title: hicar_rep3

data_processing:
Library strategy: HiCAR-seq
reads were aligned to hg38 reference genome using bwa mem with flags -SP.
Alignments were parsed and paired end tags (PET) were generated using the pairtools
PET with low mapping quality (MAPQ < 10) were filtered out. PET with the same coordinate on the genome or mapped to the same digestion fragment were removed.
Uniquely mapped PET were then flipped as side1 with the lower genomic coordinate and aggregated into contact matrices in the cooler  format using the cooler tools
MPAS is used to call the significant chromatin interaction.
Genome_build: hg38
Supplementary_files_format_and_content: Chromatin interactions  called by MAPS, provided in BEDPE formate. Raw_count for RNA-seq libraries generated by feature counts.

source_name: H1 hESC

growth_protocol: WA01 were cultured in Matrigel (corning, 354230) coated plates with Stabilized feeder-free maintenance medium mTeSRTM Plus (STEMCELL, #05825). mTeSRTM Plus was changed every other day.

extract_protocol:
For crosslinking, cells were washed once by PBS, then treated by accutase (biolegend, #423201) for 10mins at 37°C. After removing the accutase, cells were resuspended by DMEM. Formaldehyde was added to the final concentration of 1%, incubated at room temperature for 10mins. Glycine was added to the final concentration of 0.2M, incubated at room temperature for 10 mins to quench formaldehyde.
HiCAR libraries were constructed following the method in the HiCAR manuscript. RNA libraries were constructed following the SMART-seq2 protocol.

value: H1 hESC


title: HC-5 Day -7 (P1.A07)

status: Public on Mar 09 2022

type: SRA

city: Bethesda

first: William

middle: W

last: Lau

state: MD

address: 4 Memorial Drive

department: Laboratory of Immune System Biology

country: USA

institute: National Institute of Allergy and Infectious Diseases

description:
R1 and R3 are forward and reverse reads, respectively, while R2 are the UMI indices.
P1.A07

library_source: transcriptomic

data_processing:
fastq generation by Illumina bcl2fastq (2.20)
reads were adapter trimmed and standardized to 100 bp across plates using trimmomatic (0.38), then mapped to hg38 genome using the STAR aligner (2.6)
PCR duplicates were removed using UMI-tools (0.5.3)
gene-level expression quantification was performed using the featureCounts function in the subread package (1.6.2)
filtering of lowly expressed genes followed by read depth and technical effect normalization by RUVSeq (1.18)
Genome_build: hg38
Supplementary_files_format_and_content: gene expression (raw and normalized) as comma-separated values (csv)

molecule: polyA RNA

organism: Homo sapiens

source_name: Whole Blood

extract_protocol:
Blood was drawn directly into the Tempus™ Blood RNA Tube (Thermo Fisher Scientific, Waltham, MA) according to manufacturer’s protocol. Two Tempus tubes were collected at each study timepoint. The blood sample from each Tempus tube was aliquoted in to two 4.5mL cryovials (General lab supplier). These cryovials were directly stored at -80°C. RNA was isolated from tempus blood using the QIAsymphony RNA Kit (Qiagen, Gaithersburg, MD) on QIAsymphony SP instrument (Qiagen, Gaithersburg, MD). On the QIAsymphony, RNA CT 800 protocol was selected and used for RNA isolation. The instrument was set up according to the manufacturer’s protocol and the elution volume for RNA samples was set to 100µl. The final volume of the eluted RNA samples ranged from 65 – 95 µl.
RNA-seq libraries were prepared manually using Universal Plus mRNA-Seq with NuQuant, Human Globin AnyDeplete (Tecan Genomics, Redwood City, CA) according to manufacturer’s protocol. For each sample, 500ng of total RNA was used to isolate mRNA via poly(A) selection. Captured mRNA was washed, fragmented, and primed with the mix of random and oligo(dT) primers. After cDNA synthesis, ends were repaired and ligated with Unique Dual Index (UDI) adaptor pairs. Unwanted abundant transcripts from rRNA, mtRNA and globin were removed using AnyDeplete module. Remaining library was amplified by 14 cycles of PCR and purified with AMPure XP reagent (Beckman Coulter, Indianapolis, IN).

tag: tissue

value: Whole Blood

tag: subject id

tag: age at sample drawn

tag: Sex

value: Female

tag: race

value: Black

tag: ethnicity

value: Hispanic or Latino

tag: group

value: HC

tag: vaccine type

value: Flucelvax

tag: influenza vaccination count (previous 10 years)

tag: vaccine side effects

value: AE

tag: visit

value: Day -7

tag: days since vaccination

tag: library plate

tag: library well


title: hicar_rep1

status: Public on Feb 28 2022

city: Madison

first: jianhong

last: ou

state: WI

address: 330 N Orchard Street

institute: Morgridge institute for research

library_source: genomic

molecule: genomic DNA

tag: cell line


title: WT_Brain_RNAseq_rep2

status: Public on Feb 25 2022

data_processing:
RNA-Seq reads were trimmed by Trim Galore (0.6.4, with -q 15) and then mapped with TopHat (v 2.1.1, with parameters --b2-very-sensitive --no-coverage-search and supplying the UCSC danRer10 refSeq gene annotation).
Gene-level read counts were obtained using the htseq-count (v1.6.1) by the reads with MAPQ greater than 30.
ATAC-Seq reads were trimmed by Trim Galore (0.4.1, with -q 15) and then mapped with bowtie2(2.2.5, with parameters --very-sensitive) to zebrafish genome (UCSC danRer10 refSeq annotation).
The mapped reads were filtered by MAPQ greater than 30 by samtools (v 1.5) and duplicated reads were removed by picard (v 1.91). Bigwig files were generated by kentUtils.
Genome_build: danRer10
Supplementary_files_format_and_content: raw counts of sequencing reads for the features of interest for RNAseq; bigwig files were generated using kentUtils by converting the output of macs2 bedgraph

molecule: total RNA

organism: Danio rerio

source_name: Brain

growth_protocol: Embryos are raised in 28℃ egg water until 5 dpf and then transferred to the aquarium system. Adult male fish between 4~12 month old were used in this study.

extract_protocol:
Brain and whole kidney were snap freezed. Total RNA was extracted using TRI reagent (T9424, Sigma-Aldrich) and treated with DNase1 to degrade genomic DNA.  Samples were purified with Quick-RNA Miniprep kit (R1054, Zymo Research). Brain and WKM nuclei were isolated through douncer homogenization or vigorous pipette respectively. 100,000 cells/nuclei were used for library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols; ATAC library preparation was performed as described in (Buenrostro et al., 2013).

treatment_protocol: animals were incubated in 0.5~0.7uM tamoxifen for 17 h and then released from tamoxifen treatment. Tissues were collected at 7day post incubation for RNA extraction and nuclei isolation.

tag: strain

value: EK

value: Brain

tag: genotype

value: Wild type

tag: treatment

value: cardiomyocyte ablation


title: WT_Brain_RNAseq_rep3

tag: tissue


title: baf180-s81-prol2

status: Public on Mar 04 2022

city: Farmington

first: Sabriya

last: Syed

state: CT

address: 10 Discovery Dr

institute: The Jackson Laboratory for Genomic Medicine

data_processing:
Basecalling performed by BGI
Sequenced reads were processed using the SOAPnuke software.  Reads were trimmed for the adaptor sequence and filtered for low quality reads and stored in FASTQ format.
HISAT2 was used for genome mapping to mm10 after which a complete reference transcriptome was generated using StringTie, Cufflinks and CPC.
The SOAPnuke output was then mapped to the reference transcriptome using Bowtie2 and RSEM was used to calculate gene expression levels.
Differential gene expression was calculated using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Mus musculus

source_name: C2C12_Baf180 shRNAs

growth_protocol: Mouse C2C12 cells (obtained from ATCC) were maintained at sub-confluent densities in proliferation media containing Dulbecco’s Modified Eagle’s Medium (DMEM, #11965118, Gibco) supplemented with 10% calf serum (#26140079, Gibco) and 1% pen/strep (#15140163, Gibco).

extract_protocol:
TRIzol was used to harvest total RNA from proliferating C2C12 myoblasts transduced with lentivirus for scr, Brd9, Baf180 and Baf250A shRNA.
RNA libraries were prepared by the Beijing Genomics Institute (BGI) for sequencing on a BGISEQ-500

treatment_protocol: Proliferating C2C12 myoblasts were transduced with lentivirus for a control sequence shRNA (scr) and shRNA against Brd9, Baf180, Baf250A in the presence of 8 µg/ml polybrene and selected with 2 µg/ml puromycin (Invitrogen). Transduced myoblasts were maintained with 1 µg/ml puromycin.

