title: CRISPR library from Cal27 derived tumor 2 from mouse replicate 2

description: Library name: LD_Cal27_T_2_2

data_processing:
In each screen, UMI was compressed using umi_tools extract, and adaptor sequences were removed using cutadapt. Subsequently, the remaining reads were aligned on the guide sequences using bowtie (maximum error: 1, minimum length: 16). The count for each guide was collected using umi_tools count, then transformed into scc format. For in vitro screen analysis, MaGeCK MLE was performed based on the guide counts with the design matrix of comparing the timepoint of the initial collection and the post-screen collection as described in (W. Li et al. 2015). In vivo and in vitro CRISPR screens were integrated by first determining the ß scores of each sample against plasmid DNA determined by miSeq (Illumina) using the MaGeCK MLE algorithm (W. Li et al. 2015). ß scores were normalized and visualized using the MaGeCKFlute R package (B. Wang et al. 2019) following the authors’ guidelines.
Assembly: hg38
Supplementary files format and content: tab separated txt file containing unnormalized feature (guide) counts
Library strategy: CRISPR Screen

extract_protocol:
Three mice (a total of six tumors) were performed on each cell line. Based on the visual observation of subcutaneous tumor growths, the mice injected with the same cell lines were sacrificed on the same days after 3-4 weeks. (A431: 3.5 weeks, Cal27: 4.5 weeks) The tumors were surgically harvested, minced, and homogenized in an MP Biomedical lysing matrix A tube. Genomic DNA was isolated using QIAGEN DNeasy Blood and Tissue Kit
Sequencing library was made as described in (Mathiowetz et al. 2023, PMID: 37000620) with an adjustment of using <10g of gDNA in PCR1 reaction and a pair of primers matching with our sequences and manually determining PCR2 cycles based on a trial run to prevent overamplification.

tag: cell line

value: Lentivirus-mediated CRISPR library infection and a tumor grown in mouse


title: CRISPR library from_Normal Keratinocyte cells, KC library, Week 1.5, replicate 1

status: Public on Apr 28 2025

type: SRA

city: Stanford

first: Luca

last: Ducoli

state: California

address: 269 Campus Drive CCSR 2150

country: USA

institute: Stanford University

description: Library name: LD_Kerat_W1_KC1

library_source: other

molecule: other

organism: Homo sapiens

source_name: Human Keratinocyte

growth_protocol: The human A431 and Cal27 cell line was cultured in DMEM media with 10% FBS and 1% PS in 5% CO2 at 36°C. Primary human keratinocytes were obtained from fresh, surgically discarded neonatal foreskin, cultured in Keratinocyte-SFM and Medium 154 with Keratinocyte supplement, and subcultured regularly before reaching high confluency for a few cycles.

extract_protocol:
DNA was isolated from the cell pellet using QIAGEN DNeasy Blood and Tissue Kit
The sequencing library was made as described in (Ji et al. 2020) [PMID: 32579974]

treatment_protocol: Lentivirus has been produced in Lenti-X cells seeded higher than 70% in 10cm (or 15cm) dish. Cells in each 10cm dish were transfected with 7.5ug CMV, 3.5ug MDG, 7.5ug Plasmid in 625ul OptiMEM mixed with another tube containing 25ul Lipofectamine in 625ul OptiMEM. (The volume or amount were doubled for cells in 15cm dish). The media was replaced after the overnight incubation, collected after every 24h with media replacement for two times, filtered through a 0.45um PES membrane, and concentrated with Lenti-X concentrator (Takara). Cas9 transfection was performed on A431, Cal27, and Primary Keratinocytes and selected with blasticidin. Pooled guide lentivirus was titrated in each of dCas9-KRAB expressing cell lines to achieve an MOI of 0.3. Following selection with puromycin for two to three days, the transfection rates were checked with Cell Titer Blue, and triplicate of cells (with +1000x coverage) were collected, flash frozen, and stored at -80°C for each replicate as the initial screen time point. Cells were cultured by maintaining at least 1000x coverage with regular basis of subculturing for three weeks (Primary Keratinocyte for 1.5 week due to inherently limited proliferation capacity).

value: Human Keratinocyte

tag: treatment

value: Lentivirus-mediated CRISPR library infection


title: CRISPR library from A431 derived tumor 2 from mouse replicate 1

description: Library name: LD_A431_T_1_2

growth_protocol: The human A431 and Cal27 cell lines were cultured in DMEM media with 10% FBS and 1% PS in 5% CO2 at 36°C

treatment_protocol: The pooled oligo Lenti virus was made and transfected on dCas9-KRAB expressing A431 and Cal27 with MOI of 0.3.. After the 3 days of selection in puromycin, the transfection rates were chekced with Cell Titer Blue. Four million cells in 100ul were gently mixed with 50ul Matrigel (Corning) until it turned into a homogenous mixture and injected with 28G insulin syringe into both sides of rear flanks of SCID Hairless Outbred (SHO®) mice (Charles River). Triplicate of cells (with +1000x coverage) were collected, flash frozen, and stored at -80C for each replicate as the initial screen time point.


title: Panc-Smad4OFF_m1

status: Public on May 14 2025

city: New York

first: Yu-Jui

last: Ho

address: 1275 York Avenue

institute: Memorial Sloan Kettering Cancer Center

description: paired-end sequencing

library_source: genomic

data_processing:
Illumina read quality was checked for each sample using FastQC v0.11.5.
FASTQ files were trimmed with trimGalore and cutadapt (PMID: 28715235), and the filtered, pair-ended reads were aligned to mm10 with Bowtie2 (PMID: 22388286).
Peaks were called over input using MACS2 (PMID: 18798982), and only peaks with ap-value of ≤ 0.001 and outside the ENCODE blacklist region were kept. All peaks from all samples were merged by combining peaks within 500 bp of each.
featureCounts (PMID: 24227677)was used to count the mapped reads for each sample. The resulting peak atlas was normalized using DESeq2 (PMID: 25516281). For comparison to DepthNorm, samples were normalized to 10 million mapped reads. Normalized bigWig files were created using the normalization factors from DESeq2 as previously described (PMID: 30429377)and BEDTools genomeCoverageBed (PMID: 20110278). Dynamic ATAC peaks were called if they had an absolute log2-transformed fold change≥0.58 and FDR≤0.1.
Assembly: Reads were aligned to the mouse genome (mm10, GRCm38.91)
Supplementary files format and content: Tab-delimited text file includes raw count table for each sample

molecule: genomic DNA

organism: Mus musculus

source_name: PDAC Primary Tumor

growth_protocol: For pancreatic tumors, mouse hosts were placed on doxycycline chow 5-7 days before transplantation. Mice were anesthetized and a survival surgery was performed to expose the pancreas. 1 x 10^5 tumor-derived cells were resuspended in 25 uL 1:1 DMEM (Gibco) : Matrigel (Corning) mix and injected in the tail of the pancreas of each mouse. For liver metastasis assays, mice were anesthetized and a survival surgery was performed to expose the spleen. 4 x 10^5 tumor-derived cells resuspended in 20 uL PBS were injected in the splenic parenchyma of each mouse, followed by removal of the spleen and cauterization (splenectomy). For lung metastasis assays, mice were restrained, and 2.5 x 10^5 tumor-derived cells resuspended in 250 uL PBS were injected in the tail vein of each mouse.

extract_protocol:
A total of 60,000 mKate2+cells were isolated by FACS, washed once with 50 μl cold PBS and resuspended in 50 μl cold lysis buffer. Cells were then centrifuged immediately for 10 min at 500gat 4°C, and the pellet of nuclei was subjected to transposition with Nextera Tn5 transposase (Illumina #FC-121–1030) for 30 min at 37°C, according to the manufacturer’s instructions. DNA was eluted using a DNA Clean & Concentrator Kit in 21 μl elution buffer (Zymo Research #D4013).
ATAC-seq libraries were prepared using the NEBNext High-Fidelity 2X PCR Master Mix (NEB M0541) as previously described (PMID: 25559105). Purified libraries were assessed using a Bioanalyzer High-Sensitivity DNA Analysis kit (Agilent).
Approximately 50 million paired-end 150-bp reads (25 million each side) were sequenced per replicate on a HiSeq instrument (Illumina).

treatment_protocol: Mouse hosts were fed Doxycycline chow. Where applicable, doxycycline withdrawal was done at 4 (pancreas), 5 (liver) or 6 weeks (lungs) post-injection by switching the food source to regular chow.

tag: cell type

value: PDAC primary tumor cells

tag: genotype


title: CD4 T cells_AML-18

status: Public on Aug 31 2024

type: RNA

city: Bern

first: Ramin

last: Radpour

address: Murtenstrasse 35

department: Medical Oncology

country: Switzerland

institute: Bern University Hospital

description: Gene expression data

hyb_protocol: The labelled products were hybridized using GeneChip® Hybridization, Wash, and Stain Kit (Affymetrix Inc.) for 48 hours at 45°C and 60rpm.

scan_protocol: The arrays were scanned on GeneChip Scanner 3000 7G (Affymetrix Inc.).

data_processing: The expression signals were acquired using the Affymetrix GeneChip Command Console Software (AGCC). The system was used to generate the numerical values of the probe intensity (Signal). The differentially expressed mRNAs were defined using Partek Genomics Suite software (Partek Incorporated, Missouri, USA) and and RMA normalization.

label: biotin

molecule: total RNA

source_name: acute myeloid leukemia

label_protocol: Biotinylated mRNAs were prepared according to the GeneChip® Human Transcriptome Pico Assay 2.0  protocol (Affymetrix Inc.) using 50ng total RNA.

extract_protocol:
CD4+ T cells were FACS-purified from BM of newly diagnosed AML patients and also control subjects.
Total RNA was extracted using RNeasiy micro kit (QIAGEN AG) according to the manufacturer's instructions.

tag: patient id

tag: disease

value: acute myeloid leukemia

value: CD4 T cells


title: CD4 T cells_AML-21

description: Gene expression data


title: CD4 T cells_AML-16

description: Gene expression data


title: CD4 T cells_AML-15

description: Gene expression data


title: CD4 T cells_AML-19

description: Gene expression data


title: CD4 T cells_AML-12

description: Gene expression data


title: CD4 T cells_AML-14

description: Gene expression data


title: CD4 T cells_AML-13

description: Gene expression data


title: CD4 T cells_AML-17

description: Gene expression data


title: CD4 T cells_AML-20

description: Gene expression data


title: HL60_KO-2G-DMSO-2_ATAC

data_processing:
RNA-Seq and ATAC-Seq were performed using Illumina NextSeq 500.
The level of gene expression was assessed after DESeq2 normalization. For the ATAC-Seq data analysis, the genomic regions with high levels of transposition/tagging events were determined.  using the MACS2 peak calling algorithm
Genome_build: GRCh38 - hg38
Supplementary_files_format_and_content: Tab-delimited text file includes Log2 transformed DESeq2 values for RNA-Seq and avarage peak values as well as genome regions for ATAC-Seq.

source_name: AML HL60 cell line

extract_protocol: Total RNA was extracted from the treated cells for the RNA-Seq analysis using an RNeasy Mini Plus RNA isolation kit a (Qiagen). DNA from the cell lysate was isolated for the ATAC-Seq analysis.

treatment_protocol: HL60 HK3-null and Cas9 expressing control cells were treated with either 1µM of ATRA or DMSO (0.01%) for 36h. Next, treated cells were harvested for RNA-Seq and ATAC-Seq analysis.

