title: 13WTF_MB21_TAO594_posF_scRNA_2M216_BDS_S8_DGE

description: Library name: Sample 13


title: B1_NCM_neg

status: Public on Jan 06 2025

type: SRA

city: Rehovot

first: Roi

last: Avraham

address: Herzl St 234

country: Israel

institute: Weizmann Institute of Science

library_source: transcriptomic

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

molecule: total RNA

organism: Mus musculus

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.

tag: tissue

value: Splenocytes

tag: treatment

value: BCG

tag: population

value: Non-Classical-Monocytes

tag: tdtm pos/neg

value: neg

tag: replicate


title: JC_1_28 (21PG40-1)

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.

value: embryo

tag: developmental stage

tag: time

value: embryo in vitro day E4.5


title: 9092 | 008 | PanCK

city: Durham

first: Peter

last: Allen

state: NC

address: 203 Research Dr., MSRB1 Rm. 475

department: Surgery

country: USA

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

organism: Homo sapiens

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: High-grade dysplasia

tag: aoi histologocal_subtype

value: Pancreatobiliary

tag: roi segment

value: epithelial


title: B1_NCM_pos

value: pos


title: 9092 | 009 | PanCK


title: JC_1_278 (20PG4-2)

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

value: Middle blastocyst

value: embryo in vitro day E5.5


title: JC_1_277 (20PG4-2)

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


title: 9092 | 007 | Other Stroma

value: stromal


title: 9092 | 007 | CD45


title: JC_1_276 (20PG4-2)

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


title: 11TGM_MB21_TAO587_tgM_scRNA_2M216_BDS_S7_DGE

city: Belvaux

first: Enrico

last: Glaab

state: Capellen

address: 6, avenue du Swing

country: Luxembourg

institute: University of Luxembourg

description: Library name: Sample 11

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: Male

tag: genotype

value: TG


title: 12WTF_MB21_TAO588_posF_scRNA_2M216_BDS_S4_DGE

description: Library name: Sample 12

value: Female

value: WT


title: JC_1_279 (20PG4-2)

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


title: JC_1_275 (20PG4-2)

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


title: 9092 | 007 | CD3


title: Mut RU486 4

city: Oxford

first: Arne

middle: Wyndham

last: Mould

state: Oxfordshire

address: Warneford Hospital

department: Psychiatry

country: United Kingdom

institute: Oxford University

data_processing:
Paired-end reads were aligned against the mm10 genome using the STAR RNA-seq aligner in Galaxy with default parameters outputting bam files
BAM files were imported imported into Seqmonk 1.46.0 (https://www.bioinformatics.babraham.ac.uk/projects/download.html#seqmonk) and analysed using the RNA-seq quantitation pipeline
Differentially expressed genes between groups were identified using DESeq2 with FDR > 0.05 based on raw counts generated using opposing strand, paired end and merge transcripts options.
Assembly: mm10
Supplementary files format and content: [.txt] Read Counts and DESeq2 Results from SeqMonk

source_name: E6.0 whole decidua

extract_protocol:
Total RNA was extracted using an RNeasy Mini kit (Qiagen Cat#74104) with on column DNase treatment according manufacturer’s protocol.
Total RNA was ribodepleted using Ribozero and libraries prepared using standard stranded illumina RNA-seq protocols. Paired end sequencing (150 bp) was performed on an Illumina Novaseq 6000 or NextSeq 500.

treatment_protocol: WT and Blimp1 mutant (Prdm1 BEH/CA ;PRCre) females were mated with C57BL6/J studs. For staging purposes, E0.5 was defined as midday on the day of vaginal plug. At E5.5, females were administered with RU486 (150 micrograms) in mineral oil or mineral oil alone by intraperitoneal injection. Whole decidua minus the overlying myometrium were harvested 14 hrs later.

value: E6.0 whole decidua

value: Blimp1 mutant


title: 10TGM_MB21_TAO585_tgM_scRNA_2M216_BDS_S4_DGE

description: Library name: Sample 10


title: Mut RU486 3


title: JC_1_274 (20PG4-2)

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

value: embryo


title: 9092 | 007 | PanCK

value: Pancreas


title: 09TGF_MB21_TAO583_tgF_scRNA_2M216_BDS_S3_DGE

description: Library name: Sample 9


title: Mut RU486 2


title: B1_CM_pos

value: Splenocytes

value: BCG

value: Classical-Monocytes


title: JC_1_273 (20PG4-2)

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


title: 9092 | 006 | PanCK

value: Invasive IPMN

value: Low-grade dysplasia

value: Gastric Foveolar

value: epithelial


title: Mut RU486 1


title: 9092 | 005 | PanCK


title: Mut oil 4

value: Oil


title: JC_1_271 (20PG4-2)

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

value: Middle blastocyst

value: embryo in vitro day E5.5


title: 07TGM_MB21_TAO581_tgM_scRNA_2M216_BDS_S3_DGE

description: Library name: Sample 7

value: Cortex

value: Male

value: TG


title: 08TGM_MB21_TAO582_tgM_scRNA_2M216_BDS_S7_DGE

description: Library name: Sample 8


title: 9092 | 004 | Other Stroma

value: stromal


title: 06TGF_MB21_TAO580_tgF_scRNA_2M216_BDS_S6_DGE

description: Library name: Sample 6

value: Female


title: B1_CM_neg

value: neg


title: Mut oil 3

value: E6.0 whole decidua

value: Blimp1 mutant


title: 9092 | 004 | CD45

value: Pancreas


title: JC_1_27 (21PG40-1)

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

value: embryo

value: embryo in vitro day E4.5


title: Mut oil 2


title: JC_1_270 (20PG4-2)

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


title: 05WTM_MB21_TAO578_posM_scRNA_2M216_BDS_S6_DGE

description: Library name: Sample 5

value: WT


title: 04WTM_MB21_TAO576_posM_scRNA_2M216_BDS_S2_DGE

description: Library name: Sample 4


title: 9092 | 004 | CD3

value: Invasive IPMN

value: Low-grade dysplasia

value: Gastric Foveolar


title: 9092 | 004 | PanCK

value: epithelial


title: Mut oil 1

value: Oil


title: JC_1_269 (20PG4-2)

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

value: Middle blastocyst

value: embryo in vitro day E5.5


title: WT RU486 4

value: wild type


title: 9092 | 003 | PanCK

value: Normal duct

value: not applicable


title: 02TGF_MB21_TAO574_tgF_scRNA_2M216_BDS_S2_DGE

description: Library name: Sample 2

value: Cortex

value: Female

value: TG


title: WT RU486 3

value: E6.0 whole decidua


title: JC_1_267 (20PG4-2)

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

value: embryo


title: 9092 | 002 | PanCK

value: Pancreas


title: JC_1_272 (20PG4-2)

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


title: WT oil 4


title: 01WTM_MB21_TAO574_posM_scRNA_2M216_BDS_S1_DGE

description: Library name: Sample 1

value: Male

value: WT


title: 9092 | 001 | Other Stroma

value: Invasive IPMN

value: stromal


title: JC_1_265 (20PG4-2)

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


title: WT oil 3


title: WT oil 2


title: JC_1_264 (20PG4-2)

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


title: 9092 | 001 | PanCK

value: epithelial


title: WT oil 1

value: Oil


title: JC_1_263 (20PG4-2)

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

value: Middle blastocyst


title: 03WTM_MB21_TAO575_posM_scRNA_2M216_BDS_S5_DGE

description: Library name: Sample 3


title: 13167 | 015 | CD3

value: Pancreatic cancer (PDAC)

value: Pancreatobiliary


title: Diabetic mouse 2860

city: Rochester

first: Madhusudan

last: Grover

state: MN

address: 200 First St SW

institute: Mayo Clinic

description:
Library name: Mouse-2860_T1
Chromium Single Cell 3’ v3

data_processing:
10X Genomics alignment using CellRanger v4.0
Assembly: mm10
Supplementary files format and content: aligned, position sorted bam files

source_name: Blood

growth_protocol: Mouse

extract_protocol:
Chromium Single Cell 3ʹ GEM Kit v3
Chromium Single Cell 3’ v3

value: Blood

tag: cell type

value: Diabetic


title: Diabetic mouse 2863

description:
Library name: Mouse-2863_T1
Chromium Single Cell 3’ v3


title: Normal Gastric Emptying Diabetic mouse 2860

description:
Library name: Mouse-2860_T2
Chromium Single Cell 3’ v3

value: Resistant


title: Normal Gastric Emptying Diabetic mouse 2863

description:
Library name: Mouse-2863_T2
Chromium Single Cell 3’ v3


title: JC_1_268 (20PG4-2)

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

value: embryo in vitro day E5.5


title: JC_1_262 (20PG4-2)

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


title: Delayed Gastric Emptying Diabetic mouse 2416

description:
Library name: Mouse-2416_T2
Chromium Single Cell 3’ v3

value: Delayed


title: 13167 | 015 | PanCK


title: JC_1_261 (20PG4-2)

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


title: B6CBAF1/J, NP P4, uterus, H3K27me3 [USC-P4-6]

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
USC-P4_all.bw
USC-P4_peaks.broadPeak

library_source: genomic

data_processing:
Raw reads were mapped to the mouse mm10 genome using STAR alignment
BAM files were generated by STAR.
PCR duplicates were removed by Picard and peak calling was done using MACS2.
Aligned BAM files were converted to BED format with bedtools, converted to bedgraph format using bedtools. Bedgraphs were normalized and each replicate of a given experimental condition was pooled and merged. bedGraphToBigWig was used to generate the bigwig files.
Assembly: mm10
Supplementary files format and content: bigWig
Supplementary files format and content: broadPeak (except for Input samples)
Library strategy: CUT & RUN

molecule: genomic DNA

source_name: uterus

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: uterus

tag: antibody

value: fibroblast

tag: mating

value: Non-pregnant, progesterone-treated


title: 13167 | 014 | PanCK

tag: tissue

value: Pancreas

value: High-grade dysplasia


title: JC_1_266 (20PG4-2)

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

value: embryo


title: B6CBAF1/J, NP P4, uterus, H3K27me3 [USC-P4-1]


title: JC_1_260 (20PG4-2)

