title: kidney biopsy_NH646


title: kidney biopsy_NH640

status: Public on Jan 16 2026

type: RNA

city: Edmonton

first: Jessica

last: Chang

address: 250 Heritage Medical Research Centre

department: Medicine

country: Canada

institute: University of Alberta

hyb_protocol: 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

molecule: total RNA

organism: Homo sapiens

source_name: kidney 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 (Affymetrix, Santa Clara, CA).

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

tag: mmdx (abmr/mixed, no abmr/mixed)

value: No ABMR/Mixed

tag: tissue

value: kidney biopsy


title: Day 14, low MOI control, MOI10, imatinib, MiniSeq_rep2

type: SRA

city: San Francisco

first: Stefan

last: Oberlin

address: 505 Parnassus Ave

department: Department of Microbiology and Immunology

country: USA

institute: University of California, San Francisco

description:
Library name: D14_C3_MOI10_imatinib_MiniSeq_rep2
counts_sublib_screen.csv

library_source: genomic

data_processing:
Read preprocessing and counting of the sequencing data of the sub partitioned CRISPRi library used for the cell essentiality and drug tolerance screen was performed as follows. Forward reads are first trimmed with BBDuk (parameters: ktrim=l minlen=20 k=10 mink=6 hdist=1 tpe tbo skipr2) to remove the human U6 sequence trailing the spacer sequence (5’-TTGTGGAAAGGACGAAACACCG-3’). Forward and reverse reads are then hard clipped to 20 and 21 bases respectively. Forward reads are counted for perfect matches to the guide RNA library using R 4.5.0 with the packages ShortRead23  and dplyr. To validate sublibrary-specific cloning, guide RNA sequences were counted hierarchically, where reads are first counted only for the sublibrary the guide RNA is expected to originate from to avoid multiple counting of guide RNA represented in multiple of the sublibraries. Effect sizes at the gene level are estimated with MAGeCK (version 0.5.7)25  using non-target controls as control sgRNA. Within each condition day 0  samples are compared to untreated and treated samples at day 14.
Data processing of the dual guide RNA CRISPRi library used for the cell sorting screen of ICAM-1 levels was performed as follows. Forward reads are first trimmed with Cutadapt26  to remove the mouse U6 sequence trailing the spacer sequence (5’- ATCCCTTGGAGAACCACCTTGTTGG-3’). Forward, reverse and index 2 reads, representing guide RNA 1, guide RNA 2 and the associated barcode, are then hard clipped to 19, 19 and 10 bases respectively. Guide RNA 1 and guide RNA 2 to barcode combinations are individually counted for perfect matches to the guide RNA library and the 41 barcodes using R 4.5.0 with the packages ShortRead and dplyr. These individual counts are subsequently added yielding for each gene 41 individual barcode counts. These barcode counts are used to estimate gene-level score with MAGeCK again using non-target controls as control sgRNA.
Assembly: hg38
Supplementary files format and content: sgRNA quantification data per samples
Library strategy: CRISPR Screen

molecule: genomic DNA

source_name: K-562 dCas9-Zim3

growth_protocol: K-562 cells are grown in advanced RPMI (Gibco), 10%FBS (Gibco), 1x Pen-Strep (Gibco) and grown at 37 °C, 5% CO2.

extract_protocol:
gDNA of live cells is extacted with the Quick-DNA 96 Kit (Zymo). gDNA of fixed cells is extacted by Phenol/Chloroform extraction. Cell pellets are resuspended and incubated overnight at 65 °C in 400µl of ChIP lysis buffer (1% SDS, 50 mM Tris, pH 8, 10 mM EDTA) with 16 µl 5 M NaCl. 8µl of RNAse A (10mg/ml - Thermo Fisher Scientific) is added the next day and incubated at 37 °C for 1 h followed by adding 8µl of Proteinase K (20mg/ml - Thermo Fisher Scientific) and a 1 h 55 °C incubation step. Genomic DNA was then isolated with phenol:chloroform:isoamyl alcohol, ethanol precipitated and washed with 70% ethanol. DNA was resuspended in water.
Genomic DNA is PCR amplified with NEBNext Ultra II Q5 polymerase with primers amplifying the sgRNA cassette.

treatment_protocol: Cells are treated for 14 days with Imatinib at IC50 (230 nM) or a corresponding DMSO control.

tag: cell line

value: K-562 dCas9-Zim3


title: kidney biopsy_NH637

value: ABMR/Mixed


title: Day 0, low MOI control, MOI20, DMSO, MiniSeq_rep2

description:
Library name: D0_C3_MOI20_none_MiniSeq_rep2
counts_sublib_screen.csv


title: Day 0, low MOI control, MOI30, DMSO, MiniSeq_rep1

description:
Library name: D0_C3_MOI30_none_MiniSeq_rep1
counts_sublib_screen.csv


title: kidney biopsy_NH636


title: Day 0, low MOI control, MOI20, DMSO, MiniSeq_rep1

description:
Library name: D0_C3_MOI20_none_MiniSeq_rep1
counts_sublib_screen.csv


title: Flag_Cluster_Rep1

city: New Haven

first: Don

last: Nguyen

state: Connecticut

address: 310 Cedar Street

department: Pathology

institute: Yale University

description: Library name: 3D_Rep1

data_processing:
All samples were quality controlled using FastQC (Babraham Bioinformatics).
Narrow peaks (H3K27Ac, FLAG-KDM2A) were trimmed with TrimGalore (Babraham Bioinformatics) and FLAG-KDM2A reads were cleaned with SMARTCleaner. Broad peaks (H3K36me) were trimmed Trimmomatic. Experiments were aligned against hg38 using Bowtie2.
Peak calling was done using MACS2 (narrow) and MACS3 (broad).
Average coverage files were generated using deepTools tools: bamCoverage, bigwigAverage, and bigwigCompare. Prior to generation, optical duplicates were removed using Picard Tools (Broad Institute), and poor-quality reads filtered using samTools20. All coverage files were normalized for sequencing depth using the counts per million (CPM) method, and averaged using bigwigAverage.
Assembly: hg38
Supplementary files format and content: Average BigWig files of CPM normalized reads for each methylation IP  are provided. MACS2 called peaks are provided for FLAG samples.

growth_protocol: H2030-BrM3 cells were grown  under cluster forming conditions in the presence of doxycycline for 5 days.

extract_protocol:
H3K27Ac: Samples were sent to Active Motif (Carlsbad, CA) for ChIP-Seq. Active Motif prepared chromatin, performed ChIP reactions, generated libraries, sequenced the libraries and performed basic data analysis. In brief, cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by adding lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp with Active Motif’s EpiShear probe sonicator (cat# 53051). Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by SPRI beads clean up (Beckman Coulter) and quantitation by Qubit. Extrapolation to the original chromatin volume allowed determination of the total chromatin yield. An aliquot of chromatin (30 ug) was precleared with protein A agarose beads (Invitrogen). Genomic DNA regions of interest were isolated using 4ug of antibody against H3K27Ac (Active Motif, catalog number 39133, lot number 06921014). Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.   FLAG and H3K36Me: FLAG-KDM2A samples were double-fixed using 2mM ethylene glycol bis(scuccinimidyl succinate) (EGS) (Thermo Scientific cat. 21565) for 1h followed by 1% formaldehyde for ten minutes.  H3K36 methylation samples were fixed with 1% formaldehyde alone.  Reactions were quenched with glycine to a final concentration of 0.125M. Pellets were washed with PBS and lysed in complete sonication buffer (20mM Tris pH 8.0, 2mM EDTA, 0.5mM EGTA, 1x protease inhibitors (Roche), 0.5% SDS, and 0.5mM PMSF) prior to sonication with a QSonica Q800. Fragment size (200-500bp) from extracted DNA was confirmed by agarose gel and quantified by Qubit. Input was aliquoted from 20% of total material, and chromatin samples were subsequently pre-cleared for 1 hour at 4ºC with immunoprecipitation (IP) buffer (20mM Tris pH 8.0, 2mM EDTA, 0.5% Triton X-100, 150mM NaCl, and 10% Glycerol) and Protein A/G beads. IP for proteins of interest was conducted using protein A/G beads and 10µg of antibody. For H3K36 methylation IPs Drosophila spike-in chromatin (100ng)  (Active Motif cat. 53083) and spike-in antibody (5μg) (Active Motif cat. 61686)were added. IPs were washed then eluted in a buffer of 100mM NaHC03, 1% SDS. Both IP and input samples were proteinase K treated, reverse crosslinked, and purified by phenol-chloroform extraction with ethanol precipitation.
H3K27Ac: Illumina sequencing libraries (a custom type, using the same paired read adapter oligonucleotides described by Bentley et al., 2008)) were prepared from the ChIP and Input DNAs on an automated system (Apollo 342, Wafergen Biosystems/Takara). After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 500  (75 nt reads, single end).  FLAG and H3K36Me: Samples were checked by Agilent Bioanalyzer, and libraries were prepared by the using ThruPlex DNA Seq (Takara Bio. cat. R400674) for H3K36 libraries, and DNA SMART ChiP-Seq (Takara Bio.cat. 634865) for FLAG libraries. Libraries were barcoded, pooled, and sequenced (PE) on Illumina NovaSeq X and NovaSeq 6000 machines. Please note, H3K36 methylation libraries were  initially sequenced on the NovaSeq 6000 then subsequently on the NovaSeq X  for additional coverage depth. Fastq files from these runs were concatinated head to tail prior to any anaylsis, and these pooled files are provided here for convenience. Files from each individual sequencing run are available upon request.

tag: cell type

value: Human metastatic lung adenocarcinoma


title: kidney biopsy_NH638


title: kidney biopsy_NH635


title: kidney biopsy_NH633


title: kidney biopsy_NH634


title: kidney biopsy_NH632


title: Flag_Control_Input_Rep1

description: Library name: 2D_Input_Rep1


title: Flag_Control_Rep2

description: Library name: 2D_Rep2


title: Flag_Control_Rep1

description: Library name: 2D_Rep1


title: kidney biopsy_NH629


title: kidney biopsy_NH630


title: kidney biopsy_NH628


title: day6_aKG8_2

city: Okayama

first: Shigeki

last: Suzuki

state: Okayama

address: 2-5-1 Shikata-cho, Kita-ku

department: Department of Operative Dentistry

country: Japan

institute: Okayama University

description:
Library name: Sample 8
RH8_TagDir/ reads normalized to 10000000 mapped reads (0.48)
RH8

library_source: transcriptomic

data_processing:
Adapter trimming was conducted with Trim galore with default setting and then aligned to a reference genome (hg38) using HISAT2. The gene expression at exons was quantified using `analyzeRepeast.pl ` command in HOMER using `-strand both` and `-count exons` followed by `getDiffExpression.pl` in HOMER using -batch` to identify expressed genes.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for all samples

molecule: polyA RNA

source_name: periodontal ligament

growth_protocol: PDLF cells were maintained in DMEM.

extract_protocol:
RNA was isolated from PDLF with RNAiso plus. Purified RNA was DNase-treated and further used for RNA-seq analyses.
Input RNA was converted to cDNA libraries using the NEBNExt poly(A) mRNA magnetic isolation module. Libraries were sequenced using 150-bp paired-end reads on an illumine Novaseq instruments.

treatment_protocol: PDLF cells were cultured in induction medium (low glucose DMEM with ascorbic acid (100 mg/ml) and beta-glecerophosphate (10 mM) in the presence or absence of aKG.

value: periodontal ligament

value: periodontal ligament fibroblasts

value: Lonza

tag: genotype

tag: treatment

value: long-term culture with aKG 8mM

tag: batch


title: day6_aKG8_1

description:
Library name: Sample 7
RH7_TagDir/ reads normalized to 10000000 mapped reads (0.52)
RH7


title: day6_aKG4_2

description:
Library name: Sample 6
RH6_TagDir/ reads normalized to 10000000 mapped reads (0.51)
RH6

value: long-term culture with aKG 4mM


title: kidney biopsy_NH627


title: day6_aKG4_1

description:
Library name: Sample 5
RH5_TagDir/ reads normalized to 10000000 mapped reads (0.54)
RH5


title: Flag_Cluster_Rep2

description: Library name: 3D_Rep2


title: Flag_Cluster_Input_Rep2

description: Library name: 3D_Input_Rep2


title: kidney biopsy_NH622


title: kidney biopsy_NH623


title: kidney biopsy_NH631


title: Flag_Control_Input_Rep2

description: Library name: 2D_Input_Rep2


title: kidney biopsy_NH625


title: day6_aKG0_2

description:
Library name: Sample 4
RH4_TagDir/ reads normalized to 10000000 mapped reads (0.45)
RH4

value: long-term culture without aKG


title: kidney biopsy_NH647


title: Flag_Cluster_Input_Rep1

description: Library name: 3D_Input_Rep1


title: kidney biopsy_NH624


title: kidney biopsy_NH620


title: kidney biopsy_NH621


title: control_DNA_2

description:
Library name: Sample 8
ss1491_4_TagDir/ Tag Count in given bp (21052638.5 Total, normalization factor = 1, effective total = 10000000)

data_processing:
Reads were trimmed using Trimmomatic, aligned to hg38 using Bowtie2 v2.5.1, PCR duplicates were removed using MarkDuplicates, and replicate concordance was assessed using deepTools. Peaks were called using HOMER v4.11 using ultrasonicated DNA as a control. Differentially enriched peaks were identified across the groups using HOMER mergePeaks with -d given and default settings.
Assembly: hg38
Supplementary files format and content: Tag Count in given bp (normalization factor = 1, effective total = 10000000)

extract_protocol:
Cells were processed using the ATAC-seq Kit (#53150; Active Motif, Carlsbad, CA, USA) according to the manufacturer’s protocol.
Libraries were sequenced as 150-bp paired-end reads on a NovaSeq platform.