value: AML HL60 cell line

value: treated with DMSO


title: HL60_KO-2G-DMSO-1_ATAC


title: CD4 T cells_AML-11

description: Gene expression data


title: HL60_KO-2G-ATRA-2_ATAC

value: treated with ATRA


title: HL60_KO-2G-ATRA-1_ATAC


title: CD4 T cells_AML-9

description: Gene expression data


title: CD4 T cells_AML-3

description: Gene expression data


title: HL60_CAS9-DMSO-2_ATAC

value: Cas9 expressing control cells


title: CD4 T cells_AML-6

description: Gene expression data


title: CD4 T cells_AML-10

description: Gene expression data


title: HL60_CAS9-ATRA-2_ATAC


title: HL60_CAS9-DMSO-1_ATAC


title: CD4 T cells_AML-7

description: Gene expression data


title: HL60_CAS9-ATRA-1_ATAC


title: CD4 T cells_AML-4

description: Gene expression data


title: CD4 T cells_AML-5

description: Gene expression data


title: HL60_KO-2G-DMSO-3_RNASeq

library_source: transcriptomic


title: CD4 T cells_AML-1

description: Gene expression data


title: CD4 T cells_AML-2

description: Gene expression data


title: CRISPR library from_A431 cells, KC library, Week 3, replicate 1

description: Library name: LD_A431_W3_KC2


title: CRISPR library from_Cal27 cells, TSK library, Week 0, replicate 1

description: Library name: LD_Cal27_W0_TSK1


title: HL60_KO-2G-DMSO-2_RNASeq


title: HL60_KO-2G-DMSO-1_RNASeq


title: HL60_KO-2G-ATRA-3_RNASeq


title: HL60_KO-2G-ATRA-1_RNASeq


title: HL60_CAS9-DMSO-2_RNASeq


title: HL60_CAS9-DMSO-3_RNASeq


title: HL60_CAS9-DMSO-1_RNASeq


title: CD4 T cells_AML-8

description: Gene expression data


title: HL60_CAS9-ATRA-3_RNASeq


title: HL60_KO-2G-ATRA-2_RNASeq


title: HL60_CAS9-ATRA-2_RNASeq


title: Vis5-4A

city: Bethesda

first: Michael

last: Erdos

address: 50 South Dr

institute: NIH

description: Leica DMi8 brightfield/widefield

data_processing:
We used Spaceranger version 2.1.1 with default parameters, software made by 10X genomics, to process the raw Visium Spatial Gene Expression data and generate quality-controlled gene expression values associated with each spatial location (“Spatial Transcriptomics - 10x Genomics,” n.d.). We then employed SpotClean to correct for the INS bleed that we observed in the original visualization (Ni et al., 2022).
Supplementary files format and content: h5
Library strategy: Spatial transcriptomics

source_name: Pancreas

extract_protocol: 10X Genomics Visium Spatial Gene Expression protocol

treatment_protocol: tissue flash frozen with isopentane and stored in liquid nitrogen

tag: tissue

value: Pancreas

tag: disease state


title: Vis5-3B

description: Leica DMi8 brightfield/widefield

value: NGT


title: HL60_CAS9-ATRA-1_RNASeq


title: Vis5-4B

description: Leica DMi8 brightfield/widefield


title: Vis5-2B

description: Leica DMi8 brightfield/widefield


title: Vis5-3A

description: Leica DMi8 brightfield/widefield


title: Vis5-2A

description: Leica DMi8 brightfield/widefield


title: Vis5-1A

description: Leica DMi8 brightfield/widefield


title: Vis5-1B

description: Leica DMi8 brightfield/widefield


title: Vis3-D

description: Leica DMi8 brightfield/widefield


title: Vis3-C

description: Leica DMi8 brightfield/widefield


title: Vis3-A

description: Leica DMi8 brightfield/widefield


title: Vis3-B

description: Leica DMi8 brightfield/widefield


title: Vis2-D

description: Leica DMi8 brightfield/widefield


title: Vis2-C

description: Leica DMi8 brightfield/widefield


title: Vis2-B

description: Leica DMi8 brightfield/widefield


title: Vis2-A

description: Leica DMi8 brightfield/widefield


title: bulk tumor tissue from PtPRb EPO-GEMM, Sample7

status: Public on Aug 26 2024

data_processing:
Illumina read quality was checked for each sample using FastQC v0.11.5.
Raw fastq files were analyzed by removing adaptor sequences using Trimmomatic (0.36), aligned to the mouse genome using STAR (2.6.1a), and quantified transcript counts using featureCounts (1.6.3).
Assembly: Reads were aligned to the mouse transcriptome (mm10, GRCm38)
Supplementary files format and content: Tab-delimited text file includes raw count table for each sample

source_name: bulk tumor

growth_protocol: Prostate orthotopic survival surgeries were performed on male mice where 20µg of two PX330 CRISPR-Cas9 constructs, one with a guide against p53, and another with guides against Pten and Rb1, were injected into the anterior lobe in 50µL volume. The lobe was then electroporated with two pulses of electricity and mice were monitored weekly for tumor formation post-surgery. Tumors were harvested at endpoint for analysis and sequencing.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen)
PolyA mRNA was selected using beads coated with polyT oligonucleotides. Purified polyA mRNA was subsequently fragmented, and first and second strand cDNA synthesis performed using standard Illumina mRNA TruSeq library preparation protocols. Double stranded cDNA was subsequently processed for TruSeq dual-index Illumina library generation.
For sequencing, pooled multiplexed libraries were run on a HiSeq 2500 machine on RAPID mode. Approximately 10 million 76bp single-end reads were retrieved per replicate condition. Resulting RNA-Seq data was analyzed by removing adaptor sequences using Trimmomatic (29), aligning sequencing data to GRCh37.75(hg19) with STAR (30), and genome wide transcript counting using HTSeq (31) to generate a RPKM matrix of transcript counts.

value: bulk tumor

value: tumor cells


title: bulk tumor tissue from PtPRb EPO-GEMM, Sample5


title: bulk tumor tissue from PtPRb EPO-GEMM, Sample4


title: bulk tumor tissue from PtPRb EPO-GEMM, Sample8


title: bulk tumor tissue from PtPRb EPO-GEMM, Sample6


title: bulk tumor tissue from PtPRb EPO-GEMM, Sample3


title: bulk tumor tissue from PtPRb EPO-GEMM, Sample1


title: bulk tumor tissue from PtPRb EPO-GEMM, Sample2


title: B4: Co-cultured_MAF2-mCherry_DMSO

status: Public on Aug 09 2024

city: London

first: Probir

last: Chakravarty

address: 1Midland Road

country: United Kingdom

institute: Francis Crick

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw data was transformed using variance-stabilizing transformation before quantile normalisation using the lumi package in R

source_name: Melanoma-associated fibroblast co-cultured with melanoma cells and stimulated with DMSO

label_protocol: Standard Illumina biotin labelling protocol

growth_protocol: Human primary melanoma-associated fibroblasts labeled with mCherry (MAF2-mCherry) were co-culture with 5555 mouse melanoma cells labeled with mEGFP (5555-mEGFP) in DMEM on plastic dishes

extract_protocol: RNA was extracted using a Qiagen RNA extraction kit. The RNA was amplified using an Ambion Illumina TotalPrep RNA Amplification Kit.

treatment_protocol: MAF2-mCherry and 5555-mEGFP co-cultures were treated with DMSO (0.1%) or PLX4720 (1 mM) for 24 hours. Cherry-positive fraction (MAF2-mCherry) were FACS-sorted.

value: melanoma-associated fibroblast (MAF2-mCherry) co-cultured with melanoma cells (5555-mEGFP)

value: DMSO


title: B8: Co-cultured_MAF2-mCherry_PLX

source_name: Melanoma-associated fibroblast co-cultured with melanoma cells and stimulated with PLX

value: PLX


title: A6: MAF2-mCherry_PLX

source_name: Melanoma-associated fibroblast mono-cultures stimulated with PLX

value: melanoma-associated fibroblast (MAF2-mCherry) mono-cultured


title: B2: MAF2-mCherry_DMSO

source_name: Melanoma-associated fibroblast mono-cultures stimulated with DMSO


title: Reln-S4

status: Public on Jul 10 2024

city: Birmingham

first: Jeremy

last: Day

state: Alabama

address: 1825 University Blvd SHEL 910

department: Neurobiology

institute: University of Alabama at Birmingham

library_source: transcriptomic single cell

data_processing:
All raw fastq files were aligned to the Ensembl mRatBn7.2 (Rn7) genome using CellRanger v7.1.0 with the associated Ensembl gene transfer format (gtf) file (version 105). CellRanger filtered outputs were analyzed with Seurat v4.3.0.1 using R v4.3.1.
To filter out background contamination, cell-free ambient RNA was removed using SoupX v.1.6.2. Next, we continued quality filtering in R with Seurat v.4.3.0.1 by removing nuclei containing <200 genes and >5% of reads mapping to the mitochondrial genome (5,846 nuclei post-processing). The counts data for each individual were then normalized, scaled by a factor of 10,000, and log-transformed.
For each sample, we used Seurat to determine the 3,000 genes with highest cell-to-cell variability; these sets of genes were used to identify “anchor” pairs of cells between samples with a shared pattern of gene expression. We then integrated the eight individual datasets based on the identified anchors, using the first 17 principal components (PCs). Downstream analysis was performed on the integrated dataset.
Expression for each gene in the integrated dataset was scaled to a mean of 0 and variance of 1 across cells. We used Seurat for initial dimensionality reduction and clustering as detailed below. We first performed dimensionality reduction via PCA retaining 17 PCs, followed by UMAP with the 17 previously identified PCs as input. Cells were then clustered under a graph-based approach by first identifying K-nearest neighbors in PCA space, and then clustering under a Louvain algorithm with a resolution of 0.3. After initial clustering but before differential gene expression analysis, we used DoubletFinder v.2.0.3 to identify and remove heterotypic doublets, a consequence of two cells of different types being captured in a single droplet and thus presenting as a single heterotypic “cell.” We assumed a doublet formation rate of 4% based on 8,000 cells loaded per GEM well, as indicated in the 10x Genomics library preparation documentation. After removing doublets, we repeated the dimensionality reduction and clustering steps detailed above. We matched the resulting clusters to specific cell types based on known marker genes from previous work
To identify genes differentially expressed between Reln knockdown and lacZ controls, we conducted a differential expression analysis on a pseudobulked gene expression matrix created by summing counts for each gene within a sample (or single GEM well) and across cells within each cell type. Genes with mean counts <5 were removed. Differential expression analysis was conducted with DESeq2 v.1.40.2 using a likelihood ratio test (LRT) with treatment condition as the main effect and controlling for the effect of sex to ensure that identified significant differential expression could be attributed to the treatment and not confounded by differences in response between sexes. To assess differential expression among cell types, we conducted a separate LRT with cell type as the main effect and controlling for sex.
Assembly: Rn7 (Ensemble gtf version 105)
Supplementary files format and content: Cell Ranger output matrices for barcodes, features, and gene expression counts are provided for each sample.

molecule: polyA RNA

organism: Rattus norvegicus

source_name: nucleus accumbens

growth_protocol: Sprague-Dawley 90-120-day-old male or female rats were purchased from Charles River Laboratories. Male or female adult rats were co-housed in pairs in plastic filtered cages with nesting enrichment in an AAALAC-approved animal care facility maintained between 23-24°C on a 12-hour light/dark cycle with ad libitum food (Lab Diet Irradiated rat chow) and water. Bedding and enrichment were changed weekly by animal resources program staff. Animals were randomly assigned to experimental groups.

extract_protocol:
Brains were blocked in 1mm sections, and NAc punches were obtained, flash frozen, and stored at -80°C prior to nuclei isolation. 1mm brain sections were taken at the level of the nucleus accumbens, and nucleus accumbens tissue was dissected using a 2mm punch tool centered on the nucleus accumbens core subregion, and frozen for storage. Frozen tissue punches were thawed slowly on ice prior to being chopped by scalpel 100 times in 2 orthogonal directions. Tissue from one rat was transferred to 5mL of chilled (4°C) Lysis Buffer (10mM Tris-HCl, 10mM NaCl, 3mM MgCl2 (Thermo Fisher, BP214-500), 0.1% Igepal in Nuclease-Free Water (Sigma, 18896-50ML)) for 15 min, mixing the tissue by inversion every 2 min. Lysis was quenched immediately at 15 min with 5mL of complete Hibernate-A (Thermo Fisher, A1247501) supplemented with B27 and Glutamax (Life Technologies, 35050-061)). Tissue was then triturated by fire-polished Pasteur pipette (2 pipettes of decreasing diameter; 8-10 passes per pipette) for 35 min and passed through a 40µm pre-wet filter. The samples were then pelleted at 500rcf for 10 min at 4°C followed by a wash in 10mL of Nuclei Wash & Resuspension Buffer (1X PBS, 1% BSA, 0.2U/ul NxGen RNase inhibitor (Lucigen, 30281-2)). Supernatant was then removed and the pellet was gently resuspended in a total volume of 800µl prior to 7-AAD (Thermo Fisher, 00-6993-50) staining and FACS to further purify the nuclei for sequencing. Immediately after FACS, nuclei were washed a final time at 200rcf in 10mL supplemented Hibernate-A containing 1% BSA for 10 minutes at 4°C to remove any remaining fine debris and nascent RNA.
FACS-sorted nuclei were subject to 10X GEM generation and barcoding, GEM-RT cleanup and cDNA amplification, and library construction using a Chromium Single Cell 3ʹ Reagent Kit (v3 chemistry) on the Chromium iX instrument. Libraries were constructed according to manufacturer's instructions using the Chromium Single Cell 3′ Library Construction Kit (10× Genomics, PN-1000190). Nuclei (6,221 total) from adult rat NAc were sequenced on the Illumina NovaSeq6000 at the UAB Heflin Genomics core to a depth of ~300,000 reads per nuclei.

