title: F_Chronic_5xCHI+ SB_Rep6

description:
Library name: 22131R-04-14
Count


title: 2_IgA_S9

status: Public on Mar 18 2026

type: SRA

city: Barcelona

first: Júlia

last: Perera-Bel

address: Doctor Aiguader, 88

department: MARData-BU

country: Spain

institute: Hospital del Mar Research Institute

description:
2_IgA
Counts.matrix.csv

library_source: transcriptomic

data_processing:
Reads were mapped with STAR software (v.2.7.8a) against the human reference genome GRCh38 using the GRCh38-89 Ensembl annotation.
The table of counts was obtained with featureCounts function in the package subread (v.2.8.2).
Counts were normalized with log2 counts per million (CPM) with the edgeR package (v.3.14.0) with a prior.count=3. Genes with more than 10 counts in at least 4 samples were kept.
Assembly: GRCh38
Supplementary files format and content: counts

molecule: total RNA

organism: Homo sapiens

source_name: Tonsillar memory class-switched IgA, FACSorted

extract_protocol:
Cells were centrifuged and homogenized using QIAshredder (Qiagen). RNA was isolated with RNeasy Micro Kit (Qiagen) according to manufacturer’s instructions. RNA quality and quantity were assessed by Bioanalyzer using Agilent RNA 6000 Pico Kit (Agilent Technologies). Samples used for analysis had RIN ≥ 6.4.
NGS libraries with polyA capture were prepared according to the manual NEBNext® Ultra™ II Directional RNA. Library Prep Kit for Illumina® (New England Biolabs) (Version 4.0, 4/21)
RNA-seq (polyA capture)

treatment_protocol: Fresh tonsilliar cell suspensions were stained with antibodies cocktail as described in Methods. Cells were then FACSorted according to the gating strategy provided in Methods.

tag: treatment

value: IgA

tag: donor

tag: cell type

value: Tonsillar memory class-switched IgA


title: GM_P_T15_R1 [sequencing]

city: Saskatoon

first: Franco

middle: J

last: Vizeacoumar

state: Saskatchewan

address: 4D40 Health Sciences Building, 107 Wiggins Road

department: Oncology

country: Canada

institute: University of Saskatchewan

description:
Skin
T15 Timepoint Replicate 1

library_source: genomic

data_processing:
Sequenced files were demultiplexed from Illumina.
Read counts were calculated using the package from Li, et al. Genome Biology 15:554 (2014). MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens.
Supplementary files format and content: Raw_read_counts_matrix.txt: Matrix table with raw gene counts for every gene and every sample.
Library strategy: Amplicon sequencing

molecule: genomic DNA

source_name: Skin

growth_protocol: 7x10^8 cells were infected at an MOI of 0.3 with a viral library (lentiCRISPRv2_A) containing 65,000 sgRNAs to yield a library coverage of 300x. Infected cells were selected for with puromycin. T0 replicates (x2) of 2.5x10^7 cells were collected and triplicate replicates for culture in hypoxia were plated at 2x10^7 per replicate.

extract_protocol:
Genomic DNA was extracted using the QIAamp Blood Maxi kit (Qiagen #51194).
Libraries were constructed following the previously described method in Shalem O et al. Science 2014.

treatment_protocol: Cells were cultured in 1% oxygen and passaged every 72 hours for a period of 20 generations. 2x10^7 cells were collected from each replicate following each passage. 2x10^7 cells were maintained in culture for each replicate for the subsequent generation to maintain 300x library coverage.

tag: cell line

value: Infection with viral library lentiCRISPRv2_A

tag: time point

tag: condition

value: Parental


title: Stage2, 3c4FC, day7, RNASeq

city: Parkville

first: Sean

last: Wilson

state: Victoria

address: 50 Flemington Road

country: Australia

institute: MCRI

description:
(3' mRNA) library: read1 file contains cell barcode and UMI, read2 file contains transcript
RNAseq_repeat.mtx

data_processing:
Cell Ranger (v1.3.1) was used to process and aggregate raw data from each of the samples returning a count matrix and associated barcode and gene information
Cite-seq-count (v1.4.3) was used to process HTO reads
RNA-seq: The raw reads were quality and adapter trimmed using trim-galore v0.6.5
RNA-seq: The trimmed reads were mapped to the human genome (hg38) using the STAR aligner v2.7.4a in the two pass mapping mode
Assembly: hg38
Supplementary files format and content: scRNAseq: gene expression matrix and sample related metadata as a csv
Supplementary files format and content: RNAseq: gene expression matrix

molecule: polyA RNA

growth_protocol: The iPSC line used in this study was CRL2429-MAFBmTagBFP2/GATA3mCherry (32), maintained and expanded at 37oC in 5% CO2 in Essential 8 medium (Thermo Fisher) on MatrigelTM-coated (Thermo Fisher) plates with daily media changes and passaged every 3-4 days with EDTA in 1x PBS buffer as described previously49. An initial seeding density of 7 x 104 cells into 6-well culture plates was then cultured with variations based on the Takasato protocol3 modified to use TeSR-E6 medium31 (STEMCELL technologies). Organoids were cultured from D0 in 1.5ml of E6 and 7µM CHIR for 3 (3c), 4 (4c) or 5 (5c) days. Following this, organoids were cultured in one of the following conditions; 2 (2F), 3 (3F) or 4 (4F and 4FG) days of 100ng/mL FGF9, 4 days of 100ng/mL FGF9 with one of 2.5µM AGN193189 (4FA), 1µM CHIR (4FC), 0.1µM LDN193109 (4FL), or 4 days of 200ng/mL FGF9 (4F200) or base media alone (4E). All conditions were then aggregated onto transwells by dissociating to single cell and transferring 1 x 104 cells as a 1ul cell/media droplet, as 3 sets of 2 technical replicates per transwell. Organoids were cultured in 1.1ml E6 with 5µM CHIR for 1 hour before replacing media with 1.1ml E6, 200ng/mL FGF9 and 1ug/mL heparin for 5 days. An additional set of 4F organoids were generated, with these receiving 50ng/mL GDF11 during these 4 days (4FG). After 5 days culture, all organoids were maintained in E6 media alone until day 27. Media was changed every 2 days for all organoids at all times, except when a culture change occurred in between. Samples were collected at the end of the four stages of differentiation as defined by changes in media composition, with the final organoids collected at day 27 of culture.

extract_protocol:
Kidney organoids were dissociated to single cell, incubated with Totalseq-A antibodies (Biolegend; Cat# 394601, 394603, 394605, 394607, 394609, 394611, 394613, 394615) for sample hashing each samples collection day, pooled and super-loaded onto the 10x Genomics Chromium Controller (10x Genomics) to capture single cells. Briefly, 3x technical replicates for each sample were dissociated using TrypLE for 3 minutes, pooled and diluted in TEsR-E6 and centrifuged at 300 × g for three minutes. The cell pellets were resuspended in 100 µL cold Fluorescence-Activated Cell Sorting (FACS) buffer (PBS with 2% fetal bovine serum). Then, 2 µL of Totalseq-A hashing antibody was added and the cells were gently pipetted to mix before incubating for 20 min on ice. Cells were then washed twice with FACS buffer by centrifuging at 300 × g for 5 min, discarding the supernatant and resuspending the cell pellet in 100 µL cold FACS buffer. Approximately 40,000 cells were loaded onto the Chromium Single Cell Chip B (10x Genomics; Catalog Number: PN-1000073) to capture 20,000 single cells with the Gel Bead Kit V3.0 (10x Genomics; Catalog Number: PN-1000075). GEM generation, barcoding, cDNA amplification, and library construction were performed according to the 10x Genomics Chromium User Guide (CG000183).
Libraries were prepared with the Single Cell 3’ V3.0 Library and Gel Bead Kit (10x Genomics; Catalog Number: PN-1000075). The samples collected from stages 1, 2 and 3 occurred across six days, each capture multiplexed up to eight unique conditions and all were sequenced on the same run. The final collection of stage four cells occurred separately, multiplexing either 3 or 4 conditions to allow for greater cell numbers per condition for the more complex “mature” organoids.

tag: library type

value: mRNA


title: Stage4, sample capture 10, day 27, scRNAseq GEX

description:
GEX (3' mRNA) library: read1 file contains cell barcode and UMI, read2 file contains transcript
Kidney_organoid_atlas_ge_matrix.mtx
Kidney_organoid_atlas_metadata.csv

library_source: transcriptomic single cell


title: F_Chronic_5xCHI+ SB_Rep5

city: Atlanta

first: Levi

middle: B.

last: Wood

state: GA

address: 315 Ferst Dr NW Rm 3303

country: USA

institute: Georgia Institute of Technology

description:
Library name: 22131R-04-24
Count

data_processing:
Quality control was performed using an Agilent Bioanalyzer to ensure all RNA samples had an RNA Integrity Number (RIN) greater than 7. Libraries were prepared using NEBNext Poly(A) mRNA Magnetic Isolation and Ultra II Directional RNA Library Prep Kits and sequenced on the Illumina NovaSeq 6000 platform to a depth of approximately 30–40 million paired-end reads per sample. Reads from four technical replicate lanes were merged per sample. Sequencing reads were aligned to the Mus musculus genome assembly GRCm39 (mm39) using STAR aligner. Gene-level quantification was performed using featureCounts. Genes with fewer than 200 raw counts in more than 5% of total samples were excluded. Non-coding genes were also filtered out. Data were normalized using the DESeq2 R package, avaliable on Bioconductor.
Assembly: Transcripts were aligned to the Mus musculus genome assembly GRCm39 (mm39).
Supplementary files format and content: Raw count values in csv format.

organism: Mus musculus

source_name: Brain Somatosensory Cortex

growth_protocol: Mice were maintained in standard housing conditions with ad libitum access to food and water.  All procedures were approved by the Institutional Animal Care and Use Committee (IACUC) and performed in accordance with institutional guidelines.

extract_protocol:
RNA was isolated from mouse brain tissue  tissues using Qiagen RNeasy kit (217804; Qiagen; Hilden, Germany) according to the manufacturer’s protocols.
A NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490S; New England Biolab; Ipswich, MA, USA) and NEBNext Ultra II Directional RNA Library Prep Kit (E7760; New England Biolab) were used to generate libraries for sequencing.

tag: strain

tag: tissue

value: Brain Somatosensory Cortex

tag: Sex

value: F

tag: timepoint

value: Chronic

tag: cohort

tag: conditions

value: 5xCHI + SB

tag: injury

value: SB


title: GM_P_T6_R1 [sequencing]

description:
Skin
T6 Timepoint Replicate 1


title: 2_IgG_S8

description:
2_IgG
Counts.matrix.csv

source_name: Tonsillar memory class-switched IgG, FACSorted

value: IgG

value: Tonsillar memory class-switched IgG


title: F_Chronic_5xCHI+ SB_Rep4

description:
Library name: 22131R-04-39
Count


title: SCI 3 mm Below-3

city: Rochester

first: Chanil

last: Choi

state: MN

address: 200 First Street SW

department: Physical Medicine and Rehabilitation

institute: Mayo Clinic

description:
Library name: Sample 15
WT-B_sample-3

data_processing:
MAP-RSeq (Kalari et al., 2014) workflow (v1.2.1.3) was used to process mRNA-seq data, including read alignment, quality control, gene expression quantification and finally summarizing the data across samples.
Paired-end reads were aligned by TopHat (v2.0.12) against the mouse genome build (mm10) using the bowtie1aligner (Langmead et al., 2009)
The gene counts were generated using Subread package (Anders et al., 2015) (v1.4.4).
The workflow also provides detailed quality control metrics across genes using the RSeQC (Wang et al., 2012) (v2.3.2).
Differential expression analysis was performed with edgeR (Robinson et al., 2010) package (v2.6.2) to identify genes with altered expression.
Assembly: mm10
Supplementary files format and content: xlsx file include raw counts for each sample

source_name: spinal cord

extract_protocol:
At the 30 d post-SCI endpoint, a 9 mm segment of spinal cord centered on the site of injury was collected and subdivided into three 3 mm segments that encompassed the injury epicenter, or the 3 mm of adjacent tissue rostral (“Above”), or caudal (“Below”). 3 mm spans were chosen as this length essentially encompasses the injury epicenter by visual inspection. For the uninjured controls, the full 9 mm section of spinal cord corresponding to the identical anatomical levels as the SCI group (T11 – S1) was collected and processed collectively. Total RNA was prepared using RNA Stat60 (Tel-Test, Friendswood, TX) following the manufacturer’s instructions.
RNA libraries were prepared using 200 ng of total RNA using the TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego, CA).