value: sonicated chromatin


title: kidney biopsy_NH626


title: day0_2

description:
Library name: Sample 2
RH2_TagDir/ reads normalized to 10000000 mapped reads (0.54)
RH2


title: kidney biopsy_NH618


title: kidney biopsy_NH619


title: control_DNA_1

description:
Library name: Sample 7
ss1491_3_TagDir/ Tag Count in given bp (56328377.5 Total, normalization factor = 1, effective total = 10000000)


title: kidney biopsy_NH617


title: day0_1

description:
Library name: Sample 1
RH1_TagDir/ reads normalized to 10000000 mapped reads (0.52)
RH1


title: PDLF_day6_aKG8_1

description:
Library name: Sample 5
ss1664_15_TagDir/ Tag Count in given bp (47729750.0 Total, normalization factor = 1, effective total = 10000000)


title: kidney biopsy_NH616


title: kidney biopsy_NH615


title: kidney biopsy_NH613


title: PDLF_day6_aKG0_2

description:
Library name: Sample 4
ss1664_12_TagDir/ Tag Count in given bp (55619961.5 Total, normalization factor = 1, effective total = 10000000)


title: PDLF_day6_aKG0_1

description:
Library name: Sample 3
ss1664_11_TagDir/ Tag Count in given bp (53763245.5 Total, normalization factor = 1, effective total = 10000000)


title: PDLF_day0_2

description:
Library name: Sample 2
ss1664_10_TagDir/ Tag Count in given bp (27738237.5 Total, normalization factor = 1, effective total = 10000000)


title: PDLF_day6_aKG8_2

description:
Library name: Sample 6
ss1664_16_TagDir/ Tag Count in given bp (26244085.5 Total, normalization factor = 1, effective total = 10000000)


title: kidney biopsy_NH614


title: kidney biopsy_NH611


title: PDLF_day0_1

description:
Library name: Sample 1
ss1664_9_TagDir/ Tag Count in given bp (25369489.0 Total, normalization factor = 1, effective total = 10000000)


title: peripheral blood mononuclear cells, HC, sample_157

city: Hefei

first: Lanxin

last: Pan

state: Anhui

address: 96 Jinzhai Road, Baohe District

country: China

institute: The First Affiliated Hospital of University of Science and Technology of China

description: Library name: 157

library_source: transcriptomic single cell

data_processing:
Sequencing reads were processed using Cell Ranger software (v7.1.0). Reads were aligned to the GRCh38 (hg38) human reference genome and transcriptome, and gene-cell count matrices were generated and merged across samples. Downstream data preprocessing and analysis were performed using Scanpy (v1.10.3).
Genes detected in fewer than three cells were excluded, and cells with more than 6% mitochondrial gene content were removed. Doublets were identified and excluded using DoubletDetection (v4.2) with default parameters. Cells expressing between 200 and 6,000 genes were retained for normalization and logarithmic transformation.
Dimensionality reduction and clustering were performed based on a neighborhood graph, followed by Leiden clustering. Cell types were annotated using established marker genes, and differential gene expression analysis was conducted using the Wilcoxon rank-sum test with multiple testing correction.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and Matrix Market files

source_name: blood

extract_protocol:
Peripheral blood mononuclear cells were isolated from peripheral whole blood samples using standard density gradient centrifugation. Single-cell suspensions were prepared immediately after isolation, washed with phosphate-buffered saline, and assessed for cell viability prior to library preparation.
Single-cell RNA-seq libraries were constructed using the 10x Genomics Chromium Single Cell 3' Reagent Kits v3.1 according to the manufacturer’s instructions. Briefly, PBMC suspensions were loaded onto the Chromium Controller for gel bead-in-emulsion (GEM) generation, followed by reverse transcription, cDNA amplification, and library construction. Final libraries were sequenced on the Illumina NovaSeq 6000 platform to generate single-cell RNA sequencing data.

value: blood

value: peripheral blood mononuclear cells

tag: disease state

value: HC

tag: age (y)

tag: Sex

value: female

tag: disease duration_(y)


title: kidney biopsy_NH609


title: kidney biopsy_NH610


title: peripheral blood mononuclear cells, HC, sample_172

description: Library name: 172

value: male


title: peripheral blood mononuclear cells, HC, sample_170

description: Library name: 170


title: peripheral blood mononuclear cells, HC, sample_130

description: Library name: 130


title: day6_aKG0_1

description:
Library name: Sample 3
RH3_TagDir/ reads normalized to 10000000 mapped reads (0.50)
RH3


title: kidney biopsy_NH612


title: kidney biopsy_NH607

value: No ABMR/Mixed


title: peripheral blood mononuclear cells, HC, sample_163

description: Library name: 163


title: peripheral blood mononuclear cells, HC, sample_133

description: Library name: 133


title: kidney biopsy_NH606

value: kidney biopsy


title: human chordoma_3_primary

city: Chongqing

first: Lei

last: Liu

address: 1 Youyi Road, Yuanjiagang, Yuzhong District

department: Department of Breast and Thyroid Surgery

institute: The First Affiliated Hospital of Chongqing Medical University, Chongqing, China

description: Human RNA expression value derived from Primeview Human Gene Expression (Affymetrix)

hyb_protocol: Array hybridization, washing, and staining were performed using the GeneChip® Hybridization, Wash and Stain Kit (Cat# 900720, Affymetrix, Santa Clara, CA, USA). Hybridization was carried out in a GeneChip® Hybridization Oven 645 (Cat# 00-0331-220V, Affymetrix), followed by washing and staining on a GeneChip® Fluidics Station 450 (Cat# 00-0079, Affymetrix), according to the manufacturer’s instructions.

scan_protocol: Microarray slides were scanned using a GeneChip® Scanner 3000 (Cat# 00-00212, Affymetrix, Santa Clara, CA, USA). Image acquisition and primary image processing were performed using GeneChip Command Console Software version 4.0 (Affymetrix) with default settings.

data_processing: Image data were acquired using GeneChip Command Console Software version 4.0 (Affymetrix) with default settings. Raw CEL files were imported into R software and normalized using the Robust Multi-array Average (RMA) algorithm implemented in the Bioconductor “affy” package. Differential gene expression analysis was performed using standard statistical methods, and statistical significance was defined as P < 0.05.

source_name: human chordoma

label_protocol: Approximately 2 μg of total RNA was used to generate biotin-labeled cRNA targets.

growth_protocol: Primary and recurrent chordoma tissue samples were obtained directly from patients at the time of surgical resection and were immediately processed for RNA extraction without in vitro culture.

extract_protocol: Total RNA was extracted from the above-mentioned tissues using TRIzol reagent (Invitrogen) according to the manufacturer’s protocol. RNA concentration and purity were measured using a NanoDrop ND-1000 spectrophotometer, and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: No treatments were applied to the biological materials prior to extract preparation.

value: primary chordoma


title: kidney biopsy_NH605


title: peripheral blood mononuclear cells, HC, sample_128

description: Library name: 128


title: peripheral blood mononuclear cells, T1D, sample_37

description: Library name: 37


title: kidney biopsy_NH604

value: ABMR/Mixed


title: kidney biopsy_NH608


title: peripheral blood mononuclear cells, T1D, sample_14

description: Library name: 14


title: kidney biopsy_NH603


title: kidney biopsy_NH671


title: peripheral blood mononuclear cells, T1D, sample_2

description: Library name: 2


title: peripheral blood mononuclear cells, T1D, sample_60

description: Library name: 60


title: kidney biopsy_NH601


title: kidney biopsy_NH602


title: peripheral blood mononuclear cells, T1D, sample_1

description: Library name: 1


title: kidney biopsy_NH600


title: kidney biopsy_NH598


title: peripheral blood mononuclear cells, T1D, sample_63

description: Library name: 63


title: peripheral blood mononuclear cells, HC, sample_168

description: Library name: 168


title: kidney biopsy_NH599


title: peripheral blood mononuclear cells, HC, sample_140

description: Library name: 140


title: kidney biopsy_NH596


title: kidney biopsy_NH595


title: kidney biopsy_NH593


title: peripheral blood mononuclear cells, HC, sample_174

description: Library name: 174


title: kidney biopsy_NH594


title: peripheral blood mononuclear cells, T1D, sample_45

description: Library name: 45


title: kidney biopsy_NH597


title: peripheral blood mononuclear cells, HC, sample_150

description: Library name: 150


title: peripheral blood mononuclear cells, HC, sample_154

description: Library name: 154


title: peripheral blood mononuclear cells, HC, sample_169

description: Library name: 169


title: peripheral blood mononuclear cells, HC, sample_129

description: Library name: 129


title: peripheral blood mononuclear cells, HC, sample_135

description: Library name: 135


title: peripheral blood mononuclear cells, HC, sample_148

description: Library name: 148


title: kidney biopsy_NH589


title: peripheral blood mononuclear cells, HC, sample_127

description: Library name: 127


title: kidney biopsy_NH588


title: kidney biopsy_NH592


title: peripheral blood mononuclear cells, T1D, sample_46

description: Library name: 46


title: peripheral blood mononuclear cells, T1D, sample_32

description: Library name: 32


title: kidney biopsy_NH584


title: kidney biopsy_NH591


title: peripheral blood mononuclear cells, T1D, sample_7

description: Library name: 7


title: peripheral blood mononuclear cells, T1D, sample_24

description: Library name: 24


title: kidney biopsy_NH583


title: kidney biopsy_NH582


title: Day 14, low MOI control, MOI30, imatinib, MiniSeq_rep1

description:
Library name: D14_C3_MOI30_imatinib_MiniSeq_rep1
counts_sublib_screen.csv

value: K-562 dCas9-Zim3


title: peripheral blood mononuclear cells, T1D, sample_59

description: Library name: 59


title: kidney biopsy_NH585


title: peripheral blood mononuclear cells, T1D, sample_80

description: Library name: 80


title: kidney biopsy_NH587


title: kidney biopsy_NH590


title: kidney biopsy_NH580


title: peripheral blood mononuclear cells, T1D, sample_93

description: Library name: 93


title: kidney biopsy_NH578


title: peripheral blood mononuclear cells, T1D, sample_17

description: Library name: 17


title: peripheral blood mononuclear cells, T1D, sample_78

description: Library name: 78


title: kidney biopsy_NH579


title: kidney biopsy_NH639


title: peripheral blood mononuclear cells, T1D, sample_112

description: Library name: 112


title: peripheral blood mononuclear cells, HC, sample_146

description: Library name: 146


title: peripheral blood mononuclear cells, HC, sample_131

description: Library name: 131


title: kidney biopsy_NH577


title: kidney biopsy_NH575


title: kidney biopsy_NH574


title: peripheral blood mononuclear cells, HC, sample_159

description: Library name: 159


title: peripheral blood mononuclear cells, HC, sample_147

description: Library name: 147


title: peripheral blood mononuclear cells, HC, sample_173

description: Library name: 173


title: peripheral blood mononuclear cells, HC, sample_152

description: Library name: 152


title: kidney biopsy_NH573


title: kidney biopsy_NH570


title: peripheral blood mononuclear cells, HC, sample_165

description: Library name: 165


title: peripheral blood mononuclear cells, HC, sample_161

description: Library name: 161


title: kidney biopsy_NH572


title: kidney biopsy_NH569


title: kidney biopsy_NH581


title: peripheral blood mononuclear cells, HC, sample_134

description: Library name: 134


title: peripheral blood mononuclear cells, HC, sample_132

description: Library name: 132


title: kidney biopsy_NH586


title: peripheral blood mononuclear cells, T1D, sample_118

description: Library name: 118


title: kidney biopsy_NH568


title: kidney biopsy_NH566


title: peripheral blood mononuclear cells, T1D, sample_19

description: Library name: 19


title: peripheral blood mononuclear cells, T1D, sample_86

description: Library name: 86


title: kidney biopsy_NH567


title: peripheral blood mononuclear cells, T1D, sample_20

description: Library name: 20


title: kidney biopsy_NH565


title: kidney biopsy_NH564


title: peripheral blood mononuclear cells, T1D, sample_36

description: Library name: 36


title: kidney biopsy_NH562


title: peripheral blood mononuclear cells, T1D, sample_120

description: Library name: 120


title: kidney biopsy_NH563


title: kidney biopsy_NH571


title: kidney biopsy_NH561


title: peripheral blood mononuclear cells, T1D, sample_113

description: Library name: 113


title: peripheral blood mononuclear cells, T1D, sample_103

description: Library name: 103


title: kidney biopsy_NH559


title: peripheral blood mononuclear cells, T1D, sample_31

description: Library name: 31


title: kidney biopsy_NH558


title: kidney biopsy_NH557


title: CP-A, p53 KO (Clone 3) + dnMCAK, Replicate 3

city: Oxford

first: Eileen

last: Parkes

address: Off Roosevelt Drive

department: Department of Oncology

country: United Kingdom

institute: University of Oxford

description: Library name: P53c9_dn_4

data_processing:
Illumina sequencing and data processing was performed by Novogene (UK). Sequencing outputs were converted into FASTQ reads, subjected to quality control (error-rate and GC-content assessment), and filtered to remove adapter-contaminated reads, reads with >10% unknown bases, and reads with >50% low-quality bases. Clean reads were mapped to the human reference genome GRCh38 using HISAT2 (v.2.0.5). Gene-level quantification was performed using featureCounts (v.1.5.0).
Assembly: GRCh38
Supplementary files format and content: gene read counts for all samples. Column headers correspond to sample library names (indicated in the sample description field)

extract_protocol:
RNA was isolated using the RNeasy Plus Mini Kit (Qiagen). RNA quality was assessed using the 5400 Fragment Analyzer System (Agilent).
Library construction was performed using Poly(A) selection by Novogene (UK).

