title: Caulobacter crescentus, delta-lexA

city: Odense

first: Clare

last: Kirkpatrick

address: Campusvej 55, 5230 Odense

department: Biochemistry and Molecular Biology

institute: University of Southern Denmark

description: Library name: delta-lexA

data_processing:
Basecalls were performed using RTA3
The Cutadapt tool (Galaxy Version 5.2+galaxy0) was used in paired-end mode to trim the adapter sequences (Illumina TruSeq).
ChIP-seq reads were alinged to the NC_011916.1 genome using "Bowtie2" (Galaxy Version 2.5.4+galaxy0). The BAM files obtained from Bowtie2 were quality filtered using the “filter SAM or BAM, output SAM or BAM” tool so that only alignments with a MAPQ quality score of ≥ 30 were kept.
Alignment bam files were converted to bedGraph files using "bamCoverage" (Galaxy Version 3.5.4+galaxy0), followed by normalizing to reads per million (RPM).
Peaks were called using "MACS2 callpeak" (Galaxy Version 2.2.9.1+galaxy0) with the significance cut-off q-value <0.05.
NarrowPeak files were generated using using "MACS2 callpeak" (Galaxy Version 2.2.9.1+galaxy0) with the significance cut-off q-value <0.05.
Assembly: NC_011916.1
Supplementary files format and content: bedGraph, narrowPeak

source_name: Bacteria

growth_protocol: Cellc were grown in peptone-yeast extract (PYE) medium to mid-exponential phase at 30°C

extract_protocol:
Cells were crosslinked with 1% formaldehyde and sonication was carried out using a Covaris ultrasonicator with the following settings: temperature 6°C, duration 3600 seconds, peak power 75.0, duty % factor 10.0, cycles per burst 200, average power 7.5, delay 60 seconds. All of the cleared sonicated lysate was used for ChIP without taking an input sample out first.
DNA was prepared for Illumina sequencing using the NEBNext UltraExpress DNA library preparation kit (New England Biolabs) according to the manufacturer's instructions and 50 bp paired-end sequencing was carried out on a NovaSeq 6000 (Illumina).

value: Bacteria

tag: strain

value: delta-lexA

tag: chip antibody

value: anti-HigX


title: P117_ST

status: Public on Nov 25 2025

type: SRA

city: Stockholm

first: Kristina

last: Broliden

state: Solna

address: Visionsgatan 4, J7:20

department: Dept. of Medicine Solna

country: Sweden

institute: Karolinska Institutet

description:
Library name: P117
Visium (10X)

library_source: transcriptomic

data_processing:
SpaceRanger
Assembly: Homo sapiens, GRCh38
Supplementary files format and content: Gzip files containing output from SpaceRanger: .h5-files with raw and filtered feature matrix, tissue images and tissue positions
Supplementary files format and content: Gzip RDS file with Seurat object containing all samples and metadata
Library strategy: Spatial Transcriptomics

molecule: polyA RNA

organism: Homo sapiens

source_name: Ectocervix

extract_protocol:
Spatial transcriptomics protocol was performed according to manufacturer's instructions.
Library preparation for sequencing adhered to the manufacturer’s instructions (10x Genomics, Visium Spatial Transcriptomic). Sequencing was conducted on a NovaSeq6000 flowcell in ‘SP’ mode, with specification of 28 bases for Read 1, 10 bases for Index 1 and 2, and 90 bases for Read 2.

tag: tissue

value: Ectocervix

tag: luminal gr

tag: Sex

value: female


title: Caulobacter crescentus, wild-type

country: Denmark

description: Library name: WT

library_source: genomic

molecule: genomic DNA

organism: Caulobacter vibrioides

tag: cell type

value: Wild-type NA1000


title: 20MSTO-sgCTRL-TEAD-1

city: Boston

first: Zhaorong

last: Li

address: 60 Fenwood Road

country: USA

institute: Dana Farber Cancer Institute

description:
Library name: 20221014_MSTO-sgCTRL-TEAD-1_AH10424_S113
Column name in Star_Gene_Counts.csv: 20MSTO-sgCTRL-TEAD-1

data_processing:
RNA-seq analysis using the VIPER snakemake pipeline
Differential gene expression testing was performed by DESeq2 (v1.22.1).
Assembly: GRCh38
Supplementary files format and content: tab-delimited gene count files