tag: cell type

value: mouse myoblast cell line

tag: genotype/variation

value: Baf180 shRNAs


title: WKM_RNAseq_uninjured_rep1

source_name: Whole kidney marrow

value: Whole kidney marrow

value: uninjured


title: WKM_RNAseq_uninjured_rep2


title: Homo_Brain_RNAseq_rep2

value: cebpd homozygous knockout


title: Homo_Brain_RNAseq_rep3


title: WT_Brain_RNAseq_rep1


title: baf250-s06-prol2

source_name: C2C12_Baf250A shRNAs

value: Baf250A shRNAs


title: WKM_ATACseq_uninjured_rep1


title: WKM_RNAseq_regeneration_rep2


title: WKM_ATACseq_regeneration_rep1


title: WKM_RNAseq_regeneration_rep1


title: WKM_ATACseq_uninjured_rep3


title: WKM_ATACseq_uninjured_rep2


title: WKM_ATACseq_regeneration_rep3


title: Brain_RNAseq_uninjured_rep1


title: Brain_RNAseq_uninjured_rep2


title: Brain_RNAseq_regeneration_rep2


title: Brain_RNAseq_regeneration_rep1


title: Brain_ATACseq_regeneration_rep2


title: Brain_ATACseq_uninjured_rep1


title: Homo_Brain_RNAseq_rep1


title: Brain_ATACseq_uninjured_rep2


title: Brain_ATACseq_regeneration_rep1


title: CEN_Homo_Kidney_RNAseq_rep2

data_processing:
RNA-Seq reads were trimmed by Trim Galore (0.6.4, with -q 15) and then mapped with TopHat (v 2.1.1, with parameters --b2-very-sensitive --no-coverage-search and supplying the UCSC danRer10 refSeq gene annotation).
Gene-level read counts were obtained using the htseq-count (v1.6.1) by the reads with MAPQ greater than 30.
Genome_build: danRer10
Supplementary_files_format_and_content: raw counts of sequencing reads for the features of interest for RNAseq

source_name: Kidney

extract_protocol:
Whole kidney were snap freezed. Total RNA was extracted using TRI reagent (T9424, Sigma-Aldrich) and treated with DNase1 to degrade genomic DNA.  Samples were purified with Quick-RNA Miniprep kit (R1054, Zymo Research).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: animals were incubated in 0.5~0.7uM tamoxifen for 17 h and then released from tamoxifen treatment. Tissues were collected at 7day post incubation for RNA extraction.

value: Kidney

value: CEN homozygous knockout


title: CEN_Homo_Kidney_RNAseq_rep3


title: CEN_Homo_Kidney_RNAseq_rep1


title: WKM_ATACseq_regeneration_rep2


title: CEN_WT_Kidney_RNAseq_rep3


title: CEN_WT_Kidney_RNAseq_rep2


title: CEN_WT_Kidney_RNAseq_rep1


title: cebpd_WT_Kidney_RNAseq_rep3


title: cebpd_WT_Kidney_RNAseq_rep2


title: cebpd_Homo_Kidney_RNAseq_rep2


title: cebpd_Homo_Kidney_RNAseq_rep3


title: cebpd_WT_Kidney_RNAseq_rep1


title: HeLa ST8SIA1 CRISPRa-Pr+enh1 3

status: Public on Jan 01 2022

city: Berlin

first: January

last: Weiner

address: Charitéplatz 1

department: CUBI

country: Germany

institute: Berlin Institute of Health, Charité Medical University of Berlin

data_processing:
Reads were aligned to the Genome Reference Consortium Human Build 38 patch release 7 (GRCh38.p7) genome using the STAR aligner v. 2.7.5a
Quality control (QC) of the reads was inspected using the multiqc reporting tool summarizing on a number of approaches, including fastqc, dupradar, qualimap and RNA-SeqC
Raw counts were extracted using the STAR program.
For differential gene expression, the R package DESeq2, version 1.26 was used.
Genome_build: Genome Reference Consortium Human Build 38 patch release 7 (GRCh38.p7)
Supplementary_files_format_and_content: XLSX, containing raw counts, rlog normalized counts, log-cpms and gene annotation

source_name: HeLa cells

growth_protocol: HeLa cells were cultured in a growth medium of Earle’s MEM, containing 10% fetal bovine serum, 2mM L-Glutamine, 1% non-essential Amino acids and 1% penicillin-streptomycin. HeLa cells were seeded at 80,000 cells per well in 6-well plates (TPP Techno Plastic Products) and left overnight to reach around 50-60% confluence.

extract_protocol: 500-1000 ng of total RNA of the 6 transfected independent HeLa cell cultures was sequenced with 16 million reads (75bp single end) on a NextSeq 500 using the NextSeq 500/550 High Output Kit v2.5 (75 Cycles). RNA-Seq was performed at the Berlin Institute of Health Core Facility Genomics.

treatment_protocol: SgRNAs were designed with the online tool CRISPR-ERA according to the protocol described earlier. As controls, we used a scrambled sgRNA with no genomic target as well as a sgRNA that located to the microRNA hsa-miR-374b-5p on chromosome X, which did not affect ST8SIA1 expression. The sgRNAs were synthesized (Metabion International AG) and cloned into the BbsI site of sgRNA(MS2) cloning backbone vector (Addgene Plasmid #61424). SgRNAs that targeted region 1 or region 2 and the promoter of ST8SIA1 were pooled and transfected into HeLa cells in biological triplicates. Separately, the controls sgRNAs were pooled and transfected into HeLa cells in biological triplicates.


title: HeLa ST8SIA1 CRISPRa-Pr+enh1 2


title: HeLa ST8SIA1 scr miRNA10 M2


title: HeLa ST8SIA1 scr miRNA10 M3


title: HeLa ST8SIA1 CRISPRa-Pr+enh1 1


title: HeLa ST8SIA1 scr miRNA10 M1


title: PBS

city: Yiwu

first: jingjia

last: ye

state: zhejiang

address: chouzhoubeilu 1575

country: China

institute: zhejiang university

data_processing:
Reads were mapped to the mouse GrCm38 genome using Cell Ranger v.3.0.2.
Genome_build: mm10
Supplementary_files_format_and_content: matrix table with raw gene counts for every gene and every cell

organism: Rattus norvegicus

source_name: primary cell derived from spinal cord

extract_protocol:
Animals (5 animals for each condition) were anesthetized deeply with chloral hydrate, and a 5-mm section of the spinal cord centered at the injury site was dissected. Then, the tissue was chopped and incubated for 30 min at 37°C with 2 ml of collagenase (1 mg/ml in PBS) and centrifuged at 300 g for 5 min at 4°C. Two milliliters of 0.25% trypsin-EDTA solution was added to pelleted cells after collagenase removal and incubated at 37°C for 5 min. FBS (10%) was added to stop the digestion by trypsin, and the supernatant was removed by centrifugation. Precipitate dispersed in PBS with 0.5% BSA was strained through a 30-µm cell strainer twice. Cells were collected by centrifugation, and 10 ml of erythrocyte lysate was added. After 10 min, the cell suspension was centrifuged, and the cells were resuspended in PBS for counting.
The single-cell suspension was then examined using the 10X Genomics Chromium Single Cell 3′ Reagent Kit v3 (10X Genomics) according to the manufacturer’s protocol.

value: spinal cord

tag: age

value: 6-8 weeks

value: wild type

value: PBS injection at injury site


title: MPG-HD

value: MPGHD injection at injury site


title: hicar_rep2

value: H1 hESC


title: cebpd_Homo_Kidney_RNAseq_rep1

value: EK


title: heart495

status: Public on Dec 28 2021

type: RNA

city: Edmonton

first: Jessica

last: Chang

address: 250 Heritage Medical Research Centre

department: Medicine

country: Canada

institute: University of Alberta

description: heart biopsy

hyb_protocol: (Affymetrix, Santa Clara, CA).  Amplified RNA (10ug) was hybridized for 16 hr at 45C on  GeneChip® PrimeView™ Human Gene Expression Array . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Gene Array Scanner 3000 7G (Affymetrix) and processed with GeneChip® Command Console® Software (AGCC)(Affymetrix).

data_processing: Microarray data files were preprocessed using robust multi-chip averaging (RMA) implemented in Bioconductor.

label: biotin

source_name: heart biopsy

label_protocol: Total RNA (0.5µg) was labeled using GeneChip 3` IVT Express Labeling kit. Quality of labeled aRNA was assessed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) before hybridization to GeneChip® PrimeView™ Human Gene Expression Array

growth_protocol: All human heart biopsies taken for clinical indication during the period specified above were included. Tissue was immediately placed in RNA later.