treatment_protocol: Cells were seeded at a density of 5.0x10^5 cells in 100 mm cell culture dishes. After 24h, cell culture media was replaced with fresh media and incubated for an additional 48h.

value: hTERT-immortalized non-dysplastic Barrett's esophagus cell line

value: p53 KO + dnMCAK


title: CP-A, p53 KO (Clone 3) + dnMCAK, Replicate 1

description: Library name: P53c9_dn_1


title: CP-A, p53 KO (Clone 3) + dnMCAK, Replicate 2

description: Library name: P53c9_dn_2


title: CP-A, p53 KO (Clone 3) + p16 KO, Replicate 3

description: Library name: P53c9_P16_4

value: p53 KO + p16 KO


title: peripheral blood mononuclear cells, T1D, ssample_49

description: Library name: 49


title: kidney biopsy_NH556


title: kidney biopsy_NH555


title: kidney biopsy_NH552


title: kidney biopsy_NH553


title: CP-A, p53 KO (Clone 3) + p16 KO, Replicate 2

description: Library name: P53c9_P16_2


title: CP-A, p53 KO (Clone 3), Replicate 3

description: Library name: P53c9_4

value: p53 KO


title: CP-A, p53 KO (Clone 3) + p16 KO, Replicate 1

description: Library name: P53c9_P16_1


title: CP-A, p53 KO (Clone 2) + dnMCAK, Replicate 2

description: Library name: P53c4_dn_2


title: kidney biopsy_NH551


title: kidney biopsy_NH550


title: kidney biopsy_NH560


title: kidney biopsy_NH548


title: CP-A, p53 KO (Clone 3), Replicate 2

description: Library name: P53c9_2


title: kidney biopsy_NH545


title: kidney biopsy_NH546


title: kidney biopsy_NH544


title: kidney biopsy_NH547


title: kidney biopsy_NH554


title: CP-A, p53 KO (Clone 3), Replicate 1

description: Library name: P53c9_1


title: CP-A, p53 KO (Clone 2) + dnMCAK, Replicate 3

description: Library name: P53c4_dn_4


title: CP-A, p53 KO (Clone 2) + p16 KO, Replicate 1

description: Library name: P53c4_P16_1


title: CP-A, p53 KO (Clone 2) + p16 KO, Replicate 3

description: Library name: P53c4_P16_4


title: CP-A, p53 KO (Clone 2), Replicate 3

description: Library name: P53c4_4


title: kidney biopsy_NH549


title: CP-A, p53 KO (Clone 2), Replicate 1

description: Library name: P53c4_1


title: kidney biopsy_NH540


title: CP-A, p53 KO (Clone 2) + p16 KO, Replicate 2

description: Library name: P53c4_P16_2


title: CP-A, p53 KO (Clone 2), Replicate 2

description: Library name: P53c4_2


title: kidney biopsy_NH543


title: CP-A, p53 KO (Clone 1) + dnMCAK, Replicate 3

description: Library name: P53c2_dn_4


title: CP-A, p53 KO (Clone 1) + dnMCAK, Replicate 2

description: Library name: P53c2_dn_2


title: CP-A, p53 KO (Clone 1) + p16 KO, Replicate 3

description: Library name: P53c2_P16_4


title: kidney biopsy_NH541


title: kidney biopsy_NH542


title: kidney biopsy_NH536


title: kidney biopsy_NH539


title: CP-A, p53 KO (Clone 1) + p16 KO, Replicate 2

description: Library name: P53c2_P16_2


title: kidney biopsy_NH537


title: kidney biopsy_NH534


title: CP-A, p53 KO (Clone 1) + p16 KO, Replicate 1

description: Library name: P53c2_P16_1


title: kidney biopsy_NH533


title: CP-A, p53 KO (Clone 1), Replicate 2

description: Library name: P53c2_2


title: CP-A, Cas9 control, Replicate 3

description: Library name: Cas9_4


title: CP-A, Cas9 control, Replicate 1

description: Library name: Cas9_1


title: kidney biopsy_NH531


title: CP-A, p53 KO (Clone 1), Replicate 1

description: Library name: P53c2_1


title: KGN cells, siOGT2_2, 48h

city: Zhenjiang

first: Caifang

last: Ren

address: Xiangshan Road

institute: Jiangsu University

description: Library name: siOGT2_2

data_processing:
First, adapter sequences at the 3' ends were removed using Cutadapt (v1.15). Second, reads with an average quality score below Q20 were filtered out. All downstream analyses were performed using the resulting high-quality, cleaned data. Clean reads were aligned to the human reference genome (Homo_sapiens. GRCh38) using HISAT2 with default parameters. Gene expression levels were quantified as fragments per kilobase of transcript per million mapped reads (FPKM).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: Ovary

growth_protocol: The human ovarian granulosa cell line KGN was routinely cultured in DMEM/F12 complete medium supplemented with 10% fetal bovine serum (FBS) and antibiotics at 37 °C in a humidified atmosphere containing 5% CO₂.

extract_protocol:
Total RNA was extracted from KGN cells using TRIzol reagent (Thermo Fisher Scientific), and RNA integrity and purity were confirmed prior to library construction.
cDNA libraries were prepared using the NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (NEB) according to the manufacturer’s instructions.

treatment_protocol: For transfection, to knock down OGT expression, cells were transfected with small interfering RNAs (siRNAs) targeting human OGT mRNA (Shanghai GenePharma, China) using Lipofectamine 3000 (Thermo Fisher Scientific) according to the manufacturer's instructions. The siRNA sequences are listed in Supplementary File 1. Briefly, cells were subcultured one day prior to transfection, and the transfection was performed when they reached approximately 60–70% confluence. Cells were harvested 48 hours post-transfection for subsequent gene expression analysis.

value: Ovary

value: KGN

value: ovarian granulosa cells

value: WT

value: siRNA transfection


title: kidney biopsy_NH535


title: kidney biopsy_NH576


title: kidney biopsy_NH530


title: kidney biopsy_NH526


title: kidney biopsy_NH528


title: CP-A, p53 KO (Clone 1), Replicate 3

description: Library name: P53c2_4


title: CP-A, Cas9 control, Replicate 2

description: Library name: Cas9_2


title: kidney biopsy_NH532


title: kidney biopsy_NH529


title: KGN cells, siOGT2_1, 48h

description: Library name: siOGT2_1


title: kidney biopsy_NH525


title: kidney biopsy_NH527


title: KGN cells, siOGT1_2, 48h

description: Library name: siOGT1_2


title: kidney biopsy_NH524


title: kidney biopsy_NH522


title: KGN cells, siNC_2, 48h

description: Library name: siNC_2


title: SK-GT-4 cGAS KO, 500nM Reversine, Replicate 1

description:
Library name: S_KO_Rev_1
Column name in gene_count.xls: S_KO_Rev_1

data_processing:
Illumina sequencing and data processing was performed by Novogene (UK). Sequencing outputs were converted into FASTQ reads, subjected to quality control (error-rate and GC-content assessment), and filtered to remove adapter-contaminated reads, reads with >10% unknown bases, and reads with >50% low-quality bases. Clean reads were mapped to the human reference genome GRCh38 using HISAT2 (v.2.0.5). Gene-level quantification was performed using featureCounts (v.1.5.0).
Assembly: GRCh38
Supplementary files format and content: Excel file containing gene read counts for all samples (gene_count.xls), wherein column names correspond to sample library names.

treatment_protocol: Cells were seeded at a density of 5.0x10^5 cells in 100 mm cell culture dishes. After 24h, cell culture media was replaced with 0.5 μM reversine- or DMSO-treated media, and incubated for an additional 48h.

value: Esophageal adenocarcinoma

value: cGAS KO

value: 500nM Reversine, 48h


title: SK-GT-4 cGAS KO, 500nM Reversine, Replicate 2

description:
Library name: S_KO_Rev_2
Column name in gene_count.xls: S_KO_Rev_2


title: kidney biopsy_NH521


title: kidney biopsy_NH523

value: No ABMR/Mixed


title: KGN cells, siNC_1, 48h

description: Library name: siNC_1


title: SK-GT-4 cGAS KO, DMSO, Replicate 1

description:
Library name: S_KO_Ctr_1
Column name in gene_count.xls: S_KO_Ctr_1

value: DMSO, 48h


title: SK-GT-4 cGAS KO, 500nM Reversine, Replicate 3

description:
Library name: S_KO_Rev_3
Column name in gene_count.xls: S_KO_Rev_3


title: KGN cells, siOGT1_1, 48h

description: Library name: siOGT1_1


title: kidney biopsy_NH515

value: kidney biopsy


title: SK-GT-4 cGAS KO, DMSO, Replicate 2

description:
Library name: S_KO_Ctr_2
Column name in gene_count.xls: S_KO_Ctr_2


title: kidney biopsy_NH517


title: kidney biopsy_NH513


title: kidney biopsy_NH518


title: kidney biopsy_NH520


title: kidney biopsy_NH512


title: SK-GT-4 cGAS KO, DMSO, Replicate 3

description:
Library name: S_KO_Ctr_3
Column name in gene_count.xls: S_KO_Ctr_3


title: kidney biopsy_NH516


title: kidney biopsy_NH514

value: ABMR/Mixed


title: CP-A, p53 KO (Clone 1) + dnMCAK, Replicate 1

description: Library name: P53c2_dn_1


title: kidney biopsy_NH519


title: SK-GT-4 Cas9 control, 500nM Reversine, Replicate 1

description:
Library name: S_Cas9_Rev_1
Column name in gene_count.xls: S_Cas9_Rev_1

value: cGAS WT


title: SK-GT-4 Cas9 control, 500nM Reversine, Replicate 3

description:
Library name: S_Cas9_Rev_3
Column name in gene_count.xls: S_Cas9_Rev_3


title: SK-GT-4 Cas9 control, 500nM Reversine, Replicate 2

description:
Library name: S_Cas9_Rev_2
Column name in gene_count.xls: S_Cas9_Rev_2


title: SK-GT-4 Cas9 control, DMSO, Replicate 3

description:
Library name: S_Cas9_Ctr_3
Column name in gene_count.xls: S_Cas9_Ctr_3


title: SK-GT-4 Cas9 control, DMSO, Replicate 1

description:
Library name: S_Cas9_Ctr_1
Column name in gene_count.xls: S_Cas9_Ctr_1


title: SK-GT-4 Cas9 control, DMSO, Replicate 2

description:
Library name: S_Cas9_Ctr_2
Column name in gene_count.xls: S_Cas9_Ctr_2


title: OE33 cGAS KO, 500nM Reversine, Replicate 1

description:
Library name: O_KO_Rev_1
Column name in gene_count.xls: O_KO_Rev_1


title: OE33 cGAS KO, DMSO, Replicate 3

description:
Library name: O_KO_Ctr_3
Column name in gene_count.xls: O_KO_Ctr_3


title: kidney biopsy_NH511


title: OE33 cGAS KO, DMSO, Replicate 2

description:
Library name: O_KO_Ctr_2
Column name in gene_count.xls: O_KO_Ctr_2


title: kidney biopsy_NH505


title: OE33 Cas9 control, 500nM Reversine, Replicate 3

description:
Library name: O_Cas9_Rev_3
Column name in gene_count.xls: O_Cas9_Rev_3