treatment_protocol: Rats underwent stereotaxic surgery to transduce nucleus accumbens tissue with lentiviruses expressing CRISPRi machinery targeting lacZ (as a control) or Reln. Two weeks following surgery, animals (4 lacZ, 4 Reln 2M/2F per group) were euthanized prior to rapid decapitation.

tag: strain

value: Sprague-Dawley

tag: age

value: 90-120 days old

value: nucleus accumbens

tag: Sex

value: Female

value: Reln sgRNA


title: Reln-S6


title: Reln-S7

value: Male


title: Reln-S2


title: 5555-mEGFP_PLX [B5]

status: Public on Jul 29 2024

description:
replicate 2
B5

data_processing: Raw data was transformed using variance-stabilizing transformation before quantile normalisation using the lumi package in R.

source_name: 5555 melanoma cell line

growth_protocol: Melanoma cells were maintained in DMEM (Invitrogen) with 10% fetal bovine serum/1% PenStrep (GIBCO).

treatment_protocol: MAF2-mCherry and 5555-mEGFP co-cultures were treated with DMSO (0.1%) or PLX4720 (1 mM) for 24 hours. mEGFP-positive fraction (5555-mEGFP) were FACS-sorted.

tag: tag


title: B6: MAF2-mCherry_PLX


title: IntestCrypts_2DG_1month_R1_Mouse_3

status: Public on Apr 10 2025

description: Library name: IntestCrypts_2DG_1month_R1_Mouse_3

data_processing:
Illumina read quality was checked for each sample using FastQC v0.11.5.
Raw fastq files were analyzed by removing adaptor sequences using Trimmomatic (0.36), aligned to the mouse genome using STAR (2.6.1a), and quantified transcript counts using featureCounts (1.6.3).
Assembly: Reads were aligned to the mouse transcriptome (mm10, GRCm38.91)
Supplementary files format and content: Tab-delimited text file includes raw count table for each sample

source_name: Murine crypts

growth_protocol: All animal experiments in this study were performed in accordance with protocols approved by the Memorial Sloan Kettering Institutional Animal Care and Use Committee (approval number: 11-06-012). The mice were housed with a 12 h light/dark cycle between 8:00 and 20:00 in a temperature-controlled room (22 ± 1°C) with free access to water and food. Both male and female mice were used in equal proportions for all experiments. .

treatment_protocol: For glycolisis inhibition, mice were injected (intraperitoneally) with 2-deoxyglucose once daily with 500 mg/kg dissolved in PBS. For the vehicle control, mice were injected with PBS. Mice were injected 5 times per week, 4 weeks.

tag: mouse strain

value: Murine crypts

tag: time

value: 500 mg/Kg 2DG


title: A4: Co-cultured_MAF2-mCherry_DMSO


title: lacZ-S8

value: lacZ sgRNA


title: A8: Co-cultured_MAF2-mCherry_PLX


title: B3D

status: Public on Apr 26 2025

description: pre-cDCs DNGR-1 KO CD45.2 from bone marrow

data_processing:
Trimmomatic v0.36 was used to remove the adapters and filter raw reads below 36 bases long. The filtered reads were aligned to the Mus musculus genome Ensembl GRCm38 (release 86) using RSEM v1.3.0  and STAR v2.5.2 with the “--forward-prob” parameter was set to “0.5” and all other parameters were kept as default.
Raw counts were processed using the bioconductor package DESeq2 v1.18.1 in R v3.4.3. Variance stabilizing transformation was applied to obtain normalized log2 gene expression values.
Assembly: GRCm38
Supplementary files format and content: tab delimited vst normalised expression data, where columns are samples and row are ensembl mouse IDs
Supplementary files format and content: tab delimited raw_counts output of STAR alignment and RSEM quantifications. Columns are samples and rows are ensembl mouse IDs

extract_protocol:
RNeasy Micro kit [Qiagen]
Total RNA (KAPA Hyper prep with Riboerase)

treatment_protocol: No Treatment

value: KO


title: A2: MAF2-mCherry_DMSO


title: Mixed_5555-mEGFP_DMSO [B3]

description:
replicate 2
B3


title: Mixed_5555-mEGFP_PLX [A7]

description:
replicate 1
A7


title: Mixed_5555-mEGFP_PLX [B7]

description:
replicate 2
B7


title: 5555-mEGFP_DMSO [A1]

description:
replicate 1
A1


title: 5555-mEGFP_DMSO [B1]

description:
replicate 2
B1


title: 5555-mEGFP_PLX [A5]

description:
replicate 1
A5


title: Mixed_5555-mEGFP_DMSO [A3]

description:
replicate 1
A3


title: X8i

data_processing:
Raw FASTQ files were processed using nf-core/rnaseq v3.10 (doi: https://doi.org/10.5281/zenodo.1400710) of the nf-core collection of workflows using a pipeline executed with Nextflow v23.04.1.
Splice-aware alignment to the mRatBn7.2/Rn7 genome assembly was conducted using STAR v2.7.9a with the associated Ensembl gene transfer format (gtf) file (version 105).
Binary alignment map files were indexed with SAMtools (v1.16.1). Gene-level counts were generated using featureCounts (Rsubread v2.0.1)
QC metrics were collected and reviewed with MultiQC (v1.13), and a minimum of 20M mapped reads were obtained per sample (range: 22.6M to 121.4M)
Differential expression testing was conducted using DESeq2 (v1.38.3). DEG testing p-values were adjusted with the Benjamini–Hochberg method, and DEGs were designated as those genes with an adjusted p-value <0.05. Genes with unreliable/low expression estimates (basemean <50) were excluded from subsequent analysis.
Assembly: Rn7 (Ensemble gtf version 105)
Supplementary files format and content: Count_matrix.txt contains RNA-seq count values for annotated gene for each sample

source_name: Sprague-Dawley

growth_protocol: Neurons were removed from rat striatal tissue at embryonic day 18, and maintained in vitro for 12 days prior transduction with CRISPRi lentivirus components. RNA was extracted at DIV 19 and RNA-seq was performed using mRNA.

extract_protocol:
Total RNA from was extracted, DNase-treated, and purified (RNeasy, Qiagen). 1µg of total RNA underwent quality control (Bioanalyzer; all RIN values > 7.0) and library construction for polyA+ RNA sequencing.
1 μg of total RNA underwent quality control (Bioanalyzer) and was prepared for directional RNA sequencing using NEBNext reagents (New England Biolabs) according to manufacturer’s recommendations. Specifically, the NEBNext Poly(A) mRNA manetic isolation module was used to enrich polyadenylated RNA. RNA-seq libraries underwent sequencing (100 bp paired-end directional reads) on an Illumina sequencing platform (NovaSeq6000).

treatment_protocol: Primary rat striatal neurons were transduced with lentiviruses expressing CRISPRi machinery on DIV12 with a multiplicity of infection (MOI) per cell of 2000 for each virus.

value: Embryonic day 18, 19 DIV

tag: source

value: Striatum


title: lacZ-S1


title: X7i


title: X6i


title: X4i


title: X2i


title: WT Week7 3

status: Public on Jun 20 2024

city: San Francisco

first: Christina

middle: M.

last: Homer

state: CA

department: Biochemistry & Biophysics

institute: UCSF

description: Coccidioides posadasii Silveira

data_processing:
Estimated counts of each transcript were calculated for each sample by alignment-free comparison against the predicted mRNA for the published Silveira genome (de Melo Teixeira et al 2022, PMID 35137016) using KALLISTO version 0.46.2 (Bray et al 2016, PMID 27043002)
Assembly: Silveira genome (de Melo Teixeira et al 2022, PMID 35137016)
Supplementary files format and content: Processed data are Kallisto output files with estimated counts per gene.

organism: Coccidioides posadasii

source_name: liquid culture

growth_protocol: All samples are arthroconidia (spores). Arthroconidia were generated on 2x GYE agar (2% Dextrose (Fisher), 1% Yeast extract (Gibco), 1.5% Bacto-Agar (BD)) + Penicillin/Streptomycin (100 U/ml penicillin and 100 g/ml streptomycin, UCSF Media Core) in T225 tissue culture flasks for 4-6 weeks at 30˚C, 25˚C, or 37˚C. Arthroconidia were then collected through scraping and washing as previously described (Mead et al 2020, PMID 32894648).

extract_protocol:
5x10^7 arthroconidia were placed in Trizol LS (Ambion) and bead beat for 2 min. RNA was extracted using the Direct-zol RNA Miniprep Plus isolation kit (Zymo) with on-column DNAse digestion step extended for 15 min.
Sequencing libraries were prepared using the Ultra II Directional RNA Library Prep kit with dual-indexed multiplexing barcodes, with total RNA as the input, omitting the polyA selection step. Library quality and adaptor dimer contamination were analyzed using Agilent High Sensitivity DNA Chip. An additional round of library size selection was performed using homemade Serapure size selection beads (Rohland et al 2012, PMID 22267522) for libraries containing significant adaptor dimers.

treatment_protocol: For samples labeled 'Week 0-7', arthroconidia generated from 30˚C growth coniditions were incubated at 4˚C in PBS for the specified number of weeks prior to RNA harvest.

value: liquid culture

value: WT

value: Week7 at 4C

tag: replicate


title: Atlantic salmon, skin, control

status: Public on Jun 24 2024

city: Midlothian

first: Sarah

last: Salisbury

address: Easter Bush Campus

institute: The Roslin Institute, University of Edinburgh

description: Sample 11

data_processing:
Genome indexing and library mapping was performed with STAR (version 2.7.10a).
Assembly: We appended the mitochondrial genome from the ENSEMBL V2 Atlantic salmon genome (Salmo_salar.ICSASG_v2.dna_rm.toplevel.fa.gz, v2, release 105, masked genome, assembly ID: GCA_000233375.4) to the ENSEMBL V3 Atlantic salmon genome (Salmo_salar.Ssal_v3.1.dna_rm.toplevel.fa.gz, v3.1, release 106, masked genome, assembly ID: GCA_905237065.2) for both the .gff and .fna files prior to indexing. For coho salmon, we appended this species’ mitochondrial genome (version NC_009263.1, NCBI) to the ENSEMBL V2 coho salmon genome (Oncorhynchus_kisutch.Okis_V2.dna_rm.toplevel.fa.gz, v2, release 106, masked genome, assembly ID: GCA_002021735.2) for both the .gff and .fna files prior to indexing.
Supplementary files format and content: Tab-separated values file for barcodes
Supplementary files format and content: Tab-separated values file for features
Supplementary files format and content: Matrix file

molecule: nuclear RNA

organism: Salmo salar

source_name: skin

extract_protocol:
Nuclei were extracted in accordance with Ruiz Daniels et al. (2023) (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10484441/). In brief, approximately 45 mg tissue samples were cut with scissors in 1 mL of TST buffer for 10 minutes on ice before being filtered through a 40 µm Falcon™ cell strainer (Thermo Fisher Scientific, catalog no. 08-771-2). A further 1 mL of TST and 3 mL of 1X PBS + BSA buffer were added to each sample before centrifuging at 4°C for 5 minutes at 500 g. Samples were resuspended in 1 mL 1X ST buffer filtered again through a 40 µm cell strainer, stained with Hoechst 33342 Solution (Thermo Fisher Scientific, catalog no. 62249) and then nuclei integrity was visually assessed using a fluorescent microscope. A disposable flow haemocytometer (C-Chip Neubauer Improved (100 µm depth), NanoEnTek, catalog no. DHC-N01) was then used to estimate nuclei counts.
Samples were processed with Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual Index) (10X Genomics) using the protocol outlined in the User Guide (CG000315 Rev C). Samples were diluted with nuclease-free water to a target concentration that would recover approximately 7000 nuclei in the final library. Samples were then loaded on the Chromium Controller for nuclei droplet formation. After subsequent nuclei and UMI barcoding and reverse transcription, resulting cDNA was then amplified, fragmented, and indexed with Truseq adapters and Illumina sample indexes.