extract_protocol: Tissue was homogenization in 0.5ml of Trizol reagent (Invitrogen, Carlsbad, CA) and total RNA was extracted and purified using the Rneasy Micro Kit (Quiagen, Ontario, Canada) (average yield 8µg/core, (RNA integrity number >7).

treatment_protocol: The immunosuppressive treatment of the patients before the biopsy was based on individual treatment regiments; the treatment after the biopsy was adjusted based on the histopathological diagnosis.

tag: in 889? (yes, no)

value: no

tag: rejection cluster (1,2,3,4,5)

tag: injury cluster (1,2,3,4,5)

tag: mmdx (nr-normal, nr-minor, early injury, ptcmr, pabmr, abmr, tcmr, mixed)

value: NR Minor


title: heart418

description: heart biopsy

value: NR Normal


title: heart256

description: heart biopsy

value: ABMR


title: heart26

description: heart biopsy


title: heart160

description: heart biopsy


title: heart382

description: heart biopsy


title: heart887

description: heart biopsy


title: heart673

description: heart biopsy


title: heart882

description: heart biopsy


title: heart304

description: heart biopsy


title: heart852

description: heart biopsy


title: heart600

description: heart biopsy

value: pABMR


title: heart262

description: heart biopsy


title: heart783

description: heart biopsy


title: heart698

description: heart biopsy

value: TCMR


title: heart486

description: heart biopsy


title: heart637

description: heart biopsy


title: heart412

description: heart biopsy


title: heart95

description: heart biopsy


title: heart442

description: heart biopsy

value: NR Early-injury


title: heart87

description: heart biopsy


title: heart439

description: heart biopsy


title: heart251

description: heart biopsy


title: heart458

description: heart biopsy


title: heart170

description: heart biopsy


title: heart879

description: heart biopsy


title: heart136

description: heart biopsy


title: heart576

description: heart biopsy


title: heart261

description: heart biopsy


title: heart194

description: heart biopsy


title: heart714

description: heart biopsy

value: Mixed


title: heart269

description: heart biopsy

value: pTCMR


title: heart510

description: heart biopsy


title: heart353

description: heart biopsy


title: heart607

description: heart biopsy


title: heart718

description: heart biopsy


title: heart231

description: heart biopsy


title: heart287

description: heart biopsy


title: heart265

description: heart biopsy


title: heart383

description: heart biopsy


title: heart365

description: heart biopsy


title: heart781

description: heart biopsy


title: heart402

description: heart biopsy


title: heart862

description: heart biopsy


title: heart77

description: heart biopsy


title: heart3

description: heart biopsy


title: heart288

description: heart biopsy


title: heart278

description: heart biopsy


title: heart834

description: heart biopsy


title: heart82

description: heart biopsy


title: heart415

description: heart biopsy


title: heart811

description: heart biopsy


title: heart624

description: heart biopsy


title: heart831

description: heart biopsy


title: heart177

description: heart biopsy


title: heart374

description: heart biopsy


title: heart784

description: heart biopsy


title: heart138

description: heart biopsy


title: heart618

description: heart biopsy


title: heart38

description: heart biopsy


title: heart776

description: heart biopsy


title: heart99

description: heart biopsy


title: heart730

description: heart biopsy


title: heart502

description: heart biopsy


title: heart476

description: heart biopsy


title: heart379

description: heart biopsy


title: heart509

description: heart biopsy


title: heart615

description: heart biopsy


title: heart684

description: heart biopsy


title: heart41

description: heart biopsy


title: heart878

description: heart biopsy


title: heart312

description: heart biopsy


title: heart326

description: heart biopsy


title: heart687

description: heart biopsy


title: heart186

description: heart biopsy


title: heart305

description: heart biopsy


title: heart477

description: heart biopsy


title: heart37

description: heart biopsy


title: heart883

description: heart biopsy


title: heart650

description: heart biopsy


title: heart675

description: heart biopsy


title: heart649

description: heart biopsy


title: heart584

description: heart biopsy


title: heart438

description: heart biopsy


title: heart542

description: heart biopsy


title: heart539

description: heart biopsy


title: heart271

description: heart biopsy


title: heart815

description: heart biopsy


title: heart785

description: heart biopsy


title: heart459

description: heart biopsy


title: heart187

description: heart biopsy


title: heart51

description: heart biopsy


title: heart322

description: heart biopsy


title: heart792

description: heart biopsy


title: heart595

description: heart biopsy


title: heart188

description: heart biopsy


title: heart734

description: heart biopsy


title: heart594

description: heart biopsy


title: heart243

description: heart biopsy


title: heart793

description: heart biopsy


title: heart640

description: heart biopsy


title: heart768

description: heart biopsy


title: heart690

description: heart biopsy


title: heart563

description: heart biopsy


title: heart620

description: heart biopsy


title: heart593

description: heart biopsy


title: heart465

description: heart biopsy


title: heart814

description: heart biopsy


title: heart663

description: heart biopsy


title: heart772

description: heart biopsy


title: heart394

description: heart biopsy


title: heart32

description: heart biopsy


title: heart308

description: heart biopsy


title: heart515

description: heart biopsy


title: heart528

description: heart biopsy


title: heart406

description: heart biopsy


title: heart870

description: heart biopsy


title: heart167

description: heart biopsy


title: heart226

description: heart biopsy


title: heart74

description: heart biopsy


title: heart296

description: heart biopsy


title: heart132

description: heart biopsy


title: heart337

description: heart biopsy


title: heart171

description: heart biopsy


title: heart7

description: heart biopsy


title: heart651

description: heart biopsy


title: heart258

description: heart biopsy


title: heart751

description: heart biopsy


title: heart89

description: heart biopsy


title: heart546

description: heart biopsy


title: heart704

description: heart biopsy


title: heart752

description: heart biopsy


title: heart880

description: heart biopsy


title: heart668

description: heart biopsy


title: heart551

description: heart biopsy


title: heart118

description: heart biopsy


title: heart342

description: heart biopsy


title: heart788

description: heart biopsy


title: heart307

description: heart biopsy


title: heart839

description: heart biopsy


title: heart535

description: heart biopsy


title: heart222

description: heart biopsy


title: heart605

description: heart biopsy


title: heart487

description: heart biopsy


title: heart753

description: heart biopsy


title: heart39

description: heart biopsy


title: heart647

description: heart biopsy


title: heart872

description: heart biopsy


title: heart665

description: heart biopsy


title: heart401

description: heart biopsy


title: heart676

description: heart biopsy


title: heart356

description: heart biopsy


title: heart195

description: heart biopsy


title: heart164

description: heart biopsy


title: heart155

description: heart biopsy


title: heart146

description: heart biopsy


title: heart390

description: heart biopsy


title: heart416

description: heart biopsy


title: heart69

description: heart biopsy


title: heart560

description: heart biopsy


title: heart469

description: heart biopsy


title: heart108

description: heart biopsy


title: heart321

description: heart biopsy


title: heart399

description: heart biopsy


title: heart723

description: heart biopsy


title: heart822

description: heart biopsy


title: heart233

description: heart biopsy


title: heart318

description: heart biopsy


title: heart141

description: heart biopsy


title: heart446

description: heart biopsy


title: heart384

description: heart biopsy


title: heart351

description: heart biopsy


title: heart313

description: heart biopsy


title: heart530

description: heart biopsy


title: heart656

description: heart biopsy


title: heart84

description: heart biopsy


title: heart461

description: heart biopsy


title: heart589

description: heart biopsy


title: heart291

description: heart biopsy


title: heart1

description: heart biopsy


title: heart119

description: heart biopsy


title: heart859

description: heart biopsy


title: heart857

description: heart biopsy


title: heart623

description: heart biopsy


title: heart523

description: heart biopsy


title: heart522

description: heart biopsy


title: heart513

description: heart biopsy


title: heart91

description: heart biopsy


title: heart808

description: heart biopsy


title: heart455

description: heart biopsy


title: heart116

description: heart biopsy


title: heart797

description: heart biopsy


title: heart168

description: heart biopsy


title: heart570

description: heart biopsy


title: heart559

description: heart biopsy


title: heart206

description: heart biopsy


title: heart597

description: heart biopsy


title: heart683

description: heart biopsy


title: heart813

description: heart biopsy


title: heart180

description: heart biopsy


title: heart708

description: heart biopsy


title: heart617

description: heart biopsy


title: heart518

description: heart biopsy


title: heart485

description: heart biopsy


title: heart110

description: heart biopsy


title: heart209

description: heart biopsy


title: heart798

description: heart biopsy


title: heart627

description: heart biopsy


title: heart629

description: heart biopsy


title: heart445