title: OE33 cGAS KO, 500nM Reversine, Replicate 3

description:
Library name: O_KO_Rev_3
Column name in gene_count.xls: O_KO_Rev_3


title: OE33 Cas9 control, 500nM Reversine, Replicate 2

description:
Library name: O_Cas9_Rev_2
Column name in gene_count.xls: O_Cas9_Rev_2


title: kidney biopsy_NH509


title: kidney biopsy_NH507


title: OE33 Cas9 control, 500nM Reversine, Replicate 1

description:
Library name: O_Cas9_Rev_1
Column name in gene_count.xls: O_Cas9_Rev_1


title: kidney biopsy_NH510


title: kidney biopsy_NH506


title: kidney biopsy_NH504


title: OE33 cGAS KO, 500nM Reversine, Replicate 2

description:
Library name: O_KO_Rev_2
Column name in gene_count.xls: O_KO_Rev_2


title: kidney biopsy_NH501


title: kidney biopsy_NH498


title: kidney biopsy_NH508


title: OE33 cGAS KO, DMSO, Replicate 1

description:
Library name: O_KO_Ctr_1
Column name in gene_count.xls: O_KO_Ctr_1


title: OE33 Cas9 control, DMSO, Replicate 3

description:
Library name: O_Cas9_Ctr_3
Column name in gene_count.xls: O_Cas9_Ctr_3


title: kidney biopsy_NH495


title: kidney biopsy_NH503


title: kidney biopsy_NH497


title: OE33 Cas9 control, DMSO, Replicate 1

description:
Library name: O_Cas9_Ctr_1
Column name in gene_count.xls: O_Cas9_Ctr_1


title: KU036

city: New York

first: Lorenzo

last: Tomassoni

address: 1130 St Nicholas Avenue

institute: Columbia University

description:
Library name: Sample 6
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger Software and CITE-Seq count
cell metadata are included in the file SupplTable_GEO_metadata_TRAM_sc_Cell_Lines.xlsx, available on the series record.
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: KU036: HPAC - SW1990 (DMSO, TRAM, HCQ, TRAM & HCQ)

extract_protocol:
After 24h of incubation cells were collected for single cell analysis. For each single cell run, 8 samples were combined. Each pre-incubated with a human specific barcode using Total Seq B antibodies. Vehicle and treated cells for each cell line were run in the same lane. Viability for each sample was above 80%
Dissociated cells were processed for single-cell gene expression capture (scRNA-seq) using the 10X Chromium 3’ Library, following the manufacturer’s user guide

treatment_protocol: Optimal concentrations to inhibit MAPK pathway were specific to each cell line and they were optimized using pERK Western Blot analysis

value: PDA Cell Lines

value: HPAC - SW1990

value: DMSO, Trametinib, Hydroxychloroquine, Trametinib & Hydroxychloroquine


title: kidney biopsy_NH500


title: kidney biopsy_NH499


title: OE33 Cas9 control, DMSO, Replicate 2

description:
Library name: O_Cas9_Ctr_2
Column name in gene_count.xls: O_Cas9_Ctr_2


title: KA092: KP4 - scATAC

description:
Library name: Sample 2
10x Genomics
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz

library_source: genomic single cell

data_processing:
FASTQ files have been processed and aligned using Cell Ranger (pipeline arc-2.0.0). Gene expression profiles and scATAC-seq data were filtered for low quality cells using default parameters as reported on Signac website
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: PDA Cell Lines

extract_protocol:
Nuclei from KP4 were isolated using the nuclei isolation kit (CG000505, 10x Genomics) and the manufacturer protocol. Briefly, 1e6 cells were trypsinized and washed once with cold PBS. Cells were then dissociated with lysis buffer and passed through nuclei isolation column. After centrifugation at 16,000 rcf and 4C , nuclei pellet was resuspended in debris removal buffe and washed with cold PBS and 10% BSA . Next, Intact nuclei were resuspended in the resuspension buffer containing 20X Nuclei Buffer, Reducing Agent B and nuclease-free water.
Nuclei were profiled for both gene expression and open chromatin using 10x Genomics Chromium Single Cell ATAC-Seq microfluidic cell processing (10x Genomics) and sequenced on an Illumina NovaSeq 6000Multiome data were analyzed using the Signac package

tag: library type

value: ATAC


title: kidney biopsy_NH502


title: KU037

description:
Library name: Sample 7
10x Genomics

source_name: KU037: MIAPACA2 (DMSO, TRAM, HCQ, TRAM & HCQ); KP4 - PK45H - PANC1 - HPAFII (TRAM & HCQ Long Time Point)

value: MIAPACA2 - KP4 - PK45H - PANC1 - HPAFII


title: KA092: KP4 - snRNA

description:
Library name: Sample 1
10x Genomics

value: mRNA


title: KU024

description:
Library name: Sample 2
10x Genomics

source_name: KU024: KP4 - HPAFII (DMSO, TRAM, HCQ, TRAM & HCQ)

value: KP4 - HPAFII


title: KU032

description:
Library name: Sample 3
10x Genomics

source_name: KU032: PATU8988S (DMSO, TRAM, HCQ, Trametinib & HCQ); PATU8988S - PK45H - PANC1 - ASPC1 (TRAM & HCQ Long Time Point)

value: PATU8988S - PK45H - PANC1 - ASPC1


title: kidney biopsy_NH489


title: KU033

description:
Library name: Sample 4
10x Genomics

source_name: KU033: PK45H - S2013 (DMSO, TRAM, HCQ, TRAM & HCQ)


title: kidney biopsy_NH492


title: kidney biopsy_NH491


title: kidney biopsy_NH490


title: kidney biopsy_NH493


title: KU035

description:
Library name: Sample 5
10x Genomics

source_name: KU035: CAPAN1 - BXPC3 (DMSO, TRAM, HCQ, TRAM & HCQ)