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


title: type2_inh mixed sample (non-demultiplexed)

data_processing:
MARS-seq pipeline (https://www.nature.com/articles/s41596-019-0164-4) was used for demultiplexing, alignment to the genome, and gene counting
Demultiplexing into plates is based on 4bp pool-barcode for each plate which is located at R1 base-pairs 6-9 (see samples_barcodes.xlsx tab:amp_batches for pool-barcodes sequences of each plate)
Demultiplexing into samples is based on 7bp  sample-barcode for each sample which is located at R2 base-pairs 1-7 (see samples_barcodes.xlsx tab:well_cells for sample-barcodes sequences of each sample)
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 4
Replicate samples of each condition were averaged, except for 1 sample that was excluded due to low coverage (<100k reads; PBS +S.Tm + Fedratinib replicate 3).
Assembly: mm9
Supplementary files format and content: data_matrix_raw_counts.txt: tab-delimited text files include raw number of reads (linear scale) for each sample
Supplementary files format and content: normalized_data_type2_inh.txt: tab-delimited text files include normalized number of reads (linear scale) for each sample

source_name: Spleen

extract_protocol:
15 days post inoculation and 24 hours post S.Tm challenge, 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 lysing pellet directly with 350uL RLT buffer.
Libraries assembled according to the Mars-seq2.0 protocol.

treatment_protocol: Female C57/BL6J mice were inoculated with 5*10^6 BCG (Pasteur) or PBS i.p in a volume of 200ul. Four hours after initial inoculation, Fedratinib (1mg) were injected, and repeated once every 24 hours for the next 4 days. After 14 days, mice were challenged with 5*10^5 CFU of Salmonella Typhimuirum or PBS, and sacrificed 24 hours after.

value: Spleen

value: Splenocytes


title: 13167 | 013 | PanCK

value: Invasive IPMN

value: epithelial


title: 13167 | 015 | CD45

value: Pancreatic cancer (PDAC)


title: B6CBAF1/J, NP P4, uterus, H3K27me3 [USC-P4-11]


title: JC_1_26 (21PG40-1)

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

value: embryo in vitro day E4.5


title: Diabetic mouse 2416

description:
Library name: Mouse-2416_T1
Chromium Single Cell 3’ v3

value: Blood


title: 13167 | 011 | PanCK

value: Pancreatobiliary


title: B6CBAF1/J, GD0.5, uterus, Input [USC-0-I]

description:
STAR v2.7.5c, samtools v1.10, bedtools v2.29.1, bedGraphToBigWig v2.8 were used for .bw creatation
USC_0_I.bw

value: xB6 male

tag: time point


title: inhibitors experiment - mixed sample (non-demultiplexed)

description: Inhibitors experiment

data_processing:
MARS-seq pipeline (https://www.nature.com/articles/s41596-019-0164-4) was used for demultiplexing, alignment to the genome, and gene counting
Demultiplexing into plates is based on 4bp pool-barcode for each plate which is located at R1 base-pairs 6-9 (see samples_barcodes.xlsx tab:amp_batches for pool-barcodes sequences of each plate)
Demultiplexing into samples is based on 7bp  sample-barcode for each sample which is located at R2 base-pairs 1-7 (see samples_barcodes.xlsx tab:well_cells for sample-barcodes sequences of each sample)
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 2 samples of Fedratinib treatment (replicates 2&3), due to technical issues during injection that resulted in a lack of inhibition.
Assembly: mm9
Supplementary files format and content: raw_data_matrix_inhibitors.txt: tab-delimited text files include raw number of reads (linear scale) for each sample
Supplementary files format and content: normalized_data_matrix_inhibitors.txt: tab-delimited text files include normalized number of reads (linear scale) for each sample

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 lysing pellet directly with 350uL RLT buffer.
Libraries assembled according to the Mars-seq2.0 protocol.

treatment_protocol: Female C57/BL6J mice were inoculated with 5*10^6 BCG (Pasteur) or PBS i.p in a volume of 200ul. Four hours after initial inoculation, Fedratinib (1mg), Ruxolitinb (1mg), and Deucravacitinib (0.5mg) were injected, and repeated once every 24 hours for the next 4 days.


title: JC_1_259 (20PG4-2)

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

value: Middle blastocyst

value: embryo in vitro day E5.5


title: 13167 | 010 | PanCK


title: B6CBAF1/J, NP P4, uterus, Input [USC-P4-I]

description:
STAR v2.7.5c, samtools v1.10, bedtools v2.29.1, bedGraphToBigWig v2.8 were used for .bw creatation
USC_P4_I.bw

value: uterus


title: WT RU486 6

value: E6.0 whole decidua

value: wild type

tag: treatment


title: WT RU486 5


title: B6CBAF1/J, GD0.5, uterus, H3K27me3 [USC-0-8]

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
USC-0_all.bw
USC-0_peaks.broadPeak

value: fibroblast


title: 13167 | 009 | CD45

value: Pancreas

value: Low-grade dysplasia

value: Gastric Foveolar


title: 13167 | 009 | Other Stroma

value: stromal


title: JC_1_257 (20PG4-2)

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

value: embryo


title: JC_1_258 (20PG4-2)

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


title: CD8+T cells, RNA+6h

city: Matsumoto

first: Sachie

last: Hiratsuka

address: 3-1-1 Asahi

department: Medicine

country: Japan

institute: Shinshu University

data_processing:
The combined library was finally subjected to sequencing with HiSeq X Ten and Illumina Hiseq 2x150 bp sequencing configuration, per lane (~350M reads)
The reads were trimmed and clipped in Trimmomatic v0.39.
The reads were imported into STAR v2.7.6a for alignment into BAM files using human genome sequence (hg38, GRCh38).
BAM files were imported into FeatureCounts (in Subread v2.0.6) and PRKM counts were calculated.
Assembly: hg83, GRCh38
Supplementary files format and content: xlsx files include raw counts and RPKM values for each sample.

growth_protocol: Human PBMC was purchased from Roche. Thawed PBMC was maintained in HPLM (Thermo) medium supplemented with 10% FCS in humidified incubator with 5% CO2 at 37C.

extract_protocol:
0.5h or 6h after the addition of RNA, cells were FACS-sorted to isolate NK cells (CD56+CD3-) and CD8+T cells. Isolated cells were immediately placed into Trizol (Thermo) reagent to obtain total RNA.
Library preparation for RNA-Seq was performed with TAKARA SMART-Seq® HT PLUS Kit (Takara Bio Inc., Shiga, Japan). A part (0.4-1.4 ng) of total RNAs were reverse transcribed and amplified by 12 PCR cycles. Then, 3 ng of each cDNA was subjected to fragmentation, illumina index attachment to the ends, and PCR-amplified (15 cycles).

treatment_protocol: The following day, FITC labeled IL1b-mRNA (10 ng/mL) was applied in the culture media

tag: cell line

value: PBMC

value: CD8+ T cells

value: WT

tag: treatment (fitc_labeled_il1b-mrna)


title: B6CBAF1/J, GD0.5, uterus, H3K27me3 [USC-0-13]


title: CD8+T cells, RNA+0.5h

value: Blood


title: JC_1_255 (21PG76-2)

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

tag: developmental stage

value: Late blastocyst

value: embryo in vitro day E5.75


title: 13167 | 009 | PanCK

value: Invasive IPMN

value: epithelial


title: 13167 | 008 | Other Stroma


title: B6CBAF1/J, GD5.5xVAS, uterus, Input [MSC-V-5-I]

description:
STAR v2.7.5c, samtools v1.10, bedtools v2.29.1, bedGraphToBigWig v2.8 were used for .bw creatation
MSC_V_5_I.bw

value: uterus

value: xVASX


title: B6CBAF1/J, GD5.5xVAS, uterus, H3K27me3 [MSC-V-5-5]

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
MSC-V-5_all.bw
MSC-V-5_peaks.broadPeak


title: 13167 | 008 | CD45


title: NK cells, RNA+6h

value: NK cells


title: JC_1_253 (21PG49-3)

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

value: Early blastocyst

tag: time

value: embryo in vitro day E5.25


title: CD8+T cells, control

value: control


title: 13167 | 008 | PanCK

value: Pancreas

tag: ffpe block_year

value: Low-grade dysplasia

value: Gastric Foveolar


title: B6CBAF1/J, GD5.5xVAS, uterus, H3K27me3 [MSC-V-5-10]

value: fibroblast


title: JC_1_254 (21PG76-2)

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

value: embryo


title: 13167 | 007 | PanCK

tag: disease pathology


title: NK cells, control

value: PBMC

value: WT


title: B6CBAF1/J, GD5.5, IIS, Input [MSC-5-I]

description:
STAR v2.7.5c, samtools v1.10, bedtools v2.29.1, bedGraphToBigWig v2.8 were used for .bw creatation
MSC_5_I.bw

source_name: Inter-implantation site

value: Inter-implantation site

value: xB6 male


title: JC_1_251 (21PG49-3)

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


title: B6CBAF1/J, GD0.5, uterus, H3K27me3 [USC-0-3]


title: JC_1_252 (21PG49-3)

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


title: 13167 | 006 | PanCK

value: Invasive IPMN

tag: aoi pathology

value: Normal duct

value: not applicable


title: JC_1_256 (21PG76-2)

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

value: Late blastocyst

value: embryo in vitro day E5.75


title: B6CBAF1/J, GD5.5, IIS, H3K27me3 [MSC-5-9]

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
MSC-5_all.bw
MSC-5_peaks.broadPeak


title: JC_1_250 (21PG49-3)

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

value: Early blastocyst


title: 13167 | 005 | PanCK

tag: aoi histologocal_subtype

value: epithelial


title: B6CBAF1/J, GD5.5, IIS, H3K27me3 [MSC-5-4]


title: Wheat root replicate 2

city: Ghent

first: Bert

last: De Rybel

address: Technologiepark 71

department: Center for Plant Systems Biology

country: Belgium

institute: VIB

description:
10X Genomics
DRS006

data_processing:
Read alignment + counting; Cell Ranger count; version 6.0.0
Assembly: Triticum aestivum IWGSC version 2.1
Supplementary files format and content: h5 file containing raw and filtered count matrix (output Cell Ranger count)
Supplementary files format and content: Merged Seurat file in .rds format

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:
From 15-day-old seedlings, 100 root tips per sample (~0.5 cm from root tip) from all available sources (primary, lateral root) were collected and digested for 1.5 hours in enzyme buffer (0.4 M mannitol, 20 mM MeS, 20 mM KCl, 1.25% Cellulase RS (Yakult), 1.25% Cellulase R10 (Yakult), 0.3% Macerozyme R10 (Yakult), 0.12% Pectolyase Y-23 (Yakult), 10 mM CaCl2, 0.1% BSA, 0.018% beta-mercaptoethanol, pH = 5.7, the enzyme buffer were pre-heated at 60 °C for 10 minutes, cool down to room temperature before use) with gentle shaking at room temperature. The protoplasts were filtered with a cell strainer (70 μm diameter, Falcon REF #352340), centrifuged, washed with 8% mannitol, filtered again with a cell strainer (70 μm diameter, Falcon REF #352340) and centrifuged again. The pellets were resuspended in a mix of 8% mannitol and levitation buffer. PI (Propidium iodide) and Calcein were added to the suspension. Cells were sorted using the LeviCell magnetic sorter (take the upper part).
Cell suspensions were loaded into a Chromium Single Cell 3’ GEM, Library & Gel Bead Kit (V3.1 chemistry, 10X Genomics) according to the manufacturer’s instructions.

