title: Community_Plant_Touching_for_one_hour_Rep2

description:
Library name: Touch1h_2
Plant in community, touching other plants for one hour, replicate 2


title: lung alveolar organoid, Npnt knockout, plate1-3 well D03

status: Public on Jun 26 2026

type: SRA

city: South San Francisco

first: Anne

last: Biton

state: CA

address: 1 DNA way

country: USA

institute: Genentech

description: Library name: 1-3_D03_NPNT

library_source: transcriptomic

data_processing:
The sequencing reads in each fastq file were first split between mouse and human using Xenome (Conway et al., 2012). Only reads unambiguously assigned to either mouse or human were kept and respectively aligned to their reference genome (mouse: GRCm38.p5, human: GRCh38.p10) through the HTSeqGenie v4.35 Bioconductor package (Pau and Reeder, 2012, https://doi.org/10.18129/B9.bioc.HTSeqGenie). First, reads with low nucleotide qualities (70% of bases with quality <23) or matches to rRNA and adapter sequences were removed. Then, reads were aligned using GSNAP (Wu et al., 2010; Wu et al., 2016) version ‘2013-10-10-v2’, allowing maximum of two mismatches per 75 base sequence (parameters: ‘-M 2 -n 10 -B 2 -i 1 -N 1 -w 200000 -E 1 --pairmax-rna=200000 --clip-overlap'). Transcript annotation was based on the Gencode genes database (human: GENCODE 27, mouse: GENCODE M15). Reads unambiguously mapping to exons were counted to get gene-level read counts.
Assembly: GRCm38.p5, GRCh38.p10
Supplementary files format and content: gene_counts.xlsx provides gene-level counts of reads unambiguously mapping to exons. There is one table for the reads assigned by Xenome to the Mus Musculus genome (originating from the mouse alveolar type 2 cells of the organoids in the well), and one table for the reads assigned to the Homo Sapiens genome (originating from the human fibroblasts of the organoids in the well).
Supplementary files format and content: plate_design.csv contains the sgRNA sequences used to target each gene and their location on the four plates.
Supplementary files format and content: imaging_outputs.csv contains the main outputs of the image analysis performed on each well at day 7 and day 14, in terms of number or organoids in the well, average area of the organoids in the well, and estimate of the percentage of the well covered by organoids.
Supplementary files format and content: xenome_stats.csv contains the summary of the sequencing read assignment made by Xenome (Conway et al., 2012).

molecule: total RNA

organism:
Homo sapiens
Mus musculus

source_name: lung mouse alveolar type 2 cells and primary human fibroblasts

extract_protocol:
Libraries were prepared from extracted RNA using a modified Smart-seq3 protocol ( Hagemann-Jensen, M., Ziegenhain, C., Chen, P. et al. Single-cell RNA counting at allele and isoform resolution using Smart-seq3. Nat Biotechnol 38, 708–714 (2020). https://doi.org/10.1038/s41587-020-0497-0) Annealing reaction was performed with 4ul purified RNA, 0.8 ul 40% PEG 8000, 0.08 ul RNAse Inhibitor, 0.04 ul Smart-seq3 oligo dT (100µM), 0.3 ul dNTP (25mM each) and 1 ul water per 384 well reaction. 10 ul mineral oil was added on top to prevent evaporation. Reaction was sealed, spun and incubated at 70˚C for 10 min. Reverse translation was performed by adding 2 ul of RT mix (0.2ul Tris HCl, pH8.0 (1M), 0.24 ul NaCl (1M), 0.2 ul MgCl2 (100mM), 0.08 ul GTP (10mM), 0.64 ul DTT (100mM), 0.16 ul TSO (100µM), 0.08 ul Maxima H Minus RTase and 0.4 ul water) to each 384 well reaction. The RT reaction was incubated at 42°C for 90 min and repeated the following steps for 10 cycles: 50˚C for 2 min and 42˚C for 2 min, and was terminated at 85°C for 5 min.
cDNA amplification was performed by adding 12ul of PCR mix (0.1 ul cDNA fwd (100µM), 0.02 ul cDNA rev (100µM), 0.1 ul MgCl2 (100mM), 10 ul 2X Kapa HiFi Hotstart Readymix  and 1.78 ul water) to the RT reaction for a total of 20 ul. Reaction was thermal cycled at 95°C for 3 min, [98°C for 20 sec, 65°C for 30 sec, 72°C for 4 min] x 14 cycles, 72 °C 4min. cDNA was diluted 1:10 in water. 1 ul of each sample was transferred to a new 384 well plate to perform tagmentation. 3 ul of tagmentation mix (0.8 ul 5X TAPS Mg buffer, 0.1 ul Tn5 enzyme, 2.1 ul water) was added to each sample on ice. Plate was sealed, vortexed for 15 seconds and spun. The reaction mixture was incubated at 55 °C for 10 min. Reaction was quenched by adding 0.5µl of 0.2% SDS to each well, sealing, vortexing for 15 seconds, and spinning the plate. The plate was  incubated at room temperature for 5 min. Libraries were indexed by added 3.5 ul of PCR mix and 2 ul indexing primers  to each sample.  Reaction was thermal cycled at 72°C for 5 min, 95°C for 3 min, [98°C for 20 sec, 65°C for 30 sec, 72°C for 30 sec] x 10 cycles, 72 °C 4min. Libraries were pooled and sequenced on an Illumina NovaSeq X Plus system, targeting 8M reads per library.

tag: cell type

tag: genotype

value: Npnt CRISPR/Cas9 knockout

tag: batch


title: breast cancer_SM336

type: RNA

city: Houston

first: William

middle: Fraser

last: Symmans

state: TX

address: 2130 W Holcombe Blvd #11.4000

institute: University of Texas MD Anderson Cancer Center

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized overnight at 46C on Affymetrix U133A arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the diagnostic-grade Affymetrix scanner 3000DX.

data_processing:
Probe intensities were quantified with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. CEL files were normalized using global scaling with a trimmed mean target intensity of each array arbitrarily set to 600 using the MAS5 algorithm from the simpleaffy package (http://bioconductor.org/packages/2.4/bioc/html/simpleaffy.html).
MAS5.0 signal intensity for each array was log2 transformed and scaled to a reference distribution of 600 breast cancer specific genes.

label: biotin

organism: Homo sapiens

source_name: breast cancer sample

label_protocol: A single-round T7 amplification was used to generate biotin-labeled cRNA for hybridization. At least 1 ug of RNA is required for cRNA synthesis.

extract_protocol: Total RNA was extracted from tissue using Qiagen Rneasy columns

treatment_protocol: Patients consented to future tissue-based research sample collections from either prospective biopsy or surgical resection.

tag: er status

value: P

tag: pr status

tag: her2 status

value: N

tag: ajcc stage

value: IIA

tag: sample collection type

value: Tissue

tag: setting of sample collection

value: Surgical Tissue Sample


title: breast cancer_SM334

value: I


title: Individual_Plant_Rep3

city: Columbia

first: Sameep

last: Dhakal

state: MO

address: 1201 Rollins St.

department: Institute for data science and Informatics

institute: University of Missouri

description:
Library name: CT_3
Individual plant, no stress, replicate 3

data_processing:
Read quality control was performed using Trim Galore v0.6.10 and FastQC v0.12.1. Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence. Subsequently, the processed reads were mapped to the Gmax_880_v6.0 whole genome using Hisat2 v2.2.1. Samtools v1.18 was used to sort the bam files which were subjected toranscript assembly and quantification using Cufflinks v2.2.1. Differential expression analysis was performed later using Cuffdiff v2.2.1, comparing control conditions with different stress and .
Assembly: Arabidopsis_thaliana TAIR10
Supplementary files format and content: processed data files are in format txt and it contains the gene names along with the fpkm values for each of the replicates.

organism: Arabidopsis thaliana

source_name: Leaves

growth_protocol: Seeds were germinated and grown on peat pellets (Jiffy-7; Jiffy International, Kristiansand, Norway), under controlled conditions of 50 µmol photons s−1 m−2, 10-h/14-h light/dark cycle at 22 °C/20 °C day/night and 400 μmol mol−1 CO2 for 4 to 5 weeks. Plants were then distributed in different treatment groups.

extract_protocol:
For each biological repeat, leaves were pooled together from 10-15 different plants and flash frozen in liquid nitrogen. RNA from samples was isolated using RNeasy plant mini kit.
RNA libraries for sequencing were prepared using standard Illumina protocols.

treatment_protocol: Individual plants were positioned so that they did not touch any other plant. For the chain and community plant setups, where leaf-to-leaf contact was required, a solution containing 0.05 M phosphate buffer (pH 7.4), 0.01% (v/v) Silwet L-77, and 0.05% agarose was applied to ensure contact between leaves.

tag: tissue

value: Leaves

value: WT (Col-0)

tag: treatment

value: Individual plant, no stress


title: lung alveolar organoid, Bmp10 knockout, plate1-3 well C10

description: Library name: 1-3_C10_BMP10

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Bmp10 CRISPR/Cas9 knockout


title: Individual_Plant_Rep2

description:
Library name: CT_2
Individual plant, no stress, replicate 2


title: breast cancer_SM333


title: lung alveolar organoid, Tigit knockout, plate1-3 well C09

description: Library name: 1-3_C09_TIGIT

value: Tigit CRISPR/Cas9 knockout


title: breast cancer_SM332

value: L

value: IV

value: Cytology

value: Needle Biopsy Sample


title: SNT996_NJVN_955_6912f8d4ddd4d65d94f02adc3a7f96f8 Xenium normal human lung

city: Cambridge

first: Alexander

last: Tsankov

state: MA

address: 7 Divinity Drive

institute: Harvard University

description: 10x Genomics Xenium spatial transcriptomics sample SNT996_NJVN_955_6912f8d4ddd4d65d94f02adc3a7f96f8

hyb_protocol: Probe hybridization, ligation, and rolling-circle amplification were performed per the 10x Genomics Xenium In Situ Gene Expression User Guide (CG000582 Rev H). The Xenium Human Lung Gene Expression panel with a custom add-on (Design ID 77VFDX; 386 total targets including 97 custom add-on probes; v1 chemistry) was hybridized overnight, followed by post-hybridization washes, ligation, rolling-circle amplification, background fluorescence quenching, and DAPI nuclear staining per the 10x Genomics Xenium In Situ Gene Expression User Guide (CG000582 Rev H).

scan_protocol: Slides were loaded onto the Xenium Analyzer and imaged per the 10x Genomics Xenium Analyzer User Guide (CG000584 Rev G). Amplicons were read out by cyclic fluorescence imaging across the decoding cycles, with DAPI imaging for nuclear morphology. Xenium Analyzer instrument control software version 3.3.0.1 was used.

data_processing: On-instrument primary and secondary analysis was performed by Xenium Onboard Analysis v3.3.0.1, which carried out image registration, transcript decoding, nucleus (DAPI) detection, and cell segmentation by nucleus expansion (default; no cell segmentation staining module used), producing the cell-feature matrix.

label: Xenium probe set

source_name: lung

label_protocol: Xenium probe set

extract_protocol: tissue preparation protocol: A tissue microarray (TMA) block was constructed from FFPE donor tissue cores. The TMA block was sectioned at 5 µm and the section placed within the capture area of Xenium slides per the 10x Genomics Xenium In Situ for FFPE Tissue Preparation Guide (CG000578 Rev A). Sections were dried, then deparaffinized and decrosslinked per the Xenium In Situ for FFPE Deparaffinization & Decrosslinking Demonstrated Protocol (CG000580 Rev E). Serial sections were H&E-stained to assess morphology prior to Xenium processing.