value: CAPAN1 - BXPC3


title: kidney biopsy_NH486


title: plasmid

description:
Library name: plasmid
counts_ICAM1_screen_barcode.csv

value: K-562 dCas9-Zim3


title: kidney biopsy_NH538


title: kidney biopsy_NH488


title: kidney biopsy_NH496


title: kidney biopsy_NH487


title: kidney biopsy_NH494


title: MOI5, mid CD54, 250x coverage, rep 2

description:
Library name: MOI5mid50_R2
counts_ICAM1_screen_barcode.csv


title: MOI5, mid CD54, 250x coverage, rep 1

description:
Library name: MOI5mid50_R1
counts_ICAM1_screen_barcode.csv


title: MOI5, mid CD54, 25x coverage, rep 2

description:
Library name: MOI5mid5_R2
counts_ICAM1_screen_barcode.csv


title: MOI5, mid CD54, 25x coverage, rep 1

description:
Library name: MOI5mid5_R1
counts_ICAM1_screen_barcode.csv


title: kidney biopsy_NH485


title: MOI5, mid CD54, 125x coverage, rep 2

description:
Library name: MOI5mid25_R2
counts_ICAM1_screen_barcode.csv


title: kidney biopsy_NH484


title: MOI5, mid CD54, 125x coverage, rep 1

description:
Library name: MOI5mid25_R1
counts_ICAM1_screen_barcode.csv


title: kidney biopsy_NH482


title: MOI5, low CD54, 250x coverage, rep 1

description:
Library name: MOI5low50_R1
counts_ICAM1_screen_barcode.csv


title: MOI5, low CD54, 250x coverage, rep 2

description:
Library name: MOI5low50_R2
counts_ICAM1_screen_barcode.csv


title: kidney biopsy_NH483


title: CP-A, p53 KO (Clone 2) + dnMCAK, Replicate 1

description: Library name: P53c4_dn_1

value: hTERT-immortalized non-dysplastic Barrett's esophagus cell line

value: p53 KO + dnMCAK


title: kidney biopsy_NH478


title: kidney biopsy_NH481


title: MOI5, low CD54, 125x coverage, rep 1

description:
Library name: MOI5low25_R1
counts_ICAM1_screen_barcode.csv


title: MOI5, low CD54, 25x coverage, rep 2

description:
Library name: MOI5low5_R2
counts_ICAM1_screen_barcode.csv


title: MOI5, low CD54, 125x coverage, rep 2

description:
Library name: MOI5low25_R2
counts_ICAM1_screen_barcode.csv


title: kidney biopsy_NH480

value: No ABMR/Mixed


title: kidney biopsy_NH477


title: MOI5, high CD54, 250x coverage, rep 2

description:
Library name: MOI5high50_R2
counts_ICAM1_screen_barcode.csv


title: kidney biopsy_NH476


title: MOI5, low CD54, 25x coverage, rep 1

description:
Library name: MOI5low5_R1
counts_ICAM1_screen_barcode.csv


title: MOI5, high CD54, 250x coverage, rep 1

description:
Library name: MOI5high50_R1
counts_ICAM1_screen_barcode.csv


title: kidney biopsy_NH475


title: kidney biopsy_NH474


title: MOI5, high CD54, 25x coverage, rep 2

description:
Library name: MOI5high5_R2
counts_ICAM1_screen_barcode.csv


title: kidney biopsy_NH472


title: MOI5, high CD54, 125x coverage, rep 2

description:
Library name: MOI5high25_R2
counts_ICAM1_screen_barcode.csv


title: MOI5, high CD54, 125x coverage, rep 1

description:
Library name: MOI5high25_R1
counts_ICAM1_screen_barcode.csv


title: kidney biopsy_NH473


title: MOI5, high CD54, 25x coverage, rep 1

description:
Library name: MOI5high5_R1
counts_ICAM1_screen_barcode.csv


title: MOI0.3, mid CD54, 250x coverage, rep 2

description:
Library name: MOI03mid50_R2
counts_ICAM1_screen_barcode.csv


title: kidney biopsy_NH471


title: kidney biopsy_NH469


title: kidney biopsy_NH468


title: kidney biopsy_NH470


title: MOI0.3, mid CD54, 250x coverage, rep 1

description:
Library name: MOI03mid50_R1
counts_ICAM1_screen_barcode.csv


title: kidney biopsy_NH466


title: kidney biopsy_NH479


title: kidney biopsy_NH465


title: kidney biopsy_NH467


title: MOI0.3, mid CD54, 125x coverage, rep 2

description:
Library name: MOI03mid25_R2
counts_ICAM1_screen_barcode.csv


title: MOI0.3, mid CD54, 25x coverage, rep 1

description:
Library name: MOI03mid5_R1
counts_ICAM1_screen_barcode.csv


title: MOI0.3, mid CD54, 125x coverage, rep 1

description:
Library name: MOI03mid25_R1
counts_ICAM1_screen_barcode.csv


title: MOI0.3, low CD54, 250x coverage, rep 1

description:
Library name: MOI03low50_R1
counts_ICAM1_screen_barcode.csv


title: MOI0.3, low CD54, 250x coverage, rep 2

description:
Library name: MOI03low50_R2
counts_ICAM1_screen_barcode.csv


title: MOI0.3, mid CD54, 25x coverage, rep 2

description:
Library name: MOI03mid5_R2
counts_ICAM1_screen_barcode.csv


title: MOI0.3, low CD54, 25x coverage, rep 1

description:
Library name: MOI03low5_R1
counts_ICAM1_screen_barcode.csv


title: MOI0.3, low CD54, 25x coverage, rep 2

description:
Library name: MOI03low5_R2
counts_ICAM1_screen_barcode.csv


title: kidney biopsy_NH462


title: MOI0.3, low CD54, 125x coverage, rep 2

description:
Library name: MOI03low25_R2
counts_ICAM1_screen_barcode.csv


title: kidney biopsy_NH461


title: kidney biopsy_NH464


title: kidney biopsy_NH460


title: kidney biopsy_NH457


title: MOI0.3, high CD54, 250x coverage, rep 2

description:
Library name: MOI03high50_R2
counts_ICAM1_screen_barcode.csv


title: kidney biopsy_NH456


title: kidney biopsy_NH463


title: kidney biopsy_NH455


title: MOI0.3, high CD54, 250x coverage, rep 1

description:
Library name: MOI03high50_R1
counts_ICAM1_screen_barcode.csv


title: kidney biopsy_NH458


title: MOI0.3, low CD54, 125x coverage, rep 1

description:
Library name: MOI03low25_R1
counts_ICAM1_screen_barcode.csv


title: kidney biopsy_NH454


title: MOI0.3, high CD54, 25x coverage, rep 1

description:
Library name: MOI03high5_R1
counts_ICAM1_screen_barcode.csv


title: MOI0.3, high CD54, 25x coverage, rep 2

description:
Library name: MOI03high5_R2
counts_ICAM1_screen_barcode.csv


title: Day 14, low MOI control, MOI5, DMSO, rep2

description:
Library name: D14_C3_MOI5_none_rep2
counts_sublib_screen.csv


title: MOI0.3, high CD54, 125x coverage, rep 2

description:
Library name: MOI03high25_R2
counts_ICAM1_screen_barcode.csv


title: kidney biopsy_NH451


title: kidney biopsy_NH453


title: Day 14, low MOI control, MOI5, DMSO, rep1

description:
Library name: D14_C3_MOI5_none_rep1
counts_sublib_screen.csv


title: kidney biopsy_NH452


title: kidney biopsy_NH449


title: Day 14, low MOI control, MOI5, imatinib, rep2

description:
Library name: D14_C3_MOI5_imatinib_rep2
counts_sublib_screen.csv


title: MOI0.3, high CD54, 125x coverage, rep 1

description:
Library name: MOI03high25_R1
counts_ICAM1_screen_barcode.csv


title: kidney biopsy_NH447


title: kidney biopsy_NH450


title: kidney biopsy_NH446


title: Day 14, low MOI control, MOI5, imatinib, rep1

description:
Library name: D14_C3_MOI5_imatinib_rep1
counts_sublib_screen.csv


title: kidney biopsy_NH448


title: Day 14, low MOI control, MOI30, DMSO, rep2

description:
Library name: D14_C3_MOI30_none_rep2
counts_sublib_screen.csv


title: Day 14, low MOI control, MOI30, DMSO, rep1

description:
Library name: D14_C3_MOI30_none_rep1
counts_sublib_screen.csv


title: Day 14, low MOI control, MOI30, imatinib, rep1

description:
Library name: D14_C3_MOI30_imatinib_rep1
counts_sublib_screen.csv


title: kidney biopsy_NH445


title: kidney biopsy_NH444


title: Day 14, low MOI control, MOI30, imatinib, rep2

description:
Library name: D14_C3_MOI30_imatinib_rep2
counts_sublib_screen.csv


title: kidney biopsy_NH442


title: Day 14, low MOI control, MOI2p5, DMSO, rep2

description:
Library name: D14_C3_MOI2p5_none_rep2
counts_sublib_screen.csv


title: Day 14, low MOI control, MOI2p5, DMSO, rep1

description:
Library name: D14_C3_MOI2p5_none_rep1
counts_sublib_screen.csv


title: Day 14, low MOI control, MOI2p5, imatinib, rep1

description:
Library name: D14_C3_MOI2p5_imatinib_rep1
counts_sublib_screen.csv


title: Day 14, low MOI control, MOI20, DMSO, rep2

description:
Library name: D14_C3_MOI20_none_rep2
counts_sublib_screen.csv


title: kidney biopsy_NH459


title: kidney biopsy_NH440


title: Day 14, low MOI control, MOI20, DMSO, rep1

description:
Library name: D14_C3_MOI20_none_rep1
counts_sublib_screen.csv


title: Day 14, low MOI control, MOI20, imatinib, rep2

description:
Library name: D14_C3_MOI20_imatinib_rep2
counts_sublib_screen.csv


title: kidney biopsy_NH438


title: kidney biopsy_NH436


title: Day 14, low MOI control, MOI10, DMSO, rep1

description:
Library name: D14_C3_MOI10_none_rep1
counts_sublib_screen.csv


title: Day 14, low MOI control, MOI20, imatinib, rep1

description:
Library name: D14_C3_MOI20_imatinib_rep1
counts_sublib_screen.csv


title: Day 14, low MOI control, MOI2p5, imatinib, rep2

description:
Library name: D14_C3_MOI2p5_imatinib_rep2
counts_sublib_screen.csv


title: Day 14, low MOI control, MOI10, imatinib, rep2

description:
Library name: D14_C3_MOI10_imatinib_rep2
counts_sublib_screen.csv


title: Day 14, low MOI control, MOI1, DMSO, rep2

description:
Library name: D14_C3_MOI1_none_rep2
counts_sublib_screen.csv


title: kidney biopsy_NH432


title: kidney biopsy_NH431


title: Day 14, low MOI control, MOI1, DMSO, rep1

description:
Library name: D14_C3_MOI1_none_rep1
counts_sublib_screen.csv


title: Day 14, low MOI control, MOI1, imatinib, rep2

description:
Library name: D14_C3_MOI1_imatinib_rep2
counts_sublib_screen.csv


title: Day 14, low MOI control, MOI10, DMSO, rep2

description:
Library name: D14_C3_MOI10_none_rep2
counts_sublib_screen.csv


title: Day 14, low MOI control, MOI10, imatinib, rep1

description:
Library name: D14_C3_MOI10_imatinib_rep1
counts_sublib_screen.csv


title: kidney biopsy_NH435


title: kidney biopsy_NH430


title: kidney biopsy_NH426


title: Day 14, constant sgRNA, MOI5, DMSO, rep1

description:
Library name: D14_C2_MOI5_none_rep1
counts_sublib_screen.csv


title: Day 14, constant sgRNA, MOI5, imatinib, rep2

description:
Library name: D14_C2_MOI5_imatinib_rep2
counts_sublib_screen.csv


title: Day 14, low MOI control, MOI1, imatinib, rep1

description:
Library name: D14_C3_MOI1_imatinib_rep1
counts_sublib_screen.csv


title: kidney biopsy_NH424


title: Day 14, constant sgRNA, MOI5, DMSO, rep2

description:
Library name: D14_C2_MOI5_none_rep2
counts_sublib_screen.csv


title: KU023

description:
Library name: Sample 1
10x Genomics

source_name: KU023: ASPC1 - PANC1 (DMSO, TRAM, HCQ, TRAM & HCQ)