description: heart biopsy


title: heart1197

description: heart biopsy


title: heart888

description: heart biopsy


title: heart666

description: heart biopsy


title: heart367

description: heart biopsy


title: heart20

description: heart biopsy


title: heart786

description: heart biopsy


title: heart507

description: heart biopsy


title: heart573

description: heart biopsy


title: heart189

description: heart biopsy


title: heart1196

description: heart biopsy


title: heart310

description: heart biopsy


title: heart521

description: heart biopsy


title: heart264

description: heart biopsy


title: heart204

description: heart biopsy


title: heart345

description: heart biopsy


title: heart397

description: heart biopsy


title: heart536

description: heart biopsy


title: heart453

description: heart biopsy


title: heart70

description: heart biopsy


title: heart40

description: heart biopsy


title: heart829

description: heart biopsy


title: heart449

description: heart biopsy


title: heart514

description: heart biopsy


title: heart767

description: heart biopsy


title: heart706

description: heart biopsy


title: heart720

description: heart biopsy


title: heart370

description: heart biopsy


title: heart681

description: heart biopsy


title: heart764

description: heart biopsy


title: heart100

description: heart biopsy


title: heart217

description: heart biopsy


title: heart376

description: heart biopsy


title: heart428

description: heart biopsy


title: heart143

description: heart biopsy


title: heart672

description: heart biopsy


title: heart619

description: heart biopsy


title: heart750

description: heart biopsy


title: heart809

description: heart biopsy


title: heart238

description: heart biopsy


title: heart190

description: heart biopsy


title: heart612

description: heart biopsy


title: heart83

description: heart biopsy


title: heart749

description: heart biopsy


title: heart49

description: heart biopsy


title: heart724

description: heart biopsy


title: heart134

description: heart biopsy


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description: heart biopsy


title: heart1090

description: heart biopsy


title: heart1120

description: heart biopsy


title: heart1223

description: heart biopsy


title: heart1232

description: heart biopsy


title: heart1237

description: heart biopsy


title: heart1078

description: heart biopsy


title: heart1132

description: heart biopsy


title: heart1098

description: heart biopsy


title: heart1229

description: heart biopsy


title: heart1227

description: heart biopsy


title: heart1228

description: heart biopsy


title: heart1116

description: heart biopsy


title: heart1051

description: heart biopsy


title: heart989

description: heart biopsy


title: heart1106

description: heart biopsy


title: heart1226

description: heart biopsy


title: heart1126

description: heart biopsy


title: heart1225

description: heart biopsy


title: heart988

description: heart biopsy


title: heart973

description: heart biopsy


title: heart943

description: heart biopsy


title: heart1210

description: heart biopsy


title: heart1112

description: heart biopsy


title: heart901

description: heart biopsy


title: heart1070

description: heart biopsy


title: heart1257

description: heart biopsy


title: heart1119

description: heart biopsy


title: heart1221

description: heart biopsy


title: heart1125

description: heart biopsy


title: heart953

description: heart biopsy


title: heart939

description: heart biopsy


title: heart1097

description: heart biopsy


title: heart1083

description: heart biopsy


title: heart936

description: heart biopsy


title: heart1036

description: heart biopsy


title: heart1089

description: heart biopsy


title: heart921

description: heart biopsy


title: heart1105

description: heart biopsy


title: heart1033

description: heart biopsy


title: heart1222

description: heart biopsy


title: heart1118

description: heart biopsy


title: heart950

description: heart biopsy


title: heart1224

description: heart biopsy


title: heart900

description: heart biopsy


title: heart1032

description: heart biopsy


title: heart1035

description: heart biopsy


title: heart972

description: heart biopsy


title: heart1029

description: heart biopsy


title: heart1115

description: heart biopsy


title: heart947

description: heart biopsy


title: heart1104

description: heart biopsy


title: heart942

description: heart biopsy


title: heart1114

description: heart biopsy


title: heart944

description: heart biopsy


title: heart1111

description: heart biopsy


title: heart1082

description: heart biopsy


title: heart945

description: heart biopsy


title: heart1034

description: heart biopsy


title: heart946

description: heart biopsy


title: heart948

description: heart biopsy


title: heart935

description: heart biopsy


title: heart1021

description: heart biopsy


title: heart1096

description: heart biopsy


title: heart1081

description: heart biopsy


title: heart934

description: heart biopsy


title: heart1025

description: heart biopsy


title: heart1031

description: heart biopsy


title: heart1026

description: heart biopsy


title: heart938

description: heart biopsy


title: heart1028

description: heart biopsy


title: heart1023

description: heart biopsy


title: heart1101

description: heart biopsy


title: heart1027

description: heart biopsy


title: heart969

description: heart biopsy


title: heart1017

description: heart biopsy


title: heart1030

description: heart biopsy


title: heart1024

description: heart biopsy


title: heart1102

description: heart biopsy


title: heart1095

description: heart biopsy


title: heart987

description: heart biopsy


title: heart1050

description: heart biopsy


title: heart1012

description: heart biopsy


title: heart1077

description: heart biopsy


title: heart1088

description: heart biopsy


title: heart932

description: heart biopsy


title: heart1063

description: heart biopsy


title: heart1208

description: heart biopsy


title: heart1020

description: heart biopsy


title: heart937

description: heart biopsy


title: heart1203

description: heart biopsy


title: heart986

description: heart biopsy


title: heart891

description: heart biopsy


title: heart933

description: heart biopsy


title: heart1300

description: heart biopsy


title: heart899

description: heart biopsy


title: heart1015

description: heart biopsy


title: heart1014

description: heart biopsy


title: heart1019

description: heart biopsy


title: heart1018

description: heart biopsy


title: heart930

description: heart biopsy


title: heart1080

description: heart biopsy


title: heart931

description: heart biopsy


title: heart1207

description: heart biopsy


title: heart1016

description: heart biopsy


title: heart985

description: heart biopsy


title: heart1066

description: heart biopsy


title: heart928

description: heart biopsy


title: heart984

description: heart biopsy


title: heart1256

description: heart biopsy


title: heart1011

description: heart biopsy


title: heart926

description: heart biopsy


title: heart1010

description: heart biopsy


title: heart1008

description: heart biopsy


title: heart1007

description: heart biopsy


title: heart1261

description: heart biopsy


title: heart1252

description: heart biopsy


title: heart1205

description: heart biopsy


title: heart1013

description: heart biopsy


title: heart920

description: heart biopsy


title: heart1009

description: heart biopsy


title: heart1006

description: heart biopsy


title: heart1296

description: heart biopsy


title: heart1260

description: heart biopsy


title: heart1251

description: heart biopsy


title: heart1201

description: heart biopsy


title: heart904

description: heart biopsy


title: heart1255

description: heart biopsy


title: heart1254

description: heart biopsy


title: heart1259

description: heart biopsy


title: heart1250

description: heart biopsy


title: heart919

description: heart biopsy


title: heart1058

description: heart biopsy


title: heart1049

description: heart biopsy


title: heart1206

description: heart biopsy


title: heart1202

description: heart biopsy


title: heart1074

description: heart biopsy


title: heart1258

description: heart biopsy


title: heart918

description: heart biopsy


title: heart925

description: heart biopsy


title: heart1249

description: heart biopsy


title: heart906

description: heart biopsy


title: heart923

description: heart biopsy


title: heart909

description: heart biopsy


title: heart983

description: heart biopsy


title: heart1199

description: heart biopsy


title: heart917

description: heart biopsy


title: heart1200

description: heart biopsy


title: heart1076

description: heart biopsy


title: heart915

description: heart biopsy


title: heart916

description: heart biopsy


title: heart968

description: heart biopsy


title: heart1069

description: heart biopsy


title: heart924

description: heart biopsy


title: heart979

description: heart biopsy


title: heart914

description: heart biopsy


title: heart1060

description: heart biopsy


title: heart1073

description: heart biopsy


title: heart910

description: heart biopsy


title: heart1057

description: heart biopsy


title: heart1059

description: heart biopsy


title: heart1054

description: heart biopsy


title: heart1048

description: heart biopsy


title: heart1072

description: heart biopsy


title: heart1044

description: heart biopsy


title: heart981

description: heart biopsy


title: heart980

description: heart biopsy


title: heart1068

description: heart biopsy


title: heart982

description: heart biopsy


title: heart1045

description: heart biopsy


title: heart927

description: heart biopsy


title: heart905

description: heart biopsy


title: heart912

description: heart biopsy


title: heart1287

description: heart biopsy


title: heart1053

description: heart biopsy


title: heart1065

