title: Survivors-3

city: Durham

first: Nicholas

last: Heaton

address: 213 Research Drive, 426 CARL Building

department: Molecular Genetics and Microbiology

institute: Duke University School of Medicine

data_processing:
CLC Genomics Workbench 24.0.2
Sequence reads were trimmed for adaptor sequence and low quality reads.
Reads were aligned with the latest moust genome custom concatenated with the Mal04-Cre genome and tdTomato.
Read count extraction, normalization, and differential expression analysis were performed using CLC genomic benchwork
Assembly: custom concatenated mm10 and Mal04-Cre
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: primary

extract_protocol:
Total RNA was extracted from each sample utilizing the Monarch Total RNA Miniprep Kit (NEB, T2010S).
RNA libraries were prepared utilizing NEBNext Ultra II RNA Library Prep Kit (E7770S) and NEBNext Multiplex Oligos for Illumina (E7335S). harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.

treatment_protocol: Infected Cre-inducible tdTomato mice with 75,000 PFU of Mal04-Cre 14dpi before tissue collection. Alevolar type 2 pneumocytes were cultured ex vivo for 7 days before being collected for sequencing.

value: primary

value: alveolar type 2 cells

value: tdTomato

value: 75,000PFU of Mal04-Cre 14days before collection

value: Day 7


title: JC_2_146 (21PG53-2)

status: Public on Jan 06 2025

type: SRA

city: Stockholm

first: Cheng

last: Zhao

state: Stockholm

address: H9 Klinisk vetenskap,171 77 Stockholm

department: Clinical Science

country: Sweden

institute: Karolinska institute

description: Gpig.scRNAseq.counts.all.tsv.gz

library_source: transcriptomic single cell

data_processing:
For the guinea pig single-cell RNA-Seq data, adapters and low-quality reads were removed using Trimgalore with default parameters. Subsequently, high-quality reads were aligned to the guinea pig Ensembl reference genome (v.Cavpor.3.0.105, Cavia porcellus, obtained from the Ensembl website)using the HISAT2 aligner (v 2.2.0) with default settings. Only uniquely mapped reads were retained for gene expression quantification. Raw read counts were tentatively quantified using featureCounts (v1.6.3) based on Ensembl reference annotation.
Considering the incomplete guinea pig reference annotation, we decided to update the guinea pig gene annotation using the following steps: 1. Ensembl transcripts belonging to “lincRNA”, “processed_pseudogene”, “protein_coding”, and “pseudogenes” were selected as the guided annotation. The mapping bam files were used as input for Stringtie (v1.3.3b) for each individual sample. After the initial assembly, the transcripts were merged using 'stringtie --merge' and compared with the guided annotation using 'gffcompare -r'. Transcripts that overlapped with multiple reference genes were excluded, as well as transcripts with a length less than 200 bp and 'class codes' identified by gffcompare equal to ‘e’, ‘s’, ‘x’ were removed in downstream analysis. Transcripts with class codes 'j', 'k', '=', 'm', 'n', 'o', 'p', 'y' were assigned to corresponding reference genes. Novel transcripts with no clear reference annotation were blasted against human and mouse transcripts of protein coding and lncRNA with parameters '-max_target_seqs 1 -outfmt 6 -num_threads 25 -evalue 1e-20 -strand plus -max_hsps 1' to find the most similar human or mouse reference genes. If there were no orthologous genes of matched reference genes in the guinea pig Ensembl annotation, they were added. Other novel transcripts with known orthologous genes in the guinea pig Ensembl annotation were reassigned to known annotated genes based on whether the novel transcripts fell within the nearby loci (± 3 kb) of the current annotation.
Assembly: Cavpor.3.0.105
Supplementary files format and content: tab-delimited text file include raw count for each Sample

molecule: polyA RNA

organism: Cavia porcellus

source_name: embryo

growth_protocol: Hartley guinea pigs (Charles River Labs, Laval, Québec) were housed in the Animal Care Facility at the CRCHUM, maintained at 21 °C with 30-70 % humidity under a 12 h light cycle, and fed with Teklad Global Guinea Pig Diet 2040 pellets, water, and hay ad libitum.

extract_protocol:
Briefly, embryos were flushed from the oviduct (E3.5) or uterine horns (E4-E5.75) using 5-10 ml of warm M2 medium (MR-015-D, Sigma Aldrich) supplemented with 1 % Penicillin-Streptomycin (15130122, Life Technologies), washed and briefly kept in M2 drops covered with Ovoil TM (10029, Vitrolife) at the incubator at 5 % O2 5 % CO2 at 37.5 °C prior to being fixed in PFA 4 % for 15 min or single cell picking. E6 embryos were collected at E5.75 and incubated in similar conditions for 6 h to reach the desirable embryonic day, as implantation occurs around E6, and obtaining embryos by flushing the uterus was challenging.
Embryos collected from E3-E5.75 were obtained through the flushing female guinea pigs and placed in M2 drops under mineral oil until further processing. Zona pellucida was removed using tyrodes, and subsequent single-cell dissociation was achieved through enzymatic digestion with TrypLE Express (12604-013, Gibco, Life Technologies) followed by isolation using fine glass capillaries. Libraries were prepared using the Smartseq2 protocol, following established procedures 14–16. The quantity and quality of the cDNA libraries were assessed using an Agilent 2100 BioAnalyzer (Agilent Technologies). Approximately 1 ng of cDNA per cell was transformed into a single-cell library using the Nextera XT DNA Library prep kit (Illumina FC-131-1096) and following the manual instructions with slight modifications. In brief, 1 ng of cDNA (in a maximum of 5 µl of sample volume) underwent tagmentation with 2 µl of TD and 1 µl of ATM at 55 °C for 5 min. Upon completion of the program, the reaction was promptly halted by adding 1 µl of 2 % SDS and incubating for 5 min at RT. Amplification was carried out using 3 µl of NMP per sample and adding 1 µl of each dual-indexed (i7 and i5; Illumina) primer. Individual Nextera XT libraries were pooled and then purified using magnetic beads. Indexed sequence libraries were combined for multiplexing (384 samples per lane). The sequencing was performed using the NovoSeq6000 paired-end.

treatment_protocol: Embryos at each stage were retrieved from at least 3 separate Hartley guinea pig females (~500 grams, 2-3 months of age) between days 3.5 and 5.75 after natural mating.

tag: tissue

value: embryo

tag: developmental stage

tag: time

value: embryo in vitro day E4.5


title: Survivors-2

state: NC

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: cell line

tag: cell type

tag: genotype

tag: treatment


city: Houston

first: Amrit

last: Koirala

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

description: Library name: PM_CLW_RMC31N_Tissue_SNF5_Proficient_H3K27me3.WI_22445

library_source: genomic

data_processing:
Data quality was assessed using FastQC and low quality basepairs were removed using TrimGalore
ChIP-Seq reads were mapped to the humangenome build UCSC hg38 using bowtie2 and duplicate reads were removed
Peaks were called using MACS2
tdf files were generated using BEDTools
Assembly: hg38
Supplementary files format and content: tag density files (tdf)

molecule: genomic DNA

organism: Homo sapiens

source_name: kidney

extract_protocol:
Frozen tissue kept on dry ice was placed in tissue pulverizer in liquid nitrogen, then crushed. 200 mg of the powdered tissue were added into the 5 mL PBS solution containing 10% of protease & phosphatase inhibitors (Sigma #P8340, Sigma #P5726, & Sigma #P0044). Crosslinking was performed using 37% Formaldehyde with a final concentration 1.5% (Fisher Scientific #CAS 7732-18-5) for 20 minutes at room temperature. Reaction was stopped using 0.5 mL 10X Glycine for 5 minutes at room temperature. After a 5-minutes centrifugation at 1,500 rpm, pellet was washed with PBS and resuspended in a PBS solution containing 10% of protease & phosphatase inhibitors. Tissue lysate was obtained using Qiagen tissue homogenizer 25 Hz for 20 seconds. Then, after a 5-minutes centrifugation at 1,500 rpm, pellet was resuspended into a buffer containing 5mM PIPES pH 8, 85mM KCl, and 0.5% NP40. Cell lysate was obtained after incubation for 15 minutes on ice. After a 5-minutes centrifugation at 4,500 rpm, pellet was resuspended into a buffer containing 50mM Tris-HCl pH8, 10mM EDTA, and 1% SDS. Nuclear lysate was obtained after incubation for 10 minutes on ice. Sonication was performed using Bioruptor® Plus for 30 to 40 cycles of 30 seconds on and 30 seconds off. Quality of sonication was checked using a solution of 5M NaCl and RNase A (Novagen #70856) for 30 minutes at 37°C. Then, Proteinase K (Novagen #71049) helped remove any protein overnight at 65°C. DNA was purified using QIAquick PCR purification kit. Quantification of DNA was performed using Nanodrop®. DNA shearing was controlled by electrophoresis: samples were considered if the majority of DNA belonged to 100 and 400 bp.
Rubicon ThruPLEX Plasma-Seq library preparation system (p/n R400492)

value: kidney

tag: tumor type

value: Adjacent normal

tag: patient id

tag: chip antibody


title: Survivors-1


title: JC_2_144 (21PG53-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_145 (21PG53-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_143 (21PG53-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


description: Library name: PM_CLW_RMC30T_Tissue_SNF5_Deficient_H3K27me3.WI_22444

value: RMC tumor


title: JC_2_141 (21PG53-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_142 (21PG53-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


description: Library name: PM_CLW_RMC30N_Tissue_SNF5_Proficient_H3K27me3.WI_22443


title: Bystanders-2


description: Library name: PM_CLW_RMC4T_Tissue_SNF5_Deficient_H3K27me3.WI_22442


title: Bystanders-1


title: JC_2_139 (21PG49-2)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: Early blastocyst

value: embryo in vitro day E5.25


title: JC_2_138 (21PG49-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


description: Library name: PM_CLW_RMC4N_Tissue_SNF5_Proficient_H3K27me3.WI_22441


title: Pair 2, Replicate 2,CMO

city: Piscataway

first: Matthew

middle: A

last: Lawlor

state: NJ

address: 604 Allison Road

department: Genetics

institute: Rutgers University

description: CMO305: WT, CMO306: Tex14m/m

library_source: other

data_processing:
Demultiplexing, single cell expression quantification, and CMO tag assignment was performed using using the cellranger multi workflow (Cellranger v7.0.1).
Assembly: mm10
Supplementary files format and content: Cellranger output files: [sample]_barcodes.tsv.gz, [sample]_features.tsv.gz, [sample]_matrix.mtx.gz, [sample]_assignment_confidence_table.csv

molecule: other

source_name: testis

extract_protocol:
Sequencing was performed with four 10-week-old males from a single litter; two Tex14m/m and two wild-type animals. Testes were dissected and two testes from a single animal were pooled. Testes were dissociated and cells were isolated as described previously (Green et al. 2018).
Single-cell libraries were generated using the 10x Genomics Chromium Controller and following the manufacturer’s protocol for 3' v3.1 chemistry with feature barcoding technology for cell multiplexing (10x Genomics). In brief, cells from each animal were counted and tagged with unique cell multiplexing oligo barcodes. Labelled cells from one wild type and one mutant were pooled equally and processed for cell encapsulation targeting 12,000 cells (~6,000 cells per mouse), followed by library preparation. This was done in duplicate to capture ~12,000 cells per mouse. Labelled cells from the second wild type and second mutant were pooled and processed similarly. Final library quality was assessed using the LabChip GXII HT (PerkinElmer) and libraries were quantified by Qubit (ThermoFisher). Pooled libraries were subjected to 28x10x10x151 bp paired-end sequencing according to the manufacturer’s protocol (Illumina NovaSeq XPlus) to generate ~25,000 reads per cell.