value: ASPC1 - PANC1


title: kidney biopsy_NH429

value: kidney biopsy


title: Day 14, constant sgRNA, MOI5, imatinib, rep1

description:
Library name: D14_C2_MOI5_imatinib_rep1
counts_sublib_screen.csv


title: kidney biopsy_NH439

value: ABMR/Mixed


title: Day 14, constant sgRNA, MOI30, DMSO, rep1

description:
Library name: D14_C2_MOI30_none_rep1
counts_sublib_screen.csv


title: Day 14, constant sgRNA, MOI30, DMSO, rep2

description:
Library name: D14_C2_MOI30_none_rep2
counts_sublib_screen.csv


title: kidney biopsy_NH423


title: Day 14, constant sgRNA, MOI30, imatinib, rep1

description:
Library name: D14_C2_MOI30_imatinib_rep1
counts_sublib_screen.csv


title: Day 14, constant sgRNA, MOI30, imatinib, rep2

description:
Library name: D14_C2_MOI30_imatinib_rep2
counts_sublib_screen.csv


title: kidney biopsy_NH422


title: kidney biopsy_NH420


title: Day 14, constant sgRNA, MOI2p5, DMSO, rep2

description:
Library name: D14_C2_MOI2p5_none_rep2
counts_sublib_screen.csv


title: kidney biopsy_NH417


title: Day 14, constant sgRNA, MOI2p5, DMSO, rep1

description:
Library name: D14_C2_MOI2p5_none_rep1
counts_sublib_screen.csv


title: kidney biopsy_NH416


title: Day 14, constant sgRNA, MOI2p5, imatinib, rep2

description:
Library name: D14_C2_MOI2p5_imatinib_rep2
counts_sublib_screen.csv


title: Day 14, constant sgRNA, MOI20, DMSO, rep2

description:
Library name: D14_C2_MOI20_none_rep2
counts_sublib_screen.csv


title: Day 14, constant sgRNA, MOI20, DMSO, rep1

description:
Library name: D14_C2_MOI20_none_rep1
counts_sublib_screen.csv


title: Day 14, constant sgRNA, MOI2p5, imatinib, rep1

description:
Library name: D14_C2_MOI2p5_imatinib_rep1
counts_sublib_screen.csv


title: kidney biopsy_NH418


title: kidney biopsy_NH414


title: Day 14, constant sgRNA, MOI20, imatinib, rep2

description:
Library name: D14_C2_MOI20_imatinib_rep2
counts_sublib_screen.csv


title: Day 14, constant sgRNA, MOI20, imatinib, rep1

description:
Library name: D14_C2_MOI20_imatinib_rep1
counts_sublib_screen.csv


title: kidney biopsy_NH412


title: Day 14, constant sgRNA, MOI10, DMSO, rep2

description:
Library name: D14_C2_MOI10_none_rep2
counts_sublib_screen.csv


title: kidney biopsy_NH425


title: kidney biopsy_NH428


title: Day 14, constant sgRNA, MOI10, imatinib, rep2

description:
Library name: D14_C2_MOI10_imatinib_rep2
counts_sublib_screen.csv


title: kidney biopsy_NH437


title: Day 14, constant sgRNA, MOI10, DMSO, rep1

description:
Library name: D14_C2_MOI10_none_rep1
counts_sublib_screen.csv


title: Day 14, constant cells, MOI5, imatinib, rep2

description:
Library name: D14_C1_MOI5_imatinib_rep2
counts_sublib_screen.csv


title: Day 14, constant cells, MOI5, imatinib, rep1

description:
Library name: D14_C1_MOI5_imatinib_rep1
counts_sublib_screen.csv


title: kidney biopsy_NH403


title: Day 14, constant cells, MOI5, DMSO, rep2

description:
Library name: D14_C1_MOI5_none_rep2
counts_sublib_screen.csv


title: kidney biopsy_NH406


title: Day 14, constant cells, MOI30, DMSO, rep2

description:
Library name: D14_C1_MOI30_none_rep2
counts_sublib_screen.csv


title: Day 14, constant cells, MOI5, DMSO, rep1

description:
Library name: D14_C1_MOI5_none_rep1
counts_sublib_screen.csv


title: Day 14, constant sgRNA, MOI10, imatinib, rep1

description:
Library name: D14_C2_MOI10_imatinib_rep1
counts_sublib_screen.csv


title: kidney biopsy_NH401


title: Day 14, constant cells, MOI30, DMSO, rep1

description:
Library name: D14_C1_MOI30_none_rep1
counts_sublib_screen.csv


title: kidney biopsy_NH402


title: kidney biopsy_NH411


title: Day 14, constant cells, MOI30, imatinib, rep2

description:
Library name: D14_C1_MOI30_imatinib_rep2
counts_sublib_screen.csv


title: kidney biopsy_NH441


title: kidney biopsy_NH400


title: Day 14, constant cells, MOI2p5, DMSO, rep1

description:
Library name: D14_C1_MOI2p5_none_rep1
counts_sublib_screen.csv


title: Day 14, constant cells, MOI2p5, imatinib, rep2

description:
Library name: D14_C1_MOI2p5_imatinib_rep2
counts_sublib_screen.csv


title: kidney biopsy_NH397


title: Day 14, constant cells, MOI2p5, DMSO, rep2

description:
Library name: D14_C1_MOI2p5_none_rep2
counts_sublib_screen.csv


title: Day 14, constant cells, MOI30, imatinib, rep1

description:
Library name: D14_C1_MOI30_imatinib_rep1
counts_sublib_screen.csv


title: Day 14, constant cells, MOI2p5, imatinib, rep1

description:
Library name: D14_C1_MOI2p5_imatinib_rep1
counts_sublib_screen.csv


title: Day 14, constant cells, MOI20, DMSO, rep2

description:
Library name: D14_C1_MOI20_none_rep2
counts_sublib_screen.csv


title: kidney biopsy_NH419


title: kidney biopsy_NH409


title: Day 14, constant cells, MOI20, DMSO, rep1

description:
Library name: D14_C1_MOI20_none_rep1
counts_sublib_screen.csv


title: kidney biopsy_NH391


title: kidney biopsy_NH443


title: kidney biopsy_NH389


title: Day 14, constant cells, MOI20, imatinib, rep2

description:
Library name: D14_C1_MOI20_imatinib_rep2
counts_sublib_screen.csv


title: Day 14, constant cells, MOI10, DMSO, rep1

description:
Library name: D14_C1_MOI10_none_rep1
counts_sublib_screen.csv


title: kidney biopsy_NH434


title: kidney biopsy_NH404


title: Day 14, constant cells, MOI10, imatinib, rep2

description:
Library name: D14_C1_MOI10_imatinib_rep2
counts_sublib_screen.csv


title: Day 14, constant cells, MOI20, imatinib, rep1

description:
Library name: D14_C1_MOI20_imatinib_rep1
counts_sublib_screen.csv


title: kidney biopsy_NH392


title: Day 14, constant cells, MOI10, DMSO, rep2

description:
Library name: D14_C1_MOI10_none_rep2
counts_sublib_screen.csv


title: kidney biopsy_NH387


title: kidney biopsy_NH408


title: kidney biopsy_NH388


title: kidney biopsy_NH415


title: kidney biopsy_NH405


title: Day 14, constant cells, MOI10, imatinib, rep1

description:
Library name: D14_C1_MOI10_imatinib_rep1
counts_sublib_screen.csv


title: Day 14, constant cells, MOI1, DMSO, rep2

description:
Library name: D14_C1_MOI1_none_rep2
counts_sublib_screen.csv


title: kidney biopsy_NH385


title: kidney biopsy_NH393


title: Day 14, constant cells, MOI1, DMSO, rep1

description:
Library name: D14_C1_MOI1_none_rep1
counts_sublib_screen.csv


title: Day 14, constant cells, MOI1, imatinib, rep2

description:
Library name: D14_C1_MOI1_imatinib_rep2
counts_sublib_screen.csv


title: Day 14, constant cells, MOI0p3, DMSO, rep2

description:
Library name: D14_C1_MOI0p3_none_rep2
counts_sublib_screen.csv


title: kidney biopsy_NH383


title: Day 14, constant cells, MOI1, imatinib, rep1

description:
Library name: D14_C1_MOI1_imatinib_rep1
counts_sublib_screen.csv


title: kidney biopsy_NH394


title: kidney biopsy_NH433


title: Day 14, constant cells, MOI0p3, DMSO, rep1

description:
Library name: D14_C1_MOI0p3_none_rep1
counts_sublib_screen.csv


title: Day 14, constant cells, MOI0p3, imatinib, rep2

description:
Library name: D14_C1_MOI0p3_imatinib_rep2
counts_sublib_screen.csv


title: kidney biopsy_NH379


title: kidney biopsy_NH384


title: kidney biopsy_NH381


title: Day 14, constant cells, MOI0p3, imatinib, rep1

description:
Library name: D14_C1_MOI0p3_imatinib_rep1
counts_sublib_screen.csv


title: kidney biopsy_NH399


title: Day 0, low MOI control, MOI5, DMSO, rep2

description:
Library name: D0_C3_MOI5_none_rep2
counts_sublib_screen.csv


title: kidney biopsy_NH380


title: kidney biopsy_NH378


title: kidney biopsy_NH421


title: Day 0, low MOI control, MOI5, DMSO, rep1

description:
Library name: D0_C3_MOI5_none_rep1
counts_sublib_screen.csv


title: Day 0, low MOI control, MOI30, DMSO, rep1

description:
Library name: D0_C3_MOI30_none_rep1
counts_sublib_screen.csv


title: Day 0, low MOI control, MOI30, DMSO, rep2

description:
Library name: D0_C3_MOI30_none_rep2
counts_sublib_screen.csv


title: kidney biopsy_NH407


title: kidney biopsy_NH376


title: Day 0, low MOI control, MOI2p5, DMSO, rep1

description:
Library name: D0_C3_MOI2p5_none_rep1
counts_sublib_screen.csv


title: Day 0, low MOI control, MOI2p5, DMSO, rep2

description:
Library name: D0_C3_MOI2p5_none_rep2
counts_sublib_screen.csv


title: kidney biopsy_NH427


title: kidney biopsy_NH375


title: Day 0, low MOI control, MOI20, DMSO, rep2

description:
Library name: D0_C3_MOI20_none_rep2
counts_sublib_screen.csv


title: kidney biopsy_NH372


title: kidney biopsy_NH396


title: kidney biopsy_NH374


title: kidney biopsy_NH410


title: Day 0, low MOI control, MOI20, DMSO, rep1

description:
Library name: D0_C3_MOI20_none_rep1
counts_sublib_screen.csv


title: kidney biopsy_NH373


title: Day 0, low MOI control, MOI10, DMSO, rep2

description:
Library name: D0_C3_MOI10_none_rep2
counts_sublib_screen.csv


title: kidney biopsy_NH398


title: kidney biopsy_NH370


title: kidney biopsy_NH390


title: Day 0, low MOI control, MOI10, DMSO, rep1

description:
Library name: D0_C3_MOI10_none_rep1
counts_sublib_screen.csv


title: kidney biopsy_NH413


title: Day 0, constant sgRNA, MOI5, DMSO, rep2

description:
Library name: D0_C2_MOI5_none_rep2
counts_sublib_screen.csv


title: Day 0, constant sgRNA, MOI5, DMSO, rep1

description:
Library name: D0_C2_MOI5_none_rep1
counts_sublib_screen.csv


title: Day 0, constant sgRNA, MOI30, DMSO, rep2

description:
Library name: D0_C2_MOI30_none_rep2
counts_sublib_screen.csv


title: kidney biopsy_NH377


title: Day 0, constant sgRNA, MOI30, DMSO, rep1

description:
Library name: D0_C2_MOI30_none_rep1
counts_sublib_screen.csv


title: Day 0, constant sgRNA, MOI2p5, DMSO, rep2

description:
Library name: D0_C2_MOI2p5_none_rep2
counts_sublib_screen.csv


title: Day 0, low MOI control, MOI1, DMSO, rep2

description:
Library name: D0_C3_MOI1_none_rep2
counts_sublib_screen.csv


title: Day 0, low MOI control, MOI1, DMSO, rep1

description:
Library name: D0_C3_MOI1_none_rep1
counts_sublib_screen.csv


title: kidney biopsy_NH364


title: Day 0, constant sgRNA, MOI2p5, DMSO, rep1

description:
Library name: D0_C2_MOI2p5_none_rep1
counts_sublib_screen.csv


title: kidney biopsy_NH365


title: kidney biopsy_NH360


title: kidney biopsy_NH367


title: kidney biopsy_NH363


title: kidney biopsy_NH366


title: kidney biopsy_NH368


title: Day 0, constant sgRNA, MOI20, DMSO, rep1

description:
Library name: D0_C2_MOI20_none_rep1
counts_sublib_screen.csv


title: kidney biopsy_NH361


title: kidney biopsy_NH395


title: Day 0, constant sgRNA, MOI10, DMSO, rep2

description:
Library name: D0_C2_MOI10_none_rep2
counts_sublib_screen.csv


title: Day 0, constant cells, MOI5, DMSO, rep1

description:
Library name: D0_C1_MOI5_none_rep1
counts_sublib_screen.csv


title: kidney biopsy_NH371


title: Day 0, constant sgRNA, MOI10, DMSO, rep1

description:
Library name: D0_C2_MOI10_none_rep1
counts_sublib_screen.csv


title: kidney biopsy_NH357


title: Day 0, constant sgRNA, MOI20, DMSO, rep2

description:
Library name: D0_C2_MOI20_none_rep2
counts_sublib_screen.csv


title: kidney biopsy_NH359


title: Day 0, constant cells, MOI5, DMSO, rep2

description:
Library name: D0_C1_MOI5_none_rep2
counts_sublib_screen.csv


title: kidney biopsy_NH386


title: Day 0, constant cells, MOI2p5, DMSO, rep2

description:
Library name: D0_C1_MOI2p5_none_rep2
counts_sublib_screen.csv


title: kidney biopsy_NH358


title: Day 0, constant cells, MOI30, DMSO, rep2

description:
Library name: D0_C1_MOI30_none_rep2
counts_sublib_screen.csv


title: Day 0, constant cells, MOI2p5, DMSO, rep1

description:
Library name: D0_C1_MOI2p5_none_rep1
counts_sublib_screen.csv


title: Day 0, constant cells, MOI20, DMSO, rep2

description:
Library name: D0_C1_MOI20_none_rep2
counts_sublib_screen.csv


title: Day 0, constant cells, MOI10, DMSO, rep1

description:
Library name: D0_C1_MOI10_none_rep1
counts_sublib_screen.csv


title: Day 0, constant cells, MOI10, DMSO, rep2

description:
Library name: D0_C1_MOI10_none_rep2
counts_sublib_screen.csv


title: kidney biopsy_NH369


title: Day 0, constant cells, MOI20, DMSO, rep1

description:
Library name: D0_C1_MOI20_none_rep1
counts_sublib_screen.csv


title: Day 0, constant cells, MOI30, DMSO, rep1

description:
Library name: D0_C1_MOI30_none_rep1
counts_sublib_screen.csv


title: Day 0, constant cells, MOI1, DMSO, rep1

description:
Library name: D0_C1_MOI1_none_rep1
counts_sublib_screen.csv


title: Day 0, constant cells, MOI0p3, DMSO, rep2

description:
Library name: D0_C1_MOI0p3_none_rep2
counts_sublib_screen.csv


title: kidney biopsy_NH346


title: kidney biopsy_NH349


title: kidney biopsy_NH347


title: kidney biopsy_NH351


title: kidney biopsy_NH350


title: kidney biopsy_NH353


title: kidney biopsy_NH352


title: kidney biopsy_NH382


title: human neural progenetor cells, postnatal day 60, rep 1

city: Los Angeles

first: Shaughn

last: Bell

state: CA

address: 8700 Beverly Blvd

department: Regenerative Medicine Institute

institute: Cedars-Sinai Medical Center

description: Library name: 04_human_invivo_hNPC_p60_1

data_processing:
Sample demultiplexing was performed by the Cedars-Sinai Applied Genomics, Computation and Translational Core.  Raw data were delivered as multiple gzipped fastq files.
Rat samples:  demultiplexed fastq files were run via CellRanger v7.1 using the "cellranger count" command using a CellRanger reference sequence previously complied using the "cellranger mkref" command and reference sequence Rnor_6.0.102
Human samples:  demultiplexed fastq files were run via CellRanger v6.1.2 using the "cellranger count" command using the 10x-provided reference GRCh38-2020-A
Assembly: Human: GRCh38, Rat: Rnor6.0.102
Supplementary files format and content: Rat:  CellRanger output filtered_feature_bc_matrix.h5 files
Supplementary files format and content: Human:  CellRanger output filtered_feature_bc_matrix directory (barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz)

source_name: hNPCs sorted from rat retina

growth_protocol: hNPC vials were rapidly thawed in a 37 °C water bath after removal from liquid nitrogen, followed by resuspension in prewarmed Stemline medium (Sigma, St. Louis, Missouri) supplemented with rhEGF (100 ng/mL; Millipore, Billerica, MA) and rhLIF (100 ng/mL; Millipore). The cell suspension was centrifuged at 200g for 5 minutes, and the pellet was resuspended in Balanced salt solution (BSS, Alcon). Cells were then labeled using PKH26 Red Fluorescent Cell Linker Kits (Sigma, St. Louis, Missouri) according to the manufacturer's protocol, and finally resuspended at a concentration of 30,000 cells/μL in BSS. Cells were kept on ice until transplantation.

extract_protocol:
Rats retinas were pooled, digested with papain, and dissociated into single-cell suspensions by manual trituration in ovomucoid solution. Single-cell suspensions from hNPC-treated and untreated retinas were labeled with DAPI. PKH26-labeled hNPCs, along with hNPC-treated and untreated retinal cells, were sorted using a FACS sorter and collected into 1.7 mL RNase-free tubes containing 2% BSA in PBS.
Library preparation was performed using the 10x Chromium v3 single-cell reagent kit, following the manufacturer's protocol.

treatment_protocol: 2 μL of the hNPC suspension (6 × 10^4 cells/eye) was injected into the subretinal space of both left and right eyes through a small scleral incision using a fine glass pipette (internal diameter 75-150μm) attached via tubing to a 25-μL syringe (Hamilton). To reduce intraocular pressure and minimize cell efflux, the cornea was punctured prior to injection. Immediately after injection, the fundus was examined for retinal damage or signs of vascular distress. Animals showing such issues were excluded from further study.