value: lung

tag: tissue preservation method

value: FFPE


title: lung alveolar organoid, Prkn knockout, plate1-3 well C08

description: Library name: 1-3_C08_PRKN

value: Prkn CRISPR/Cas9 knockout


title: SNT795_RDXZ_895_ab5b29342a6318c669d72bf528f2b969 Xenium normal human lung

description: 10x Genomics Xenium spatial transcriptomics sample SNT795_RDXZ_895_ab5b29342a6318c669d72bf528f2b969


title: SNT953_RHPB_762_f6c505eaed18256c58e79c6dceb19f25 Xenium normal human lung

description: 10x Genomics Xenium spatial transcriptomics sample SNT953_RHPB_762_f6c505eaed18256c58e79c6dceb19f25


title: SNT779_CQZQ_942_59c99fcb8f72e857d4bf721439ae247b Xenium normal human lung

description: 10x Genomics Xenium spatial transcriptomics sample SNT779_CQZQ_942_59c99fcb8f72e857d4bf721439ae247b


title: breast cancer_SM330

value: P

value: N


title: Individual_Plant_Rep1

description:
Library name: CT_1
Individual plant, no stress, replicate 1


title: SNT635_LWJG_639_6540632fe43706acb801db14d4df98b6 Xenium normal human lung

description: 10x Genomics Xenium spatial transcriptomics sample SNT635_LWJG_639_6540632fe43706acb801db14d4df98b6


title: breast cancer_SM331

value: Tissue

value: Surgical Tissue Sample


title: SNT827_VSJM_725_b292cb29384424d0de895d89475968e4 Xenium normal human lung

description: 10x Genomics Xenium spatial transcriptomics sample SNT827_VSJM_725_b292cb29384424d0de895d89475968e4


title: Community_Plant_Touching_for_one_hour_Rep1

description:
Library name: Touch1h_1
Plant in community, touching other plants for one hour, replicate 1

value: Leaves

value: Community 1 hour, no stress


title: lung alveolar organoid, Il1a knockout, plate1-3 well C07

description: Library name: 1-3_C07_IL1A

value: Il1a CRISPR/Cas9 knockout


title: SNT729_MJXR_538_17d33b94bdee121e9239781423811f03 Xenium normal human lung

description: 10x Genomics Xenium spatial transcriptomics sample SNT729_MJXR_538_17d33b94bdee121e9239781423811f03


title: breast cancer_SM329

value: IIA


title: lung alveolar organoid, Trp63 knockout, plate1-3 well C06

description: Library name: 1-3_C06_TRP63

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Trp63 CRISPR/Cas9 knockout


title: SNT665_MSZP_496_43d3b1de3c21cd32fe5c762dc3ce2d19 Xenium normal human lung

description: 10x Genomics Xenium spatial transcriptomics sample SNT665_MSZP_496_43d3b1de3c21cd32fe5c762dc3ce2d19


title: lung alveolar organoid, Sftpd knockout, plate1-3 well C05

description: Library name: 1-3_C05_SFTPD

value: Sftpd CRISPR/Cas9 knockout


title: SNT638_GNLL_459_bfec902d45098c033eb018c03eb80847 Xenium normal human lung

description: 10x Genomics Xenium spatial transcriptomics sample SNT638_GNLL_459_bfec902d45098c033eb018c03eb80847


title: breast cancer_ANON 13B

value: IIB


title: breast cancer_SM327


title: SNT588_NRZH_473_77dbc949ecf2ed54d73dcd5e50042eed Xenium normal human lung

description: 10x Genomics Xenium spatial transcriptomics sample SNT588_NRZH_473_77dbc949ecf2ed54d73dcd5e50042eed


title: lung alveolar organoid, Huwe1 knockout, plate1-3 well C04

description: Library name: 1-3_C04_HUWE1

value: Huwe1 CRISPR/Cas9 knockout


title: SNT586_GWVQ_588_acdc8a344bd0194e6295e2e57dd78858 Xenium normal human lung

description: 10x Genomics Xenium spatial transcriptomics sample SNT586_GWVQ_588_acdc8a344bd0194e6295e2e57dd78858


title: lung alveolar organoid, Mecom knockout, plate1-3 well C03

description: Library name: 1-3_C03_MECOM

value: Mecom CRISPR/Cas9 knockout


title: SNT545_GBMS_643_b8d5cf9a5906add2c218a89eaffa52e4 Xenium normal human lung

description: 10x Genomics Xenium spatial transcriptomics sample SNT545_GBMS_643_b8d5cf9a5906add2c218a89eaffa52e4

value: lung


title: breast cancer_SM326

value: Cytology


title: SNT542_ZSGK_763_432cf60cc168271e26a0bcccbb681099 Xenium normal human lung

description: 10x Genomics Xenium spatial transcriptomics sample SNT542_ZSGK_763_432cf60cc168271e26a0bcccbb681099

value: FFPE


title: breast cancer_ANON 13A

value: P


title: SNT537_HDFP_842_82b92b99ea6e4d1834379777408158be Xenium normal human lung

description: 10x Genomics Xenium spatial transcriptomics sample SNT537_HDFP_842_82b92b99ea6e4d1834379777408158be


title: lung alveolar organoid, Tead1 knockout, plate1-3 well C02

description: Library name: 1-3_C02_TEAD1

value: Tead1 CRISPR/Cas9 knockout


title: SNT455_MJZC_582_ac5045f43c97d32079fe208b82a2436d Xenium normal human lung

description: 10x Genomics Xenium spatial transcriptomics sample SNT455_MJZC_582_ac5045f43c97d32079fe208b82a2436d


title: breast cancer_SM324

value: N

value: III

value: Tissue

value: Needle Biopsy Sample


title: breast cancer_SM322

value: Surgical Tissue Sample


title: SNT436_KZZF_362_438154eae4bceec977e7bf0e52b5272c Xenium normal human lung

description: 10x Genomics Xenium spatial transcriptomics sample SNT436_KZZF_362_438154eae4bceec977e7bf0e52b5272c


title: Body, exposed to pathogen and ant food, 05

city: Graz

first: Danae

last: Nyckees

address: Universitätsplatz 2

country: Austria

institute: University of Graz

description: Library name: sample30

data_processing:
The raw paired-end sequencing reads from the released RNA-Seq library was subject to processing. First, sequencing adaptors and low-quality nucleotides (Phred score threshold 30, stringency 2) were trimmed using Trim Galore (v. 0.6.0). Reads shorter than 70 bp were discarded and only intact pairs were retained for further processing. Secondly, the genome of F. fusca was retrieved from the GAGA project (Vizueta et al., 2025) and used to generate a genome index with STAR (v. 2.7.10b). Read mapping to the indexed reference genome for each sample was performed with the same software. Thirdly, PCR duplicate removal was performed using Picard (v. 2.18.7). Finally, the total reads from exon were transformed into counts using featureCounts (v. 2.0.6).
Assembly: GCA_048541905.1
Supplementary files format and content: each processed data file contains the gene name and the respective number of reads

organism: Formica fusca

source_name: thorax and abdomen

extract_protocol:
RNA was isolated from each sample with a phenol-chlorophorm extraction method. First, samples were homogenized with 500 µl TRI Reagent (T9424, Sigma-Aldrich, Missouri, United States) with a TissueLyser II (Qiagen, Venlo, Netherlands) for 1min at 30/s. Then, the volume was adjusted to 1 ml with TRI Reagent and the samples were vortexed. A volume of 150 µl of chloroform (C2432, Sigma-Aldrich, Missouri, United States) was added and the samples were vortexed vigorously. The samples were incubated at room temperature for 2 min and then on ice for 5 min. The samples are then centrifuged for 10 min at 14,000 rpm and at 4 °C. The supernatant was then carefully transferred to a new clean tube and 500 µl of isopropanol (190764, Sigma-Aldrich, Missouri, United States) was added. The samples are then vortexed vigorously and stored at -20 °C for approx. 24 h. The samples were centrifuged for 30 min at 14,000 rpm and at 4 °C. The isopropanol was removed and 500 µl of 80 % ethanol was added. The samples were centrifuged for 10 min at 14,000 rpm and at 4 °C. The ethanol was removed, and the samples were spined down to allow a second removal of the remaining solution. The RNA pellets were allowed to air dry for approx. 10 min with open cap. Finally, 40 µl of miliQ H2O were added and the RNA concentration and purity were measured with the Nanodrop Onec (Thermo Fisher Scientific, Massachusetts, United States). RNA extracts that were under 1.8 from the 260/280 ratio were subjected to a clean-up with GeneJET RNA Cleanup and Concentration Micro Kit (K0842, Thermo Fisher Scientific, Massachusetts, United States). Twenty microliters of RNA extracts were used and adjusted with nuclease-free water to reach a volume of 200 µl. Then, the manufacturer protocol was followed. As the amount of RNA was large, 20 µl of nuclease-free water was added instead of 10 for the final elution volume. RNA concentration and purity were measured with a Nanodrop and the RNA extracts with low purity levels were subjected to another round of clean-up.
Library construction was performed by Novogen using Illumina NovaSeq™ X Plus instruments and a paired-end 150 bp sequencing strategy.

treatment_protocol: Ten ants per experimental box were collected on day 4. Each ant was decapitated. Heads and bodies (thorax + abdomen) from each experimental colony and day were pooled respectively and conserved in RNAlater (R0901, Sigma-Aldrich, Missouri, United States). They were first stored at -20 °C for one night to allow the ants to sink and then at -80 °C until further analysis.

value: thorax and abdomen

value: exposed to Beauveria bassiana + ant food


title: breast cancer_SM321

value: IIA


title: SNT379_WBLL_744_f4ae89493af530f20bc0c810d74a79e5 Xenium normal human lung

description: 10x Genomics Xenium spatial transcriptomics sample SNT379_WBLL_744_f4ae89493af530f20bc0c810d74a79e5


title: lung alveolar organoid, Ccbe1 knockout, plate1-3 well B10

description: Library name: 1-3_B10_CCBE1

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Ccbe1 CRISPR/Cas9 knockout


title: lung alveolar organoid, Gdf2 knockout, plate1-3 well B11

description: Library name: 1-3_B11_GDF2

value: Gdf2 CRISPR/Cas9 knockout


title: breast cancer_SM319


title: breast cancer_SM317

value: L


title: SNT424_VLKP_238_ca8bde4a33b94275899fc7da8472d7e0 Xenium normal human lung

description: 10x Genomics Xenium spatial transcriptomics sample SNT424_VLKP_238_ca8bde4a33b94275899fc7da8472d7e0

value: lung


title: d25 normoxia with 5% imacs replicate 3

city: Clayton

first: Wei

last: Shi

state: VIC

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology

country: Australia

institute: Monash University

hyb_protocol: As per 10x Genomics protocols

scan_protocol: As per 10x Genomics protocols

data_processing:
Raw spatial transcriptomics count data, generated by the Xenium onboard analysis software, was loaded into R. All individual sample transcript counts were pooled and normalized with SCTransform using the Seurat package. Unsupervised clustering was then performed using two resolutions: 0.8 and 0.3.  Final clustering results were derived by integrating these results, selectively using the 0.8 resolution for nephron clusters and the 0.3 resolution for non-nephron clusters.
To integrate samples from different conditions and/or slides, we used multiple methods within the Seurat package. These included Harmony, Joint PCA, and Reciprocal PCA (RPCA). For RPCA, we performed the integration using either all variable genes or a specific set of marker genes previously identified from normoxia cell clusters.
Cell types were then mapped onto the Xenium data by integrating with a reference scRNA-seq dataset of the same type of sample, utilizing both RCTD and Seurat's anchor-based cell type transfer methods.
.tar.gz: Xenium raw data from onboard analysis software
CellClusters-*.tsv.gz: TAB-delimited table giving cluster of each cell
Cells-*.tsv.gz: TAB-delimited table giving centroid coordinates of each cell
Counts-*.tsv.gz: TAB-delimited table giving transcript count of each gene in each cell
Molecules-*.tsv.gz: TAB-delimited table giving coordinates and cell assignment of each transcript
PseudoBulk-log2CPM-*.tsv.gz: TAB-delimited table giving normalised log2CPM values of each gene on pseudo-bulk mode, using all cells, nephrons, stromal cells, endothelial or immune cells (if detected in this sample).

source_name: kidney organoid

label_protocol: Samples were labelled with the 10X Genomics Xenium Human Immuno-Oncology panel containing probes to 380 genes, then with the Xenium Cell Segmentation kit as per the 10x protocol.

growth_protocol: Kidney organoids were differentiated from 522 iPSC lines using a protocol based on https://doi.org/10.1038/nature15695, iMacs were differentiated using a protocol based on 10.3390/ijms232416087.

extract_protocol: Deparaffinization and decrosslinking was performed to make subcellular RNA targets accessible (10X Genomics Demonstrated Protocol CG000580).

treatment_protocol: Details on the experimental treatment (hypoxia) +/- iMacs are outlined above, with futher information available in https://doi.org/10.1101/2023.10.04.558359. Equipment and instruments were cleaned using RNase Away before use. A 5 micron section of each FFPE block containing replicate samples from an experimental group was cut and carefully arranged on the Xenium slide and left to dry overnight. Slides were baked at 42°C for 3 hours, then stored in a sealed container at room temperature.