value: testis

value: mixed sample (Tex14 m/m, WT)


title: JC_2_135 (21PG49-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_136 (21PG49-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


description: Library name: PM_CLW_RMC31T_Tissue_SNF5_Deficient_H3K27me3.WI_22446


description: Library name: PM_CLW_RMC36N_Tissue_SNF5_Proficient_H3K27me3.WI_22447


description: Library name: PM_CLW_RMC2T_Tissue_SNF5_Deficient_H3K27me3.WI_22440


title: JC_2_134 (21PG49-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


description: Library name: PM_CLW_RMC2N_Tissue_SNF5_Proficient_H3K27me3.WI_22439


title: JC_2_14 (21PG77-1)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: 16 cell

value: embryo in vitro day E4


title: Pair 2, Replicate 1, CMO

description: CMO305: WT, CMO306: Tex14m/m


title: JC_2_133 (21PG49-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_140 (21PG49-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_130 (21PG49-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


description: Library name: PM_CLW_RMC36T_Tissue_SNF5_Deficient_H3K4me3.WI_22438


title: JC_2_131 (21PG49-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_13 (21PG77-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_129 (21PG49-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: Pair 2, Replicate 1, GEX

description: CMO305: WT, CMO306: Tex14m/m


description: Library name: PM_CLW_RMC36N_Tissue_SNF5_Proficient_H3K4me3.WI_22437


title: JC_2_128 (21PG49-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: Pair 1, Replicate 2, CMO

description: CMO307: WT, CMO308:Tex14m/m


title: JC_2_127 (21PG49-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: Pair 1, Replicate 2, GEX

description: CMO307: WT, CMO308:Tex14m/m


title: Bystanders-3


description: Library name: PM_CLW_RMC31T_Tissue_SNF5_Deficient_H3K4me3.WI_22436


title: JC_2_126 (21PG49-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_125 (21PG49-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: Pair 1, Replicate 1, CMO

description: CMO307: WT, CMO308:Tex14m/m


title: JC_2_124 (21PG49-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


description: Library name: PM_CLW_RMC30T_Tissue_SNF5_Deficient_H3K4me3.WI_22434


title: JC_2_123 (21PG49-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: Pair 2, Replicate 2, GEX

description: CMO305: WT, CMO306: Tex14m/m


title: JC_2_132 (21PG49-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: Pair 1, Replicate 1, GEX

description: CMO307: WT, CMO308:Tex14m/m


title: JC_2_122 (21PG49-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_121 (21PG49-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_12 (21PG77-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_120 (21PG49-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


description: Library name: PM_CLW_RMC30N_Tissue_SNF5_Proficient_H3K4me3.WI_22433


description: Library name: PM_CLW_RMC4T_Tissue_SNF5_Deficient_H3K4me3.WI_22432


title: Untreated MC3T3-E1 (mouse pre-osteoblastic) cells cultured in the OC medium replicate 3

city: Iowa City

first: Erliang

last: Zeng

state: IOWA

address: 801 Newton Rd, DSB N101-9, College of Dentistry

institute: University of Iowa

description: Library name: OC3

data_processing:
Cutadapt and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC.
HISAT2 was used to map reads to the genome of Mus_musculus.GRCm38 V101. StringTie was used to perform expression level for mRNAs by calculating FPKM. mRNAs differential expression analysis were performed by R package DESeq2 between two different groups.
Assembly: Mus_musculus.GRCm38 V101
Supplementary files format and content: CSV file format with gene expression measured by FPKM

source_name: mouse MC3T3-E1

growth_protocol: Mouse-calvaria-derived pre-osteoblasts (MC3T3-E1, from ATCC) cells were cultured in osteogenic medium containing α-MEM containing 10% FBS, 10 mm β-glycerophosphate and 50 mg/mL ascorbic acid-2-phosphate (Sigma–Aldrich, St. Louis, MO).

extract_protocol:
RNA was extracted and purified using the miRNeasy Mini kit (Qiagen) following the manufacturer's protocol.
Poly(A) RNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol. RNA integrity was checked with Agilent Technologies 2100 Bioanalyzer. Poly(A) tail-containing mRNAs were purified using oligo-(dT) magnetic beads with two rounds of purification. After purification, poly(A) RNA was fragmented using divalent cation buffer in elevated temperature.

value: mouse MC3T3-E1

value: pre-osteoblasts

value: Control


title: Untreated MC3T3-E1 (mouse pre-osteoblastic) cells cultured in the OC medium replicate 2

description: Library name: OC2


title: JC_2_119 (21PG49-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


description: Library name: PM_CLW_RMC4N_Tissue_SNF5_Proficient_H3K4me3.WI_22431


title: JC_2_118 (21PG49-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: Untreated MC3T3-E1 (mouse pre-osteoblastic) cells cultured in the OC medium replicate 1

description: Library name: OC1


title: JC_2_117 (21PG49-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: MC3T3-E1 (mouse pre-osteoblastic) cells treated with PAKG–8diol–PEG(S) MPs (30 μg/ml) replicate 3

description: Library name: pAKG3

value: PAKG–8diol–PEG(S) MPs (30 microg/ml)


description: Library name: PM_CLW_RMC2T_Tissue_SNF5_Deficient_H3K4me3.WI_22430


description: Library name: PM_CLW_RMC31N_Tissue_SNF5_Proficient_H3K4me3.WI_22435


title: JC_2_115 (21PG55-3)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: Late blastocyst

value: embryo in vitro day E5.75


title: JC_2_114 (21PG55-3)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: embryo


description: Library name: PM_CLW_RMC2N_Tissue_SNF5_Proficient_H3K4me3.WI_22429


title: MC3T3-E1 (mouse pre-osteoblastic) cells treated with PAKG–8diol–PEG(S) MPs (30 μg/ml) replicate 2

description: Library name: pAKG2


description: Library name: PM_CLW_RMC36T_Tissue_SNF5_Deficient_H3K27ac.WI_22428


title: JC_2_112 (21PG55-3)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_113 (21PG55-3)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: MC3T3-E1 (mouse pre-osteoblastic) cells treated with PAKG–8diol–PEG(S) MPs (30 μg/ml) replicate 1

description: Library name: pAKG1


title: JC_2_111 (21PG55-3)

description: Gpig.scRNAseq.counts.all.tsv.gz


description: Library name: PM_CLW_RMC36N_Tissue_SNF5_Proficient_H3K27ac.WI_22427


title: JC_2_110 (21PG55-3)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: KO3 M1

city: Chicago

first: Sarah

last: Tersey

state: IL

department: Medicine

institute: University of Chicago

description: Library name: KO3 M1

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

source_name: bone marrow derived macrophages

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

treatment_protocol: WT or Gpr31b KO M0 or M1 macrophages.

value: bone marrow derived macrophages

value: macrophages

value: KO


title: JC_2_11 (21PG77-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


description: Library name: PM_CLW_RMC31T_Tissue_SNF5_Deficient_H3K27ac.WI_22426

value: kidney

value: RMC tumor


description: Library name: PM_CLW_RMC31N_Tissue_SNF5_Proficient_H3K27ac.WI_22425

value: Adjacent normal


title: KO3 M0

description: Library name: KO3 M0


title: JC_2_108 (21PG55-3)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_107 (21PG55-3)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_106 (21PG55-3)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: KO2 M1

description: Library name: KO2 M1


description: Library name: PM_CLW_RMC30T_Tissue_SNF5_Deficient_H3K27ac.WI_22424


title: KO2 M0

description: Library name: KO2 M0


title: JC_2_104 (21PG55-3)

description: Gpig.scRNAseq.counts.all.tsv.gz


description: Library name: PM_CLW_RMC30N_Tissue_SNF5_Proficient_H3K27ac.WI_22423


title: JC_2_116 (21PG49-1)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: Early blastocyst

value: embryo in vitro day E5.25


title: KO1 M1

description: Library name: KO1 M1


description: Library name: PM_CLW_RMC4T_Tissue_SNF5_Deficient_H3K27ac.WI_22422


title: JC_2_103 (21PG55-3)

description: Gpig.scRNAseq.counts.all.tsv.gz


description: Library name: PM_CLW_RMC4N_Tissue_SNF5_Proficient_H3K27ac.WI_22421


title: KO1 M0

description: Library name: KO1 M0


title: JC_2_10 (21PG77-1)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: 16 cell


title: JC_2_100 (21PG55-3)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_102 (21PG55-3)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_193 (21PG57-2)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: Middle blastocyst

value: embryo in vitro day E5.5


title: JC_2_1 (21PG50-3)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: 8 cell

value: embryo in vitro day E3.5


title: WT3 M1

description: Library name: WT3 M1

value: WT


description: Library name: PM_CLW_RMC2T_Tissue_SNF5_Deficient_H3K27ac.WI_22420


title: WT3 M0

description: Library name: WT3 M0


title: JC_2_109 (21PG55-3)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: Late blastocyst


description: Library name: PM_CLW_RMC2N_Tissue_SNF5_Proficient_H3K27ac.WI_22419


title: JC_1_97 (21PG55-2)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: embryo in vitro day E5.75


title: JC_1_98 (21PG55-2)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: embryo


title: WT2 M1

description: Library name: WT2 M1

value: bone marrow derived macrophages


title: JC_1_96 (21PG76-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_105 (21PG55-3)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: PooledInput-H3K27me3.WI-22018_S50

description: Library name: PooledInput-H3K27me3.WI-22018_S50

extract_protocol:
After removing culture media and adding 20 mL of PBS, crosslinking was performed using 16% Paraformaldehyde (Thermo Scientific REF 28908) with a final concentration 1% for 10 minutes at room temperature. Reaction was stopped using 2 mL 10X Glycine for 5 minutes at room temperature. Cells were then scrapped and transferred into a tube. After a 5-minutes centrifugation at 1,500 rpm, pellet was washed with PBS and resuspended in a PBS solution containing 10% of protease & phosphatase inhibitors. After a 5-minutes centrifugation at 1,500 rpm, pellet was resuspended into a buffer containing 50mM Tris-HCl pH 8, 10mM EDTA, and 1% SDS. Nuclear lysate was obtained after incubation for 10 minutes on ice. Sonication was performed using Bioruptor® Plus for 7 to 10 cycles of 30 seconds on and 30 seconds off. Quality of sonication was checked using a solution of 5M NaCl and RNase A (Novagen #70856) for 30 minutes at 37°C. Then, Proteinase K (Novagen #71049) helped remove any protein overnight at 65°C. DNA was purified using QIAquick PCR purification kit. Quantification of DNA was performed using Nanodrop®. DNA shearing was controlled by electrophoresis: samples were considered if the majority of DNA belonged to 100 and 400 bp.
Rubicon ThruPLEX Plasma-Seq library preparation system (p/n R400492)

tag: transfected with

value: input


title: WT2 M0

description: Library name: WT2 M0

value: macrophages


title: RMC219-SNF5.H3K27me3.WI-22017_S49

description: Library name: RMC219-SNF5.H3K27me3.WI-22017_S49

value: kidney

value: SNF5 (SMARCB1)


title: JC_1_95 (21PG76-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_1_93 (21PG76-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_2_101 (21PG55-3)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: WT1 M1

description: Library name: WT1 M1


title: JC_1_92 (21PG76-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: RMC2C1-SNF5.H3K27me3.WI-22016_S48

description: Library name: RMC2C1-SNF5.H3K27me3.WI-22016_S48


title: JC_1_91 (21PG76-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: WT1 M0

description: Library name: WT1 M0


title: JC_1_90 (21PG76-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: RMC219-EV.H3K27me3.WI-22015_S47

description: Library name: RMC219-EV.H3K27me3.WI-22015_S47

value: Empty vector


title: JC_1_9 (21PG39-1)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: embryo in vitro day E4


title: T532M, rep3

first: Federica

last: Mosti

address: 213 Research Dr

institute: Duke University

description:
RM_T532M
T532M_DESeq2.star_salmon.diff.xls
Table S2.xlsx

data_processing:
Sequence reads were trimmed for adaptor sequence using cutadapt
Trimmed sequence reads were mapped to rRNA using bowtie2  v2.4.4, and remaining reads were maped to mm10 supplied with GENCODE22 annotation using STAR v2.7.9a (Dobin, 2013).
Reads were nomalized on "no virus" condition
Assembly: mm10
Supplementary files format and content: Supplementary files format and content: excel files include average log2FC and average CPM for ctrl and missense mutations condition