value: skin

value: control


title: WT Week7 2

description: Coccidioides posadasii Silveira


title: WT Week7 1

description: Coccidioides posadasii Silveira


title: lacZ-S3

value: Sprague-Dawley


title: X1i


title: WT Week5 2

description: Coccidioides posadasii Silveira

value: Week5 at 4C


title: WT Week3 3

description: Coccidioides posadasii Silveira

value: Week3 at 4C


title: X3i


title: WT Week3 1

description: Coccidioides posadasii Silveira


title: WT Week2 3

description: Coccidioides posadasii Silveira

value: Week2 at 4C


title: WT Week2 2

description: Coccidioides posadasii Silveira


title: WT Week2 1

description: Coccidioides posadasii Silveira


title: WT Week1 2

description: Coccidioides posadasii Silveira

value: Week1 at 4C


title: WT Week1 1

description: Coccidioides posadasii Silveira


title: WT Week1 3

description: Coccidioides posadasii Silveira


title: WT Week0 1

description: Coccidioides posadasii Silveira

value: Week0 at 4C


title: WT 25 2-1

description: Coccidioides posadasii Silveira


title: WT 25 2-3

description: Coccidioides posadasii Silveira


title: WT 37 2-1

description: Coccidioides posadasii Silveira


title: WT 25 2-2

description: Coccidioides posadasii Silveira


title: WT 37 2-3

description: Coccidioides posadasii Silveira


title: WT Week0 2

description: Coccidioides posadasii Silveira


title: WT 25 1-3

description: Coccidioides posadasii Silveira


title: WT 25 1-1

description: Coccidioides posadasii Silveira


title: LN308, Control, replicate 4

status: Public on Oct 05 2025

city: Boston

first: Ryan

middle: A.

last: Flynn

state: MA

address: 1 Blackfan Circle

department: Department of Pediatrics

institute: Boston Children's Hospital

description:
Library name: 12h
count_matrix_homo.csv
counts_long.csv

data_processing:
FASTQ files were demultiplexed by Illumina software. Reads were trimmed with cutadapt (v4.9) to remove UMIs, adapters, poly(A/G) tails, and low-quality bases, discarding reads <15 nt. Trimmed reads were aligned with bowtie2 (v2.5.4) to curated small ncRNA transcriptomes (human, mouse, or dog), retaining multimappers. Multi-mapped reads were resolved by an EM-based probabilistic assignment scheme adapted from salmon/alevin, yielding transcript-level counts. After EM hard-assignment, per-base pileups were generated from BAM files using samtools (v1.21) mpileup and processed with cpup (https://github.com/y9c/cpup) to extract per-position base counts (reference vs. non-reference bases, insertions, deletions, skips, mismatches). Count matrices were annotated with sample metadata (Input, IP, Control) and deposited as processed data. Software: cutadapt v4.9; bowtie2 v2.5.4; samtools v1.21; cpup v0.1; R v4.3.3
Assembly: Curated small ncRNA transcriptomes (see GitHub: www.github.com/FlynnLab/rPAL-seq)
Supplementary files format and content: count_matrix_homo.csv, count_matrix_mus.csv, count_matrix_canis.csv: Species-specific, EM-assigned transcript-level raw read counts (rounded to nearest integer). Each row corresponds to a transcript. Each column corresponds to a library. Values are raw counts used for DESeq2 analysis.
Supplementary files format and content: counts_long.csv: Per-base variant count matrix in long format. Each row represents one genomic position within a transcript. Columns include transcript/position identifiers (chr_pos, chr, pos, ref_base), sample metadata (super_group, group_name, replicates, pair_id, sample_id, sample, condition), sequencing depth (depth_raw), reference counts (REF), variant subcategories (SGID, A_star, C_star, G_star, T_star), and summary totals (mismatches, total_variant, nonvariant). Values are raw base counts used as input for variant enrichment analyses.

growth_protocol: OCI-AML2, OCI-AML3, Molm13, Jurkat, Jeko1, Nalm6, and EMT6 cells were cultured in RPMI-1640 medium (Gibco, cat. no. 61870036); HeLa, A549, 293T, Huh7, LPS853 and LN308 were cultured in DMEM medium (Gibco, cat. no. 10566024). DiFi and MDCK cells were cultured in DMEM medium supplemented with 1% L-glutamine (Gibco, cat. no. 25030081) and 1% non-essential amino acids (Gibco, cat. no. 11140050). All media were supplemented with 10% FBS (R&D Systems, cat. no. S11150) and 1% penicillin-streptomycin (Gibco, cat. no. 15140122). Cells were maintained at 37 °C, 5% CO2. All cell lines tested negative for mycoplasma contamination (Universal mycoplasma detection kit; ATCC, cat. no. 30-1012K).

extract_protocol:
Cells were washed with PBS and lysed directly in RNAzol (Molecular Research Center) without trypsinization (1 mL per 10 cm plate of adherent cells or per 5 × 10^6 suspension cells). Lysates were homogenized, clarified by centrifugation, and crude small RNA was precipitated with isopropanol and water. RNA was purified on Zymo Research spin columns using guanidine/ethanol washes, on-column Proteinase K digestion, and water elution. Purified RNA was further treated with StcE mucinase (Sigma) followed by an additional Zymo column cleanup. Small RNAs were fractionated by mixing RNA with adjusted RNA binding buffer (Zymo RNA binding buffer mixed with one volume of ethanol) and recovered from the flow-through on a second Zymo column._x000B_To obtain secreted fractions, cells were cultured to ~80% confluence, washed with PBS, and incubated in serum-free medium for 48 h. Conditioned medium was cleared by centrifugation and filtration, concentrated with a 100 kDa cutoff filter, and ultracentrifuged to obtain small EVs (sEVs). Exomeres were isolated from the supernatant by additional ultracentrifugation, and supermeres were recovered from the exomere supernatant by higher-speed ultracentrifugation. Crude sEVs were further purified by iodixanol (Sigma) density-gradient centrifugation, and pooled fractions containing sEVs were washed and pelleted in PBS.
Total or small RNA (50 ng–2 µg) was 3' polyadenylated with end blocking and purified. Polyadenylated RNA was subjected to enhanced rPAL labeling, biotin enrichment on neutravidin beads, and sialidase-mediated release of sialoglycoRNA. Released RNA was reverse-transcribed using anchored oligo-dT primers with template switching, followed by PCR amplification with dual-indexed primers. Amplicons (200–500 bp) were purified by gel extraction and bead clean-up. Libraries were assessed by TapeStation, pooled by concentration, and sequenced on an Illumina NovaSeq X (single-end 100 bp, dual 8 bp indexes).

treatment_protocol: For production of extracellular vesicles (EVs) and non-vesicular extracellular nanoparticles (NVEPs), cells were cultured until 80% confluent. The cells were then washed three times with PBS and cultured in serum-free medium for 48 h.

value: neural (glial)

tag: sample group

value: LN308, Control


title: WT 37 1-3

description: Coccidioides posadasii Silveira


title: WT 37 1-2

description: Coccidioides posadasii Silveira


title: WT 37 1-1

description: Coccidioides posadasii Silveira


title: WT 30 1-3

description: Coccidioides posadasii Silveira


title: WT 30 1-1

description: Coccidioides posadasii Silveira


title: C57BL6 mouse aortic arch intima lesser curvature (18hr LPS)

status: Public on Feb 22 2024

city: Toronto

first: Stylianos

last: Prattas

address: 101 College Street

country: Canada

institute: Toronto General Hospital Research Institute

data_processing:
Digital gene expression matrices were generated with the Cell Ranger Pipeline v3.1 and aligned to the mm10-2020-A reference transcriptome. The resulting digital gene expression matrix was filtered, normalized, and clustered using R 4.2.1 and Seurat 4.2.0. Features that were detected in less than 3 cells and cells with less than 200 features were excluded. We further filtered out cells with less than 500 transcripts, greater than 5000 features or a mitochondrial transcriptome of >25%. Normalization was performed using LogNormalize feature with a scale factor of 100000. PCA was performed on the top 2000 variable features that were identified using the “vst” selection method. The datasets were integrated using the Harmony algorithm based on the first 20 principal components. Cells were clustered using the Louvain algorithm based on the first 20 harmony dimensions with a resolution of 0.5. UMAP was used for non-linear reduction and two-dimensional data visualization.
Digital gene expression matrices were generated with the Cell Ranger Pipeline v3.1 and aligned to the mm10-2020-A reference transcriptome, for the 18hrLPS sample the number of GEMs analyzed was forced to 6000 cells.
Assembly: mm10-2020A
Supplementary files format and content: filtered feature matrix files

source_name: Aortic arch intima

extract_protocol:
Briefly, aortas were harvested from mice perfused with ice-cold PBS-/- supplemented with 1 μg/mL actinomycin D and 1% heparin. The ascending aorta was isolated and pinned en face in a dish with PBS-/- supplemented with 2 μg/mL actinomycin D. The dissection buffer was washed off, then the tissue was digested for 10 minutes at 37°C with a mixture of Collagenase D and DNAse I in PBS. Following digestion, aortas were washed twice; first with PBS + 2mM EDTA to inactivate the enzymes, followed by PBS alone to remove excess EDTA. Cells from the lesser curvature were gently dislodged and aspirated into PBS-/- (with 0.05% BSA to minimize cell loss and aggregation) with a P10 pipet tip.
Libraries where constructed as per the v3 ChromiumTM Single Cell 3’ Library Kit manufacturer's protocol.

treatment_protocol: For the 18hr LPS sample, mice were injected intravenously with 30 ug ultrapure LPS 18 hours prior to tissue harvest.

value: Aortic arch intima

value: 12-13 weeks

value: pooled male and female

value: Intimal cells

value: C57Bl/6J wildtype

value: 30 ug ultrapure LPS (i.v.), 18 hours prior to harvest


title: WT 30 1-2

description: Coccidioides posadasii Silveira

value: liquid culture

value: WT


title: C57BL6 mouse aortic arch intima lesser curvature (untreated control-replicate)


title: 2-year-old, Mxra7 KO, scRNAseq

status: Public on Feb 04 2024

city: Suzhou

first: Yiqiang

last: Wang

state: Jiangsu

address: 111 Renai Road

country: China

institute: Xi'an Jiaotong-Liverpool University

description: 10x Genomics

data_processing:
The Cell Ranger software (version 2.0.1, 10X Genomics) was employed for data processing. It facilitated the demultiplexing of cellular barcodes, mapping of reads to the genome and transcriptome using the STAR aligner, and down-sampling of reads as necessary. This process generated normalized aggregate data across samples, ultimately producing a matrix of gene counts.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: bone marrow

extract_protocol:
Bone marrow samples from 2-month-old and 2-year-old wild-type and Mxra7KO mice (n = 3 to 5 per group) were digested using tissue dissociation solution (RPMI 1640, Thermo Fisher Scientific) to obtain single-cell suspensions. These suspensions were subsequently filtered through 40-μm nylon sterile filters. Cell counts and viability were automatically determined and quality-controlled using a Countess® II Automated Cell Counter.
In accordance with the manufacturer's protocol, Chromium Single Cell 3′ Reagent v2 kits (10X Genomics) were employed to generate barcoded single-cell RNA sequencing (scRNA-seq) libraries. The prepared cell suspension, 10X barcode gel magnetic beads, and oil were added to separate chambers of the Chromium Chip B. Subsequently, gel beads-in-emulsion (GEM) were formed using a microfluidic "double cross" system. The GEMs were then transferred to a thermal cycler for reverse transcription. The 30nt oligo-dT reverse transcription primer on the gel magnetic beads facilitated the conversion of poly-A RNA within the cells into cDNA strands containing barcode and unique molecular identifier (UMI) information. Following this, magnetic bead purification was performed to isolate the cDNA. The purified cDNA was then amplified via PCR, and its concentration and fragment size were assessed using a Qubit fluorometer and an Agilent 2100 Bioanalyzer, respectively.

value: bone marrow

value: bone marrow cell

value: Mxra7 KO


title: C57BL6 mouse aortic arch intima lesser curvature (untreated control)


title: 2-year-old, WT, scRNAseq

description: 10x Genomics


title: 2-month-old, WT, scRNAseq

description: 10x Genomics


title: Amor_P2_uPAR_positive

status: Public on Dec 08 2023

description: 10x Genomics

data_processing:
Sequencing data was demultiplexed, mapped, and processed into gene/cell expression matrices using 10X Genomics' Cell Ranger software v7.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger). Gene expression reads were aligned to the mouse reference genome version gex-mm10-2020-A, available from the 10X Genomics website.
Assembly: mm10
Supplementary files format and content: Filtered single cell 3' cell/gene matrices in .h5 format generated by Cell Ranger for Liver + Adipose tissues
Supplementary files format and content: Filtered single cell 3' cell/gene matrices in .h5 format generated by Cell Ranger for Pancreas tissue

extract_protocol:
Live uPAR positive or negative cells were sorted by uPAR staining (R&D, FAB531P) on a SONY SH800 cell sorter, stained with AO/PI (acridine orange/propidium iodide, Nexcelon ViaStain) and checked for viability >80% using a Countess FL II Automated cell counter.
10X Genomics NextGEM v3.1 Single Cell 3' Gene Expression libraries were prepared from sorted cells according to the manufacturer's instructions and sequenced on Illumina NextSeq2000 flow cells.