value: spinal cord

value: female

tag: age

value: 12 weeks old

tag: time

value: 30 days after SCI


title: Stage4, sample capture 8, day 27, scRNAseq GEX


title: SCI 3 mm Below-2

description:
Library name: Sample 14
WT-B_sample-2


title: F_Chronic_5xCHI+ SB_Rep7

description:
Library name: 22131R-04-23
Count


title: 8-IgA_S20

description:
8-IgA
Counts.matrix.csv


title: Stage4, sample capture 12, day 27, scRNAseq GEX


title: 2-naive_S7

description:
2-naive
Counts.matrix.csv

source_name: Tonsillar naive B cells, FACSorted

value: naive

value: Tonsillar naive B cells


title: F_Chronic_5xCHI+ SB_Rep2

description:
Library name: 22131R-04-37
Count


title: SCI 3 mm Below-4

description:
Library name: Sample 16
WT-B_sample-4


title: SCI 3 mm Below-1

description:
Library name: Sample 13
WT-B_sample-1


title: Stage4, sample capture 9, day 27, scRNAseq GEX


title: Stage3, sample capture 7, day14, scRNAseq GEX


title: 2-IgD_S10

description:
2-IgD
Counts.matrix.csv

source_name: Tonsillar memory class-switched IgD, FACSorted

value: IgD

value: Tonsillar memory class-switched IgD


title: F_Chronic_5xCHI+ SB_Rep3

description:
Library name: 22131R-04-38
Count


title: 8-IgG_S22

description:
8-IgG
Counts.matrix.csv


title: Stage3, sample capture 6, day13, scRNAseq GEX


title: SCI Epicenter-4

description:
Library name: Sample 12
WT-E_sample-4


title: 8-naive_S21

description:
8-naive
Counts.matrix.csv


title: SCI Epicenter-3

description:
Library name: Sample 11
WT-E_sample-3


title: Stage3, sample capture 5, day12, scRNAseq GEX


title: SCI Epicenter-2

description:
Library name: Sample 10
WT-E_sample-2


title: NHOS cells, IL10RB-transfected (NHOS-TR)

city: Tokyo

first: Chie

last: Kudo-Saito

address: 5-1-1 Tsukiji, Chuo-ku

department: Department of Immune Medicine

country: Japan

institute: National Cancer Center Research Institute

description:
Library name: HHMF5DSX3_PR3072_02A0284
Colomun name in Processed data (CKS-IL10RB).xlsx: PR3072_02_a

data_processing:
DRAGEN Bio-IT Platform ver. 3.7.5
Sequence reads were mapped using DRAGEN Bio-IT Platform ver. 3.7.5
Read count extraction and normalization to TPM values were performed using DRAGEN Bio-IT Platform ver. 3.7.5
Assembly: m28
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: NHOS

growth_protocol: NHOS cells were maintained in DMEM medium containing 10% FBS and 1 mg/ml Geneticin/G418 at 37°C under humidified conditions with 5% CO2.

extract_protocol:
RNAs were extracted using Rneasy mini kit (Qiagen), and were used for the construction of sequencing libraries.
cDNA libraries were prepared using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech) according to the manufacturer’s protocols.

value: NHOS

value: Osteosarcoma

tag: genetic modification

value: IL10RB transfectant


title: NHOS cells, Mock control (NHOS-mock)

description:
Library name: HHMF5DSX3_PR3072_01A0283
Colomun name in Processed data (CKS-IL10RB).xlsx: PR3072_01_a

value: Mock


title: Stage2, sample capture 3, day8, scRNAseq GEX

value: mRNA


title: 16-IgD_S2

description:
16-IgD
Counts.matrix.csv

tag: treatment


title: SCI Epicenter-1

description:
Library name: Sample 9
WT-E_sample-1


title: F_Chronic_5xCHI+ SB_Rep1

description:
Library name: 22131R-04-15
Count

value: Brain Somatosensory Cortex

value: F

value: Chronic

value: 5xCHI + SB


title: 20-IgD_S4

description:
20-IgD
Counts.matrix.csv

tag: donor


title: SCI 3 mm Above-4

description:
Library name: Sample 8
WT-A_sample-4

value: spinal cord


title: 16-naive_S1

description:
16-naive
Counts.matrix.csv

tag: cell type


title: 20-IgA_S3

description:
20-IgA
Counts.matrix.csv

value: IgA

value: Tonsillar memory class-switched IgA


title: Stage1, sample capture 1, day 0 to 5, scRNAseq GEX

tag: cell line


title: 20-naive_S5

description:
20-naive
Counts.matrix.csv


title: Stage2, sample capture 2, day 7, scRNAseq GEX


title: 20-IgG_S6

description:
20-IgG
Counts.matrix.csv

value: IgG

value: Tonsillar memory class-switched IgG


title: SCI 3 mm Above-1

description:
Library name: Sample 5
WT-A_sample-1

value: female

value: 12 weeks old

value: 30 days after SCI


title: Muscle,Intermittent_fasting,Female,rep4

city: Melbourne

first: Yibo

last: Fan

state: VIC

address: Science Dr, Bundoora VIC 3083

institute: La Trobe University

description: Library name: MIF36

data_processing:
Base Calling,CASAVA base recognition
Data Filtering,Remove reads with adapter contamination.Remove reads when uncertain nucleotides constitute more than 10 percent of either read (N > 10%).Remove reads when low quality nucleotides (Base Quality less than 5) constitute more than 50 percent of the read.
Alignment,HISAT2
Assembly: mm39
Supplementary files format and content: txt file includes raw counts for each sample

source_name: Muscle

extract_protocol:
RNA was extracted using TRIzol Reagent.
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 using either dUTP for directional library.For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification

value: Muscle

tag: diet

value: IF


title: SCI 3 mm Above-2

description:
Library name: Sample 6
WT-A_sample-2


title: Stage2, sample capture 4, day9, scRNAseq GEX


title: Muscle,Intermittent_fasting,Female,rep5

description: Library name: MIF37


title: 23-6-IgA_S13

description:
23-6-IgA
Counts.matrix.csv


title: Muscle,Intermittent_fasting,Female,rep6

description: Library name: MIF38


title: Muscle,Intermittent_fasting,Female,rep7

description: Library name: MIF39


title: THP-1, LMAs, rep3

city: Shenzhen

first: Zhe

last: Dai

address: Xueyuan Avenue 1088

department: School of Medicine

country: China

institute: Southern University of Science and Technology

data_processing:
Raw RNA-seq reads underwent quality control and length selection using Trimmomatic (http://www.usadellab.org/cms/index.php?page=trimmomatic). Subsequently, they were aligned to the GRCh38 (hg38) reference genome using HISAT2 (http://daehwankimlab.github.io/hisat2/). Count tables were generated employing featureCounts (http://subread.sourceforge.net/).
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

extract_protocol:
Total RNA was extracted from LAMs or control cells using TRIzol® Reagent following the manufacturer’s instructions (Magen). RNA samples were assessed for purity using the A260/A280 absorbance ratio with a Nanodrop ND-2000 system (Thermo Scientific, USA), and RNA integrity was evaluated using an Agilent Bioanalyzer 4150 system (Agilent Technologies, CA, USA). Only samples meeting quality criteria were selected for library construction. 1 ug of total RNA was used for the construction of sequencing libraries.
Paired-end libraries were prepared using a ABclonal mRNA-seq Lib Prep Kit (ABclonal, China) following the manufacturer’s instructions.


title: SCI 3 mm Above-3

description:
Library name: Sample 7
WT-A_sample-3


title: Muscle,Intermittent_fasting,Female,rep3

description: Library name: MIF35


title: THP-1, Control, rep3


title: THP-1, LAMs, rep1


title: THP-1, LAMs, rep2


title: uninjured spinal cord-4

description:
Library name: Sample 4
WT-UI_sample-4


title: 23-6-IgG_S12

description:
23-6-IgG
Counts.matrix.csv


title: Muscle,Intermittent_fasting,Female,rep2

description: Library name: MIF34


title: uninjured spinal cord-3

description:
Library name: Sample 3
WT-UI_sample-3


title: THP-1, Control, rep2


title: 23-6-naive_S11

description:
23-6-naive
Counts.matrix.csv

value: naive

value: Tonsillar naive B cells


title: 23_IgG_S16

description:
23_IgG
Counts.matrix.csv


title: Muscle,Ad_libtum,Female,rep8

description: Library name: MAL32

value: AL


title: Muscle,Intermittent_fasting,Female,rep1

description: Library name: MIF33


title: 25-IgA_S18

description:
25-IgA
Counts.matrix.csv


title: Muscle,Ad_libtum,Female,rep6

description: Library name: MAL30


title: U-2 OS, shFTSJ3 model, H3K27ac Replicate 2

data_processing:
Data from different lanes (lanes 3 and 4) were pooled into a single FASTQ file with samtools
ChIP-seq reads were trimmed from 3' end using Cutadapt version 4.2.
Bowtie version 2.5.0 was used to align the reads to the hg38 (GRCh38.p14) reference genome with the --very-sensitive settings profile.
SAMtools verson 1.16.1 was used to convert the SAM files to BAM and sort the subsequent BAM files.
Peaks were called using epic2 with the default settings, comparing the treatments vs. the inputs. Input-1 was used for H3K9Me3-1 only, where as input-2 was used for K3K9Me3-2 and both acetylation samples.
Output bed6 files were manually converted into bedGraph files using the standard Unix command awk.
bigWig files were generated UCSC's bedGraphToBigWig tool. Score represents the coverage of DNA fragments at a given genomic coordinate relative to the input control.
Assembly: GRCh38.p14
Supplementary files format and content: bigWig, bedGraph

source_name: Human female osteosarcoma

growth_protocol: As described in Abuhussein et al. 2023

extract_protocol:
As described in Abuhussein et al. 2023
As described in Abuhussein et al. 2023

treatment_protocol: As described in Abuhussein et al. 2023

value: U-2 OS

value: Human female osteosarcoma

tag: chip antibody

value: shFTSJ model


title: 23_naive_S14

description:
23_naive
Counts.matrix.csv


title: U-2 OS, shFTSJ3 model, H3K27ac Replicate 1


title: LVFW_R403Q_12mo_2

city: Boston

first: Jonathan

last: Seidman

state: Massachusetts

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

description:
Library name: Sample 32
10x Genomics

data_processing:
FASTQ files were processed with Cell Ranger (v9.0.0) using the --include-introns option and aligned to the Sus scrofa reference genome (Sscrofa11.1, Ensembl). Count matrices were refined with CellBender (v0.2.1).
Filtered gene-barcode matrices were imported into R (v4.3.1) and analyzed with Seurat v5.0.1. Doublets were detected and excluded using Solo (v0.3). Quality control thresholds retained nuclei with 300–25,000 counts, 300–6,000 genes, ≤2% mitochondrial transcripts, and Solo softmax ≤0.5.
Data were log-normalized, highly variable genes were selected, and mitochondrial content and total counts were regressed out. Principal component analysis was performed, and Harmony (v1.2.0) was applied to correct batch effects across subjects.
Assembly: Sus scrofa (pig) genome assembly Sscrofa11.1
Supplementary files format and content: For each sample, processed data are provided as filtered_feature_bc_matrix.h5 files generated by Cell Ranger (v9.0.0). These HDF5 files contain filtered gene-by-barcode count matrices, representing expression counts per gene and nucleus after quality control and preprocessing.

organism: Sus scrofa

growth_protocol: Yucatan minipigs carrying the MYH7-R403Q mutation and wild-type littermates were studied between 2 and 13 months of age. Animals were maintained under standardized housing conditions with free access to food and water and regular veterinary monitoring. At defined time points, tissue samples from the left ventricular free wall were collected, immediately transferred into cold cardioplegia solution, and snap-frozen at –80 °C.

extract_protocol:
Porcine cardiac tissue samples were processed by an experimenter blinded to genotype. Nuclei were isolated from unfixed frozen tissue using detergent-based lysis, purified by fluorescence-activated cell sorting, and microscopically inspected to confirm integrity and purity. Nuclei were quantified with a Countess II system (Life Technologies), kept on ice, and immediately used for single-nucleus RNA-sequencing
Single-nucleus suspensions were loaded onto a Chromium Controller (10x Genomics) targeting a recovery of 5,000–10,000 nuclei per reaction. 3′ gene expression libraries were prepared using the Chromium Single Cell 3′ Reagent Kits v3 (10x Genomics) following the manufacturer’s instructions. cDNA quality was assessed with the Agilent Bioanalyzer High Sensitivity DNA Analysis Kit, and libraries were quantified using the KAPA Library Quantification Kit. Sequencing was performed on an Illumina NovaSeq 6000 platform at a target depth of 30,000–50,000 reads per nucleus.

value: mixed cardiac cell types

value: Yucatan minipig

tag: genotype

value: MYH7 R403Q (heterozygous, knock-in)

value: male


title: Muscle,Ad_libtum,Female,rep4

description: Library name: MAL28


title: U-2 OS, shFTSJ3 model, H3K9me3 Replicate 2


title: Muscle,Ad_libtum,Female,rep7

description: Library name: MAL31


title: Muscle,Ad_libtum,Female,rep5

description: Library name: MAL29


title: 25-IgG_S19

description:
25-IgG
Counts.matrix.csv

value: IgG


title: 23_IgA_S15

description:
23_IgA
Counts.matrix.csv

value: IgA

value: Tonsillar memory class-switched IgA


title: LVFW_R403Q_12mo_1

description:
Library name: Sample 31
10x Genomics

tag: strain


title: THP-1, Control, rep1


title: uninjured spinal cord-1

description:
Library name: Sample 1
WT-UI_sample-1

tag: tissue

value: spinal cord

value: female

value: 12 weeks old


title: uninjured spinal cord-2

description:
Library name: Sample 2
WT-UI_sample-2

tag: Sex

value: 30 days after SCI


title: U-2 OS, shFTSJ3 model, H3K9me3 Replicate 1


title: U-2 OS, shFTSJ3 model, input-2

value: shFTSJ model, input


title: 25-naive_S17

description:
25-naive
Counts.matrix.csv

value: naive

value: Tonsillar naive B cells


title: Muscle,Ad_libtum,Female,rep3

description: Library name: MAL27

value: Muscle

value: AL


title: LVFW_R403Q_10mo_2

description:
Library name: Sample 30
10x Genomics


title: LVFW_R403Q_10mo_1

description:
Library name: Sample 29
10x Genomics


title: LVFW_R403Q_13mo

description:
Library name: Sample 33
10x Genomics


title: Muscle,Ad_libtum,Female,rep2

description: Library name: MAL26


title: KPPC sgCCR1A 3A

city: St Louis

first: Kian-Huat

last: Lim

state: MO

address: 4566 Scott Avenue

institute: Washington University Medical school

description:
Library name: Sample 18
KPPC_sgCCR2A_3.LIB012835.LIB012835_22G37CLT3_S247_L005_R1_001.fastq

