title: T23-071_Rucaparib_High_6

description: GeoMX Nanostring

value: Omentum

value: High


title: C3_EOT_ER

status: Public on Jan 05 2026

type: SRA

city: Cambridge

first: Jason

last: Carroll

address: Li Ka Shing Centre, Robinson Way

country: United Kingdom

institute: Cancer Research UK, Cambridge Institute

description: Library name: jc6674

library_source: genomic

data_processing:
Reads were mapped to hg38 using Bowtie2 version 2.2.6 (Langmead B and  Salzberg S., 2012).
Aligned reads with the mapping quality less than 5 were filtered out.
Peaks were called with MACS2 version 2.1.1.20160309 (Zhang Y1 at al., 2008) using sequences from the corresponding input as a background control
Peaks yielded with MACS2 q value <= 1e-4 were selected for downstream analysis.  For visualizing tag density and signal distribution heatmap the read coverage in a window of +/- 2.5 or 5 kb region flanking the tag midpoint was generated using the bin size of 1/100 of the window length.
Assembly: GRCh38
Supplementary files format and content: bed/text

molecule: genomic DNA

organism: Homo sapiens

source_name: breast cancer

extract_protocol:
ChIP-Seq was performed at described in Ross-Innes CS et al. Nature. 2012 and in the materials and methods of Burrell et al. Antibodies used are a 50:50 mixture of Millipore: 06-935, Abcam: ab3575, as validated in Glont et al. PloS One 2019.
DNA was prepared for Illumina sequencing on the HiSeq 4000 using the ThruPLEX DNA-seq kit according to the manufacturer's instructions.

treatment_protocol: samples are either baseline biopsies from untreated patients enrolled in the PIONEER trial, or end of treatment biopsies after 15 days of trial treatment (either letrozole only (Arm A), letrozole + megestrol 40mg (Arm B), or letrozole + megestrol 160mg (Arm C))

tag: tissue

value: breast cancer

tag: sample type

value: breast core biopsy

tag: treatment

value: Letrozole + Megestrol 160mg

tag: timepoint

value: end of treatment

tag: chip antibody

value: Millipore:06-935, Abcam:ab3575

tag: antibody lot_number


title: C2_EOT_Input

description: Library name: jc6593

value: Input


title: bone and BM, control, lane1

city: Tokorozawa

first: Masahiro

last: Shinohara

state: Saitama

address: 4-1 Namiki

country: Japan

institute: National Rehabilitation Center for Persons with Disabilities

description:
Library name: 4_Control_L1
10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting were performed using the Cell Ranger software v7.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

organism: Mus musculus

source_name: bone, bone marrow

extract_protocol:
Femurs and tibias from Tnfsf11tTA/+; LC1; Rosa26LSL-tdTomato mice were isolated from both limbs, and bone marrow was flushed out with PBS. The remaining bones were minced using scissors and forceps, then incubated in 5 mM EDTA in PBS at room temperature for 1 hour. Dissociated cells were collected every 30 minutes and pooled with the bone marrow cells isolated from the same mouse. Cells were collected by centrifugation and treated with Red Blood Cell Lysis Buffer, followed by incubation in DMEM containing 1 mg/mL Collagenase P, 0.025 mg/mL Liberase TH and 0.1 mg/mL DNase I at 37ºC with gentle shaking for 1 hour. Dissociated cells were collected every 20 minutes and passed through a 100 μm nylon mesh. The cells were then collected by centrifugation, resuspended in 2% FBS/2 mM EDTA/PBS. The isolated cells were stained with antibodies against Ter119 and CD45.2. Fixable Viability Dye (eBioscience) was used to stain dead cells. Live CD45.2-Ter119-tdTomato+ cells were sorted for single cell 3' gene expression library construction.
Library construction was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics) with slight modification.  Cells up to 10,000 were directly sorted into the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM).

value: bone, bone marrow

tag: cell type

tag: strain

tag: genotype

value: Control

tag: age


title: T23-071_Rucaparib_Low_5

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

institute: MRC London Institute of Medical Sciences

description: GeoMX Nanostring

library_source: transcriptomic

data_processing:
Sequenced data was analysed using the GeoMx NGS pipeline v2.3.3.10. Quality control thresholds: 100,000 raw reads and 50% sequencing saturation.
Quartile3 normalisation was applied across all targets to account for differing ROI size and cellularity which impact transcript abundance.
Data analysis performed wuthin R-environment, and differential gene expression analysed based on Linear Mixed Model. Significant genes defined as FDR<0.05
Assembly: GRCh38
Supplementary files format and content: DCC files produced by GeoMX NGS Pipeline
Library strategy: Spatial Transcriptomics

source_name: Omentum

growth_protocol: PDEs were placed onto inserts (0.4 μm porosity, Millipore PICM01250) within 6-well plates and just submerged in media before acclimatising overnight in complete medium (RPMI 1640, 20% FCS (foetal calf serum), 2 mM sodium pyruvate, 100 U/mL penicillin, 100 μg/mL streptomycin, 2.5 μg/mL insulin) at 37°C, 5% CO2.

extract_protocol:
sample processing step: To aid cryosection, frozen PDEs were embedded in a hydrogel (7.5% hydroxypropyl methylcellulose, 2.5% PVP)60. Polymer blocks were snap-frozen using dry ice-chilled isopropyl alcohol. 10-12 μm serial sections of were cut using a Leica CM3050s cryostat (-17°C), thaw-mounted onto slides (Thermo Fisher, 12-550-15) prior to storage at -80°C.
Adjacent tissue sections to those used for MSI were processed as recommended by Nanostring. In average, 5 high- and 5 low-drug  areas  were selected per sample,  inferred differential drug accumulation according to mass spectrometry imaging data.
PCR amplification/library preparations was carried out according to manufacturer’s instructions. Pooled libraries were purified using AMPure XP beads (Beckman Coulter), and final library quality and quantity assessed using the Agilent 2100 High Sensitivity DNA, and Qubit High-Sensitivity DNA assays. Sequencing was performed using the Illumina NextSeq2000 platform (Paired End 27bp + dual 8bp indexing).

treatment_protocol: Explants were treated with Niraparib, Olaparib and Rucaparib at 20 μM in complete media or with 0.1% DMSO as vehicle. PDEs were incubated with drug (37°C, 5% CO2) for 24 hours.

value: Cancer

tag: patient id

tag: drug treatment

value: Rucaparib

tag: absorbtion

value: Low


title: T23-071_Rucaparib_Low_4

description: GeoMX Nanostring


title: C2_Baseline_Input

description: Library name: jc6592

value: baseline


title: bone and BM, immoblized, lane2

description:
Library name: 3_SWI_L2
10x Genomics

value: hindlimb immobilization


title: bone and BM, immoblized, lane1

description:
Library name: 3_SWI_L1
10x Genomics


title: T23-071_Rucaparib_Low_3

description: GeoMX Nanostring


title: C2_EOT_ER

description: Library name: jc6585


title: T23-071_Rucaparib_Low_2

description: GeoMX Nanostring


title: C2_Baseline_ER

description: Library name: jc6584


title: KO2 Cytokines

city: Chicago

first: Sarah

middle: A

last: Tersey

state: IL

department: Medicine

country: USA

institute: University of Chicago

description: Library name: KO2 Cytokines

data_processing:
Data was analyzed using Galaxy.
Reads were trimmed using trimmomatic. Quality scores were assessed using FastQC.
Individual sample reads were quantified using Htseq and normalized via Relative Log Expression using DESeq2 R library.
Assembly: mm10
Supplementary files format and content: excel file with raw counts

molecule: polyA RNA

source_name: primary islets

extract_protocol:
RNA was extracted using Qiagen RNAeasy Mini Kit.
RNA quality and quantity was assessed using the Agilent bio-analyzer. Strand-specfiic RNA-seq libraries were prepared using an TruSEQ mRNA-SEQ library protocol (Illumina provided).
Library quality and quantity was assessed using the Agilent bio-analyzer and libraries were seqenced using an Illumina NovaSEQ6000.

treatment_protocol: WT or Gpr31b KO primary islets were treated with vehicle or cytokine mix (TNF-α, IFN-γ, IL-1β) for 24 hours

value: primary islets

value: islets

value: KO

value: cytokines


title: C1_EOT_Input

description: Library name: jc5903

value: breast cancer


title: KO3 Cytokines

description: Library name: KO3 Cytokines


title: BO112-SARC-004_pre-RT_T2

city: Stanford

first: Anusha

last: Kalbasi

state: CA

address: 269 Campus Drive

department: Radiation Oncology

institute: Stanford

description:
Library name: BO112-SARC-004_pre-RT_T2
10X Genomics FFPE spatial transcriptomics

data_processing:
Regions of interest were selected based on H&E quality and IHC data on immune cell infiltration from adjacent sections. RNA quality was confirmed by DV200 assessment prior to processing.
Two specimens were placed per Visium HD slide (6.5 × 6.5 mm capture area), and libraries were prepared according to the manufacturer’s protocol (Visium HD CytAssist Spatial GEX 6.5 mm workflow; 10x Genomics).
Libraries underwent Qubit fluorometric quantification and TapeStation fragment analysis and were sequenced on an Illumina NovaSeq (PE50), generating ~550M reads per sample.
FASTQ files were processed using Space Ranger (v4.0.1) with alignment to the GRCh38-2020-A reference and quantification using the Visium Human Transcriptome Probe Set v2.0.
CytAssist alignment images were registered to corresponding brightfield H&E images using the supplied JSON files with manual refinement using loupe Browser 9. Resulting feature matrices and spatial metadata were used for downstream analysis.
All four specimens were imported into Seurat, and one baseline sample with low transcript capture was excluded. Cells expressing <50 unique genes were removed.
Remaining cells were normalized using SCTransform with cell area (total 2-µm bins per cell) regressed as a technical covariate.
Cell clustering (resolution 0.8) and differential expression analysis enabled manual cell-type annotation.
Tumor cell identity was confirmed via inferCNV using immune cells as reference.
Putative T–myeloid doublets were subclustered (resolution 0.3) and reannotated. Final annotated cell maps were exported for spatial visualization in Loupe Browser.
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned fudicials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected tissue image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors json.json: scalefactors in jason format
Supplementary files format and content: tissue hires image.png: hi-res image of tissue
Supplementary files format and content: tissue lowres image.png: low-res image of tissue
Supplementary files format and content: cell_segmentations.geojson: per-cell polygon coordinates representing segmentation boundaries.
Supplementary files format and content: filtered_feature_bc_matrix.h5: HDF5 format count matrix following Space Ranger / spaceranger-compatible processing.
Library strategy: Spatial Transcriptomics

source_name: Tumor

extract_protocol:
Tissues were formalin fixed and paraffin embedded.
Spatial transcriptomic profiling was performed using the 10x Genomics Visium HD platform on four FFPE longitudinal tumor specimens from a single patient.

treatment_protocol: Patients were treated with Radiation therapy ( 6 Gy x 5 fractions), and/or intratumoral BO-112. Samples were taken before, during and after treatment before each BO-112 administration and at surgical resection of the tumor..

value: Tumor

tag: patient

value: Patient 004

tag: cohort

value: Cohort -2

tag: batch


title: KO1 Cytokines

description: Library name: KO1 Cytokines


title: BO112-SARC-004_post-RT_T3

description:
Library name: BO112-SARC-004_post-RT_T3
10X Genomics FFPE spatial transcriptomics

value: Radiation (6 Gy x 5), BO-112 (2 doses)


title: BO112-SARC-004_surgery_T4

description:
Library name: BO112-SARC-004_surgery_T4
10X Genomics FFPE spatial transcriptomics

value: Radiation (6 Gy x 5), BO-112 (3 doses)


title: T23-071_Rucaparib_High_13

description: GeoMX Nanostring

value: Omentum

value: High


title: T23-071_Rucaparib_High_11

description: GeoMX Nanostring

value: Cancer


title: C1_Baseline_Input

description: Library name: jc5902

value: breast core biopsy

value: Letrozole + Megestrol 160mg

value: Input


title: C1_Baseline_ER

description: Library name: jc5896

value: baseline

value: Millipore:06-935, Abcam:ab3575


title: T23-071_Rucaparib_High_12

description: GeoMX Nanostring

value: Rucaparib


title: BO112-SARC-004_baseline_T1

description:
Library name: BO112-SARC-004_baseline_T1
10X Genomics FFPE spatial transcriptomics


title: WT1 Cytokines

description: Library name: WT1 Cytokines

value: primary islets

value: islets

value: WT


title: T23-071_Rucaparib_High_10

description: GeoMX Nanostring


title: T23-071_Niraparib_High_9

description: GeoMX Nanostring

value: Niraparib


title: Control_miRNAseq_rep3

city: Québec

first: Lucie

last: Jeannotte

state: QC

address: 2260, boulevard Henri Bourassa

department: Biologie moléculaire, Biochimie médicale & Pathologie

country: Canada

institute: Université Laval

description:
Library name: CTL3b_S27
Column_name in miRNA_PPB_CTL_count.txt : CTL3b_miRNA.bam

data_processing:
miRNA sequencing was performed using paired-end sequencing. However, given the uselessness of paired reads in miRNAseq analysis, only R1 reads were analyzed.
Quality of sequencing reads was evaluated using FastQC software (v0.12.1). Reads were trimmed and filtered using Trim Galore with --stringency 1 --max_length 25 --fastqc --length 15 parameters (v0.6.5).
Only R1 reads were mapped with Bowtie1 aligner (v1.3.1) with --best -v 2 parameters to the human reference genome from ENSEMB GRCh38.p14.
The mapped sequencing data were then processed with the software featureCounts (v2.0.3; Liao et al., Bioinformatics 2014) with -t miRNA -g product parameters with a gff file.
miRNA expression levels were represented as reads per million (RPMs).
Assembly: GRCh38.p14
Supplementary files format and content: All_miRNA_expression_RPM.txt : Tab-delimited text file include RPM miRNA expression for each sample

source_name: Normal lung tissue

growth_protocol: Human specimens were obtained fresh-frozen or embedded in Optimal Cutting Temperature (OCT) compound.