source_name: Mouse fetal cortex

extract_protocol:
RNA-seq: RNA was harvested using the RNAeasy kit (Qiagen, 74034). 50 ng of total RNA was used for the construction of sequencing libraries.
RNAseq: cDNA libraries for RNA-seq were prepared using the Kapa mRNA HyperPrep kit with mRNA capture (KapaBiosystems, KR1352)

value: Mouse fetal cortex

value: neuroprogenitor primary culture

value: DDX3X T532M lentiviral delivery


title: JC_1_88 (21PG76-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_1_89 (21PG76-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_1_99 (21PG55-2)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: Middle blastocyst


title: RMC219.H3K27me3.WI-22014_S46

description: Library name: RMC219.H3K27me3.WI-22014_S46

value: none/parental


title: T532M, rep2

description:
RB_T532M
T532M_DESeq2.star_salmon.diff.xls
Table S2.xlsx


title: RMC2C1-EV.H3K27me3.WI-22013_S45

description: Library name: RMC2C1-EV.H3K27me3.WI-22013_S45


title: JC_1_87 (21PG76-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_1_86 (21PG76-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_1_84 (21PG76-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_1_94 (21PG76-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_1_83 (21PG76-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: R488H, rep3

description:
RM_R488H
R488H_DESeq2.star_salmon.diff.xls
Table S2.xlsx

value: DDX3X R488H lentiviral delivery


title: RMC2C1.H3K27me3.WI-22012_S44

description: Library name: RMC2C1.H3K27me3.WI-22012_S44


title: JC_1_82 (21PG76-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: PooledInput-H3K27ac.WI-22011_S43

description: Library name: PooledInput-H3K27ac.WI-22011_S43


title: JC_1_80 (21PG76-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: RMC219-SNF5.H3K27ac.WI-22010_S42

description: Library name: RMC219-SNF5.H3K27ac.WI-22010_S42


title: R488H, rep2

description:
RB_R488H
R488H_DESeq2.star_salmon.diff.xls
Table S2.xlsx

value: WT


title: JC_1_8 (21PG50-2)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: 8 cell

value: embryo in vitro day E3.5


title: R488H, rep1

description:
BM_R488H
R488H_DESeq2.star_salmon.diff.xls
Table S2.xlsx


title: RMC2C1-SNF5.H3K27ac.WI-22009_S41

description: Library name: RMC2C1-SNF5.H3K27ac.WI-22009_S41


title: JC_1_79 (21PG76-2)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: embryo

value: Late blastocyst

value: embryo in vitro day E5.75


title: JC_1_78 (21PG76-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: RMC219-EV.H3K27ac.WI-22008_S40

description: Library name: RMC219-EV.H3K27ac.WI-22008_S40


title: JC_1_77 (21PG76-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_1_76 (21PG76-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: RMC219.H3K27ac.WI-22007_S39

description: Library name: RMC219.H3K27ac.WI-22007_S39


title: JC_1_75 (21PG76-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: T532M, rep1

description:
BM_T532M
T532M_DESeq2.star_salmon.diff.xls
Table S2.xlsx


title: JC_2_137 (21PG49-2)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: Early blastocyst

value: embryo in vitro day E5.25


title: JC_1_74 (21PG76-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: R326H, rep3

description:
RM_R326H
R326H_DESeq2.star_salmon.diff.xls
Table S2.xlsx

value: DDX3X R326H lentiviral delivery


title: JC_1_85 (21PG76-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: R376C, rep2

description:
RB_R376C
R376C_DESeq2.star_salmon.diff.xls
Table S2.xlsx

value: DDX3X R376C lentiviral delivery


title: RMC2C1-EV.H3K27ac.WI-22006_S38

description: Library name: RMC2C1-EV.H3K27ac.WI-22006_S38

value: kidney

value: Empty vector


title: R376C, rep1

description:
BM_R376C
R376C_DESeq2.star_salmon.diff.xls
Table S2.xlsx

value: Mouse fetal cortex

value: neuroprogenitor primary culture


title: JC_1_71 (21PG51-3)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: embryo in vitro day E4.5


title: RMC2C1.H3K27ac.WI-22005_S37

description: Library name: RMC2C1.H3K27ac.WI-22005_S37

value: none/parental


title: JC_1_81 (21PG76-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_1_72 (21PG51-3)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_1_73 (21PG51-3)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: R326H, rep2

description:
RB_R326H
R326H_DESeq2.star_salmon.diff.xls
Table S2.xlsx


title: JC_1_70 (21PG51-3)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: R326H, rep1

description:
BM_R326H
R326H_DESeq2.star_salmon.diff.xls
Table S2.xlsx


title: JC_1_7 (21PG50-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_1_68 (21PG51-3)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: PooledInput-H3K9me3.WI-22004_S36

description: Library name: PooledInput-H3K9me3.WI-22004_S36

value: input


title: RMC219-SNF5.H3K9me3.WI-22003_S35

description: Library name: RMC219-SNF5.H3K9me3.WI-22003_S35

value: SNF5 (SMARCB1)


title: R376C, rep3

description:
RM_R376C
R376C_DESeq2.star_salmon.diff.xls
Table S2.xlsx

value: WT


title: JC_1_69 (21PG51-3)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: RMC2C1-SNF5.H3K9me3.WI-22002_S34

description: Library name: RMC2C1-SNF5.H3K9me3.WI-22002_S34


title: JC_1_67 (21PG51-3)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_1_66 (21PG51-3)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: WT, rep3

description:
RM_WT
WT_DESeq2.star_salmon.diff.xls
Table S2.xlsx

value: DDX3X WT lentiviral delivery


title: WT, rep2

description:
RB_WT
WT_DESeq2.star_salmon.diff.xls
Table S2.xlsx


title: RMC219-EV.3K9me3.WI-22001_S33

description: Library name: RMC219-EV.3K9me3.WI-22001_S33


title: JC_1_64 (21PG51-3)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: embryo


title: WT, rep1

description:
BM_WT
WT_DESeq2.star_salmon.diff.xls
Table S2.xlsx


title: RMC219.H3K9me3.WI-22000_S32

description: Library name: RMC219.H3K9me3.WI-22000_S32


title: JC_1_63 (21PG51-3)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: No virus, rep3

description:
RM_no_virus
WT_DESeq2.star_salmon.diff.xls
Table S2.xlsx

value: No lentiviral trasduction


title: JC_1_62 (21PG51-3)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: No virus, rep2

description:
RB_no_virus
WT_DESeq2.star_salmon.diff.xls
Table S2.xlsx


title: RMC2C1.H3K9me3.WI-21998_S30

description: Library name: RMC2C1.H3K9me3.WI-21998_S30


title: JC_1_6 (21PG50-2)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: 8 cell

value: embryo in vitro day E3.5


title: JC_1_60 (21PG51-2)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: Early blastocyst


title: No virus, rep1

description:
BM_no_virus
WT_DESeq2.star_salmon.diff.xls
Table S2.xlsx


title: JC_1_58 (21PG51-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_1_61 (21PG51-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: PooledInput-H3K4me3.WI-21997_S29

description: Library name: PooledInput-H3K4me3.WI-21997_S29


title: JC_1_57 (21PG51-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_1_59 (21PG51-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_1_56 (21PG51-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: RMC2C1-SNF5.H3K4me3.WI-21995_S27

description: Library name: RMC2C1-SNF5.H3K4me3.WI-21995_S27


title: JC_1_53 (21PG51-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_1_54 (21PG51-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: phthmix

city: Newark

first: Genoa

middle: R

last: Warner

address: 161 Warren St Tiernan Hall #366 Tiernan Hall #366

institute: New Jersey Institute of Technology

data_processing:
The final 10x single cell pool was sequenced on the Illumina NovaSeq 6000, using one lane of an S4 flowcell, as paired-reads with 150nt in length. The first read of the single cell library is used for the UMI and 10x barcode only, the 2nd read contains the RNA sequencing information.
Basecalling and demultiplexing of raw data was done with the mkfastq command of the software Cell Ranger 6.0.1 (10x Genomics).
CellRanger count used to generate feature-barcode matrix
Processing in R as per methods
Assembly: GRCm38
Supplementary files format and content: fastq.gz: filtered raw data to reduce file size
Supplementary files format and content: h5: feature-barcode matrix, to be read into R
Supplementary files format and content: rds: fully processed data, ready for DGE analysis

source_name: ovary

extract_protocol:
Following culture, follicles were immediately dissociated into a single cell suspension for single cell sequencing. Follicles from each treatment group were shredded using watchmaker forceps in a dissociation solution composed of DMEM/F12 (Thermo Fisher Scientific) containing 20 mg/mL of collagenase II (Thermo Fisher Scientific) and 50 U/mL DNAse 1 (Thermo Fisher Scientific). Cells were pipette mixed, incubated at 37 °C for 40 minutes, and then pipette mixed again. After centrifugation and removal of the supernatant, 0.25% trypsin-ethylenediaminetetraacetic acid (EDTA) (Thermo Fisher Scientific) was added to the cells, pipette mixed, and incubated for 5 minutes. Cells were washed with cell culture media and strained through a 100 μm cell strainer. Cells were counted and concentration adjusted to 700 cells/μl for sequencing.
Single-cell 3 cDNA libraries were prepared at the DNA Services laboratory of the Roy J. Carver Biotechnology Center at the University of Illinois at Urbana-Champaign. Single-cell suspensions were delivered to the facility and were counted and checked for viability >80% using the Nexcelom K2 brightfield/dual florescence cell counter (Nexcelom Biosciences, Lawrence MA) with AO/PI staining, then washed with PBS buffer containing 2.0% BSA, then recounted for library preparation. The cells were individually labeled with the 10x Cell Plex Multiplexing Oligo labels, washed, and pooled per the manufacturers instructions. The target number of labeled cells (30,000, to target 5,000 from each population) were converted into a single barcoded cDNA library with the Single-Cell 3 NextGEM v3.1 Chromium kit from 10X Genomics (Pleasanton, CA) following the manufacturers protocols. Following ds-cDNA synthesis, an individually-barcoded dual-index library compatible with the Illumina chemistry was constructed in parallel with the CellPlex library. The final libraries were quantitated on Qubit (Life Technologies, Grand Island, NY) and the average size determined on the AATI Fragment Analyzer (Agilent Technologies, Santa Clara, CA). The final libraries were then diluted to 5nM final concentration and further quantitated by qPCR on a BioRad CFX Connect Real-Time System (Bio-Rad Laboratories, Inc. CA), then pooled for sequencing. The final 10x single cell pool was sequenced on the Illumina NovaSeq 6000, using one lane of an S4 flowcell, as paired-reads with 150nt in length. The first read of the single cell library is used for the UMI and 10x barcode only, the 2nd read contains the RNA sequencing information. Basecalling and demultiplexing of raw data was done with the mkfastq command of the software Cell Ranger 6.0.1 (10x Genomics). Sorted data was posted to a password-secured AWS site for download and downstream processing.

value: ovary

tag: strain


title: epithelial cells, Mal04-Cre infected mice, 28 dpi, bystander

data_processing:
Basecalls: CellRanger mkfastq (version 3.1.0)
Alignment: CellRanger count (version 3.1.0)
Resulting raw count maxtrix was filtered for contaminating mRNA using the R SoupX pipeline (version 1.6.2)
The filtered count matrix was then imported into Seurat (version 5.0.3)
Assembly: custom concatenated mm10 and Mal04-Cre
Supplementary files format and content: Normalized counts for cells included in analyses

source_name: respiratory epithelium

extract_protocol:
Mice were anesthetized with ketamine-xylazine followed by cervical dislocation and lung removal. The lungs were perfused with PBS then inflated with digestion enzymes. Lungs were removed minxed finely with a razor blade then incubated in digestion enzyme 30 minutes. The tissue mixture is filtered through a 70-µm filter and red blood cells were lysed with RBC lysis buffer and the remaining cells were filtered through a 40-µm filter. Spin the cells down and resuspend in 2% FBS with advanced DMEM/F-12 to be sorted on a BD DiVA.
Sorted cells were prepared for library generation (10x Genomics) according to manufacturers protocols.