molecule: total RNA

growth_protocol: MSTO-211H cells were maintained in RPMI supplemented with 10% FBS and antibiotics in humidified atmosphere with 5% CO2  at 37oC

extract_protocol:
Total RNAs were extracted and purified using the RNeasy Mini Kit (Qiagen; 74106). rRNA depletion was performed from 100ng of purified RNA using QIAseq FastSelect rRNA HMR reagents
Libraries were prepared using Roche Kapa Biosystems RNA HyperPrep sample preparation kits on a Beckman Coulter Biomek i7. Finished dsDNA libraries were quantified by Qubit fluorometer and Agilent TapeStation 4200. Uniquely dual indexed libraries were pooled in an equimolar ratio and shallowly sequenced on an Illumina MiSeq to further evaluate library quality and pool balance. The final pool was sequenced with paired-end 150 bp reads on an Illumina NovaSeq 6000 at the Dana-Farber Cancer Institute Molecular Biology Core Facilities.

treatment_protocol: MSTO-211H malignant pleural mesothelioma cells were transiently transfected with Cas9 and either an sgRNA control guide (sgCTRL) or a guide targeting EZH2 (EZH2-KO). sgCTRL and EZH2-KO cells were treated with DMSO or a TEAD inhibitor, MYF-03-69 for 24h.

tag: cell line

value: Malignant Pleural Mesothelioma

tag: genotype

tag: treatment

value: DMSO


title: 20MSTO-sgCTRL-DMSO-1

description:
Library name: 20221014_MSTO-sgCTRL-DMSO-1_AH10424_S115
Column name in Star_Gene_Counts.csv: 20MSTO-sgCTRL-DMSO-1


title: WGBS_LOS_#4

city: Columbia

first: Rocío

middle: Melissa

last: Rivera

state: MO

address: 920 East Campus Drive

department: Division of Animal Sciences

institute: University of Missouri, Columbia

data_processing:
For WGBS data, raw sequencing reads were deduplicated using the clumpify function of BBMap 38.90 and trimmed for adapter sequences and low quality bases using trimmomatic 0.39 with parameters ‘ILLUMINACLIP:adapter_seq:2:30:10:1:true LEADING:20 TRAILING:20 AVGQUAL:20 MAXINFO:0:0.5’. Trimmed reads were aligned to the corresponding reference genome using BSBolt 1.5.0 with default setting. Trimmed reads were also aligned to lambda phage genome to determine bisulfite conversion rates. Samtools 1.13 was used to convert, sort, filter, and index bam files. MarkDuplicates function of picard 2.25.5 was used with parameter ‘--OPTICAL_DUPLICATE_PIXEL_DISTANCE 2500’ to further remove duplicated reads after alignment. CpG methylation information was extracted from the bam files using the function CallMethylation of BSBolt with parameter ‘-CG -min 1 -BQ 20’. For each sample, CpG methylation at C/T SNPs detected in their corresponding Hi-C data were excluded for sense strand reads, and CpG methylation at G/A SNPs were excluded for antisense strand reads. For bovine samples, SNPs identified from Hi-C dataset were also used to assign alleles for WGBS reads using custom Perl scripts. C/T SNPs (based on sense strand sequence) were only applied for antisense strand reads, and G/A SNPs were only applied for sense strand reads. Other types of SNP were applied for both strands. Reads that cover multiple SNPs and have conflicting allele assignments were excluded. For both overall and allele-specific comparisons, statistical analyses were conducted using R package hummingbird with parameter ‘minCpGs = 10, minLength = 100, maxGap = 300’ to identify differentially methylated regions (DMRs) between groups. DMRs with at least 15% difference in methylation level (both gain and loss of methylation) and at least 4 mean read coverage at CpG sites in all the samples were reported. For allele-specific analyses, the read coverage filtering was not applied since only about 20% of the usable SNPs are shared by all the sample. The sex chromosomes were excluded from analyses to circumvent confounding created by X chromosome inactivation.
Assembly: ARS-UCD1.2
Supplementary files format and content: Read coverage and DNA methylation percentage for CpG sites in BEDGRAPH format.