extract_protocol:
Total RNA was isolated from fresh frozen specimens with TRIzol reagent according to the manufacturer's instructions (Invitrogen). Samples in OCT were cut in 20 µm-thick sections and 20-30 sections per specimen were used for extraction with TRIzol (Invitrogen) according to manufacturer’s instructions.
The NEBNext multiplex small RNA library prep ((New Englands Biolabs Inc., USA) was used to prepare miRNA sequencing libraries, according to manufacturer’s instructions. Libraries were prepared using 500ng of total RNA. Briefly, RNA 3’ adapter was first ligated to the 3’ end of miRNA followed by the ligation of RNA 5’ adapter to the 5’end of miRNA-3’ adaptors, which were further used for the reverse transcription step. Following the reverse transcription step, an amplification of 14 cycles was performed to incorporate specific indexes for multiplexing. After a purification step with GenElutePCR clean-up kit (Sigma-Aldrich, USA), the appropriate range of cDNA fragments was extracted on a 3% gel using a Pippin Prep instrument (Sage Science, USA). Llibrary quantification was done on a QBit 3.0 fluorometer (ThermoFisher Scientific, Canada). miRNA libraries were pooled together in equimolar ratio and the quality was examined with a DNA screentape D1000 HS on a TapeStation2200 (Agilent technologies, USA). Subsequently, miRNA librairies with unique index were sequenced for paired-end 100pb sequencing on an Illumina Novaseq 6000.

treatment_protocol: no treatment

value: Normal lung tissue


title: B9_EOT_Input

description: Library name: jc6531

value: breast cancer

value: Letrozole + Megestrol 40mg

value: end of treatment


title: Control_miRNAseq_rep1

description:
Library name: CTL1b_S11
Column_name in miRNA_PPB_CTL_count.txt : CTL1b_miRNA.bam


title: B9_EOT_ER

description: Library name: jc6525


title: T23-071_Rucaparib_Low_1

description: GeoMX Nanostring

value: Omentum

value: Low


title: B9_Baseline_Input

description: Library name: jc6530


title: KO3 Vehicle

description: Library name: KO3 Vehicle

value: KO

value: vehicle


title: WT2 Cytokines

description: Library name: WT2 Cytokines

value: cytokines


title: Control_miRNAseq_rep4

description:
Library name: CTL4b_13
Column_name in miRNA_PPB_CTL_count.txt : CTL4b_miRNA.bam


title: C1_EOT_ER

description: Library name: jc5897

value: breast core biopsy

value: Letrozole + Megestrol 160mg


title: PPB_miRNAseq_rep3

description:
Library name: PPB3b_S28
Column_name in miRNA_PPB_CTL_count.txt : PPB3b_miRNA.bam

source_name: Pleuropulmonary blastoma lung lesion

value: Pleuropulmonary blastoma lung lesion


title: T23-071_Niraparib_Low_6

description: GeoMX Nanostring

value: Cancer


title: KO2 Vehicle

description: Library name: KO2 Vehicle

value: primary islets


title: WT3 Cytokines

description: Library name: WT3 Cytokines

value: islets


title: B9_Baseline_ER

description: Library name: jc6524

value: baseline

value: Millipore:06-935, Abcam:ab3575


title: Control_miRNAseq_rep2

description:
Library name: CTL2b_S12
Column_name in miRNA_PPB_CTL_count.txt : CTL2b_miRNA.bam

value: Normal lung tissue


title: T23-071_Niraparib_Low_7

description: GeoMX Nanostring

value: Niraparib


title: WT3 Vehicle

description: Library name: WT3 Vehicle

value: WT


title: PPB_miRNAseq_rep2

description:
Library name: PPB2b_S15
Column_name in miRNA_PPB_CTL_count.txt : PPB2b_miRNA.bam


title: T23-071_Niraparib_High_8

description: GeoMX Nanostring

value: High


title: B8_Baseline_Input

description: Library name: jc6719

value: breast cancer

value: Letrozole + Megestrol 40mg

value: Input


title: PPB_miRNAseq_rep1

description:
Library name: PPB1b_S14
Column_name in miRNA_PPB_CTL_count.txt : PPB1b_miRNA.bam


title: B8_EOT_Input

description: Library name: jc6720

value: end of treatment


title: KO1 Vehicle

description: Library name: KO1 Vehicle

value: KO

value: vehicle


title: WT2 Vehicle

description: Library name: WT2 Vehicle


title: B8_EOT_ER

description: Library name: jc6688

value: breast core biopsy


title: Control_RNAseq_rep4

description:
Library name: CTL4_S82
Column_name in Raw_count_RNA_PPB_CPAM_CTL.txt : CTL4

data_processing:
Quality of sequencing reads was evaluated using FastQC software (v0.12.1). Reads were trimmed and filtered using Trim Galore with default parameters (v0.6.5).
Trimmed reads were mapped with STAR aligner (v2.7.9a) to the human reference genome from ENSEMBL GRCh38.p14 (release Feb3, 2022; Martin et al., Nucleic Acid Res. 2023)
The mapped sequencing data were then processed with the software featureCounts (v2.0.3; Liao et al., Bioinformatics 2014) with -t exon -g gene -p parameters to obtain the number of reads associated with genes.
Assembly: GRCh38.p14
Supplementary files format and content: Tab-delimited text file include raw counts for each sample

extract_protocol:
Total RNA was isolated from fresh frozen specimens with TRIzol reagent according to the manufacturer's instructions (Invitrogen). Samples in OCT were cut in 20 µm-thick sections and 20-30 sections per specimen were used for extraction with TRIzol (Invitrogen) according to manufacturer’s instructions.
The cDNA libraries were first constructed using SMART-Seq v4 Ultra low input RNA Kit (Clontech Laboratories, Takara Bio Company; Mountain View, CA, USA) according to manufacturer’s instructions. Briefly, the first-strand cDNA was synthesized using total RNA from the tissue by the 3’ SMART-Seq CDS Primer II A and template switching was performed by SMART-Seq v4 Oligonucleotide at the 5’ end of the transcript.  Then, cDNA from SMART sequences was amplified by PCR Primer II A. After 17 cycles of long-distance PCR, amplified cDNA was purified using the Agencourt AMPure XP Kit (Beckman Coulter, Cat.No. A63882). The quality of cDNA construction was validated using Agilent Tapestation 2200 system. Subsequently, 150pg of amplified cDNA was used for Illumina library preparation using Nextera XT DNA Library Preparation Kits (Illumina Inc., San Diego, CA, USA). Libraries with unique index were pooled together in equimolar ratio and sequenced for paired-end 100pb sequencing on an Illumina Novaseq 6000 system.


title: WT1 Vehicle

description: Library name: WT1 Vehicle


title: T23-071_Niraparib_Low_4

description: GeoMX Nanostring

value: Omentum

value: Low


title: Control_RNAseq_rep3

description:
Library name: CTL3_S81
Column_name in Raw_count_RNA_PPB_CPAM_CTL.txt : CTL3


title: T23-071_Niraparib_Low_3

description: GeoMX Nanostring

value: Cancer


title: B8_Baseline_ER

description: Library name: jc6687


title: T23-071_Niraparib_Low_5

description: GeoMX Nanostring


title: Subject_6_LP4GC (BCR-Seq)

city: New Haven

first: Hailong

last: Meng

state: CT

address: 300 George Str

institute: Yale University

description:
Library name: Sample 27
mouse4_airr_rearrangement.tsv

data_processing:
Pair-end FASTQ reads were preprocessed using the “cellranger vdj” command from 10x Genomics’ Cell Ranger v6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome) for alignment against the mouse reference (vdj_GRCm38_alts_ensembl-4.0.0). Initial germline V(D)J gene annotation was conducted using IgBLAST v1.17.0 against the C57BL/6 mouse vjd germline reference (Ye et al., 2013; Giudicelli et al., 2005). IgBLAST output was further processed with Change-O v1.3.0 (Gupta et al., 2015). Quality control was performed to ensure only productively rearranged sequences with valid V and J gene annotations and junction lengths divisible by 3 were retained. Additionally, cells containing one heavy chain sequence paired with at least one light chain sequence were kept, while cells with the same barcode and sequence from different samples were excluded.
Assembly: vdj_GRCm38_alts_ensembl-4.0.0
Supplementary files format and content: Processed files contains BCR data in AIRR format

source_name: Intestinal Lamina Propria

extract_protocol:
MLNs and PPs were crushed between frosted glass slides and passed through filter paper to create single cell suspensions suspended in FACS Buffer (2% FBS 1mM EDTA) in PBS. To avoid loss of the PP cell pellet, cells were filtered immediately prior to any centrifugation steps until adding the surface stain. LP lymphocytes were isolated as described in. Cells were stained for flow cytometry using the antibodies listed in the Key Resources Table diluted in FACS Buffer. Surface staining was done at room temperature for 20 minutes, after which cells were fixed with the Cytofix/Cytoperm Fixation/Permeabilization Kit (BD Biosciences) for 15 minutes at 4˚C. Intracellular staining was performed on fixed cells overnight at 4˚C. Identifying OVA-specific B cells was achieved by staining cells with OVA-AF647, OVA-AF488 and/or OVA-Texas Red (Invitrogen) on both the surface and intracellularly. Flow cytometry for OVA-specific B cells in the LP was done with OVA-AF647, and OVA-specific B cell detection in the MLN and PPs used dual OVA-AF647 and OVA-Texas Red staining. Identifying NP-specific B cells was achieved by staining cells with NP-APC on both the surface and intracellularly. MLN, PP, and LP tissues were prepared as for flow cytometry and stained for sorting markers without any enrichment. Samples were sorted using a FACSAria (BD Biosciences) and used for library preparation.
we followed the 10x protocol described in https://cdn.10xgenomics.com/image/upload/v1722286172/support-documents/CG000331_Chromium_Next_GEM_Single_Cell_5_v2_UserGuide_RevF.pdf

value: Intestinal Lamina Propria

value: B-Lymphocyte

value: S1PR2CreERT2 Rosa-lsl-tdTomato


title: Subject_6_LP4nonGC (BCR-Seq)

description:
Library name: Sample 26
mouse4_airr_rearrangement.tsv


title: B7_Baseline_Input

description: Library name: jc6596

value: baseline


title: T23-071_Niraparib_High_28

description: GeoMX Nanostring

source_name: Bladder

value: Bladder

value: Niraparib


title: Control_RNAseq_rep1

description:
Library name: CTL1_S79
Column_name in Raw_count_RNA_PPB_CPAM_CTL.txt : CTL1

value: Normal lung tissue


title: T23-071_Niraparib_High_26

description: GeoMX Nanostring

value: High


title: B7_EOT_ER

description: Library name: jc6589

value: breast cancer

value: Letrozole + Megestrol 40mg

value: Millipore:06-935, Abcam:ab3575


title: Subject_5_LP3nonGC (BCR-Seq)

description:
Library name: Sample 24
mouse3_airr_rearrangement.tsv


title: B7_Baseline_ER

description: Library name: jc6588


title: Subject_4_LP2GC (BCR-Seq)

description:
Library name: Sample 23
mouse2_airr_rearrangement.tsv


title: Subject_5_LP3GC (BCR-Seq)

description:
Library name: Sample 25
mouse3_airr_rearrangement.tsv


title: CPAM_RNAseq_rep4

description:
Library name: MAKP4_S113
Column_name in Raw_count_RNA_PPB_CPAM_CTL.txt : CPAM4

source_name: Congenital pulmonary airway malformation lung lesion


title: T23-071_Niraparib_High_24

description: GeoMX Nanostring


title: B7_EOT_Input

description: Library name: jc6597

value: end of treatment

value: Input


title: T23-071_Niraparib_Low_27

description: GeoMX Nanostring


title: Subject_4_LP2nonGC (BCR-Seq)