value: kidney organoid

tag: days

tag: condition

value: Normoxia

tag: proportion of imacs

tag: slide number


title: d25 normoxia with 5% imacs replicate 4


title: SNT334_KMRB_286_cce63e0aa77dfff766f699a40cfb3719 Xenium normal human lung

description: 10x Genomics Xenium spatial transcriptomics sample SNT334_KMRB_286_cce63e0aa77dfff766f699a40cfb3719

value: FFPE


title: lung alveolar organoid, Pink1 knockout, plate1-3 well B08

description: Library name: 1-3_B08_PINK1

value: Pink1 CRISPR/Cas9 knockout


title: d25 normoxia with 5% imacs replicate 2


title: lung alveolar organoid, Eif2ak3 knockout, plate1-3 well B09

description: Library name: 1-3_B09_EIF2AK3

value: Eif2ak3 CRISPR/Cas9 knockout


title: SNT228_DHGQ_454_f035455ac6a5eaae1c81efb72571eac9 Xenium normal human lung

description: 10x Genomics Xenium spatial transcriptomics sample SNT228_DHGQ_454_f035455ac6a5eaae1c81efb72571eac9


title: d25 normoxia with 5% imacs replicate 1


title: breast cancer_SM316

value: P

value: N


title: lung alveolar organoid, Acp6 knockout, plate1-3 well B07

description: Library name: 1-3_B07_ACP6

value: Acp6 CRISPR/Cas9 knockout


title: d25 hypoxia with 5% imacs replicate 4

value: Hypoxia


title: breast cancer_SM313

value: Tissue

value: Needle Biopsy Sample


title: Head, sham and caffeinated ant food, 04

description: Library name: sample37

source_name: head

value: head

value: sham + ant food spiked with 100 ppm caffeine


title: d25 hypoxia with 5% imacs replicate 3


title: lung alveolar organoid, Trp53 knockout, plate1-3 well B06

description: Library name: 1-3_B06_TRP53

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Trp53 CRISPR/Cas9 knockout


title: d25 hypoxia with 5% imacs replicate 2


title: breast cancer_SM311

value: IIA

value: Cytology


title: d25 hypoxia with 5% imacs replicate 1

value: kidney organoid


title: d25 normoxia replicate 6

value: Normoxia


title: lung alveolar organoid, Tdtomato knockout, plate1-3 well B05

description: Library name: 1-3_B05_TDTOMATO

value: Tdtomato CRISPR/Cas9 knockout


title: d25 normoxia replicate 5


title: breast cancer_SM309

value: Surgical Tissue Sample


title: lung alveolar organoid, Tigit knockout, plate1-3 well B04

description: Library name: 1-3_B04_TIGIT

value: Tigit CRISPR/Cas9 knockout


title: breast cancer_SM303

value: P

value: III


title: d25 normoxia replicate 3


title: lung alveolar organoid, Glis3 knockout, plate1-3 well B03

description: Library name: 1-3_B03_GLIS3

value: Glis3 CRISPR/Cas9 knockout


title: d25 normoxia replicate 2


title: d25 normoxia replicate 4


title: breast cancer_SM301

value: N


title: breast cancer_SM305

value: I

value: Tissue


title: d25 normoxia replicate 1


title: d25 hypoxia replicate 6

value: Hypoxia


title: Head, exposed to pathogen and ant food, 03

description: Library name: sample25

value: head

value: exposed to Beauveria bassiana + ant food


title: lung alveolar organoid, Met knockout, plate1-3 well B02

description: Library name: 1-3_B02_MET

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Met CRISPR/Cas9 knockout


title: lung alveolar organoid, Tdtomato knockout, plate1-2 well G10

description: Library name: 1-2_G10_TDTOMATO


title: d25 hypoxia replicate 5


title: d25 hypoxia replicate 4


title: breast cancer_SM299


title: d25 hypoxia replicate 3


title: lung alveolar organoid, Becn1 knockout, plate1-2 well G09

description: Library name: 1-2_G09_BECLN1

value: Becn1 CRISPR/Cas9 knockout


title: d25 hypoxia replicate 2

value: kidney organoid


title: breast cancer_SM298


title: d25 hypoxia replicate 1


title: d20 normoxia replicate 2

value: Normoxia


title: lung alveolar organoid, Ern1 knockout, plate1-2 well G08

description: Library name: 1-2_G08_ERN1

value: Ern1 CRISPR/Cas9 knockout


title: breast cancer_SM293

value: Surgical Tissue Sample


title: Head, sham and ant food, 01

description: Library name: sample11

value: sham + ant food


title: lung alveolar organoid, Nr1d2 knockout, plate1-2 well G07

description: Library name: 1-2_G07_NR1D2

value: Nr1d2 CRISPR/Cas9 knockout


title: d20 hypoxia replicate 3


title: d20 hypoxia replicate 2


title: d20 hypoxia replicate 1


title: breast cancer_SM292

value: P

value: L

value: IIA


title: lung alveolar organoid, Hhip knockout, plate1-2 well G06

description: Library name: 1-2_G06_HHIP

value: Hhip CRISPR/Cas9 knockout


title: breast cancer_SM289

value: N

value: Tissue


title: Isocortex, Hippocampus, 6h, NMEC, rep3

city: Tianjin

first: zhiyue

last: Wu

address: No. 288 Nanjing Road, Heping District, Tianjin, China

country: China

institute: Institute of Hematology & Blood Diseases Hospital

description:
Library name: Sample 6
10x Genomics

data_processing:
Quality filtering：Raw reads were quality-filtered with fastp (v0.20.0) to remove adapters, poly-N sequences, and low-quality bases (Q < 15 for >40% of read length; length < 18 bp).
Alignment：Trimmed reads were aligned to the mm10/GRCm38 mouse genome using Bowtie2 (v2.4.2, parameter: --very-sensitive).
Duplicate removal：Duplicates were removed with Picard MarkDuplicates (v2.26.0). Reads with a mapping quality score < 30 were removed.
Peak calling：Genrich (v0.6.1) was used with parameters: -j -p 0.01 -a 20 -l 100 -r to detect open chromatin regions (peaks). Peaks overlapping with blacklisted regions were filtered out.
Assembly: Mouse mm10
Supplementary files format and content: .bw (bigWig) files：Normalized coverage tracks for visualization in genome browsers, representing genome-wide chromatin accessibility signals.

organism: Mus musculus

source_name: Isocortex, Hippocampus

growth_protocol: 18-day-old wide type C57BL/6N mice were maintained under specific pathogen-free conditions with free access to food and water.

extract_protocol:
Frozen mouse brain tissues were thawed in a 37°C water bath. Cells were centrifuged at 500 g for 5 min at 4°C. For each sample, 50,000 live cells were lysed in 50 µL lysis buffer on ice for 5 min, followed by addition of 1 mL wash buffer and centrifugation (500 g, 5 min). Tissue samples were homogenized in 1 mL 1× HB buffer, filtered, and centrifuged (500 g, 5 min, 4°C). Nuclei were further purified by density gradient centrifugation for 10 min and counted with LUNA-FL. A total of 50,000 nuclei were collected for downstream applications.
ATAC-seq was performed as previously described. Isolated nuclei were resuspended in Tn5 transposase reaction mix and incubated at 37°C for 30 min. After transposition, equimolar Adapter 1 and Adapter 2 were added, followed by PCR amplification. Libraries were purified with AMPure beads, and concentration was measured using Qubit. Indexed libraries were clustered on an Illumina cBot system with TruSeq PE Cluster Kit v3-cBot-HS.

treatment_protocol: Escherichia coli (NMEC) infection in mice

value: Isocortex, Hippocampus

value: infected, NMEC, 6h


title: breast cancer_SM286

value: IIB

value: Needle Biopsy Sample


title: Isocortex, Hippocampus, 6h, PBS, rep1

description:
Library name: Sample 1
10x Genomics

value: infected, PBS, 6h


title: breast cancer_SM282

value: Cytology


title: Casp3-/-Mlkl-/-Bid-/- P815 cells CTL_treated, rep1

city: Lørenskog

first: Shixiong

last: Wang

address: Sykehusveien 25

country: Norway

institute: Akershus University Hospital

description: Library name: Sample4

library_source: other

data_processing:
Screening data were analyzed using MAGeCK-VISPR  to identify significantly enriched or depleted sgRNAs/genes. In brief, sgRNA counting was first performed with mageck count function on Fastq files with option --trim-5 22,23,24,25,26,28,29,30 to trim the 5 prime stagger sequences.
CD8 T cells treated and control treatments were compared with mageck test function, and the normalization was performed by using control sgRNAs.
Assembly: mm10
Supplementary files format and content: tab-delimited text file with gene ranking summary
Library strategy: CRISPR Screen

molecule: other

extract_protocol:
Genomic DNA was extracted from 2 × 10⁷ cells per replicate using the NucleoSpin™ Blood L Midi kit (Macherey-Nagel; #740954.20).
sgRNA sequences were amplified and prepared for next-generation sequencing (NGS) using a two-step PCR strategy. In the first PCR (30–45 cycles), sgRNA-containing regions were amplified from genomic DNA using eight staggered forward primers (PCR1_Fwd_1–8) together with a vector-specific reverse primer, using Q5® High-Fidelity DNA Polymerase (New England Biolabs; M0491S). PCR products were pooled and purified using the NucleoSpin™ Gel and PCR Clean-up Midi kit (Macherey-Nagel; #740986.20). In the second PCR (8 cycles), Illumina P5 and P7 adapters and sample-specific indices were added. Final libraries were purified using SpeedBeads (GE65152105050250, Cytiva), quantified using a Qubit fluorometer (Thermo Fisher Scientific), and quality-checked using TapeStation system with D1000 ScreenTape (5067-5582, Agilent). Libraries were pooled equimolarly and sequenced on a NovaSeq X platform (Illumina), targeting a depth of 20–30 million reads per sample.

treatment_protocol: 7.5 × 10⁷ Casp3-/-Mlkl-/-Bid-/- P815 cells were transduced with the Brie lentiviral library at a multiplicity of infection (MOI) of 0.3 to ensure single integration events per cell. 48 hours post-transduction, cells were selected with puromycin (0.6 µg/mL). After 48 h of selection, surviving cells were pooled, cultured in puromycin-free medium, and subjected to cytotoxic T lymphocyte (CTL) selection. For CTL selection, 8 × 10⁶ target cells were co-cultured with activated human CD8⁺ T cells at equal effector-to-target ratios in the presence of 5 µg/mL anti-CD3 antibody. After 48 h of co-culture, cells were collected and treated with puromycin to eliminate residual CD8⁺ T cells. Surviving P815 cells were expanded, and CTL selection was repeated twice. Following selection, surviving cells were expanded, and genomic DNA was extracted from 2 × 10⁷ cells per replicate.

tag: cell line

value: Mastocytoma

value: CTL


title: Casp3-/-Mlkl-/-Bid-/- P815 cells CTL_treated, rep3

description: Library name: Sample6

tag: cell type


title: Casp3-/-Mlkl-/-Bid-/- P815 cells CTL_treated, rep2

description: Library name: Sample5


title: lung alveolar organoid, Xbp1 knockout, plate1-2 well F10

description: Library name: 1-2_F10_XBP1

value: lung mouse alveolar type 2 cells and primary human fibroblasts

tag: genotype

value: Xbp1 CRISPR/Cas9 knockout


title: breast cancer_SM280

value: I

value: Surgical Tissue Sample


title: Casp3-/-Mlkl-/-Bid-/- P815 cells Control, rep2

description: Library name: Sample2

value: Control


title: Casp3⁻/⁻ P815 cells CTL_treated, rep4

description: Library name: Sample7

treatment_protocol: 7.5 × 10⁷ Casp3⁻/⁻ P815 cells were transduced with the Brie lentiviral library at a multiplicity of infection (MOI) of 0.3 to ensure single integration events per cell. 48 hours post-transduction, cells were selected with puromycin (0.6 µg/mL). After 48 h of selection, surviving cells were pooled, cultured in puromycin-free medium, and subjected to cytotoxic T lymphocyte (CTL) selection. For CTL selection, 8 × 10⁶ target cells were co-cultured with activated human CD8⁺ T cells at equal effector-to-target ratios in the presence of 5 µg/mL anti-CD3 antibody. After 24 h of co-culture, cells were collected and treated with puromycin to eliminate residual CD8⁺ T cells. Surviving P815 cells were expanded, and CTL selection was repeated three times. Following selection, surviving cells were expanded, and genomic DNA was extracted from 2 × 10⁷ cells per replicate.


title: breast cancer_SM279

value: P


title: breast cancer_ANON 12N

value: IIA


title: lung alveolar organoid, Eif2b1 knockout, plate1-2 well F08

description: Library name: 1-2_F08_EIF2B1

value: Eif2b1 CRISPR/Cas9 knockout

tag: batch


title: breast cancer_SM278

tag: er status

value: L

value: N

value: Tissue


title: Casp3⁻/⁻ P815 cells CTL_treated, rep2

description: Library name: Sample5


title: Casp3⁻/⁻ P815 cells CTL_treated, rep1

description: Library name: Sample4


title: breast cancer_SM274

tag: pr status


title: Body, sham and ant food, 01

description: Library name: sample12

value: thorax and abdomen

value: sham + ant food


title: lung alveolar organoid, Fam13a knockout, plate1-2 well F06

description: Library name: 1-2_F06_FAM13A

value: Fam13a CRISPR/Cas9 knockout


title: breast cancer_SM273

tag: her2 status


title: lung alveolar organoid, Terf1 knockout, plate1-2 well F05

description: Library name: 1-2_F05_TERF1

value: Terf1 CRISPR/Cas9 knockout


title: CD8+ T cell transduced with Runx3 wt construct replicate 1

city: Jupiter

first: Wuyue

last: Zhou

address: 110 Scripps Way

institute: The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology

description:
Library name: WT_REP1
See corresponding column

data_processing:
Reads were processed using nf-core/rnaseq v3.14.0. Briefly, raw read quality was assessed with FastQC v0.12.1, and adapter sequences and low-quality bases were trimmed using Trim Galore! v0.6.7. Trimmed reads were aligned to the GRCm38 reference genome with STAR, and the resulting transcriptome-level alignments were quantified with Salmon v1.10.1. Genome alignments were coordinate-sorted and indexed with SAMtools v1.17, duplicate reads were marked with Picard v3.0.0, and normalized genome coverage tracks were generated with BEDTools v2.30.0. Post-alignment quality control included read distribution, gene-body coverage, and strand-specificity metrics (RSeQC, Qualimap, and inference via Salmon), duplication assessment (dupRadar), library-complexity estimation (Preseq), and gene-biotype quantification with featureCounts (Subread v2.0.1). Sample-to-sample similarity was evaluated by principal component analysis and hierarchical clustering of regularized log-transformed counts using DESeq2 v1.40.2. Differential gene expression analysis was performed in R using DESeq2 v1.40.2. Gene-level counts from the star_salmon quantification were filtered to retain genes with a mean raw count ≥ 5 across all samples, and a model of the form “~ group” was fit to test pairwise contrasts between each RUNX3 fusion construct (FT, LOV, APEX, ULTRA, MINI, TID) and the empty-vector (EV) and wild-type RUNX3 (WT) controls using the Wald test. Genes with a Benjamini–Hochberg-adjusted p-value ≤ 0.05 and |log₂ fold-change| ≥ 1 were considered differentially expressed.
Assembly: GRCm38 (mouse)
Supplementary files format and content: Tab-separated values (TSV) file containing gene-level raw counts from Salmon/STAR quantification. Rows represent genes (n = 45,706), with columns for Ensembl gene ID, gene name, and raw read counts for 2 biological replicates across 7 conditions (APEX, EV, FT, LOV, MINI, TID, ULTRA, WT)

source_name: primary cell

growth_protocol: CD8+ T cells were isolated from splenocytes and cultured ex vivo with anti-CD3/CD28 stimulation and transduced with RUNX3 retroviral constructs as described in the CD8+ T cell transduction protocol.