treatment_protocol: Mice were treated with 40 uL PBS or 75,000PFU of Mal04-Cre intranasally 14 days prior to tissue collection.

value: respiratory epithelium

value: epithelial cell

value: tdTomato

value: 75,000 PFU Mal04-Cre


title: epithelial cells, Mal04-Cre infected mice, 28 dpi, survivor

tag: fluorescent marker

value: tdTomato+


title: JC_1_52 (21PG51-2)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: embryo in vitro day E4.5


title: JC_1_65 (21PG51-3)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_1_51 (21PG51-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: epithelial cells, Mal04-Cre infected mice, 14 dpi, survivor


title: JC_1_50 (21PG51-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: RMC2C1-EV.H3K9me3.WI-21999_S31

description: Library name: RMC2C1-EV.H3K9me3.WI-21999_S31

value: kidney

value: Empty vector


title: RMC219.H3K4me3.WI-21993_S25

description: Library name: RMC219.H3K4me3.WI-21993_S25

value: none/parental


title: JC_1_5 (21PG50-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_1_49 (21PG51-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: epithelial cells, Mal04-Cre infected mice, 14 dpi, bystander


title: JC_1_48 (21PG51-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_1_47 (21PG51-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_1_46 (21PG51-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: RMC2C1.H3K4me3.WI-21991_S23

description: Library name: RMC2C1.H3K4me3.WI-21991_S23


title: epithelial cells, Mal04-Cre infected mice, 3 dpi, infected


title: RMC219-SNF5.H3K4me3.WI-21996_S28

description: Library name: RMC219-SNF5.H3K4me3.WI-21996_S28

value: SNF5 (SMARCB1)


title: RMC2C1-EV.H3K4me3.WI-21992_S24

description: Library name: RMC2C1-EV.H3K4me3.WI-21992_S24


title: epithelial cells, Mal04-Cre infected mice, 3 dpi, bystander


title: PooledInput-H3K4me1.WI-21990_S22

description: Library name: PooledInput-H3K4me1.WI-21990_S22

value: input


title: JC_1_45 (21PG51-2)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: embryo


title: JC_1_44 (21PG51-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: epithelial cells, mock infected mice

value: PBS


title: JC_1_43 (21PG51-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_1_55 (21PG51-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_1_42 (21PG40-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: RMC219-EV.H3K4me3.WI-21994_S26

description: Library name: RMC219-EV.H3K4me3.WI-21994_S26


title: RMC2C1-SNF5.H3K4me1.WI-21988_S20

description: Library name: RMC2C1-SNF5.H3K4me1.WI-21988_S20


title: JC_1_40 (21PG40-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_1_41 (21PG40-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: Unexposed animals, sample 6b

city: Boston

first: Lisa

middle: V

last: Goodrich

state: MA

address: 220 Longwood Ave

department: Neurobiology

institute: Harvard Medical School

description: Unexposed littermate controls of sample 6a

data_processing:
Sequencing reads were demultiplexed and aligned to a modified mm10-3.0.0 transcriptome that included intronic reads using the cellranger package from 10x Genomics (v. 7.0.0).
Quality filtering: Raw gene counts were imported into the Seurat package (v. 4.2.1) in R (v.4.2.2). Cells and genes were initially filtered by eliminating all genes detected in fewer than 3 cells and removing cells with fewer than 500 unique genes. Additionally, nuclei were excluded if the number of genes or unique molecular identifiers (UMI) detected was greater than two standard deviations above the mean. Next, we eliminated additional low-quality cells by excluding nuclei with fewer than 1,000 UMI or 750 genes. Finally, we excluded all nuclei in which more than 1% of reads mapped to the mitochondrial genome.
Clustering: Each sample was initially normalized independently using regularized negative binomial regression, implemented in the scTransform package in Seurat (v. 0.3.5). Normalized datasets were integrated with canonical correlation analysis (CCA) referenced to a subset of noise-exposed and control nuclei using 30 principal components (PCs) and 3,000 variable genes. Prior to clustering, we performed principal component analysis (PCA) on the integration vectors from the CCA pipeline above. We included 20 PCs as input to a graph-based clustering algorithm, implemented with the FindNeighbors and FindClusters algorithms in Seurat, using a resolution of 0.4. To refine our assessment of OCN subtypes, we subset this larger dataset to include only the 1,757 nuclei called as either MOCs or LOCs in the full dataset. We then repeated the PCA and clustering analysis on the subsetted data, again using 20 PCs and a resolution of 0.4. Cluster identities denoted in the processed data file include the subclustered OCN identity when applicable and a numeric cluster ID for all remaining cells.
Normalization: The processed data file includes normalized values established by dividing the counts for each gene by the total number of counts for each cell. These values were then multiplied by 10,000 and natural-log transformed.
Assembly: mm10-3.0.0
Supplementary files format and content: A comma-separated value (.csv) file containing a matrix of log-normalized data and associated cell-type identities, established as described in the data processing steps above. Column names include the originating sample, exposure condition, timepoint, cell-type cluster ID, and a cellular barcode, separated by an underscore.

molecule: nuclear RNA

source_name: Brain

extract_protocol:
Portions of the ventral brainstem were dissected and tissue was manually dissociated with a dounce homogenizer. Nuclei were then isolated using differential centrifugation. Enrichment for cholinergic nuclei was achieved by collecting GFP+ nuclei via FACS. Individual nuclei were captured through the 10x Genomics Platform (3' Kit v. 3.1).
Libraries were generated following manufacturer's directions (10x Single Cell 3' v3.1). Some samples were sequenced multiple times to achieve sufficient coverage. Paired experimental and control samples were always multiplexed and sequenced together on a flow cell.

value: Brain

tag: animal

value: sample 6b

value: unexposed


title: 7 days post-exposure, sample 6a

value: sample 6a

value: 7 days post exposure


title: JC_1_4 (21PG50-2)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: 8 cell

value: embryo in vitro day E3.5


title: RMC219-EV.H3K4me1.WI-21987_S19

description: Library name: RMC219-EV.H3K4me1.WI-21987_S19


title: JC_1_38 (21PG40-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_1_39 (21PG40-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: Unexposed animals, sample 5b

description: Unexposed littermate controls of sample 5a

value: sample 5b


title: RMC219.H3K4me1.WI-21986_S18

description: Library name: RMC219.H3K4me1.WI-21986_S18


title: 7 days post-exposure, sample 5a

value: sample 5a


title: JC_1_362 (21PG41-1)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: embryo in vitro day E4.75


title: Unexposed animals, sample 4b

description: Unexposed littermate controls of sample 4a

value: sample 4b


title: P12 Pancreatic Cyst Fluid

city: Dublin

first: Laura

middle: E

last: Kane

state: Dublin

address: Trinity St. James's Cancer Institute

department: Department of Surgery

country: Ireland

institute: Trinity College Dublin

data_processing:
The sequencing data on miRNA expression of target genes were imported into HTG EdgeSeq Parser software. The HTG EdgeSeq Reveal Application was utilized to quality check and normalize data. The data were normalised using counts per million normalisation in R.
Assembly: Targeted probe list
Supplementary files format and content: Tab deliminated .txt file in a count per million (CPM) normalised format.

source_name: Pancreatic Cyst Fluid

extract_protocol:
N/A no extraction
Each processed sample from the stop plate was used as a template to set up PCR reactions with specially designed primers, referred to as tags. These tags share common sequences that are complementary to 5'-end and 3'-end "wing" sequences of the probes and common adaptors required for cluster generation on an Illumina sequencing platform. In addition, each tag contains a unique barcode that is used for sample identification and multiplexing. HTG has developed 12 forward and eight reverse primer tags; therefore, up to 96 samples can be analyzed simultaneously on an Illumina sequencing platform. The library was prepared in accordance with OP-00035, HTG EdgeSeq PCR processing. Clean-up procedures were performed according to OP-00037, HTG EdgeSeq AMPure cleanup of Illumina Sequencing Libraries.
HTG Molecular Diagnostics Inc. proprietary quantitative nuclease protection assay (qNPA) chemistry with a next generation sequencing platform.

value: Pancreatic Cyst Fluid

tag: risk level

value: Low


title: RMC2C1.H3K4me1.WI-21984_S16

description: Library name: RMC2C1.H3K4me1.WI-21984_S16

value: kidney

value: none/parental


title: 7 days post-exposure, sample 4a

value: sample 4a


title: P56 Pancreatic Cyst Fluid

value: High


title: JC_1_360 (21PG41-1)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: embryo


title: RMC219-SNF5.H3K4me1.WI-21989_S21

description: Library name: RMC219-SNF5.H3K4me1.WI-21989_S21

value: SNF5 (SMARCB1)


title: Unexposed animals, sample 3b

description: Unexposed littermate controls of sample 3a

value: Brain

value: sample 3b

value: unexposed


title: JC_1_36 (21PG40-1)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: embryo in vitro day E4.5


title: Pooled_HSCR_ganglionic_aganglionic_sample02

city: Rotterdam

first: Maria

last: Alves

address: Wytemaweg 80

department: Departments of Clinical Genetics and Pediatric Surgery

country: Netherlands

institute: Erasmus University Medical Center-Sophia Children’s Hospital

description:
Library name: Pooled_HSCR_s02
JW_HSCR_02_raw_feature_bc_matrix.tar

data_processing:
Illumina bcl2fastq was used to convert raw bcl files to fastq format
Fastq files were processed using 10x Genomics Cellranger software
Assembly: hg38
Supplementary files format and content: compressed raw UMI counts matrices from Cellranger outputs for mRNA and antibody libraries.

source_name: Intestine

extract_protocol:
Cryopreserved tissue was rapidly thawed in a 37°C water bath and processed to yield high viablity single cells. Cells were stained with fluorescent antibodies and ENS cells were enriched by FACS. Cells were then loaded onto the 10X platform for single-cell RNA sequencing.
Libraries were made according to the manufacter’s instructions (Single Cell 3' v3 chemistry, 10x Genomics)

value: Intestine

value: Neurons and Glia

tag: library type

value: Gene Expression


title: 7 days post-exposure, sample 3a

value: sample 3a

value: 7 days post exposure


title: P64 Pancreatic Cyst Fluid

value: Pancreatic Cyst Fluid


title: JC_1_359 (21PG41-1)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: embryo in vitro day E4.75


title: Ileum_control_sample03

description:
Library name: Ileum_s03
R2_Windster_ENS02_raw_feature_bc_matrix.tar


title: JC_1_358 (21PG41-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: P2 Pancreatic Cyst Fluid


title: Ileum_control_sample02

description:
Library name: Ileum_s02
R2_Windster_ENS01_raw_feature_bc_matrix.tar


title: Unexposed animals, sample 2b

description: Unexposed littermate controls of sample 2a

value: sample 2b


title: JC_1_37 (21PG40-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_1_357 (21PG41-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: P13 Pancreatic Cyst Fluid

value: Low


title: 1 day post-exposure, sample 2a

value: sample 2a

value: 1 day post exposure


title: JC_1_361 (21PG41-1)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: embryo


title: Unexposed animals, sample 1b

description: Unexposed littermate controls of sample 1a

value: sample 1b


title: RMC2C1-EV.H3K4me1.WI-21985_S17

description: Library name: RMC2C1-EV.H3K4me1.WI-21985_S17

value: kidney

value: Empty vector


title: Ileum_control_sample01

description:
Library name: Ileum_s01
JW1_NCAMp_raw_feature_bc_matrix.tar


title: JC_1_355 (21PG41-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: P90 Pancreatic Cyst Fluid


title: P1 Pancreatic Cyst Fluid

value: High


title: P37 Pancreatic Cyst Fluid


title: Colon_control_sample02

description:
Library name: Colon_s02
JW_Colon_Ctrl2_raw_feature_bc_matrix.tar


title: P81 Pancreatic Cyst Fluid


title: 1 day post-exposure, sample 1a

value: Brain

value: sample 1a


title: JC_1_354 (21PG41-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_1_356 (21PG41-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: P15 Pancreatic Cyst Fluid


title: P78 Pancreatic Cyst Fluid


title: Kdm6bf/f, GD5.5, IIS, Input

city: San Francisco

first: Adrian

last: Erlebacher

state: CA

address: 513 Parnasssus

institute: UCSF

description:
STAR v2.7.5c, samtools v1.10, bedtools v2.29.1, bedGraphToBigWig v2.8 were used for .bw creatation and peaks were called with macs2 v2.2.7.1
1256-GD5-5-CTRL-I

data_processing:
Reads were mapped to mouse mm10 genome using STAR
BAM files were also generated by STAR
PCR duplicates removed by Picard
Peak calling was performed using MACS2
bedGraphToBigWig was used to generate bigwig files
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&RUN

source_name: Inter-implantation site

extract_protocol:
H3K27me3 CUT&RUN was performed using the CUT&RUN Assay Kit (Cell Signaling Technology, cat no: 86652) following the manufacturer’s instructions.
CUT&RUN libraries were prepared using the Nextera Flex Library Prep Kit (Illumina)

treatment_protocol: Myometrium/endometrium tissue was digested in a cocktail of liberase, DNase I and trypsin and then fibroblasts were purified using magnetic beads.