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.0.4b
Gene counts derived with Subread:featureCount 1.45.  RPKM and CPM calculated from gene counts with custom R scripting.
Assembly: Ensembl Release 76 GRCm38.76
Supplementary files format and content: Gene counts in tab-delimitted text format

source_name: Pancreatic cancer

growth_protocol: All cells were cultured in DMEM/10% FBS, 1% Pen/Strep.

extract_protocol:
RNA was harvested using Purelink RNA Mini isolation kit. mRNA is extracted form total RNA using a Dynal mRNA Direct kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Pancreatic cancer

value: KPPC Cell line

value: Murine KPPC Cell line

value: KPPC cells espressing sgCCR1A 1 replicate3

tag: batch

value: KPPC sgCCR1A 3


title: KPPC sgCCR1A 2A

description:
Library name: Sample 17
KPPC_sgCCR2A_2.LIB012834.LIB012834_22G37CLT3_S252_L005_R1_001.fastq

value: KPPC cells espressing sgCCR1A 1 replicate2

value: KPPC sgCCR1A 2


title: Muscle,Ad_libtum,Female,rep1

description: Library name: MAL25


title: U-2 OS, non-targeting shRFP control, H3K27ac Replicate 2

value: U-2 OS

value: Human female osteosarcoma

value: non-targeting shRFP


title: Muscle,Intermittent_fasting,Female,rep8

description: Library name: MIF40

value: female

value: IF


title: LVFW_R403Q_9mo_1

description:
Library name: Sample 27
10x Genomics

value: mixed cardiac cell types

value: Yucatan minipig

value: MYH7 R403Q (heterozygous, knock-in)

value: male


title: KPPC sgCCR1A 1A

description:
Library name: Sample 16
KPPC_sgCCR2A_1.LIB012833.LIB012833_22G37CLT3_S249_L005_R1_001.fastq

value: KPPC cells espressing sgCCR1A 1 replicate1

value: KPPC sgCCR1A 1


title: Muscle,Intermittent_fasting,Male,rep8

description: Library name: MIF16

value: Muscle


title: U-2 OS, non-targeting shRFP control, H3K27ac Replicate 1


title: LVFW_R403Q_8mo

description:
Library name: Sample 26
10x Genomics


title: U-2 OS, shFTSJ3 model, input-1

value: shFTSJ model, input


title: U-2 OS, non-targeting shRFP control, H3K9me3 Replicate 1


title: LVFW_R403Q_6mo_4

description:
Library name: Sample 25
10x Genomics


title: LVFW_R403Q_6mo_3

description:
Library name: Sample 24
10x Genomics


title: U-2 OS, non-targeting shRFP control, H3K9me3 Replicate 2


title: U-2 OS, non-targeting shRFP control, input-2

value: non-targeting shRFP, input


title: LVFW_R403Q_9mo_2

description:
Library name: Sample 28
10x Genomics


title: KPPC sgCCR2A 2A

description:
Library name: Sample 14
KPPC_sgCCR1A_2.LIB012837.LIB012837_22G37CLT3_S251_L005_R1_001.fastq

value: Pancreatic cancer

value: KPPC Cell line

value: Murine KPPC Cell line

value: KPPC cells espressing sgCCR2A 2 replicate 2

value: KPPC sgCCR2A 2


title: Muscle,Intermittent_fasting,Male,rep6

description: Library name: MIF14


title: LVFW_R403Q_6mo_2

description:
Library name: Sample 23
10x Genomics


title: KPPC vector Control 3A

description:
Library name: Sample 12
KPPC_vector_Control_3.LIB012832.LIB012832_22G37CLT3_S246_L005_R1_001.fastq

value: KPPC cells expressing empty vector replicate 3

value: KPPC vector Control 3


title: Muscle,Intermittent_fasting,Male,rep4

description: Library name: MIF12

value: IF


title: Muscle,Intermittent_fasting,Male,rep5

description: Library name: MIF13


title: U-2 OS, non-targeting shRFP control, input-1

value: U-2 OS

value: Human female osteosarcoma


title: KPPC  vector Control 1A

description:
Library name: Sample 10
KPPC_vector_Control_1.LIB012830.LIB012830_22G37CLT3_S248_L005_R1_001.fastq

value: KPPC cells expressing empty vector replicate 1

value: KPPC  vector Control 1


title: LVFW_R403Q_6mo_1

description:
Library name: Sample 22
10x Genomics

value: mixed cardiac cell types

value: Yucatan minipig

value: MYH7 R403Q (heterozygous, knock-in)

value: male


title: KPPC sgCCR2A 3A

description:
Library name: Sample 15
KPPC_sgCCR1A_3.LIB012838.LIB012838_22G37CLT3_S245_L005_R1_001.fastq

value: KPPC cells espressing sgCCR2A 3 replicate 3

value: KPPC sgCCR2A 3


title: MIA PaCa-2, shFTSJ3 model, H3K27ac Replicate 2

source_name: Human male pancreas carcinoma

value: MIA PaCa-2

value: Human male pancreas carcinoma

value: shFTSJ model


title: KPPC sgCCR1A 3

description:
Library name: Sample 9
KPPC_sgCCR2A_3.LIB012835.LIB012835_22G2NGLT3_S51_L001_R1_001.fastq

value: Pancreatic cancer

value: KPPC Cell line

value: Murine KPPC Cell line

value: KPPC cells espressing sgCCR1A 1 replicate3

value: KPPC sgCCR1A 3


title: LVFW_R403Q_4mo

description:
Library name: Sample 19
10x Genomics


title: KPPC sgCCR1A 1

description:
Library name: Sample 7
KPPC_sgCCR2A_1.LIB012833.LIB012833_22G2NGLT3_S53_L001_R1_001.fastq

value: KPPC cells espressing sgCCR1A 1 replicate1

value: KPPC sgCCR1A 1


title: LVFW_R403Q_5mo_1

description:
Library name: Sample 20
10x Genomics


title: MIA PaCa-2, shFTSJ3 model, H3K9me3 Replicate 2


title: Muscle,Ad_libtum,Male,rep8

description: Library name: MAL8

value: Muscle

value: AL


title: LVFW_R403Q_2mo_1

description:
Library name: Sample 17
10x Genomics

value: mixed cardiac cell types

value: Yucatan minipig


title: MIA PaCa-2, shFTSJ3 model, input-2

value: shFTSJ model, input


title: LVFW_R403Q_2mo_2

description:
Library name: Sample 18
10x Genomics

value: MYH7 R403Q (heterozygous, knock-in)

value: male


title: KPPC vector Control 2A

description:
Library name: Sample 11
KPPC_vector_Control_2.LIB012831.LIB012831_22G37CLT3_S250_L005_R1_001.fastq

value: KPPC cells expressing empty vector replicate 2

value: KPPC vector Control 2


title: MIA PaCa-2, shFTSJ3 model, H3K27ac Replicate 1

value: MIA PaCa-2

value: Human male pancreas carcinoma

value: shFTSJ model


title: LVFW_WT_13mo

description:
Library name: Sample 16
10x Genomics

value: WT

value: none (wild-type)


title: LVFW_R403Q_5mo_2

description:
Library name: Sample 21
10x Genomics


title: Muscle,Intermittent_fasting,Male,rep7

description: Library name: MIF15

value: IF


title: Muscle,Intermittent_fasting,Male,rep3

description: Library name: MIF11


title: LVFW_WT_12mo_2

description:
Library name: Sample 15
10x Genomics


title: KPPC sgCCR2A 1A

description:
Library name: Sample 13
KPPC_sgCCR1A_1.LIB012836.LIB012836_22G37CLT3_S253_L005_R1_001.fastq

value: Pancreatic cancer

value: KPPC Cell line

value: Murine KPPC Cell line

value: KPPC cells espressing sgCCR2A 1 replicate 1

value: KPPC sgCCR2A 1


title: Muscle,Ad_libtum,Male,rep5

description: Library name: MAL5

value: Muscle

value: AL


title: Muscle,Ad_libtum,Male,rep7

description: Library name: MAL7


title: Muscle,Ad_libtum,Male,rep4

description: Library name: MAL4


title: KPPC sgCCR2A 3

description:
Library name: Sample 6
KPPC_sgCCR1A_3.LIB012838.LIB012838_22G2NGLT3_S49_L001_R1_001.fastq

value: KPPC cells espressing sgCCR2A 3 replicate 3

value: KPPC sgCCR2A 3


title: MIA PaCa-2, non-targeting shRFP control, H3K9me3 Replicate 2

value: non-targeting shRFP


title: Muscle,Intermittent_fasting,Male,rep1

description: Library name: MIF9

value: male


title: LVFW_WT_10mo_2

description:
Library name: Sample 13
10x Genomics

value: mixed cardiac cell types

value: Yucatan minipig


title: KPPC vector Control 2

description:
Library name: Sample 2
KPPC_vector_Control_2.LIB012831.LIB012831_22G2NGLT3_S54_L001_R1_001.fastq

value: KPPC cells expressing empty vector replicate 2

value: KPPC vector Control 2


title: KPPC sgCCR2A 2

description:
Library name: Sample 5
KPPC_sgCCR1A_2.LIB012837.LIB012837_22G2NGLT3_S55_L001_R1_001.fastq

value: KPPC cells espressing sgCCR2A 2 replicate 2

value: KPPC sgCCR2A 2


title: Muscle,Intermittent_fasting,Male,rep2

description: Library name: MIF10

value: IF


title: LVFW_WT_12mo_1

description:
Library name: Sample 14
10x Genomics

value: WT

value: none (wild-type)


title: KPPC vector Control 3

description:
Library name: Sample 3
KPPC_vector_Control_3.LIB012832.LIB012832_22G2NGLT3_S50_L001_R1_001.fastq

value: Pancreatic cancer

value: KPPC Cell line

value: Murine KPPC Cell line

value: KPPC cells expressing empty vector replicate 3

value: KPPC vector Control 3


title: KPPC sgCCR2A 1

description:
Library name: Sample 4
KPPC_sgCCR1A_1.LIB012836.LIB012836_22G2NGLT3_S57_L001_R1_001.fastq

value: KPPC cells espressing sgCCR2A 1 replicate 1

value: KPPC sgCCR2A 1


title: MIA PaCa-2, non-targeting shRFP control, input-2

value: MIA PaCa-2

value: Human male pancreas carcinoma

value: non-targeting shRFP, input


title: MIA PaCa-2, non-targeting shRFP control, H3K27ac Replicate 1

value: non-targeting shRFP


title: KPPC sgCCR1A 2

description:
Library name: Sample 8
KPPC_sgCCR2A_2.LIB012834.LIB012834_22G2NGLT3_S56_L001_R1_001.fastq

value: KPPC cells espressing sgCCR1A 1 replicate2

value: KPPC sgCCR1A 2


title: MIA PaCa-2, non-targeting shRFP control, H3K9me3 Replicate 1


title: MIA PaCa-2, shFTSJ3 model, input-1

value: shFTSJ model, input


title: LVFW_WT_10mo_1

description:
Library name: Sample 12
10x Genomics

value: mixed cardiac cell types

value: Yucatan minipig

value: male


title: MIA PaCa-2, non-targeting shRFP control, H3K27ac Replicate 2


title: KPPC  vector Control 1

description:
Library name: Sample 1
KPPC_vector_Control_1.LIB012830.LIB012830_22G2NGLT3_S52_L001_R1_001.fastq

value: Pancreatic cancer

value: KPPC cells expressing empty vector replicate 1

value: KPPC  vector Control 1


title: Muscle,Ad_libtum,Male,rep2

description: Library name: MAL2

value: Muscle

value: AL


title: Muscle,Ad_libtum,Male,rep6

description: Library name: MAL6


title: LVFW_WT_9mo_3

description:
Library name: Sample 11
10x Genomics

value: WT

value: none (wild-type)


title: MIA PaCa-2, non-targeting shRFP control, input-1

value: MIA PaCa-2


title: Muscle,Ad_libtum,Male,rep1

description: Library name: MAL1


title: MIA PaCa-2, shFTSJ3 model, H3K9me3 Replicate 1

value: Human male pancreas carcinoma

value: shFTSJ model


title: Muscle,Ad_libtum,Male,rep3

description: Library name: MAL3


title: Liver,Intermittent_fasting,Female,rep8

description: Library name: LIF40

source_name: Liver

value: Liver

value: female

value: IF


title: Luc-A549 tumor, 24h 5Gy treatment, rep3

city: Hamilton

first: Theodoros

last: Tsakiridis

address: 699 Concession St

institute: McMaster University

description:
Library name: Sample 12
24h post-5Gy C

data_processing:
Sequencing was conducted on the Illumina NextSeq 2000 (1x50bp, XLEAP-SBS chemistry), generating ~31 million clusters per sample.
Reads were assessed with FastQC (v0.12.1) and  trimmed using Cutadapt (v4.9).
Reads were aligned to human (hg38) and mouse (mm10) genomes using HISAT2 (v2.2.1).
Disambiguate was employed to separate xenograft (human) and host (mouse) reads.
Read counts were generated using featureCounts (v2.0.3) and differential expression analysis was done using the DESeq2 (v1.46.0) in R, to identify differentially expressed genes (DEGs), defined by a Benjamini-Hochberg adjusted P-value (p-adj) < 0.05.
Assembly: hg38 and mm10
Supplementary files format and content: There are 4 processed data files in Excel format that contain DESeq1 results, raw counts and VST normalized counts for the following comparisons: 1) 7d post-0Gy vs 7d post-5Gy (human transcripts), 2) 7d post-0Gy vs 7d post-5Gy (mouse transcripts), 3) 24h post-0Gy vs 24h post-5Gy (human transcripts), and 4) 24h post-0Gy vs 24h post-5Gy (mouse transcripts).