extract_protocol:
T cells were collected and centrifuged at 750 × g for 5 minutes. Cells were lysed with DNA/RNA Shield (Zymo Research, #1100-50) at a density of 1 × 10⁶ cells per 50 µL. Lysed samples were submitted to Plasmidsaurus for library construction and sequencing.
Library construction and RNA-seq sequencing (10 million reads/sample) were performed by Plasmidsaurus. In brief, they converted mRNA into complementary DNA (cDNA) via reverse transcription and second-strand synthesis, followed by tagmentation and library indexing and amplification.

treatment_protocol: Sixteen hours post-activation, cells were spinfected with retroviral supernatant to express different Runx3-tagged constructs: FT(FlAsH-tag), LOV*, APEX2, ultraID, miniTurbo, TurboID, WT, and Empty vector control.

value: primary cell

value: primary CD8+ T cells were isolated from splenocytes

value: C57BL/6J mice

value: transduced with Runx3 wt construct


title: CD8+ T cell transduced with Runx3-ultraID construct replicate 1

description:
Library name: ULTRA_REP1
See corresponding column

value: transduced with Runx3-ultraID construct


title: breast cancer_SM269

tag: ajcc stage

value: IIB

value: Cytology

value: Needle Biopsy Sample


title: Isocortex, Hippocampus, 6h, NMEC, rep2

description:
Library name: Sample 5
10x Genomics

value: Isocortex, Hippocampus

value: infected, NMEC, 6h


title: lung alveolar organoid, Rbms3 knockout, plate1-2 well F03

description: Library name: 1-2_F03_RBMS3

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Rbms3 CRISPR/Cas9 knockout


title: Casp3-/-Mlkl-/-Bid-/- P815 cells Control, rep3

description: Library name: Sample3

value: Mastocytoma

value: Control


title: breast cancer_SM281

value: P

value: N

value: IIA

tag: sample collection type

value: Tissue

value: Surgical Tissue Sample


title: CD8+ T cell transduced with Runx3-TurboID construct replicate 1

description:
Library name: TID_REP1
See corresponding column

value: primary cell

value: primary CD8+ T cells were isolated from splenocytes

value: C57BL/6J mice

value: transduced with Runx3-TurboID construct


title: lung alveolar organoid, Atg16l1 knockout, plate1-2 well F09

description: Library name: 1-2_F09_ATG16L1

value: Atg16l1 CRISPR/Cas9 knockout


title: breast cancer_SM267

value: L

value: I

value: Cytology

tag: setting of sample collection


title: lung alveolar organoid, Lgr4 knockout, plate4-4 well G03

description: Library name: 4-4_G03_LGR4

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Lgr4 CRISPR/Cas9 knockout


title: lung alveolar organoid, Nr1d1 knockout, plate1-2 well F07

description: Library name: 1-2_F07_NR1D1

value: Nr1d1 CRISPR/Cas9 knockout


title: lung alveolar organoid, Tigit knockout, plate1-2 well F02

description: Library name: 1-2_F02_TIGIT

value: Tigit CRISPR/Cas9 knockout


title: CD8+ T cell transduced with Runx3-miniTurbo construct replicate 2

description:
Library name: MINI_REP2
See corresponding column


title: Body, sham and ant food, 03

description: Library name: sample16

tag: tissue

value: thorax and abdomen

value: sham + ant food


title: CD8+ T cell transduced with Runx3-miniTurbo construct replicate 1

description:
Library name: MINI_REP1
See corresponding column

tag: treatment


title: breast cancer_SM265

value: P

value: N

value: III

value: Needle Biopsy Sample


title: Murine aortic smooth muscle cellswith Knockdown long CASC22 and no treatment; P19

city: Pittsburgh

first: Delphine

last: Gomez

state: Pennsylvania

address: 203 Lothrop Street

department: Vascular Medicine Institute

institute: University of Pittsburgh

description:
Library name: seqrun3_KD_lCAS_no-trt_rep4
Column name in rsem.merged.gene_counts.tsv: seqrun3_KD_lCAS_no-trt_rep4

data_processing:
Preprocessing was conducted with nf-core/rnaseq: v3.22.2’s standard parameters unless otherwise stated. The 75 bp paired-end reads were mapped to Mus musculus reference genome, GRCm39 primary assembly with the STAR aligner v2.7.11b and quantified with RSEM 1.3.1.
Assembly: mm10
Supplementary files format and content: tab-delimited text file contains STAR-RSEM counts for each sample

source_name: aortic smooth muscle cells

growth_protocol: Mouse and rat aortic smooth muscle cells (mSMC) were cultured in growth medium (DMEM: F12, Gibco, 11320-033) supplemented with fetal bovine serum (10%, Corning, 35-015-CV), L-glutamine (1.6 mM, Gibco, 25030081), and penicillin-streptomycin (100 U/mL, Gibco, 15140122) in a humidified sterile incubator at 37 C with 5% CO2. . For all experiments, mouse and rat SMCs were starved in serum-free media supplemented with L-glutamine (1.6 mM, Gibco, 25030081), Apo-Transferrin (5 mg/ml, Sigma Aldrich, T5391), L-ascorbic acid (0.2 mM, Sigma Aldrich, A4403), and Na Selenite (6.25 ng/ml, Sigma-Aldrich, S5261) for 48 hours.

extract_protocol:
Total RNA was extracted, and column-purified using RNeasy Mini Kit (Qiagen, 74104) based on the manufacturer’s protocol. Genomic DNA was removed using DNase I (Qiagen). RNA quantification was performed using nanodrop (ThermoFisher).
Libraries were sequenced with illumina NextSeq High Output 150 cycle kit (2 x 75 bp) with reading depth of 20 million reads per sample.

treatment_protocol:
GapmeR transfections were performed using Fugene HD transfection reagent (Promega, PRE2311) and Opti-MEM reduced-serum medium (Fisher, 31985062). siRNA transfection was performed with Lipofectamine RNAiMax transfection reagent (Invitrogen, 31985062) and Opti-MEM reduced serum medium (Fisher, 31985062). Gapmers and plasmids DNA were transfected at 1ug/mL while siRNA control was transfected at 10 ng/mL. All transfections were performed for at least 24 hours prior to the experimental endpoints.
Human Platelet-Derived Growth Factor-BB (PDGF-BB; Sigma Aldrich, SRP3138) recombinant was reconstituted in 10 mM Acetic Acid and used at 10-30 ng/ml for treatment. Human Angiotensin II (Sigma Aldrich, A9525-50MG) recombinant was reconstituted in distilled water and used at 10ng/ml for treatment. Cells were treated for 24 hours.

value: aortic smooth muscle cells

value: Knockdown long CASC22

value: no treatment


title: Casp3⁻/⁻ P815 cells Control, rep2

description: Library name: Sample2

value: Mastocytoma

value: Control


title: lung alveolar organoid, Manf knockout, plate1-2 well E11

description: Library name: 1-2_E11_MANF

value: Manf CRISPR/Cas9 knockout


title: CD8+ T cell transduced with Runx3-LOV* construct replicate 2

description:
Library name: LOV_REP2
See corresponding column

value: primary cell

value: primary CD8+ T cells were isolated from splenocytes

value: C57BL/6J mice

value: transduced with Runx3-LOV* construct


title: Murine aortic smooth muscle cellswith Knockdown long CASC21 and no treatment; P18

description:
Library name: seqrun3_KD_lCAS_no-trt_rep3
Column name in rsem.merged.gene_counts.tsv: seqrun3_KD_lCAS_no-trt_rep3

value: Knockdown long CASC21


title: breast cancer_SM263

value: IIB

value: Tissue


title: lung alveolar organoid, Inhba knockout, plate1-2 well E10

description: Library name: 1-2_E10_INHBA

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Inhba CRISPR/Cas9 knockout


title: Murine aortic smooth muscle cellswith Knockdown long CASC20 and no treatment; P17

description:
Library name: seqrun3_KD_lCAS_no-trt_rep2
Column name in rsem.merged.gene_counts.tsv: seqrun3_KD_lCAS_no-trt_rep2

value: Knockdown long CASC20


title: lung alveolar organoid, Ulk1 knockout, plate1-2 well E09

description: Library name: 1-2_E09_ULK1

value: Ulk1 CRISPR/Cas9 knockout


title: CD8+ T cell transduced with Runx3-FlAsH tag construct replicate 2

description:
Library name: FT_REP2
See corresponding column


title: lung alveolar organoid, Nfe2l2 knockout, plate1-2 well E08

description: Library name: 1-2_E08_NFE2L2

value: Nfe2l2 CRISPR/Cas9 knockout


title: breast cancer_SM260

value: P

value: N

value: IIA

value: Surgical Tissue Sample


title: Murine aortic smooth muscle cellswith Knockdown long CASC18 and Angiotensin II; P19

description:
Library name: seqrun3_KD_lCAS_angio2_rep4
Column name in rsem.merged.gene_counts.tsv: seqrun3_KD_lCAS_angio2_rep4

value: aortic smooth muscle cells

value: Knockdown long CASC18

value: Angiotensin II


title: lung alveolar organoid, Usp30 knockout, plate1-2 well E07

description: Library name: 1-2_E07_USP30

value: Usp30 CRISPR/Cas9 knockout


title: CD8+ T cell transduced with empty vector replicate 2

description:
Library name: EV_REP2
See corresponding column

value: primary cell

value: primary CD8+ T cells were isolated from splenocytes

value: C57BL/6J mice

value: transduced with empty vector


title: Murine aortic smooth muscle cellswith Knockdown long CASC17 and Angiotensin II; P18

description:
Library name: seqrun3_KD_lCAS_angio2_rep3
Column name in rsem.merged.gene_counts.tsv: seqrun3_KD_lCAS_angio2_rep3

value: Knockdown long CASC17


title: lung alveolar organoid, Nkx21 knockout, plate1-2 well E06

description: Library name: 1-2_E06_NKX21

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Nkx21 CRISPR/Cas9 knockout


title: CD8+ T cell transduced with empty vector replicate 1

description:
Library name: EV_REP1
See corresponding column


title: breast cancer_SM255

value: L

value: III

value: Cytology

value: Needle Biopsy Sample


title: Murine aortic smooth muscle cellswith Knockdown long CASC16 and Angiotensin II; P17

description:
Library name: seqrun3_KD_lCAS_angio2_rep2
Column name in rsem.merged.gene_counts.tsv: seqrun3_KD_lCAS_angio2_rep2

value: Knockdown long CASC16


title: lung alveolar organoid, Twist1 knockout, plate1-2 well E05

description: Library name: 1-2_E05_TWIST1

value: Twist1 CRISPR/Cas9 knockout


title: CD8+ T cell transduced with Runx3-APEX2 construct replicate 2

description:
Library name: APEX_REP2
See corresponding column

value: transduced with Runx3-APEX2 construct


title: breast cancer_SM254

value: P

value: N

value: IIA

value: Tissue

value: Surgical Tissue Sample


title: breast cancer_SM264


title: CD8+ T cell transduced with Runx3-LOV* construct replicate 1

description:
Library name: LOV_REP1
See corresponding column

value: primary cell

value: primary CD8+ T cells were isolated from splenocytes

value: C57BL/6J mice

value: transduced with Runx3-LOV* construct


title: Murine aortic smooth muscle cellswith Knockdown long CASC15 and Angiotensin II; P16

description:
Library name: seqrun3_KD_lCAS_angio2_rep1
Column name in rsem.merged.gene_counts.tsv: seqrun3_KD_lCAS_angio2_rep1

value: aortic smooth muscle cells

value: Knockdown long CASC15

value: Angiotensin II


title: lung alveolar organoid, Sox4 knockout, plate1-2 well E04

description: Library name: 1-2_E04_SOX4

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Sox4 CRISPR/Cas9 knockout


title: breast cancer_SM262

value: III

value: Needle Biopsy Sample


title: breast cancer_SM252

value: I

value: Cytology


title: d20 normoxia replicate 1

value: kidney organoid

value: Normoxia


title: Murine aortic smooth muscle cellswith Knockdown long CASC19 and no treatment; P16

description:
Library name: seqrun3_KD_lCAS_no-trt_rep1
Column name in rsem.merged.gene_counts.tsv: seqrun3_KD_lCAS_no-trt_rep1