value: Inter-implantation site

tag: cut&run antibody

value: fibroblast

value: Kdm6b f/f

tag: mating

value: xB6 male

tag: timepoint


title: Kdm6bf/f, GD5.5, IIS, H3K27me3,7

description:
STAR v2.7.5c, samtools v1.10, bedtools v2.29.1, bedGraphToBigWig v2.8 were used for .bw creatation and peaks were called with macs2 v2.2.7.1
1256-GD5-5-CTRL-7

tag: tissue


title: HSCR_sample01_ganglionic

description:
Library name: HSCR_s01_ganglionic
JW_HSCR_01_raw_feature_bc_matrix.tar

value: Intestine

value: Neurons and Glia

value: Gene Expression


title: JC_1_353 (21PG41-1)

description: Gpig.scRNAseq.counts.all.tsv.gz

tag: developmental stage

tag: time

value: embryo in vitro day E4.75


title: Kdm6bf/f, GD5.5, IIS, H3K27me3,15

description:
STAR v2.7.5c, samtools v1.10, bedtools v2.29.1, bedGraphToBigWig v2.8 were used for .bw creatation and peaks were called with macs2 v2.2.7.1
1256-GD5-5-CTRL-15

tag: cell type

tag: genotype


title: JC_1_352 (21PG52-2)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: Late blastocyst

value: embryo in vitro day E5.75


title: P85 Pancreatic Cyst Fluid

value: Pancreatic Cyst Fluid

value: Low


title: Ileum_control_sample_4

description:
Library name: Ileum_s04
ENS04_raw_feature_bc_matrix.tar


title: Kdm6bf/f, GD5.5, IIS, H3K27me3,11

description:
STAR v2.7.5c, samtools v1.10, bedtools v2.29.1, bedGraphToBigWig v2.8 were used for .bw creatation and peaks were called with macs2 v2.2.7.1
1256-GD5-5-CTRL-11


title: P3 Pancreatic Cyst Fluid


title: JC_1_351 (21PG52-2)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: embryo


title: Pooled_colon_control_sample03_HSCR_ganglionic_aganglionic_sample03_Feature_Barcoding

description:
Library name: Pooled_Colon_s03_HSCR_s03_Feature_Barcoding
hashed2_raw_feature_bc_matrix.tar

molecule: protein

value: Feature Barcoding

tag: multiplexed sample_info


title: Colon_control_sample01

description:
Library name: Colon_s01
Windster_ColonControl1_raw_feature_bc_matrix.tar


title: Pgr-cre Kdm6bf/f, GD5.5, IIS, Input

description:
STAR v2.7.5c, samtools v1.10, bedtools v2.29.1, bedGraphToBigWig v2.8 were used for .bw creatation and peaks were called with macs2 v2.2.7.1
1256-GD5-5-CKO-I

value: Pgr-cre Kdm6b f/f


title: Pooled_colon_control_sample03_HSCR_ganglionic_aganglionic_sample03

description:
Library name: Pooled_Colon_s03_HSCR_s03
hashed2_raw_feature_bc_matrix.tar


title: JC_1_350 (21PG52-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: P20 Pancreatic Cyst Fluid


title: JC_1_35 (21PG40-1)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: embryo in vitro day E4.5


title: P92 Pancreatic Cyst Fluid

value: High


title: Pgr-cre Kdm6bf/f, GD5.5, IIS, H3K27me3,8

description:
STAR v2.7.5c, samtools v1.10, bedtools v2.29.1, bedGraphToBigWig v2.8 were used for .bw creatation and peaks were called with macs2 v2.2.7.1
1256-GD5-5-CKO-8

value: Inter-implantation site


title: JC_1_349 (21PG52-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: Pgr-cre Kdm6bf/f, GD5.5, IIS, H3K27me3,4

description:
STAR v2.7.5c, samtools v1.10, bedtools v2.29.1, bedGraphToBigWig v2.8 were used for .bw creatation and peaks were called with macs2 v2.2.7.1
1256-GD5-5-CKO-4

value: fibroblast


title: HSCR_sample01_aganglionic

description:
Library name: HSCR_s01_aganglionic
JW_HSCR_01_AG_raw_feature_bc_matrix.tar


title: Pooled_HSCR_ganglionic_aganglionic_sample02_Feature_barcoding

description:
Library name: Pooled_HSCR_s02_Feature_barcoding
JW_HSCR_02_raw_feature_bc_matrix.tar


title: Pgr-cre Kdm6bf/f, GD5.5, IIS, H3K27me3,16

description:
STAR v2.7.5c, samtools v1.10, bedtools v2.29.1, bedGraphToBigWig v2.8 were used for .bw creatation and peaks were called with macs2 v2.2.7.1
1256-GD5-5-CKO-16


title: P59 Pancreatic Cyst Fluid


title: Kdm6bf/f, GD0.5, UT, Input

description:
STAR v2.7.5c, samtools v1.10, bedtools v2.29.1, bedGraphToBigWig v2.8 were used for .bw creatation and peaks were called with macs2 v2.2.7.1
1256-GD0-5-CTRL-I

source_name: uterus

value: uterus

value: Kdm6b f/f


title: JC_1_348 (21PG52-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: P18 Pancreatic Cyst Fluid


title: 36697 | 011 | Other Stroma

first: Peter

last: Allen

address: 203 Research Dr., MSRB1 Rm. 475

department: Surgery

institute: Duke Medical Center

description: FFPE spatial whole transcriptome sequencing

data_processing:
Raw fastq files were run through the GeoMx NGS pipeline to produce DCC files which were uploaded to the DSP instrument.
The DCC files produce a raw count matrix that was downloaded from the DSP.
Assembly: GRCh38.p13
Supplementary files format and content: Iyer_GeoMx_WTA_2022_GEO_matrix.xlsx: Initial raw dataset downloaded from the DSP (includes count matrix)
Supplementary files format and content: Iyer_WTA_2022_GEO_DCC.tar.gz: Raw read counts with probe barcodes
Library strategy: Spatial Transcriptomics

source_name: Pancreas

extract_protocol:
On average, 2x 5 um-thick FFPE sections were cut and placed on a slide from each IPMN patient surgical tissue block, which were identified by a surgical pathologist (CS). One slide was stained with H&E for pathological annotation and the other slide was stained with the GeoMx morphology markers and RNA probes.
Libraries were constructed with Nanostring DSP reagents and in accordance with the Illumina GeoMx library preparation protocol.

value: Pancreas

tag: ffpe block_year

tag: disease pathology

value: Invasive IPMN

tag: aoi pathology

value: Pancreatic cancer (PDAC)

tag: aoi histologocal_subtype

value: Pancreatobiliary

tag: roi segment

value: stromal


title: P83 Pancreatic Cyst Fluid


title: JC_1_347 (21PG52-2)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: Late blastocyst

value: embryo in vitro day E5.75


title: 36697 | 012 | PanCK

value: epithelial


title: 36697 | 011 | CD45


title: Kdm6bf/f, GD0.5, UT, H3K27me3,5

description:
STAR v2.7.5c, samtools v1.10, bedtools v2.29.1, bedGraphToBigWig v2.8 were used for .bw creatation and peaks were called with macs2 v2.2.7.1
1256-GD0-5-CTRL-5-1

value: xB6 male


title: P73 Pancreatic Cyst Fluid

value: Pancreatic Cyst Fluid

value: Low


title: 36697 | 010 | Other Stroma


title: JC_1_346 (21PG52-2)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: embryo


title: Kdm6bf/f, GD0.5, UT, H3K27me3,24

description:
STAR v2.7.5c, samtools v1.10, bedtools v2.29.1, bedGraphToBigWig v2.8 were used for .bw creatation and peaks were called with macs2 v2.2.7.1
1256-GD0-5-CTRL-24-1


title: 36697 | 010 | CD45


title: P24 Pancreatic Cyst Fluid


title: JC_1_345 (21PG52-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: Kdm6bf/f, GD0.5, UT, H3K27me3,22

description:
STAR v2.7.5c, samtools v1.10, bedtools v2.29.1, bedGraphToBigWig v2.8 were used for .bw creatation and peaks were called with macs2 v2.2.7.1
1256-GD0-5-CTRL-22-1


title: P77 Pancreatic Cyst Fluid

value: High


title: JC_1_344 (21PG52-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 36697 | 010 | CD3


title: Pgr-cre Kdm6bf/f, GD0.5, UT, Input

description:
STAR v2.7.5c, samtools v1.10, bedtools v2.29.1, bedGraphToBigWig v2.8 were used for .bw creatation and peaks were called with macs2 v2.2.7.1
1256-GD0-5-CKO-I

value: Pgr-cre Kdm6b f/f


title: 36697 | 010 | PanCK


title: JC_1_343 (21PG52-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: Pgr-cre Kdm6bf/f, GD0.5, UT, H3K27me3,2

description:
STAR v2.7.5c, samtools v1.10, bedtools v2.29.1, bedGraphToBigWig v2.8 were used for .bw creatation and peaks were called with macs2 v2.2.7.1
1256-GD0-5-CKO-2

value: fibroblast


title: 36697 | 011 | PanCK


title: JC_1_342 (21PG52-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: P54 Pancreatic Cyst Fluid


title: 36697 | 008 | PanCK

value: High-grade dysplasia


title: JC_1_341 (21PG52-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: P46 Pancreatic Cyst Fluid


title: Pgr-cre Kdm6bf/f, GD0.5, UT, H3K27me3,10

description:
STAR v2.7.5c, samtools v1.10, bedtools v2.29.1, bedGraphToBigWig v2.8 were used for .bw creatation and peaks were called with macs2 v2.2.7.1
1256-GD0-5-CKO-10

value: uterus


title: 36697 | 007 | Other Stroma

value: Pancreas


title: JC_1_340 (21PG52-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: P71 Pancreatic Cyst Fluid


title: P60 Pancreatic Cyst Fluid


title: 36697 | 007 | CD45

value: Invasive IPMN


title: LK,WT,Rep3

city: La Jolla

first: Zhen

last: Dong

state: California

address: 9420 Athena Circle

department: Department of Signaling and Gene Expression

institute: La Jolla Institute for Immunology

data_processing:
Trimmed sequencing reads were aligned against the mouse reference genome (mm10) using the STAR aligner in two configurations 1) to allow unique aligments for gene expression quantification and 2) to allow multi mappers for Transposable Elements (TEs) expression quantification
To measure the expression of genes, we used HT-Seq and then perform the differential expression (DE) analysis with DESeq2.
To measure the expression of TEs, we used the TEtranscript package with the option -multi to quantify ambiguously mapped reads and then perform the DE analysis with DESeq2
For TE analysis, we specifically used the mm10 repeatMasker annotation
Assembly: mm10
Supplementary files format and content: Tab delimited file of gene counts for each sample
Supplementary files format and content: Tab delimited file of TEs counts for each sample

source_name: LK (lineage-negative, c-Kit+)

growth_protocol: Cells were isolated from mouse bone marrow and used for experiments immediately

extract_protocol:
RNA was harvested from cells using RNeasy Mini plus kit (Qiagen). 200 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared using NEBNextUltra II Directional RNA Library Prep Kit for Illumina following manufacture’s protocols.