source_name: tumor

growth_protocol: Luc-A549 cells were maintained in DMEM (Wisent) supplemented with 10% fetal bovine serum (FBS) and 1% antibiotic-antimycotic in a humidified incubator with 5% CO2 at 37C.

extract_protocol:
Total RNA was purified using the RNease Mini Kit with on-column DNase digestion (QIAGEN). RNA quality and quantity were assessed with a NanoPhotometer (Implen Inc: Westlake Village, CA) and cDNA synthesis was performed using SuperScript IV (Invitrogen). 1 ug of total RNA was used for construction of sequencing libraries.
RNA-seq libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: One million Luc-A549 cells were subcutaneously injected into the rear flank of NRG mice (1:1 Matrigel:PBS). Once tumors reached 200mm3, mice were stratified into one of four treatment groups based on tumor volume (n=3/group): 1) 7d post-0Gy (non-irradiated), 2) 7d post-5Gy (irradiated), 3) 24h post-0Gy (non-irradiated), and 4) 24h post-5Gy (irradiated). The timepoint (7d or 24h) refers to the time tumors were harvested after a single fraction 0Gy or 5Gy irradiation. Radiotherapy was delivered with 6MV parallel opposed X-ray beams using a TrueBeam linear accelerator.

value: tumor

value: NSCLC cells

tag: cells genotype

value: enhanced firefly luciferase-expressing

tag: mouse strain

value: NRG

tag: mouse sex

tag: mouse genotype

tag: timepoint

value: 24 hours


title: Luc-A549 tumor, 24h 5Gy treatment, rep2

description:
Library name: Sample 11
24h post-5Gy B


title: LVFW_WT_9mo_2

description:
Library name: Sample 10
10x Genomics

value: mixed cardiac cell types

value: Yucatan minipig

tag: genetic modification

tag: age

value: male


title: LVFW_WT_9mo_1

description:
Library name: Sample 9
10x Genomics


title: Sensitive 1564

city: Houston

first: Chi Lam

last: Au Yeung

state: TX

address: 1515 Holcombe Blvd

institute: The University of Texas MD Anderson Cancer Center

description: Library name: Sample 23

data_processing:
Ion Torrent reads were collected using Ion Torrent Suite software, which also sorted the data according to the barcodes.
The software scores the quality of the reads by assigning Q17 and Q20 scores according to the quality scoring computation.
Fastq files from the Ion Torrent server were imported to the CLC Genomics Workbench (version 5.1; Life Technologies Corp.).
Sequence reads were trimmed to remove reads with ambiguous nucleotides and to create a sequence length of 15 to 55 nucleotides. Trimmed sequence reads were aligned to a miRNA database (miRBase, release 18). Mapped reads were annotated and counted.
Assembly: hg19
Supplementary files format and content: Ion Torrent reads were then normalized to the number of cells in each sample and presented as the total reads per 1000 cells in xlsx files.

source_name: Ovarian cancer

extract_protocol:
Total RNA was extracted from microdissected chemo-refractory and chemo-sensitive HGSC tumor tissues using the RNAqueous-Micro kit (Thermo Fisher Scientific, Waltham, MA, USA), and the amount and quality of small RNA in the total RNA samples were determined using an Agilent small RNA kit (Agilent Technologies, Santa Clara, CA, USA) on an Agilent 2100 Bioanalyzer (Agilent Technologies).
5 ng of small RNAs were subjected to library construction using the Ion Total RNA-Seq kit v2 (Life Technologies Corp., Carlsbad, CA, USA), according to the manufacturer’s small RNA protocol.

value: Ovarian cancer


title: Sensitive 1933

description: Library name: Sample 24


title: LVFW_WT_6mo_3

description:
Library name: Sample 8
10x Genomics

value: WT


title: Sensitive 1449

description: Library name: Sample 22


title: Sensitive 841

description: Library name: Sample 21


title: Liver,Intermittent_fasting,Female,rep7

description: Library name: LIF39


title: Luc-A549 tumor, 24h 0Gy control, rep2

description:
Library name: Sample 8
24h post-0Gy B

tag: treatment


title: Sensitive 816

description: Library name: Sample 19


title: Luc-A549 tumor, 7d 5Gy treatment, rep3

description:
Library name: Sample 6
7d post-5Gy C

tag: cell type

value: 7 days


title: Liver,Intermittent_fasting,Female,rep6

description: Library name: LIF38


title: Liver,Intermittent_fasting,Female,rep4

description: Library name: LIF36


title: Liver,Intermittent_fasting,Female,rep5

description: Library name: LIF37


title: Liver,Intermittent_fasting,Female,rep3

description: Library name: LIF35


title: LVFW_WT_5mo_1

description:
Library name: Sample 4
10x Genomics

value: none (wild-type)


title: LVFW_WT_5mo_2

description:
Library name: Sample 5
10x Genomics


title: Sensitive 800

description: Library name: Sample 18


title: Luc-A549 tumor, 7d 5Gy treatment, rep2

description:
Library name: Sample 5
7d post-5Gy B

tag: cell line


title: Luc-A549 tumor, 24h 0Gy control, rep1

description:
Library name: Sample 7
24h post-0Gy A


title: Liver,Intermittent_fasting,Female,rep1

description: Library name: LIF33

tag: diet


title: LVFW_WT_6mo_2

description:
Library name: Sample 7
10x Genomics


title: Sensitive 819

description: Library name: Sample 20


title: LVFW_WT_6mo_1

description:
Library name: Sample 6
10x Genomics


title: Liver,Intermittent_fasting,Female,rep2

description: Library name: LIF34


title: Luc-A549 tumor, 24h 5Gy treatment, rep1

description:
Library name: Sample 10
24h post-5Gy A


title: LVFW_WT_4mo

description:
Library name: Sample 3
10x Genomics


title: Sensitive 715

description: Library name: Sample 17


title: Luc-A549 tumor, 24h 0Gy control, rep3

description:
Library name: Sample 9
24h post-0Gy C


title: LVFW_WT_2mo_2

description:
Library name: Sample 2
10x Genomics


title: Sensitive 386

description: Library name: Sample 14


title: Luc-A549 tumor, 7d 5Gy treatment, rep1

description:
Library name: Sample 4
7d post-5Gy A


title: Sensitive 443

description: Library name: Sample 16


title: Liver,Ad_libtum,Female,rep4

description: Library name: LAL28

value: AL


title: Liver,Ad_libtum,Female,rep8

description: Library name: LAL32


title: Sensitive 412

description: Library name: Sample 15


title: Liver,Ad_libtum,Female,rep7

description: Library name: LAL31


title: LVFW_WT_2mo_1

description:
Library name: Sample 1
10x Genomics


title: lERM3, 36H, snRNAseq

city: St. John's

first: Touati

last: Benoukraf

state: NL

address: Craig L. Dobbin Genetics Research Centre,

department: Faculty of Medicine, Division of BioMedical Sciences

institute: Memorial University of Newfoundland

description:
Library name: Sample 36
10x Genomics

data_processing:
The demultiplexing, alignment, filtering, barcoding, and UMI counting were done using the 10x Genomics Cell Ranger v7.2.0 pipeline (https://www.10xgenomics.com/support/software/cell-ranger/7.2), then the filtered matrix.h5 (.h5) files were analyzed with Seurat and Scanpy
All the steps are mentioned here; https://github.com/ziahasanz/hippocampus_paper
Assembly: mRatBN7.2
Supplementary files format and content: matrix.h5 (.h5)

organism: Rattus norvegicus

source_name: Hippocampus

extract_protocol:
Nuclei were isolated from the dissected frozen hippocampus of six experimental groups; AAV-GFP, AAV-htauE14, early stress + AAV-htauE14 (eSTR), early enrichment +  AAV-htauE14 (eER), late stress +  AAV-htauE14 (lSTR), late enrihment +  AAV-htauE14 (lER). The detailed protcol is described here https://www.protocols.io/private/BE210BE858B311ED9CED0A58A9FEAC02
Library construction was completed using the Chromium Next GEM Single Cell 3' Kit v3.1 (10x Genomics). The libraries were then sequenced (paired-end) on the Illumina NovaSeq 6000.

value: Hippocampus

value: Brain cells

value: Male

value: late enrihment +  AAV-htauE14


title: Luc-A549 tumor, 7d 0Gy control, rep1

description:
Library name: Sample 1
7d post-0Gy A

value: tumor

value: female


title: lERM2, 35H, snRNAseq

description:
Library name: Sample 35
10x Genomics


title: NKTCL tumor tissue, NKTL9

city: Singapore

first: Jason

middle: Yongsheng

last: Chan

address: 30 Hospital Blvd

country: Singapore

institute: National Cancer Centre Singapore

description: Library name: NKTL9

data_processing:
Reads aligned by STAR and transcript abundance estimation using RSEM
Assembly: hg38
Supplementary files format and content: tab delimited txt file includes raw counts for each samples

extract_protocol:
RNeasy Mini Kit (Qiagen)
TruSeq Stranded Total RNA LT Sample Prep Kit


title: Liver,Ad_libtum,Female,rep6

description: Library name: LAL30

value: Liver


title: Luc-A549 tumor, 7d 0Gy control, rep3

description:
Library name: Sample 3
7d post-0Gy C

value: NSCLC cells

value: enhanced firefly luciferase-expressing

value: NRG


title: NKTCL tumor tissue, NKTL7

description: Library name: NKTL7


title: Luc-A549 tumor, 7d 0Gy control, rep2

description:
Library name: Sample 2
7d post-0Gy B


title: lERM1, 34H, snRNAseq

description:
Library name: Sample 34
10x Genomics


title: Sensitive 351

description: Library name: Sample 13


title: Sensitive 324

description: Library name: Sample 12


title: lERF3, 33H, snRNAseq

description:
Library name: Sample 33
10x Genomics

value: Female


title: Liver,Ad_libtum,Female,rep5

description: Library name: LAL29


title: NKTCL tumor tissue, NKTL8

description: Library name: NKTL8


title: Liver,Ad_libtum,Female,rep3

description: Library name: LAL27


title: Sensitive 317

description: Library name: Sample 11


title: Liver,Ad_libtum,Female,rep2

description: Library name: LAL26


title: Refractory 2512

description: Library name: Sample 10


title: lERF2, 32H, snRNAseq

description:
Library name: Sample 32
10x Genomics


title: Liver,Ad_libtum,Female,rep1

description: Library name: LAL25


title: Refractory 2487

description: Library name: Sample 9


title: NKTCL tumor tissue, NKTL68

description: Library name: NKTL68


title: NKTCL tumor tissue, NKTL67

description: Library name: NKTL67


title: Liver,Intermittent_fasting,Male,rep7

description: Library name: LIF15

value: male

value: IF


title: lSTRF3, 30H, snRNAseq

description:
Library name: Sample 30
10x Genomics

value: late stress +  AAV-htauE14


title: NKTCL tumor tissue, NKTL65

description: Library name: NKTL65


title: Liver,Intermittent_fasting,Male,rep5

description: Library name: LIF13


title: lERF1, 31H, snRNAseq

description:
Library name: Sample 31
10x Genomics


title: lSTRM3, 27H, snRNAseq

description:
Library name: Sample 27
10x Genomics


title: NKTCL tumor tissue, NKTL62

description: Library name: NKTL62


title: Liver,Intermittent_fasting,Male,rep3

description: Library name: LIF11


title: Liver,Intermittent_fasting,Male,rep6

description: Library name: LIF14


title: Liver,Intermittent_fasting,Male,rep2

description: Library name: LIF10


title: Liver,Intermittent_fasting,Male,rep8

description: Library name: LIF16


title: Refractory 2143

description: Library name: Sample 7

value: Ovarian cancer


title: lSTRF2, 29H, snRNAseq

description:
Library name: Sample 29
10x Genomics


title: cGFPM3, 24H, snRNAseq

description:
Library name: Sample 24
10x Genomics

value: AAV-GFP


title: Refractory 691

description: Library name: Sample 2


title: Refractory 1293

description: Library name: Sample 4


title: NKTCL tumor tissue, NKTL59

description: Library name: NKTL59


title: NKTCL tumor tissue, NKTL63

description: Library name: NKTL63


title: cGFPM2, 23H, snRNAseq

description:
Library name: Sample 23
10x Genomics


title: Refractory 2411

description: Library name: Sample 8


title: NKTCL tumor tissue, NKTL58

description: Library name: NKTL58


title: Refractory 799

description: Library name: Sample 3


title: Liver,Ad_libtum,Male,rep8

description: Library name: LAL8

value: AL


title: lSTRM2, 26H, snRNAseq

description:
Library name: Sample 26
10x Genomics

value: Hippocampus


title: NKTCL tumor tissue, NKTL54

description: Library name: NKTL54


title: cGFPM1, 22H, snRNAseq

description:
Library name: Sample 22
10x Genomics

value: Brain cells


title: NKTCL tumor tissue, NKTL57

description: Library name: NKTL57


title: lSTRM1, 25H, snRNAseq

description:
Library name: Sample 25
10x Genomics

value: Male


title: Refractory 1660

description: Library name: Sample 6


title: cGFPF3, 21H, snRNAseq

description:
Library name: Sample 21
10x Genomics


title: lSTRF1, 28H, snRNAseq

description:
Library name: Sample 28
10x Genomics


title: NKTCL tumor tissue, NKTL56

description: Library name: NKTL56


title: NKTCL tumor tissue, NKTL41

description: Library name: NKTL41


title: Refractory 1450

description: Library name: Sample 5


title: 15bp+H3 DiNucleosome sense strand

city: Grand Rapids

first: Peter

middle: A

last: Jones

state: MI

address: 333 Bostwick Ave NE

department: Center of Epigenetics

institute: Van Andel Research Institute

description: Library name: NS3A15

library_source: other

data_processing:
The sequencing data were analyzed using BISCUIT software (https://huishenlab.github.io/biscuit/)
Supplementary files format and content: TXT file with beta value for the CpGs