description:
Library name: Sample 22
mouse2_airr_rearrangement.tsv


title: Control_RNAseq_rep2

description:
Library name: CTL2_S80
Column_name in Raw_count_RNA_PPB_CPAM_CTL.txt : CTL2


title: CPAM_RNAseq_rep3

description:
Library name: MAKP3_S85
Column_name in Raw_count_RNA_PPB_CPAM_CTL.txt : CPAM3

value: Congenital pulmonary airway malformation lung lesion


title: Subject_6_PP4nonGC (BCR-Seq)

description:
Library name: Sample 20
mouse4_airr_rearrangement.tsv

source_name: Peyer's Patch

value: Peyer's Patch


title: CPAM_RNAseq_rep2

description:
Library name: MAKP2_S112
Column_name in Raw_count_RNA_PPB_CPAM_CTL.txt : CPAM2


title: T23-071_Niraparib_Low_21

description: GeoMX Nanostring

value: Low


title: B6_EOT_Input

description: Library name: jc6708

value: breast core biopsy


title: T23-071_Niraparib_Low_22

description: GeoMX Nanostring

value: Cancer


title: CPAM_RNAseq_rep1

description:
Library name: MAKP1_S83
Column_name in Raw_count_RNA_PPB_CPAM_CTL.txt : CPAM1


title: T23-071_Niraparib_High_25

description: GeoMX Nanostring


title: B5_EOT_Input

description: Library name: jc6539


title: T23-071_Niraparib_High_23

description: GeoMX Nanostring


title: Subject_6_PP4GC (BCR-Seq)

description:
Library name: Sample 21
mouse4_airr_rearrangement.tsv

value: B-Lymphocyte


title: Subject_5_PP3GC (BCR-Seq)

description:
Library name: Sample 19
mouse3_airr_rearrangement.tsv

value: S1PR2CreERT2 Rosa-lsl-tdTomato


title: B6_Baseline_ER

description: Library name: jc6675

value: baseline


title: PPB_RNAseq_rep3

description:
Library name: PPB3_S89
Column_name in Raw_count_RNA_PPB_CPAM_CTL.txt : PPB3

value: Pleuropulmonary blastoma lung lesion


title: T23-071_Niraparib_Low_20

description: GeoMX Nanostring

value: Bladder

value: Niraparib


title: PPB_RNAseq_rep1

description:
Library name: PPB1_S87
Column_name in Raw_count_RNA_PPB_CPAM_CTL.txt : PPB1


title: B5_Baseline_Input

description: Library name: jc6538


title: B6_Baseline_Input

description: Library name: jc6707


title: MCF-7, WT, biol rep 1

city: Houston

first: Suzanne

last: Fuqua

state: Texas

address: 1 Baylor Plaza

institute: Baylor College of Medicine

description: Library name: MCF7_parental_26651

data_processing:
Paired-end reads were trimmed using TrimGalore
Reads were mapped to the UCSC hg38 genome build using HISAT2
Aligned reads were counted against the Gencode gene model annotation to obtain expression values by using FeatureCounts
Assembly: hg38
Supplementary files format and content: Combined FeatureCounts gene expression .csv file for all samples

source_name: breast

growth_protocol: Cells were cultured in MEM (Corning MT10-010-CV) media supplemented with 10% fetal bovine serum (GeminiBio 100-500-500), 100 U/mL penicillin and 100 mg/mL streptomycin (GeminiBio 400-109-100), 1X MEM non-essential amino acids (Corning MT-25-025-CI), 50 mg/mL Gentamicin (ThermoFisher, 15750060), and 5 mg/mL Plasmocin Prophylactic (InvivoGen, NC9886956).

extract_protocol:
RNA was extracted using the Qiagen Rneasy kit following the manufacturer's protocol
Hamilton NGS STAR for automated NGS library preparation

treatment_protocol: Cells with long-term treatment exposure to Fulv (100 nM) or Abemaciclib (Abema) (500 nM) were treated twice per week.

value: breast

tag: cell line

value: mammary epithelial adenocarcinoma

value: WT ESR1

value: Untreated


title: MCF-7, FulvR AbemaR 12 months, tech rep 1

description: Library name: MCF7_FulvR_AbemaR_12month_YS_26661

tag: tissue

value: Fulv and Abema


title: MCF-7, FulvR AbemaR 8 months, biol rep 1

description: Library name: MCF7_FulvR_AbemaR_8month_26659


title: MCF-7, AbemaR, biol rep 2

description: Library name: MCF7_AbemaR_26658

value: Abema


title: MCF-7, FulvR AbemaR 8 months, biol rep 2

description: Library name: MCF7_FulvR_AbemaR_8month_26660


title: B6_EOT_ER

description: Library name: jc6676

value: breast cancer

tag: sample type

value: Letrozole + Megestrol 40mg

value: end of treatment

value: Millipore:06-935, Abcam:ab3575


title: MCF-7, FulvR AbemaR 12 months, tech rep 2

description: Library name: MCF7_FulvR_AbemaR_12month_YS_26662

tag: treatment


title: MCF-7, WT, biol rep 2

description: Library name: MCF7_parental_26652


title: MCF-7, AbemaR, biol rep 1

description: Library name: MCF7_AbemaR_26657


title: MCF-7, WT, biol rep 3

description: Library name: MCF7_parental_26653


title: PPB_RNAseq_rep2

description:
Library name: PPB2_S88
Column_name in Raw_count_RNA_PPB_CPAM_CTL.txt : PPB2


title: B5_EOT_ER

description: Library name: jc6533

value: breast core biopsy

tag: timepoint


title: T23-071_Niraparib_Low_19

description: GeoMX Nanostring

value: Cancer

value: Low


title: T23-071_Niraparib_Low_2

description: GeoMX Nanostring

value: Omentum


title: LREX_sh_MECOM-2 Run 1

city: Buffalo

first: Remi

last: Adelaiye-Ogala

state: New York

address: 875 Ellicot Street

department: Department of Medicine

institute: University at Buffalo

description:
Library name: RAO_M004  Run 1
RAO_M004.bigWig

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed using Trimmomatic v0.33.
Reads were aligned to UCSC hg38 genome using Bowtie version 1.1.2.
Peaks were called using MACS v2.1.0.
Assembly: GRCh38
Supplementary files format and content: bigWig

source_name: LREX

growth_protocol: LREX are  Castrate resistant and enzalutamide prostate cancer cell lines were cultured in RPMI, 10%CSFBS, 1% Penstrep in humdified atmosphere with 5%CO2 at 37C

extract_protocol: We crosslinked protein to DNA in live cells by using 1% formaldehyde for 10 minutes. After quenching and cell lysis. Chromatin was sonicated using  ME220 Focused-ultrasonicator(Covaris)

value: LREX

value: prostate cancer cell line


title: PPB_RNAseq_rep4

description:
Library name: PPB4_S213
Column_name in Raw_count_RNA_PPB_CPAM_CTL.txt : PPB4

value: Pleuropulmonary blastoma lung lesion


title: Subject_4_PP2nonGC (BCR-Seq)

description:
Library name: Sample 16
mouse2_airr_rearrangement.tsv

value: Peyer's Patch

value: B-Lymphocyte

value: S1PR2CreERT2 Rosa-lsl-tdTomato


title: LREX_sh_MECOM-1 Run 2

description:
Library name: RAO_M003  Run 2
RAO_M003.bigWig


title: LREX_sh_MECOM-2 Run 2

description:
Library name: RAO_M004  Run 2
RAO_M004.bigWig


title: B4_EOT_Input

description: Library name: jc6712

tag: chip antibody

value: Input


title: B5_Baseline_ER

description: Library name: jc6532

value: baseline

tag: antibody lot_number


title: Subject_6_MLN4GC (BCR-Seq)

description:
Library name: Sample 15
mouse4_airr_rearrangement.tsv

source_name: Mesenteric Lymph Node

value: Mesenteric Lymph Node

tag: cell type


title: Subject_5_PP3nonGC (BCR-Seq)

description:
Library name: Sample 18
mouse3_airr_rearrangement.tsv


title: T23-071_Niraparib_Low_17

description: GeoMX Nanostring

value: Bladder

value: Niraparib


title: T23-071_Niraparib_High_15

description: GeoMX Nanostring

value: High


title: T23-071_Niraparib_Low_16

description: GeoMX Nanostring


title: B4_Baseline_Input

description: Library name: jc6711

value: breast cancer

value: Letrozole + Megestrol 40mg


title: LREX-Control-2 Run 1

description:
Library name: RAO_M002  Run 1
RAO_M002.bigWig


title: Subject_4_MLN2GC (BCR-Seq)

description:
Library name: Sample 11
mouse2_airr_rearrangement.tsv


title: Subject_6_MLN4nonGC (BCR-Seq)

description:
Library name: Sample 14
mouse4_airr_rearrangement.tsv


title: Subject_4_PP2GC (BCR-Seq)

description:
Library name: Sample 17
mouse2_airr_rearrangement.tsv


title: LREX_sh_MECOM-1 Run 1

description:
Library name: RAO_M003  Run 1
RAO_M003.bigWig


title: Subject_5_MLN3GC (BCR-Seq)

description:
Library name: Sample 13
mouse3_airr_rearrangement.tsv


title: T23-071_Niraparib_Low_18

description: GeoMX Nanostring

value: Cancer


title: LREX-Control-2 Run 2

description:
Library name: RAO_M002  Run 2
RAO_M002.bigWig


title: Subject_4_MLN2nonGC (BCR-Seq)

description:
Library name: Sample 10
mouse2_airr_rearrangement.tsv


title: B4_EOT_ER

description: Library name: jc6680

value: breast core biopsy

value: end of treatment

value: Millipore:06-935, Abcam:ab3575


title: T23-071_Niraparib_High_13

description: GeoMX Nanostring

value: Omentum


title: LREX-Control-1 Run 2

description:
Library name: RAO_M001  Run 2
RAO_M001.bigWig

value: LREX

value: prostate cancer cell line


title: T23-071_Niraparib_High_14

description: GeoMX Nanostring


title: Subject_3_LP (BCR-Seq)

description:
Library name: Sample 9
BCR_data.tsv

value: Intestinal Lamina Propria

value: B-Lymphocyte

value: C57BL/6N WT


title: B4_Baseline_ER

description: Library name: jc6679

value: baseline


title: T23-071_Niraparib_High_12

description: GeoMX Nanostring


title: Subject_5_MLN3nonGC (BCR-Seq)

description:
Library name: Sample 12
mouse3_airr_rearrangement.tsv

value: Mesenteric Lymph Node

value: S1PR2CreERT2 Rosa-lsl-tdTomato


title: T23-071_Niraparib_High_11

description: GeoMX Nanostring

value: Niraparib


title: LREX-Control-1 Run 1

description:
Library name: RAO_M001  Run 1
RAO_M001.bigWig


title: B3_EOT_ER

description: Library name: jc6587


title: Input (pulled) Run 2

description:
Library name: Input_004 Run 2
Input_004.bigWig

value: Input (pulled)


title: B3_Baseline_Input

description: Library name: jc6594

value: breast cancer

value: Input


title: B3_EOT_Input

description: Library name: jc6595

value: Letrozole + Megestrol 40mg


title: Input (pulled) Run 1

description:
Library name: Input_004 Run 1
Input_004.bigWig


title: Subject_2_LP (BCR-Seq)

description:
Library name: Sample 8
BCR_data.tsv


title: Old, SA-ßGal-High, ATAC-Seq, donor 4

city: Piscataway

first: Ricardo

middle: Iván

last: Martínez Zamudio

state: New Jersey

address: 675 Hoes Lane West

department: Pharmacology

institute: Rutgers Biomedical and Health Sciences | Rutgers-Robert Wood Johnson Medical School

description: Library name: O_H_4_ATAC

data_processing:
In-house pipeline
Adaptors were trimmed using cutadapt version 5.1.
Trimmed reads were mapped to GRCh38.d1.v1 using bowtie2 with the following parameters: -no-mixed --no-discordant --maxins 2000
Alignments de-deduplicated using Picard and Samtools and subsequently blacklisted regions were removed using Bedtools.
Cleaned alignments were then used as input for peak calling using MACS2 with a relaxed threshold of q-value = 0.01 and a master peakset was constructed using bedops with individual sample peak sets as input. Differential accessibility was performed with DESeq2 and the differentially accessible regions (DARs) were used as input for TF footprinting using RGT-HINT.
Assembly: GRCh38.d1.v1
Supplementary files format and content: 1X normalized signal tracks per sample are provided. These were generated using deeptools normalized against the effective GRCh38 genome size.
Supplementary files format and content: BW

source_name: Peripheral blood

growth_protocol: Cells were isolated from peripheral blood and immediately stained for SA-ßGal and isolated via FACS.

extract_protocol:
Nuclei were isolated and transposed as in Buenrostro et al, Nature Methods, 2013, from ~50,000 CD8+ T cells
Libraries were constructed by PCR amplification of tagmented DNA as in Buenrostro et al, Nature Methods, 2013.