value: LK (lineage-negative, c-Kit+)

tag: age

value: 18 month old


title: LK,WT,Rep2


title: JC_1_339 (21PG52-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 36697 | 007 | CD3

value: Pancreatobiliary


title: P14 Pancreatic Cyst Fluid

tag: risk level


title: 36697 | 006 | PanCK

value: Low-grade dysplasia

value: Gastric Foveolar


title: LK,WT,Rep1


title: JC_1_338 (21PG52-2)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: Late blastocyst

value: embryo in vitro day E5.75


title: P45 Pancreatic Cyst Fluid

value: Pancreatic Cyst Fluid


title: P47 Pancreatic Cyst Fluid

value: Low


title: LK,MT,Rep3


title: P44 Pancreatic Cyst Fluid


title: JC_1_337 (21PG52-2)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: embryo


title: 36697 | 009 | PanCK

value: epithelial


title: Pgr-cre Kdm6bf/f, GD0.5, UT, H3K27me3,18

description:
STAR v2.7.5c, samtools v1.10, bedtools v2.29.1, bedGraphToBigWig v2.8 were used for .bw creatation and peaks were called with macs2 v2.2.7.1
1256-GD0-5-CKO-18

value: Pgr-cre Kdm6b f/f

value: xB6 male


title: P33 Pancreatic Cyst Fluid


title: LK,MT,Rep2


title: JC_1_336 (21PG52-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 36697 | 005 | CD3


title: LK,MT,Rep1


title: P44 Serum

source_name: Peripheral blood serum

value: Peripheral blood serum

value: High


title: JC_1_34 (21PG40-1)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: embryo in vitro day E4.5


title: 36697 | 005 | PanCK

value: Pancreas

value: Invasive IPMN


title: JC_1_335 (21PG52-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: Cd11b,old,WT,Rep3

source_name: myeloid (Cd11b+)

value: myeloid (Cd11b+)

value: 18 month old


title: 36697 | 004 | PanCK

value: Low-grade dysplasia


title: Cd11b,old,WT,Rep2


title: P56 Serum


title: P78 Serum


title: 36697 | 003 | Other Stroma

value: Normal duct

value: not applicable

value: stromal


title: Cd11b,old,WT,Rep1


title: JC_1_332 (21PG75-1)

description: Gpig.scRNAseq.counts.all.tsv.gz

source_name: embryo

value: Late blastocyst

value: embryo in vitro day E6


title: JC_1_334 (21PG75-1)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: embryo


title: Cd11b,old,MT,Rep3


title: 36697 | 005 | Other Stroma

value: Gastric Foveolar


title: P24 Serum

value: Low


title: Cd11b,old,MT,Rep2


title: 36697 | 003 | PanCK

value: epithelial


title: JC_1_331 (21PG75-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: P73 Serum

value: Peripheral blood serum


title: JC_1_330 (21PG75-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 36697 | 002 | PanCK


title: P33 Serum


title: P90 Serum


title: Cd11b,old,MT,Rep1


title: JC_1_33 (21PG40-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 36697 | 001 | PanCK


title: 37622 C18 | 010 | PanCK


title: Cd11b,young,WT,Rep4

value: 4 month old


title: 37622 C18 | 009 | PanCK


title: P77 Serum

value: High


title: 37622 C18 | 008 | Other Stroma

value: Pancreas


title: JC_1_328 (21PG75-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: P20 Serum


title: JC_1_333 (21PG75-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: Cd11b,young,WT,Rep3


title: JC_1_327 (21PG75-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_1_329 (21PG75-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: P83 Serum


title: Cd11b,young,WT,Rep1


title: JC_1_326 (21PG75-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: P18 Serum


title: 37622 C18 | 008 | CD3

value: Invasive IPMN


title: Cd11b,young,MT,Rep3

value: myeloid (Cd11b+)


title: 37622 C18 | 008 | PanCK


title: P2 Serum


title: P64 Serum


title: P45 Serum


title: P60 Serum


title: 37622 C18 | 007 | CD45


title: Cd11b,young,MT,Rep2


title: 37622 C18 | 007 | PanCK


title: P4_RP_pos

city: Rehovot

first: Roi

last: Avraham

address: Herzl St 234

country: Israel

institute: Weizmann Institute of Science

data_processing:
The cel-seq pipeline (https://github.com/yanailab/CEL-Seq-pipeline) was used for sample demultiplexing, alignment to the genome (GRCh38), and gene counting.
The CEL-seq protocol is paired-end, with read1 (R1) contains the sample barcode and UMI sequence, and read2 (R2) contains the mRNA sequence. Demultiplexing was done based on read1 and alignment to the genome and gene counting was done by read2 alone, therefore only read2 (R2) was submitted
Data was normalized to a library size factor. Factors were calculated by dividing the total number of reads from each sample to the median total number of reads across all samples.
Data was transformed to log2 scale, and minimal expression threshold was set to 3
Replicate samples of each condition were averaged, except for 1 sample that was excluded due to low coverage (<150k reads; control NCM-Tdtm+ replicate 4).
Assembly: mm9
Supplementary files format and content: tab-delimited text files include normalized number of reads (log2 scale) for each sample

source_name: Splenocytes

extract_protocol:
14 days post inoculation, mice were sacrificed with CO2, and spleens were isolated whole. Extracted spleens were mashed on 70um screens with 5mL FACs buffer (1% FBS, 5uM EDTA). Cells were pelleted, treated with RBS lysis buffer, and washed 2x with FACs buffer before proceeding to sorting. Using a FACs Aria III, cells were bulk sorted (~8K cells/tube) based on expression of Ly6C, F4/80, and TdTomato.
RNA-seq libraries were prepared according to Cel-seq libraries protocol (Hashimshony, T. et al Genome Biology 2016)

treatment_protocol: Female C57/BL6J Ms4a3-Tdtomato mice were inoculated with 5*10^6 BCG (Pasteur) or PBS i.p in a volume of 200ul.

value: Splenocytes

tag: treatment

value: PBS

tag: population

value: Red pulp macrophages

tag: tdtm pos/neg

value: pos

tag: replicate


title: JC_1_323 (21PG75-1)

description: Gpig.scRNAseq.counts.all.tsv.gz

tag: tissue


title: JC_1_324 (21PG75-1)

description: Gpig.scRNAseq.counts.all.tsv.gz

tag: developmental stage


title: P4_NCM_neg

value: Non-Classical-Monocytes

value: neg


title: Cd11b,young,MT,Rep1


title: P1 Serum


title: 37622 C18 | 008 | CD45

value: Low-grade dysplasia


title: P4_RP_neg


title: 37622 C18 | 007 | CD3


title: JC_1_321 (21PG75-1)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: embryo

value: Late blastocyst

tag: time

value: embryo in vitro day E6


title: 37622 C18 | 006 | PanCK

value: Normal duct

value: not applicable

value: epithelial


title: Cd11b,young,WT,Rep2

tag: cell type

value: 4 month old


title: JC_1_325 (21PG75-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 37622 C18 | 007 | Other Stroma

value: Pancreas

value: Gastric Foveolar

value: stromal


title: P13 Serum

value: Peripheral blood serum

value: Low


title: JC_1_322 (21PG75-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: P4_CM_pos

value: Splenocytes

value: PBS

value: Classical-Monocytes


title: JC_1_32 (21PG40-1)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: embryo in vitro day E4.5


title: 37622 C18 | 005 | Other Stroma

value: Invasive IPMN


title: P3 Serum

value: High


title: P4_CM_neg

value: neg


title: P37 Serum


title: 37622 C18 | 005 | PanCK


title: JC_1_320 (21PG75-1)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: embryo

value: Late blastocyst

value: embryo in vitro day E6


title: P3_RP_pos

value: Red pulp macrophages

value: pos


title: JC_1_319 (21PG75-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: P3_RP_neg


title: JC_1_317 (21PG75-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: P46 Serum


title: P3_CM_pos


title: P85 Serum


title: JC_1_316 (21PG75-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_1_314 (21PG75-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_1_318 (21PG75-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: P3_NCM_pos

value: Non-Classical-Monocytes


title: P47 Serum


title: P81 Serum


title: 37622 C18 | 002 | PanCK

value: Pancreas

value: Normal duct

value: not applicable

value: epithelial


title: P3_NCM_neg

value: Splenocytes


title: 37622 C18 | 004 | PanCK


title: JC_1_315 (21PG75-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 37622 C18 | 001 | PanCK


title: P92 Serum

value: Peripheral blood serum


title: 37622 C18 | 003 | PanCK


title: 37622 C18 | 001 | Other Stroma

value: stromal


title: JC_1_313 (21PG75-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 37622-C11 | 008 | Other Stroma

value: Pancreatic cancer (PDAC)

value: Pancreatobiliary


title: P3_CM_neg

value: PBS

value: Classical-Monocytes


title: P71 Serum

value: High


title: P2_RP_pos


title: 37622-C11 | 008 | CD45

value: Invasive IPMN


title: P14 Serum


title: P12 Serum

value: Low


title: JC_1_311 (20PG4-1)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: embryo

value: Middle blastocyst

value: embryo in vitro day E5.5


title: P59 Serum


title: P2_RP_neg

value: Red pulp macrophages

value: neg


title: P54 Serum


title: JC_1_31 (21PG40-1)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: embryo in vitro day E4.5


title: 37622-C11 | 008 | CD3

value: Pancreas


title: P2_CM_pos

value: Splenocytes

value: pos


title: 37622-C11 | 007 | CD3


title: JC_1_309 (20PG4-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: P2_NCM_pos

value: Non-Classical-Monocytes


title: 37622-C11 | 007 | Other Stroma

value: Pancreatic cancer (PDAC)

value: stromal


title: P15 Serum

value: Peripheral blood serum


title: JC_1_308 (20PG4-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: P2_CM_neg

value: PBS

value: Classical-Monocytes


title: 37622-C11 | 004 | PanCK

value: Invasive IPMN

value: Pancreatobiliary

value: epithelial


title: P1_RP_neg


title: 37622-C11 | 006 | PanCK


title: P2_NCM_neg


title: No template control A

organism: blank sample

source_name: not applicable

value: not applicable


title: No template control B


title: JC_1_306 (20PG4-1)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: embryo

value: Middle blastocyst

value: embryo in vitro day E5.5


title: 37622-C11 | 005 | PanCK


title: JC_1_312 (20PG4-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: JC_1_310 (20PG4-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 37622-C11 | 003 | PanCK

value: High-grade dysplasia


title: Wheat root, distal root region

city: Ghent

first: Bert

last: De Rybel

address: Technologiepark 71

department: Center for Plant Systems Biology

country: Belgium

institute: VIB

description: BGI Stereo-seq

data_processing:
Quality control, genome alignment and quantification of gene expression of the sequencing data were done using STOmics Analysis Workflow (SAW) (https://github.com/BGIResearch/SAW)
Assembly: Triticum aestivum IWGSC version 2.1
Supplementary files format and content: raw.gem: SAW pipeline output gem file
Supplementary files format and content: barcodeToPos.h5: Stereo-seq mask file
Supplementary files format and content: regist.tif: nuclei staining image aligned to transcriptomics coordinate space
Supplementary files format and content: FB.regist.tif: cell wall staining image aligned to transcriptomics coordinate space
Library strategy: Spatial Transcriptomics

organism: Triticum aestivum

source_name: Root

growth_protocol: Seeds were pre-soaked in milli-Q water for 4 days in the dark at 4 °C, followed by 10-min treatment at 50 °C in a water bath. Seeds were then transferred onto a MS (Murashige and Skoog) medium plate, grown in a tissue culture room (24 °C,  06.00-22.00 light). After germination, seeds were transferred to soil (Jiffy) in a growth room (20 °C,  06.00-22.00 light).