organism: Bos indicus x Bos taurus

source_name: skin fibroblast primary cell

growth_protocol: Day 105 Bos taurus indicus (B. t. indicus; Brahman breed) x Bos taurus taurus (B. t. taurus; Angus breed) F1 hybrid fetuses were generated by our laboratory in 2019 (PMID: 35542046) and used as tissue donors. Fetal skins were collected to establish fibroblast primary cell line using protocol adapted from a publication (PMID: 24198123). Fibroblast cells were cultured in bovine embryonic fibroblast medium (89% (v/v) DMEM (Gibco, 11885084), 10% (v/v) fetal bovine serum (Atlanta Biologicalsa, S11150H), and 1% (v/v) Antibiotic-antimycotic (Gibco, 15240062)) at 38.5°C with 5% CO2.

extract_protocol:
Bovine fibroblast cells were lysed in lysis buffer (0.05 M Tris-HCl (pH 8.0), 0.1 M EDTA, and 0.5% (w/v) SDS) with proteinase K (Fisher BioReagents, BP1700) at 55°C for four hours. Genomic DNA was extracted with Phenol:Chloroform:Isoamyl Alcohol (SIGMA, P3803) following the manufacturer’s instructions. The concentration of DNA was measured by using a NanoDrop® ND-1000 Spectrophotometer and DNA integrity was confirmed by electrophoresis on a 0.7% agarose gel. Genomic DNA samples were stored at -20°C.
WGBS for fibroblast cells was conducted by CD Genomics (Shirley, NY, USA). Information on library preparation and sequencing obtained from the company is as follows: Genomic DNA was fragmented by sonication to a mean size of approximately 200-400 bp. Fragmented DNA was end-repaired, 5'-phosphorylated, 3'-dA-tailed and then ligated to methylated adapters. The methylated adapter-ligated DNAs were purified using 0.8× Agencourt AMPure XP magnetic beads and subjected to bisulfite conversion by ZYMO EZ DNA Methylation-Gold Kit (Zymo Research). The converted DNAs then have the addition of 8-bp index primers to create the final cDNA library. Equimolar pooling of libraries was performed based on QC values and sequenced on Novaseq6000 sequencer (Illumina) with a read length configuration of 150 PE for 300M PE reads per sample (300M in each direction). 0.1-1% lambda DNA were added during the library preparation to monitor bisulfite conversion rate.

treatment_protocol: For bovine fetuses, artificial insemination was used to generate the control group and assisted reproductive technologies (ART) were used to generate the ART group (PMID: 35732675). The large offspring syndrome (LOS) group was defined as individuals from the ART group with body weight greater than 97th centile of controls.

tag: original fetal_id

value: skin fibroblast primary cell

tag: developmental stage

value: D105 fetus

tag: conception method

value: Assisted reproductive technology

tag: disease status

value: LOS

value: Male


title: foregut endoderm 500nM RA treated NF15-25 rep2

city: Cincinnati

first: Aaron

last: Zorn

state: OH

address: 240 Albert Sabin Way, Bld S

department: Developmental Biology

institute: Cincinnati Children's Hospital and Medical Center

description:
Library name: laevis_NF25_fg_endo_explant_500nM_RA_rep2
laevis_NF25_fg_endo_explant_500nM_RA_rep2

data_processing:
Quality of reads was asessed with factqc
Quality trimmed reads in fastq format were mapped and quantified using RSEM (v1.3.0)  with bowtie2
Assembly: Xenopus Laevis v10
Supplementary files format and content: Raw counts and TPM files in .txt format

organism: Xenopus laevis

source_name: embryo

growth_protocol: foregut endoderm explants cultured at 15 degrees C for 16 hours from stage NF15 to stage NF25

extract_protocol:
RNA was extracted using Macherey-Nagel Nucleospin Kit according to manufacturer's instructions
Illumina's TruSeq stranded mRNA library prep kit was used according to manufacturer's instruction

treatment_protocol: foregut endoderm explants were treated with either 0.1% DMSO, 25nM RA, 200nM RA or 500nM RA

value: embryo

value: wild type embryo

value: foregut endoderm

value: 500nM RA (Sigma R2625)

tag: batch


title: foregut endoderm 500nM RA treated NF15-25 rep3

description:
Library name: laevis_NF25_fg_endo_explant_500nM_RA_rep3
laevis_NF25_fg_endo_explant_500nM_RA_rep3


title: 20MSTO-sgCTRL-DMSO-2

description:
Library name: 20221014_MSTO-sgCTRL-DMSO-2_AH10424_S116
Column name in Star_Gene_Counts.csv: 20MSTO-sgCTRL-DMSO-2