description: heart biopsy


title: heart971

description: heart biopsy


title: heart1062

description: heart biopsy


title: heart1285

description: heart biopsy


title: heart1291

description: heart biopsy


title: heart1292

description: heart biopsy


title: heart1283

description: heart biopsy


title: heart1280

description: heart biopsy


title: heart1061

description: heart biopsy


title: heart1293

description: heart biopsy


title: heart1271

description: heart biopsy


title: heart1269

description: heart biopsy


title: heart1274

description: heart biopsy


title: heart1290

description: heart biopsy


title: heart1282

description: heart biopsy


title: heart1284

description: heart biopsy


title: heart967

description: heart biopsy


title: heart1286

description: heart biopsy


title: heart1281

description: heart biopsy


title: heart1272

description: heart biopsy


title: heart163

description: heart biopsy


title: heart1047

description: heart biopsy


title: heart499

description: heart biopsy


title: heart1056

description: heart biopsy


title: heart1064

description: heart biopsy


title: heart263

description: heart biopsy


title: heart913

description: heart biopsy


title: heart1273

description: heart biopsy


title: heart806

description: heart biopsy


title: heart448

description: heart biopsy


title: heart688

description: heart biopsy


title: heart274

description: heart biopsy


title: heart849

description: heart biopsy


title: heart642

description: heart biopsy


title: heart475

description: heart biopsy


title: heart354

description: heart biopsy


title: heart389

description: heart biopsy


title: heart375

description: heart biopsy


title: heart429

description: heart biopsy


title: heart856

description: heart biopsy


title: heart320

description: heart biopsy


title: heart660

description: heart biopsy


title: heart525

description: heart biopsy


title: heart599

description: heart biopsy


title: heart504

description: heart biopsy


title: heart73

description: heart biopsy


title: heart881

description: heart biopsy


title: heart381

description: heart biopsy


title: heart407

description: heart biopsy


title: heart179

description: heart biopsy


title: heart62

description: heart biopsy


title: heart488

description: heart biopsy


title: heart253

description: heart biopsy


title: heart257

description: heart biopsy


title: heart421

description: heart biopsy


title: heart172

description: heart biopsy


title: heart58

description: heart biopsy


title: heart634

description: heart biopsy


title: heart695

description: heart biopsy


title: heart565

description: heart biopsy


title: heart473

description: heart biopsy


title: heart53

description: heart biopsy


title: heart130

description: heart biopsy


title: heart842

description: heart biopsy


title: heart18

description: heart biopsy


title: heart10

description: heart biopsy


title: heart22

description: heart biopsy


title: heart611

description: heart biopsy


title: heart861

description: heart biopsy


title: heart232

description: heart biopsy


title: heart731

description: heart biopsy


title: heart836

description: heart biopsy


title: heart484

description: heart biopsy


title: heart405

description: heart biopsy


title: heart483

description: heart biopsy


title: heart745

description: heart biopsy


title: heart249

description: heart biopsy


title: heart348

description: heart biopsy


title: heart361

description: heart biopsy


title: heart552

description: heart biopsy


title: heart727

description: heart biopsy


title: heart8

description: heart biopsy


title: heart165

description: heart biopsy


title: heart315

description: heart biopsy


title: heart16

description: heart biopsy


title: heart807

description: heart biopsy


title: heart769

description: heart biopsy


title: heart340

description: heart biopsy


title: heart700

description: heart biopsy


title: heart221

description: heart biopsy


title: heart701

description: heart biopsy


title: heart413

description: heart biopsy


title: heart789

description: heart biopsy


title: heart34

description: heart biopsy


title: heart154

description: heart biopsy


title: heart493

description: heart biopsy


title: heart162

description: heart biopsy


title: heart482

description: heart biopsy


title: heart248

description: heart biopsy


title: heart865

description: heart biopsy


title: heart27

description: heart biopsy


title: heart771

description: heart biopsy


title: heart123

description: heart biopsy


title: heart447

description: heart biopsy


title: heart667

description: heart biopsy


title: heart372

description: heart biopsy


title: heart142

description: heart biopsy


title: heart1043

description: heart biopsy


title: heart219

description: heart biopsy


title: heart722

description: heart biopsy


title: heart795

description: heart biopsy


title: heart685

description: heart biopsy


title: heart355

description: heart biopsy


title: heart90

description: heart biopsy


title: heart112

description: heart biopsy


title: heart759

description: heart biopsy


title: heart140

description: heart biopsy


title: heart54

description: heart biopsy


title: heart431

description: heart biopsy


title: heart717

description: heart biopsy


title: heart92

description: heart biopsy


title: heart543

description: heart biopsy


title: heart588

description: heart biopsy


title: heart331

description: heart biopsy


title: heart46

description: heart biopsy


title: heart443

description: heart biopsy


title: heart598

description: heart biopsy


title: heart441

description: heart biopsy


title: heart47

description: heart biopsy


title: heart677

description: heart biopsy


title: heart869

description: heart biopsy


title: heart555

description: heart biopsy


title: heart787

description: heart biopsy


title: heart658

description: heart biopsy


title: heart474

description: heart biopsy


title: heart126

description: heart biopsy


title: heart885

description: heart biopsy


title: heart250

description: heart biopsy


title: heart64

description: heart biopsy


title: heart317

description: heart biopsy


title: heart234

description: heart biopsy


title: heart347

description: heart biopsy


title: heart2

description: heart biopsy


title: heart799

description: heart biopsy


title: heart693

description: heart biopsy


title: heart424

description: heart biopsy


title: heart648

description: heart biopsy


title: heart639

description: heart biopsy


title: heart425

description: heart biopsy


title: heart526

description: heart biopsy


title: heart867

description: heart biopsy


title: heart344

description: heart biopsy


title: heart420

description: heart biopsy


title: heart237

description: heart biopsy


title: heart835

description: heart biopsy


title: heart520

description: heart biopsy


title: heart503

description: heart biopsy


title: heart433

description: heart biopsy


title: heart393

description: heart biopsy


title: heart697

description: heart biopsy


title: heart183

description: heart biopsy


title: heart211

description: heart biopsy


title: heart227

description: heart biopsy


title: heart655

description: heart biopsy


title: heart109

description: heart biopsy


title: heart327

description: heart biopsy


title: heart686

description: heart biopsy


title: heart554

description: heart biopsy


title: heart654

description: heart biopsy


title: heart732

description: heart biopsy


title: heart422

description: heart biopsy


title: heart224

description: heart biopsy


title: heart323

description: heart biopsy


title: heart689

description: heart biopsy


title: heart494

description: heart biopsy


title: heart716

description: heart biopsy


title: heart396

description: heart biopsy


title: heart711

description: heart biopsy


title: heart423

description: heart biopsy


title: heart756

description: heart biopsy


title: heart491

description: heart biopsy


title: heart339

description: heart biopsy


title: heart201

description: heart biopsy


title: heart531

description: heart biopsy


title: heart456

description: heart biopsy


title: heart1005

description: heart biopsy


title: heart762

description: heart biopsy


title: heart820

description: heart biopsy


title: heart553

description: heart biopsy


title: heart79

description: heart biopsy


title: heart297

description: heart biopsy


title: heart794

description: heart biopsy


title: heart17

description: heart biopsy


title: heart359

description: heart biopsy


title: heart606

description: heart biopsy


title: heart67

description: heart biopsy


title: heart275

description: heart biopsy


title: heart863

description: heart biopsy


title: heart561

description: heart biopsy


title: heart1004

description: heart biopsy


title: heart548

description: heart biopsy


title: heart133

description: heart biopsy


title: heart437

description: heart biopsy


title: heart336

description: heart biopsy


title: heart273

description: heart biopsy


title: heart763

description: heart biopsy


title: heart635

description: heart biopsy


title: heart871

description: heart biopsy


title: heart457

description: heart biopsy


title: heart715

description: heart biopsy


title: heart519

description: heart biopsy


title: heart333

description: heart biopsy


title: heart472

description: heart biopsy


title: heart876

description: heart biopsy


title: heart242

description: heart biopsy


title: heart529

description: heart biopsy


title: heart524

description: heart biopsy


title: heart664

description: heart biopsy


title: heart332

description: heart biopsy


title: heart541

description: heart biopsy


title: kidney biopsy [N78]

status: Public on Dec 23 2021

source_name: kidney biopsy

treatment_protocol: All human kidney biopsies taken for clinical indication during the period specified above were included. Tissue was immediately placed in RNA later.