value: Pancreas

value: Untreated

value: Male


title: Amor_P1_uPAR_positive

description: 10x Genomics

value: Female


title: Amor_L3_uPAR_positive

description: 10x Genomics

source_name: Liver

value: Liver


title: Amor_AT1_uPAR_positive

description: 10x Genomics

source_name: Gonadal adipose tissue

value: Gonadal adipose tissue


title: Amor_AT3_uPAR_positive

description: 10x Genomics


title: Amor_L1_uPAR_positive

description: 10x Genomics


title: Amor_P1_uPAR_negative

description: 10x Genomics


title: Amor_AT1_uPAR_negative

description: 10x Genomics


title: Amor_AT3_uPAR_negative

description: 10x Genomics


title: Amor_L3_uPAR_negative

description: 10x Genomics


title: Amor_L1_uPAR_negative

description: 10x Genomics


title: BONEMARROW pre-cDCs

status: Public on Nov 29 2023

description: 10x Genomics

data_processing:
Library generation for 10x Genomics analysis were performed following the Chromium Single Cell 3′ Reagents Kits (10x Genomics) and sequenced on an Hiseq4000 (Illumina)
Raw reads were initially processed by the Cell Ranger v.3.0.2 pipeline, aligning to the mm10 transcriptome + eGFP sequence using STAR (v.2.5.1b)
All subsequent analyses were performed in R v.3.6.1  using the Seurat (v3) package
Assembly: mm10
Supplementary files format and content: Tab-separated barcodes ID's, features files and count files

source_name: Bone Marrow

extract_protocol:
Spleens, and lungs  were cut into small pieces and digested with collagenase VIII (1 mg/ml; Sigma-Aldrich) and deoxyribonuclease I (0.4 mg/ml; Roche) in RPMI 1640 for 15 min (spleen) or 25 min (lung) at 37°C. Digested tissues were passed through a 70-μm cell strainer (BD Biosciences) and washed with FACS buffer (3% FCS and 5 mM EDTA in PBS). For lung, leukocytes were enriched by Percoll gradient centrifugation (GE Healthcare). For BM, the femur, tibia and hip extremities were cut and spun for 30 s at 10,000 rpm. Cells were resuspended in FACS buffer after centrifugation. Single cell suspensions from the bone marrow, spleen and lung were enriched for pre-cDCs by staining lineage-restricted markers with FITC-conjugated antibodies (CD3, Ly6G, SiglecF, B220, CD19, Ly6D, NK1.1, and Ter119) and depleting T, B, plasmacytoid, and red blood cells, neutrophils, eosinophils, and their precursors using the EasySep Mouse FITC Positive Selection Kit II (Stemcell technologies). Cells were stained and FACS sorted on an Aria Fusion (BD) with a 100um nozzle.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics).

value: pre-cDC

value: Bone Marrow

value: 6-8 weeks old


title: LUNG scRNASEQ pre-cDCs

description: 10x Genomics

source_name: Lung

value: Lung


title: SPLEEN pre-cDCs

description: 10x Genomics

source_name: Spleen

value: Spleen


title: AXSham48hrs

status: Public on Oct 12 2023

description: 10x Genomics

data_processing:
Library generation for 10x Genomics analysis were performed following the Chromium Single Cell 3′ Reagents Kits (10x Genomics) and sequenced on an Hiseq4000 or Novaseq (Illumina)
Raw reads were initially processed by the Cell Ranger v.3.0.2 pipeline, aligning to the mm10 transcriptome + eGFP sequence using STAR (v.2.5.1b)
All subsequent analyses were performed in R v.3.6.1  using the Seurat (v3) package
Assembly: mm10
Supplementary files format and content: Tab-separated barcodes ID's, features files and count files

source_name: Pituitary

extract_protocol:
The anterior lobe of freshly dissected pituitaries was minced and incubated for 15mn at 37ºC in 1mg/ml Papain (Sigma 10108014001), 10mg/ml DNAse I (Sigma 10104159001) and 10mg/ml Rock inhibitor (Abmole Bioscience M1817) in HBSS (Sigma H9394). pH was adjusted by addition of NaOH. The enzymatic solution was removed, and the cells were mechanically resuspended in HBSS supplemented with DNAse I and Rock inhibitor, as above. Cells were FACsorted for GFP using a large nozzle (100mm) and low pressure (20psi) for optimal cell survival.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics).

value: Sox9iresGFP positive

value: Pituitary

value: 7 to 10 w-old


title: AX48hrs

description: 10x Genomics


title: AXGX4days

description: 10x Genomics


title: AX4days

description: 10x Genomics


title: GX4days

description: 10x Genomics


title: Unchallenged

description: 10x Genomics


title: Normal_Stomach.3

status: Public on Sep 03 2023

data_processing:
Illumina read quality was checked for each sample using FastQC v0.11.5.
Raw fastq files were analyzed by removing adaptor sequences using Trimmomatic (0.36), aligned to the mouse genome using STAR (2.5.3a), and quantified transcript counts using featureCounts (1.6.3).
Assembly: Reads were aligned to the mouse transcriptome (mm10, GRCm38.91)
Supplementary files format and content: Tab-delimited text file includes raw count table for each sample

source_name: WT stomach

growth_protocol: 8- to 12-week-old WT C57BL/6 mice were starved for two hours prior to the procedure. Mice were anesthetized with isoflurane and the surgical site (epigastrium) scrubbed with a povidone-iodine scrub (Betadine) and rinsed with 70% alcohol. After opening the peritoneal cavity, the stomach was mobilized and opened up in the area of the forestomach. Afterwards the inside of the stomach was rinsed with saline to remove any residual food. Subsequently, the plasmid mix (50ul; see specifications below) was injected into the epithelial compartment in the corpus/antrum region using a 30-gauge syringe and tweezer electrodes were tightly placed around the injection bubble. Two pulses of electrical current (75V) given for 35-milisecond lengths at 500-milisecond intervals were then applied using an in vivo electroporator (NepaGene NEPA21 Type II Electroporator). After electroporation, the stomach was closed with absorbable sutures and the peritoneal cavity was rinsed with 0.5 mL of prewarmed saline. The peritoneal cavity was sutured, and the skin closed with skin staples. The mice were kept at 37°C until awoke, and post-surgery pain management was done with injections of buprenorphine and/or meloxicam for the 3 following days. Tumor formation was assessed by palpation or ultrasound imaging, and mice were sacrificed following early tumor development or at endpoint. Genome editing in EPO-GEMM tumors was confirmed by Sanger sequencing, and RNA collected from whole stomach tissue.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen)
PolyA mRNA was selected using beads coated with polyT oligonucleotides. Purified polyA mRNA was subsequently fragmented, and first and second strand cDNA synthesis performed using standard Illumina mRNA TruSeq library preparation protocols. Double stranded cDNA was subsequently processed for TruSeq dual-index Illumina library generation.
For sequencing, pooled multiplexed libraries were run on a HiSeq 2500 machine on RAPID mode. Approximately 10 million 76bp single-end reads were retrieved per replicate  condition. Resulting RNA-Seq data was analyzed by removing adaptor sequences using Trimmomatic (29), aligning sequencing data to GRCh37.75(hg19) with STAR (30), and genome wide transcript counting using HTSeq (31) to generate a RPKM matrix of transcript counts.

value: Whole tissue

value: non-treated


title: Normal_Stomach.2


title: Normal_Stomach.1


title: MPMsh2.6

source_name: MYC;sgp53;sgMsh2 gastric EPO-GEMM tumor


title: MPMsh2.5


title: MPMsh2.2


title: MPMsh2.4


title: MApc.4

source_name: MYC;sgApc gastric EPO-GEMM tumor


title: LPS853, IP, replicate 1

description:
Library name: 5p
count_matrix_homo.csv
counts_long.csv

tag: cell line

value: mesenchymal

value: LPS853, IP


title: MApc.1

tag: treatment


title: MP.6

source_name: MYC;sgp53 gastric EPO-GEMM tumor


title: MP.5


title: X5i

value: Sprague-Dawley

value: Embryonic day 18, 19 DIV

value: Striatum

value: Reln sgRNA


title: WT Week5 3

description: Coccidioides posadasii Silveira

value: liquid culture

value: WT

value: Week5 at 4C


title: MP.3


title: WT Week5 1

description: Coccidioides posadasii Silveira


title: WT Week3 2

description: Coccidioides posadasii Silveira

value: Week3 at 4C


title: MP.2


title: LN308, Control, replicate 3

description:
Library name: 11h
count_matrix_homo.csv
counts_long.csv

tag: cell type

value: neural (glial)

value: LN308, Control


title: Molm13, Control, replicate 2

description:
Library name: 18h
count_matrix_homo.csv
counts_long.csv

value: hematopoietic

value: Molm13, Control


title: WT Week0 3

description: Coccidioides posadasii Silveira

tag: genotype

value: Week0 at 4C


title: WT 37 2-2

description: Coccidioides posadasii Silveira


title: MEF_CTNS-KD-rescue_rep2

status: Public on Aug 30 2023

city: Ithaca

first: Saori

last: Uematsu

address: 526 Campus Road, Cornell University

department: Division of Nutritional Sciences

institute: Cornell University

data_processing:
The sequencing results were demultiplexed and converted to FASTQ format using Illumina bcl2fastq (v2.20.0.422) software.
The 5’ and 3’ adapters of the reads were trimmed by Cutadapt (version 2.8) using the following parameters: -g “^GGG” -a “A{10}” -n 2 -m 15 –max-n=0.1. The trimmed reads with length shorter than 15 nucleotides were excluded from the analysis.
The trimmed reads were first aligned to rRNAs using Bowtie (version 1.2.3) with the following parameters: -v 0 –norc.
The reads unaligned to rRNAs were then mapped to the custom mouse transcriptome using STAR (version 2.7.10a) with default parameters. To avoid ambiguity, reads mapped to multiple positions or with >2 mismatches were disregarded for further analysis.
Read count extraction and normalization were performed using the custom Python script.
Assembly: GRCm39.106
Supplementary files format and content: tab-delimited text files including raw count values for each sample.

source_name: MEF cells

extract_protocol:
Total RNA was extracted using TRIzol reagent from cell lysates. Messanger RNA (mRNA) was isolated by oligo (dT) magnetic beads (NEB) and separated on a 15% polyacrylamide TBE-urea gel (Invitrogen). The mRNA at 50-100 nt was excised.
The RNA was dephosphorylated by T4 PNK (NEB) followed by poly(A) tailing by PAP1 (NEB). After adapter ligation by T4 RNA ligase 2 truncated KQ (NEB), cDNA synthesis was performed by m-MLV-mut5. The synthesized cDNA was amplified by PCR using barcoded sequencing primers. The PCR products were separated on a 8% polyacrylamide TBE gel (Invitrogen). Expected DNA was excised and recovered from DNA gel elution.

value: MEF cells

value: transfected with sh-CTNS and CTNS plasmid


title: MEF_CTNS-KD_rep2

value: transfected with sh-CTNS


title: MEF_Cysteamine_rep2

value: cysteamina treatment


title: WT 25 1-2

description: Coccidioides posadasii Silveira


title: MEF_CTNS-KD-rescue_rep1


title: MEF_CTNS-KD_rep1


title: MEF_AA_rep2

value: full amino acid starvation


title: MEF_Cys_rep2

value: cysteine starvation


title: MEF_NT_rep2

value: no treatment


title: MEF_AA_rep1


title: AML25-U

status: Public on Aug 28 2023

description: BM AML1/ETO positive LSPCs untreated

data_processing:
Primary data analysis was performed with the Illumina RTA v2.4.11 .
The  sequence assembly and alignment was performed using the SeqMan NGen software  and analyzed using ArrayStar software (DNASTAR, USA).
The level of gene expression was assessed after Reads Per Kilobase Million (RPKM) normalization.
Genome_build: GRCh38 - hg38
Supplementary_files_format_and_content: Tab-delimited text file includes linear total RPKM  normalized values.