extract_protocol:
Roots were harvested fresh and embedded in pre-cooled OCT (Sakura) and stored at -80 °C until processed. The pre-frozen root tissues in OCT were cross-sectioned at 10 μm thickness using a Leica CM1950 cryostat.
All following steps were performed according to the protocols from (Chen et al., 2022; Xia et al., 2022) with small modifications.  Stereo-seq chip was pretreated with 0.01% poly-lysine for 10 minutes at room temperature before use. Tissue sections were adhered to the Stereo-seq chip surface and incubated on a slide warmer at 37 °C for 8 minutes. Then, tissues were fixed in methanol and incubated at -20 °C for 30 minutes and afterwards stained with Fluorescent Brightener 28 (FB) and Qubit ssDNA. Imaging was performed with a Motic fluorescence microscope. Then the tissue sections were permeabilized at 37 °C for 12 minutes followed by a washing step with 0.1x SSC buffer (Thermo, AM9770) containing 0.05 U/μL RNase inhibitor (NEB, M0314L). RNA was reverse transcribed for 3 hours at 42 °C, tissue sections were washed twice with 0.1x SSC buffer and digested with Tissue Removal buffer at 55 °C for 10 minutes. cDNA release mix was added and the cDNA was released during an overnight treatment  at 55 °C. cDNA was purified using DNA Cleanup Beads AMPure(R)  XP (Agencourt), and amplified using PCR. A total of 30 ng of DNA were used for fragmentation, performed at 55 °C for 10 minutes. Fragmentation products were amplified using PCR,  purified using the DNA Cleanup Beads AMPure(R)  XP, and sequenced (paired-end 100 bp) on an MGI-DNBSEQ-Tx sequencer.

value: Root

tag: ecotype

value: Chinese spring


title: P1_NCM_pos

value: Splenocytes

value: pos


title: JC_1_304 (20PG4-1)

description: Gpig.scRNAseq.counts.all.tsv.gz

extract_protocol:
Briefly, embryos were flushed from the oviduct (E3.5) or uterine horns (E4-E5.75) using 5-10 ml of warm M2 medium (MR-015-D, Sigma Aldrich) supplemented with 1 % Penicillin-Streptomycin (15130122, Life Technologies), washed and briefly kept in M2 drops covered with Ovoil TM (10029, Vitrolife) at the incubator at 5 % O2 5 % CO2 at 37.5 °C prior to being fixed in PFA 4 % for 15 min or single cell picking. E6 embryos were collected at E5.75 and incubated in similar conditions for 6 h to reach the desirable embryonic day, as implantation occurs around E6, and obtaining embryos by flushing the uterus was challenging.
Embryos collected from E3-E5.75 were obtained through the flushing female guinea pigs and placed in M2 drops under mineral oil until further processing. Zona pellucida was removed using tyrodes, and subsequent single-cell dissociation was achieved through enzymatic digestion with TrypLE Express (12604-013, Gibco, Life Technologies) followed by isolation using fine glass capillaries. Libraries were prepared using the Smartseq2 protocol, following established procedures 14–16. The quantity and quality of the cDNA libraries were assessed using an Agilent 2100 BioAnalyzer (Agilent Technologies). Approximately 1 ng of cDNA per cell was transformed into a single-cell library using the Nextera XT DNA Library prep kit (Illumina FC-131-1096) and following the manual instructions with slight modifications. In brief, 1 ng of cDNA (in a maximum of 5 µl of sample volume) underwent tagmentation with 2 µl of TD and 1 µl of ATM at 55 °C for 5 min. Upon completion of the program, the reaction was promptly halted by adding 1 µl of 2 % SDS and incubating for 5 min at RT. Amplification was carried out using 3 µl of NMP per sample and adding 1 µl of each dual-indexed (i7 and i5; Illumina) primer. Individual Nextera XT libraries were pooled and then purified using magnetic beads. Indexed sequence libraries were combined for multiplexing (384 samples per lane). The sequencing was performed using the NovoSeq6000 paired-end.


title: 37622-C11 | 002 | Other Stroma

value: Pancreas


title: JC_1_305 (20PG4-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: Wheat root, root cap region

description: BGI Stereo-seq


title: JC_1_307 (20PG4-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 10x lib 85, donor N387, cytopenia

first: Liran

last: Shlush

address: 234 Herzl Street

description: Library name: 10x_lib_85_donor_N387_blood_sample_225

data_processing:
Count matrices were generated using 10x Genomics' Cell Ranger v7.0.1 (https://www.10xgenomics.com/support/software/cell-ranger/latest).
As each 10x scRNA library contained pooled cells of multiple individuals, both Vireo (https://github.com/single-cell-genetics/vireo) and Souporcell (https://github.com/wheaton5/souporcell) were used (on each 10x library separately) to cluster cells based on SNPs found in the sequenced RNA. Cells that were identified as doublets by Vireo or Souporcell were discarded. Resulting clusters were matched to targeted genotype data obtained for each donor.
Cells with high mitochondrial content (>20%), platelet signature (PPBP > 0.2%), neutrophil signature (LCN2, CAMP, LTF), erythrocyte signature (HBB, HBA1, HBA2), or with low signature of nuclear RNAs were excluded. As part of additional doublet detection, cells were excluded if their UMI count was higher than 2.5-fold of their cluster median computed (thereby compensating for variable cell sizes across types), as well as if they exhibited high expression of both monocyte and MEBEMP gene programs.
Assembly: GRCh38-3.0.0
Supplementary files format and content: h5ad file (https://anndata.readthedocs.io/en/stable/) containing count matrix and cell metadata.

source_name: peripheral blood

extract_protocol:
Peripheral blood was drawn into lithium-heparin tubes. PBMCs were isolated via Ficoll, using Lymphoprep filled Sepmate tubes (StemCell technologies), followed by CD34 magnetic bead-based enrichment using the EasySep human CD34 positive selection kit II (StemCell technologies). 3-6 individual samples were pooled on each experiment day such that CD34-enrichment was performed on the entire pool of PBMCs produced. Few samples were not pooled due to logistical issues of timing blood donations, as sampling was restricted to fresh blood.
Single cell RNA libraries were generated using the 10x Genomics scRNA-seq platform (Chromium Next Gem single cell 3’ reagent kit V3.1) according to the manufacturer's instructions, except that we "super-loaded" each chromium chip lane, loading cells at a significantly higher concentration than recommended, with an expected yield of ~20-25k single cells.

value: peripheral blood

tag: Sex

value: male

value: PBMC

tag: disease state

value: cytopenia

tag: batch


title: P1_NCM_neg

value: PBS

value: Non-Classical-Monocytes

value: neg


title: JC_1_303 (20PG4-1)

description: Gpig.scRNAseq.counts.all.tsv.gz

data_processing:
For the guinea pig single-cell RNA-Seq data, adapters and low-quality reads were removed using Trimgalore with default parameters. Subsequently, high-quality reads were aligned to the guinea pig Ensembl reference genome (v.Cavpor.3.0.105, Cavia porcellus, obtained from the Ensembl website)using the HISAT2 aligner (v 2.2.0) with default settings. Only uniquely mapped reads were retained for gene expression quantification. Raw read counts were tentatively quantified using featureCounts (v1.6.3) based on Ensembl reference annotation.
Considering the incomplete guinea pig reference annotation, we decided to update the guinea pig gene annotation using the following steps: 1. Ensembl transcripts belonging to “lincRNA”, “processed_pseudogene”, “protein_coding”, and “pseudogenes” were selected as the guided annotation. The mapping bam files were used as input for Stringtie (v1.3.3b) for each individual sample. After the initial assembly, the transcripts were merged using 'stringtie --merge' and compared with the guided annotation using 'gffcompare -r'. Transcripts that overlapped with multiple reference genes were excluded, as well as transcripts with a length less than 200 bp and 'class codes' identified by gffcompare equal to ‘e’, ‘s’, ‘x’ were removed in downstream analysis. Transcripts with class codes 'j', 'k', '=', 'm', 'n', 'o', 'p', 'y' were assigned to corresponding reference genes. Novel transcripts with no clear reference annotation were blasted against human and mouse transcripts of protein coding and lncRNA with parameters '-max_target_seqs 1 -outfmt 6 -num_threads 25 -evalue 1e-20 -strand plus -max_hsps 1' to find the most similar human or mouse reference genes. If there were no orthologous genes of matched reference genes in the guinea pig Ensembl annotation, they were added. Other novel transcripts with known orthologous genes in the guinea pig Ensembl annotation were reassigned to known annotated genes based on whether the novel transcripts fell within the nearby loci (± 3 kb) of the current annotation.
Assembly: Cavpor.3.0.105
Supplementary files format and content: tab-delimited text file include raw count for each Sample


title: 37622-C11 | 002 | CD3

tag: ffpe block_year

tag: disease pathology

value: Invasive IPMN

tag: aoi pathology

value: Pancreatobiliary


title: P1_RP_pos

value: Red pulp macrophages


title: RA-FLS shNFATc2 3

city: Wenzhou

first: Wu

last: Gan

address: Chashan Street, Ouhai District

country: China

institute: Wenzhou Medical University

description:
Library name: KD3
FPKM.KD3

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality was also verified using fastp. We used HISAT2 (https://ccb.jhu.edu/software/hisat2) to map reads to the reference genome of Homo sapiens GRCh38. The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/). After the final transcriptome was generated, StringTie and was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]). The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and with parametric F-test comparing nested linear models (p value < 0.05) by R package edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html).
Assembly: hg38
Supplementary files format and content: excel file include FPKM value of each sample

source_name: fibroblast-like synoviocytes

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification.
The poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: fibroblast-like synoviocytes

tag: genotype

value: NFATc2 knock down


title: 37622-C11 | 001 | PanCK

value: High-grade dysplasia

tag: aoi histologocal_subtype

tag: roi segment

value: epithelial


title: RA-FLS shNFATc2 2

description:
Library name: KD2
FPKM.KD2


title: P1_CM_pos

value: Splenocytes

tag: treatment

tag: population

value: Classical-Monocytes


title: P1_CM_neg

tag: tdtm pos/neg

tag: replicate


title: JC_1_302 (20PG4-1)

first: Cheng

last: Zhao

description: Gpig.scRNAseq.counts.all.tsv.gz

tag: tissue

value: embryo

tag: developmental stage

value: Middle blastocyst

value: embryo in vitro day E5.5


title: 37507 | 008 | PanCK

value: Pancreas

value: Low-grade dysplasia

value: Normal duct

value: not applicable


title: RA-FLS shNFATc2 1

description:
Library name: KD1
FPKM.KD1

tag: cell type


title: B5_RP_pos

value: BCG

value: pos


title: 37622-C11 | 002 | PanCK

value: Invasive IPMN

value: Pancreatobiliary


title: JC_1_301 (20PG4-1)

description: Gpig.scRNAseq.counts.all.tsv.gz

tag: time


title: JC_1_300 (20PG4-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 37507 | 007 | PanCK

value: Gastric Foveolar


title: RA-FLS shNC 3

description:
Library name: NC3
FPKM.NC3

value: fibroblast-like synoviocytes

value: WT


title: B5_NCM_pos

value: Non-Classical-Monocytes


title: JC_1_30 (21PG40-1)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: embryo in vitro day E4.5


title: 37507 | 006 | Other Stroma

value: stromal


title: RA-FLS shNC 2

description:
Library name: NC2
FPKM.NC2


title: B5_NCM_neg

value: Splenocytes

value: neg


title: 37507 | 006 | PanCK

value: epithelial


title: JC_1_3 (21PG50-2)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: embryo

value: 8 cell

value: embryo in vitro day E3.5


title: B5_CM_pos

value: Classical-Monocytes


title: JC_1_299 (20PG4-1)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: Middle blastocyst

value: embryo in vitro day E5.5


title: OH17582, dauer, solvent control, rep5

city: New York

first: Surojit

last: Sural

state: NY

address: 1212 Amsterdam Avenue

department: Biological Sciences

institute: Howard Hughes Medical Institute, Columbia University

description: Library name: TIR1 no auxin n5

data_processing:
Quality control of raw RNA-seq reads were performed using FastQC. Adapter sequences were trimmed using Trimmomatic. Reads were aligned to the C. elegans genome (WS284) usin STAR. Read counts were assigned to genes using featureCounts. Differential expression of genes across conditions was determined using DESeq2.
Assembly: C. elegans WS284
Supplementary files format and content: comma-separated values file with normalized read counts for all samples

organism: Caenorhabditis elegans

source_name: Whole animal

growth_protocol: All animals carrying the daf-2(e1370) mutation were synchronized using alkaline bleaching method and embryos were grown on nematode growth media (NGM) plates with E. coli OP50 bacteria in a 25°C incubator for 3 days till all animals were arrested in the dauer stage.