value: Root

tag: ecotype

value: Chinese spring


title: 13167 | 003 | PanCK

value: Pancreas

tag: roi segment


title: JC_1_25 (21PG40-1)

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

value: embryo in vitro day E4.5


title: B6CBAF1/J, GD5.5, IIS, H3K27me3 [MSC-5-14]

value: fibroblast

tag: genotype


title: JC_1_249 (21PG49-3)

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

value: embryo

value: embryo in vitro day E5.25


title: B6CBAF1/J, GD5.5xVAS, uterus, H3K27me3 [MSC-V-5-15]

value: uterus

tag: cell type

value: xVASX


title: Wheat root replicate 1

description:
10X Genomics
DRS003


title: Kdm6b f/f, GD8.5, IIS, Input [8WT_I_15]

description:
STAR v2.7.5c, samtools v1.10, bedtools v2.29.1, bedGraphToBigWig v2.8 were used for .bw creatation
8WT_I_15.bw

value: Inter-implantation site

tag: antibody

value: Kdm6b f/f control

value: xB6 male


title: NK cells, RNA+0.5h

value: Blood

value: PBMC

value: NK cells

value: WT


title: 9505 E13 | 006 | PanCK

value: Invasive IPMN

value: Pancreatic cancer (PDAC)

value: Pancreatobiliary

value: epithelial


title: JC_1_248 (21PG49-3)

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

value: Early blastocyst


title: 9505 E13 | 005 | Other Stroma

value: Pancreas

value: stromal


title: Kdm6b f/f, GD8.5, IIS, H3K27me3 [8WT_3]

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
8WT_all.bw
1137_8WT_ext400_BC0.5_peaks.broadPeak

value: fibroblast

tag: mating


title: Kdm6b f/f, GD8.5, IIS, H3K27me3 [8WT_28]

tag: tissue


title: JC_1_247 (21PG49-3)

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

value: embryo

value: embryo in vitro day E5.25


title: 9505 E13 | 005 | CD3

description: FFPE spatial whole transcriptome sequencing


title: JC_1_246 (21PG49-3)

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


title: 13167 | 002 | Other Stroma

value: Normal duct

value: not applicable


title: Pgr-cre Kdm6b f/f, GD8.5, IIS, Input [8KO_I_25]

description:
STAR v2.7.5c, samtools v1.10, bedtools v2.29.1, bedGraphToBigWig v2.8 were used for .bw creatation
8KO_I_25.bw

value: Inter-implantation site

value: Kdm6b cKO

value: xB6 male

tag: time point


title: Wheat root replicate 3

description:
10X Genomics
DRS007

value: Root

value: Chinese spring


title: 9505 E13 | 005 | PanCK

value: Invasive IPMN


title: JC_1_245 (21PG49-3)

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


title: Kdm6b f/f, GD8.5, IIS, H3K27me3 [8WT_15]

value: Kdm6b f/f control


title: Pgr-cre Kdm6b f/f, GD8.5, IIS, H3K27me3 [8KO_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
8KO_all.bw
1137_8KO_ext400_BC0.5_peaks.broadPeak


title: 9505 E13 | 004 | CD3

value: Pancreatic cancer (PDAC)

value: Pancreatobiliary


title: JC_1_243 (21PG49-3)

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

value: Early blastocyst


title: JC_1_242 (21PG49-3)

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


title: Pgr-cre Kdm6b f/f, GD8.5, IIS, H3K27me3 [8KO_30]


title: 9505 E13 | 004 | PanCK

value: Pancreas

value: epithelial


title: Pgr-cre Kdm6b f/f, GD8.5, IIS, H3K27me3 [8KO_25]

value: fibroblast


title: JC_1_241 (21PG49-3)

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

value: embryo


title: 9505 E13 | 003 | PanCK

value: High-grade dysplasia


title: Kdm6b f/f, GD5.5, IIS, Input [5WT_I_13]

description:
STAR v2.7.5c, samtools v1.10, bedtools v2.29.1, bedGraphToBigWig v2.8 were used for .bw creatation
5WT_I_13.bw


title: JC_1_240 (21PG49-3)

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

value: embryo in vitro day E5.25


title: 9505 E13 | 002 | PanCK


title: Kdm6b f/f, GD5.5, IIS, H3K27me3 [5WT_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
5WT_all.bw
1137_5WT_ext400_BC0.5_peaks.broadPeak


title: Kdm6b f/f, GD5.5, IIS, H3K27me3 [5WT_45]


title: 9505 E13 | 001 | Other Stroma

value: stromal


title: JC_1_24 (21PG40-1)

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

value: embryo in vitro day E4.5


title: 9505 E13 | 001 | CD3


title: Kdm6b f/f, GD5.5, IIS, H3K27me3 [5WT_13]

value: Inter-implantation site


title: JC_1_244 (21PG49-3)

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


title: JC_1_239 (21PG49-3)

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


title: Pgr-cre Kdm6b f/f, GD5.5, IIS, Input [5KO_I_14]

description:
STAR v2.7.5c, samtools v1.10, bedtools v2.29.1, bedGraphToBigWig v2.8 were used for .bw creatation
5KO_I_14.bw

value: Kdm6b cKO

value: xB6 male


title: JC_1_237 (21PG49-3)

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


title: 9505 E13 | 004 | Other Stroma


title: 9505 E13 | 001 | PanCK


title: JC_1_238 (21PG49-3)

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


title: Pgr-cre Kdm6b f/f, GD5.5, IIS, H3K27me3 [5KO_36]

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
5KO_all.bw
1137_5KO_ext400_BC0.5_peaks.broadPeak


title: repeat_Bryostatin_33

city: Rotterdam

middle: D.

last: Katsikis

state: Zuid-Holland

address: Dr. Molewaterplein 40

department: Department of Immunology

country: Netherlands

institute: Erasmus University Medical Center

description:
Library name: r_Bryo_33
repeat peptide stimulated

data_processing:
Raw fastq files were processed with the nf-core rnaseq pipeline (v3.0). Briefly:
Reads were quality trimmed using Trim Galore! for bases with a Phred score lower than 30.
The reads were aligned for each sample seperately using STAR2.7.6a to the mouse reference genome (GRCm38).
BAM files were converted using Samtools 1.10.
Alignment files were annotated and counts were esimated with RSEM 1.3.1 using GRCm38.81.gtf from Ensembl file for gene annotation.
Assembly: Ensembl GRCm38 / Ensembl GRCm38.81.gtf
Supplementary files format and content: RSEM estimated gene counts

source_name: purified CD8+ T cells

growth_protocol: CD8+ T cells were isolated from single-cell suspensions of splenocytes from OT-I mice by negative selection (EasySep, Stemcell Technologies). Cells were cultured in RPMI 1640 media containing 10% FBS (Gibco), 2mM L-glutamine (Life Technologies), 10 mM HEPES (Life Technologies), 100 mM Sodium Pyruvate (Life Technologies), 1% non-essential amino acides (Gibco), 100 U/ml penicillin (Gibco) and 100 μg/ml Streptomycin-sulfate (Gibco), 0.05mM Betamercaptoethanol (Sigma). Cytokines IL-7 (5ng/ml, Peprotech, Cat 210–07) and IL-15 (5ng/ml, Peprotech, Cat 210–15) were added in the media to avoid cell apoptosis. Cells received repeat OVA(257-264) peptide stimulation daily at the concentration of 10 ng/ml for five days from day 0 to day 5 which inducing T cell exhaustion (Repeat peptide stimulated cells). The cells received only a single peptide stimulation on day 0 were washed after 48 hours, resulting in a non-exhausted effector phenotype (Single peptide stimulated cells). On day 4, cultures from both repeat and single peptide stimulations were 1:1 split and put fresh media with IL-15 and IL-7. On day 5, both single peptide and repeat peptide stimulated cells were washed and 0.5x10^5 cells per well in 24well plates were then cultured with bryostatin-1 or DMSO treatments for additional 3 days. 10 ng/ml OVA(257-264)  peptide was added to repeat peptide stimulation cultures to maintain the chronic antigenic stimulation environment from day 5 to day 8.

extract_protocol:
1x10^6 live (Annexin V-) CD8+ T cells were sorted from the 4 different culture conditions and immediately lysed with TRIzol LS reagent (Life Technologies) and stored at -80°C. RNA was extracted according to manufacturer’s instructions and a bioanalyzer (Agilent) was used to determine the integrity of the extracted RNA.
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina" (NEB #E7760S/L).
mRNA was isolated from total RNA using the oligo-dT magnetic beads. After fragmentation of the mRNA, a cDNA synthesis was performed. This was used for ligation with the sequencing adapters and PCR amplicification of the resulting product. The quality and yield after sample preparation was measured with the Fragment Analyzer (see appendices). The size of the resulting products was consistent with the expected size distribution (a broad peak between 300-500 bp).

treatment_protocol: On day 5, both single peptide and repeat peptide stimulated cells were treated either with 10 nM bryostatin-1 (sc-201407, Santa Cruz Biotechnology) or DMSO for additional 3 days. On day 8, the cells were harvested.

value: purified CD8+ T cells

value: OT-1 mice WT

tag: treatment

value: Bryostatin 10nM


title: repeat_Bryostatin_49

description:
Library name: r_Bryo_49
repeat peptide stimulated


title: 9505 E12 | 005 | PanCK

value: Invasive IPMN

value: Low-grade dysplasia

value: Gastric Foveolar


title: 9505 E12 | 004 | PanCK

value: Pancreas


title: JC_1_236 (21PG49-3)

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

value: Early blastocyst


title: Pgr-cre Kdm6b f/f, GD5.5, IIS, H3K27me3 [5KO_24]

value: fibroblast


title: JC_1_235 (21PG49-3)

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

value: embryo


title: 9505 E12 | 003 | Other Stroma


title: repeat_Bryostatin_20

description:
Library name: r_Bryo_20
repeat peptide stimulated


title: JC_1_234 (21PG49-3)

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


title: 9505 E12 | 003 | CD3


title: Kdm6b f/f, GD18.5, IS, Input [18WT_I_21]

description:
STAR v2.7.5c, samtools v1.10, bedtools v2.29.1, bedGraphToBigWig v2.8 were used for .bw creatation
18WT_I_21.bw

value: Kdm6b f/f control


title: repeat_Bryostatin_14b

description:
Library name: r_Bryo_14b
repeat peptide stimulated


title: JC_1_233 (21PG49-3)

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

value: embryo in vitro day E5.25


title: repeat_DMSO_43

description:
Library name: r_DMSO_43
repeat peptide stimulated

value: DMSO


title: JC_1_232 (21PG49-3)