molecule: other

organism: synthetic construct

source_name: Synthesized DNA

extract_protocol:
The DNA was then immobilized on Agencourt AMPure XP Beads (Beckman Coulter), washed twice with 80% ethanol, eluted with water, and subjected to bisulfite conversion using the EZ DNA Methylation Kit (Zymo Research) following the manufacturer’s instructions. Bisulfite-converted DNA was then amplified by PCR using the ZymoTaq DNA Polymerase (Zymo Research).
PCR products were then sent out for next-generation sequencing (Genewiz) using the Amplicon-EZ service.

treatment_protocol: To assess the activity of the DNMT3A2/3B3 complex on di-nucleosomes with variable linker lengths, 10 pmol of each di-nucleosome (100nM) or its corresponding naked DNA was incubated with 100 pmol of purified DNMT3A2/3B3 tetramer (1mM) in 100 ml binding buffer (20 mM HEPES pH7.8, 50 mM NaCl, 1% glycerol, 1 mM DTT, 0.1 mg/ml BSA, 100 mM SAM, and 1 mM histone H3 peptides (residues 1–20)) at 37 °C for 4 hours. To remove free DNA from the reaction with the di-nucleosomes, one unit of AluI (New England Biolabs) was added to the reaction and incubated at 37 °C for 15 minutes. The 601 DNA sequence contains a single AluI site that is blocked by histone binding, allowing for specific cleavage of free DNA not bound to the nucleosome. All reactions were then terminated by heating at 80°C for 20 minutes.

value: Synthesized DNA


title: 10bp+H3 DiNucleosome sense strand

description: Library name: NS3A10


title: NKTCL tumor tissue, NKTL6

description: Library name: NKTL6

value: tumor


title: Liver,Intermittent_fasting,Male,rep1

description: Library name: LIF9


title: NKTCL tumor tissue, NKTL42

description: Library name: NKTL42


title: 8bp+H3 DiNucleosome sense strand

description: Library name: NS3A8


title: 20bp+H3 DiNucleosome sense strand R1

description: Library name: NS3A20


title: Liver,Ad_libtum,Male,rep7

description: Library name: LAL7


title: Liver,Intermittent_fasting,Male,rep4

description: Library name: LIF12


title: Liver,Ad_libtum,Male,rep4

description: Library name: LAL4


title: Refractory 332

description: Library name: Sample 1


title: cE14M2, 17H, snRNAseq

description:
Library name: Sample 17
10x Genomics


title: Liver,Ad_libtum,Male,rep3

description: Library name: LAL3


title: Liver,Ad_libtum,Male,rep2

description: Library name: LAL2


title: 25bp+H3 DiNucleosome antisense strand

description: Library name: NAS3A25


title: cE14M1, 16H, snRNAseq

description:
Library name: Sample 16
10x Genomics


title: NKTCL tumor tissue, NKTL40

description: Library name: NKTL40


title: 25bp+H3 DiNucleosome sense strand

description: Library name: NS3A25


title: cGFPF2, 20H, snRNAseq

description:
Library name: Sample 20
10x Genomics


title: cE14M3, 18H, snRNAseq

description:
Library name: Sample 18
10x Genomics


title: cE14F3, 15H, snRNAseq

description:
Library name: Sample 15
10x Genomics


title: Liver,Ad_libtum,Male,rep5

description: Library name: LAL5


title: cE14F2, 14H, snRNAseq

description:
Library name: Sample 14
10x Genomics


title: NKTCL tumor tissue, NKTL39

description: Library name: NKTL39


title: cE14F1, 13H, snRNAseq

description:
Library name: Sample 13
10x Genomics


title: Cortex,Intermittent_fasting,Female,rep7

description: Library name: CIF39

source_name: Cortex

value: Cortex

value: female


title: Cortex,Intermittent_fasting,Female,rep6

description: Library name: CIF38


title: 8bp+H3 DiNucleosome antisense strand

description: Library name: NAS3A8


title: eERM3, 12H, snRNAseq

description:
Library name: Sample 12
10x Genomics

value: early enrichment +  AAV-htauE14


title: eERM2, 11H, snRNAseq

description:
Library name: Sample 11
10x Genomics


title: NKTCL tumor tissue, NKTL4

description: Library name: NKTL4


title: Liver,Ad_libtum,Male,rep6

description: Library name: LAL6

value: Liver


title: NKTCL tumor tissue, NKTL24

description: Library name: NKTL24


title: NKTCL tumor tissue, NKTL37

description: Library name: NKTL37


title: NKTCL tumor tissue, NKTL38

description: Library name: NKTL38


title: 25bp+H3 DNA sense strand

description: Library name: DS3A25


title: eERM1, 10H, snRNAseq

description:
Library name: Sample 10
10x Genomics


title: NKTCL tumor tissue, NKTL3

description: Library name: NKTL3


title: Cortex,Intermittent_fasting,Female,rep2

description: Library name: CIF34


title: eERF3, 9H, snRNAseq

description:
Library name: Sample 9
10x Genomics


title: 5bp+H3 DiNucleosome sense strand

description: Library name: NS3A5


title: Cortex,Intermittent_fasting,Female,rep8

description: Library name: CIF40


title: 10bp+H3 DiNucleosome antisense strand

description: Library name: NAS3A10


title: cGFPF1, 19H, snRNAseq

description:
Library name: Sample 19
10x Genomics


title: 20bp+H3 DiNucleosome antisense strand R1

description: Library name: NAS3A20


title: NKTCL tumor tissue, NKTL22

description: Library name: NKTL22


title: 15bp+H3 DiNucleosome antisense strand

description: Library name: NAS3A15


title: NKTCL tumor tissue, NKTL34

description: Library name: NKTL34


title: NKTCL tumor tissue, NKTL23

description: Library name: NKTL23


title: Cortex,Intermittent_fasting,Female,rep4

description: Library name: CIF36


title: NKTCL tumor tissue, NKTL35

description: Library name: NKTL35


title: Liver,Ad_libtum,Male,rep1

description: Library name: LAL1


title: NKTCL tumor tissue, NKTL21

description: Library name: NKTL21


title: 10bp+H3 DNA sense strand

description: Library name: DS3A10


title: 15bp+H3 DNA sense strand

description: Library name: DS3A15


title: 8bp+H3 DNA sense strand

description: Library name: DS3A8


title: 5bp+H3 DiNucleosome antisense strand

description: Library name: NAS3A5


title: Cortex,Intermittent_fasting,Female,rep5

description: Library name: CIF37


title: Cortex,Ad_libtum,Female,rep6

description: Library name: CAL30


title: eERF2, 8H, snRNAseq

description:
Library name: Sample 8
10x Genomics


title: Cortex,Ad_libtum,Female,rep5

description: Library name: CAL29


title: 25bp+H3 DNA antisense strand

description: Library name: DAS3A25


title: 20bp+H3 DNA sense strand R1

description: Library name: DS3A20


title: NKTCL tumor tissue, NKTL2

description: Library name: NKTL2


title: 20bp+H3 DNA antisense strand R1

description: Library name: DAS3A20


title: eSTRM1, 4H, snRNAseq

description:
Library name: Sample 4
10x Genomics

value: early stress + AAV-htauE14


title: Cortex,Intermittent_fasting,Female,rep3

description: Library name: CIF35


title: Cortex,Intermittent_fasting,Female,rep1

description: Library name: CIF33


title: eSTRM3, 6H, snRNAseq

description:
Library name: Sample 6
10x Genomics


title: NKTCL tumor tissue, NKTL18

description: Library name: NKTL18


title: NKTCL tumor tissue, NKTL20

description: Library name: NKTL20


title: Cortex,Ad_libtum,Female,rep7

description: Library name: CAL31


title: Cortex,Ad_libtum,Female,rep8

description: Library name: CAL32


title: eERF1, 7H, snRNAseq

description:
Library name: Sample 7
10x Genomics

value: Female


title: Cortex,Ad_libtum,Female,rep4

description: Library name: CAL28


title: NKTCL tumor tissue, NKTL19

description: Library name: NKTL19


title: NKTCL tumor tissue, NKTL17

description: Library name: NKTL17


title: eSTRF3, 3H, snRNAseq

description:
Library name: Sample 3
10x Genomics


title: 5bp+H3 DNA sense strand

description: Library name: DS3A5


title: 15bp+H3 DNA antisense strand

description: Library name: DAS3A15


title: NKTCL tumor tissue, NKTL15

description: Library name: NKTL15


title: eSTRM2, 5H, snRNAseq

description:
Library name: Sample 5
10x Genomics


title: SNT-8 cells, control

description: Library name: SNT8

source_name: cell line

extract_protocol:
RNeasy Mini Kit (Qiaen)
TruSeq Stranded Total RNA LT Sample Prep Kit