source_name: AML1/ETO positive LSPCs untreated

extract_protocol:
Total RNA was extracted from the treated AML LSPCs, using the RNeasy Micro Kit (QIAGEN AG, Switzerland).
Libraries were generated from total RNA using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Bio, Japan).

treatment_protocol: FACS-purified AML1/ETO positive LSPCs were harvested and LSPCs treated w/o rhIL-33. Treated LSPCs were then harvested for the RNA extraction.

tag: population

value: AML1/ETO positive LSPCs

value: Bone marrow (BM) derived LSPCs


title: 2-month-old, Mxra7 KO, scRNAseq

description: 10x Genomics

value: bone marrow

value: bone marrow cell

value: Mxra7 KO


title: AML20-U

description: BM AML1/ETO positive LSPCs untreated


title: AML25-T

description: BM AML1/ETO positive LSPCs treated +rhIL-33


title: AML24-T

source_name: AML1/ETO positive LSPCs treated +rhIL-33


title: AML20-T


title: Female_Saline_1

status: Public on Aug 07 2023

description: snATAC-seq

data_processing:
snATAC-seq data was aligned to the mRatBN7.2/Rn7 reference assembly using cellranger-atac v2.1.0 and the procedure outlined by 10X Genomics.
Analysis of the cellranger-atac output was analyzed using Signac v1.9.068 and Seurat v4.3.063. Counts, fragments, and barcode information for each treatment group were loaded and combined into Seurat objects as outlined by the Stuart lab website (https://stuartlab.org/signac/).
Using Signac and Suerat functions, samples were merged into one object based on a common set of features and the standard Signac dimensionality reduction and clustering workflow was performed using 2:30 dimensions and a resolution value of 0.2. Data was then integrated with the snRNA-seq data from the same samples (available at GSE222418). Common anchors between the two were used to predict and label the cell types present in the snATAC-seq data.
Assembly: Rn7 (Ensemble gtf version 105)
Supplementary files format and content: Cell Ranger Arc outputs including  matrices for barcodes (.tsv), ATAC matrix (.mtx), and peak locations (.bed) are provided for each sample.

source_name: Sprague-Dawley

extract_protocol:
Flash-frozen NAc tissue was added to a tube containing 500µl lysis buffer (1mM Tris-HCl pH 7.4, 1mM NAc, 0.3 mM MgCl2, 0.01% Tween-20, 0.01% Igepal in nuclease free water, 0.001% Digitonin, 0.1% BSA), homogenized using a motorized homogenizer and RNase free pestle, and incubated on ice for 5 minutes. Samples were then pipette mixed 15x and incubated on ice for an additional 10 minutes. Following lysis, 4 samples from same sex and treatment were grouped into a single sample, and 2mL chilled wash buffer (10mM Tris-HCl pH 7.4, 10mM NACl, 3mM MgCl2, 1% BSA, 0.1% Tween-20) was added. Samples were then passed through 70µM and 40µM Scienceware Flowmi Cell Strainers. Samples were then centrifuged at 250 rcf for 5 min at 4°C. Supernatant was removed and the pellet was resuspended in 1mL of chilled wash buffer (10mM Tris-HCl pH 7.4, 10mM NACl, 3mM MgCl2, 1% BSA, 0.1% Tween-20). 100µL of sample was then stained with 7-aminoactinomycin D and used to set a representative gate for fluorescence activated cell sorting (FACs). This gate was then used to purify nuclei further. Following FACs, samples were spun at 250 rcf for 10 min at 4°C to remove any remaining debris. Samples were then loaded into individual wells of the Chromium NextGem Single Cell Chip using 4 of the 8 available wells.
FACS-sorted nuclei were subject to 10X GEM generation, transposase barcoding, and library construction using a Chromium Next GEM Single Cell ATAC Kit v2. Libraries were quantified and underwent sequencing on an Illumina sequencing platform (NextSeq 500) using a dual-indexed, paired-end strategy (Read 1N, 50 cycles; i7 index, 8 cycles; i5 index, 16 cycles; Read 2N, 50 cycles).

treatment_protocol: Rats were injected with either cocaine (20mg/kg, dissolved in physiological saline) intraperitoneally or equal volumes of physiological saline and placed in an open field for behavioral tracking. Injections occured daily across 7 consecutive days. Tissue was harvested 1hr after the final (7th) injection, when rats were sacrificed, the brain was blocked into 1mm sections, abd the NAc was harvested and flash frozen. A total of 16 rats (8 male, 8 female, 4 per GEMwell) were used for this experiment.

value: Sprague-Dawley

value: Nucleus accumbens

value: Saline

value: Female


title: Male_Cocaine_1

description: snATAC-seq

value: Cocaine

value: Male


title: RNA K4

data_processing:
Paired-end FASTQ files were analyzed using a custom bioinformatics pipeline built with Snakemake (v6.1.0). Read quality was assessed using FastQC before and after trimming with Trim_Galore! (v0.6.7). Splice-aware alignment to the mRatBn7.2/Rn7 reference assembly for cultured embryonic rat striatal neurons was performed using Ensembl gene transfer format (gtf) file (version 105) with STAR (v2.7.9a).
Binary alignment map (BAM) files were indexed with SAMtools (v1.13)
Gene-level counts were generated using the featureCounts function within the Rsubread package (v2.6.1) in R (v4.1.1)
QC metrics were collected and reviewed with MultiQC(v1.11).
Differential expression testing was conducted using DeSeq2 (v1.38.3). DEG testing p-values were adjusted with the Benjamini-Hochberg method. DEGs were designated as those genes with an adjusted p-value < 0.05 and a |log2FoldChange| > 0.5.
Assembly: Rn7 (Ensemble gtf version 105)
Supplementary files format and content: Str_4h_KCl_count_matrix.txt contains RNA-seq count values for annotated gene for each sample

growth_protocol: Neurons were removed from rat striatal tissue at embryonic day 18, and maintained in vitro for 11 days prior to RNA-seq. Each culture well contained ~250,000 cells.

extract_protocol:
Total RNA from was extracted, DNase-treated, and purified (RNeasy, Qiagen). 1µg of total RNA underwent quality control (Bioanalyzer; all RIN values > 7.0) and library construction for total RNA sequencing.
1 μg of total RNA underwent quality control (Bioanalyzer) and was prepared for directional RNA sequencing using NEBNext reagents (New England Biolabs) according to manufacturer’s recommendations. Specifically, the NEBnext rRNA depletion kit was used to remove ribosomal RNA to include both polyadenylated and non-polyadenylated RNA. RNA-seq libraries underwent sequencing (75 bp paired-end directional reads) on an Illumina sequencing platform (NextSeq500).

treatment_protocol: Neurons were treated as described with neurobasal media (vehicle) or potassium chloride (KCl; 10mM) for 4 hours on DIV 11.

value: Embryonic day 18, 11 DIV

value: Striatum

value: KCl (10mM)


title: RNA K3


title: MApc.3

value: Whole tissue

value: non-treated


title: MApc.5


title: RNA K2


title: LPS853, Input, replicate 1

description:
Library name: 5i
count_matrix_homo.csv
counts_long.csv

value: mesenchymal

value: LPS853, Input


title: RNA V3

value: Vehicle


title: RNA V4


title: RNA V2


title: RNA V1


title: AK4

description: ATAC-seq

data_processing:
Low-quality bases (Phred <20) and Nextera adapters (5’-CTGTCTCTTATA-3’) were identified and trimmed using FastQC and TrimGalore (v0.6.7).
FASTQ files containing trimmed sequences were then aligned to Rn7 Ensembl genome assembly (v105) to generate binary alignment map (BAM) files with Bowtie2 (v.2.4.4).
PCR duplicates and reads mapping to the mitochondrial genome were removed using SAMtools52 (v1.13)
BigWig files were generated with deeptools v3.5.1. QC metrics were collected and reviewed with MultiQC54 (v1.11)
ATAC peaks were called using MACS2 (v 2.1.1.20160309) callpeak with options - -qvalue  0.01 - -gsize 2626580772 - -format BAMPE.
Differential accessibility analysis was performed with Diffbind (v3.8.4). DARs were defined as regions with an adjusted p-value < 0.05. Reads within peaks were counted using the dba.count() function with options bParallel=TRUE, summits=250, bUseSummarizeOverlaps=TRUE, and score = DBA_SCORE_TMM_READS_FULL_CPM.
Assembly: Rn7 (Ensemble gtf version 105)
Supplementary files format and content: 4_Hour_ATAC_Counts.txt contains ATAC count values for defined peaks for each sample
Supplementary files format and content: 4_Hour_Aniso_ATAC_Counts.txt contains ATAC count values for defined peaks for each sample

growth_protocol: Neurons were removed from rat striatal tissue at embryonic day 18, and maintained in vitro for 11 days prior to ATAC-seq. Each culture well contained ~250,000 cells.

extract_protocol:
Following treatment, media was aspirated, and cells were washed with 1x cold PBS. Then, 600 µl of Lysis Buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630, Molecular Grade H2O) was added to cell culture wells and incubated for 5 mins on ice. Lysed cells were then transferred to a 1.5 ml Eppendorf tube and centrifuged at 500 g for 10 mins in a swinging bucket centrifuge. Following removal of supernatant containing lysis buffer and cell debris, 500 µl of 1x cold PBS was added to each tube, and nuclei were counted using the Countess II (Life Technologies). The approximate volume needed to achieve 50,000 nuclei was then placed in new Eppendorf tube, and centrifuged at 500 g for 10 mins in a swinging bucket centrifuge.
The nuclei pellet was then resuspended in 22.5 µl of tagmentation reaction mix containing Molecular Grade H2O, 2x Tagment DNA Buffer (Illumina), 0.011% Digitonin, 0.1% Tween-20, followed by the addition of 2.5 µl TDE1 (Illumina) and incubated at 37°C for 1 hr. Following tagmentation, libraries were PCR amplified and purified using the Qiagen Minelute PCR purification kit (Qiagen). To remove primer dimers, libraries were bead purified using one round of 1.0X Ampure XP beads with 80% ethanol, followed by a second round of 0.8X Ampure beads with 80% ethanol. Libraries were sequenced (75-bp paired end reads) on the NextSeq500 platform (Illumina).

treatment_protocol: Neurons from experiment 1 were treated as described with neurobasal media (vehicle) or potassium chloride (KCl; 10mM) for 4 hours on DIV 11. Neurons from experiment 2 were treated with DMSO or anisomycin (40µM) for 30 minutes prior to a second treatment with either vehicle or 10mM KCl. 50,000 cells per sample were harvested for ATAC-seq.

tag: experiment id

tag: treatment 1

value: Anisomycin (40microM)

tag: treatment 2


title: AK3

description: ATAC-seq

tag: strain


title: AK2

description: ATAC-seq

tag: age


title: DK2

description: ATAC-seq

value: DMSO


title: DK1

description: ATAC-seq


title: DV3

description: ATAC-seq


title: lacZ-S5

data_processing:
All raw fastq files were aligned to the Ensembl mRatBn7.2 (Rn7) genome using CellRanger v7.1.0 with the associated Ensembl gene transfer format (gtf) file (version 105). CellRanger filtered outputs were analyzed with Seurat v4.3.0.1 using R v4.3.1.
To filter out background contamination, cell-free ambient RNA was removed using SoupX v.1.6.2. Next, we continued quality filtering in R with Seurat v.4.3.0.1 by removing nuclei containing <200 genes and >5% of reads mapping to the mitochondrial genome (5,846 nuclei post-processing). The counts data for each individual were then normalized, scaled by a factor of 10,000, and log-transformed.
For each sample, we used Seurat to determine the 3,000 genes with highest cell-to-cell variability; these sets of genes were used to identify “anchor” pairs of cells between samples with a shared pattern of gene expression. We then integrated the eight individual datasets based on the identified anchors, using the first 17 principal components (PCs). Downstream analysis was performed on the integrated dataset.
Expression for each gene in the integrated dataset was scaled to a mean of 0 and variance of 1 across cells. We used Seurat for initial dimensionality reduction and clustering as detailed below. We first performed dimensionality reduction via PCA retaining 17 PCs, followed by UMAP with the 17 previously identified PCs as input. Cells were then clustered under a graph-based approach by first identifying K-nearest neighbors in PCA space, and then clustering under a Louvain algorithm with a resolution of 0.3. After initial clustering but before differential gene expression analysis, we used DoubletFinder v.2.0.3 to identify and remove heterotypic doublets, a consequence of two cells of different types being captured in a single droplet and thus presenting as a single heterotypic “cell.” We assumed a doublet formation rate of 4% based on 8,000 cells loaded per GEM well, as indicated in the 10x Genomics library preparation documentation. After removing doublets, we repeated the dimensionality reduction and clustering steps detailed above. We matched the resulting clusters to specific cell types based on known marker genes from previous work
To identify genes differentially expressed between Reln knockdown and lacZ controls, we conducted a differential expression analysis on a pseudobulked gene expression matrix created by summing counts for each gene within a sample (or single GEM well) and across cells within each cell type. Genes with mean counts <5 were removed. Differential expression analysis was conducted with DESeq2 v.1.40.2 using a likelihood ratio test (LRT) with treatment condition as the main effect and controlling for the effect of sex to ensure that identified significant differential expression could be attributed to the treatment and not confounded by differences in response between sexes. To assess differential expression among cell types, we conducted a separate LRT with cell type as the main effect and controlling for sex.
Assembly: Rn7 (Ensemble gtf version 105)
Supplementary files format and content: Cell Ranger output matrices for barcodes, features, and gene expression counts are provided for each sample.