tag: cfdna>1 (yes, no)

tag: mmdx (abmr, tcmr, mixed, nr, pabmr, ptcmr)

value: NR

tag: in n=280? (yes, no)

tag: dsa status (positive, negative, na)

value: negative


title: heart178

description: heart biopsy


title: heart303

description: heart biopsy


title: heart450

description: heart biopsy


title: heart78

description: heart biopsy


title: kidney biopsy [N209]


title: kidney biopsy [N77]

value: positive


title: kidney biopsy [N281]


title: kidney biopsy [N290]


title: kidney biopsy [N33]


title: kidney biopsy [N174]


title: heart76

description: heart biopsy


title: kidney biopsy [N58]


title: kidney biopsy [N132]


title: heart400

description: heart biopsy


title: kidney biopsy [N166]


title: heart335

description: heart biopsy


title: kidney biopsy [N218]


title: kidney biopsy [N256]


title: kidney biopsy [N199]


title: kidney biopsy [N176]


title: kidney biopsy [N297]


title: kidney biopsy [N230]


title: kidney biopsy [N131]


title: kidney biopsy [N201]


title: kidney biopsy [N300]


title: kidney biopsy [N296]


title: kidney biopsy [N27]


title: kidney biopsy [N87]


title: kidney biopsy [N124]


title: kidney biopsy [N269]


title: kidney biopsy [N145]


title: kidney biopsy [N161]


title: kidney biopsy [N53]


title: kidney biopsy [N247]


title: kidney biopsy [N46]


title: kidney biopsy [N153]


title: kidney biopsy [N39]


title: kidney biopsy [N232]


title: kidney biopsy [N139]


title: kidney biopsy [N134]


title: kidney biopsy [N55]


title: kidney biopsy [N223]


title: kidney biopsy [N76]


title: kidney biopsy [N5]


title: kidney biopsy [N206]


title: kidney biopsy [N108]


title: kidney biopsy [N73]


title: kidney biopsy [N194]


title: kidney biopsy [N37]


title: kidney biopsy [N138]


title: kidney biopsy [N180]


title: kidney biopsy [N217]


title: kidney biopsy [N149]


title: kidney biopsy [N273]


title: kidney biopsy [N268]


title: kidney biopsy [N246]


title: kidney biopsy [N213]


title: kidney biopsy [N13]


title: kidney biopsy [N129]


title: kidney biopsy [N70]


title: kidney biopsy [N95]


title: kidney biopsy [N75]


title: kidney biopsy [N152]


title: kidney biopsy [N265]


title: kidney biopsy [N21]


title: kidney biopsy [N86]


title: kidney biopsy [N116]


title: kidney biopsy [N119]


title: kidney biopsy [N205]


title: kidney biopsy [N208]


title: kidney biopsy [N97]


title: kidney biopsy [N114]


title: kidney biopsy [N64]


title: kidney biopsy [N298]


title: kidney biopsy [N151]


title: kidney biopsy [N222]


title: kidney biopsy [N225]


title: kidney biopsy [N165]


title: kidney biopsy [N137]


title: kidney biopsy [N189]


title: kidney biopsy [N34]


title: kidney biopsy [N52]


title: kidney biopsy [N211]


title: kidney biopsy [N26]


title: kidney biopsy [N93]


title: kidney biopsy [N99]


title: kidney biopsy [N45]


title: kidney biopsy [N173]


title: kidney biopsy [N259]


title: kidney biopsy [N221]


title: heart223

description: heart biopsy


title: kidney biopsy [N94]


title: kidney biopsy [N272]


title: kidney biopsy [N150]


title: kidney biopsy [N196]


title: kidney biopsy [N12]


title: kidney biopsy [N83]


title: kidney biopsy [N128]


title: kidney biopsy [N72]


title: kidney biopsy [N271]


title: kidney biopsy [N32]


title: kidney biopsy [N299]


title: kidney biopsy [N264]


title: kidney biopsy [N62]


title: kidney biopsy [N291]


title: kidney biopsy [N170]


title: kidney biopsy [N283]


title: kidney biopsy [N242]


title: kidney biopsy [N188]


title: kidney biopsy [N210]


title: kidney biopsy [N294]


title: kidney biopsy [N81]


title: kidney biopsy [N18]


title: kidney biopsy [N103]


title: kidney biopsy [N252]


title: kidney biopsy [N162]


title: kidney biopsy [N251]


title: kidney biopsy [N267]


title: kidney biopsy [N80]


title: kidney biopsy [N198]


title: kidney biopsy [N263]


title: kidney biopsy [N51]


title: kidney biopsy [N178]


title: kidney biopsy [N179]


title: kidney biopsy [N200]


title: kidney biopsy [N15]


title: kidney biopsy [N262]


title: kidney biopsy [N19]


title: kidney biopsy [N192]


title: kidney biopsy [N31]


title: kidney biopsy [N24]


title: kidney biopsy [N136]


title: kidney biopsy [N156]


title: kidney biopsy [N220]


title: kidney biopsy [N287]


title: kidney biopsy [N258]


title: kidney biopsy [N204]


title: kidney biopsy [N3]


title: kidney biopsy [N216]


title: kidney biopsy [N202]


title: kidney biopsy [N169]


title: kidney biopsy [N261]


title: kidney biopsy [N233]


title: kidney biopsy [N167]


title: kidney biopsy [N177]


title: kidney biopsy [N118]


title: kidney biopsy [N61]


title: kidney biopsy [N102]


title: kidney biopsy [N234]


title: kidney biopsy [N90]


title: kidney biopsy [N253]


title: kidney biopsy [N164]


title: kidney biopsy [N219]


title: kidney biopsy [N109]


title: kidney biopsy [N243]


title: kidney biopsy [N245]


title: kidney biopsy [N49]


title: kidney biopsy [N30]


title: kidney biopsy [N125]


title: kidney biopsy [N48]


title: kidney biopsy [N284]


title: kidney biopsy [N224]


title: kidney biopsy [N187]


title: kidney biopsy [N227]


title: kidney biopsy [N241]


title: kidney biopsy [N98]


title: kidney biopsy [N43]


title: kidney biopsy [N191]


title: kidney biopsy [N79]


title: kidney biopsy [N175]


title: kidney biopsy [N250]


title: kidney biopsy [N226]


title: kidney biopsy [N56]


title: kidney biopsy [N104]


title: kidney biopsy [N121]


title: kidney biopsy [N231]


title: kidney biopsy [N44]


title: kidney biopsy [N22]


title: kidney biopsy [N229]


title: kidney biopsy [N69]


title: kidney biopsy [N154]


title: kidney biopsy [N92]


title: kidney biopsy [N67]


title: kidney biopsy [N28]


title: kidney biopsy [N249]


title: kidney biopsy [N8]


title: kidney biopsy [N127]


title: kidney biopsy [N112]


title: kidney biopsy [N74]


title: kidney biopsy [N17]


title: kidney biopsy [N274]


title: kidney biopsy [N54]


title: kidney biopsy [N123]


title: kidney biopsy [N197]


title: kidney biopsy [N255]


title: kidney biopsy [N172]


title: kidney biopsy [N96]


title: kidney biopsy [N237]


title: kidney biopsy [N2]


title: kidney biopsy [N279]


title: kidney biopsy [N207]


title: kidney biopsy [N107]


title: kidney biopsy [N254]


title: kidney biopsy [N82]


title: kidney biopsy [N184]


title: kidney biopsy [N10]


title: kidney biopsy [N190]


title: kidney biopsy [N6]


title: kidney biopsy [N68]


title: kidney biopsy [N50]


title: kidney biopsy [N38]


title: kidney biopsy [N215]


title: kidney biopsy [N120]


title: kidney biopsy [N270]


title: kidney biopsy [N11]


title: kidney biopsy [N106]


title: kidney biopsy [N236]


title: kidney biopsy [N186]


title: kidney biopsy [N66]


title: kidney biopsy [N238]


title: kidney biopsy [N35]


title: kidney biopsy [N257]


title: kidney biopsy [N115]


title: kidney biopsy [N212]


title: kidney biopsy [N260]


title: kidney biopsy [N89]


title: kidney biopsy [N47]


title: kidney biopsy [N239]


title: kidney biopsy [N133]


title: kidney biopsy [N111]


title: kidney biopsy [N42]


title: kidney biopsy [N130]


title: kidney biopsy [N203]


title: kidney biopsy [N293]


title: kidney biopsy [N248]


title: kidney biopsy [N16]


title: kidney biopsy [N85]


title: kidney biopsy [N105]


title: kidney biopsy [N63]


title: kidney biopsy [N277]


title: kidney biopsy [N101]


title: kidney biopsy [N282]


title: kidney biopsy [N275]


title: kidney biopsy [N158]


title: kidney biopsy [N147]


title: kidney biopsy [N29]


title: kidney biopsy [N288]


title: kidney biopsy [N143]


title: kidney biopsy [N171]


title: kidney biopsy [N122]


title: kidney biopsy [N146]


title: kidney biopsy [N135]


title: kidney biopsy [N110]


title: kidney biopsy [N295]


title: kidney biopsy [N183]


title: kidney biopsy [N182]


title: kidney biopsy [N71]


title: kidney biopsy [N193]


title: kidney biopsy [N286]


title: kidney biopsy [N65]


title: kidney biopsy [N159]


title: kidney biopsy [N181]


title: kidney biopsy [N84]


title: kidney biopsy [N20]