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


title: 9505 E12 | 003 | PanCK

value: epithelial


title: Kdm6b f/f, GD18.5, IS, H3K27me3 [18WT_43]

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
18WT_all.bw
1137_18WT_ext400_BC0.5_peaks.broadPeak


title: JC_1_231 (21PG49-3)

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


title: Kdm6b f/f, GD18.5, IS, H3K27me3 [18WT_10]


title: repeat_DMSO_37

description:
Library name: r_DMSO_37
repeat peptide stimulated


title: 9505 E12 | 002 | Other Stroma

value: Normal duct

value: not applicable

value: stromal


title: 9505 E12 | 002 | PanCK


title: Kdm6b f/f, GD18.5, IS, H3K27me3 [18WT_21]

value: xB6 male


title: repeat_Bryostatin_25

description:
Library name: r_Bryo_25
repeat peptide stimulated

value: purified CD8+ T cells

value: OT-1 mice WT


title: Pgr-Cre Kdm6bf/f, GD18.5, IS, Input [18KO_I_29]

description:
STAR v2.7.5c, samtools v1.10, bedtools v2.29.1, bedGraphToBigWig v2.8 were used for .bw creatation
18KO_I_29.bw

value: Kdm6b cKO


title: 9505 E12 | 001 | PanCK

description: FFPE spatial whole transcriptome sequencing

value: Invasive IPMN


title: repeat_DMSO_30

description:
Library name: r_DMSO_30
repeat peptide stimulated


title: repeat_DMSO_18

description:
Library name: r_DMSO_18
repeat peptide stimulated


title: JC_1_230 (21PG49-3)

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


title: Pgr-Cre Kdm6bf/f, GD18.5, IS, H3K27me3 [18KO_35]

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
18KO_all.bw
1137_18KO_ext400_BC0.5_peaks.broadPeak


title: repeat_DMSO_23

description:
Library name: r_DMSO_23
repeat peptide stimulated


title: JC_1_23 (21PG40-1)

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

value: embryo in vitro day E4.5


title: Pgr-cre Kdm6b f/f, GD5.5, IIS, H3K27me3 [5KO_14]

value: Inter-implantation site


title: 40593 | 006 | PanCK

value: Pancreas

value: Low-grade dysplasia

value: Gastric Foveolar


title: Pgr-Cre Kdm6bf/f, GD18.5, IS, H3K27me3 [18KO_29]

value: fibroblast


title: repeat_DMSO_11

description:
Library name: r_DMSO_11
repeat peptide stimulated


title: JC_1_210 (21PG57-1)

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

value: embryo

value: Late blastocyst

value: embryo in vitro day E5.5


title: 40593 | 005 | PanCK

value: epithelial


title: single_Bryostatin_47

description:
Library name: s_Bryo_47
single peptide stimulated

value: Bryostatin 10nM


title: Pgr-Cre Kdm6bf/f, GD18.5, IS, H3K27me3 [18KO_11]


title: JC_1_21 (21PG40-1)

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


title: Kdm6b f/f, GD14.5, IS, Input [14WT_I_16]

description:
STAR v2.7.5c, samtools v1.10, bedtools v2.29.1, bedGraphToBigWig v2.8 were used for .bw creatation
14WT_I_16.bw

value: Kdm6b f/f control


title: single_Bryostatin_29

description:
Library name: s_Bryo_29
single peptide stimulated


title: 40593 | 004 | Other Stroma

value: stromal


title: JC_1_209 (21PG57-1)

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


title: 9505 E12 | 001 | Other Stroma

value: Normal duct

value: not applicable


title: 40593 | 004 | CD45


title: 40593 | 004 | CD3


title: single_Bryostatin_10

description:
Library name: s_Bryo_10
single peptide stimulated

value: purified CD8+ T cells

value: OT-1 mice WT


title: JC_1_206 (21PG57-1)

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


title: Kdm6b f/f, GD14.5, IIS, Input [14WT_IIS_I_18]

description:
STAR v2.7.5c, samtools v1.10, bedtools v2.29.1, bedGraphToBigWig v2.8 were used for .bw creatation
14WT_IIS_I_18.bw

value: xB6 male


title: Kdm6b f/f, GD14.5, IIS, H3K27me3 [14WT_IIS_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
14WT_IIS_all.bw
1137_14WT_IIS_ext400_BC0.5_peaks.broadPeak

value: Inter-implantation site


title: 40593 | 003 | PanCK

value: Pancreas


title: JC_1_202 (21PG57-1)

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


title: single_DMSO_40

description:
Library name: s_DMSO_40
single peptide stimulated

value: DMSO


title: single_DMSO_46

description:
Library name: s_DMSO_46
single peptide stimulated


title: Kdm6b f/f, GD14.5, IIS, H3K27me3 [14WT_IIS_18]


title: Kdm6b f/f, GD14.5, IIS, H3K27me3 [14WT_IIS_31]


title: single_Bryostatin_50

description:
Library name: s_Bryo_50
single peptide stimulated


title: Kdm6b f/f, GD14.5, IS, H3K27me3 [14WT_47]

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
14WT_all.bw
1137_14WT_ext400_BC0.5_peaks.broadPeak


title: 40593 | 004 | PanCK

value: Low-grade dysplasia

value: Gastric Foveolar


title: single_DMSO_34

description:
Library name: s_DMSO_34
single peptide stimulated


title: JC_1_200 (21PG57-1)

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

value: embryo


title: 40593 | 002 | PanCK

description: FFPE spatial whole transcriptome sequencing


title: JC_1_2 (21PG50-2)

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

value: 8 cell

value: embryo in vitro day E3.5


title: single_DMSO_7

description:
Library name: s_DMSO_7
single peptide stimulated


title: 40593 | 001 | PanCK

value: epithelial


title: JC_1_198 (21PG57-1)

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

value: Late blastocyst

value: embryo in vitro day E5.5


title: Kdm6b f/f, GD14.5, IS, H3K27me3 [14WT_26]

value: fibroblast

value: Kdm6b f/f control


title: 25212 | 016 | Other Stroma

value: Invasive IPMN

value: Pancreatic cancer (PDAC)

value: Pancreatobiliary

value: stromal


title: single_DMSO_26b

description:
Library name: s_DMSO_26b
single peptide stimulated

value: purified CD8+ T cells

value: OT-1 mice WT


title: NGS40 HT22 +Ox +121

city: La Jolla

first: K. Garrett

last: Evensen

address: 10010 N Torrey Pines Rd

institute: The Salk Institute for Biological Studies

data_processing:
RNA-Seq reads were mapped by STAR [v2.5.3a, ref: 10.1093/bioinformatics/bts635. pmid:23104886] to the mm10 reference genome with default parameters and flag “--outFilterIntronMotifs RemoveNoncanonical”.
Homer [v4.9.1, ref: PMID: 20513432; http://homer.ucsd.edu/homer/] commands “makeTagDirectory” and “analyzeRepeats” were used to quantify gene expression by counting uniquely mapped reads across all exons of RefSeq genes.
Mitochondrial gene reads were quantified using STAR with flag “--quantMode GeneCounts” to the 10X cell ranger mm10 v1.2.0 STAR index because they were not included in Homer annotation.
Assembly: mm10
Supplementary files format and content: tab-delimited file includes raw counts for each sample

source_name: HT-22 Mouse Hippocampal Neuronal Cell Line

growth_protocol: HT22 mouse hippocampal nerve cells were cultured in high-glucose Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal calf serum (FCS), and incubated at 37ºC in an atmosphere with 10% CO2.

extract_protocol:
RNA was isolated from HT22 nerve cells using the RNeasy Plus Universal mini kit (Qiagen).
RNA-Seq libraries were prepared using the Illumina TruSeq Stranded mRNA Sample Prep Kit according to the manufacturer’s instructions.

treatment_protocol: After 24 h of culture, the medium was exchanged with fresh medium, and 5 mM glutamate was added in the absence and presence of 1uM CMS121.

tag: cell line

value: Hippocampal nerve cells

value: WT

value: Oxytosis + CMS124


title: JC_1_201 (21PG57-1)

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

value: embryo


title: NGS39 HT22 +Ox +121

value: HT-22 Mouse Hippocampal Neuronal Cell Line


title: Pgr-Cre Kdm6bf/f, GD14.5, IIS, Input [14KO_IIS_I_19]

description:
STAR v2.7.5c, samtools v1.10, bedtools v2.29.1, bedGraphToBigWig v2.8 were used for .bw creatation
14KO_IIS_I_19.bw

value: Inter-implantation site

value: Kdm6b cKO

value: xB6 male


title: JC_1_196 (21PG57-1)

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

value: Late blastocyst

value: embryo in vitro day E5.5


title: Pgr-Cre Kdm6bf/f, GD14.5, IIS, H3K27me3 [14KO_IIS_32]

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
14KO_IIS_all.bw
1137_14KO_IIS_ext400_BC0.5_peaks.broadPeak

value: fibroblast


title: Pgr-Cre Kdm6bf/f, GD14.5, IS, Input [14KO_I_17]

description:
STAR v2.7.5c, samtools v1.10, bedtools v2.29.1, bedGraphToBigWig v2.8 were used for .bw creatation
14KO_I_17.bw


title: 25212 | 016 | PanCK

value: Pancreas

value: Invasive IPMN

value: epithelial


title: 25212 | 016 | CD3

value: Pancreatic cancer (PDAC)

value: Pancreatobiliary


title: JC_1_195 (21PG57-1)

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


title: NGS38 HT22 +Ox +121

value: Oxytosis + CMS123


title: 40593 | 001 | Other Stroma

value: Low-grade dysplasia

value: Normal duct

value: not applicable

value: stromal


title: 25212 | 015 | PanCK


title: NGS37 HT22 +Ox +121

value: HT-22 Mouse Hippocampal Neuronal Cell Line

value: Hippocampal nerve cells

value: WT

value: Oxytosis + CMS122


title: JC_1_193 (21PG57-1)

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

value: embryo

value: Late blastocyst


title: Pgr-Cre Kdm6bf/f, GD14.5, IIS, H3K27me3 [14KO_IIS_19]

value: Inter-implantation site

value: fibroblast

value: Kdm6b cKO

value: xB6 male


title: JC_1_22 (21PG40-1)

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

value: embryo in vitro day E4.5


title: JC_1_20 (21PG40-1)

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


title: 25212 | 014 | PanCK

value: Pancreas

value: Invasive IPMN

value: Pancreatic cancer (PDAC)

value: Pancreatobiliary

value: epithelial


title: Kdm6b f/f, GD14.5, IS, H3K27me3 [14WT_16]

value: Kdm6b f/f control


title: JC_1_192 (21PG50-1)