source_name: nucleus accumbens

extract_protocol:
Brains were blocked in 1mm sections, and NAc punches were obtained, flash frozen, and stored at -80°C prior to nuclei isolation. 1mm brain sections were taken at the level of the nucleus accumbens, and nucleus accumbens tissue was dissected using a 2mm punch tool centered on the nucleus accumbens core subregion, and frozen for storage. Frozen tissue punches were thawed slowly on ice prior to being chopped by scalpel 100 times in 2 orthogonal directions. Tissue from one rat was transferred to 5mL of chilled (4°C) Lysis Buffer (10mM Tris-HCl, 10mM NaCl, 3mM MgCl2 (Thermo Fisher, BP214-500), 0.1% Igepal in Nuclease-Free Water (Sigma, 18896-50ML)) for 15 min, mixing the tissue by inversion every 2 min. Lysis was quenched immediately at 15 min with 5mL of complete Hibernate-A (Thermo Fisher, A1247501) supplemented with B27 and Glutamax (Life Technologies, 35050-061)). Tissue was then triturated by fire-polished Pasteur pipette (2 pipettes of decreasing diameter; 8-10 passes per pipette) for 35 min and passed through a 40µm pre-wet filter. The samples were then pelleted at 500rcf for 10 min at 4°C followed by a wash in 10mL of Nuclei Wash & Resuspension Buffer (1X PBS, 1% BSA, 0.2U/ul NxGen RNase inhibitor (Lucigen, 30281-2)). Supernatant was then removed and the pellet was gently resuspended in a total volume of 800µl prior to 7-AAD (Thermo Fisher, 00-6993-50) staining and FACS to further purify the nuclei for sequencing. Immediately after FACS, nuclei were washed a final time at 200rcf in 10mL supplemented Hibernate-A containing 1% BSA for 10 minutes at 4°C to remove any remaining fine debris and nascent RNA.
FACS-sorted nuclei were subject to 10X GEM generation and barcoding, GEM-RT cleanup and cDNA amplification, and library construction using a Chromium Single Cell 3ʹ Reagent Kit (v3 chemistry) on the Chromium iX instrument. Libraries were constructed according to manufacturer's instructions using the Chromium Single Cell 3′ Library Construction Kit (10× Genomics, PN-1000190). Nuclei (6,221 total) from adult rat NAc were sequenced on the Illumina NovaSeq6000 at the UAB Heflin Genomics core to a depth of ~300,000 reads per nuclei.

value: 90-120 days old

tag: tissue

value: nucleus accumbens

tag: Sex

value: lacZ sgRNA


title: K4

description: ATAC-seq

value: Sprague-Dawley


title: DK4

description: ATAC-seq


title: AK1

description: ATAC-seq


title: K3

description: ATAC-seq


title: DK3

description: ATAC-seq


title: V4

description: ATAC-seq


title: DV4

description: ATAC-seq


title: V3

description: ATAC-seq


title: K2

description: ATAC-seq


title: V1

description: ATAC-seq


title: DV2

description: ATAC-seq


title: Amor_P2_uPAR_negative

description: 10x Genomics

source_name: Pancreas

value: Pancreas

value: WT

value: Untreated


title: BT20-Dox-mRNA

status: Public on Jun 07 2023

data_processing:
The adaptor AAAAAAAAAAAA was trimmed by Cutadapt. The reads with length <15 nt were not included. The trimmed reads were aligned to human transcriptome, using STAR with default parameters. The uniquely mapped reads were used for analysis. TRNA-seq was analyzed following PMID: 33581077.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include RPKM values for each sample

source_name: BT20 cells

extract_protocol:
For tRNA-seq, total RNA was extacted with Trizol, deacylated in 50 mM Tris-HCl (pH 9.0) at 37 °C for 45 min and then resolved by 10% polyacrylamide TBE-urea gel (Invitrogen). tRNA (60 to 100 nt) were collected by gel excision and resolved in RNA elution buffer (300 mM NaOAc pH 5.2, 1 mM EDTA, 0.1 U/μL SUPERase In) overnight. After ethanol precipitation, tRNA was treated with demethylase (rtStarTM tRNA-optimized First-Strand cDNA Synthesis Kit, ArrayStar) and cleaned up. 1 μg tRNA was used for library construction. For ribo-seq, ribosome fractions separated by sucrose gradient sedimentation were pooled and digested with E. coli RNase I (Ambion, 750 U per 100 A260 units) by incubation at 4°C for 1 h. SUPERase inhibitor (50 U per 100 U RNase I) was then added into the reaction mixture to stop the digestion. Total RNA was extracted using TRIzol reagent. RNA was separated on a 15% polyacrylamide TBE-urea gel (Invitrogen) and the ribosome protected fractions were excised (25-35 nt).
RNA was dephosphorylated. Poly(A) tailing, 5’ adenylation, adaptor ligation, and library construction were carried out as described in PMID: 36824937.

value: BT20 cells

value: Dox-inducible SAMD9 R1293W

value: treatment with Dox for 12 hours

tag: fraction

value: mRNA


title: BT20-Dox-RPF (rep2)

data_processing:
The adaptor AAAAAAAAAAAA was trimmed by Cutadapt. The reads with length <15 nt were not included. The trimmed reads were aligned to human transcriptome, using STAR with default parameters. The uniquely mapped reads were used for analysis. TRNA-seq was analyzed following PMID: 33581077.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include RPKM values for each sample
Library strategy: Ribo-seq

value: Ribosome protected fragment


title: BT20-Con-mRNA

value: nontreated


title: BT20-Con-RPF (rep2)


title: BT20-Dox-RPF (rep1)


title: DV1

description: ATAC-seq

value: Embryonic day 18, 11 DIV

value: Striatum


title: Normal_Stomach.4

value: Whole tissue

value: non-treated


title: BT20-Con-RPF (rep1)


title: HeLa-WT-VACV-tRNA (rep2)

source_name: HeLa cells

value: HeLa cells

tag: infection

value: WT VACV

value: tRNA


title: MApc.6


title: HeLa-WT-VACV-tRNA (rep1)


title: HeLa-VACV-tRNA (rep2)

value: vK1-C7- VACV


title: HeLa-VACV-tRNA (rep1)


title: HeLa-uninfected-tRNA (rep1)

value: uninfected


title: MPMsh2.1


title: MPMsh2.3


title: MApc.2


title: HeLa-uninfected-tRNA (rep2)

value: WT


title: Skin1

status: Public on May 08 2023

city: Roslin

first: rose

middle: ruiz

last: daniels

address: The University Of Edinburgh

institute: The University of Edinburgh

description:
snRNA-seq 10x
skin1

data_processing:
Supplementary files format and content: Raw sequencing data were aligned to the unmasked ICSASG_v2 reference assembly (Ensembl release 104) of the Atlantic salmon genom
The analysis used just protein coding genes. Mapping of reads to the genome, assignment of reads to cellular barcodes, and collapsing of unique molecular identifiers (UMIs) was performed using STARsolo v2.7.7a
The top 100,000 cell barcodes ranked by UMI number were retained to ensure the capture of transcriptionally quiet nuclei, these are normally lost when using the automated STARsolo filtering algorithm
Assembly: S.salar V2 emsbl
Supplementary files format and content: Tab-separated values files and matrix files

source_name: skin

extract_protocol:
for libraries S3 and s6 we followed the nuclei extraction protocol of Taylor & Ruiz Daniels 2022
For libraries PElv2 and Skin1 we followed the nuclei extratraction protocol of dx.doi.org/10.17504/protocols.io.261genwm7g47/v2
Nuclei were processed through the 10X Chromium™ Single Cell Platform using the Chromium™ Single Cell 3` Library and Gel Bead Kit v3.1 and Chromium™ Single Cell A Chip Kit (both 10X Genomics) as per the manufacturer’s protocol with the aim of recovery of 7000 nuclei.

value: skin

value: frozen tissue

value: nucleus

value: single nucleus

value: Ruiz Daniels 2023


title: PIL C4

status: Public on Mar 13 2023

data_processing:
Illumina read quality was checked for each sample using FastQC v0.11.5.
Raw fastq files were analyzed by removing adaptor sequences using Trimmomatic (0.36), aligned to the mouse genome using STAR (2.5.3a), and quantified transcript counts using featureCounts (1.6.3).
Assembly: Reads were aligned to the mouse transcriptome (mm10, GRCm38)
Supplementary files format and content: Tab-delimited text file includes raw count table for each sample

source_name: tumor cells from KPCmut PDAC tumors transplanted into lungs (PIL)

growth_protocol: To generate pancreatic tumors, 5x104 KrasG12D/+;Trp53R172H/wt (KPCmut) PDAC cells (PIP) or KrasG12D/+;p53-/- (KP) lung cancer cells expressing luciferase and GFP (LUC-GFP) were transplanted into the pancreas of 8-10 week old C57BL/6 female mice. Mice were monitored for tumor development (5-8 days post-transplantation) by bioluminescence imaging (BLI) on a Xenogen IVIS Spectrum imager (PerkinElmer) before being randomized into various study cohorts. To generate lung tumors, 5x105 KPCmut PDAC cells (PIL) or 4x104 KP lung cancer cells expressing luciferase and GFP (LUC-GFP) were tail vein injected into 8-10 week old C57BL/6 female mice. Mice were monitored for tumor development (5-8 days post-transplantation) by bioluminescence imaging (BLI) on a Xenogen IVIS Spectrum imager (PerkinElmer) before being randomized into various study cohorts.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen)
PolyA mRNA was selected using beads coated with polyT oligonucleotides. Purified polyA mRNA was subsequently fragmented, and first and second strand cDNA synthesis performed using standard Illumina mRNA TruSeq library preparation protocols. Double stranded cDNA was subsequently processed for TruSeq dual-index Illumina library generation.
For sequencing, pooled multiplexed libraries were run on a HiSeq 2500 machine on RAPID mode. Approximately 10 million 76bp single-end reads were retrieved per replicate  condition. Resulting RNA-Seq data was analyzed by removing adaptor sequences using Trimmomatic, aligning sequencing data to GRCh37.75(hg19) with STAR, and genome wide transcript counting using HTSeq to generate a RPKM matrix of transcript counts.

treatment_protocol: Tumor-bearing mice were treated with vehicle or combined trametinib (1 mg/kg body weight), and palbociclib (100 mg/kg body weight) per os for 4 consecutive days followed by 3 days off treatment for 2 weeks before sacrafice.