title: foregut endoderm 500nM RA treated NF15-25 rep1

description:
Library name: laevis_NF25_fg_endo_explant_500nM_RA_rep1
laevis_NF25_fg_endo_explant_500nM_RA_rep1


title: P024_ST

description:
Library name: P024
Visium (10X)


title: foregut endoderm 25nM RA treated NF15-25 rep2

description:
Library name: laevis_NF25_fg_endo_explant_25nM_RA_rep2
laevis_NF25_fg_endo_explant_25nM_RA_rep2

value: 25nM RA (Sigma R2625)


title: P021_ST

description:
Library name: P021
Visium (10X)


title: P087_ST

description:
Library name: P087
Visium (10X)


title: foregut endoderm 25nM RA treated NF15-25 rep1

description:
Library name: laevis_NF25_fg_endo_explant_25nM_RA_rep1
laevis_NF25_fg_endo_explant_25nM_RA_rep1


title: foregut endoderm 25nM RA treated NF15-25 rep3

description:
Library name: laevis_NF25_fg_endo_explant_25nM_RA_rep3
laevis_NF25_fg_endo_explant_25nM_RA_rep3


title: P081_ST

description:
Library name: P081
Visium (10X)


title: P018_ST

description:
Library name: P018
Visium (10X)


title: WGBS_CON_B_#3

value: Artificial insemination

value: Healthy


title: foregut endoderm 200nM RA treated NF15-25 rep1

description:
Library name: laevis_NF25_fg_endo_explant_200nM_RA_rep1
laevis_NF25_fg_endo_explant_200nM_RA_rep1

value: 200nM RA (Sigma R2625)


title: foregut endoderm 200nM RA treated NF15-25 rep3

description:
Library name: laevis_NF25_fg_endo_explant_200nM_RA_rep3
laevis_NF25_fg_endo_explant_200nM_RA_rep3


title: foregut endoderm 200nM RA treated NF15-25 rep2

description:
Library name: laevis_NF25_fg_endo_explant_200nM_RA_rep2
laevis_NF25_fg_endo_explant_200nM_RA_rep2


title: P001_ST

description:
Library name: P001
Visium (10X)

value: Ectocervix

value: female


title: P057_ST

description:
Library name: P057
Visium (10X)


title: foregut endoderm control DMSO treated NF15-25 rep2

description:
Library name: laevis_NF25_fg_endo_explant_DMSO_rep2
laevis_NF25_fg_endo_explant_DMSO_rep2


title: foregut endoderm control DMSO treated NF15-25 rep3

description:
Library name: laevis_NF25_fg_endo_explant_DMSO_rep3
laevis_NF25_fg_endo_explant_DMSO_rep3


title: P014_ST

description:
Library name: P014
Visium (10X)


title: P050_ST

description:
Library name: P050
Visium (10X)


title: foregut endoderm control DMSO treated NF15-25 rep1

description:
Library name: laevis_NF25_fg_endo_explant_DMSO_rep1
laevis_NF25_fg_endo_explant_DMSO_rep1


title: P045_ST

description:
Library name: P045
Visium (10X)


title: KPC Pancreas, grade 4, mouse 4

city: Munich

first: Julian

last: Frädrich

address: Ismaninger Strasse 22

department: Institute of Experimental Oncology & Therapy Research

country: Germany

institute: TUM School of Medicine and Health

description:
Library name: KPC_24
Column in normCounts_Pancreata_KPC_Controls.txt: KPC_24

data_processing:
All data processing steps were performed using the Galaxy platform (http://usegalaxy.org and https://usegalaxy.eu)
FastQC tool was used to evaluate read quality, GC content, sequence duplication levels, and adapter contamination
Poor-quality reads and adapter sequences were removed using Cutadapt with parameters set to trim bases ≤20 bp
Quality reports were aggregated using MultiQC
DESeq2 was used to normalize read counts and extract DEGs
Assembly: Reads were mapped to the reference genome (Mus musculus, GRCm39) using STAR
Supplementary files format and content: tab-delimited text file including normalized counts for each sample

organism: Mus musculus

source_name: Pancreas (tumor)

extract_protocol:
Total RNA was isolated using RNeasy Plus Mini Kit (Qiagen)
Libraries were prepared using the NGS RNA Library Prep Set (PT042; Novogene GmbH)

treatment_protocol: Mice of both sexes were employed in this study and kept at the animal facility of TUM Universitätsklinikum Klinikum rechts der Isar (Munich, Germany) at RT (21°C) under specific pathogen-free conditions. Mice were maintained in filter-topped cages with autoclaved food and water.