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

value: 8 cell

value: embryo in vitro day E3.5


title: 25212 | 013 | PanCK

value: High-grade dysplasia


title: NGS36 HT22 +Ox +121

value: HT-22 Mouse Hippocampal Neuronal Cell Line

value: Hippocampal nerve cells

value: WT

value: Oxytosis + CMS121


title: Pgr-Cre Kdm6bf/f, GD14.5, IS, H3K27me3 [14KO_6]

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
14KO_all.bw
1137_14KO_ext400_BC0.5_peaks.broadPeak

value: fibroblast


title: Pgr-Cre Kdm6bf/f, GD14.5, IIS, H3K27me3 [14KO_IIS_12]

value: Inter-implantation site

value: Kdm6b cKO


title: JC_1_191 (21PG50-1)

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

value: embryo


title: 25212 | 012 | Other Stroma

value: Pancreas

value: stromal


title: NGS35 HT22 +Ox -121

value: Oxytosis


title: 25212 | 012 | CD3

value: Invasive IPMN

value: Pancreatic cancer (PDAC)

value: Pancreatobiliary


title: NGS33 HT22 +Ox -121


title: Pgr-Cre Kdm6bf/f, GD14.5, IS, H3K27me3 [14KO_17]

value: xB6 male


title: JC_1_190 (21PG50-1)

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

value: 8 cell

value: embryo in vitro day E3.5


title: Pgr-Cre Kdm6bf/f, GD14.5, IS, H3K27me3 [14KO_27]


title: JC_1_19 (21PG40-1)

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

value: embryo in vitro day E4.5


title: NGS31 HT22 +Ox -121

value: HT-22 Mouse Hippocampal Neuronal Cell Line

value: Hippocampal nerve cells


title: JC_1_188 (21PG50-1)

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


title: Kdm6b f/f, GD14.5, IS, H3K27me3 [14FRA_WT_38]

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
14FRA_WT_all.bw
1137_14FRA_WT_ext400_BC0.5_peaks.broadPeak

value: Kdm6b f/f control


title: 25212 | 011 | PanCK

value: High-grade dysplasia

value: epithelial


title: Kdm6b f/f, GD14.5, IS, H3K27me3 [14FRA_WT_41]

value: fibroblast


title: NGS29 HT22 -Ox +121

value: WT

value: Control + CMS124


title: JC_1_194 (21PG57-1)

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

value: embryo

value: Late blastocyst

value: embryo in vitro day E5.5


title: 25212 | 010 | Other Stroma

value: Pancreas

value: Invasive IPMN

value: stromal


title: NGS34 HT22 +Ox -121

value: Oxytosis


title: JC_1_187 (21PG50-1)

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

value: 8 cell

value: embryo in vitro day E3.5


title: 25212 | 010 | CD45

value: Pancreatobiliary


title: JC_1_186 (21PG50-1)

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


title: 25212 | 010 | CD3


title: NGS28 HT22 -Ox +121

value: HT-22 Mouse Hippocampal Neuronal Cell Line

value: Hippocampal nerve cells

value: Control + CMS123


title: JC_1_185 (21PG77-2)

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

value: 16 cell

value: embryo in vitro day E4


title: Pdgfra-Cre Kdm6bf/f, GD14.5, IS, Input [14FRA_KO_I_20]

description:
STAR v2.7.5c, samtools v1.10, bedtools v2.29.1, bedGraphToBigWig v2.8 were used for .bw creatation
14FRA_KO_I_20.bw

value: fibroblast

value: Pdgfra-cre Kdm6b f/f

value: xB6 male


title: 25212 | 010 | PanCK

value: High-grade dysplasia

value: epithelial


title: NGS27 HT22 -Ox +121

value: WT

value: Control + CMS122


title: NGS32 HT22 +Ox -121


title: 25212 | 012 | PanCK

value: Pancreas

value: Invasive IPMN

value: Pancreatic cancer (PDAC)


title: JC_1_189 (21PG50-1)

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

value: embryo

value: 8 cell

value: embryo in vitro day E3.5


title: NGS30 HT22 -Ox +121

value: HT-22 Mouse Hippocampal Neuronal Cell Line

value: Hippocampal nerve cells

value: Control + CMS125


title: Kdm6b f/f, GD14.5, IS, Input [14FRA_WT_I_8]

description:
STAR v2.7.5c, samtools v1.10, bedtools v2.29.1, bedGraphToBigWig v2.8 were used for .bw creatation
14FRA_WT_I_8.bw

value: Kdm6b f/f control


title: Pdgfra-Cre Kdm6bf/f, GD14.5, IS, H3K27me3 [14FRA_KO_9]

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
14FRA_KO_all.bw
1137_14FRA_KO_ext400_BC0.5_peaks.broadPeak

value: fibroblast


title: 25212 | 009 | Other Stroma

value: Pancreatobiliary

value: stromal


title: 25212 | 009 | CD45

value: High-grade dysplasia


title: JC_1_184 (21PG77-2)

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

value: 16 cell

value: embryo in vitro day E4


title: JC_1_183 (21PG77-2)

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


title: NGS25 HT22 -Ox -121

value: WT

value: Control


title: NGS24 HT22 -Ox -121


title: JC_1_182 (21PG77-2)

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


title: NGS26 HT22 -Ox +121

value: Control + CMS121


title: 25212 | 009 | PanCK

value: Pancreas

value: Invasive IPMN

value: epithelial


title: JC_1_181 (21PG77-2)

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

value: embryo


title: Kdm6b f/f, GD14.5, IS, H3K27me3 [14FRA_WT_37]

value: xB6 male


title: Pdgfra-Cre Kdm6bf/f, GD14.5, IS, H3K27me3 [14FRA_KO_20]

value: Pdgfra-cre Kdm6b f/f


title: 25212 | 008 | PanCK

value: Low-grade dysplasia

value: Gastric Foveolar


title: 25212 | 009 | CD3


title: NGS23 HT22 -Ox -121

value: HT-22 Mouse Hippocampal Neuronal Cell Line

value: Hippocampal nerve cells


title: NGS22 HT22 -Ox -121


title: JC_1_180 (21PG77-2)

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


title: JC_1_18 (21PG40-1)

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

value: embryo in vitro day E4.5


title: NGS21 HT22 -Ox -121


title: 25212 | 007 | PanCK


title: Mouse 96 L uninj

type: RNA

city: North Grafton

first: Jillian

middle: M

last: Richmond

state: Massachusetts

address: 200 Westboro Road

department: Comparative Pathobiology

institute: Tufts Cummings School of Veterinary Medicine

hyb_protocol: Hybridizations were performed per NanoString manufacturer's protocol overnight for 18h in a BioRad C1000 touch thermocycler

scan_protocol: Cartridges were run on a NanoString Sprint machine.

data_processing: Data were analyzed with nSolver software version 4.0

label: fluorescent probe

source_name: Uninjected control

label_protocol: Probe labeling was performed per NanoString manufacturer's protocol.

growth_protocol: For OT1 transfers, CD8+ T cells were isolated from donor spleens using Biolegend MojoSort kits and 1 million cells were transfered into recipient mice. For OT2 cultures, CD4+ T cells were isolated from donor spleens, activated with anti-CD3/28 antibodies, skewed with cytokines and antibodies towards Th2, and expanded with IL-2 for a total of 10 days (see also PMIDs: 29889098, 35833127). Ten million OT2 Th2 cells were transfered into recipient mice. Lesional skin tissue was isolated from all recipient mice at the indicated time points and frozen for future analysis. Skin was also isolated from littermate injected mice and uninjected controls from similar anatomical sites.

extract_protocol: RNA was extracted from skin using Qiagen RNEasy mini kits per the manufacturer's instructions.

value: frozen skin

tag: t cell donor type

value: N/A (uninjected)

tag: mouse score

tag: time point first or flare

value: First

tag: Sex

value: Male


title: Mouse 93 L uninj


title: 25212 | 006 | PanCK

tag: ffpe block_year

tag: disease pathology


title: JC_1_179 (21PG77-2)

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

tag: developmental stage

value: 16 cell

tag: time

value: embryo in vitro day E4


title: Pdgfra-Cre Kdm6bf/f, GD14.5, IS, H3K27me3 [14FRA_KO_34]

value: fibroblast


title: VEEV, 8dpi, 12mkd, Rep4

city: Memphis

first: Evan

middle: Peter

last: Williams

state: TN

address: 858 Madison Ave

department: Dept. of Microbiology, Immunology, and Biochemistry

institute: University of Tennessee Health Science Center

data_processing:
CLC Genomics Workbench v 23.0
Sequence reads were trimmed  and filter using default parameters in CLC Genomic Workbench
Trimmed and filter sequence reads were mapped to GRCm39/virus species concatinated genome using default parameters in CLC Genomic Workbench
Read count results were collected in  CLC Genomic Workbench
Read count were normalized and fold change calculated using DESeq2
Assembly: GRCM38 concatinated with lab reference genome of each virus
Supplementary files format and content: tab-delimited text files include total counts, TPM, CPM, and RPKM values for each sample

source_name: Brain

extract_protocol:
Total RNA was isolated using TRIzol
Libraries were constructed using Illumina TruSeq Stranded mRNA

value: Brain

value: BALB/c

value: Infected, 12 mk/kg/day


title: Mouse 138 L uninj

value: Flare


title: Mouse 132 R uninj


title: VEEV, 8dpi, 12mkd, Rep3


title: 25212 | 005 | Other Stroma

value: Pancreas

value: Invasive IPMN

tag: aoi pathology

tag: aoi histologocal_subtype

tag: roi segment

value: stromal


title: Mouse 81 L littermate

source_name: CD8 injected littermate female

value: CD8 (OT1)

value: Female


title: 25212 | 005 | CD45

value: Low-grade dysplasia

value: Gastric Foveolar


title: JC_1_176 (21PG77-2)

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

value: embryo


title: VEEV, 8dpi, 12mkd, Rep2

tag: genotype


title: 25212 | 005 | CD3


title: JC_1_175 (21PG77-2)

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


title: Mouse 116 O littermate

source_name: CD8 injected littermate male

value: frozen skin

value: First


title: VEEV, 8dpi, 12mkd, Rep1


title: JC_1_177 (21PG77-2)

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

value: 16 cell


title: VEEV, 4dpi, 12mkd, Rep4


title: JC_1_174 (21PG77-2)

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

value: embryo in vitro day E4


title: 25212 | 004 | Other Stroma

value: Normal duct

value: not applicable


title: Mouse 98 O littermate

value: Male


title: VEEV, 4dpi, 12mkd, Rep3

value: Brain

value: BALB/c

value: Infected, 12 mk/kg/day


title: Mouse 110 R littermate


title: JC_1_173 (21PG77-2)

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


title: 25212 | 004 | PanCK

value: Pancreas

value: Invasive IPMN

value: epithelial


title: 25212 | 005 | PanCK


title: VEEV, 4dpi, 12mkd, Rep2


title: Mouse 80 O PCA

source_name: CD8 injected primary disease female

value: CD8 (OT1)

value: Female


title: JC_1_172 (21PG77-2)