treatment_protocol: No treatment.

value: Peripheral blood

value: CD8+ T cell


title: T23-071_Niraparib_High_10

description: GeoMX Nanostring

value: Cancer

value: High


title: Subject_3_PP (BCR-Seq)

description:
Library name: Sample 6
BCR_data.tsv

value: Peyer's Patch


title: B2_EOT_Input

description: Library name: jc6591

value: breast core biopsy

value: end of treatment


title: Subject_1_LP (BCR-Seq)

description:
Library name: Sample 7
BCR_data.tsv

value: Intestinal Lamina Propria

value: B-Lymphocyte


title: Subject_1_PP (BCR-Seq)

description:
Library name: Sample 4
BCR_data.tsv

value: C57BL/6N WT


title: T23-071_Niraparib_Low_1

description: GeoMX Nanostring

value: Omentum

value: Low


title: Old, SA-ßGal-High, ATAC-Seq, donor 3

description: Library name: O_H_3_ATAC


title: Subject_2_PP (BCR-Seq)

description:
Library name: Sample 5
BCR_data.tsv


title: B3_Baseline_ER

description: Library name: jc6586

value: baseline

value: Millipore:06-935, Abcam:ab3575


title: T23-037_Rucaparib_Low_7

description: GeoMX Nanostring

value: Rucaparib


title: Old, SA-ßGal-High, ATAC-Seq, donor 1

description: Library name: O_H_1_ATAC


title: B2_Baseline_Input

description: Library name: jc6590

value: breast cancer

value: Input


title: B1_EOT_Input

description: Library name: jc5901

value: Letrozole + Megestrol 40mg


title: Subject_3_MLN (BCR-Seq)

description:
Library name: Sample 3
BCR_data.tsv

value: Mesenteric Lymph Node


title: T23-037_Rucaparib_Low_8

description: GeoMX Nanostring

value: Cancer


title: Old, SA-ßGal-High, ATAC-Seq, donor 2

description: Library name: O_H_2_ATAC

value: Peripheral blood

value: CD8+ T cell


title: T23-037_Rucaparib_High_5

description: GeoMX Nanostring

value: High


title: T23-037_Rucaparib_Low_6

description: GeoMX Nanostring


title: Subject_2_MLN (BCR-Seq)

description:
Library name: Sample 2
BCR_data.tsv


title: B1_Baseline_Input

description: Library name: jc5900

value: breast core biopsy


title: Young, SA-ßGal-High, ATAC-Seq, donor 4

description: Library name: O_L_4_ATAC


title: B2_EOT_ER

description: Library name: jc6583

value: end of treatment


title: B2_Baseline_ER

description: Library name: jc6582


title: T23-037_Rucaparib_High_4

description: GeoMX Nanostring


title: T23-037_Rucaparib_Low_9

description: GeoMX Nanostring


title: Young, SA-ßGal-High, ATAC-Seq, donor 2

description: Library name: O_L_2_ATAC


title: Subject_6_LP4GC (scRNA-seq)

description:
Library name: Sample 27
gex_data_ct_anno.rds

data_processing:
Pair-end FASTQ reads were first preprocessed on a by-sample basis using the “cellranger count” command from 10x Genomics’ Cell Ranger v6.1.2 for alignment against the mouse reference genome (refdata-gex-mm10-2020-a). The feature biotypes were retrieved using biomaRt v2.42.0 from Ensembl release 93.
Assembly: refdata-gex-mm10-2020-a
Supplementary files format and content: rds objects with cell annotations

value: Intestinal Lamina Propria

value: B-Lymphocyte

value: S1PR2CreERT2 Rosa-lsl-tdTomato


title: Subject_1_MLN (BCR-Seq)

description:
Library name: Sample 1
BCR_data.tsv

value: C57BL/6N WT


title: B1_EOT_ER

description: Library name: jc5895


title: T23-037_Rucaparib_Low_31

description: GeoMX Nanostring

value: Low


title: T23-037_Rucaparib_Low_30

description: GeoMX Nanostring


title: B1_Baseline_ER

description: Library name: jc5894

value: baseline

value: Millipore:06-935, Abcam:ab3575


title: Old, SA-ßGal-Low, ATAC-Seq, donor 4

description: Library name: Y_H_4_ATAC


title: T23-037_Rucaparib_High_3

description: GeoMX Nanostring

value: Rucaparib


title: Young, SA-ßGal-High, ATAC-Seq, donor 1

description: Library name: O_L_1_ATAC


title: Subject_6_LP4nonGC (scRNA-seq)

description:
Library name: Sample 26
gex_data_ct_anno.rds


title: Young, SA-ßGal-High, ATAC-Seq, donor 3

description: Library name: O_L_3_ATAC


title: T23-037_Rucaparib_Low_29

description: GeoMX Nanostring


title: Old, SA-ßGal-Low, ATAC-Seq, donor 3

description: Library name: Y_H_3_ATAC


title: Subject_5_LP3GC (scRNA-seq)

description:
Library name: Sample 25
gex_data_ct_anno.rds


title: Subject_4_LP2nonGC (scRNA-seq)

description:
Library name: Sample 22
gex_data_ct_anno.rds


title: Old, SA-ßGal-Low, ATAC-Seq, donor 2

description: Library name: Y_H_2_ATAC


title: A7_Baseline_Input

description: Library name: jc6540

value: breast cancer

value: Letrozole

value: Input


title: Subject_4_LP2GC (scRNA-seq)

description:
Library name: Sample 23
gex_data_ct_anno.rds


title: A7_EOT_ER

description: Library name: jc6535


title: A7_Baseline_ER

description: Library name: jc6534


title: T23-037_Rucaparib_Low_28

description: GeoMX Nanostring

value: Cancer


title: Old, SA-ßGal-Low, ATAC-Seq, donor 1

description: Library name: Y_H_1_ATAC

value: Peripheral blood


title: T23-037_Rucaparib_Low_27

description: GeoMX Nanostring


title: A6_EOT_Input

description: Library name: jc6724


title: Young, SA-ßGal-Low, ATAC-Seq, donor 4

description: Library name: Y_L_4_ATAC

value: CD8+ T cell


title: Young, SA-ßGal-Low, ATAC-Seq, donor 3

description: Library name: Y_L_3_ATAC


title: A6_Baseline_Input

description: Library name: jc6723


title: Subject_6_PP4nonGC (scRNA-seq)

description:
Library name: Sample 20
gex_data_ct_anno.rds

value: Peyer's Patch


title: A7_EOT_Input

description: Library name: jc6541

value: breast core biopsy


title: Subject_5_PP3GC (scRNA-seq)

description:
Library name: Sample 19
gex_data_ct_anno.rds


title: T23-037_Rucaparib_High_25

description: GeoMX Nanostring

value: High


title: T23-037_Rucaparib_High_24

description: GeoMX Nanostring


title: Young, SA-ßGal-Low, ATAC-Seq, donor 2

description: Library name: Y_L_2_ATAC


title: T23-037_Rucaparib_Low_26

description: GeoMX Nanostring


title: Subject_5_LP3nonGC (scRNA-seq)

description:
Library name: Sample 24
gex_data_ct_anno.rds

value: Intestinal Lamina Propria


title: Young, SA-ßGal-Low, ATAC-Seq, donor 1

description: Library name: Y_L_1_ATAC


title: A6_EOT_ER

description: Library name: jc6692

value: end of treatment


title: A5_EOT_Input

description: Library name: jc6527


title: Subject_6_PP4GC (scRNA-seq)

description:
Library name: Sample 21
gex_data_ct_anno.rds

value: B-Lymphocyte

value: S1PR2CreERT2 Rosa-lsl-tdTomato


title: Old, SA-ßGal-High, donor 2

description:
Library name: O_H_2
column name in RLD_WGCNA_Modules.txt: O_H_2

data_processing:
In-house pipeline
Adaptors were trimmed using cutadapt version 5.1.
Trimmed reads were mapped to GRCh38.d1.v1 using bowtie2 with the local option.
Alignments were analyzed for differential expression using DESeq2 and clustered using WGCNA.
Assembly: GRCh38.d1.v1
Supplementary files format and content: We include a tab-delimited text file that contains the RLD-transformed, normalized and debatched values of the compasiron 'SA-ßgal-low versus SA-ßgal-high' which is reported on the paper. The file contains the gene expression modules identified by WGCNA with their RLD values and annotated.

extract_protocol:
Macherey-Nagel RNA XS plus columns  from ~100,000 cells.
SMART-seq V4 as per the manufacturer's instructions.


title: Subject_5_PP3nonGC (scRNA-seq)

description:
Library name: Sample 18
gex_data_ct_anno.rds


title: Old, SA-ßGal-High, donor 3

description:
Library name: O_H_3
column name in RLD_WGCNA_Modules.txt: O_H_3


title: A5_Baseline_Input

description: Library name: jc6526


title: A6_Baseline_ER

description: Library name: jc6691


title: T23-037_Rucaparib_High_22

description: GeoMX Nanostring


title: Subject_4_PP2nonGC (scRNA-seq)

description:
Library name: Sample 16
gex_data_ct_anno.rds


title: Subject_6_MLN4GC (scRNA-seq)

description:
Library name: Sample 15
gex_data_ct_anno.rds

value: Mesenteric Lymph Node


title: T23-037_Rucaparib_High_21

description: GeoMX Nanostring


title: Subject_4_PP2GC (scRNA-seq)

description:
Library name: Sample 17
gex_data_ct_anno.rds


title: A5_EOT_ER

description: Library name: jc6521


title: A5_Baseline_ER

description: Library name: jc6520

value: baseline


title: T23-037_Rucaparib_High_23

description: GeoMX Nanostring


title: Old, SA-ßGal-High, donor 1

description:
Library name: O_H_1
column name in RLD_WGCNA_Modules.txt: O_H_1


title: Young, SA-ßGal-High, donor 3

description:
Library name: Y_H_3
column name in RLD_WGCNA_Modules.txt: Y_H_3


title: Subject_6_MLN4nonGC (scRNA-seq)

description:
Library name: Sample 14
gex_data_ct_anno.rds


title: T23-037_Rucaparib_Low_19

description: GeoMX Nanostring

value: Low


title: T23-037_Rucaparib_Low_20

description: GeoMX Nanostring

value: Rucaparib


title: T23-037_Rucaparib_Low_17

description: GeoMX Nanostring


title: Subject_5_MLN3nonGC (scRNA-seq)

description:
Library name: Sample 12
gex_data_ct_anno.rds


title: Subject_4_MLN2nonGC (scRNA-seq)

description:
Library name: Sample 10
gex_data_ct_anno.rds


title: A4_EOT_Input

description: Library name: jc6007

value: breast cancer


title: A3_EOT_Input

description: Library name: jc6282

value: Letrozole


title: Young, SA-ßGal-High, donor 4

description:
Library name: Y_H_4
column name in RLD_WGCNA_Modules.txt: Y_H_4


title: T23-037_Rucaparib_Low_18

description: GeoMX Nanostring


title: Subject_4_MLN2GC (scRNA-seq)

description:
Library name: Sample 11
gex_data_ct_anno.rds


title: A3_EOT_ER

description: Library name: jc6275

value: Millipore:06-935, Abcam:ab3575


title: Young, SA-ßGal-High, donor 2

description:
Library name: Y_H_2
column name in RLD_WGCNA_Modules.txt: Y_H_2


title: A3_Baseline_Input

description: Library name: jc6281

value: Input


title: Subject_5_MLN3GC (scRNA-seq)

description:
Library name: Sample 13
gex_data_ct_anno.rds


title: T23-037_Rucaparib_High_2

description: GeoMX Nanostring

value: Cancer


title: Young, SA-ßGal-High, donor 1

description:
Library name: Y_H_1
column name in RLD_WGCNA_Modules.txt: Y_H_1

value: Peripheral blood

value: CD8+ T cell


title: A4_Baseline_Input

description: Library name: jc6006

value: breast core biopsy


title: A3_Baseline_ER

description: Library name: jc6274


title: T23-037_Rucaparib_High_13

description: GeoMX Nanostring

value: High


title: Subject_3_PP (scRNA-seq)

description:
Library name: Sample 6
emilyMouse2.rds

value: Peyer's Patch

value: C57BL/6N WT


title: A4_EOT_ER

description: Library name: jc6001

value: end of treatment


title: Old, SA-ßGal-Low, donor 2

description:
Library name: O_L_2
column name in RLD_WGCNA_Modules.txt: O_L_2


title: T23-037_Rucaparib_Low_16

description: GeoMX Nanostring


title: T23-037_Rucaparib_High_11

description: GeoMX Nanostring


title: Subject_2_LP (scRNA-seq)

description:
Library name: Sample 8
emilyMouse2.rds

value: Intestinal Lamina Propria

value: B-Lymphocyte


title: Old, SA-ßGal-Low, donor 3

description:
Library name: O_L_3
column name in RLD_WGCNA_Modules.txt: O_L_3


title: T23-037_Rucaparib_High_15

description: GeoMX Nanostring


title: T23-037_Rucaparib_High_14

description: GeoMX Nanostring


title: A2_EOT_ER

description: Library name: jc6682


title: Young, SA-ßGal-Low, donor 2

description:
Library name: Y_L_2
column name in RLD_WGCNA_Modules.txt: Y_L_2


title: Old, SA-ßGal-Low, donor 4

description:
Library name: O_L_4
column name in RLD_WGCNA_Modules.txt: O_L_4


title: Subject_3_LP (scRNA-seq)

description:
Library name: Sample 9
emilyMouse2.rds


title: ISG20_rep_3, HFF/ISG20, biological replicate 3

city: Ulm

first: Thomas

last: Stamminger

address: Albert Einstein Allee 11

country: Germany

institute: Institute of Virology, Ulm University

description: Library name: Sample 6

data_processing:
Raw data (raw reads) of Fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analysis were based on clean data with high quality
Index of the reference genome was built using Hisat 2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat 2 v2.0.5.
Mapped reads of each sample were assembled by StringTie (v.1.3.3b) in a reference-based approach.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene
differential expression analysis was performed using the DESeq2 R package (1.20.0).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: connective tissue

growth_protocol: Primary human foreskin fibroblasts (HFF) cells were cultivated in 5% CO2 in minimal essential medium containing 7% fetal calf serum, 1% GlutaMAX (Gibco) and penicillin-streptomycin. After lentiviral transduction culturing was performed in the presence of 500 µg/ml geneticin (InvivoGen).