value: hNPCs sorted from rat retina

value: hNPCs

tag: strain

tag: time point


title: kidney biopsy_NH343


title: kidney biopsy_NH339


title: kidney biopsy_NH356


title: Day 0, constant cells, MOI0p3, DMSO, rep1

description:
Library name: D0_C1_MOI0p3_none_rep1
counts_sublib_screen.csv


title: human neural progenetor cells, postnatal day 90, rep 1

description: Library name: 06_human_invivo_hNPC_p90_1


title: kidney biopsy_NH340


title: kidney biopsy_NH341


title: kidney biopsy_NH344


title: kidney biopsy_NH338


title: kidney biopsy_NH348


title: human neural progenetor cells, postnatal day 60, rep 2

description: Library name: 05_human_invivo_hNPC_p60_2


title: human neural progenetor cells, pre-transplantation, rep 2

description: Library name: 02_human_invitro_hNPC_2

source_name: hNPCs


title: Day 0, constant cells, MOI1, DMSO, rep2

description:
Library name: D0_C1_MOI1_none_rep2
counts_sublib_screen.csv


title: kidney biopsy_NH336


title: human neural progenetor cells, pre-transplantation, rep 1

description: Library name: 01_human_invitro_hNPC_1


title: kidney biopsy_NH354


title: kidney biopsy_NH355


title: HAP1, SETX WT, DRIP(INPUT)

city: San Antonio

first: Hanzhou

last: Wang

state: TX

address: 8403 Floyd Curl Drive, MSC 7784

institute: UT Health at San Antonio

description: Library name: HAP1_WT_Input_S72

data_processing:
All data processing was performed using the RPipes workflow (v0.9.1) (https://github.com/Bishop-Laboratory/RLPipes).
Reads were aligned to the hg38 reference genome using bwa-mem within the RPipes framework.
Peak calling was conducted with MACS2 (v2.0) as part of the workflow,
bigWig files were generated using bamCoverage from deepTools. All computational steps were executed within the RPipes pipeline to ensure consistency and reproducibility.
Assembly: hg38
Supplementary files format and content: bigWig

growth_protocol: HAP1 wild-type (WT) and SETX knockout (KO) cells were cultured to 75–80% confluency (~6 × 10⁶ cells per 10-cm dish) before harvesting. Cells were washed with pre-warmed (37°C) DPBS, dissociated using 0.6 mL trypsin-express at 37°C for 2 minutes, and collected by centrifugation at 300g for 1 minute. The reaction was stopped by adding 1.5 mL of complete medium, and cells were washed twice with DPBS before being snap-frozen in dry ice and stored at -80°C until DRIP-seq

extract_protocol:
Genomic DNA was extracted from 5–8 million cells per replicate using SDS and proteinase K digestion, followed by phenol/chloroform/ethanol purification. DNA was digested overnight with XbaI, EcoRI, BsrGI, HindIII, and SspI in rCutSmart buffer. RNase H treatment was used as a negative control to degrade DNA-RNA hybrids. Post-cleanup, 12 μg of digested DNA per sample was incubated with 30 μL of S9.6 antibody to capture R-loops. Immunoprecipitation was performed by overnight rotation at 4°C, followed by binding to protein A/G beads for 2.5–4 hours. Bound DNA was eluted using proteinase K digestion at 55°C for 45 minutes, purified via phenol/chloroform/ethanol extraction, and resuspended in 10 mM Tris-HCl (pH 8.0). DNA was stored at -80°C until sequencing.
Library preparation was performed using the NEBNext® Ultra™ DNA Library Prep Kit for Illumina following the manufacturer’s instructions.

treatment_protocol: HAP1 wild-type and SETX KO cells were harvested without additional treatment.

value: Human cell line

tag: chip antibody


title: HAP1, SETX WT, DRIP(REP3)

description: Library name: HAP1_WT_3_S70


title: shKDM2A_H3K27Ac_Rep3

description: Library name: shKDM2A_H3K27Ac_Rep3

value: Human metastatic lung adenocarcinoma


title: shControl_H3K27Ac_Rep3

description: Library name: shControl_H3K27Ac_Rep3


title: kidney biopsy_NH335


title: shKDM2A_H3K27Ac_Rep2

description: Library name: shKDM2A_H3K27Ac_Rep2


title: kidney biopsy_NH334


title: kidney biopsy_NH345


title: HAP1, SETX WT, DRIP(RNH)

description: Library name: HAP1_WT_RNH_S71

value: RNH


title: shControl_H3K27Ac_Rep2

description: Library name: shControl_H3K27Ac_Rep2


title: HAP1, SETX WT, DRIP(REP2)

description: Library name: HAP1_WT_2_S69


title: Pooled_Input_Rep2

description: Library name: Yale_Pooled_Input_Rep2


title: kidney biopsy_NH362


title: shControl_H3K27Ac_Rep1

description: Library name: shControl_H3K27Ac_Rep1


title: HAP1, SETX KO, DRIP(RNH)

description: Library name: HAP1_KO_RNH_S76


title: Pooled_Input_Rep1

description: Library name: Yale_Pooled_Input_Rep1


title: HAP1, SETX WT, DRIP(REP1)

description: Library name: HAP1_WT_1_S68


title: shKDM2A_H3K27Ac_Rep1

description: Library name: shKDM2A_H3K27Ac_Rep1


title: RNA-seq, leaf, J2_233, chemical fertilizer, Year 2022

city: Tsukuba

first: Hirofunmi

last: Fukuda

state: Ibaraki

address: 1-31-1 Kannondai

institute: National Agriculture and Food Research Organization (NARO)

description:
Library name: J2_233
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_233

data_processing:
The libraries were sequenced using the Illumina NovaSeq X Plus. Sequencing was performed on the 25B flow cell with paired-end 150-bp and unique dual-index reads. The reads were preprocessed by CLC Genomics Workbench version 25.0 (Qiagen). Reads were first trimmed using the following parameters: quality limit of 0.05, maximum number of ambiguities 2. Next, raw reads were mapped to the genome assembly and gene sets of “Os-Nipponbare-Reference-IRGSP-1.0" with the following parameters: mismatch cost of 2, insertion–deletion cost of 3, length fraction of 0.8, similarity fraction of 0.8, and maximum number of hits of a read of 10. Then, uniquely mapped read counts were quantified. Genes with at least one raw read count in all of the library samples for each comparison were analyzed.
Assembly: Os-Nipponbare-IRGSP-1.0
Supplementary files format and content: csv file includes RNA-seq raw count on whole transcripts for each sample.

organism: Oryza sativa

source_name: leaf

growth_protocol: A hundred of  JAM2 lines (F5 and F6) in 2022 and 2023 were used in this study. Seeds soaked in water at 30°C for 2 days were sown in trays filled with soils and incubated at 30°C in the dark for 2 days. Seedlings were grown in a paddy field in Kannondai, Tsukuba, for a month, and then 33 seedlings per line were transplanted (11 plants 18 cm apart × 3 rows 30 cm apart, no replicates) into a nearby paddy field and cultivated for 5 months The dates of sowing was April 18 in 2022 and April 17 in 2023.

extract_protocol:
The most expanded leaf was collected from 9:00 to 11:00 am as one biological replicate, immediately frozen in liquid N, and stored at -80 °C until sample crushing. Frozen samples were crushed by multi-specimen cell disruption device (BMS-A20TP, BMS) just before RNA extraction. Total RNAs from each sample were extracted using RNeasy Plant Mini Kit (QIAGEN), referring to the manufacture’s protocol. One biological replicate was obtained for each JAM2 line at 6 weeks after transplanting:  July 1, 2022 and June 29, 2023.
RNA-sequencing (RNA-seq) libraries were prepared using the NEBNext Ultra II Directional mRNA-seq kit for Illumina (New England Biolabs), following the manufacturer’s protocols.

treatment_protocol: Chemical fertilizer was applied as a basal dressing at 56:176:56:90:120 kg/ha (N:PO4:K:Mg:SiO2).

value: leaf

value: Akidawara x Iwaidawara x Tachiharuka x Toyomeki

value: control


title: kidney biopsy_NH331

source_name: kidney biopsy


title: HAP1, SETX KO, DRIP(INPUT)

description: Library name: HAP1_KO_Input_S77


title: kidney biopsy_NH330


title: RNA-seq, leaf, J2_322, chemical fertilizer, Year 2022

description:
Library name: J2_322
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_322


title: RNA-seq, leaf, J2_294, chemical fertilizer, Year 2022

description:
Library name: J2_294
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_294


title: kidney biopsy_NH342


title: kidney biopsy_NH329


title: RNA-seq, leaf, J2_260, chemical fertilizer, Year 2022

description:
Library name: J2_260
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_260


title: kidney biopsy_NH333


title: RNA-seq, leaf, J2_227, chemical fertilizer, Year 2022

description:
Library name: J2_227
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_227


title: HAP1, SETX KO, DRIP(REP3)

description: Library name: HAP1_KO_3_S75


title: RNA-seq, leaf, J2_209, chemical fertilizer, Year 2022

description:
Library name: J2_209
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_209


title: HAP1, SETX KO, DRIP(REP2)

description: Library name: HAP1_KO_2_S74


title: AM045: T2 Trametinib - Batch 2B

description:
Library name: Sample 6
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger Software followed by additional downstream analyses
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
UMI-bc containing lentiviral constructs were transduced into KP4 cell line with MOI <0.1 followed by puromycin selection. After all the non-transduced cells were dead, we seeded 8000 cells / well (multiple wells in total), followed by incubation which lasted approx. 1-2 population doublings (daughter cells were created for each UMI-BC containing cell). At this point we performed the 1st 10x chromium run (time point 1) so that 50% of the cells were used for this this initial time point run, and the remaining 50% of the cells were cultured further for the 2nd time point. The 2nd time point chromium run was done approx. 10 population doublings later.
Portion of amplified cDNA-library was re-amplified with specific ORF_BC_amplif_oligo_F & ORF_BC_amplif_R to enrich for the lineage tracing UMI-BC (the same oligos were used in the Pooled TF overexpression assay in our publication). Finally this amplified fragment was spiked in to the whole-transcriptome part of the library with estimated 10% abundance.
scRNA-seq based bar-coded lineage tracing

value: PDA Cell Line

value: Time Point 2 - Trametinib


title: RNA-seq, leaf, J2_264, chemical fertilizer, Year 2022

description:
Library name: J2_264
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_264


title: HAP1, SETX KO, DRIP(REP1)

description: Library name: HAP1_KO_1_S73

value: STEX KO


title: AM044: T2 Trametinib - Batch 2B

description:
Library name: Sample 5
10x Genomics


title: RNA-seq, leaf, J2_273, chemical fertilizer, Year 2022

description:
Library name: J2_273
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_273


title: RNA-seq, leaf, J2_218, chemical fertilizer, Year 2022

description:
Library name: J2_218
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_218


title: RNA-seq, leaf, J2_262, chemical fertilizer, Year 2022

description:
Library name: J2_262
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_262


title: kidney biopsy_NH327


title: kidney biopsy_NH326


title: RNA-seq, leaf, J2_277, chemical fertilizer, Year 2022

description:
Library name: J2_277
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_277


title: kidney biopsy_NH324


title: RNA-seq, leaf, J2_235, chemical fertilizer, Year 2022

description:
Library name: J2_235
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_235


title: human neural progenetor cells, pre-transplantation, rep 3

description: Library name: 03_human_invitro_hNPC_3


title: RNA-seq, leaf, J2_255, chemical fertilizer, Year 2022

description:
Library name: J2_255
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_255


title: kidney biopsy_NH322


title: RNA-seq, leaf, J2_221, chemical fertilizer, Year 2022

description:
Library name: J2_221
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_221


title: kidney biopsy_NH328


title: AM043: T2 DMSO - Batch 2A

description:
Library name: Sample 4
10x Genomics

value: Time Point 2 - DMSO


title: RNA-seq, leaf, J2_274, chemical fertilizer, Year 2022

description:
Library name: J2_274
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_274


title: kidney biopsy_NH337


title: AM042: T2 DMSO - Batch 2A

description:
Library name: Sample 3
10x Genomics


title: RNA-seq, leaf, J2_206, chemical fertilizer, Year 2022

description:
Library name: J2_206
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_206


title: RNA-seq, leaf, J2_275, chemical fertilizer, Year 2022

description:
Library name: J2_275
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_275


title: RNA-seq, leaf, J2_229, chemical fertilizer, Year 2022

description:
Library name: J2_229
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_229


title: RNA-seq, leaf, J2_202, chemical fertilizer, Year 2022

description:
Library name: J2_202
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_202


title: kidney biopsy_NH320


title: RNA-seq, leaf, J2_212, chemical fertilizer, Year 2022

description:
Library name: J2_212
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_212


title: kidney biopsy_NH323


title: RNA-seq, leaf, J2_213, chemical fertilizer, Year 2022

description:
Library name: J2_213
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_213


title: kidney biopsy_NH318


title: AM040: T1 - Batch 1A

description:
Library name: Sample 1
10x Genomics

value: Time Point 1


title: UVA174  Coronary artery bulk ATAC

city: Charlottesville

first: Clint

middle: L

last: Miller

state: VA

department: Center for Public Health Genomics

institute: University of Virginia

description: UVA174 _ATAC

data_processing:
Bulk ATAC-seq sample processing was all conducted using the PEPATAC pipeline (version 0.8.6). This includes alignment, duplicate removal, mitochondrial read removal, and peak-calling.
Assembly: hg38
Supplementary files format and content: Supplementary_files_format_and_content: narrowPeak (peaks from each individual sample)

source_name: human coronary artery

extract_protocol:
Frozen coronary artery segments were broken down into small pieces using mortar and pestle under dry ice and liquid nitrogen. Nuclei were isolated using iodixanol/sucrose gradients following the Omni-ATAC protocol (Corces et al. Nature Methods 2017). 50,000 nuclei were washed in cold ATAC Resuspension Buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) + 0.1% Tween-20 and centrifuged for 10 minutes at 500 g at 4°C. 50,000 nuclei were then resuspended in 50 µl of transposition mix (25 µl 2X TD buffer, 2.5 µl of Tn5 transposase (Illumina), 16.5 µl PBS, 0.01% digitonon, 0.1% Tween-20). Samples were subsequently transposed for 30 minutes at 37°C with shaking (1000 rpm).
50,000 nuclei per sample were used for Tn5 transposition reactions, incubated for 30 minutes at 37C. Transposed DNA was purified using the Zymo DNA Clean and Concentrator-5 Kit and bulk ATAC-seq libraries were generated by PCR amplification and uniquely indexed barcodes. Bulk ATAC-seq libraries were sequenced on an Illumina NovaSeq 6000.
Transposed DNA was first purified using the Zymo DNA Clean and Concentrator-5 Kit. Libraries were subsequently constructed and amplified according to Supplementary Protocol 1 in the Omni-ATAC protocol (Corces et al. Nature Methods 2017). Each library underwent 5 cycles of pre-amplification and then additional amplification cycles (determined by qPCR of pre-amplified mixtures)