value: Knockdown long CASC19

value: no treatment


title: CD8+ T cell transduced with Runx3-FlAsH tag construct replicate 1

description:
Library name: FT_REP1
See corresponding column

value: primary cell


title: CD8+ T cell transduced with Runx3-APEX2 construct replicate 1

description:
Library name: APEX_REP1
See corresponding column

value: primary CD8+ T cells were isolated from splenocytes

value: transduced with Runx3-APEX2 construct


title: Murine aortic smooth muscle cellswith Knockdown control and PDGF-BB; P19

description:
Library name: seqrun3_KD_ctrl_pdgfBB_rep4
Column name in rsem.merged.gene_counts.tsv: seqrun3_KD_ctrl_pdgfBB_rep4

value: Knockdown control

value: PDGF-BB


title: breast cancer_SM290

value: P

value: N

value: IIB

value: Tissue

value: Surgical Tissue Sample


title: lung alveolar organoid, Tigit knockout, plate1-2 well E03

description: Library name: 1-2_E03_TIGIT

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Tigit CRISPR/Cas9 knockout


title: Tumor, GEX

city: Minneapolis

first: Ingunn

last: Stromnes

state: Minnesota

address: 2-186 Wallin Medical Biosciences Building, 2101 6th St SE

department: Medical School

institute: University of Minnesota

description: Library name: Tumor_GEX

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were preprocessed and demultiplexed using CellRanger multi (v8.0.0; 10x Genomics) with cell-multiplexing oligo (CMO) references (Supplementary Table 1) and a tumor-specific configuration file. Mapped BAM files for each tumor sample (TIL_1 through TIL_4) were converted to fastq format using bamtofastq (v1.4.1) and reprocessed individually using CellRanger multi against the mouse reference genome (mm10, Ensembl v98).
Assembly: mm10 Ensembl mouse v98
Supplementary files format and content: tumor_barcodes.tsv.gz cell-level data from cellranger run
Supplementary files format and content: tumor_features.tsv.gz cell-level data from cellranger run
Supplementary files format and content: tumor_matrix.mtx.gz cell-level data from cellranger run

molecule: polyA RNA

source_name: Tumor

extract_protocol:
Spleen and tumor single cell suspensions were prepared. Immune cells were enriched from the tumor single cell suspensions using a 44/67% percoll density gradient. Briefly, samples were resuspended in 3 mL of 44% percoll in a 15 mL conical tube and then underlaid with 3 mL of 67% percoll using a glass Pasteur pipette. Samples were centrifuged for 20 minutes at 600 x g at 22°C with an acceleration of 1 and brake of 0. After spinning, cells at the density interface were isolated with a P100 pipette and transferred to 20 mL of complete media for washing. T cells were enriched from the percoll sample using a mouse pan T cell negative selection kit (Miltenyi Biotec 130-095-130). For each tissue (tumor or spleen) samples from individual treatment groups (control, aTNFa, dual, triple) were stained with unique hashtags (TotalSeq C, Biolegend) at a concentration of 0.2 mg per 1 x 106 cells. Next, samples were pooled by tissue containing the 4 treatment groups for proceeding with 2 independent captures. magnetic enrichment or orthotopic KPC2 PDA tumors using collagenase digestion and percoll enrichment. Samples were uniquely barcoded with oligo tagged antibodies prior to capture and single cell RNA sequencing.
Cells were captured and the library was constructed with the 10X Genomics Chromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index) according to the manufacturer's instructions.

value: Tumor

tag: library type

value: Gene Expression (GEX)

value: Pooled sample (untreated (Untx), aTNFa, aPD-L1 & agCD40 ,aPD-L1 & agCD40 & aTNFa)

tag: fb

value: TotalSeq-C0301 anti-mouse Tumor-Untx, TotalSeq-C0302 anti-mouse Tumor-aTNFa, TotalSeq-C0303 anti-mouse Tumor-aPDL1_agCD40, TotalSeq-C0304 anti-mouse Tumor-aPDL1_agCD40_aTNFa


title: lung alveolar organoid, Chrm3 knockout, plate1-2 well G05

description: Library name: 1-2_G05_CHRM3

value: Chrm3 CRISPR/Cas9 knockout


title: Isocortex, Hippocampus, 6h, NMEC, rep1

description:
Library name: Sample 4
10x Genomics

value: Isocortex, Hippocampus

value: infected, NMEC, 6h


title: lung alveolar organoid, Cacna2d3 knockout, plate1-2 well G04

description: Library name: 1-2_G04_CACNA2D3

value: Cacna2d3 CRISPR/Cas9 knockout


title: breast cancer_SM251

value: I

value: Cytology


title: mouse HSPCs with shRen rep3, treated with FAS, batch5

city: Chengdu

first: Yiman

last: Peng

state: Sichuan

address: No.1, Keyuan 4th Road, Gaopeng Avenue, Chengdu, Sichuan, China

department: State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University

institute: Sichuan University

description: Library name: shRen_FAS_rep3

data_processing:
For RNA-Seq, after removing the adapters, ploy-N, and low-quality reads, clean data were aligned against the reference mouse genome (mm10) using STAR_2.7.10b. Following this, raw counts were normalized and significance scores as well as log2-fold change values were calculated using the DESeq2 (v1.26.0).
Assembly: mm10
Supplementary files format and content: csv files include raw counts and DESeq2 normalized data of RNAseq.

source_name: HSPC

growth_protocol: For Utx KO/WT samples, WBM cells were freshly isolated from Utxf/f and Utxf/f; Mx1-Cre mice, and then HSPCs were sorted with mouse CD117 magnetic microbeads. Primary mouse cells were cultured in BCM medium (50% IMDM+50% DMEM+10% FBS+5% PS+0.34% BME) with 10% Stem Cell Medium (SCM) including 10% FBS, IL3 (10ng/mL; 1:1000), IL6 (10ng/mL; 1:500), and SCF (50ng/mL; 1:1000). For other RNA-Seq samples, mouse cKit+ HSPCs and AML cells were cultured at 37 °C with 7.5% CO2 in BCM medium [45% IMDM + 45% DMEM + 10% FBS + 50 × 10-6 M β-mercaptoethanol + penicillin (100 U mL-1)/streptomycin (0.1 mg mL-1)] supplemented with 10% stem cell medium (SCM) including mIL-3 (10 ng mL-1, Cat# 403-ML; R&D Systems), mIL-6 (10 ng mL-1, Cat# 406-ML; R&D Systems), and mSCF (50 ng mL-1, Cat# 455-MC; R&D Systems)

extract_protocol: RNA-seq libraries were constructed using an Illumina stranded mRNA sample preparation kits (NEB, E7770) according to the manufacturer's protocol.

value: HSPC

value: shRen

value: FAS


title: breast cancer_SM284

value: P

value: N

value: IIA

value: Tissue


title: lung alveolar organoid, Pid1 knockout, plate1-2 well G02

description: Library name: 1-2_G02_PID1

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Pid1 CRISPR/Cas9 knockout


title: Murine aortic smooth muscle cellswith Knockdown control and PDGF-BB; P18

description:
Library name: seqrun3_KD_ctrl_pdgfBB_rep3
Column name in rsem.merged.gene_counts.tsv: seqrun3_KD_ctrl_pdgfBB_rep3

value: aortic smooth muscle cells

value: Knockdown control

value: PDGF-BB


title: Isocortex, Hippocampus, 6h, PBS, rep3

description:
Library name: Sample 3
10x Genomics

value: Isocortex, Hippocampus

value: infected, PBS, 6h


title: Isocortex, Hippocampus, 6h, PBS, rep2

description:
Library name: Sample 2
10x Genomics


title: Tumor, FB

description: Library name: Tumor_FB

molecule: protein

value: Tumor

value: Feature Barcode (FB) Multiplexing capture

value: Pooled sample (untreated (Untx), aTNFa, aPD-L1 & agCD40 ,aPD-L1 & agCD40 & aTNFa)

value: TotalSeq-C0301 anti-mouse Tumor-Untx, TotalSeq-C0302 anti-mouse Tumor-aTNFa, TotalSeq-C0303 anti-mouse Tumor-aPDL1_agCD40, TotalSeq-C0304 anti-mouse Tumor-aPDL1_agCD40_aTNFa


title: lung alveolar organoid, Serpina1a knockout, plate1-2 well G03

description: Library name: 1-2_G03_SERPINA1A

value: Serpina1a CRISPR/Cas9 knockout


title: breast cancer_SM248

value: III

value: Needle Biopsy Sample


title: lung alveolar organoid, Rad21 knockout, plate1-2 well F11

description: Library name: 1-2_F11_RAD21

value: Rad21 CRISPR/Cas9 knockout


title: lung alveolar organoid, Tfcp2l1 knockout, plate1-2 well E02

description: Library name: 1-2_E02_TFCP2L1

value: Tfcp2l1 CRISPR/Cas9 knockout


title: breast cancer_SM257

value: P

value: N

value: Tissue


title: lung alveolar organoid, Il1a knockout, plate1-2 well D11

description: Library name: 1-2_D11_IL1A

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Il1a CRISPR/Cas9 knockout


title: Murine aortic smooth muscle cellswith Knockdown control and PDGF-BB; P17

description:
Library name: seqrun3_KD_ctrl_pdgfBB_rep2
Column name in rsem.merged.gene_counts.tsv: seqrun3_KD_ctrl_pdgfBB_rep2

value: aortic smooth muscle cells

value: Knockdown control

value: PDGF-BB


title: breast cancer_SM247

value: IIB

value: Cytology


title: D27_2F_2

city: San Francisco

last: Mohapatra

department: Medicine

institute: University of California, San Francisco

hyb_protocol: A total of 429 genes were included in the analysis. Gene panel probe hybridization occurred overnight for 16 hours at 50o C. Slides were washed to remove unbound probes. Ligase was added to circularize the paired ends of bound probes (2 hours at 37o C), followed by enzymatic rolling circle amplification (2 hours at 30o C). Slides were washed in TE buffer before cell segmentation staining (16 hours at 4o C). Background fluorescence was then chemically quenched.

scan_protocol: Image processing, decoding, quality score generation, and cell segmentation was automatically performed by the Xenium Analyzer system. Data was acquired on instrument software version 4.0.1.4 and analysis version xenium-4.0.1.0.

data_processing: Xenium Onboard Analysis: 4.0.1.0. R using Seurat 5.4.0 and SpNeigh 0.99.42 packages.

extract_protocol: tissue preparation protocol: Lung sections were cut at a thickness of 5 mm and placed onto a Xenium slide followed by deparaffinization and decrosslinking

value: lung

tag: tissue preservation method

value: FFPE

tag: mtb strain

tag: mouse strain

tag: mtb infection duration

value: 27 days

tag: Sex

value: female


title: Murine aortic smooth muscle cellswith Knockdown control and PDGF-BB; P16

description:
Library name: seqrun3_KD_ctrl_pdgfBB_rep1
Column name in rsem.merged.gene_counts.tsv: seqrun3_KD_ctrl_pdgfBB_rep1

tag: cell type


title: Casp3-/-Mlkl-/-Bid-/- P815 cells Control, rep1

description: Library name: Sample1

tag: cell line

value: Mastocytoma

value: Control


title: lung alveolar organoid, Fgf7 knockout, plate1-2 well D10

description: Library name: 1-2_D10_FGF7

tag: genotype

value: Fgf7 CRISPR/Cas9 knockout

tag: batch


title: D27_2F_1


title: breast cancer_SM245

tag: er status

value: P

tag: pr status

tag: her2 status

value: IIA

value: Needle Biopsy Sample


title: lung alveolar organoid, Tfeb knockout, plate1-2 well D09

description: Library name: 1-2_D09_TFEB

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Tfeb CRISPR/Cas9 knockout


title: Murine aortic smooth muscle cellswith Knockdown control and no treatment; P19

description:
Library name: seqrun3_KD_ctrl_no-trt_rep4
Column name in rsem.merged.gene_counts.tsv: seqrun3_KD_ctrl_no-trt_rep4

value: aortic smooth muscle cells

value: no treatment


title: D27_1M_2

value: male


title: Murine aortic smooth muscle cellswith Knockdown control and no treatment; P18

description:
Library name: seqrun3_KD_ctrl_no-trt_rep3
Column name in rsem.merged.gene_counts.tsv: seqrun3_KD_ctrl_no-trt_rep3

value: Knockdown control


title: lung alveolar organoid, Keap1 knockout, plate1-2 well D08

description: Library name: 1-2_D08_KEAP1

value: Keap1 CRISPR/Cas9 knockout


title: breast cancer_SM243

value: N

tag: ajcc stage

value: III

tag: sample collection type

value: Tissue

tag: setting of sample collection

value: Surgical Tissue Sample


title: breast cancer_SM242


title: lung alveolar organoid, Tigit knockout, plate1-2 well D07

description: Library name: 1-2_D07_TIGIT

value: Tigit CRISPR/Cas9 knockout


title: breast cancer_SM237


title: lung alveolar organoid, Tns1 knockout, plate1-2 well D05

description: Library name: 1-2_D05_TNS1

value: Tns1 CRISPR/Cas9 knockout


title: breast cancer_SM239


title: Murine aortic smooth muscle cellswith Knockdown control and Angiotensin II; P19

description:
Library name: seqrun3_KD_ctrl_angio2_rep4
Column name in rsem.merged.gene_counts.tsv: seqrun3_KD_ctrl_angio2_rep4

tag: treatment

value: Angiotensin II


title: breast cancer_SM236

value: P

value: IIB


title: Murine aortic smooth muscle cellswith Knockdown control and no treatment; P17