extract_protocol:
Total RNA was isolated using the Direct-zol Miniprep (Zymo Research) according to the manufacturer's instructions including an extended on-column Dnase digestion for 30 min
Library construction was performed by Novogene (Cambridge, UK). Including mRNA enrichment.

treatment_protocol: Cells were treated with doxycycline (500 ng/ml) for 24 h before total RNA was isolated

value: connective tissue

value: primary human foreskin fibroblasts

value: ISG20 overexpression


title: Subject_1_LP (scRNA-seq)

description:
Library name: Sample 7
emilyMouse2.rds


title: Subject_2_MLN (scRNA-seq)

description:
Library name: Sample 2
emilyMouse2.rds

value: Mesenteric Lymph Node


title: Old, SA-ßGal-Low, donor 1

description:
Library name: O_L_1
column name in RLD_WGCNA_Modules.txt: O_L_1


title: A1_EOT_Input

description: Library name: jc6704

value: breast cancer

value: Letrozole


title: A4_Baseline_ER

description: Library name: jc6000

value: baseline

value: Millipore:06-935, Abcam:ab3575


title: T23-015_Niraparib_Low_8

description: GeoMX Nanostring

value: Cancer

value: Niraparib

value: Low


title: T23-037_Rucaparib_High_12

description: GeoMX Nanostring

value: Rucaparib

value: High


title: ISG20_rep_1, HFF/ISG20, biological replicate 1

description: Library name: Sample 4


title: T23-015_Niraparib_Low_7

description: GeoMX Nanostring


title: Young, SA-ßGal-Low, donor 4

description:
Library name: Y_L_4
column name in RLD_WGCNA_Modules.txt: Y_L_4

value: Peripheral blood

value: CD8+ T cell


title: A1_EOT_ER

description: Library name: jc6672

value: breast core biopsy

value: end of treatment


title: Subject_1_PP (scRNA-seq)

description:
Library name: Sample 4
emilyMouse2.rds

value: Peyer's Patch

value: B-Lymphocyte

value: C57BL/6N WT


title: A1_Baseline_ER

description: Library name: jc6671


title: Young, SA-ßGal-Low, donor 3

description:
Library name: Y_L_3
column name in RLD_WGCNA_Modules.txt: Y_L_3


title: T23-037_Rucaparib_High_1

description: GeoMX Nanostring


title: 1802b_b, Ttc22-/-

city: Beijing

first: Wei

last: Tian

state: Beijing

address: Fu-Cheng-Lu #52, Haidian District

country: China

institute: Peking University Beijing cancer hospital

data_processing:
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the reference genome with hisat2 software (v2.0.4). Then, guided by the Ensembl gtf gene annotation file, cuffdiff software (part of cufflinks) was used to get the gene level FPKM as the expression profiles of mRNA.
Assembly: mm10
Supplementary files format and content: mRNA Expression Profiling.xlsx reports FPKM Values

source_name: colon

growth_protocol: Mice were housed in animal facility (with SPF condition) at the Peking University Cancer Hospital & Institute.

extract_protocol:
Total RNA was isolated from the colon tissues of Ttc22+/+/Ttc22+/-/Ttc22-/- mice (n=3) using an RNA Extraction Kit.
RNA high throughput sequencing was performed by Cloud-Seq Biotech (Shanghai, China). Briefly, total RNA was used for removing the rRNAs with NEBNext rRNA Depletion Kit (New England Biolabs, Inc., Massachusetts, USA) following the manufacturer's instructions. RNA libraries were constructed by using NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, Inc., Massachusetts,USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA).
Library sequencing was performed on an illumina NovaSeq 6000 instrument with 150bp paired end reads. Paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30.

value: colon


title: A2_EOT_Input

description: Library name: jc6714

source_name: breast cancer

value: breast cancer

value: Input


title: T23-037_Rucaparib_Low_10

description: GeoMX Nanostring


title: Old, SA-ßGal-High, donor 4

description:
Library name: O_H_4
column name in RLD_WGCNA_Modules.txt: O_H_4


title: T23-015_Niraparib_High_5

description: GeoMX Nanostring


title: T23-015_Niraparib_Low_9

description: GeoMX Nanostring


title: Subject_2_PP (scRNA-seq)

description:
Library name: Sample 5
emilyMouse2.rds


title: A2_Baseline_Input

description: Library name: jc6713

value: Letrozole

value: baseline


title: T23-015_Niraparib_Low_6

description: GeoMX Nanostring

value: Cancer


title: 1824a_b, Ttc22+/-


title: 1801a_b, Ttc22+/-


title: Subject_1_MLN (scRNA-seq)

description:
Library name: Sample 1
emilyMouse2.rds

value: Mesenteric Lymph Node


title: A2_Baseline_ER

description: Library name: jc6681

value: Millipore:06-935, Abcam:ab3575


title: CTRL_rep_3, HFF/CTRL, biological replicate 3

description: Library name: Sample 3

value: connective tissue

value: primary human foreskin fibroblasts

value: WT


title: CWR R1 NS Input

description: Library name: CWR_R1_NS_Input

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed using Trimmomatic v0.33.
Reads were aligned to UCSC hg38 genome using Bowtie version 1.1.2.
Peaks were called using MACS v2.1.0.
Assembly: GRCh38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample).

growth_protocol: LREX, C42B-ER and CWR-R1 are  Castrate resistant and enzalutamide prostate cancer cell lines were cultured in RPMI, 10%CSFBS, 1% Penstrep in humdified atmosphere with 5%CO2 at 37C

value: prostate cancer

value: NS


title: 1791a_b, Ttc22+/-


title: Subject_3_MLN (scRNA-seq)

description:
Library name: Sample 3
emilyMouse2.rds


title: T23-015_Niraparib_High_2

description: GeoMX Nanostring

value: Niraparib

value: High


title: siWdr82_expB_RNAseq_Rep2

city: New York

first: Robert

last: Sebra

address: 1 Gustave L. Levy Place

institute: Icahn School of Medicine at Mount Sinai

description: Library name: siWdr82_expB_RNAseq_Rep2

data_processing:
Illumina adapters were trimmed from reads using Trim Galore (v0.5.0). Reads were aligned to the GRCm38/mm10 reference genome using STAR (v2.7.5b) with the following custom parameters: --outFilterMultimapNmax 100 –winAnchorMultimapNmax 100. Gene and TE-level counts were calculated using TEcount (v2.2.1) using the Ensembl GRCm38 v102 transcript annotation and the GRCm38 RepeatMasker annotation downloaded from UCSC table browser.
Assembly: mm10
Supplementary files format and content: Supplementary files format and content: TSV file containing gene counts

source_name: mESC

extract_protocol:
For RNA extraction, cells were washed 3x with DPBS and lysed directly on the plate with 1mL of TRIzol reagent (Invitrogen, 15596026). Subsequently, RNA was purified using Direct-zol RNA Miniprep Plus Kits (Zymo, R2072) following manufacturer instructions. In brief, lysed cells in TRIzol were mixed 1:1 with 100% ethanol. Mixed lysates were added to the Zymo-spin columns, treated with DNase I, and washed with provided buffers. RNA was eluted with UltraPure DNase/RNase-Free Distilled Water (Invitrogen, 10977015). For DNA extraction, PureLink™ Genomic DNA Mini Kit (Invitrogen, K1820-00) was used followed manufacturer instructions. In brief, cells were washed 3x with DPBS and lysed directly on the plates using supplied Lysis/Binding buffer. Lysates were subsequently applied to the column and washed with buffers provided. DNA was eluted in PureLink Genomic Elution Buffer provided in the kit.
For complementary DNA synthesis, 100-200 µg of DNase I treated RNA was reverse transcribed using High-Capacity cDNA Reverse Transcription Kit (Applied Biosystems, 4368814). Random hexamers were used to capture total RNA.

value: mESC

tag: group

value: Experiment B


title: 1817b_b, Ttc22-/-

value: colon

tag: genotype


title: T23-015_Niraparib_Low_10

description: GeoMX Nanostring

value: Low


title: A1_Baseline_Input

description: Library name: jc6703

data_processing:
Reads were mapped to hg38 using Bowtie2 version 2.2.6 (Langmead B and  Salzberg S., 2012).
Aligned reads with the mapping quality less than 5 were filtered out.
Peaks were called with MACS2 version 2.1.1.20160309 (Zhang Y1 at al., 2008) using sequences from the corresponding input as a background control
Peaks yielded with MACS2 q value <= 1e-4 were selected for downstream analysis.  For visualizing tag density and signal distribution heatmap the read coverage in a window of +/- 2.5 or 5 kb region flanking the tag midpoint was generated using the bin size of 1/100 of the window length.
Assembly: GRCh38
Supplementary files format and content: bed/text

value: breast cancer

value: breast core biopsy

value: Input


title: CWR R1 ShMECOM 2 Input

description: Library name: CWR_R1_shMECOM_2_Input

value: shMECOM


title: C. elegans DJ101A control

city: Nanjing

first: Josef

last: Voglmeir

state: Jiangsu

address: 1 Weigang

institute: Nanjing Agricultural University

description:
Library name: DJ101A
biological replicate 1 and 2

data_processing:
Raw sequencing reads were assessed for quality using FastQC and summarized with MultiQC.
Reads were aligned to the C. elegans reference genome using HISAT2.
Gene-level read counts were generated using featureCounts.
Differential expression analysis was performed using DESeq2 in R.
Gene set enrichment analysis was performed using ReactomePA and clusterProfiler.
Assembly: Caenorhabditis elegans reference genome (WormBase)
Supplementary files format and content: Processed data include gene-level count tables, differential expression results, and pathway enrichment results provided as comma-separated value (CSV) files.