title: kidney biopsy [N1]


title: kidney biopsy [N36]


title: kidney biopsy [N14]


title: kidney biopsy [N292]


title: kidney biopsy [N235]


title: kidney biopsy [N289]


title: kidney biopsy [N57]


title: kidney biopsy [N60]


title: kidney biopsy [N278]


title: kidney biopsy [N168]


title: kidney biopsy [N4]


title: kidney biopsy [N88]


title: kidney biopsy [N9]


title: kidney biopsy [N23]


title: kidney biopsy [N148]


title: kidney biopsy [N228]


title: kidney biopsy [N280]


title: kidney biopsy [N244]


title: kidney biopsy [N240]


title: kidney biopsy [N40]


title: kidney biopsy [N41]


title: kidney biopsy [N195]


title: kidney biopsy [N117]


title: kidney biopsy [N157]


title: RTS_B1_DMSO

status: Public on Dec 01 2021

city: Houston

first: An

last: Xu

state: TX

institute: UThealth Houston

data_processing:
QC: FastQC v0.11.5. Sequenced reads were then trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
RNAeq Alignment: RNAStar
RNAseq normalization: Featurecounts
Genome_build: Genome_build: hg19
Supplementary_files_format_and_content: Supplementary_files_format_and_content: RNASeq: tab-delimited text files include FPKM values for each Sample .csv

source_name: late osteoblasts_DMSO

growth_protocol: MSCs and Obs were differentiated from iPSCs using defined mesenchymal stem cell medium or osteoblast differentiation medium as appropriate, and then collected at MSC day 60, OB day 15, and OB day 24.

extract_protocol:
mRNA were extracted using Trizol (Invitrogen, 10296010).
For RNASeq, library construction was performed using NEBNext Ultra II RNA Library Prep Kit (E7770) following manufacturer’s instructions. Libraries were submitted to PE150 high-throughput sequencing.

treatment_protocol: Day 24 OBs were treated with DMSO

value: iPSC-derived osteoblasts

value: RECQL4 mut/ mut

tag: disease state

value: Rothmund-Thomson Syndrome


title: RTS_B2_DMSO


title: kidney biopsy [N142]


title: F_B3_D24OB

source_name: late osteoblasts

value: RECQL4 mut/wt

value: healthy carrier


title: RTS_B2_IACS

source_name: late osteoblasts_IACS-010759 treated

treatment_protocol: Day 24 OBs were treated with 100nM IACS-010759 for 48 hours


title: kidney biopsy [N266]


title: kidney biopsy [N285]


title: kidney biopsy [N141]


title: kidney biopsy [N59]


title: kidney biopsy [N214]

value: no


title: F_A2_D24OB


title: F_B2_D24OB


title: F_B1_D24OB


title: F_A3_D24OB


title: F_A1_D24OB


title: kidney biopsy [N163]


title: kidney biopsy [N113]


title: kidney biopsy [N276]


title: kidney biopsy [N100]


title: kidney biopsy [N7]


title: kidney biopsy [N140]


title: kidney biopsy [N144]


title: kidney biopsy [N126]


title: kidney biopsy [N155]


title: kidney biopsy [N25]


title: RTS_B1_IACS


title: RTS_A1_D24OB


title: RTS_B1_D24OB


title: F_B3_D15OB

source_name: early osteoblasts


title: RTS_A2_D24OB


title: RTS_B2_D24OB


title: RTS_A3_D24OB


title: F_B2_D15OB


title: RTS_A3_D15OB


title: RTS_A1_D15OB


title: F_B1_D15OB


title: F_A2_D15OB


title: RTS_B3_D15OB


title: F_A1_D15OB


title: RTS_B1_D15OB


title: F_B2_MSC

source_name: mesenchymal stem cells

value: iPSC-derived MSCs


title: F_A3_D15OB


title: F_B3_MSC


title: F_B1_MSC


title: kidney biopsy [N91]


title: F_A3_MSC


title: kidney biopsy [N185]


title: RTS_B3_D24OB


title: kidney biopsy [N160]


title: RTS_B3_MSC


title: RTS_B2_MSC


title: RTS_B1_MSC


title: RTS_A2_MSC


title: RTS_A3_MSC


title: RTS_A2_D15OB


title: RTS_A1_MSC


title: BLCA_Nac_269

status: Public on Nov 19 2021

city: Lund

first: Gottfrid

last: Sjodahl

address: Medicon Village

department: Department of Translational Medicine

country: Sweden

institute: Lund Univeristy

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials â€¢ Heat cocktails at 99Â° for 5 minutes, then 42Â° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). â€¢ Transfer 200Î¼l of hyb solution to each array, then tape holes and parafilm. â€¢ Hybridize 16 hours at 45Â° at 60rpmâ€¢ Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Raw data was RNA normalized, adjusted for labeling batch using ComBat and merged by median probe set values per gene symbol.
Platform design info was retrieved via bioconductor: pd.hugene.1.0.st.v1
Platform design info was retrieved via bioconductor: pd.hugene.1.0.st.v1
Raw data from RMA was quantile normalized, adjusted for labeling batch using ComBat, and merged by median probe set values per gene symbol.

source_name: FFPE tissue specimen

label_protocol: SensationPlus FFPE Amplification and WT labeling kit (samples 1-32) or GeneChip WT Pico kit (samples 33-149)

growth_protocol: not applicable

extract_protocol: Total RNA was extracted using the HighPure FFPET kit (Roche)

treatment_protocol: not applicable

tag: overlap with previous submisson gse83586

tag: labeling kit

value: GeneChip WT Pico kit

tag: labeling batch

tag: clinical tnm-staging

tag: neoadjuvant vs induction chemotherapy

value: neoadjuvant

tag: pathologic tn stage rc specimen

tag: lundtax rna subtype

value: UroB

tag: lundtax ihc subtype

value: GU

tag: consensus classifier subtype

value: StromaRich


title: BLCA_Nac_147

value: Uro


title: RTS_B2_D15OB

tag: cell type

tag: genotype


title: BLCA_Nac_206

value: LumU


title: BLCA_Nac_145

value: Ba/Sq

value: BASQ


title: BLCA_Nac_125

value: induction


title: BLCA_Nac_127


title: F_A2_MSC


title: BLCA_Nac_126

value: UroC

value: LumP


title: BLCA_Nac_121

value: NE-like


title: BLCA_Nac_116


title: F_A1_MSC

value: RECQL4 mut/wt


title: BLCA_Nac_110

value: UroA


title: BLCA_Nac_109


title: BLCA_Nac_122

value: Mes-like


title: BLCA_Nac_103


title: BLCA_Nac_98


title: BLCA_Nac_97


title: BLCA_Nac_108


title: BLCA_Nac_88


title: BLCA_Nac_55


title: BLCA_Nac_46


title: BLCA_Nac_47


title: BLCA_Nac_45


title: BLCA_Nac_42


title: BLCA_Nac_52


title: BLCA_Nac_80


title: BLCA_Nac_76

value: pTCisNx


title: BLCA_Nac_138

value: GeneChip WT Pico kit


title: BLCA_Nac_85

value: neoadjuvant


title: BLCA_Nac_123

value: LumNS


title: BLCA_Nac_33


title: BLCA_Nac_19


title: BLCA_Nac_111


title: BLCA_Nac_41


title: BLCA_Nac_22


title: BLCA_Nac_120


title: BLCA_Nac_143


title: BLCA_Nac_11

value: GU


title: BLCA_Nac_10


title: BLCA_Nac_6

value: UroB


title: BLCA_Nac_3


title: BLCA_Nac_144

value: StromaRich


title: BLCA_Nac_2

value: Uro


title: 3T3_t0_rep1_atac

first: Michael

middle: Joseph

last: Guertin

address: 400 Farmington Ave

department: Center for Cell Analysis and Modeling

institute: University of Connecticut

description: accessible DNA

data_processing:
adapter trimming: cutadapt 1.8.1
FASTQ deduplication: https://raw.githubusercontent.com/WarrenDavidAnderson/genomeAnalysis/master/PROseq/deduplicator.py
FASTX trimming and reverse complementing: fastx_trimmer, fastx_reverse_complement 0.0.14. Note that the first 8 bases of the read are a UMI and need to be trimmed.
alignment: bowtie2 2.2.5
file manipulation: samtools 1.2
file manipulation: seqOutBias v1.1.3
all PRO-seq details and code: https://github.com/WarrenDavidAnderson/genomeAnalysis/tree/master/PROseq
all ATAC-seq details and code: https://github.com/WarrenDavidAnderson/genomeAnalysis/tree/master/ATACseq
Genome_build: mm10
Supplementary_files_format_and_content: PRO: stranded bigWig counts files; ATAC: bigWig counts file