value: Pancreas (tumor)


title: P020_ST

description:
Library name: P020
Visium (10X)


title: KPC Pancreas, grade 4, mouse 3

description:
Library name: KPC_23
Column in normCounts_Pancreata_KPC_Controls.txt: KPC_23


title: KPC Pancreas, grade 4, mouse 2

description:
Library name: KPC_22
Column in normCounts_Pancreata_KPC_Controls.txt: KPC_22


title: me4CL_OTX2-KO-ne2

city: luzhou

last: Jiang

state: sichuan

address: 1st xianglinlu

country: China

institute: southwest medical university

description: Library name: OTX2-KO-ne2

data_processing:
RNAseqv1
Adapter of sequence reads were trimmed and poor quality reads  were removed by TrimGalore(quality <20 or length <30),
Paired-end RNA-seq reads were trimmed and then mapped to hg38 genome by STAR (v.2.7.4a)
Raw count tables of genes were computed using featureCounts (v2.0.1)
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: hPSCs

extract_protocol:
Total RNA was isolated using RNA isolater Total RNA Extraction Reagent (Vazyme, R401) according to the manufacturer’s instructions.
TRIzol was used to extract total RNA, and libraries were constructed using the VAHTS Universal V8 RNA-seq Library Prep Kit (Vazyme, NR605) according to the manufacturer’s instructions. 500 ng total RNA was used to construct libraries. Library samples were subjected to the Illumina NovaSeq 6000 sequencing system.

value: hPSCs

value: me4CL cells


title: me4CL_OTX2-KO-ne3

description: Library name: OTX2-KO-ne3


title: me4CL_OTX2-KO-ne1

description: Library name: OTX2-KO-ne1


title: KPC Pancreas, grade 4, mouse 1

description:
Library name: KPC_21
Column in normCounts_Pancreata_KPC_Controls.txt: KPC_21


title: KPC Pancreas, grade 3, mouse 8

description:
Library name: KPC_19
Column in normCounts_Pancreata_KPC_Controls.txt: KPC_19


title: me4CL_OTX2-KO-GFP2

description: Library name: OTX2-KO-GFP2


title: me4CL_OTX2-KO-GFP3

description: Library name: OTX2-KO-GFP3


title: KPC Pancreas, grade 3, mouse 7

description:
Library name: KPC_18
Column in normCounts_Pancreata_KPC_Controls.txt: KPC_18


title: KPC Pancreas, grade 3, mouse 9

description:
Library name: KPC_20
Column in normCounts_Pancreata_KPC_Controls.txt: KPC_20


title: KPC Pancreas, grade 3, mouse 6

description:
Library name: KPC_17
Column in normCounts_Pancreata_KPC_Controls.txt: KPC_17


title: me4CL_OTX2-KO-GFP1

description: Library name: OTX2-KO-GFP1


title: KPC Pancreas, grade 3, mouse 5

description:
Library name: KPC_16
Column in normCounts_Pancreata_KPC_Controls.txt: KPC_16


title: OTX2_KO_H3K4me3

description: Library name: OTX2_KO_K4

data_processing:
cuttag_pipeline
The raw FASTQ files were preprocessed using Cutadapt (v1.18) with stringent parameters (-e 0.1 for maximum error rate and -m 5 for minimum read length)
High-quality reads were then aligned to the hg38 human reference genome using Bowtie2 (v2.2.2)
The resulting alignments were processed using SAMtools (v.1.7) to filter out low-quality mappings (Q < 30). The filtered reads were converted to BAM format and PCR duplicates were removed using Picard Tools (v.2.8.0) with the REMOVE_DUPLICATES = true.
For peak identification, we employed MACS2 (v.2.2.7.1)    with specific parameters: --narrow for narrow peak calling, --keep-dup all to retain all duplicates during model building, -B for storing fragment pileup information, and --SPMR for signal per million scaling.
Assembly: Finally, genome-wide visualization profiles were generated using deepTools (v3.1.3) to facilitate comprehensive analysis of the sequencing data.
Supplementary files format and content: hg38
Supplementary files format and content: bigwig
Library strategy: CUT&TAG