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


title: JC_1_178 (21PG77-2)

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


title: 25212 | 003 | PanCK


title: Mouse 110 O PCA

source_name: CD8 injected primary disease male


title: VEEV, 4dpi, 12mkd, Rep1


title: JC_1_171 (21PG77-2)

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

source_name: embryo


title: 25212 | 002 | PanCK

source_name: Pancreas


title: Mouse 123 O PCA


title: VEEV, 2dpi, 12mkd, Rep4


title: JC_1_170 (21PG53-1)

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

value: embryo in vitro day E4.5


title: VEEV, 2dpi, 12mkd, Rep3


title: Mouse 127 R CLE flare

source_name: CD4 injected flare disease male

value: CD4 (OT2 Th2)

value: Flare


title: VEEV, 2dpi, 12mkd, Rep2


title: 25212 | 001 | PanCK


title: JC_1_17 (21PG39-2)

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

value: embryo


title: 25212 | 001 | Other Stroma

value: stromal


title: Mouse 141 O CLE flare

source_name: CD4 injected flare disease female

value: frozen skin


title: VEEV, 2dpi, 12mkd, Rep1


title: Mouse 113 O PCA

value: First


title: Mouse 123 RL CLE flare


title: 38859 | 007 | PanCK

value: Low-grade dysplasia

value: Gastric Foveolar


title: JC_1_169 (21PG53-1)

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


title: VEEV, 5dpi, 0mkd, Rep4

value: Brain

value: Infected, 0 mk/kg/day


title: JC_1_167 (21PG53-1)

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


title: Mouse 123 L CLE flare

value: Male


title: VEEV, 5dpi, 0mkd, Rep3

value: BALB/c


title: Mouse 67 RL CLE primary

source_name: CD4 injected primary disease female


title: JC_1_166 (21PG53-1)

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


title: 38859 | 005 | PanCK

value: Pancreas

value: Normal duct

value: not applicable


title: VEEV, 5dpi, 0mkd, Rep2


title: Mouse 53 L CLE primary

value: Female


title: JC_1_165 (21PG53-1)

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

value: embryo in vitro day E4.5


title: 38859 | 004 | PanCK

value: epithelial


title: Mouse 95 O CLE primary

source_name: CD4 injected primary disease male

value: CD4 (OT2 Th2)


title: 38859 | 008 | PanCK


title: JC_1_164 (21PG53-1)

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

value: embryo


title: JC_1_168 (21PG53-1)

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


title: 38859 | 003 | Other Stroma

value: stromal


title: VEEV, 4dpi, 0mkd, Rep4


title: JC_1_163 (21PG53-1)

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


title: 38859 | 003 | CD45


title: VEEV, 4dpi, 0mkd, Rep2


title: VEEV, 4dpi, 0mkd, Rep3


title: Mouse 93 O CLE primary

value: frozen skin


title: Mouse 71 O littermate

source_name: CD4 injected littermate female

value: First


title: JC_1_161 (21PG53-1)

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


title: 38859 | 003 | CD3

value: Low-grade dysplasia


title: JC_1_162 (21PG53-1)

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


title: Mouse 152 R littermate

value: Flare


title: 38859 | 003 | PanCK

value: Gastric Foveolar


title: Mouse 122 O littermate

source_name: CD4 injected littermate male


title: 38859 | 006 | PanCK


title: JC_1_160 (21PG53-1)

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


title: 38859 | 002 | PanCK


title: VEEV, 2dpi, 0mkd, Rep4

value: Brain

value: Infected, 0 mk/kg/day


title: VEEV, 4dpi, 0mkd, Rep1

value: BALB/c


title: A3B_SPIseq_lipid

city: London

first: Chi

last: Zhang

address: 15 Cotswold Road

department: Division of Cancer Therapeutics

institute: The Institute of Cancer Research

description: SPI-seq, lipid-treated cells

data_processing:
library strategy: ssDNA protein immunoprecipitation (SPI)-seq
Single-end raw reads were aligned to GRCh37 genome assembly using BWA, followed by file format exchange by SAMtools.
Peak calling was carried out using MACS2 package, where both input/IP sequence reads were used and the fragment length was set to 200 bp.
Genome_build: GRCh37
Supplementary_files_format_and_content: peak files generated by MACS2
Supplementary_files_format_and_content: bigwig files generated by MACS2, score represent fold enrichment over input control

source_name: T-47D BRCA cell line

growth_protocol: T-47D (ATCC HTB-133) cells were obtained from ATCC, and maintained in RPMI-1640 medium supplemented with 10% v/v FBS (PAA), 0.2 Units/ml bovine insulin (Sigma) and 0.5% v/v pen/strep (Gibco). Cells were transduced with lentiviral inducible 3×Flag-A3B-P2A-hUGI-HA cassette, which was maintained with 1 µg/ml puromycin (Gibco).

extract_protocol:
ChIP protocol was adopted from Myer’s Lab at HudsonAlpha (protocol version v011014) which contributed to the ENCODE project. Except that: i), cells were lysed in ChromaTrap lysis buffer that designed for sonication (Porvair Science, 100001), and chromatin fragmentation was carried out on a Covaris E220 instrument with optimised settings for ChIP purpose; 2), ChIP-grade protein A/G beads (Pierce 26162) were used to perform immuno-precipitation experiments; 3), Flag-M2 (Sigma F1804) antibody was used, and the following buffer was used for chromatin binding and washing: 100 mM Tris pH 7.5; 500 mM LiCl; 1% NP-40; 1% sodium deoxycholate. For SPI, the immunoprecipitated complex from ChIP were subjected to denaturing and adapter ligation following the protocol reported by the developers of SPI-seq (PMID: 23249883).
Library was constructed following the protocol reported by the developers of SPI-seq (PMID: 23249883).

treatment_protocol: T-47D cells were plated in a 6-well plate at a density of 5×10^4 cells per well and incubated for 24 h before transfected with 1.5 µg of the vector or 30 nM siRNA by Lipofectamine 2000 (Invitrogen) according to the manufacturer's instructions. 1 µg/ml doxycycline was added 24 hours after transfection, and ChIP/SPI experiments were carried out 48 hours after transfection.

value: Transfection lipid (lipofectamine 2000)


title: VEEV, 5dpi, 0mkd, Rep1


title: JC_1_16 (21PG39-1)

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

value: 16 cell

value: embryo in vitro day E4


title: 38859 | 001 | Other Stroma

value: Pancreas

value: Normal duct

value: not applicable


title: VEEV, 2dpi, 0mkd, Rep3


title: A3B_SPIseq_RNaseH_input

description: input, RNaseH1-overexpressed cells

value: RNaseH1-overexpressing plasmid


title: 38859 | 001 | CD45


title: JC_1_159 (21PG53-1)

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

value: embryo

value: embryo in vitro day E4.5


title: VEEV, 2dpi, 0mkd, Rep2


title: JC_1_158 (21PG53-1)

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


title: VEEV, 2dpi, 0mkd, Rep1


title: A3B_SPIseq_ChIPseq_lipid_input

description: Input for lipid-treated cells, ChIP-seq and SPI-seq


title: 38859 | 001 | PanCK

value: epithelial


title: A3B_SPIseq_RNaseH

description: SPI-seq, RNaseH1-overexpressed cells


title: 38859 | 001 | CD3


title: IgG_for_H3K4me3,WT,Rep2,CUT&RUN

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:
Trimemd reads were aligned against a combined version of the mouse genome reference (mm10) and the Drosophila melanogaster reference genome (build5.41) using Bowtie2, duplicated reads and unassembled contigs were removed using Picard.
The number of reads aligning to mouse or Drosophila melanogaster chromosomes were obtained using Samtools and were used to calculate normalization factors.
deepTools and UCSC utilities were used to generate the bigwig tracks. To remove the technical noise, averaged IgG signals were removed from the from the CUT&RUN signals using bigwigCompare.
Average tracks per condition were estimated by using BigwigMerge and considering the number of samples. To measure genome-wide changes, we used a 10kb approach, using bedtools map.
Assembly: mm10
Supplementary files format and content: Normalized coverage files in bigWig format
Library strategy: Cut&Run

source_name: myeloid (Cd11b+)

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

extract_protocol:
Cells were washed twice and immobilized on concanavalin A-coated magnetic beads. Cells were then incubated overnight at 4°C with primary antibody in antibody binding buffer. After washing with dig-wash, cells were incubated with pA-MNase complex in wash buffer for 1 hour at 4°C.
Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina. Five nanograms (5 ng) of DNA was used for library preparation, and the libraries were amplified using 13 cycles on the thermocycler. The final libraries were cleaned up using AMPureXP beads, validated using the Agilent High Sensitivity DNA kit, and the concentrations were measured by Qubit.

tag: antibody

value: IgG

tag: cell type

value: myeloid (Cd11b+)

tag: age

value: 18-20 months old


title: Pool2_rep3

city: New York

first: Sofie

last: Delbare

state: NY

address: 435 East 30th Street

institute: NYU Langone

data_processing:
Read quality was assessed using FastQC (v.0.11.9). Reads were trimmed to remove adapter sequences using fastp.
Trimmed reads were mapped to hg38 using bowtie2 (v.2.5.1).
MACS2 (v.2.2.7.1)  was run to call peaks in pulldown samples, using whole genome input samples as control, and with q-value cutoff 0.05.
Assembly: hg38
Supplementary files format and content: Processed data file contains narrowPeak output from MACS2 for all samples except input samples.
Library strategy: ChIRP-seq

growth_protocol: THP were cultivated in RPMI (ATCC) with 10% non-heat inactivated FBS and 1% P/S.

extract_protocol:
DNA was eluted from hybridized magnetic beads and subjected for Illumina sequencing. In short, beads were washed at room temperature with ChIRP wash buffer (EMD Millipore, #17-10494). Beads were subsequently captured using a DynaMag magnet (Thermo Fisher Scientific) and DNA was eluted by suspending beads in elution buffer (20 mM Tris pH 7.4, 1% SDS, 50 mM NaHCO3, 1 mM EDTA). ChIRP eluates were reverse cross-linked at 65C for 4h, digested with Proteinase K (EMD Millipore) at 55C followed by incubation with RNase cocktail (Ambion). ChIRP purified DNA was cleaned using PCR purification columns (Zymo Research) and subjected to Illumina sequencing.
Illumina

treatment_protocol: cells were not treated

value: monocytic cell

tag: group

value: odd probe for IRF1-AS1


title: A3B-SPI-seq-siTDRD3

description: SPI-seq, TDRD3 siRNA-treated cells

tag: cell line

tag: treatment

value: TDRD3-targeting siRNA


title: JC_1_155 (21PG53-1)