treatment_protocol: Human hearts were obtained from heart transplant recipients or rejected donor hearts. Hearts were all placed in cardioplegic solution prior to dissection of the left anterior descending (LAD), left circumflex (LCX), and right coronary arteries (RCA). All coronary artery samples were flash frozen in liquid nitrogen in the same manner

value: human coronary artery

value: ATAC-Seq


title: UVA173  Coronary artery bulk ATAC

description: UVA173 _ATAC


title: RNA-seq, leaf, J2_236, chemical fertilizer, Year 2022

description:
Library name: J2_236
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_236


title: RNA-seq, leaf, J2_225, chemical fertilizer, Year 2022

description:
Library name: J2_225
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_225


title: kidney biopsy_NH321

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

value: kidney biopsy


title: RNA-seq, leaf, J2_246, chemical fertilizer, Year 2022

description:
Library name: J2_246
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_246


title: kidney biopsy_NH316

value: ABMR/Mixed


title: AM041: T1 - Batch 1B

description:
Library name: Sample 2
10x Genomics


title: RNA-seq, leaf, J2_307, chemical fertilizer, Year 2022

description:
Library name: J2_307
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_307


title: UVA171  Coronary artery bulk ATAC

description: UVA171 _ATAC


title: kidney biopsy_NH319

value: No ABMR/Mixed


title: UVA170  Coronary artery bulk ATAC

description: UVA170 _ATAC


title: UVA175  Coronary artery bulk ATAC

description: UVA175 _ATAC


title: RNA-seq, leaf, J2_252, chemical fertilizer, Year 2022

description:
Library name: J2_252
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_252


title: RNA-seq, leaf, J2_250, chemical fertilizer, Year 2022

description:
Library name: J2_250
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_250


title: kidney biopsy_NH317


title: RNA-seq, leaf, J2_270, chemical fertilizer, Year 2022

description:
Library name: J2_270
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_270


title: RNA-seq, leaf, J2_310, chemical fertilizer, Year 2022

description:
Library name: J2_310
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_310


title: kidney biopsy_NH314


title: RNA-seq, leaf, J2_309, chemical fertilizer, Year 2022

description:
Library name: J2_309
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_309


title: RNA-seq, leaf, J2_248, chemical fertilizer, Year 2022

description:
Library name: J2_248
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_248


title: RNA-seq, leaf, J2_216, chemical fertilizer, Year 2022

description:
Library name: J2_216
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_216


title: kidney biopsy_NH312


title: RNA-seq, leaf, J2_285, chemical fertilizer, Year 2022

description:
Library name: J2_285
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_285


title: RNA-seq, leaf, J2_335, chemical fertilizer, Year 2022

description:
Library name: J2_335
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_335


title: kidney biopsy_NH313


title: RNA-seq, leaf, J2_280, chemical fertilizer, Year 2022

description:
Library name: J2_280
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_280


title: UVA165  Coronary artery bulk ATAC

description: UVA165 _ATAC


title: RNA-seq, leaf, J2_348, chemical fertilizer, Year 2022

description:
Library name: J2_348
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_348


title: RNA-seq, leaf, J2_312, chemical fertilizer, Year 2022

description:
Library name: J2_312
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_312


title: RNA-seq, leaf, J2_204, chemical fertilizer, Year 2022

description:
Library name: J2_204
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_204


title: RNA-seq, leaf, J2_342, chemical fertilizer, Year 2022

description:
Library name: J2_342
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_342


title: UVA167  Coronary artery bulk ATAC

description: UVA167 _ATAC


title: kidney biopsy_NH311


title: UVA168  Coronary artery bulk ATAC

description: UVA168 _ATAC


title: UVA163  Coronary artery bulk ATAC

description: UVA163 _ATAC


title: RNA-seq, leaf, J2_410, chemical fertilizer, Year 2023

description:
Library name: Ogawa_319
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_410


title: kidney biopsy_NH309


title: RNA-seq, leaf, J2_323, chemical fertilizer, Year 2023

description:
Library name: Ogawa_320
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_323


title: kidney biopsy_NH310


title: RNA-seq, leaf, J2_210, chemical fertilizer, Year 2022

description:
Library name: J2_210
column name in JAM2_RNA_rawdata_UniqueExonReads_2022R.csv: J2_210


title: UVA161  Coronary artery bulk ATAC

description: UVA161 _ATAC


title: RNA-seq, leaf, J2_370, chemical fertilizer, Year 2023

description:
Library name: Ogawa_318
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_370


title: RNA-seq, leaf, J2_342, chemical fertilizer, Year 2023

description:
Library name: Ogawa_316
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_342


title: RNA-seq, leaf, J2_334, chemical fertilizer, Year 2023

description:
Library name: Ogawa_317
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_334


title: UVA157  Coronary artery bulk ATAC

description: UVA157 _ATAC


title: RNA-seq, leaf, J2_412, chemical fertilizer, Year 2023

description:
Library name: Ogawa_315
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_412


title: UVA156  Coronary artery bulk ATAC

description: UVA156 _ATAC


title: UVA159  Coronary artery bulk ATAC

description: UVA159 _ATAC


title: RNA-seq, leaf, J2_317, chemical fertilizer, Year 2023

description:
Library name: Ogawa_314
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_317


title: RNA-seq, leaf, J2_417, chemical fertilizer, Year 2023

description:
Library name: Ogawa_312
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_417


title: RNA-seq, leaf, J2_418, chemical fertilizer, Year 2023

description:
Library name: Ogawa_311
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_418


title: UVA155  Coronary artery bulk ATAC

description: UVA155 _ATAC


title: RNA-seq, leaf, J2_362, chemical fertilizer, Year 2023

description:
Library name: Ogawa_310
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_362


title: kidney biopsy_NH306


title: RNA-seq, leaf, J2_403, chemical fertilizer, Year 2023

description:
Library name: Ogawa_309
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_403


title: kidney biopsy_NH304


title: RNA-seq, leaf, J2_416, chemical fertilizer, Year 2023

description:
Library name: Ogawa_308
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_416


title: UVA152  Coronary artery bulk ATAC

description: UVA152 _ATAC


title: kidney biopsy_NH305


title: RNA-seq, leaf, J2_304, chemical fertilizer, Year 2023

description:
Library name: Ogawa_306
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_304


title: kidney biopsy_NH303


title: UVA150  Coronary artery bulk ATAC

description: UVA150 _ATAC


title: RNA-seq, leaf, J2_349, chemical fertilizer, Year 2023

description:
Library name: Ogawa_305
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_349


title: RNA-seq, leaf, J2_389, chemical fertilizer, Year 2023

description:
Library name: Ogawa_303
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_389


title: UVA151  Coronary artery bulk ATAC

description: UVA151 _ATAC


title: UVA146  Coronary artery bulk ATAC

description: UVA146 _ATAC


title: RNA-seq, leaf, J2_330, chemical fertilizer, Year 2023

description:
Library name: Ogawa_307
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_330


title: UVA141  Coronary artery bulk ATAC

description: UVA141 _ATAC


title: UVA140  Coronary artery bulk ATAC

description: UVA140 _ATAC


title: kidney biopsy_NH301


title: RNA-seq, leaf, J2_306, chemical fertilizer, Year 2023

description:
Library name: Ogawa_301
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_306


title: kidney biopsy_NH300


title: UVA138  Coronary artery bulk ATAC

description: UVA138 _ATAC


title: RNA-seq, leaf, J2_395, chemical fertilizer, Year 2023

description:
Library name: Ogawa_296
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_395


title: RNA-seq, leaf, J2_397, chemical fertilizer, Year 2023

description:
Library name: Ogawa_298
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_397


title: kidney biopsy_NH332


title: RNA-seq, leaf, J2_391, chemical fertilizer, Year 2023

description:
Library name: Ogawa_297
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_391


title: RNA-seq, leaf, J2_346, chemical fertilizer, Year 2023

description:
Library name: Ogawa_304
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_346


title: RNA-seq, leaf, J2_309, chemical fertilizer, Year 2023

description:
Library name: Ogawa_294
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_309


title: kidney biopsy_NH298


title: UVA164  Coronary artery bulk ATAC

description: UVA164 _ATAC


title: RNA-seq, leaf, J2_318, chemical fertilizer, Year 2023

description:
Library name: Ogawa_300
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_318


title: kidney biopsy_NH299


title: RNA-seq, leaf, J2_325, chemical fertilizer, Year 2023

description:
Library name: Ogawa_299
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_325


title: RNA-seq, leaf, J2_415, chemical fertilizer, Year 2023

description:
Library name: Ogawa_302
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_415


title: RNA-seq, leaf, J2_337, chemical fertilizer, Year 2023

description:
Library name: Ogawa_293
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_337


title: kidney biopsy_NH297


title: RNA-seq, leaf, J2_315, chemical fertilizer, Year 2023

description:
Library name: Ogawa_292
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_315


title: RNA-seq, leaf, J2_413, chemical fertilizer, Year 2023

description:
Library name: Ogawa_295
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_413


title: UVA134  Coronary artery bulk ATAC

description: UVA134 _ATAC


title: UVA136  Coronary artery bulk ATAC

description: UVA136 _ATAC


title: UVA132  Coronary artery bulk ATAC

description: UVA132 _ATAC


title: RNA-seq, leaf, J2_365, chemical fertilizer, Year 2023

description:
Library name: Ogawa_289
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_365


title: RNA-seq, leaf, J2_404, chemical fertilizer, Year 2023

description:
Library name: Ogawa_291
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_404


title: UVA133  Coronary artery bulk ATAC

description: UVA133 _ATAC


title: RNA-seq, leaf, J2_400, chemical fertilizer, Year 2023

description:
Library name: Ogawa_288
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_400


title: RNA-seq, leaf, J2_381, chemical fertilizer, Year 2023

description:
Library name: Ogawa_290
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_381


title: kidney biopsy_NH294


title: RNA-seq, leaf, J2_382, chemical fertilizer, Year 2023

description:
Library name: Ogawa_287
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_382


title: UVA131  Coronary artery bulk ATAC

description: UVA131 _ATAC


title: kidney biopsy_NH293


title: RNA-seq, leaf, J2_298, chemical fertilizer, Year 2023

description:
Library name: Ogawa_286
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_298


title: RNA-seq, leaf, J2_378, chemical fertilizer, Year 2023

description:
Library name: Ogawa_284
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_378


title: kidney biopsy_NH325


title: UVA130  Coronary artery bulk ATAC

description: UVA130 _ATAC


title: RNA-seq, leaf, J2_385, chemical fertilizer, Year 2023

description:
Library name: Ogawa_285
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_385


title: UVA129  Coronary artery bulk ATAC

description: UVA129 _ATAC


title: RNA-seq, leaf, J2_359, chemical fertilizer, Year 2023

description:
Library name: Ogawa_283
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_359


title: RNA-seq, leaf, J2_379, chemical fertilizer, Year 2023

description:
Library name: Ogawa_281
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_379


title: RNA-seq, leaf, J2_414, chemical fertilizer, Year 2023

description:
Library name: Ogawa_280
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_414


title: UVA123  Coronary artery bulk ATAC

description: UVA123 _ATAC


title: RNA-seq, leaf, J2_387, chemical fertilizer, Year 2023

description:
Library name: Ogawa_282
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_387


title: kidney biopsy_NH291


title: RNA-seq, leaf, J2_411, chemical fertilizer, Year 2023

description:
Library name: Ogawa_279
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_411


title: kidney biopsy_NH295


title: UVA122  Coronary artery bulk ATAC

description: UVA122 _ATAC


title: RNA-seq, leaf, J2_374, chemical fertilizer, Year 2023

description:
Library name: Ogawa_277
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_374


title: RNA-seq, leaf, J2_314, chemical fertilizer, Year 2023

description:
Library name: Ogawa_275
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_314


title: RNA-seq, leaf, J2_348, chemical fertilizer, Year 2023

description:
Library name: Ogawa_276
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_348


title: UVA121  Coronary artery bulk ATAC

description: UVA121 _ATAC


title: UVA120  Coronary artery bulk ATAC

description: UVA120 _ATAC


title: RNA-seq, leaf, J2_211, chemical fertilizer, Year 2023

description:
Library name: Ogawa_272
column name in JAM2_RNA_rawdata_UniqueExonReads_2023R.csv: J2_211