source_name: 3T3-L1 cells

growth_protocol: 3T3-L1 cells are from Dr. Thurl Harris and were were grown in high glucose Dulbecco’s Modified Eagle Medium containing 10% newborn calf serum, 1% fetal calf serum, 100 U/mL penicillin g-sodium, and 100 μg/mL streptomycin sulfate

treatment_protocol: A final concentration of 0.25 U/mL Insulin, 250 nM dexamethasone, and 0.5 mM 3-isobutyl-1-methylxanthine was added at indicated times

tag: cell line

value: 3T3-L1 cells

tag: treatment


title: 3T3_t0_rep3_atac

description: accessible DNA


title: 3T3_6d_rep3_atac

description: accessible DNA

value: 6 days adipogenesis cocktail


title: 3T3_t0_rep2_atac

description: accessible DNA


title: 3T3_60min_rep1_atac

description: accessible DNA

value: 60 minutes adipogenesis cocktail


title: 3T3_60min_rep2_atac

description: accessible DNA


title: 3T3_6d_rep1_atac

description: accessible DNA


title: BLCA_Nac_13


title: BLCA_Nac_7

value: Ba/Sq

value: BASQ


title: Primed hiPSC well day 7 rep. 2

status: Public on Nov 11 2021

city: Santander

first: Lucio

last: Di Filippo

state: Cantabria

address: PCTCAN - Cl. Albert Einstein, 22

country: Spain

institute: IBBTEC

description: 3'DGE mRNA-seq

data_processing:
Illumina novaSeq base call (BCL) files are converted in fastq file through bcl2fastq (version v2.20.0.422)
Sequence reads were trimmed using bbduk software (bbmap suite 37.31)
Alignment was performed with STAR 2.6.0a.
The expression levels of genes were determined with HTseq-counts 0.9.1.
Differential expression analysis was performed using edgeR
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample

source_name: HPD06 induced primed (isogenic, naïve hiPSCs-derived)

extract_protocol:
RNA was extracted with RNeasy Plus Micro Kit (Qiagen) following manufacturer instructions.
NEGEDIA Digital mRNA-seq research grade sequencing service (Next Generation Diagnostics srl).

value: Human primed induced pluripotent stem cells

tag: culture system

value: Glass coverslip in standard plate

tag: culture conditions

value: On 2.5percent Matrigel growth factor reduced (MRF, Corning), cultured in Essential 8 medium (E8, Stemcell Technologies)

tag: time point

value: Day 7 after seeding


title: 3T3_40min_rep3_atac

description: accessible DNA

value: 40 minutes adipogenesis cocktail


title: Primed hiPSC well day 7 rep. 3

description: 3'DGE mRNA-seq


title: 3T3_4hr_rep1_atac

description: accessible DNA

value: 4 hours adipogenesis cocktail


title: 3T3_40min_rep1_atac

description: accessible DNA


title: 3T3_4hr_rep2_atac

description: accessible DNA


title: Primed hiPSC microfluidics day 7 rep. 3

description: 3'DGE mRNA-seq

value: Microfluidics


title: 3T3_2hr_rep3_atac

description: accessible DNA

value: 2 hours adipogenesis cocktail


title: Primed hiPSC well day 7 rep. 1

description: 3'DGE mRNA-seq


title: 3T3_20min_rep1_atac

description: accessible DNA

value: 20 minutes adipogenesis cocktail


title: 3T3_2hr_rep1_atac

description: accessible DNA


title: 3T3_3hr_rep2_atac

description: accessible DNA

value: 3 hours adipogenesis cocktail


title: 3T3_20min_rep2_atac

description: accessible DNA


title: 3T3_2hr_rep2_atac

description: accessible DNA


title: 3T3_20min_rep3_atac

description: accessible DNA


title: 3T3_3hr_rep1_atac

description: accessible DNA


title: 3T3_3hr_rep3_atac

description: accessible DNA


title: 3T3_6d_rep2_atac

description: accessible DNA


title: 3T3_60min_rep3_atac

description: accessible DNA


title: 3T3_4hr_rep3_atac

description: accessible DNA


title: 3T3_40min_rep2_atac

description: accessible DNA


title: Primed hiPSC microfluidics day 7 rep. 1

description: 3'DGE mRNA-seq


title: Primed hiPSC well day 4 rep. 2

description: 3'DGE mRNA-seq

value: Day 4 after seeding


title: Primed hiPSC microfluidics day 4 rep. 3

description: 3'DGE mRNA-seq


title: Primed hiPSC microfluidics day 7 rep. 2

description: 3'DGE mRNA-seq


title: Primed hiPSC microfluidics day 4 rep. 2

description: 3'DGE mRNA-seq


title: Primed hiPSC well day 4 rep. 3

description: 3'DGE mRNA-seq


title: Primed hiPSC microfluidics day 4 rep. 1

description: 3'DGE mRNA-seq


title: Primed hiPSC well day 4 rep. 1

description: 3'DGE mRNA-seq


title: Primed hiPSC well day 1 rep. 3

description: 3'DGE mRNA-seq

value: Day 1 after seeding


title: Naive hiPSC well day 7 rep. 2

description: 3'DGE mRNA-seq

source_name: Human naïve induced pluripotent stem cells (naïve hiPSCs, HPD06, from Nat Cell Biol. 2019 Feb;21(2):275-286)

value: Human naive induced pluripotent stem cells

value: On a confluent layer of mitotically inactive MEFs (DR4, ATCC) in RSeT medium (Stemcell Technologies)


title: Naive hiPSC microfluidics day 7 rep. 3

description: 3'DGE mRNA-seq


title: Naive hiPSC microfluidics day 7 rep. 1

description: 3'DGE mRNA-seq


title: Naive hiPSC well day 7 rep. 1

description: 3'DGE mRNA-seq


title: Naive hiPSC microfluidics day 4 rep. 3

description: 3'DGE mRNA-seq


title: Naive hiPSC well day 4 rep. 1

description: 3'DGE mRNA-seq


title: Primed hiPSC microfluidics day 1 rep. 1

description: 3'DGE mRNA-seq


title: Naive hiPSC microfluidics day 4 rep. 1

description: 3'DGE mRNA-seq


title: Naive hiPSC well day 1 rep. 3

description: 3'DGE mRNA-seq


title: Primed hiPSC microfluidics day 1 rep. 3

description: 3'DGE mRNA-seq


title: Naive hiPSC well day 7 rep. 3

description: 3'DGE mRNA-seq


title: Naive hiPSC well day 1 rep. 2

description: 3'DGE mRNA-seq


title: Primed hiPSC well day 1 rep. 1

description: 3'DGE mRNA-seq


title: Naive hiPSC well day 4 rep. 3

description: 3'DGE mRNA-seq


title: Naive hiPSC microfluidics day 4 rep. 2

description: 3'DGE mRNA-seq


title: Naive hiPSC well day 4 rep. 2

description: 3'DGE mRNA-seq


title: Naive hiPSC well day 1 rep. 1

description: 3'DGE mRNA-seq


title: Naive hiPSC microfluidics day 1 rep. 3

description: 3'DGE mRNA-seq


title: Naive hiPSC microfluidics day 1 rep. 2

description: 3'DGE mRNA-seq


title: Naive hiPSC microfluidics day 1 rep. 1

description: 3'DGE mRNA-seq


title: HFF microfluidics day 7 rep. 1

description: 3'DGE mRNA-seq

source_name: fibroblasts (HFF-1, ATCC)

value: Fibroblast

value: On Vitronectin (25 microg/ml) in High Glucose Dulbecco’s modified Eagle Medium (DMEM, ThermoFisher Scientific) supplemented with 10percent Fetal Bovine Serum (FBS, ThermoFisher Scientific)


title: HFF well day 7 rep. 3

description: 3'DGE mRNA-seq


title: HFF well day 7 rep. 1

description: 3'DGE mRNA-seq


title: HFF microfluidics day 7 rep. 2

description: 3'DGE mRNA-seq


title: HFF microfluidics day 7 rep. 3

description: 3'DGE mRNA-seq


title: Primed hiPSC well day 1 rep. 2

description: 3'DGE mRNA-seq


title: HFF well day 4 rep. 3

description: 3'DGE mRNA-seq


title: HFF well day 4 rep. 2

description: 3'DGE mRNA-seq


title: Naive hiPSC microfluidics day 7 rep. 2

description: 3'DGE mRNA-seq


title: HFF microfluidics day 4 rep. 2

description: 3'DGE mRNA-seq


title: HFF microfluidics day 1 rep. 2

description: 3'DGE mRNA-seq


title: HFF well day 1 rep. 3

description: 3'DGE mRNA-seq


title: HFF microfluidics day 1 rep. 3

description: 3'DGE mRNA-seq