description:
Library name: seqrun3_KD_ctrl_no-trt_rep2
Column name in rsem.merged.gene_counts.tsv: seqrun3_KD_ctrl_no-trt_rep2


title: D27_1M_1

tag: tissue

value: lung

value: FFPE

value: 27 days


title: lung alveolar organoid, Ttf1 knockout, plate1-2 well D06

description: Library name: 1-2_D06_TTF1

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Ttf1 CRISPR/Cas9 knockout


title: breast cancer_SM232


title: Murine aortic smooth muscle cellswith Knockdown control and Angiotensin II; P18

description:
Library name: seqrun3_KD_ctrl_angio2_rep3
Column name in rsem.merged.gene_counts.tsv: seqrun3_KD_ctrl_angio2_rep3

value: aortic smooth muscle cells


title: Murine aortic smooth muscle cellswith Knockdown control and Angiotensin II; P17

description:
Library name: seqrun3_KD_ctrl_angio2_rep2
Column name in rsem.merged.gene_counts.tsv: seqrun3_KD_ctrl_angio2_rep2

value: Knockdown control


title: lung alveolar organoid, Npnt knockout, plate1-2 well D03

description: Library name: 1-2_D03_NPNT

value: Npnt CRISPR/Cas9 knockout


title: breast cancer_SM231

value: N

value: Cytology

value: Needle Biopsy Sample


title: Murine aortic smooth muscle cellswith Knockdown control and Angiotensin II; P16

description:
Library name: seqrun3_KD_ctrl_angio2_rep1
Column name in rsem.merged.gene_counts.tsv: seqrun3_KD_ctrl_angio2_rep1


title: breast cancer_SM227

value: Tissue


title: lung alveolar organoid, Ror1 knockout, plate1-2 well D02

description: Library name: 1-2_D02_ROR1

value: Ror1 CRISPR/Cas9 knockout


title: Murine aortic smooth muscle cellswith Overexpression total CASC17 and no treatment; P19

description:
Library name: seqrun2_OE_tCAS_no-trt_rep3
Column name in rsem.merged.gene_counts.tsv: seqrun2_OE_tCAS_no-trt_rep3

value: Overexpression total CASC17

value: no treatment


title: lung alveolar organoid, Pla2g15 knockout, plate1-2 well C11

description: Library name: 1-2_C11_PLA2G15

value: Pla2g15 CRISPR/Cas9 knockout


title: breast cancer_SM225

value: P

value: III


title: breast cancer_SM222

value: I

value: Surgical Tissue Sample


title: breast cancer_SM219


title: Murine aortic smooth muscle cellswith Overexpression total CASC16 and no treatment; P18

description:
Library name: seqrun2_OE_tCAS_no-trt_rep2
Column name in rsem.merged.gene_counts.tsv: seqrun2_OE_tCAS_no-trt_rep2

value: Overexpression total CASC16


title: Murine aortic smooth muscle cellswith Overexpression control and no treatment; P19

description:
Library name: seqrun2_OE_ctrl_no-trt_rep3
Column name in rsem.merged.gene_counts.tsv: seqrun2_OE_ctrl_no-trt_rep3

value: Overexpression control


title: lung alveolar organoid, Prkn knockout, plate1-2 well C08

description: Library name: 1-2_C08_PRKN

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Prkn CRISPR/Cas9 knockout


title: PD-NC4 E212m subclone 3

first: Megan

last: Mahlke

address: 5115 Centre Ave

institute: UPMC

description:
Library name: PD-NC4 E212m subclone 3
This data was aligned to the PDNC4 chromosome 4 assembly.

library_source: genomic

data_processing:
aligned to PD-NC4 or T2T assembly with Bwa, Peak calling with MACS2
Assembly: T2T CHM13 v 2.0 (GCF_009914755.1), PD-NC4 Chr4 assembly (https://www.biorxiv.org/content/10.64898/2025.12.23.696241v1.full)
Supplementary files format and content: bigwig, CENP-A read pileup
Library strategy: CUT&Run

molecule: genomic DNA

extract_protocol:
ChIP-seq or CUT&RUN antibody-directed DNA isolation
NEB Next Ultra II

value: fibroblast


title: Murine aortic smooth muscle cellswith Overexpression total CASC15 and no treatment; P17

description:
Library name: seqrun2_OE_tCAS_no-trt_rep1
Column name in rsem.merged.gene_counts.tsv: seqrun2_OE_tCAS_no-trt_rep1

value: aortic smooth muscle cells

value: Overexpression total CASC15


title: Murine aortic smooth muscle cellswith Overexpression control and no treatment; P18

description:
Library name: seqrun2_OE_ctrl_no-trt_rep2
Column name in rsem.merged.gene_counts.tsv: seqrun2_OE_ctrl_no-trt_rep2


title: lung alveolar organoid, Tigit knockout, plate1-2 well C09

description: Library name: 1-2_C09_TIGIT

value: Tigit CRISPR/Cas9 knockout


title: breast cancer_SM216

value: N

value: Tissue


title: lung alveolar organoid, Il1a knockout, plate1-2 well C07

description: Library name: 1-2_C07_IL1A

value: Il1a CRISPR/Cas9 knockout


title: lung alveolar organoid, Bmp10 knockout, plate1-2 well C10

description: Library name: 1-2_C10_BMP10

value: Bmp10 CRISPR/Cas9 knockout


title: breast cancer_SM217


title: Murine aortic smooth muscle cellswith Overexpression control and no treatment; P17

description:
Library name: seqrun2_OE_ctrl_no-trt_rep1
Column name in rsem.merged.gene_counts.tsv: seqrun2_OE_ctrl_no-trt_rep1

value: no treatment


title: PD-NC4 E212m subclone 1

description:
Library name: PD-NC4 E212m subclone 1
This data was aligned to the PDNC4 chromosome 4 assembly.


title: lung alveolar organoid, Trp63 knockout, plate1-2 well C06

description: Library name: 1-2_C06_TRP63

value: Trp63 CRISPR/Cas9 knockout


title: breast cancer_SM215

value: P

value: III

value: Needle Biopsy Sample


title: Murine aortic smooth muscle cellswith Knockdown total CASC16 and no treatment; P18

description:
Library name: seqrun2_KD_tCAS_no-trt_rep2
Column name in rsem.merged.gene_counts.tsv: seqrun2_KD_tCAS_no-trt_rep2

value: Knockdown total CASC16


title: lung alveolar organoid, Sftpd knockout, plate1-2 well C05

description: Library name: 1-2_C05_SFTPD

value: Sftpd CRISPR/Cas9 knockout


title: PD-NC4 C212m subclone 3

description:
Library name: PD-NC4 C212m subclone 3
This data was aligned to the PDNC4 chromosome 4 assembly.


title: breast cancer_SM214

value: IIB


title: Murine aortic smooth muscle cellswith Knockdown total CASC15 and no treatment; P17

description:
Library name: seqrun2_KD_tCAS_no-trt_rep1
Column name in rsem.merged.gene_counts.tsv: seqrun2_KD_tCAS_no-trt_rep1

value: Knockdown total CASC15


title: PD-NC4 C212m subclone 2

description:
Library name: PD-NC4 C212m subclone 2
This data was aligned to the PDNC4 chromosome 4 assembly.

value: fibroblast


title: lung alveolar organoid, Huwe1 knockout, plate1-2 well C04

description: Library name: 1-2_C04_HUWE1

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Huwe1 CRISPR/Cas9 knockout


title: breast cancer_SM213


title: Murine aortic smooth muscle cellswith Knockdown control GapmeR and no treatment; P18

description:
Library name: seqrun2_KD_ctrl_no-trt_rep2
Column name in rsem.merged.gene_counts.tsv: seqrun2_KD_ctrl_no-trt_rep2

value: aortic smooth muscle cells

value: Knockdown control GapmeR


title: breast cancer_SM211

value: N

value: IIA

value: Cytology


title: Murine aortic smooth muscle cellswith Knockdown control GapmeR and no treatment; P17

description:
Library name: seqrun2_KD_ctrl_no-trt_rep1
Column name in rsem.merged.gene_counts.tsv: seqrun2_KD_ctrl_no-trt_rep1

value: no treatment


title: lung alveolar organoid, Mecom knockout, plate1-2 well C03

description: Library name: 1-2_C03_MECOM

value: Mecom CRISPR/Cas9 knockout


title: PD-NC4 C212m subclone 1

description:
Library name: PD-NC4 C212m subclone 1
This data was aligned to the PDNC4 chromosome 4 assembly.


title: lung alveolar organoid, Tead1 knockout, plate1-2 well C02

description: Library name: 1-2_C02_TEAD1

value: Tead1 CRISPR/Cas9 knockout


title: breast cancer_SM209

value: P

value: Tissue

value: Surgical Tissue Sample


title: lung alveolar organoid, Ccbe1 knockout, plate1-2 well B10

description: Library name: 1-2_B10_CCBE1

value: Ccbe1 CRISPR/Cas9 knockout


title: PD-NC4 C2Y subclone 1

description:
Library name: PD-NC4 C2Y subclone 1
This data was aligned to the PDNC4 chromosome 4 assembly.


title: FPC, 0.05% Chol, 24 weeks

city: Los Angeles

first: Ana

middle: C

last: Maretti-Mira

address: 1450 Biggy Street, NRT 3514

institute: USC

description:
Library name: FNA_1_C
10X Genomics

data_processing:
Raw data processing: Cell by gene count matrices were generated by processing FASTQ files using the Cell Ranger count pipeline (version 9.0.1, 10X Genomics) with the GRCm39 mouse reference genome (GRCm39-2024-A, 10X Genomics) for each sample. Count matrices were corrected for ambient RNA contamination using SoupX with default parameters. Quality control was performed using Seurat (version 5.3) in a two-step process. First, genes detected in fewer than 3 cells were removed. Second, low-quality cells were filtered by removing cells with fewer than 500 UMIs, fewer than 300 detected genes, and greater than 10% mitochondrial reads.
Data integration: Samples were integrated into a unified data set using sctransform normalization and Harmony (version 1.2.3) integration implemented in Seurat. Differences in mitochondrial gene content among cells were corrected during normalization by regressing out the percentage of mitochondrial reads using the vars.to.regress parameter in the SCTransform function. Clustering was performed using the first 30 PCs as input dimensions for the Seurat FindNeighbors function. Optimal clustering resolution was determined by evaluating a range of resolution values from 0 to 1 (by increments of 0.1) using the R package clustree (version 0.5.1) and a final resolution value of 0.4 was selected for downstream analysis. Clusters were embedded in two-dimensional space using UMAP and visualized in Seurat.
Cell annotation: Cell types were annotated manually by examining the expression of canonical marker genes across each cluster.
Assembly: GRCm39-2024-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: liver

extract_protocol:
FNA procedure: FNA was performed with a 0.60 × 25 needle coupled to a 10 ml syringe, which was attached to a hand-grip syringe holder. The procedure consisted of the introduction of the needle into the tissue and suction while moving the needle back and forth repeatedly. Enough material was considered to have been obtained when the hub of the needle was filled with aspirate, then pressure applied on the syringe was released, and the needle is removed from the lesion. We harvested tissue from the 4 largest lobes of the liver (Right Lobe, Left Lobe, and 2 Middle Lobes). FNAs were placed into RPMI+10% FBS and kept on ice until processing. Cell dissociation: FNA biopsies were added to 10mL of liver digestion buffer pre-heated to 37°C. The liver digestion buffer was composed of 0.05% Collagenase type IV (Cat#17104-019, Gibco,) and 0.02% DNase (Cat#DN25, Sigma-Aldrich) in RPMI 1640 (Cat#22440, Invitrogen). Biopsies were dissociated into single-cell suspension for 15 minutes at 37°C on rocker. Red cells were removed using 1X BD Pharm Lyse™ Lysing Buffer (Cat#555899, BD Biosciences) and dead cells were removed using Dead Cell Removal Kit microbead solution (Cat#130–090-101, Miltenyi Biotech). Viable cells were particioned using 10x Chromium Controller and kit 3' v3.1.
Library was performed according to the manufacter’s instructions

treatment_protocol: Two groups of mice (n = 3 each) were fed the Fructose, Palmitate, Cholesterol, and Trans-Fat (FPC) diet with varying cholesterol content for a total of 32 weeks. During the first 24 weeks (Progression phase), one group received low dietary cholesterol (0.05%), and the other received high cholesterol (1.25%). At week 24, they transitioned to an FPC diet with 0.05% cholesterol for an additional 8 weeks (Intervention phase).