value: cell line

value: Lymphoma

value: WT


title: eSTRF1, 1H, snRNAseq

description:
Library name: Sample 1
10x Genomics


title: eSTRF2, 2H, snRNAseq

description:
Library name: Sample 2
10x Genomics


title: Cortex,Ad_libtum,Female,rep2

description: Library name: CAL26


title: 8bp+H3 DNA antisense strand

description: Library name: DAS3A8


title: Cortex,Ad_libtum,Female,rep3

description: Library name: CAL27


title: NKTCL tumor tissue, NKTL10

description: Library name: NKTL10


title: NKTCL tumor tissue, NKTL16

description: Library name: NKTL16


title: 5bp+H3 DNA antisense strand

description: Library name: DAS3A5


title: HANK-1 cells, control

description: Library name: HANK1


title: 10bp+H3 DNA antisense strand

description: Library name: DAS3A10


title: YT cells, control

description: Library name: YT

value: YT


title: NKTCL tumor tissue, NKTL_FTKK

description: Library name: NKTL_FTKK


title: NKTCL tumor tissue, NKTL_FYAL

description: Library name: NKTL_FYAL


title: Cortex,Intermittent_fasting,Male,rep8

description: Library name: CIF16

value: male

value: IF


title: 35bp+H3 DiNucleosome sense strand

description: Library name: S8


title: Cortex,Intermittent_fasting,Male,rep6

description: Library name: CIF14


title: Cortex,Ad_libtum,Female,rep1

description: Library name: CAL25

value: AL


title: NKTCL tumor tissue, NKTL_FLAB

description: Library name: NKTL_FLAB


title: Cortex,Intermittent_fasting,Male,rep7

description: Library name: CIF15


title: NKTCL tumor tissue, NKTL_FPTH

description: Library name: NKTL_FPTH


title: SNK-1 cells, control

description: Library name: SNK1


title: NKTCL tumor tissue, NKTL_FKV

description: Library name: NKTL_FKV


title: 35bp+H3 DNA sense strand

description: Library name: S6


title: 35bp-H3 DiNucleosome sense strand

description: Library name: S7


title: 35bp-H3 DNA sense strand

description: Library name: S5


title: KHYG-1 cells, control

description: Library name: KHYG1


title: SNK-6 cells, control

description: Library name: SNK6


title: 20bp+H3 DiNucleosome sense strand

description: Library name: S4


title: Cortex,Intermittent_fasting,Male,rep5

description: Library name: CIF13


title: MEC-04 cells, control

description: Library name: MEC04


title: NKTCL tumor tissue, NKTL_FESJ

description: Library name: NKTL_FESJ


title: NKTCL tumor tissue, NKTL_FESL

description: Library name: NKTL_FESL


title: Cortex,Intermittent_fasting,Male,rep4

description: Library name: CIF12


title: NK-92 cells, control

description: Library name: NK92


title: Cortex,Intermittent_fasting,Male,rep3

description: Library name: CIF11


title: 20bp-H3 DNA sense strand

description: Library name: S1


title: NK-S1 cells, control

description: Library name: NKS1


title: KI-JK cells, control

description: Library name: KIJK

value: KI-JK


title: NKTCL tumor tissue, NKTL_F29

description: Library name: NKTL_F29


title: 20bp-H3 DiNucleosome sense strand

description: Library name: S3


title: 20bp+H3 DNA sense strand

description: Library name: S2


title: 35bp-H3 DiNucleosome antisense strand

description: Library name: A7


title: Cortex,Ad_libtum,Male,rep8

description: Library name: CAL8


title: Cortex,Ad_libtum,Male,rep7

description: Library name: CAL7


title: NKTCL tumor tissue, NKTL_F33

description: Library name: NKTL_F33


title: 35bp+H3 DNA antisense strand

description: Library name: A6


title: NKTCL tumor tissue, NKTL_F28

description: Library name: NKTL_F28


title: NK-YS cells, control

description: Library name: NKYS

value: NK-YS


title: Cortex,Intermittent_fasting,Male,rep2

description: Library name: CIF10


title: NKTCL tumor tissue, NKTL_F32

description: Library name: NKTL_F32


title: 35bp+H3 DiNucleosome antisense strand

description: Library name: A8

value: Synthesized DNA


title: 35bp-H3 DNA antisense strand

description: Library name: A5


title: PT-S2 cells, control

description: Library name: PTS2


title: KAI-3 cells, control

description: Library name: KAI3


title: HH cells, control

description: Library name: HH

value: HH


title: Cortex,Intermittent_fasting,Male,rep1

description: Library name: CIF9

value: Cortex


title: Cortex,Ad_libtum,Male,rep6

description: Library name: CAL6


title: K-299 cells, control

description: Library name: K299


title: 20bp+H3 DiNucleosome antisense strand

description: Library name: A4


title: Cortex,Ad_libtum,Male,rep4

description: Library name: CAL4


title: NKTCL tumor tissue, NKTL_F23

description: Library name: NKTL_F23

value: tumor


title: 20bp-H3 DiNucleosome antisense strand

description: Library name: A3


title: NKTCL tumor tissue, NKTL_F25

description: Library name: NKTL_F25


title: 20bp+H3 DNA antisense strand

description: Library name: A2


title: Cortex,Ad_libtum,Male,rep3

description: Library name: CAL3


title: NKTCL tumor tissue, NKTL_F22

description: Library name: NKTL_F22


title: SMZ-1 cells, control

description: Library name: SMZ1


title: Cortex,Ad_libtum,Male,rep2

description: Library name: CAL2


title: NKTCL tumor tissue, NKTL_F24

description: Library name: NKTL_F24


title: L-82 cells, control

description: Library name: L82


title: Cortex,Ad_libtum,Male,rep5

description: Library name: CAL5


title: NKTCL tumor tissue, NKTL_F1

description: Library name: NKTL_F1


title: NKTCL tumor tissue, NKTL_F21

description: Library name: NKTL_F21


title: Dhx9f/f;MX1 Lin- cells, rep5

city: Hefei

first: Minhui

last: Shi

state: Anhui

address: University of Science and Technology of China

department: Division of Life Sciences and Medicine

data_processing:
Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1).
Pass filter data of fastq format were processed by Cutadapt to be high quality clean data.
Clean data were aligned to reference genome GRCm39 via software Hisat2 (v2.0.1).
Read count extraction and normalization were performed using HTSeq (v0.6.1).
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample.

source_name: Bone marrow

extract_protocol:
Total cellular RNA was isolated using TRIzol reagent (Invitrogen, 15596018CN).
Transcriptome libraries were constructed according to the manufacturer's instructions (Azenta Life Sciences).

treatment_protocol: Lineage negative cells were sorted by Lineage Cell Depletion Kit mouse from Dhx9f/f (WT) or Dhx9f/f;MX1 (cKO) mice bone marrow cells.

value: Bone marrow

value: lineage negative cells

value: Dhx9 knock down


title: NK-S1 cells, 1000ng/ml, replicate 3

description: Library name: NKS11000-3

value: Brincidofovir treatment


title: DEL cells, control

description: Library name: DEL

value: cell line

value: DEL


title: 20bp-H3 DNA antisense strand

description: Library name: A1


title: Dhx9f/f;MX1 Lin- cells, DHX9, ChIP

institute: University of Science and Technology of China

data_processing:
Pass filter data of fastq format were processed by fastp (v0.19.6) to be high quality clean data.
Clean data were aligned to reference genome GRCm39 via software Bowtie2 (v2.2.7).
Use MACS3 (version 3.0.0a6) to analyze peaks quality control, peaks calling and peaks annotation.
Assembly: mm39
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

extract_protocol:
CUT&Tag product (Vazyme, TD904) was used for extracting DNA.
CUT&Tag product (Vazyme, TD904) was used for library preparation.


title: LN_AMP-dT_72h_1

type: RNA

first: Martin

middle: P

last: Steinbuck

address: 451D Street, Ste 501

department: Research

institute: Elicio Therapeutics

hyb_protocol: Performed by Canopy Biosciences following the NanoString protocols

data_processing:
NanoString generated raw values of dT and AMP-dT samples were analyzed against Mock samples using Rosalind software. Volcano plots show Rosalind-generated p-values (log2) and fold-changes (-log10). For heat maps, Z-scores were calculated for the raw expression data. These were then averaged among biological duplicates and mock-subtracted.
Rosalind computed expression values.

label: NanoString Probes

extract_protocol: Inguinal lymph nodes were harvested from immunized C57BL/6J mice at the indicated time points, processed into single cell suspensions, and lysed with RLT buffer (Qiagen, cat# 79216)

treatment_protocol: In vivo - vaccine injection into mouse

tag: vaccine

value: AMP-dT

tag: time


title: NK-S1 cells, 1000ng/ml, replicate 2

description: Library name: NKS11000-2

value: Lymphoma

tag: genotype

value: WT


title: Dhx9f/f;MX1 Lin- cells, rep4

tag: tissue


title: SUDHL-1 cells, control

description: Library name: SUDHL1


title: SUP-M2 cells, control

description: Library name: SUPM2


title: NK-S1 cells, 1000ng/ml, replicate 1

description: Library name: NKS11000-1


title: PT-S1 cells, control

description: Library name: PTS1


title: Dhx9f/f;MX1 Lin- cells, rep3


title: LN_AMP-dT_24h_1

scan_protocol: Performed by Canopy Biosciences following the NanoString protocols


title: LN_AMP-dT_72h_2

label_protocol: Performed by Canopy Biosciences following the NanoString protocols


title: K-562 cells, control

description: Library name: K562


title: FE-PD cells, control

description: Library name: FEPD

value: FE-PD


title: NK-S1 cells, 100ng/ml, replicate 2

description: Library name: NKS1100-2


title: Dhx9f/f;MX1 Lin- cells, rep1


title: Dhx9f/f;MX1 Lin- cells, rep2


title: LN_AMP-dT_2h_2


title: LN_AMP-dT_6h_1


title: NK-S1 cells, control, replicate 3

description: Library name: NKS1C3

value: Mock treatment


title: Dhx9f/f Lin- cells, rep5


title: NK-S1 cells, 100ng/ml, replicate 3

description: Library name: NKS1100-3


title: K-231 cells, control

description: Library name: K231


title: NK-S1 cells, 100ng/ml, replicate 1

description: Library name: NKS1100-1


title: SC-1 cells, control

description: Library name: SC1


title: LN_dT_72h_2

value: dT


title: NK-S1 cells, control, replicate 2

description: Library name: NKS1C2


title: LN_AMP-dT_24h_2


title: Cortex,Ad_libtum,Male,rep1

description: Library name: CAL1

tag: Sex

value: male

value: AL


title: Dhx9f/f Lin- cells, rep4


title: Dhx9f/f Lin- cells, rep3


title: LN_AMP-dT_2h_1


title: HT cells, control

description: Library name: HT

value: HT

tag: batch


title: NK-S1 cells, control, replicate 1

description: Library name: NKS1C1


title: LN_dT_24h_2


title: LN_AMP-dT_6h_2


title: Dhx9f/f Lin- cells, rep2


title: SUDHL-16 cells, control

description: Library name: SUDHL16


title: LN_dT_24h_1


title: Dhx9f/f Lin- cells, rep1


title: U2932 cells, control

description: Library name: U2932


title: LN_dT_72h_1


title: DAUDI cells, control

description: Library name: DAUDI

value: DAUDI


title: LN_dT_6h_1


title: KAI-3 cells, 1000ng/ml, replicate 3

description: Library name: KAI31000-3


title: LN_dT_6h_2


title: KAI-3 cells, 100ng/ml, replicate 3

description: Library name: KAI3100-3


title: KAI-3 cells, 1000ng/ml, replicate 2

description: Library name: KAI31000-2


title: Dhx9f/f Lin- cells, H3K27ac, ChIP


title: Dhx9f/f;MX1 Lin- cells, H3K27ac, ChIP


title: RAJI cells, control

description: Library name: RAJI

value: RAJI


title: CL1956_DKO_ERY

city: Washington

first: Alexandros

last: Tzatsos

state: DC

address: 800 22nd St NW SEH 8850

department: GW Cancer Center

institute: George Washington University

description: 10x Genomics

data_processing:
Demultiplexing, barcode processing, alignment, filtering, UMI counting, and aggregation took place with Cell Ranger (v7.1.0) using the ‘intron mode’ and the ‘mm10-2020-A’ reference genome.
Assembly: GRCm38/mm10
Supplementary files format and content: Filtered_feature_bc_matrix (*.h5 format)

source_name: sorted LinnegcKit+ bone marrow cells

growth_protocol: None. Bone marrow was isolated from the femur and LinnegcKit+ cells were sorted for scRNA-seq using the 10x Genomics platform.

extract_protocol:
Bone marrow was isolated from the femur and LinnegcKit+ cells were sorted for scRNA-seq using the 10x Genomics platform.
Libraries were constructed according to 10x Genomics instructions using Single Cell 3' v3 chemistry (catalog number 1000268).

value: sorted LinnegcKit+ bone marrow cells

value: Hematopietic progenitors

value: A-1155463 (BCL-XL inhibitor)


title: KAI-3 cells, 100ng/ml, replicate 2

description: Library name: KAI3100-2

value: Brincidofovir treatment


title: KAI-3 cells, 100ng/ml, replicate 1

description: Library name: KAI3100-1

value: cell line


title: Dhx9f/f Lin- cells, DHX9, ChIP

value: Bone marrow

value: lineage negative cells


title: SUDHL-4 cells, control

description: Library name: SUDHL4

value: Lymphoma


title: KAI-3 cells, 1000ng/ml, replicate 1

description: Library name: KAI31000-1

value: WT


title: SR-786 cells, control

description: Library name: SR786


title: LN_dT_2h_2


title: Dhx9f/f Lin- cells, IgG, ChIP


title: KAI-3 cells, control, replicate 2

description: Library name: KAI3C2


title: WSU-NHL cells, control

description: Library name: WSUNHL

value: WSU-NHL


title: SUDHL-6 cells, control

description: Library name: SUDHL6


title: KAI-3 cells, control, replicate 1

description: Library name: KAI3C1

value: Mock treatment


title: KAI-3 cells, control, replicate 3

description: Library name: KAI3C3


title: RL cells, control

description: Library name: RL

value: RL


title: CL1937_DKO_AML

description: 10x Genomics

value: female

value: no


title: OCI-LY3 cells, control

description: Library name: OCILY3


title: OCI-LY18 cells, control

description: Library name: OCILY18


title: RKO-DMSO-rep-3

city: Mannheim

first: Siche

last: Chen

address: Stockhornstrasse 55, 55

department: Dept. of Experimental Surgery - Cancer Metastasis

country: Germany

institute: Medical Faculty Mannheim, Ruprecht-Karls University of Heidelberg

data_processing:
Raw reads were filtered and cleaned by fastp software. Aliments were performed following STAR instruction. analyzeRepeats.pl function were used for counting.R was used for visualization.
Assembly: hg38
Supplementary files format and content: TXT file contain counts for each sample

source_name: RKO

growth_protocol: RKO cells were grown in EMEM medium (GIBCO/ Thermo Fisher, Germany, 16600082) with the addition of 10% Fetal Bovine Serum (FBS) (GIBCO/ Thermo Fisher, Germany, 10500064) and 1% penicillin/streptomycin (PS) (GIBCO/ Thermo Fisher, Germany, 10378016).

extract_protocol:
total RNA was extracted using miRNeasy Mini Kit (Qiagen), according to the manufacturer’s protocol, without the separation step between mRNAs and microRNAs.
RNA libraries were prepared using standard Illumina protocols.

treatment_protocol: RKO cells were plated into 6-well plate 24 h before treated with DMSO and Olaparib.