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

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.

tag: tissue


title: IgG_for_H3K4me3,MT,Rep2,CUT&RUN


title: JC_1_154 (21PG53-1)

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


title: LacZ_rep3

value: LacZ


title: Pool1_rep3

value: even probe for IRF1-AS1


title: TDRD3_ChIP-seq_rep2_input

description: input control for TDRD3 ChIP seq rep2

data_processing:
Raw reads were aligned to GRCh37 genome assembly using BWA and processed by SAMtools.
MACS2 was used to perform peak calling, with modelled narrow peak settings and an extended fragment length of 200 bp.
For replicated expriment of TDRD3 ChIP-seq, MSPC was used to generate list of consensus peaks.
Genome_build: GRCh37
Supplementary_files_format_and_content: bigwig generated by MACS2 software, score represents fold enrichment over input control.
Supplementary_files_format_and_content: Bed generated by MSPC software, only peaks with score of >20 was included.

growth_protocol: T-47D (ATCC HTB-133) cells were obtained from ATCC, and were maintained in RPMI-1640 medium supplemented with 10% v/v FBS (PAA), 0.2 Units/ml bovine insulin (Sigma) and 0.5% v/v pen/strep (Gibco).

extract_protocol:
ChIP protocol was adopted from Myer’s Lab at HudsonAlpha (protocol version v011014) which contributed to the ENCODE project. Except that: i), cells were lysed in ChromaTrap lysis buffer that designed for sonication (Porvair Science, 100001), and chromatin fragmentation was carried out on a Covaris E220 instrument with optimised settings for ChIP purpose; 2), ChIP-grade protein A/G beads (Pierce 26162) were used to perform immuno-precipitation experiments; 3), the following buffers were used for binding and washing of chromatin: H3R17me2a and CARM1 (100 mM Tris pH 7.5; 500 mM LiCl; 1% NP-40; 0.1% sodium deoxycholate); TDRD3 (100 mM Tris pH 7.5; 500 mM LiCl; 0.5% NP-40; 0.5% sodium deoxycholate); 4), the following antibodies were used: TDRD3 (Proteintech 13359-1-AP), H3R27me2a (Active Motif 39709), CARM1 (Active Motif 39251).
Libraries were constructed by Beijing Genomics Institute Hong Kong, using standard Illumina TruSeq protocol.

tag: chip antibody


title: IgG_for_H3K4me3,MT,Rep1,CUT&RUN


title: JC_1_153 (21PG53-1)

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


title: A3B-SPI-seq-siTDRD3-input

description: Input for TDRD3 siRNA-treated cells


title: IgG_for_H3K27me3,WT,CUT&RUN


title: JC_1_152 (21PG53-1)

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


title: Mouse 125 RL littermate

value: frozen skin

tag: t cell donor type

value: CD4 (OT2 Th2)

tag: mouse score

tag: time point first or flare

value: Flare

tag: Sex

value: Male


title: Pool2_rep2


title: TDRD3_ChIP-seq_rep2

description: TDRD3 ChIPseq rep2

value: TDRD3 (polyclonal, Proteintech, 13359-1-AP)


title: TDRD3_ChIP-seq_rep1_input

description: input control for TDRD3 ChIP seq rep1


title: IgG_for_H3K27me3,MT,CUT&RUN


title: Pool1_rep2


title: JC_1_157 (21PG53-1)

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

tag: developmental stage

tag: time


title: JC_1_151 (21PG55-2)

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

value: Middle blastocyst

value: embryo in vitro day E5.75


title: LacZ_rep2


title: JC_1_156 (21PG55-2)

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

value: embryo


title: IgG_for_H3K9me3,WT,Rep2,CUT&RUN


title: TDRD3_ChIP-seq_rep1

description: TDRD3 ChIPseq rep1


title: IgG_for_H3K4me3,WT,Rep1,CUT&RUN


title: JC_1_150 (21PG53-1)

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

value: embryo in vitro day E4.5


title: Pool2_rep1


title: IgG_for_H3K9me3,WT,Rep1,CUT&RUN

value: IgG


title: H3R17me2a_ChIP-seq

description: H3R17me2a ChIPseq

value: H3R17me2a (polyclonal, Active Motif, 39709)


title: Pool1_rep1


title: Input_for_CARM1_H3R17me2a_ChIP-seq

description: input control for CARM1 ChIPseq


title: IgG_for_H3K9me3,MT,Rep1,CUT&RUN

value: myeloid (Cd11b+)

value: 18-20 months old


title: IgG_for_H3K9me3,MT,Rep2,CUT&RUN


title: CARM1_ChIP-seq

description: CARM1 ChIPseq

value: CARM1 (polyclonal, Active Motif, 39251)


title: JC_1_149 (21PG53-1)

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


title: LacZ_rep1

value: monocytic cell


title: input_rep3


title: JC_1_147 (21PG53-1)

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


title: input_rep2


title: DOX-E2-4

description: induced estradiol-treated replicate4

data_processing:
Raw reads were aligned to GRCh38 genome assembly and GENCODE GRCh38.p13 annotation using STAR programme, followed by processing of the resultant file using SAMtools.
Read counting on genomic features was carried out using Rsubread, and the R package DESeq2 was used to perform statistic-based quantification.
Genome_build: GRCh38
Supplementary_files_format_and_content: Excel table with quantification results, generated by DESeq2

extract_protocol:
Total RNA from T-47D cells were extracted using MagNA pure 96 instrument (Roche), and RNA integrity number was measured by BioAnalyzer 2100 (Agilent).
RNA libraries were constructed and sequenced by BGI using poly-dT enrichment in conjunction with DNB technology on BGISEQ-500 instrument.

treatment_protocol: Adherent T-47D cells were washed with warm PBS before change of growth media with RPMI-1640 medium supplemented with 10% charcoal-stripped FBS. 30 nM siRNA were transfected to the cells and incubated for 48 hours. Cells were then treated with DMSO or 100 nM E2 for 2 hours.

tag: hugi induction

value: Induced with doxycycline

tag: drug treatment

value: estradiol


title: IgG_for_H3K9me2,WT,Rep2,CUT&RUN


title: IgG_for_H3K9me2,WT,Rep3,CUT&RUN


title: JC_1_146 (21PG53-1)

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


title: JC_1_148 (21PG53-1)

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


title: IgG_for_H3K9me2,WT,Rep1,CUT&RUN


title: input_rep1


title: IgG_for_H3K9me2,MT,Rep2,CUT&RUN


title: JC_1_145 (21PG53-1)

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


title: Control_for_CMML,72N

data_processing:
Trimmed sequencing reads were aligned against the human reference genome (T2T-CHM13v2.0) 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 T2T-CHM13v2.0 repeatMasker annotation
Assembly: T2T-CHM13v2.0
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: blood

extract_protocol:
RNA was extracted using the Rneasy Plus Mini Kit (Qiagen) following the manufacturer's instructions. 200 - 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for RNA-seq using TruSeq RNA Exome (Illumina) kit following the manufacturer's protocols.

value: blood

value: primary cells

value: Peripheral blood mononuclear cells

tag: genotype

value: healthy


title: JC_1_144 (21PG53-1)

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


title: JC_1_15 (21PG39-1)

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

value: 16 cell

value: embryo in vitro day E4


title: DOX-E2-1

description: induced estradiol-treated replicate1


title: Control_for_CMML,70N


title: A3B_ChIPseq_lipid

description: ChIP-seq, lipid-treated cells

data_processing:
Single-end raw reads were aligned to GRCh37 genome assembly using BWA, followed by file format exchange by SAMtools.
Peak calling was carried out using MACS2 package, where both input/IP sequence reads were used and the fragment length was set to 200 bp.
Genome_build: GRCh37
Supplementary_files_format_and_content: peak files generated by MACS2
Supplementary_files_format_and_content: bigwig files generated by MACS2, score represent fold enrichment over input control

value: Transfection lipid (lipofectamine 2000)


title: DOX-E2-2

description: induced estradiol-treated replicate2


title: Control_for_CMML,69N


title: JC_1_143 (21PG53-1)

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

value: embryo


title: IgG_for_H3K9me2,MT,Rep1,CUT&RUN

tag: antibody


title: IgG_for_H2AK119ub,WT,CUT&RUN

tag: cell type


title: DOX-DMSO-3

description: induced DMSO-treated replicate 3

value: DMSO


title: Control_for_CMML,68N


title: IgG_for_H2AK119ub,MT,CUT&RUN

value: IgG

tag: age


title: JC_1_142 (21PG53-1)

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

value: embryo in vitro day E4.5


title: DOX-E2-3

description: induced estradiol-treated replicate3


title: JC_1_141 (21PG37-3)

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

value: Early blastocyst

value: embryo in vitro day E5.25


title: DOX-DMSO-2

description: induced DMSO-treated replicate 2


title: DOX-DMSO-1

description: induced DMSO-treated replicate 1


title: H3K4me3,WT,Rep2,CUT&RUN

value: myeloid (Cd11b+)

value: 18-20 months old


title: Control_for_CMML,64N


title: Control_for_CMML,62N


title: JC_1_140 (21PG37-3)

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


title: DMSO-E2-4

description: non-induced estradiol-treated replicate4

value: non-induced


title: DOX-DMSO-4

description: induced DMSO-treated replicate 4

value: Induced with doxycycline


title: normal scar sample 3

city: GuangZhou

first: Yan

state: GuangDong

address: Road LuJing

country: China

institute: Dermatology Hospital of Southern Medical University

description: 10X Genomics

data_processing:
The 10x GenomicsCell Ranger toolkit (v6.1.2) was carried out to process 10X genomics raw data for read alignment and UMI matrix generation. Reads were aligned to human reference genome (GRCh38) download from 10X Genomics official website with SATR algorithm.  The aligned reads were quantified as gene expression matrix based on the number of UMIs detected in individual cells. Filtered gene-cell UMI matrices were generated for further single cell analysis.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and barcode files
Supplementary files format and content: Tab-separated values files and features files
Supplementary files format and content: Tab-separated values files and matrix files

source_name: dermal skin

extract_protocol:
The keloid skin was washed with phosphate-buffered saline (PBS; Gibco, USA,C20012500BT) on ice and removing fat tissue .Then cut into 1cm2 pieces in digestion medium composed of 2.5 mg/ml DispaseII (Roche, USA, 04942078001) in PBS and incubate at 37℃ for 2h . Remove the epidermis, The dermal portion was further cut and digested in 2.5 mg/ml collagenase IV (Yeasen Biotechnology, China; 40510ES60) at 37℃ for 2h. The cell suspension was filtered through a 70um- cell strainer, then neutralizing the enzymes with buffer (PBS with 1% fetal bovine serum), The cells were centrifuged for 2000 rpm for 10min at 4℃ and resuspended in buffer (PBS with 1%FBS).
Single-cell cDNA, library preparation, and 3′-end single-cell RNA-sequencing were performed by Novogene (Beijing, China).  For experiments using the 10× Genomics platform, the Chromium Single Cell 3′ Library & Gel Bead Kit v3.1, Chromium Single Cell 3′ Chip kit v3.1, and Chromium i7 Multiplex Kit were used according to the manufacturer’s instructions in the Chromium Single Cell 3′ Reagents Kits v3.1 User Guide.  The single-cell suspension was washed twice with 1×PBS + 0.04% BSA.  The cell number and concentration were confirmed with a TC20™ Automated Cell Counter. Approximately 10000 cells were immediately subjected to the 10× Genomics Chromium Controller machine for Gel Beads-in-Emulsion (GEM) generation.  mRNA was prepared using 10×Genomics Chromium Single Cell 3′ reagent kit (V3 chemistry).  During this step, cells were partitioned into the GEMs along with Gel Beads coated with oligos.  These oligos provide poly-dT sequences to capture mRNAs released after cell lysis inside the droplets, as well as cell-specific and transcript-specific barcodes (16 bp 10× Barcode and 10 bp Unique Molecular Identifier (UMI), respectively). After RT-PCR, cDNA was recovered, purified, and amplified to generate sufficient quantities for library preparation.  Library quality and concentration were assessed using Agilent Bioanalyzer 2100.