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: C. elegans were maintained under standard laboratory conditions prior to experimental treatment.

extract_protocol:
Total RNA was extracted from whole animals using TRIzol reagent according to the manufacturer’s instructions.
RNA sequencing libraries were prepared using a standard poly(A)-selected RNA-seq library preparation protocol compatible with Illumina sequencing.

treatment_protocol: Animals were exposed to bacteria expressing PNGaseDJ, PNGaseF, or the inactive PNGase mutant DJ101A prior to RNA extraction.

value: whole animal

value: wild-type

value: DJ101A inactive PNGase


title: C. elegans PNGaseDJ treatment

description:
Library name: PNGaseDJ
biological replicate 1 and 2

value: PNGaseDJ


title: CWR R1 ShMECOM 1 Input

description: Library name: CWR_R1_shMECOM_1_Input


title: 1815b_b, Ttc22-/-


title: ISG20_rep_2, HFF/ISG20, biological replicate 2

description: Library name: Sample 5

value: connective tissue

value: primary human foreskin fibroblasts

value: ISG20 overexpression


title: T23-015_Niraparib_High_4

description: GeoMX Nanostring

data_processing:
Sequenced data was analysed using the GeoMx NGS pipeline v2.3.3.10. Quality control thresholds: 100,000 raw reads and 50% sequencing saturation.
Quartile3 normalisation was applied across all targets to account for differing ROI size and cellularity which impact transcript abundance.
Data analysis performed wuthin R-environment, and differential gene expression analysed based on Linear Mixed Model. Significant genes defined as FDR<0.05
Assembly: GRCh38
Supplementary files format and content: DCC files produced by GeoMX NGS Pipeline
Library strategy: Spatial Transcriptomics

value: Cancer

value: Niraparib


title: siWdr82_expB_RNAseq_Rep1

description: Library name: siWdr82_expB_RNAseq_Rep1

value: mESC


title: CTRL_rep_2, HFF/CTRL, biological replicate 2

description: Library name: Sample 2

value: WT


title: mouse primary lung fibroblasts KD2

city: JiNan

first: Kaige

last: Lyu

state: ShanDong

address: SCHOOL OF PHARMACY ROOM 612, NEW SCIENTIFIC RESEARCH BUILDING OF PHARMACY  NO.44 WENHUA XI ROAD JINAN SHANDONG 250012 CHINA

institute: ShanDong University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.0.5。
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: mouse primary fibroblasts

extract_protocol:
WT or calumenin-KO mouse primary fibroblasts were lysed in TRIzol reagent, and total RNA was extracted by using a Rapid RNA Extraction Kit per the manufacturer's protocol.   The integrity of the RNA was verified via agarose gel electrophoresis, and the RNA concentrations were quantified with a NanoDrop spectrophotometer.
RNA-Seq libraries were prepared and sequenced on an Illumina NovaSeq 6000. The index of the reference genome was built by using HISAT2 (v2.0.5), and paired-end clean reads were aligned to the reference genome.

value: mouse primary fibroblasts

value: Mouse fibroblasts

value: Calu-KO


title: HDT820_kidney_1_a

type: RNA

city: Vancouver

first: David

last: Huntsman

state: BC

address: 675 W 10th Ave

department: Molecular Oncology

institute: BC Cancer Research Centre

description:
tma_2_transcripts.zarr.zip
tma_2_barcodes.tsv.gz
tma_2_features.tsv.gz
tma_2_matrix.mtx.gz
tma_2_morphology_focus.ome.tif
tma_2_morphology.ome.tif
dicer1_xenium_mus_musculus_all.rds
dicer1_xenium_mus_musculus_slide_map.xlsx
Raw data resulting from Xenium run, segmented with 5 micrometer expansion distance, without re-segmentation or processing by Proseg. Seurat object contains results after first re-segmenting with Proseg.

hyb_protocol: On day two, slides were subjected to a post-hybridization wash (37°C for 2 h), ligation (37°C for 2 h), amplification (30°C for 2 h), autofluorescence quenching and nuclei staining steps. Slides were then stored in PBS-T, overnight, at 4°C, in the dark.

scan_protocol: The following day, slides and consumables were loaded onto the Xenium Analyzer instrument according to the Xenium Analyzer (10X Genomics, CG000584, version Rev B) protocol. The whole slide area was selected for probe decoding and image acquisition, and the run was initiated.

data_processing: The Xenium bundles were segmented with Xenium Ranger 1.7.1.1, with the expansion distance around nuclei set to 5 µm.

label: 10X Genomics, Mouse Tissue Atlassing Panel, PN1000682

source_name: Kidney

label_protocol: The slides were processed, over a two-day span, as per the Xenium In Situ for FFPE – Deparaffinization and Decrosslinking (10X Genomics, CG000580 version Rev C) and Xenium In Situ Gene Expression (10X Genomics, CG000582 version Rev C) protocols. On day one, slides were incubated at 60°C for 2 h on a Xenium thermocycler adaptor plate (BioRad, C1000 Touch Thermocycler), followed by deparaffinized through a series of immersions in xylene, 100%, 96% and 70% ethanol, and rehydration with nuclease-free water. Slides were assembled into Xenium cassettes for all downstream steps, starting with decrosslinking and permeabilization.

extract_protocol: Tissue sections were prepared as per the Xenium In Situ for FFPE – Tissue Preparation Guide (10X Genomics, CG000578 version Rev C) protocol. 5 μm sections were cut and mounted onto the Sample Area of a Xenium slide. The slides were air dried, followed by 3 h incubation at 42°C.

treatment_protocol: Mice were injected intraperitoneally with tamoxifen (dose: 1 mg/kg, 5 consecutive days for mice > 3 weeks old; 2 mg/kg, 3 consecutive days for mice <2 weeks old). The cohort received a tamoxifen injection within first 2 months of birth (<=61 days).

tag: histology

value: Non-neoplastic kidney

value: Dicer1 mutant

tag: Sex

value: Female

tag: days after tamoxifen injection

tag: section

tag: tma core id


title: T23-015_Niraparib_High_3

description: GeoMX Nanostring

tag: patient id

tag: drug treatment

tag: absorbtion

value: High


title: C42B ER NS Input

description: Library name: C42B_ER_NS_Input

tag: cell line

value: prostate cancer

value: NS


title: CTRL_rep_1, HFF/CTRL biological replicate 1

description: Library name: Sample 1

tag: tissue


title: LREX NS Input

description: Library name: LREX_NS_Input

value: LREX


title: C. elegans PNGaseF treatment

description:
Library name: PNGaseF
biological replicate 1 and 2

value: whole animal

value: wild-type

tag: treatment

value: PNGaseF


title: HDT339_kidney_2_tumor

description:
kidney_section_4_transcripts.zarr.zip
kidney_section_4_barcodes.tsv.gz
kidney_section_4_features.tsv.gz
kidney_section_4_matrix.mtx.gz
kidney_section_4_morphology_focus.ome.tif
kidney_section_4_morphology.ome.tif
dicer1_xenium_mus_musculus_all.rds
dicer1_xenium_mus_musculus_slide_map.xlsx
Raw data resulting from Xenium run, segmented with 5 micrometer expansion distance, without re-segmentation or processing by Proseg. Seurat object contains results after first re-segmenting with Proseg.

label: 10X Genomics, Mouse Tissue Atlassing Panel, PN1000684

source_name: Renal tumor

value: Low-grade mesenchymal neoplasm

value: Male

value: Whole kidney section 4


title: C42B ER ShMECOM  2 Input

description: Library name: C42B_ER_shMECOM_2_Input

value: shMECOM


title: 1781a_a, Ttc22+/+

value: colon


title: 1843a_a, Ttc22+/+


title: T23-015_Niraparib_High_1

description: GeoMX Nanostring

value: Cancer

value: Niraparib


title: T23-037_Niraparib_Low_9

description: GeoMX Nanostring

value: Low


title: T23-037_Niraparib_Low_8

description: GeoMX Nanostring


title: HDT820_kidney_1_b

label: 10X Genomics, Mouse Tissue Atlassing Panel, PN1000683

value: Non-neoplastic kidney

value: Dicer1 mutant


title: LREX ShMECOM 2 Input

description: Library name: LREX_shMECOM_2_Input


title: HDT863_kidney_1_a

label: 10X Genomics, Mouse Tissue Atlassing Panel, PN1000681


title: T23-037_Niraparib_Low_6

description: GeoMX Nanostring


title: T23-037_Niraparib_Low_7

description: GeoMX Nanostring


title: C42B ER ShMECOM 1 Input

description: Library name: C42B_ER_shMECOM_1_Input


title: mouse primary lung fibroblasts KD1

value: mouse primary fibroblasts

value: Mouse fibroblasts

value: Calu-KO


title: CWR R1 ShMECOM 2  AR

description: Library name: CWR_R1_shMECOM_2_AR

value: prostate cancer

tag: antibody

value: AR


title: HDT872_kidney_1_a

label: 10X Genomics, Mouse Tissue Atlassing Panel, PN1000680


title: LREX ShMECOM 1 Input

description: Library name: LREX_shMECOM_1_Input

value: LREX


title: HDT868_kidney_2

label: 10X Genomics, Mouse Tissue Atlassing Panel, PN1000679

value: Female


title: 1826a_a, Ttc22+/+


title: T23-037_Niraparib_Low_40

description: GeoMX Nanostring


title: HDT868_kidney_1

label: 10X Genomics, Mouse Tissue Atlassing Panel, PN1000678


title: mouse primary lung fibroblasts NC1

value: Calu-WT


title: T23-037_Niraparib_High_5

description: GeoMX Nanostring

value: High


title: mouse primary lung fibroblasts NC2


title: PEG4

city: Eugene

first: Sam

middle: G

last: Horst

state: OR

address: 1229 University of Oregon, Room 273 Onyx Bridge

department: Institute of Molecular Biology

institute: University of Oregon

description: Library name: PEG4

data_processing:
Aligned to GRCz11 using TopHat 2.1.1 and bowtie2 2.33
Read counts were collected using HTSeq 0.6.1
Differential gene analysis done using EdgeR 4.3.2
Assembly: GRCz11
Supplementary files format and content: tab delimited text file includes raw counts for each sample.
Supplementary files format and content: tab delimited text file includes normalized cpm counts for each sample.

organism: Danio rerio

source_name: Caudal Fin

extract_protocol:
Tissue was homogenized in Trizol and frozen. Then, it was phase separated with chloroform, spun down, and the aqueous phase was extracted. Glycogen and isapropanol was added to the RNA, incubated for 10 minutes, and it was spun down. Supernatant was removed and RNA was washed with 70 percent ethanol. Finally, RNA was allowed to air dry and was suspended in RNAse-free water.
RNA libraries for RNA-Seq were prepared using the Kapa mRNA Seq Kit following manufacturer's protocols.

treatment_protocol: Intraperitoneal injection of 40mg/kg of BMS-833923 suspended in injection buffer (50% PEG-400, 5% Propylene Glycol, 0.5% Tween-80) or an equal volume of injection buffer. Fins were collected 5 hours after injection.

value: Caudal Fin

value: Control

value: PEG


title: C42B ER ShMECOM 2 AR

description: Library name: C42B_ER_shMECOM_2_AR

value: shMECOM


title: BMS4

description: Library name: BMS4

value: Smoothened Inhibited


title: HDT539_kidney_1_tumor

label: 10X Genomics, Mouse Tissue Atlassing Panel, PN1000677

value: Low-grade mesenchymal neoplasm


title: PEG3

description: Library name: PEG3


title: T23-037_Niraparib_Low_39

description: GeoMX Nanostring

extract_protocol:
sample processing step: To aid cryosection, frozen PDEs were embedded in a hydrogel (7.5% hydroxypropyl methylcellulose, 2.5% PVP)60. Polymer blocks were snap-frozen using dry ice-chilled isopropyl alcohol. 10-12 μm serial sections of were cut using a Leica CM3050s cryostat (-17°C), thaw-mounted onto slides (Thermo Fisher, 12-550-15) prior to storage at -80°C.
Adjacent tissue sections to those used for MSI were processed as recommended by Nanostring. In average, 5 high- and 5 low-drug  areas  were selected per sample,  inferred differential drug accumulation according to mass spectrometry imaging data.
PCR amplification/library preparations was carried out according to manufacturer’s instructions. Pooled libraries were purified using AMPure XP beads (Beckman Coulter), and final library quality and quantity assessed using the Agilent 2100 High Sensitivity DNA, and Qubit High-Sensitivity DNA assays. Sequencing was performed using the Illumina NextSeq2000 platform (Paired End 27bp + dual 8bp indexing).

value: Cancer

value: Niraparib

value: Low


title: HDT344_kidney_1_tumor

label: 10X Genomics, Mouse Tissue Atlassing Panel, PN1000674

value: Dicer1 mutant


title: HDT348_kidney_1_tumor_b

label: 10X Genomics, Mouse Tissue Atlassing Panel, PN1000675

value: Male


title: PEG2

description: Library name: PEG2


title: C42B ER ShMECOM 1 AR

description: Library name: C42B_ER_shMECOM_1_AR

value: prostate cancer


title: T23-037_Niraparib_High_4

description: GeoMX Nanostring


title: BMS2

description: Library name: BMS2


title: HDT339_kidney_1_tumor_b

label: 10X Genomics, Mouse Tissue Atlassing Panel, PN1000673


title: T23-037_Niraparib_Low_38

description: GeoMX Nanostring


title: T23-037_Niraparib_Low_36

description: GeoMX Nanostring

source_name: Omentum

value: Omentum


title: BMS3

description: Library name: BMS3


title: T23-037_Niraparib_Low_37

description: GeoMX Nanostring


title: C42B ER NS AR

description: Library name: C42B_ER_NS_AR

value: NS

value: AR


title: CWR R1 NS AR with AR

description: Library name: CWR_R1_NS_AR


title: CWR R1 ShMECOM 1 AR

description: Library name: CWR_R1_shMECOM_1_AR


title: LREX shMECOM 2  AR

description: Library name: LREX_shMECOM_2_AR

value: LREX


title: T23-037_Niraparib_High_35

description: GeoMX Nanostring

value: High


title: HDT395_kidney_2_tumor

label: 10X Genomics, Mouse Tissue Atlassing Panel, PN1000671

value: Female


title: HDT339_kidney_1_tumor_a

label: 10X Genomics, Mouse Tissue Atlassing Panel, PN1000672


title: IVR10-2014 - Rep3

city: Toulouse

first: Rémy

last: Betous

address: 23 Chemin des Capelles

department: Animal Health

country: France

institute: INRAE

description:
Library name: RS2159.58
RS2159.58

data_processing:
BaseCalls were converted and demultiplexed using Illumina bcl2fastq software to generate raw fastq files.
The analysis pipeline was executed with Nextflow v22.12.0-edge (Di Tommaso et al., 2017) and processed using nf-core/rnaseq v3.12.0 (doi: https://doi.org/10.5281/zenodo.7998767) of the nf-core collection of workflows (Ewels et al., 2020).
C. elegans genome reference PRJNA13758.WBPS18 and GTF annotation file  were used as reference sequences for nf-core/rnaseq pipeline.
Biostatistics treatments were performed under R v4.2.2 (R Core Team, 2022), edgeR package (Robinson et al., 2010) and Bioconductor packages (Huber et al. 2015). Briefly, raw count table was filtered to eliminate undetected genes using filterByExpr function with min.count=10 parameters. Normalization factors were calculated using TMM method. Then the common, trended and tagwise negative binomial dispersions were estimated with the robust mode of estimateDisp function. Normalized log2 CPM (counts per million reads) were exported to generate the normalized data file which is provided as 'processed data file'.
Assembly: PRJNA13758.WBPS18
Supplementary files format and content: Matrix table (tab separated tsv file) with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table (semicolon separated csv file) with log2CPM values for every gene and every sample