extract_protocol:
24,000 dauer stage animals per sample were lyzed in TRIzol reagent and total RNA was extracted using RNeasy Micro Kit (Qiagen) using the manufacturer's protocol.
100 ng of total RNA per sample was used for library prep using Universal RNA-seq with NuQuant kit (Tecan) using the manufacturer's protocol with custom AnyDeplete (IC0149S) to deplete rRNA.

treatment_protocol: Animals were treated with either solvent (ethanol) only or 100μM 5-phenyl-indole-3-acetic acid (5-Ph-IAA) by spreading a solution of 5-Ph-IAA on the NGM plates one day prior to seeding them with E. coli OP50 bacteria. The final ethanol concentration on the plates was 0.2% (v/v).

value: Whole animal

value: Ethanol


title: B5_CM_neg

value: BCG


title: B5_RP_neg

value: Red pulp macrophages


title: OH17582, dauer, 100 uM 5PhIAA, rep5

description: Library name: TIR1 PhIAA n5

value: 100 uM 5-Ph-IAA


title: JC_1_298 (20PG4-1)

address: H9 Klinisk vetenskap,171 77 Stockholm

institute: Karolinska institute

description: Gpig.scRNAseq.counts.all.tsv.gz


title: B4_RP_pos

value: pos


title: OH14654, dauer, 100 uM 5PhIAA, rep5

description: Library name: no TIR1 PhIAA n5


title: JC_1_296 (20PG4-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: OH14654, dauer, solvent control, rep5

description: Library name: no TIR1 no auxin n5


title: JC_1_297 (20PG4-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 37507 | 005 | PanCK

value: Pancreas

value: Low-grade dysplasia

value: Gastric Foveolar


title: 37507 | 004 | Other Stroma

value: stromal


title: B4_RP_neg

value: Splenocytes

value: neg


title: 37507 | 003 | PanCK

value: Normal duct

value: not applicable

value: epithelial


title: OH17582, dauer, 100 uM 5PhIAA, rep4

description: Library name: TIR1 PhIAA n4


title: B4_NCM_neg

value: Non-Classical-Monocytes


title: JC_1_294 (20PG4-1)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: embryo

value: Middle blastocyst

value: embryo in vitro day E5.5


title: 37507 | 002 | PanCK


title: 37507 | 004 | PanCK


title: OH17582, dauer, solvent control, rep4

description: Library name: TIR1 no auxin n4

value: Whole animal

value: Ethanol


title: RA-FLS shNC 1

description:
Library name: NC1
FPKM.NC1

value: fibroblast-like synoviocytes

value: WT


title: 37507 | 005 | Other Stroma

value: Pancreas


title: JC_1_293 (20PG4-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 37507 | 001 | Other Stroma

value: Low-grade dysplasia


title: B4_CM_pos

value: BCG

value: Classical-Monocytes

value: pos


title: OH14654, dauer, 100 uM 5PhIAA, rep4

description: Library name: no TIR1 PhIAA n4

value: 100 uM 5-Ph-IAA


title: JC_1_292 (20PG4-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: B4_CM_neg

value: Splenocytes

value: neg


title: B4_NCM_pos


title: 34453 | 006 | PanCK

value: Gastric Foveolar

value: epithelial


title: JC_1_295 (20PG4-1)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: embryo


title: B3_RP_neg

value: Red pulp macrophages


title: 37507 | 001 | PanCK

value: Normal duct

value: not applicable


title: JC_1_291 (20PG4-1)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: Middle blastocyst

value: embryo in vitro day E5.5


title: B3_RP_pos


title: OH17582, dauer, solvent control, rep3

description: Library name: TIR1 no auxin n3

value: Whole animal

value: Ethanol


title: 34453 | 005 | PanCK

value: Pancreas

value: Low-grade dysplasia


title: JC_1_290 (20PG4-1)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: B3_NCM_pos

value: BCG

value: Non-Classical-Monocytes


title: OH17582, dauer, 100 uM 5PhIAA, rep3

description: Library name: TIR1 PhIAA n3

value: 100 uM 5-Ph-IAA


title: B3_NCM_neg

value: Splenocytes


title: 34453 | 004 | PanCK


title: JC_1_29 (21PG40-1)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: embryo in vitro day E4.5


title: OH14654, dauer, solvent control, rep3

description: Library name: no TIR1 no auxin n3


title: B3_CM_pos

value: Classical-Monocytes

value: pos


title: JC_1_289 (20PG4-1)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: embryo


title: 34453 | 003 | PanCK

value: Gastric Foveolar

value: epithelial


title: OH17582, dauer, 100 uM 5PhIAA, rep2

description: Library name: TIR1 PhIAA n2


title: OH17582, dauer, solvent control, rep2

description: Library name: TIR1 no auxin n2


title: 34453 | 002 | PanCK

value: Normal duct

value: not applicable


title: JC_1_287 (20PG4-2)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: Middle blastocyst

value: embryo in vitro day E5.5


title: OH14654, dauer, solvent control, rep4

description: Library name: no TIR1 no auxin n4

value: Whole animal

value: Ethanol


title: B2_RP_pos

value: Red pulp macrophages


title: 34453 | 001 | Other Stroma

value: Pancreas

value: Low-grade dysplasia

value: stromal


title: JC_1_285 (20PG4-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: OH14654, dauer, 100 uM 5PhIAA, rep3

description: Library name: no TIR1 PhIAA n3

value: 100 uM 5-Ph-IAA


title: B2_RP_neg

value: Splenocytes

value: BCG

value: neg


title: OH14654, dauer, 100 uM 5PhIAA, rep2

description: Library name: no TIR1 PhIAA n2


title: 34453 | 004 | Other Stroma


title: OH14654, dauer, solvent control, rep2

description: Library name: no TIR1 no auxin n2


title: OH17582, dauer, 100 uM 5PhIAA, rep1

description: Library name: TIR1 PhIAA n1


title: 34453 | 001 | PanCK


title: JC_1_284 (20PG4-2)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: embryo


title: B2_NCM_pos

value: Non-Classical-Monocytes

value: pos


title: B2_NCM_neg


title: JC_1_283 (20PG4-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: OH17582, dauer, solvent control, rep1

description: Library name: TIR1 no auxin n1


title: B2_CM_pos

value: Classical-Monocytes


title: 9092 | 011 | PanCK

value: Invasive IPMN

value: Pancreatic cancer (PDAC)

value: Pancreatobiliary

value: epithelial


title: OH14654, dauer, 100 uM 5PhIAA, rep1

description: Library name: no TIR1 PhIAA n1

value: Whole animal


title: 9092 | 010 | Other Stroma


title: B3_CM_neg


title: JC_1_282 (20PG4-2)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: Middle blastocyst

value: embryo in vitro day E5.5


title: JC_1_288 (21PG57-1)

description: Gpig.scRNAseq.counts.all.tsv.gz

value: Late blastocyst


title: JC_1_281 (20PG4-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: B2_CM_neg


title: 9092 | 010 | CD45

value: Pancreas


title: OH14654, dauer, solvent control, rep1

description: Library name: no TIR1 no auxin n1

value: Ethanol


title: JC_1_280 (20PG4-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: B1_RP_pos

value: Splenocytes

value: Red pulp macrophages


title: 9092 | 010 | CD3


title: 9092 | 012 | PanCK


title: JC_1_286 (20PG4-2)

description: Gpig.scRNAseq.counts.all.tsv.gz


title: 16WTF_MB22_TAO501_posF_scRNA_2M216_BDS_S5_DGE

city: Belvaux

first: Enrico

last: Glaab

state: Capellen

address: 6, avenue du Swing

country: Luxembourg

institute: University of Luxembourg

description: Library name: Sample 16

data_processing:
Raw sequencing data was processed using Drop-seq tools (version 1.12, http://mccarrolllab.com/dropseq/). Reads were aligned to the mouse genome (mm10) following the Drop-seq Alignment Cookbook (version 1.2, January 2016).
Assembly: mm10
Supplementary files format and content: Processed data is provided in the .txt file format containing the normalized gene count matrix for each sample.

source_name: Cortex

growth_protocol: THY-Tau22 mouse breeding pairs were obtained from the University of Lille, France. The line was rederived at the University of Luxembourg mouse facility and maintained by crossing heterozygous males with C57Bl6/J females (RRID:MGI:3028467). Animals were housed in pathogen-free facilities with unrestricted access to standard mouse chow (Ssniff, # V 1534-300) and water. The mice were aged to 17 months for this study.

extract_protocol:
RNA was extracted from cortical tissue using the RNeasy Universal Kit (Qiagen) following established protocols. Quality control criteria for RNA samples included an RNA integrity value above 8.5 and absorbance ratios at 260/230 and 260/280 equal to or greater than 1.8 and 2, respectively. Validated samples were stored at -80°C. For single-cell transcriptomics, fresh cortical tissue was dissociated using the Adult Brain Dissociation kit (Miltenyi Biotec) before proceeding with DropSeq analysis.
The 3′ end enriched cDNA libraries were prepared by tagmentation reaction of 600 pg cDNA library using the standard Nextera XT tagmentation kit (Illumina). Reactions were performed according to the manufacturer’s instructions. The PCR amplification cycling programme used was 95 °C 30 s, and 12 cycles of 95 °C (10 s), 55 °C (30 s), and 72 °C (30 s), followed by a final extension step of 72 °C (5 min). Libraries were purified twice to reduce primers and short DNA fragments with 0.6 × and 1 × Agencourt AMPure XP beads (Beckman Coulter), respectively, in accordance with the manufacturer’s protocol. Finally, purified libraries were eluted in 10 μl Molecular Grade Water. Quality and quantity of the tagmented cDNA library were evaluated using Bioanalyzer High Sensitivity DNA Chip. The average size of the tagmented libraries prior to sequencing was between 400 and 700 bps.
Purified DropSeq libraries were sequenced on an Illumina NextSeq machine using paired-end sequencing. Read 1 (20 bases) covered cell barcodes (bases 1-12) and unique molecular identifiers (UMIs, bases 13-20), while Read 2 captured 60 bases of gene sequences. A custom primer (GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC) was used for Read 1 at 6pM concentration.

value: Cortex

tag: Sex

value: Female

value: WT


title: B1_RP_neg

value: BCG

value: neg


title: 15TGF_MB22_TAO500_tgF_scRNA_2M216_BDS_S1_DGE

description: Library name: Sample 15

value: TG


title: 9092 | 010 | PanCK

city: Durham

value: Invasive IPMN

value: Pancreatic cancer (PDAC)


title: 14TGF_MB21_TAO595_tgF_scRNA_2M216_BDS_S8_DGE

description: Library name: Sample 14