value: liver

value: non-parenchymal

value: FPC, 0.05% Chol, 24 weeks


title: lung alveolar organoid, Eif2ak3 knockout, plate1-2 well B09

description: Library name: 1-2_B09_EIF2AK3

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Eif2ak3 CRISPR/Cas9 knockout


title: FPC, 1.25% Chol, 24 weeks

description:
Library name: FNA_1_A
10X Genomics

value: FPC, 1.25% Chol, 24 weeks


title: lung alveolar organoid, Pink1 knockout, plate1-2 well B08

description: Library name: 1-2_B08_PINK1

value: Pink1 CRISPR/Cas9 knockout


title: breast cancer_SM201

value: N

value: I


title: Citrobactor infected SpiB+ epithelila cells, scRNAseq, rep4

city: Brisbane

first: M. Zeeshan

last: Chaudhry

state: Queensland

address: 37 Kent Street

institute: The University of Queensland

data_processing:
RunHarmony 19 wrapped in Seurat was performed using the 30PCs to integrate data sets from each batch. The first 40 harmony dimension reductions were applied to construct a shared nearest neighbour graph and FindClusters with Louvain algorithms using a standard Seurat analysis pipeline. Uniform manifold approximation and projection (UMAP) was also generated with the first 40 harmony dimension reductions to embed the data sets into two dimensions for visualization.
To annotate each cluster, we used FindAllMarkers in Seurat to find marker genes for each cluster. We also checked the expression level of marker genes of expected cell type cells from literatures.
Differential expression (DE) analysis between M cells and Tuft cells, and between cells from different locations including PP, SI and LI compared to other M cells without any stimulus was performed with MAST 20. Genes with P values < 0.01 were regarded as DE genes. Adjusted P values were then used in volcano plots. GO analysis was conducted on up-regulated genes using goana in limma (3.50.3)
Assembly: ScRNA-sequencing reads were mapped to the GRCm38.p8 mouse genome and external RNA controls consortium (ERCC) spike-in sequences using the Subread aligner (v2.4.3)13 and assigned to genes using scPipe (v1.12.0) 14 with GENCODE 38 primary assembly annotation
Supplementary files format and content: sce file containing the raw count for each individual cell
Supplementary files format and content: sce file containing the raw count for each individual cell

source_name: Peyer's patch, small intestine and large intestine

extract_protocol:
Single-cell (sc)-RNA-seq using a modified CEL-Seq2 protocol. Cell were sorted into into a chilled 384-well PCR plate (Greiner, 785290) containing 1.2μl of primer/lysis mix [20 nM indexed polydT primer (custom made, IDT), 1:6.000.000 dilution of ERCC RNA spike-in mix (Ambion - 4456740), 1 mM dNTPs (NEB - N0446S), 1.2 units SUPERaseIN Rnase Inhibitor (Thermo Fisher - AM2696), 0.2 % Triton X-100 solution (Sigma Aldrich – 93443-100ml), DEPC water (Thermo Fisher - AM9920)]
Single cell transcriptome libraries were generated by adapting the CelsSeq2 protocol [Hashimshony et al., 2016] as follows: Samples were pooled after first strand cDNA synthesis, treated with Exonuclease 1 for 30 minutes, followed by a 1.2X bead clean-up. Second strand synthesis was performed using NEBNext Second Strand Synthesis module (NEB #E6111S) in a final reaction volume of 20 ul and NucleoMag NGS Clean-up and Size select magnetic beads (Macherey-Nagel - 7449970.5) were used for all DNA purification and size selection steps.]

value: Citrobactor


title: breast cancer_SM200


title: PD-NC4 C2Y subclone 2

description:
Library name: PD-NC4 C2Y subclone 2
This data was aligned to the PDNC4 chromosome 4 assembly.

value: fibroblast


title: Citrobactor infected SpiB+ epithelila cells, scRNAseq, rep3

value: Peyer's patch, small intestine and large intestine


title: lung alveolar organoid, Trp53 knockout, plate1-2 well B06

description: Library name: 1-2_B06_TRP53

value: Trp53 CRISPR/Cas9 knockout


title: breast cancer_SM195

value: P

value: IIA

value: Cytology


title: lung alveolar organoid, Tdtomato knockout, plate1-2 well B05

description: Library name: 1-2_B05_TDTOMATO

value: Tdtomato CRISPR/Cas9 knockout


title: Citrobactor infected SpiB+ epithelila cells, scRNAseq, rep2


title: breast cancer_SM194

value: Tissue

value: Needle Biopsy Sample


title: Citrobactor infected SpiB+ epithelila cells, scRNAseq, rep1


title: lung alveolar organoid, Glis3 knockout, plate1-2 well B03

description: Library name: 1-2_B03_GLIS3

value: Glis3 CRISPR/Cas9 knockout


title: breast cancer_SM193

value: Surgical Tissue Sample


title: Salmoenlla infected SpiB+ epithelila cells, scRNAseq, rep4

value: Salmoenella


title: breast cancer_SM192


title: lung alveolar organoid, Met knockout, plate1-2 well B02

description: Library name: 1-2_B02_MET

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Met CRISPR/Cas9 knockout


title: lung alveolar organoid, Tigit knockout, plate1-1 well G11

description: Library name: 1-1_G11_TIGIT

value: Tigit CRISPR/Cas9 knockout


title: Salmoenlla infected SpiB+ epithelila cells, scRNAseq, rep3


title: breast cancer_SM188

value: N

value: III


title: lung alveolar organoid, Tdtomato knockout, plate1-1 well G10

description: Library name: 1-1_G10_TDTOMATO


title: breast cancer_SM187

value: IIB


title: Salmoenlla infected SpiB+ epithelila cells, scRNAseq, rep1

value: Peyer's patch, small intestine and large intestine


title: lung alveolar organoid, Becn1 knockout, plate1-1 well G09

description: Library name: 1-1_G09_BECLN1

value: Becn1 CRISPR/Cas9 knockout


title: breast cancer_SM186

value: P

value: IV


title: lung alveolar organoid, Ern1 knockout, plate1-1 well G08

description: Library name: 1-1_G08_ERN1

value: Ern1 CRISPR/Cas9 knockout


title: breast cancer_SM185

value: I


title: naïve SpiB+ epithelila cells, scRNAseq, rep3


title: naïve SpiB+ epithelila cells, scRNAseq, rep2


title: breast cancer_SM184

value: IIA

value: Tissue


title: lung alveolar organoid, Hhip knockout, plate1-1 well G06

description: Library name: 1-1_G06_HHIP

value: Hhip CRISPR/Cas9 knockout


title: breast cancer_SM183

value: L

value: Surgical Tissue Sample


title: naïve SpiB+ epithelila cells, scRNAseq, rep1


title: lung alveolar organoid, Chrm3 knockout, plate1-1 well G05

description: Library name: 1-1_G05_CHRM3

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Chrm3 CRISPR/Cas9 knockout


title: breast cancer_SM182


title: Type 2 diabetic, myocardial biopsy from patient, biol rep 47

city: Pierre Bénite

first: emmanuelle

last: meugnier

address: Cens Eli Bat 2 D- Hopital Lyon Sud

country: France

data_processing:
Illumina
Base Calling and quality assessement were performes using NCS v4.0.1 & RTA v2.4.11. demultiplexing was realized usign Bxl2fastq v2.17.1.14.Quality Analysis was performed using FastQC tool v0.11.9. Sequenced reads were trimmed for adapters using cutadapt v4.0 with default parameters. Mapping to Homo Sapiens GRCHh38  was performed using STAR v2.7.5a.  Gene count Table was realized using STAR v2.7.5a
raw Reads
Assembly: GRCHh38
Supplementary files format and content: tab-delimited text files include raw count for each sample

source_name: Left cardiac ventricular biopsy from patient

extract_protocol:
Total RNA extraction was performed using miRNeasy mini kit (Qiagen) following manufacturer’s instructions
100ng of total RNA were used for library construction using Lexogen QuantSeq 3 mRNA seq Library Prep kit (Illumina) following manufacturer's instruction
RNA-Seq SingleEnd 75bp with Illumina NextSeq500

value: Left Ventricular myocardial biopsy

tag: disease state

value: Type 2 diabetic


title: lung alveolar organoid, Cacna2d3 knockout, plate1-1 well G04

last: Biton

description: Library name: 1-1_G04_CACNA2D3

data_processing:
The sequencing reads in each fastq file were first split between mouse and human using Xenome (Conway et al., 2012). Only reads unambiguously assigned to either mouse or human were kept and respectively aligned to their reference genome (mouse: GRCm38.p5, human: GRCh38.p10) through the HTSeqGenie v4.35 Bioconductor package (Pau and Reeder, 2012, https://doi.org/10.18129/B9.bioc.HTSeqGenie). First, reads with low nucleotide qualities (70% of bases with quality <23) or matches to rRNA and adapter sequences were removed. Then, reads were aligned using GSNAP (Wu et al., 2010; Wu et al., 2016) version ‘2013-10-10-v2’, allowing maximum of two mismatches per 75 base sequence (parameters: ‘-M 2 -n 10 -B 2 -i 1 -N 1 -w 200000 -E 1 --pairmax-rna=200000 --clip-overlap'). Transcript annotation was based on the Gencode genes database (human: GENCODE 27, mouse: GENCODE M15). Reads unambiguously mapping to exons were counted to get gene-level read counts.
Assembly: GRCm38.p5, GRCh38.p10
Supplementary files format and content: gene_counts.xlsx provides gene-level counts of reads unambiguously mapping to exons. There is one table for the reads assigned by Xenome to the Mus Musculus genome (originating from the mouse alveolar type 2 cells of the organoids in the well), and one table for the reads assigned to the Homo Sapiens genome (originating from the human fibroblasts of the organoids in the well).
Supplementary files format and content: plate_design.csv contains the sgRNA sequences used to target each gene and their location on the four plates.
Supplementary files format and content: imaging_outputs.csv contains the main outputs of the image analysis performed on each well at day 7 and day 14, in terms of number or organoids in the well, average area of the organoids in the well, and estimate of the percentage of the well covered by organoids.
Supplementary files format and content: xenome_stats.csv contains the summary of the sequencing read assignment made by Xenome (Conway et al., 2012).

extract_protocol:
Libraries were prepared from extracted RNA using a modified Smart-seq3 protocol ( Hagemann-Jensen, M., Ziegenhain, C., Chen, P. et al. Single-cell RNA counting at allele and isoform resolution using Smart-seq3. Nat Biotechnol 38, 708–714 (2020). https://doi.org/10.1038/s41587-020-0497-0) Annealing reaction was performed with 4ul purified RNA, 0.8 ul 40% PEG 8000, 0.08 ul RNAse Inhibitor, 0.04 ul Smart-seq3 oligo dT (100µM), 0.3 ul dNTP (25mM each) and 1 ul water per 384 well reaction. 10 ul mineral oil was added on top to prevent evaporation. Reaction was sealed, spun and incubated at 70˚C for 10 min. Reverse translation was performed by adding 2 ul of RT mix (0.2ul Tris HCl, pH8.0 (1M), 0.24 ul NaCl (1M), 0.2 ul MgCl2 (100mM), 0.08 ul GTP (10mM), 0.64 ul DTT (100mM), 0.16 ul TSO (100µM), 0.08 ul Maxima H Minus RTase and 0.4 ul water) to each 384 well reaction. The RT reaction was incubated at 42°C for 90 min and repeated the following steps for 10 cycles: 50˚C for 2 min and 42˚C for 2 min, and was terminated at 85°C for 5 min.
cDNA amplification was performed by adding 12ul of PCR mix (0.1 ul cDNA fwd (100µM), 0.02 ul cDNA rev (100µM), 0.1 ul MgCl2 (100mM), 10 ul 2X Kapa HiFi Hotstart Readymix  and 1.78 ul water) to the RT reaction for a total of 20 ul. Reaction was thermal cycled at 95°C for 3 min, [98°C for 20 sec, 65°C for 30 sec, 72°C for 4 min] x 14 cycles, 72 °C 4min. cDNA was diluted 1:10 in water. 1 ul of each sample was transferred to a new 384 well plate to perform tagmentation. 3 ul of tagmentation mix (0.8 ul 5X TAPS Mg buffer, 0.1 ul Tn5 enzyme, 2.1 ul water) was added to each sample on ice. Plate was sealed, vortexed for 15 seconds and spun. The reaction mixture was incubated at 55 °C for 10 min. Reaction was quenched by adding 0.5µl of 0.2% SDS to each well, sealing, vortexing for 15 seconds, and spinning the plate. The plate was  incubated at room temperature for 5 min. Libraries were indexed by added 3.5 ul of PCR mix and 2 ul indexing primers  to each sample.  Reaction was thermal cycled at 72°C for 5 min, 95°C for 3 min, [98°C for 20 sec, 65°C for 30 sec, 72°C for 30 sec] x 10 cycles, 72 °C 4min. Libraries were pooled and sequenced on an Illumina NovaSeq X Plus system, targeting 8M reads per library.

value: Cacna2d3 CRISPR/Cas9 knockout


title: PD-NC4 clone E2 12mo

description:
Library name: PD-NC4 clone E2 12mo
This data was aligned to the PDNC4 chromosome 4 assembly.

value: fibroblast


title: lung alveolar organoid, Serpina1a knockout, plate1-1 well G03

description: Library name: 1-1_G03_SERPINA1A

value: Serpina1a CRISPR/Cas9 knockout


title: Type 2 diabetic, myocardial biopsy from patient, biol rep 46


title: PD-NC4 clone E1 12mo

description:
Library name: PD-NC4 clone E1 12mo
This data was aligned to the PDNC4 chromosome 4 assembly.

data_processing:
aligned to PD-NC4 or T2T assembly with Bwa, Peak calling with MACS2
Assembly: T2T CHM13 v 2.0 (GCF_009914755.1), PD-NC4 Chr4 assembly (https://www.biorxiv.org/content/10.64898/2025.12.23.696241v1.full)
Supplementary files format and content: bigwig, CENP-A read pileup


title: breast cancer_SM178

last: Symmans

data_processing:
Probe intensities were quantified with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. CEL files were normalized using global scaling with a trimmed mean target intensity of each array arbitrarily set to 600 using the MAS5 algorithm from the simpleaffy package (http://bioconductor.org/packages/2.4/bioc/html/simpleaffy.html).
MAS5.0 signal intensity for each array was log2 transformed and scaled to a reference distribution of 600 breast cancer specific genes.