value: dermal skin

tag: tissue type

value: normal scar sample

value: CD45+ cells


title: H3K4me3,WT,Rep1,CUT&RUN


title: H3K4me3,MT,Rep2,CUT&RUN


title: JC_1_139 (21PG37-3)

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


title: JC_1_14 (21PG39-1)

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


title: DMSO-E2-2

description: non-induced estradiol-treated replicate2

tag: cell line

value: estradiol


title: H3K4me3,MT,Rep1,CUT&RUN


title: JC_1_138 (21PG37-3)

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


title: normal scar sample 2

description: 10X Genomics


title: JC_1_137 (21PG37-3)

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


title: H3K27me3,WT,CUT&RUN


title: keloid sample 3

description: 10X Genomics

value: keloid sample


title: H3K27me3,MT,Rep2,CUT&RUN


title: H3K27me3,MT,Rep1,CUT&RUN


title: DMSO-DMSO-4

description: non-induced DMSO-treated replicate 4


title: keloid sample 2

description: 10X Genomics


title: DMSO-DMSO-3

description: non-induced DMSO-treated replicate 3


title: JC_1_135 (21PG37-3)

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


title: H3K9me3,WT,Rep2,CUT&RUN


title: keloid sample 1

description: 10X Genomics


title: DMSO-DMSO-2

description: non-induced DMSO-treated replicate 2


title: T47D, Resistant, biol rep 3

city: Liège

first: Nor Eddine

last: Sounni

address: avenue de l'Hôpital 11

department: Medical oncology

institute: Liège University (ULG - ULiège)

data_processing:
Sequencing was performed on a Illumina NovaSeq 6000 instrument producing 50 bp paired-end reads running Control Software 1.7.0
Demultiplexing of the samples was perfomed with bcl2fastq v2.20.0.422
Sequence reads were trimmed for adaptor sequence/low quality sequence with Trim galore (version 0.6.6)
Trimmed sequence reads were aligned in paired-end mode to the GRCh38/hg38 reference genome using STAR aligner (version 2.7.9a) and default parameters
Read count extraction was performed using featureCounts (version 2.0.0)
Normalization of the read count was carried out using the DESeq2 R package
Assembly: hg38
Supplementary files format and content: tab-delimited text file including raw counts for each sample
Supplementary files format and content: tab-delimited text file including DESeq2-normalized (median of ratios) counts for each sample, ensembl geneID and gene name

growth_protocol: Cell lines were tested by MycoALert Kit (Lonza) to ensure that they were Mycoplasma-free. Cells were grown in red-phenol free DMEM supplemented with 10% FBS, L-glutamine (2 mmol/L), penicillin (100 U/mL), and streptomycin (100 mg/mL) at 37°C, in a 5% CO2 humid atmosphere. All culture reagents were purchased from Gibco/Thermo Fisher.

extract_protocol:
After the end of the treatment, each dish was washed twice with PBS, then a scraper was made in the center of the dish and recovered in 200 μl of PBS. 400 μl of Lysis/binding Buffer from the Roche “High pure RNA isolation Kit (11828665001)” kit was added, and the solution was frozen at −80°. The rest of the extraction was performed according to the protocol of the previously mentioned Roche kit. RNA concentration was measured with the NanoDrop One.
Library preparation has been done with 400ng of input RNA using: NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490) followed by NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7760) and NEBNext® Multiplex Oligos for Illumina® (96 Unique Dual Index Primer Pairs) (NEB# E6440).

value: epithelial cells

value: WT

tag: treatment

value: 0.3 µM of Palbociclib and 30 nM of Fulvestrant for 1 year

value: 3 year - resistant


title: DMSO-E2-3

description: non-induced estradiol-treated replicate3


title: H3K9me3,WT,Rep1,CUT&RUN


title: DMSO-DMSO-1

description: non-induced DMSO-treated replicate 1

value: DMSO


title: JC_1_134 (21PG37-3)

address: H9 Klinisk vetenskap,171 77 Stockholm

institute: Karolinska institute

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

tag: tissue

value: embryo


title: H3K9me3,MT,Rep2,CUT&RUN


title: T47D, Resistant, biol rep 2

value: 2 year - resistant


title: ssDRIP_siNT_E2_rep3

description: ssDRIP, replicate 3

data_processing:
library strategy: strand-specific DNA:RNA immunoprecipitation sequencing (ssDRIP-seq)
Pair-end raw reads were aligned to GRCh37 genome assembly using BWA, followed by file format exchange by SAMtools.
The resultant alignment reads were separated by first-in-pair strand into two files corresponding to (+) or (-) strand R-loop (or input) reads using SAMtools flag identifiers.
Peak calling was carried out using MACS2 package using pair-end fragment setting with input and ssDRIP samples. The resultant peaks were served as input for MSPC, and recurrent peaks were filtered using parameters ‘–w 1E-4 –s 1E-8 –c 4’.
Peaks on the same strand and within a distance of 1000 bp were merged using BEDTools, and converted to GTF format using UCSC tools (bedtogenepred and genepredtogtf).
Read counting was conducted using Subread, and raw counts were analysed by DEseq2 using a generalized linear model with an interaction term.
Genome_build: GRCh37
Supplementary_files_format_and_content: Excel table with quantification results, generated by DESeq2

extract_protocol:
DRIP was performed on T-47D cells using an optimised method previously reported by Halász et al (PMID: 28341774). The best-performing protocol number 5 was adopted. In this experiment, S9.6 antibody from Kerafast (ENH002) was used.
To enable strand-specificity, DRIP product was subjected to second-strand DNA synthesis with uracil incorporation. More specifically, DNA:RNA hybrid was reconstituted in 1× NEB first-strand synthesis buffer (NEB E7525) without the addition of primer and enzyme to a final volume of 20 µl. The product was immediately used as the starting material of NEB’s directional second-strand synthesis method following manufacturer’s instructions (NEB E7550). The resultant DNA was purified using SPRI beads (Thermo Fisher) at a volume ratio of 2.0 and eluted using TE buffer. After quality inspections by BioAnalyzer 2100 (Agilent), the product was sent to BGI, Hong Kong, where strand-specific libraries were constructed using DNB technology.

treatment_protocol: T-47D cells were transfected with 30 nM non-targeting or A3B-targeting siRNA using RNAiMAX reagent (Thermo Fisher) in RPMI-1640 medium supplemented with 10% charcoal-stripped FBS. 48 hours after siRNA transfection, cells were treated with DMSO or 100 nM E2 for 2 hours before proceeding to ssDRIP-seq protocol.

tag: sirna treatment

value: non-targeting

tag: molecule subtype

value: DNA:RNA hyprid


title: normal scar sample 1

description: 10X Genomics


title: DMSO-E2-1

description: non-induced estradiol-treated replicate1


title: JC_1_132 (21PG37-3)

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

value: Early blastocyst

value: embryo in vitro day E5.25


title: H3K9me3,MT,Rep1,CUT&RUN

value: myeloid (Cd11b+)

value: 18-20 months old


title: ssDRIP_siNT_E2_rep2

description: ssDRIP, replicate 2


title: T47D, Resistant, biol rep 1

value: 1 year - resistant


title: JC_1_133 (21PG37-3)

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


title: JC_1_131 (21PG37-3)

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


title: JC_1_130 (21PG37-3)

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


title: T47D, Day20, biol rep2

value: 0.3 µM of Palbociclib and 30 nM of Fulvestrant for 20 days


title: ssDRIP_siNT_E2_rep1

description: ssDRIP, replicate 1

value: estradiol


title: H3K9me2,WT,Rep3,CUT&RUN


title: T47D, Day20, biol rep3


title: H3K9me2,WT,Rep2,CUT&RUN


title: ssDRIP_siNT_DMSO_rep3

description: ssDRIP, replicate 3


title: JC_1_13 (21PG39-1)

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

value: 16 cell

value: embryo in vitro day E4


title: JC_1_136 (21PG37-3)

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


title: H3K9me2,MT,Rep3,CUT&RUN


title: T47D, Day20, biol rep1

value: epithelial cells

value: WT


title: H3K9me2,WT,Rep1,CUT&RUN


title: T47D, Day5, biol rep3

value: 0.3 µM of Palbociclib and 30 nM of Fulvestrant for 5 days


title: JC_1_128 (21PG37-3)

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


title: T47D, Day5, biol rep2


title: ssDRIP_siNT_DMSO_rep1

description: ssDRIP, replicate 1

value: DMSO


title: H3K9me2,MT,Rep2,CUT&RUN


title: ssDRIP_siA3B_E2_rep3

description: ssDRIP, replicate 3


title: JC_1_129 (21PG37-3)

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

value: embryo


title: ssDRIP_siA3B_E2_rep2

description: ssDRIP, replicate 2


title: H3K9me2,MT,Rep1,CUT&RUN


title: JC_1_126 (21PG37-3)

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


title: JC_1_125 (21PG37-3)

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


title: H2AK119ub,WT,Rep2,CUT&RUN


title: T47D, Untreated, biol rep2

value: Untreated


title: JC_1_127 (21PG37-3)

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


title: ssDRIP_siA3B_E2_rep1

description: ssDRIP, replicate 1


title: T47D, Untreated, biol rep1


title: H2AK119ub,WT,Rep1,CUT&RUN


title: ssDRIP_siA3B_DMSO_rep3

description: ssDRIP, replicate 3


title: ssDRIP_siA3B_DMSO_rep2

description: ssDRIP, replicate 2