extract_protocol:
L4 stage worms were homogenized using a FastPrep-24 (MP Biomedicals, Irvine, USA) with lysis matrix D; three runs of 10 seconds at 6 m/s were performed, with 2 minutes of cooling on ice between runs. Subsequently, RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany).
RNAseq libraries were constructed from 1000 ng of total RNA at the GeT‐TRiX facility (GénoToul, Génopole Toulouse Midi-Pyrénées) using Illumina® Stranded mRNA Prep kit (Illumina, San Diego, CA, USA) following the manufacturer's instructions. Briefly, mRNAs were captures, then fragmented, converted to double stranded cDNAs and sequencing adaptors were ligated. Libraries were amplified with eleven cycles of PCR.

tag: strain

tag: Stage

value: whole animal

tag: phenotype

value: Resistant

tag: batch


title: IVR10-2022 - Rep3

description:
Library name: RS2159.57
RS2159.57


title: T23-037_Niraparib_High_33

description: GeoMX Nanostring

tag: cell type


title: HDT395_kidney_1_tumor

label: 10X Genomics, Mouse Tissue Atlassing Panel, PN1000670

tag: histology

value: Sarcoma

tag: genotype

tag: group


title: T23-037_Niraparib_High_34

description: GeoMX Nanostring


title: HDT359_kidney_1_tumor_b

label: 10X Genomics, Mouse Tissue Atlassing Panel, PN1000668

tag: Sex

tag: days after tamoxifen injection

tag: section


title: IVR10-2009 - Rep3

description:
Library name: RS2159.56
RS2159.56


title: LREX NS AR with AR

description: Library name: LREX_NS_AR


title: T23-037_Niraparib_High_31

description: GeoMX Nanostring

tag: patient id

tag: drug treatment


title: T23-037_Niraparib_High_32

description: GeoMX Nanostring

tag: absorbtion


title: T23-037_Niraparib_Low_30

description: GeoMX Nanostring

tag: tissue


title: HDT318_kidney_2_tumor_b_2

label: 10X Genomics, Mouse Tissue Atlassing Panel, PN1000663

tag: tma core id


title: T23-037_Niraparib_High_3

description: GeoMX Nanostring


title: N2B - Rep3

description:
Library name: RS2159.55
RS2159.55

value: WT


title: HDT359_kidney_1_tumor_c

label: 10X Genomics, Mouse Tissue Atlassing Panel, PN1000669


title: LREX shMECOM 1  AR

description: Library name: LREX_shMECOM_1_AR

tag: cell line

value: shMECOM

tag: antibody


title: CWRR1_shMECOM_REP2

description: Library name: Sample17

data_processing:
Adapter trimming and quality control were performed using Trim Galore with default parameters
Reads were aligned to the human reference genome (GRCh37) using the STAR aligner with default settings.
Gene-level quantification was performed using RSEM to generate raw counts and normalized FPKM/TPM values.
Differential expression analysis was conducted using edgeR .
Quality control was performed using FastQC, and multiQC reports were generated.
Assembly: GRCh37
Supplementary files format and content: Tab delimiated text file contaning raw counts for each gene across all samples.
Supplementary files format and content: Csv file contaning normalized expression vlaues for each genes.
Supplementary files format and content: rsem.merged.gene_counts.tsv: gene count
Supplementary files format and content: Sample_Sheet_RnaSeq.xlsx: sample sheet
Supplementary files format and content: mean_countPM.csv: mean count per million
Supplementary files format and content: differential_gene_expression.csv: diffrerntial gene expression
Supplementary files format and content: top_genes_LREX_shMECOM_v_control.csv: top genes for volcano plot
Supplementary files format and content: top_genes_C42B_ER_shMECOM_v_control.csv: top genes for volcano plot
Supplementary files format and content: top_genes_CWRR1_shMECOM_v_control.csv: top genes for volcano plot
Supplementary files format and content: All_UpandDown_regulatedGenes_Selected_Contrasts.csv: common down regulated genes
Supplementary files format and content: GSEA_data.csv: Gense set enrichment data

extract_protocol:
RNA Was harvested and extracted by using TRIzol reagent and RNA integrity and Qunatinty was determined by usnig Qubit RNA reagents
RNA libraries for sequencing were prepared using the SMARTer mRNA-Seq Library Prep Kit, following the manufacturer’s instructions.

treatment_protocol:
shMECOM RNA transfection
RNA was extracted following the manufacturer's instructions. RNA purity and concentration were assessed using spectrophotometry.

value: CRPC

tag: treatment

value: control

value: knookdown shRNA


title: CWRR1_Control_REP2

description: Library name: Sample14


title: IVR10-2009 - Rep2

description:
Library name: RS2159.50
RS2159.50

tag: strain

tag: Stage

tag: phenotype


title: CWRR1_Control_REP1

description: Library name: Sample13

tag: cell type

tag: batch


title: IVR10-2014 - Rep1

description:
Library name: RS2159.46
RS2159.46


title: CWRR1_Control_REP3

description: Library name: Sample15

tag: genotype


title: HDT318_kidney_1_tumor_a

label: 10X Genomics, Mouse Tissue Atlassing Panel, PN1000661

tag: histology

tag: group

value: Dicer1 mutant

tag: Sex


title: IVR10-2022 - Rep1

description:
Library name: RS2159.45
RS2159.45


title: T23-037_Niraparib_Low_27

description: GeoMX Nanostring

value: Cancer

tag: patient id

value: Niraparib

value: Low


title: CWRR1_shMECOM_REP3

description: Library name: Sample18


title: T23-037_Niraparib_Low_26

description: GeoMX Nanostring

tag: drug treatment


title: IVR10-2009 - Rep1

description:
Library name: RS2159.44
RS2159.44


title: CWRR1_shMECOM_REP1

description: Library name: Sample16


title: T23-037_Niraparib_Low_28

description: GeoMX Nanostring

tag: absorbtion


title: HDT967_kidney_2

description:
kidney_section_1_transcripts.zarr.zip
kidney_section_1_barcodes.tsv.gz
kidney_section_1_features.tsv.gz
kidney_section_1_matrix.mtx.gz
kidney_section_1_morphology_focus.ome.tif
kidney_section_1_morphology.ome.tif
dicer1_xenium_mus_musculus_all.rds
dicer1_xenium_mus_musculus_slide_map.xlsx
Raw data resulting from Xenium run, segmented with 5 micrometer expansion distance, without re-segmentation or processing by Proseg. Seurat object contains results after first re-segmenting with Proseg.

label: 10X Genomics, Mouse Tissue Atlassing Panel, PN1000631

value: Non-neoplastic kidney

tag: days after tamoxifen injection

tag: section

value: Whole kidney section 1


title: HDT318_kidney_2_tumor_b_1

label: 10X Genomics, Mouse Tissue Atlassing Panel, PN1000662

tag: tma core id


title: IVR10-2014 - Rep2

description:
Library name: RS2159.52
RS2159.52

tag: tissue


title: N2B - Rep2

description:
Library name: RS2159.49
RS2159.49


title: C42B-ER_Control_REP3

description: Library name: Sample9

tag: cell line

tag: treatment


title: HDT359_kidney_1_tumor_a

label: 10X Genomics, Mouse Tissue Atlassing Panel, PN1000667

value: Male


title: T23-037_Niraparib_High_25

description: GeoMX Nanostring

value: High


title: 35S:HY5K87R-GFP/hy5 after 2h of the control condition, biological rep3

city: Münster

first: Jie

last: Shen

address: Schlossplatz 7,  48149 Münster

institute: University of Muenster

description:
Library name: Sample21
JS015

data_processing:
Raw reads in FASTQ format were processed using the fastp software to remove adapter sequences, reads containing poly-N, and low-quality reads. Additionally, quality metrics Q30 and GC content of the clean data were calculated.
High-quality reads were mapped to the Arabidopsis thaliana TAIR10 reference genome using Hisat2 (v2.0.5).
The mapped reads for each sample were assembled using StringTie (v1.3.3b) (79) in a reference-guided approach. Gene-level quantification was performed using the featureCounts tool (v1.5.0-p3), which counted the number of reads mapped to each gene.
To compare gene expression levels quantitatively, FPKM (Fragments Per Kilobase of transcript sequence per Million base pairs) values were calculated for each gene based on gene length and the mapped read count using default parameters.
Differential expression analysis between two conditions or groups was conducted using the DESeq2 R package (v1.20.0) with three biological replicates per group.
Assembly: TAIR10
Supplementary files format and content: Matrix table with count file for every sample

organism: Arabidopsis thaliana

source_name: seeding

growth_protocol: Arabidopsis thaliana seeds were surface-sterilized by chlorine gas, then cultured in Petri dishes on solid ½ Murashige and Skoog (MS) medium for 7 days. Plants were grown in the growth chamber with the 16-h light /8-h dark cycles (23 °C/18 °C) at a light intensity of 100 μmol m-2 s-1.

extract_protocol:
Total RNA was extracted using the Trizol reagent (Invitrogen) and reverse-transcribed into first-strand cDNA using SuperScript II Reverse Transcriptase (Invitrogen).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection

treatment_protocol: For high light experiments, plants were initially grown for one week in a growth light (100 µmol m-2 s-1) before increasing the irradiance to 500 µmol m-2 s-1 for 2 h.

value: seeding

value: Growth light


title: T23-037_Niraparib_High_24

city: London

first: LMS

last: Bioinformatics Core

institute: MRC London Institute of Medical Sciences

description: GeoMX Nanostring


title: C42B-ER_shMECOM_REP2

description: Library name: Sample11


title: IVR10-2022 - Rep2

description:
Library name: RS2159.51
RS2159.51

tag: strain

tag: Stage

value: whole animal

value: Resistant


title: 35S:HY5K87R-GFP/hy5 after 2h of the control condition, biological rep2

description:
Library name: Sample20
JS014


title: HDT293_kidney_1_a

label: 10X Genomics, Mouse Tissue Atlassing Panel, PN1000628


title: HDT340_kidney_2_b

label: 10X Genomics, Mouse Tissue Atlassing Panel, PN1000664


title: C42B-ER_shMECOM_REP3

description: Library name: Sample12

tag: cell type


title: T23-037_Niraparib_Low_29

description: GeoMX Nanostring


title: HDT289_kidney_2_b

label: 10X Genomics, Mouse Tissue Atlassing Panel, PN1000627

value: Female


title: N2B - Rep1

description:
Library name: RS2159.43
RS2159.43

tag: phenotype

value: WT

tag: batch


title: HDT294_kidney_2

description:
kidney_section_2_transcripts.zarr.zip
kidney_section_2_barcodes.tsv.gz
kidney_section_2_features.tsv.gz
kidney_section_2_matrix.mtx.gz
kidney_section_2_morphology_focus.ome.tif
kidney_section_2_morphology.ome.tif
dicer1_xenium_mus_musculus_all.rds
dicer1_xenium_mus_musculus_slide_map.xlsx
Raw data resulting from Xenium run, segmented with 5 micrometer expansion distance, without re-segmentation or processing by Proseg. Seurat object contains results after first re-segmenting with Proseg.