value: RKO

value: colorectal cancer cells

value: DMSO


title: RKO-DMSO-rep-2


title: L-428 cells, control

description: Library name: L428


title: LN_Mock_72h_1

value: Mock


title: LN_Mock_72h_2


title: CL1786_DKO_ERY

description: 10x Genomics

value: sorted LinnegcKit+ bone marrow cells

value: male

value: Hematopietic progenitors


title: LN_dT_2h_1

value: dT


title: CL1777_DKO_ERY

description: 10x Genomics


title: CL1936_DKO_ERY

description: 10x Genomics

value: A-1155463 (BCL-XL inhibitor)


title: LN_Mock_24h_2


title: LN_Mock_6h_2


title: CL1801_BAP1

description: 10x Genomics


title: OCI-LY19 cells, control

description: Library name: OCILY19


title: CL1785_DKO_ERY

description: 10x Genomics


title: CL2016_DKO_AML

description: 10x Genomics


title: RKO-Ola-rep-2

value: Olaparib


title: RKO-DMSO-rep-1


title: LN_Mock_2h_2


title: BJAB cells, control

description: Library name: BJAB

value: BJAB

value: Lymphoma


title: LN_Mock_2h_1


title: LN_Mock_24h_1


title: CL1859_p53

description: 10x Genomics


title: SUDHL-5 cells, control

description: Library name: SUDHL5

value: WT


title: LN_Mock_6h_1


title: SQ1023_WT

description: 10x Genomics


title: H99 WT cells, 37°C-shift, hour1, rep2

status: Public on Mar 17 2026

city: Buffalo

first: Sean

middle: R

last: Duffy

state: NY

address: 955 Main Street

department: Microbiology and Immunology

institute: SUNY at Buffalo

description:
Library name: Sample 6
Column name in matrix_FPKMs-all.txt: 16
column G

data_processing:
FASTQ files were processed to generate a counts matrix using the following software in command-line: Cutadapt/3.2 (adapter trimming and quality control), STAR/2.7.2b (alignment), and RSEM/1.2.20 (read counting)
Assembly: FungiDB C. neoformans H99 genome build v.63
Supplementary files format and content: Single txt file containing FPKM values
Supplementary files format and content: Column A contains locus tag of genes from C. neoformans. Other columns (column B-I) correspond to their respective sample in order (Sample 1-8).

organism: Cryptococcus neoformans

source_name: yeast

growth_protocol: C. neoformans cells were grown in YPD media at 30°C

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen). ERCC RNA Spike-in mix (ThermoFisher) was added to samples at a 1:100 ratio but was not used in for data processing. Poly(a) selection was perfomed by Azenta/Genewiz.
RNA libraries for RNA-seq were prepared by Azenta/Genewiz.

treatment_protocol: Cells were pelleted, spent media decanted, and then resuspended in pre-warmed YPD media at 37°C

tag: strain

value: yeast

value: mid-log growth at 30°C then shifted to 37°C

value: hour 1


title: RKO-Ola-rep-3


title: RKO-Ola-rep-1


title: H99 WT cells,mid-log 30°C, hour0, rep2

description:
Library name: Sample 5
Column name in matrix_FPKMs-all.txt: 15
column F

value: mid-log growth at 30°C

value: hour 0


title: H99 upf1 cells, 37°C-shift, hour1, rep1

description:
Library name: Sample 4
Column name in matrix_FPKMs-all.txt: 13
column E

value: upf1 knockout


title: H99 upf1 cells,mid-log 30°C, hour0, rep1

description:
Library name: Sample 3
Column name in matrix_FPKMs-all.txt: 12
column D


title: TK6 cells, 4 µg/mL 3-MCA, rep3

city: Kawasaki

first: Yuko

last: Ogata

state: Kanagawa

address: 6-21-1 Nagao, Tama-Ku

department: Division of Chemical Information, Research Center for Chemical Information and Management

institute: National Institute of Occupational Safety and Health, Japan

description: Library name: 3MCA_highconcentration_rep3

data_processing:
Preprocessing and quality control of sequencing reads were performed using fastp version 0.23.4 and MultiQC version 1.27.
Trimmed sequence reads were mapped to the human genome assembly GRCh38.p14 (NCBI RefSeq assembly ID: GCF_000001405.40) using HISAT2 version 2.2.1.
Gene expression was quantified using featureCounts version 2.0.6.
Assembly: GRCh38.p14 (NCBI RefSeq assembly ID: GCF_000001405.40)
Supplementary files format and content: tab-delimited text file includes CPM values for each Sample

source_name: TK6 (IVGT)

extract_protocol:
Total RNA was isolated using an RNeasy Mini Kit (Qiagen).
RNA-Seq libraries were prepared using KAPA mRNA Capture Kit (Kapa Biosystems), MGIEasy Fast RNA Library Prep Set (MGI Tech), and a DNBSEQ-G400RS High-throughput Sequencing Kit (FCL PE150) (MGI Tech).

value: TK6 (IVGT)

value: Suspension cells


title: H99 WT cells, 37°C-shift, hour1, rep1

description:
Library name: Sample 2
Column name in matrix_FPKMs-all.txt: 10
column C


title: TK6 cells, 0.0004 µg/mL 3-MCA, rep2

description: Library name: 3MCA_lowconcentration_rep2


title: DB cells, control

description: Library name: DB

value: DB


title: TK6 cells, 0.04 µg/mL 3-MCA, rep3

description: Library name: 3MCA_mediumconcentration_rep3


title: TK6 cells, 0 µg/mL 3-MCA, rep2

description: Library name: control_rep2

value: control


title: H99 WT cells,mid-log 30°C, hour0, rep1

description:
Library name: Sample 1
Column name in matrix_FPKMs-all.txt: 9
column B


title: H99 upf1 cells,mid-log 30°C, hour0, rep2

description:
Library name: Sample 7
Column name in matrix_FPKMs-all.txt: 18
column H


title: TK6 cells, 0.0004 µg/mL 3-MCA, rep3

description: Library name: 3MCA_lowconcentration_rep3


title: TK6 cells, 0 µg/mL 3-MCA, rep3

description: Library name: control_rep3


title: TK6 cells, 4 µg/mL 3-MCA, rep2

description: Library name: 3MCA_highconcentration_rep2


title: H99 upf1 cells, 37°C-shift, hour1, rep2

description:
Library name: Sample 8
Column name in matrix_FPKMs-all.txt: 19
column I


title: TK6 cells, 0.0004 µg/mL 3-MCA, rep1

description: Library name: 3MCA_lowconcentration_rep1


title: TK6 cells, 0 µg/mL 3-MCA, rep1

description: Library name: control_rep1


title: TK6 cells, 4 µg/mL 3-MCA, rep1

description: Library name: 3MCA_highconcentration_rep1


title: TK6 cells, 0.04 µg/mL 3-MCA, rep2

description: Library name: 3MCA_mediumconcentration_rep2


title: L. interrogans, sHPLM, 4 hours, rep4

city: St. Louis

first: Matthew

middle: Harrison

last: Ward

state: Missouri

address: 1 Brookings Dr.

department: Chemistry

institute: Washington University in St. Louis

description: Library name: sHPLM_4h_4

data_processing:
Illumina bcl2fastq software used for Basecalls and demultiplexing with threshold of max 1 mismatch in indexing reads.
Alignment with STAR version 2.7.11b
Gene counts calculated with Subread:featureCount version 2.0.8
Assembly: Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130 GCF_000007685.1 (ASM768v1) primary assembly
Supplementary files format and content: each tab-deliited text file includes gene counts (in CPM, FPKM, and TPM) for each sample

organism: Leptospira interrogans

source_name: Bacterial culture

growth_protocol: L. interrogans serovar Copenhageni strain Fiocruz L1-130 was grown in Difco EMJH at 30 degrees Celsius without shaking in 50mL conical tubes.

extract_protocol:
Bacteria were pelleted at 3700 RCF for 30 minutes, and RNA isolated by TRIzol and chloroform extraction. 500ng to 1ug of total RNA was used for library preparation.
cDNA libraries were prepared using the Qiagen FastSelect kit and Life Technologies SuperScript III RT enzyme.

treatment_protocol: Leptospira interrogans grown in standard EMJH medium at 30 degrees Celsius was cultured for four hours at late exponential phase density in either fresh EMJH, sHPLM at 37 degrees Celsius, or EMJH with 550uM L-glutamine.

value: Bacterial culture

value: sHPLM


title: L. interrogans, sHPLM, 4 hours, rep2

description: Library name: sHPLM_4h_2

value: serovar Copenhageni strain Fiocruz L1-130


title: L. interrogans, sHPLM, 4 hours, rep3

description: Library name: sHPLM_4h_3


title: VAL cells, control

description: Library name: VAL

value: VAL


title: L. interrogans, EMJH + 550uM L-glutamine, 4 hours, rep3

description: Library name: EMJH_550uMGln_4h_3

value: EMJH + 550uM L-glutamine


title: L. interrogans, EMJH + 550uM L-glutamine, 4 hours, rep1

description: Library name: EMJH_550uMGln_4h_1


title: L. interrogans, sHPLM, 4 hours, rep1

description: Library name: sHPLM_4h_1


title: L. interrogans, EMJH, 4 hours, rep4

description: Library name: EMJH_4h_4

value: EMJH


title: L. interrogans, EMJH + 550uM L-glutamine, 4 hours, rep2

description: Library name: EMJH_550uMGln_4h_2


title: L. interrogans, EMJH, 4 hours, rep3

description: Library name: EMJH_4h_3


title: TK6 cells, 0.04 µg/mL 3-MCA, rep1

description: Library name: 3MCA_mediumconcentration_rep1


title: L. interrogans, EMJH, 4 hours, rep2

description: Library name: EMJH_4h_2


title: L. interrogans, EMJH, 4 hours, rep1

description: Library name: EMJH_4h_1


title: ORG-0159_BC360_20230117 histologically normal breast tissue

city: Jacksonville

first: Derek

middle: Charles

last: Radisky

state: Florida

address: 4500 San Pablo Road

department: Cancer Biology

institute: Mayo Clinic

description: Original RCC file: 20230117_Radisky35 BC360 run3_ORG-0159_11.RCC; Selected renamed RCC file: ORG-0159_BC360_20230117.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20230117; Cartridge: Radisky35 BC360 run3; Lane: 11; MD5: c45b7dd9e0ebb121829bf3b619008f7b

hyb_protocol: RNA was hybridized for 18 h at 65°C to the NanoString BC360 or IO360 CodeSet. Cartridges were processed on the nCounter Prep Station.

scan_protocol: Cartridges were scanned at 555 fields of view on the nCounter Digital Analyzer. All samples passed manufacturer QC thresholds used in the manuscript: imaging QC score > 0.85, binding density 0.1–2.25 spots/µm², and positive-control linearity R² > 0.95.

data_processing: The BC360_Raw_Matrix.xlsx values are complete raw NanoString counts extracted directly from the selected BC360 RCC files. This BC360 matrix contains 790 probes/features across 74 specimens (758 endogenous genes, 18 housekeeping probes, 8 negative controls, 6 positive controls). Raw RCC files were matched to specimens by exact specimen ID; when multiple candidate raw RCC files existed for the same specimen and panel, the latest RCC date was selected. The processed workbook sample ORG-0098 was matched to raw IO360 specimen ORG-0098 R per submitter instruction. Supplementary file BC360_processed_matrix.tsv retains the analyzed normalized values supplied in Combined IO360 and BC360.xlsx.

label: nanostring

source_name: histologically normal breast tissue

label_protocol: NanoString nCounter direct digital counting with panel-specific reporter and capture probes according to the manufacturer protocol; no separate external labeling step was performed.

growth_protocol: Not applicable. These are human surgical FFPE specimens and were not grown or cultured before RNA extraction.

extract_protocol: From each FFPE block, three consecutive 10 µm scrolls (approximately 50 mm² total tissue area) were deparaffinized in xylene and rehydrated through graded ethanol. RNA was extracted using the Qiagen RNeasy FFPE Kit (Cat. 73504) according to the manufacturer instructions. RNA integrity was assessed by spectrophotometry (A260/280 > 1.8) and DV200 (>40% required for inclusion). One hundred nanograms of RNA were used per hybridization.

treatment_protocol: Not applicable. Tissue was collected at surgery with no experimental ex vivo treatment before NanoString profiling.