source_name: me4CL cells

extract_protocol:
Fresh cells were collected and washed with 500 μl wash buffer and centrifuged at 500×g for 5 min at room temperature. Cell pellets were resuspended with 100 μl wash buffer.
The CUT&Tag assay was performed according to the manual of the Hyperactive Universal CUT&Tag Assay Kit for Illumina (TD904, Vazyme Biotech). 1 × 105 cells were used as starting material for every sample. Libraries were amplified using 12 cycles on the thermocysler. Post amplification libraries were size select at 250-450bp in length using DNA Clean Beads  (N411, Vazyme Biotech). Libraries were validated using the dsDNA HS Assay Kit (EQ121, Vazyme Biotech).


title: KPC Pancreas, grade 3, mouse 4

description:
Library name: KPC_15
Column in normCounts_Pancreata_KPC_Controls.txt: KPC_15


title: OTX2_KO_H3K9me3

description: Library name: OTX2_KO_K9


title: WT_H3K4me3

description: Library name: WT_K4


title: KPC Pancreas, grade 3, mouse 3

description:
Library name: KPC_14
Column in normCounts_Pancreata_KPC_Controls.txt: KPC_14


title: WT_H3K9me3

description: Library name: WT_K9


title: KPC Pancreas, grade 3, mouse 1

description:
Library name: KPC_12
Column in normCounts_Pancreata_KPC_Controls.txt: KPC_12


title: KPC Pancreas, grade 3, mouse 2

description:
Library name: KPC_13
Column in normCounts_Pancreata_KPC_Controls.txt: KPC_13


title: KPC Pancreas, grade 2, mouse 3

description:
Library name: KPC_11
Column in normCounts_Pancreata_KPC_Controls.txt: KPC_11


title: WT_H3K27me3

description: Library name: WT_K27


title: OTX2_KO_H3K27me3

description: Library name: OTX2_KO_K27


title: KPC Pancreas, grade 2, mouse 2

description:
Library name: KPC_10
Column in normCounts_Pancreata_KPC_Controls.txt: KPC_10


title: KPC Pancreas, grade 2, mouse 1

description:
Library name: KPC_9
Column in normCounts_Pancreata_KPC_Controls.txt: KPC_9


title: Replicate 3 UT-SCC-103 CTRL

city: Turku

first: Johanna

last: Ivaska

address: Tykistökatu 6

department: Turku Bioscience Centre

country: Finland

institute: University of Turku

description:
Library name: UT-SCC-103_CTRL_3
Column name in normalizedData.csv: UT-SCC-103_CTRL_3

data_processing:
read trimming: FastQC (v.0.11.8) default parameters
read alingment: Rsubread(v.2.0.0) default parameters
read counting: Rsubread(v.2.0.0) [4]::featureCount
data normalization: edgeR(v.3.28.0) [6, 8]::calcNormFactors
differential gene expression: ROTS(v.1.14.0)
Assembly: hg38
Supplementary files format and content: CSV format; tab-delimited; normalized counts as cpm (counts per million) values

source_name: Vocal fold

growth_protocol: HaCat, UT-SCC-11 and UT-SCC-103 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 1 % non-essential amino acids (NEAA) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was isolated using Macherey-Nagel #740955.250 NucleoSpin RNA -kit
Illumina stranded total RNA prep library was prepared using 100 ng of RNA as per the manufacturer’s instructions (Illumina Stranded mRNA Preparation and Ligation kit)

treatment_protocol: No vibration, 30 min of vibration or 6 hours of vibration

value: Vocal fold

value: laryngeal cancer cell

value: WT

value: no vibration


title: KPC Pancreas, early PDAC, mouse 8

description:
Library name: KPC_8
Column in normCounts_Pancreata_KPC_Controls.txt: KPC_8


title: Replicate 3 UT-SCC-11 6h

description:
Library name: UT_SCC11_6h_3
Column name in normalizedData.csv: UT_SCC11_6h_3

value: 6h vibration


title: Replicate 3 UT-SCC-103 30 min

description:
Library name: UT-SCC-103_30min_3
Column name in normalizedData.csv: UT-SCC-103_30min_3

value: 30 min vibration


title: Replicate 3 UT-SCC-11 30 min

description:
Library name: UT_SCC11_30min_3
Column name in normalizedData.csv: UT_SCC11_30min_3