label: 10X Genomics, Mouse Tissue Atlassing Panel, PN1000632

tag: histology

tag: genotype

value: Whole kidney section 2


title: T23-037_Niraparib_High_21

description: GeoMX Nanostring


title: T23-037_Niraparib_Low_20

description: GeoMX Nanostring


title: HDT289_kidney_1_b

tag: group

value: control

tag: Sex


title: C42B-ER_Control_REP1

description: Library name: Sample7

value: CRPC

value: knookdown shRNA


title: C42B-ER_shMECOM_REP1

description: Library name: Sample10

value: shMECOM


title: 35S:HY5K87Q-GFP/hy5  after 2h of the control condition, biological rep1

description:
Library name: Sample16
hy5_Q


title: 35S:HY5K87K-GFP/hy5 after 2h of the control condition, biological rep3

description:
Library name: Sample15
JS009


title: 35S:HY5K87R-GFP/hy5 after 2h of the control condition, biological rep1

description:
Library name: Sample19
hy5_R


title: C42B-ER_Control_REP2

description: Library name: Sample8


title: HDT293_kidney_1_b

label: 10X Genomics, Mouse Tissue Atlassing Panel, PN1000629


title: HDT289_kidney_1_c


title: HDT293_kidney_1_c

label: 10X Genomics, Mouse Tissue Atlassing Panel, PN1000630


title: HDT799_kidney_1_a


title: LREX_shMECOM_REP1

description: Library name: Sample4

value: LREX


title: LREX_shMECOM_REP3

description: Library name: Sample6


title: LREX_shMECOM_REP2

description: Library name: Sample5


title: T23-037_Niraparib_High_2

description: GeoMX Nanostring

value: Cancer

tag: patient id

tag: drug treatment

value: Niraparib


title: LREX_Control_REP2

description: Library name: Sample2


title: T23-037_Niraparib_Low_18

description: GeoMX Nanostring

tag: absorbtion

value: Low


title: HDT789_kidney_1_b

value: Non-neoplastic kidney

value: Male

tag: days after tamoxifen injection

tag: section


title: LREX_Control_REP3

description: Library name: Sample3


title: LREX_Control_REP1

description: Library name: Sample1


title: 35S:HY5K87Q-GFP/hy5 after 2h of the control condition, biological rep2

description:
Library name: Sample17
JS011

tag: tissue

value: seeding


title: 35S:HY5K87K-GFP/hy5 after 2h of the control condition, biological rep1

description:
Library name: Sample13
hy5_0

value: Growth light


title: HDT799_kidney_1_b

tag: tma core id


title: T23-037_Niraparib_High_22

description: GeoMX Nanostring

value: High


title: MSI2-KO, replicate 2

city: Boston

first: Gaurav

last: Agarwal

state: MA

address: 1 Blackfan Circle

department: Division of Hematology/Oncology

institute: Boston Children's Hospital

description:
Library name: KO-rep2
10X Genomics

data_processing:
The raw scRNA-seq FASTQ files were processed with the CellRanger (v8.0.1) pipeline to map in the reference genome (GRCh38). We excluded cells with unique molecular identifier (UMI) counts less than 2,000 or greater than 25,000, or mitochondrial UMI fraction higher than 20%, and removed potential doublets by a threshold of doublet score > 0.25 using ScrubletR, which resulted in a total of 58,810 cells across AAVS1 (donor 1 = 10,267 and donor 2 = 12,771), ENH-1 (donor 1 = 7,425 and donor 2 = 8,522), and MSI2-KO (donor 1 = 11,553 and donor 2 = 8,272) edited cells. Symphony R package60 was used to project the cells on a human BM reference (https://github.com/andygxzeng/BoneMarrowMap), to annotate molecularly defined HSCs. A standard Seurat framework (v4.4.0) was used to conduct normalization, principal component analysis (PCA), and dimensionality reduction. The feature-barcode matrix was normalized by the total read count and log-transformed, and the top 3,000 variable features were selected by the vst method in the FindVariableFeatures function. The normalized expression was scaled by Seurat’s ScaleData function, and PCA was performed using the RunPCA function (npc = 30). The sample-dependent technical variation was corrected by using Harmony (PMID: 31740819). Uniform Manifold Approximation and Projection (UMAP) was conducted to reduce dimensions to embed the cells into two-dimensional space.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Primary Human HSPC

growth_protocol: Serum-free HSPC expansion media

extract_protocol:
72 hours after editing, viable cells (negative for DAPI) were sorted with a 100 um nozzle - on a FACSymphony S6 Cell Sorter (BD Biosciences) - according to the surface expression of CD34+CD45RA-CD90+ markers. The sorted cells were counted and roughly 16,000 cells from each sample were utilized for the subsequent procedure (estimated recovery: 10,000 cells/sample).
Libraries were prepared by Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 (10X Genomics) according to manufacturer’s instructions.

treatment_protocol: Primary human CD34+ HSPCs were edited (on day 2 of culture) with CRISPR/Cas9 for ENH-1 microdeletion, MSI2-knockout, or at the AAVS1 safe-harbor locus.

value: Primary Human HSPC

value: CD34+CD45RA-CD90+ HSPCs

tag: treatment

value: CRISPR/Cas9 MSI2-knockout


title: T23-037_Niraparib_High_23

address: Hammersmith Hospital Campus, Du Cane Road

description: GeoMX Nanostring


title: T23-037_Niraparib_Low_17

description: GeoMX Nanostring


title: T23-037_Niraparib_Low_19

description: GeoMX Nanostring


title: hy5 after 2h of high light, biological rep3

description:
Library name: Sample12
JS021

value: High light


title: hy5 after 2h of high light, biological rep2

description:
Library name: Sample11
JS020


title: 35S:HY5K87Q-GFP/hy5 after 2h of the control condition, biological rep3

description:
Library name: Sample18
JS012


title: HDT968_kidney_1_b

value: control


title: HDT968_kidney_1_a


title: HDT967_kidney_1_b

value: Female


title: T23-037_Niraparib_Low_16

description: GeoMX Nanostring


title: 35S:HY5K87K-GFP/hy5 after 2h of the control condition, biological rep2

description:
Library name: Sample14
JS008


title: HDT789_kidney_1_a


title: ENH-1 microdeletion, replicate 2

description:
Library name: ENH1-rep2
10X Genomics

value: CRISPR/Cas9 ENH-1 microdeletion at MSI2 enhancer


title: T23-037_Niraparib_High_14

description: GeoMX Nanostring


title: hy5 after 2h of high light, biological rep1

description:
Library name: Sample10
hy5HL


title: T23-037_Niraparib_High_15

description: GeoMX Nanostring


title: AAVS1 edited, replicate 2

description:
Library name: AAVS1-rep2
10X Genomics

value: CRISPR/Cas9 editing at AAVS1


title: ENH-1 microdeletion, replicate 1

description:
Library name: ENH1-rep1
10X Genomics


title: hy5after 2h of the control condition, biological rep3

description:
Library name: Sample9
JS006


title: T23-037_Niraparib_High_13

description: GeoMX Nanostring


title: T23-037_Niraparib_High_12

description: GeoMX Nanostring


title: HDT964_kidney_1_b

value: Hic1-CreERT2+/+;tdtomato fl/fl


title: WT after 2h of high light, biological rep3

description:
Library name: Sample6
JS018

value: Col-0 (WT)


title: MSI2-KO, replicate 1

description:
Library name: KO-rep1
10X Genomics


title: HDT967_kidney_1_a


title: HDT963_kidney_1_a


title: hy5 after 2h of the control condition, biological rep1

description:
Library name: Sample7
hy5


title: WT after 2h of high light, biological rep2

description:
Library name: Sample5
WTHL


title: hy5 after 2h of the control condition, biological rep2

description:
Library name: Sample8
JS005


title: HDT964_kidney_1_a


title: HDT963_kidney_1_b


title: AAVS1 edited, replicate 1

description:
Library name: AAVS1-rep1
10X Genomics


title: D4 WGS

city: Cincinnati

first: Artem

last: Barski

state: OH

address: 3333 Burnet Av

department: Allergy

institute: Cincinnati Children's Hospital

description:
Library name: E05830_D4
Genomic DNA was isolated using a PureLink Genomic DNA Kit (Thermo Fisher) and quality/quantity verified by Qubit and gel electrophoresis. WGS libraries were prepped and sequenced PE150 using the Illumina NovaSeq 6000.

data_processing:
Sequencing reads were aligned, and variants were identified using the Genome Analysis Toolkit (GATK) Unified Genotyper following GATK Best Practices 3.3.
Assembly: GRCh38/hg38
Supplementary files format and content: A Variant Call Format (VCF v4.2) file that includes SNP and indels from all 3 datasets: E05828_D2, E05829_D3, and E05830_D4.
Supplementary files format and content: TBI index for a VCF file.

source_name: blood

extract_protocol:
Genomic DNA was isolated using a PureLink Genomic DNA Kit (Thermo Fisher) following the manufacturer’s guidelines.
Genomic DNA was sent to NovoGene for Human Whole Genome Sequencing (WOBI).

value: blood

value: CD4 T cells


title: T23-037_Niraparib_High_11

description: GeoMX Nanostring

value: Cancer

value: Niraparib


title: S71_LoGated_Ruc_24h

data_processing:
Reads were processed using cutadapt v4.7 (Martin 2011) to remove Illumina adapters, trim, and filter on quality with the settings: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA, -n 1, -m 31, --nextseq-trim 20, --max-n 0
Processed reads were quantified against the GRCh38 transcriptome (Ensembl 107 annotations) by Salmon (Patro et al. 2017) with the following settings: -l A, --softclip, --softclipOverhangs, --allowDovetail, --seqBias, --gcBias.
Within DESeq2 v1.44.0 (Love, Huber, and Anders 2014), independent hypothesis weighting was conducted to optimise the power of p value filtering using IHW v1.32.0 (Ignatiadis et al. 2016) and log2 fold-change shrinkage was performed using ashr v2.2-63 (Stephens 2017). Multiple correction testing adjustments were optimised by passing FDR and log2FC thresholds at the point of results generation.
Assembly: GRCh38
Supplementary files format and content: Transcript-level expression estimates

growth_protocol: Cell lines were maintained in RPMI 1640 supplemented with 2 mM Glutamine, 100 U/mL penicillin, 100 µg/mL streptomycin, 10% FCS at 37°C, 5% CO2 and passaged three times per week using TrypLE express.

extract_protocol:
After treatment, with or without FACS-sorting to separate rucaparib-high and low (top and bottom 20% of population), cells were washed in ice-cold PBS before extraction RNA using the RNeasy purification kit (Qiagen, 74106) according to manufacturer’s instructions. Unsorted controls cells were scraped directly into lysis buffer (RLT) using a cell scraper.
The NEBNext Ultra II Directional RNA Library Prep Kit with NEBNext Poly(A) mRNA Magnetic Isolation Module was used to generate RNA-Seq libraries according to the manufacturer’s protocol. Library quality was checked using the Agilent 2100 High-Sensitivity DNA assay, before checking concentrations with the Qubit dsDNA HS Assay Kit. Libraries were sequenced on a NextSeq 2000 after pooling in equimolar quantities.

treatment_protocol: PEO1 cells were treated for 2 or 24h with DMSO (vehicle) or the fluorescent compound Rucaparib at 8.5 µM. After incubation, the different conditions were harvested to FACS-sort the bottom and top 20% of the Rucaparib treated population when ranked according to the drug fluorescence intensity.

tag: cell line

tag: facs gate

value: Lo

value: Ruc

tag: timepoint

tag: replicate


title: WT after 2h of the control condition, biological rep3

description:
Library name: Sample3
JS003

value: seeding

value: Growth light


title: D3 WGS

description:
Library name: E05829_D3
Genomic DNA was isolated using a PureLink Genomic DNA Kit (Thermo Fisher) and quality/quantity verified by Qubit and gel electrophoresis. WGS libraries were prepped and sequenced PE150 using the Illumina NovaSeq 6000.

tag: cell type


title: HDT365_kidney_2_tumor

data_processing:
The Xenium bundles were segmented with Xenium Ranger 1.7.1.1, with the expansion distance around nuclei set to 5 µm.
Raw data resulting from Xenium run, segmented with 5 micrometer expansion distance, without re-segmentation or processing by Proseg. Seurat object contains results after first re-segmenting with Proseg.

label: Xenium Mouse Probe Set

value: Renal tumor

tag: histology

value: Sarcoma

value: HDT tumor

value: F

tag: tma core map


title: HDT361_kidney_1_tumor_b

tag: genotype

tag: group

value: M


title: T23-037_Niraparib_High_1

description: GeoMX Nanostring

tag: patient id

value: High


title: T23-037_Niraparib_Low_10

description: GeoMX Nanostring

tag: drug treatment

value: Low


title: WT after 2h of the control condition, biological rep1

description:
Library name: Sample1
WT


title: D2 WGS

description:
Library name: E05828_D2
Genomic DNA was isolated using a PureLink Genomic DNA Kit (Thermo Fisher) and quality/quantity verified by Qubit and gel electrophoresis. WGS libraries were prepped and sequenced PE150 using the Illumina NovaSeq 6000.


title: HDT291_kidney_1_tumor

tag: Sex


title: WT after 2h of high light, biological rep1

description:
Library name: Sample4
JS016

value: High light


title: WT after 2h of the control condition, biological rep2

description:
Library name: Sample2
JS002

value: Col-0 (WT)


title: HDT325_kidney_1_tumor

tag: days after tamoxifen injection