extract_protocol: Total RNA was extracted from tissue using Qiagen Rneasy columns

value: N

value: IIB

value: Cytology

value: Needle Biopsy Sample


title: Type 2 diabetic, myocardial biopsy from patient, biol rep 45


title: lung alveolar organoid, Pid1 knockout, plate1-1 well G02

description: Library name: 1-1_G02_PID1

value: Pid1 CRISPR/Cas9 knockout


title: breast cancer_SM177

value: P


title: lung alveolar organoid, Rad21 knockout, plate1-1 well F11

description: Library name: 1-1_F11_RAD21

value: Rad21 CRISPR/Cas9 knockout


title: PD-NC4 clone D2 12mo

description:
Library name: PD-NC4 clone D2 12mo
This data was aligned to the PDNC4 chromosome 4 assembly.


title: breast cancer_SM175

value: III

value: Tissue


title: Type 2 diabetic, myocardial biopsy from patient, biol rep 43


title: lung alveolar organoid, Xbp1 knockout, plate1-1 well F10

description: Library name: 1-1_F10_XBP1

value: Xbp1 CRISPR/Cas9 knockout


title: lung alveolar organoid, Atg16l1 knockout, plate1-1 well F09

description: Library name: 1-1_F09_ATG16L1

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Atg16l1 CRISPR/Cas9 knockout


title: Type 2 diabetic, myocardial biopsy from patient, biol rep 42

value: Left Ventricular myocardial biopsy


title: PD-NC4 clone C3 12mo

description:
Library name: PD-NC4 clone C3 12mo
This data was aligned to the PDNC4 chromosome 4 assembly.


title: breast cancer_SM173

value: Surgical Tissue Sample


title: Type 2 diabetic, myocardial biopsy from patient, biol rep 41

value: Type 2 diabetic


title: lung alveolar organoid, Eif2b1 knockout, plate1-1 well F08

description: Library name: 1-1_F08_EIF2B1

value: Eif2b1 CRISPR/Cas9 knockout


title: PD-NC4 clone C2 12mo

description:
Library name: PD-NC4 clone C2 12mo
This data was aligned to the PDNC4 chromosome 4 assembly.

value: fibroblast


title: breast cancer_SM169

value: N


title: Type 2 diabetic, myocardial biopsy from patient, biol rep 40


title: Type 2 diabetic, myocardial biopsy from patient, biol rep 44


title: lung alveolar organoid, Nr1d1 knockout, plate1-1 well F07

description: Library name: 1-1_F07_NR1D1

value: Nr1d1 CRISPR/Cas9 knockout


title: breast cancer_SM168

value: IIB


title: Type 2 diabetic, myocardial biopsy from patient, biol rep 39


title: PD-NC4 clone D1 12mo

description:
Library name: PD-NC4 clone D1 12mo
This data was aligned to the PDNC4 chromosome 4 assembly.


title: lung alveolar organoid, Fam13a knockout, plate1-1 well F06

description: Library name: 1-1_F06_FAM13A

value: Fam13a CRISPR/Cas9 knockout


title: PD-NC4 clone A1 12mo

description:
Library name: PD-NC4 clone A1 12mo
This data was aligned to the PDNC4 chromosome 4 assembly.


title: Murine aortic smooth muscle cellswith Knockdown control and no treatment; P16

description:
Library name: seqrun3_KD_ctrl_no-trt_rep1
Column name in rsem.merged.gene_counts.tsv: seqrun3_KD_ctrl_no-trt_rep1

value: aortic smooth muscle cells

value: Knockdown control

value: no treatment


title: breast cancer_SM163

value: P

value: I


title: Type 2 diabetic, myocardial biopsy from patient, biol rep 38


title: PD-NC4 clone C4 12mo

description:
Library name: PD-NC4 clone C4 12mo
This data was aligned to the PDNC4 chromosome 4 assembly.


title: lung alveolar organoid, Terf1 knockout, plate1-1 well F05

description: Library name: 1-1_F05_TERF1

value: Terf1 CRISPR/Cas9 knockout


title: lung alveolar organoid, Rnf43 knockout, plate1-2 well D04

description: Library name: 1-2_D04_RNF43

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Rnf43 CRISPR/Cas9 knockout


title: breast cancer_SM174

value: E

value: III

value: Cytology

value: Needle Biopsy Sample


title: breast cancer_SM161

value: Tissue

value: Surgical Tissue Sample


title: PD-NC4 clone E2 6mo

description:
Library name: PD-NC4 clone E2 6mo
This data was aligned to the PDNC4 chromosome 4 assembly.

value: fibroblast


title: Type 2 diabetic, myocardial biopsy from patient, biol rep 37

value: Left Ventricular myocardial biopsy

value: Type 2 diabetic


title: lung alveolar organoid, Ager knockout, plate1-1 well F04

description: Library name: 1-1_F04_AGER

value: Ager CRISPR/Cas9 knockout


title: PD-NC4 E212m subclone 2

description:
Library name: PD-NC4 E212m subclone 2
This data was aligned to the PDNC4 chromosome 4 assembly.


title: PD-NC4 clone E1 6mo

description:
Library name: PD-NC4 clone E1 6mo
This data was aligned to the PDNC4 chromosome 4 assembly.


title: breast cancer_SM160

value: N

value: IIB


title: Type 2 diabetic, myocardial biopsy from patient, biol rep 36


title: lung alveolar organoid, Rbms3 knockout, plate1-1 well F03

description: Library name: 1-1_F03_RBMS3

value: Rbms3 CRISPR/Cas9 knockout


title: PD-NC4 clone D2 6mo

description:
Library name: PD-NC4 clone D2 6mo
This data was aligned to the PDNC4 chromosome 4 assembly.


title: lung alveolar organoid, Tigit knockout, plate1-1 well F02

description: Library name: 1-1_F02_TIGIT

value: Tigit CRISPR/Cas9 knockout


title: breast cancer_SM157

value: P

value: I


title: Type 2 diabetic, myocardial biopsy from patient, biol rep 35


title: PD-NC4 clone D1 6mo

description:
Library name: PD-NC4 clone D1 6mo
This data was aligned to the PDNC4 chromosome 4 assembly.


title: breast cancer_SM156


title: Type 2 diabetic, myocardial biopsy from patient, biol rep 34


title: lung alveolar organoid, Manf knockout, plate1-1 well E11

description: Library name: 1-1_E11_MANF

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Manf CRISPR/Cas9 knockout


title: PD-NC4 clone C4 6mo

description:
Library name: PD-NC4 clone C4 6mo
This data was aligned to the PDNC4 chromosome 4 assembly.


title: breast cancer_SM155


title: breast cancer_SM208

value: IIA


title: lung alveolar organoid, Gdf2 knockout, plate1-2 well B11

description: Library name: 1-2_B11_GDF2

value: Gdf2 CRISPR/Cas9 knockout


title: Type 2 diabetic, myocardial biopsy from patient, biol rep 33


title: lung alveolar organoid, Inhba knockout, plate1-1 well E10

description: Library name: 1-1_E10_INHBA

value: Inhba CRISPR/Cas9 knockout


title: breast cancer_SM205

value: Tissue


title: PD-NC4 clone C3 6mo

description:
Library name: PD-NC4 clone C3 6mo
This data was aligned to the PDNC4 chromosome 4 assembly.


title: breast cancer_SM152

value: L

value: Cytology

value: Surgical Tissue Sample


title: FPC, 1.25% Chol - 24 weeks, 0.05% Chol - 8 weeks

description:
Library name: FNA_R_A
10X Genomics

value: liver

value: non-parenchymal


title: Type 2 diabetic, myocardial biopsy from patient, biol rep 32

value: Left Ventricular myocardial biopsy

value: Type 2 diabetic


title: lung alveolar organoid, Ulk1 knockout, plate1-1 well E09

description: Library name: 1-1_E09_ULK1

value: Ulk1 CRISPR/Cas9 knockout


title: breast cancer_SM150

value: N

value: Needle Biopsy Sample


title: lung alveolar organoid, Acp6 knockout, plate1-2 well B07

description: Library name: 1-2_B07_ACP6

value: Acp6 CRISPR/Cas9 knockout


title: PD-NC4 clone C2 6mo

description:
Library name: PD-NC4 clone C2 6mo
This data was aligned to the PDNC4 chromosome 4 assembly.

value: fibroblast


title: Type 2 diabetic, myocardial biopsy from patient, biol rep 31


title: breast cancer_SM204

value: P

value: IIB


title: breast cancer_SM149

value: I


title: PD-NC4 clone C1 6mo

description:
Library name: PD-NC4 clone C1 6mo
This data was aligned to the PDNC4 chromosome 4 assembly.


title: Non-diabetic, myocardial biopsy from patient, biol rep 30

value: Non  diabetic


title: lung alveolar organoid, Usp30 knockout, plate1-1 well E07

description: Library name: 1-1_E07_USP30

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Usp30 CRISPR/Cas9 knockout


title: Non-diabetic, myocardial biopsy from patient, biol rep 29


title: breast cancer_SM148

value: Tissue


title: PD-NC4 clone A1 6mo

description:
Library name: PD-NC4 clone A1 6mo
This data was aligned to the PDNC4 chromosome 4 assembly.


title: lung alveolar organoid, Nkx21 knockout, plate1-1 well E06

description: Library name: 1-1_E06_NKX21

value: Nkx21 CRISPR/Cas9 knockout


title: FPC, 0.05% Chol, 32 weeks

description:
Library name: FNA_R_C
10X Genomics

value: liver

value: FPC, 0.05% Chol, 32 weeks


title: PD-NC4 clone E2 young

description:
Library name: PD-NC4 clone E2 young
This data was aligned to the PDNC4 chromosome 4 assembly.


title: breast cancer_SM147

value: IIA

value: Surgical Tissue Sample


title: PD-NC4 C2Y subclone 3

description:
Library name: PD-NC4 C2Y subclone 3
This data was aligned to the PDNC4 chromosome 4 assembly.


title: lung alveolar organoid, Twist1 knockout, plate1-1 well E05

description: Library name: 1-1_E05_TWIST1

value: Twist1 CRISPR/Cas9 knockout


title: Non-diabetic, myocardial biopsy from patient, biol rep 28

value: Left Ventricular myocardial biopsy


title: PD-NC4 clone E1 young

description:
Library name: PD-NC4 clone E1 young
This data was aligned to the PDNC4 chromosome 4 assembly.


title: Non-diabetic, myocardial biopsy from patient, biol rep 27


title: breast cancer_SM146

value: L

value: N

value: Cytology


title: lung alveolar organoid, Sox4 knockout, plate1-1 well E04

description: Library name: 1-1_E04_SOX4

value: Sox4 CRISPR/Cas9 knockout


title: breast cancer_SM143

value: P

value: III

value: Needle Biopsy Sample


title: PD-NC4 clone D2 young

description:
Library name: PD-NC4 clone D2 young
This data was aligned to the PDNC4 chromosome 4 assembly.

value: fibroblast


title: lung alveolar organoid, Nfe2l2 knockout, plate1-1 well E08

description: Library name: 1-1_E08_NFE2L2

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Nfe2l2 CRISPR/Cas9 knockout


title: breast cancer_SM141

value: Tissue


title: lung alveolar organoid, Tigit knockout, plate1-1 well E03

description: Library name: 1-1_E03_TIGIT

value: Tigit CRISPR/Cas9 knockout


title: Non-diabetic, myocardial biopsy from patient, biol rep 26

value: Non  diabetic


title: PD-NC4 clone D1 young

description:
Library name: PD-NC4 clone D1 young
This data was aligned to the PDNC4 chromosome 4 assembly.


title: Non-diabetic, myocardial biopsy from patient, biol rep 25


title: lung alveolar organoid, Tfcp2l1 knockout, plate1-1 well E02

description: Library name: 1-1_E02_TFCP2L1

value: Tfcp2l1 CRISPR/Cas9 knockout


title: Non-diabetic, myocardial biopsy from patient, biol rep 24


title: lung alveolar organoid, Il1a knockout, plate1-1 well D11

description: Library name: 1-1_D11_IL1A

value: Il1a CRISPR/Cas9 knockout


title: PD-NC4 clone C3 young

description:
Library name: PD-NC4 clone C3 young
This data was aligned to the PDNC4 chromosome 4 assembly.


title: breast cancer_SM139

value: I

value: Surgical Tissue Sample


title: lung alveolar organoid, Fgf7 knockout, plate1-1 well D10

description: Library name: 1-1_D10_FGF7

value: Fgf7 CRISPR/Cas9 knockout


title: PD-NC4 clone C2 young

description:
Library name: PD-NC4 clone C2 young
This data was aligned to the PDNC4 chromosome 4 assembly.


title: Non-diabetic, myocardial biopsy from patient, biol rep 22

value: Left Ventricular myocardial biopsy


title: PD-NC4 clone C1 young

description:
Library name: PD-NC4 clone C1 young
This data was aligned to the PDNC4 chromosome 4 assembly.


title: lung alveolar organoid, Keap1 knockout, plate1-1 well D08

description: Library name: 1-1_D08_KEAP1

value: Keap1 CRISPR/Cas9 knockout