value: breast

value: FFPE surgical specimen

value: not specified

tag: panel

value: NHW

value: White

tag: ethnicity

value: Not Hispanic/Latino

value: Pre

tag: parity

value: Parous

tag: breastfed

value: Yes

tag: density

value: HD

tag: involution

value: Partial

value: Other

tag: diagnosis

value: L IDC w/ DCIS

value: L DCIS

value: no


title: ORG-0151_R1_BC360_20230117 histologically normal breast tissue

description: Original RCC file: 20230117_Radisky35 BC360 run3_ORG-0151 R1_08.RCC; Selected renamed RCC file: ORG-0151_R1_BC360_20230117.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20230117; Cartridge: Radisky35 BC360 run3; Lane: 8; MD5: 4631452a8293b9d37f26404d2fd75024

value: Nulliparous

value: unknown

value: Unknown

value: Fg

value: L IDC


title: ORG-0163_BC360_20230117 histologically normal breast tissue

description: Original RCC file: 20230117_Radisky35 BC360 run3_ORG-0163_12.RCC; Selected renamed RCC file: ORG-0163_BC360_20230117.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20230117; Cartridge: Radisky35 BC360 run3; Lane: 12; MD5: 6140bfd294384f03e43f53624a735999

value: breast

value: FFPE surgical specimen

value: not specified

value: NHB

value: Black

value: Post

value: Breast Reduction


title: ORG-0150_BC360_20230117 histologically normal breast tissue

description: Original RCC file: 20230117_Radisky35 BC360 run3_ORG-0150_07.RCC; Selected renamed RCC file: ORG-0150_BC360_20230117.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20230117; Cartridge: Radisky35 BC360 run3; Lane: 7; MD5: d31c78dbcfc5d4e7ab14377debaa46ca

value: NHW

value: White

value: Not Hispanic/Latino

value: Pre

value: Parous

value: Yes

value: HD

value: Partial


title: ORG-0152_BC360_20230117 histologically normal breast tissue

description: Original RCC file: 20230117_Radisky35 BC360 run3_ORG-0152_09.RCC; Selected renamed RCC file: ORG-0152_BC360_20230117.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20230117; Cartridge: Radisky35 BC360 run3; Lane: 9; MD5: 5379aa399524e3c148ca21e00be275b0

value: ED

value: Right Mastectomy, Left Prophylactic Mastectomy

value: R IDC

value: unknown

value: no


title: ORG-0154_L3_BC360_20230117 histologically normal breast tissue

description: Original RCC file: 20230117_Radisky35 BC360 run3_ORG-0154 L3_10.RCC; Selected renamed RCC file: ORG-0154_L3_BC360_20230117.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20230117; Cartridge: Radisky35 BC360 run3; Lane: 10; MD5: d9996adb028ba6a281907e9ed65139f8

value: breast

value: FFPE surgical specimen

value: Nulliparous

value: Unknown

value: Other

value: R IDC w/ DCIS


title: ORG-0147_R4_BC360_20230117 histologically normal breast tissue

description: Original RCC file: 20230117_Radisky35 BC360 run3_ORG-0147 R4_05.RCC; Selected renamed RCC file: ORG-0147_R4_BC360_20230117.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20230117; Cartridge: Radisky35 BC360 run3; Lane: 5; MD5: 734387aec246a1cda8ffc99438fb72d7

value: NHB

value: Black

value: Not Hispanic/Latino

value: IDC


title: ORG-0148_R1_BC360_20230117 histologically normal breast tissue

description: Original RCC file: 20230117_Radisky35 BC360 run3_ORG-0148 R1_06.RCC; Selected renamed RCC file: ORG-0148_R1_BC360_20230117.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20230117; Cartridge: Radisky35 BC360 run3; Lane: 6; MD5: 0aa38cc9a9fb66911ddeb58c6092afd8

value: NHW

value: White

value: Pre

value: Parous

value: Yes

value: HD


title: ORG-0139_L1_BC360_20230117 histologically normal breast tissue

description: Original RCC file: 20230117_Radisky35 BC360 run3_ORG-0139 L1_01.RCC; Selected renamed RCC file: ORG-0139_L1_BC360_20230117.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20230117; Cartridge: Radisky35 BC360 run3; Lane: 1; MD5: f9090b265d34246c22f5c3ba2e81959b

value: Partial

value: Left Mastectomy, Right Prophylactic Mastectomy

value: unknown

value: no


title: ORG-0143_L2_BC360_20230117 histologically normal breast tissue

description: Original RCC file: 20230117_Radisky35 BC360 run3_ORG-0143 L2_03.RCC; Selected renamed RCC file: ORG-0143_L2_BC360_20230117.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20230117; Cartridge: Radisky35 BC360 run3; Lane: 3; MD5: 5de2539273e36e90bfc20a7ba6fd0b06

value: breast

value: FFPE surgical specimen

value: Fg

value: Right Mastectomy, Left Prophylactic Mastectomy


title: ORG-0136_R2_BC360_20230117 histologically normal breast tissue

description: Original RCC file: 20230117_Radisky35 BC360 run2_ORG-0136 R2_11.RCC; Selected renamed RCC file: ORG-0136_R2_BC360_20230117.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20230117; Cartridge: Radisky35 BC360 run2; Lane: 11; MD5: 91ed73fc85309f6ae6c6234b73e2d7b5

value: Post

value: No


title: ORG-0141_R4_BC360_20230117 histologically normal breast tissue

description: Original RCC file: 20230117_Radisky35 BC360 run3_ORG-0141 R4_02.RCC; Selected renamed RCC file: ORG-0141_R4_BC360_20230117.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20230117; Cartridge: Radisky35 BC360 run3; Lane: 2; MD5: 47d26fed7de445b35bbfed05bf924617

value: Not Hispanic/Latino

value: Nulliparous

value: Unknown

value: ED

value: IDC w/ DCIS


title: ORG-0138_R1_BC360_20230117 histologically normal breast tissue

description: Original RCC file: 20230117_Radisky35 BC360 run2_ORG-0138 R1_12.RCC; Selected renamed RCC file: ORG-0138_R1_BC360_20230117.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20230117; Cartridge: Radisky35 BC360 run2; Lane: 12; MD5: 7818cb0dd13bb228923bff773898af56

value: NHW

value: White

value: Pre

value: Parous

value: Breast Reduction

value: No (Reduc)


title: ORG-0146_R1_BC360_20230117 histologically normal breast tissue

description: Original RCC file: 20230117_Radisky35 BC360 run3_ORG-0146 R1_04.RCC; Selected renamed RCC file: ORG-0146_R1_BC360_20230117.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20230117; Cartridge: Radisky35 BC360 run3; Lane: 4; MD5: 1e0c43bc74eb7f172b67e246df60f426

value: breast

value: NHB

value: Black

value: Yes

value: Missing

value: Partial

value: unknown

value: no


title: ORG-0131_L2_BC360_20230117 histologically normal breast tissue

description: Original RCC file: 20230117_Radisky35 BC360 run2_ORG-0131 L2_06.RCC; Selected renamed RCC file: ORG-0131_L2_BC360_20230117.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20230117; Cartridge: Radisky35 BC360 run2; Lane: 6; MD5: 06e7a4fc13b9ad6ad618d1fd9fcb86fd

value: FFPE surgical specimen

value: Right Mastectomy, Left Prophylactic Mastectomy

value: DCIS


title: ORG-0136_L1_BC360_20230117 histologically normal breast tissue

description: Original RCC file: 20230117_Radisky35 BC360 run2_ORG-0136 L1_10.RCC; Selected renamed RCC file: ORG-0136_L1_BC360_20230117.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20230117; Cartridge: Radisky35 BC360 run2; Lane: 10; MD5: b1db9097c23f418a01c2d5faa3929c04

value: NHW

value: Not Hispanic/Latino

value: Post

value: No

value: HD

value: IDC


title: ORG-0135_L_BC360_20230117 histologically normal breast tissue

description: Original RCC file: 20230117_Radisky35 BC360 run2_ORG-0135 L_09.RCC; Selected renamed RCC file: ORG-0135_L_BC360_20230117.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20230117; Cartridge: Radisky35 BC360 run2; Lane: 9; MD5: c7bd747b7d560aea8ad9e19d9073c501

value: breast

value: L

value: Pre

value: Nulliparous

value: Unknown

value: Breast Reduction


title: ORG-0133_L2_BC360_20230117 histologically normal breast tissue

description: Original RCC file: 20230117_Radisky35 BC360 run2_ORG-0133 L2_07.RCC; Selected renamed RCC file: ORG-0133_L2_BC360_20230117.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20230117; Cartridge: Radisky35 BC360 run2; Lane: 7; MD5: 32bfd45ab148276bc372fbde35e456fe

value: White

value: Parous

value: unknown


title: ORG-0123_R1_BC360_20230117 histologically normal breast tissue

description: Original RCC file: 20230117_Radisky35 BC360 run2_ORG-0123 R1_04.RCC; Selected renamed RCC file: ORG-0123_R1_BC360_20230117.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20230117; Cartridge: Radisky35 BC360 run2; Lane: 4; MD5: b42aa714eab930f10e73265726cd73c2

value: FFPE surgical specimen

value: Yes

value: ED

value: Left Mastectomy, Right Prophylactic Mastectomy

value: no


title: ORG-0128_R_BC360_20220608 histologically normal breast tissue

description: Original RCC file: 20220608_Radisky BC360 IO360 run2_ORG-0128 R_09.RCC; Selected renamed RCC file: ORG-0128_R_BC360_20220608.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20220608; Cartridge: Radisky BC360 IO360 run2; Lane: 9; MD5: b696feb6dd39eef504785b9960bb64b4

value: R

value: NHW

value: Hispanic/Latino

value: Post

value: Fg

value: Complete

value: No


title: ORG-0134_R1_BC360_20230117 histologically normal breast tissue

description: Original RCC file: 20230117_Radisky35 BC360 run2_ORG-0134 R1_08.RCC; Selected renamed RCC file: ORG-0134_R1_BC360_20230117.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20230117; Cartridge: Radisky35 BC360 run2; Lane: 8; MD5: f92cc2744f70d21a4dccd5b622f2a59f

value: breast

value: Not Hispanic/Latino

value: Pre

value: HD

value: Partial

value: IDC


title: ORG-0119_L4_BC360_20230117 histologically normal breast tissue

description: Original RCC file: 20230117_Radisky35 BC360 run2_ORG-0119 L4_01.RCC; Selected renamed RCC file: ORG-0119_L4_BC360_20230117.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20230117; Cartridge: Radisky35 BC360 run2; Lane: 1; MD5: 9eb620e39aaafa57b1ac65e91dedb72a

value: FFPE surgical specimen

value: White

value: Nulliparous

value: unknown

value: Unknown

value: Right Mastectomy, Left Prophylactic Mastectomy

value: DCIS


title: ORG-0115_L2_BC360_20230117 histologically normal breast tissue

description: Original RCC file: 20230117_Radisky35 BC360 run1_ORG-0115 L2_11.RCC; Selected renamed RCC file: ORG-0115_L2_BC360_20230117.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20230117; Cartridge: Radisky35 BC360 run1; Lane: 11; MD5: 365e91614a3d501fd1c2464ca14a8504

value: NHW

value: Parous

value: Yes

value: Left Mastectomy, Right Prophylactic Mastectomy

value: PD (padget's disease)

value: no


title: ORG-0118_L1_BC360_20230117 histologically normal breast tissue

description: Original RCC file: 20230117_Radisky35 BC360 run1_ORG-0118 L1_12.RCC; Selected renamed RCC file: ORG-0118_L1_BC360_20230117.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20230117; Cartridge: Radisky35 BC360 run1; Lane: 12; MD5: 82943e11b91cae7f52b798f3b5ce34b1

value: breast

value: Pre

value: Breast Reduction

value: No


title: ORG-0121_R4_BC360_20230117 histologically normal breast tissue

description: Original RCC file: 20230117_Radisky35 BC360 run2_ORG-0121 R4_03.RCC; Selected renamed RCC file: ORG-0121_R4_BC360_20230117.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20230117; Cartridge: Radisky35 BC360 run2; Lane: 3; MD5: 3f2d43fbae28cf6a89f0191766d5c2a3

value: FFPE surgical specimen

value: Asian/White

value: Not Hispanic/Latino

value: HD

value: Partial

value: IDC


title: ORG-0112_BC360_20210921 histologically normal breast tissue

description: Original RCC file: 20210921_Radisky 52 samples BC360 6_ORG-112_02.RCC; Selected renamed RCC file: ORG-0112_BC360_20210921.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20210921; Cartridge: Radisky 52 samples BC360 6; Lane: 2; MD5: 7eaab717921a9f21d2a8f500bcf69c73

value: not specified

value: White

value: R IDC


title: ORG-0110_BC360_20210917 histologically normal breast tissue

description: Original RCC file: 20210917_Radisky 52 samples BC360 5_ORG-110_03.RCC; Selected renamed RCC file: ORG-0110_BC360_20210917.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20210917; Cartridge: Radisky 52 samples BC360 5; Lane: 3; MD5: f33588e95177d694eb27e39cdd49b31c

value: NHB

value: Black

value: Nulliparous

value: unknown

value: Unknown


title: ORG-0104_L2_BC360_20230117 histologically normal breast tissue

description: Original RCC file: 20230117_Radisky35 BC360 run1_ORG-0104 L2_09.RCC; Selected renamed RCC file: ORG-0104_L2_BC360_20230117.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20230117; Cartridge: Radisky35 BC360 run1; Lane: 9; MD5: 9f5410a5e518e0ba77a26d15c98d6c23

value: breast

value: NHW

value: Pre

value: ED

value: Complete

value: Left Mastectomy, Right Prophylactic Mastectomy

value: IDC & DCIS

value: no


title: ORG-0111_BC360_20210917 histologically normal breast tissue

description: Original RCC file: 20210917_Radisky 52 samples BC360 5_ORG-111_04.RCC; Selected renamed RCC file: ORG-0111_BC360_20210917.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20210917; Cartridge: Radisky 52 samples BC360 5; Lane: 4; MD5: e5d7b319d2b489266543c04b287b77b2

value: FFPE surgical specimen

value: Not Hispanic/Latino

value: Post

value: Parous

value: No

value: HD

value: Partial

value: DCIS


title: ORG-0120_L_BC360_20230117 histologically normal breast tissue

description: Original RCC file: 20230117_Radisky35 BC360 run2_ORG-0120 L_02.RCC; Selected renamed RCC file: ORG-0120_L_BC360_20230117.RCC; Panel: nCounter Breast Cancer 360 Panel [NS_BC_360_v2.0]; Run date: 20230117; Cartridge: Radisky35 BC360 run2; Lane: 2; MD5: 2f20807c23f5a21565aa1ff9764fa3a2

value: L

value: White

value: unknown

value: Yes

value: Breast Reduction