value: tumor cells

value: T/P (C)


title: PIL C3


title: PIL C2


title: MP.9


title: MP.8


title: MP.7


title: MP.4


title: PIL C1


title: PIL V2

value: Vehicle (V)


title: PIL V1


title: LIL C3

source_name: tumor cells from KP lung tumors transplanted into lungs (LIL)


title: LIL C4


title: PIL V4


title: LIL C2


title: LIL C1


title: LIL V2


title: MP.1


title: PIL V3


title: LIP C4

source_name: tumor cells from KP lung tumors transplanted into pancreas (LIP)


title: LIL V1


title: LIP C3


title: LIP C2


title: LIP C1


title: LIP V4


title: LIP V3


title: LIP V2


title: LIP V1


title: Immune_p53 Off 3

status: Public on Jan 28 2023

description: 10x Genomics (3' kit, v2.0)

data_processing:
All scRNAseq data were processed into count matrices using 10x Genomics CellRanger All scRNAseq data were processed into count matrices using 10x Genomics CellRanger 6.0.0 with default parameters using reference mouse genome GRCm38/mm10 augmented with BioLegend TotalSeqB hashtag oligonucleotide barcode sequences for demultiplexing cellular compartments in downstream analysis oligonucleotide barcode sequences for demultiplexing cellular compartments in downstream analysis. Count matrices were processed to remove empty and low quality droplets by removing (in order): transcripts with more than 10 million or fewer than 100 total reads, droplets with library size greater than 150,000 or lower than 300 total read count, and droplets with fewer than 15 distinct expressed transcripts.
Potential doublets were removed using Solo version 1.2 (76) by training one doublet classification model per sample using default parameters for Solo and removing droplets using a threshold of 0.5. Subsequently, dead / dying cells were filtered by removing droplets with high mitochondrial RNA content (greater than 20% of transcript counts mapped to MT genes) or high ribosomal transcript count (greater than 15% of total transcript counts mapped to ribosomal genes). After pre-processing, poor quality samples with either low numbers of recovered cells or low number of distinct transcripts recovered were removed.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: liver tumor

growth_protocol: GFP-expressing NSP tumor cells were cultured off Dox to suppress p53 expression and orthotopically injected into liver of C57B/6 mice fed with Dox food. After 2-3 weeks tumor growth, the mice were randomized either keeping on Dox or removing Dox diet to control p53 expression in tumor cells

extract_protocol:
Single-cell encapsulation and scRNA-seq library prep of Flow cytometry-sorted cell suspensions was performed on the Chromium instrument (10x Genomics) following the user manual (Reagent Kit 3’ v2). Each sample loaded onto the cartridge contained approximately 40,000 cells at a final dilution of ~600 cells/μl. Transcriptomes of encapsulated cells were barcoded during reverse transcription.
cDNA was purified with DynaBeads, followed by amplification per the user manual (Reagent Kit 3’ v2). Next, the PCR-amplified product was fragmented, A-tailed, purified with 1.2X SPRI beads, ligated to sequencing adapters and indexed by PCR. Indexed DNA libraries were double-size purified (0.6–0.8X) with SPRI beads.
scRNA-seq (3' kit, v 2.0)

treatment_protocol: Liver tumors were harvested from the indicated mouse models and processed for FACS using Collagenase IV (1 mg/mL) & Dispase II (2 U/mL) mix digestion solution and Gentle-MACS dissociator (mTDK_1 protocol), followed by a 0.05% Trypsin-EDTA step. Cell suspensions were incubated with Fc block and CD45-APC or CD45-APC-Cy7 antibody to mark immune cells. Live immune cells from liver tumor (marked as GFP-negative, CD45-positive and DAPI-negative) were sorted using Sony or Aria 1 sorter, and collected in 2% 1x PBS buffer containing 2% fetal bovine serum (FBS).  Single-cell suspensions were spun down and resuspended in 0.05% BSA containing 1 U/µL Invitrogen Ambion RNase Inhibitor (AM2682, Thermo Fisher Scientific).

value: sorted primary immune cells (CD45+)

value: liver tumor

tag: condition

value: orthotopic liver injection

value: p53 Off

tag: sorting strategy

value: GFP-; Cd45+;DAPI-

tag: mouse strain

value: Female


title: MEF_NT2_rep2

tag: cell line

value: MEF cells

value: no treatment


title: MEF_Cysteamine_rep1

value: WT

tag: treatment

value: cysteamina treatment


title: Immune_p53 Off 2

description: 10x Genomics (3' kit, v2.0)

tag: cell type


title: Immune_p53 On 1

description: 10x Genomics (3' kit, v2.0)

value: p53 On 8 days


title: Immune_p53 On 2

description: 10x Genomics (3' kit, v2.0)


title: Immune_p53 Off 1

description: 10x Genomics (3' kit, v2.0)


title: NSP_SEN_IFNG_1 ng_2

source_name: in vitro senescent NSP cells + IFNg high dose

growth_protocol: NSP cells were cultured in DMEM supplemented with 10% FBS and 1% penicillin and streptomycin (GIBCO) on plates that were collagen-coated (PurCol, Advanced Biomatrix, 0.1 mg/ml) for 30’ at 37 C and maintained by the addition of 1 μg/ml doxycycline to suppress p53 expression. In order to restore p53 expression and therefore induce senescence, doxycycline-containing media was replaced with doxycycline-free media for 6 days and senescent cells were seeded and collected on day 8 after doxycycline withdrawal. For IFN-γ of proliferating or senescent populations, the indicated doses of mouse recombinant IFN-γ was administrated to proliferating and senescent (p53-restored) NSP cells after 24 h of cell seeding and cells were harvested after 24 h of IFN-γ treatment.

extract_protocol:
PolyA mRNA was selected using beads coated with polyT oligonucleotides. Purified polyA mRNA was subsequently fragmented, and first and second strand cDNA synthesis performed using standard Illumina mRNA TruSeq library preparation protocols. Double stranded cDNA was subsequently processed for TruSeq dual-index Illumina library generation.
For sequencing, pooled multiplexed libraries were run on a HiSeq 2500 machine on RAPID mode. Approximately 10 million 76bp single-end reads were retrieved per replicate  condition. Resulting RNA-Seq data was analyzed by removing adaptor sequences using Trimmomatic (29), aligning sequencing data to GRCh37.75(hg19) with STAR (30), and genome wide transcript counting using HTSeq (31) to generate a RPKM matrix of transcript counts.

value: Cell line

value: Doxycycline Off


title: NSP_SEN_IFNG_1 ng_1

growth_protocol: NSP cells were cultured in DMEM supplemented with 10% FBS and 1% penicillin and streptomycin (GIBCO) on plates that were collagen-coated (PurCol, Advanced Biomatrix, 0.1 mg/ml) for 30’ at 37 C and maintained by the addition of 1 μg/ml doxycycline to suppr


title: NSP_SEN_IFNG_1 ng_3


title: NSP_SEN_No IFNG_3

source_name: in vitro senescent NSP cells + no IFNg


title: NSP_PRO_IFNG_1 ng_3

source_name: in vitro proliferating NSP cells + IFNg high dose

value: Doxycycline On


title: NSP_PRO_IFNG_1 ng_1


title: MEF_NT2_rep1

tag: genotype


title: NSP_SEN_No IFNG_1


title: NSP_PRO_No IFNG_3

source_name: in vitro proliferating NSP cells + no IFNg


title: NSP_SEN_No IFNG_2


title: NSP_PRO_IFNG_1 ng_2


title: MEF_NT_rep1

source_name: MEF cells


title: MEF_Cys_rep1

value: cysteine starvation


title: NSP_PRO_No IFNG_1


title: SC29_Dox_Combo_2_(7_days) [NSP_SEN_COMBO_2]

status: Public on Jan 17 2023

organism: Mus

source_name: in vitro senescent NSP (trametinib/palbociclib) cells

growth_protocol: NSP cells were cultured in DMEM supplemented with 10% FBS and 1% penicillin and streptomycin (GIBCO) on plates that were collagen-coated (PurCol, Advanced Biomatrix, 0.1 mg/ml) for 30’ at 37 C and maintained by the addition of 1 μg/ml doxycycline to suppress p53 expression. In order to restore p53 expression and therefore induce senescence, doxycycline-containing media was replaced with doxycycline-free media for 6 days and senescent cells were seeded and collected on day 8 after doxycycline withdrawal. For perturbing BRD4-dependent transcriptional programs, cells were treated with 500 nM of JQ1 (S7110, Selleck Chem) for 48 h prior to harvest, starting JQ1 at day 6 after restoring p53 (off-dox), when NSP cells are fully senescent. For drug-induced senescence experiments, p53-suppressed (on-dox) NSP cells were treated with trametinib + palbociclib, or cisplatin for 7 days. The concentration of DMSO corresponded to the drug treatment and does not exceed 1:1,000 dilution of total media volume, which shows no discernable toxicity to cultured cells. For IFN-γ of proliferating or senescent populations, the indicated doses of mouse recombinant IFN-γ was administrated to proliferating and senescent (p53-restored) NSP cells after 24 h of cell seeding and cells were harvested after 24 h of IFN-γ treatment.

extract_protocol:
Total RNA was extracted using using TRIzol (Thermo Fisher Scientific) following the manufacturer’s instructions.
PolyA mRNA was selected using beads coated with polyT oligonucleotides. Purified polyA mRNA was subsequently fragmented, and first and second strand cDNA synthesis performed using standard Illumina mRNA TruSeq library preparation protocols. Double stranded cDNA was subsequently processed for TruSeq dual-index Illumina library generation.
For sequencing, pooled multiplexed libraries were run on a HiSeq 2500 machine on RAPID mode. Approximately 10 million 76bp single-end reads were retrieved per replicate condition.

tag: sample type


title: SC28_Dox_Combo_1_(7_days) [NSP_SEN_COMBO_1]


title: SC27_Dox_DMSO_3_(7_days) [NSP_PRO_DMSO_3]

source_name: in vitro proliferating (DMSO) NSP cells


title: NSP_PRO_IFNg_50pg_2 [NSP_PRO_IFNG_2]

source_name: in vitro proliferating NSP cells + IFNg


title: NSP_PRO_IFNg_0pg_2 [NSP_PRO_UT_2]

source_name: in vitro proliferating NSP cells untreated


title: NSP_PRO_IFNg_0pg_1 [NSP_PRO_UT_1]


title: In vitro_SEN_JQ1_500nM_2_(2days) [NSP_SEN_JQ1_2]

source_name: in vitro senescent (p53-restored) NSP cells + JQ1


title: In vitro_SEN_DMSO_3_(2days) [NSP_SEN_3]

source_name: in vitro senescent (p53-restored) NSP cells


title: In vitro_SEN_DMSO_2_(2days) [NSP_SEN_2]


title: NSP_SEN_IFNg_0pg_1 [NSP_SEN_UT_1]

source_name: in vitro senescent (p53-restored) NSP cells untreated


title: In vitro_PRO_JQ1_500nM_3_(2_days) [NSP_PRO_JQ1_3]

source_name: in vitro proliferating NSP cells + JQ1


title: In vitro_PRO_DMSO_3_(2_days) [NSP_PRO_3]

source_name: in vitro proliferating NSP cells


title: In vitro_PRO_JQ1_500nM_1_(2_days) [NSP_PRO_JQ1_1]


title: In vitro_PRO_DMSO_1_(2_days) [NSP_PRO_1]


title: In vivo NSP_47 [NSP_47]

source_name: in vivo bulk tumor (p53-restored)

growth_protocol: C57BL/6N female mice aged 8-9 weeks old were injected via hydrodynamic tail vein injection (HTVI) with a sterile 2 ml (or 1/10 of mouse body weight) 0.9% NaCl solution containing 5 μg of pT3-EF1a-NrasG12D-IRES-rtTA (Tet-On system) and 20 ug of pT3-TRE-tRFP-shp53 transposon vectors along with 5ug CMV-SB13 transposase (5:1 ratio) through the lateral tail vein. Doxycycline was administered to mice via 625 mg/kg doxycycline-containing food pellets (Harlan Teklad) at least 4 days before injection. The tumor was harvested at 5-7 weeks after injection for cell line isolation.

extract_protocol:
To extract tissue RNA, freshly isolated tumor chunk was first stored in RNA-later solution (AM7024, Thermo Scientific) to preserve RNA integrity until extraction and RNeasy kit (74106, Quiagen) was used to purified tissue RNA following the manufacturer instructions
PolyA mRNA was selected using beads coated with polyT oligonucleotides. Purified polyA mRNA was subsequently fragmented, and first and second strand cDNA synthesis performed using standard Illumina mRNA TruSeq library preparation protocols. Double stranded cDNA was subsequently processed for TruSeq dual-index Illumina library generation.
For sequencing, pooled multiplexed libraries were run on a HiSeq 2500 machine on RAPID mode. Approximately 10 million 76bp single-end reads were retrieved per replicate condition.

value: Whole tissue


title: In vivo NSP_42 [NSP_42]


title: In vivo NSP_44 [NSP_44]


title: In vivo NSP_40 [NSP_40]

source_name: in vivo bulk tumor (p53-suppressed)


title: In vivo NSP_45 [NSP_45]


title: In vivo NSP_52 [NSP_52]


title: In vivo NSP_43 [NSP_43]


title: In vivo NSP_41 [NSP_41]