title: Replicate 3 UT-SCC-11 CTRL

description:
Library name: UT_SCC11_CTRL_3
Column name in normalizedData.csv: UT_SCC11_CTRL_3


title: KPC Pancreas, early PDAC, mouse 7

description:
Library name: KPC_7
Column in normCounts_Pancreata_KPC_Controls.txt: KPC_7


title: KPC Pancreas, early PDAC, mouse 5

description:
Library name: KPC_5
Column in normCounts_Pancreata_KPC_Controls.txt: KPC_5


title: KPC Pancreas, early PDAC, mouse 4

description:
Library name: KPC_4
Column in normCounts_Pancreata_KPC_Controls.txt: KPC_4


title: Replicate 3 Hacat 6h

description:
Library name: Hacat_6h_3
Column name in normalizedData.csv: Hacat_6h_3

source_name: Skin

value: Skin

value: HaCat

value: epidermal keratinocyte


title: Replicate 3 Hacat 30 min

description:
Library name: Hacat_30min_3
Column name in normalizedData.csv: Hacat_30min_3


title: KPC Pancreas, early PDAC, mouse 3

description:
Library name: KPC_3
Column in normCounts_Pancreata_KPC_Controls.txt: KPC_3


title: KPC Pancreas, early PDAC, mouse 2

description:
Library name: KPC_2
Column in normCounts_Pancreata_KPC_Controls.txt: KPC_2


title: KPC Pancreas, early PDAC, mouse 1

description:
Library name: KPC_1
Column in normCounts_Pancreata_KPC_Controls.txt: KPC_1


title: Replicate 3 Hacat CTRL

description:
Library name: Hacat_CTRL_3
Column name in normalizedData.csv: Hacat_CTRL_3


title: Replicate 2 UT-SCC-103 30 min

description:
Library name: UT-SCC-103_30min_2
Column name in normalizedData.csv: UT-SCC-103_30min_2


title: Replicate 2 UT-SCC-103 6h

description:
Library name: UT-SCC-103_6h_2
Column name in normalizedData.csv: UT-SCC-103_6h_2


title: Replicate 3 UT-SCC-103 6h

description:
Library name: UT-SCC-103_6h_3
Column name in normalizedData.csv: UT-SCC-103_6h_3


title: Control Pancreas, mouse 11

description:
Library name: Control_11
Column in normCounts_Pancreata_KPC_Controls.txt: Control_11

source_name: Pancreas

value: Pancreas

value: Cre-; Kras+/+; Trp53+/LSL-R172H


title: Replicate 2 UT-SCC-103 CTRL

description:
Library name: UT-SCC-103_CTRL_2
Column name in normalizedData.csv: UT-SCC-103_CTRL_2


title: Control Pancreas, mouse 10

description:
Library name: Control_10
Column in normCounts_Pancreata_KPC_Controls.txt: Control_10


title: Replicate 2 UT-SCC-11 CTRL

description:
Library name: UT_SCC11_CTRL_2
Column name in normalizedData.csv: UT_SCC11_CTRL_2


title: Control Pancreas, mouse 8

description:
Library name: Control_8
Column in normCounts_Pancreata_KPC_Controls.txt: Control_8


title: Replicate 2 UT-SCC-11 6h

description:
Library name: UT_SCC11_6h_2
Column name in normalizedData.csv: UT_SCC11_6h_2


title: Replicate 2 UT-SCC-11 30 min

description:
Library name: UT_SCC11_30min_2
Column name in normalizedData.csv: UT_SCC11_30min_2


title: Replicate 2 Hacat 6h

description:
Library name: Hacat_6h_2
Column name in normalizedData.csv: Hacat_6h_2


title: KPC Pancreas, early PDAC, mouse 6

description:
Library name: KPC_6
Column in normCounts_Pancreata_KPC_Controls.txt: KPC_6


title: Replicate 2 Hacat 30 min

description:
Library name: Hacat_30min_2
Column name in normalizedData.csv: Hacat_30min_2


title: Replicate 2 Hacat CTRL

description:
Library name: Hacat_CTRL_2
Column name in normalizedData.csv: Hacat_CTRL_2


title: Control Pancreas, mouse 4

description:
Library name: Control_4
Column in normCounts_Pancreata_KPC_Controls.txt: Control_4


title: Control Pancreas, mouse 5

description:
Library name: Control_5
Column in normCounts_Pancreata_KPC_Controls.txt: Control_5


title: Control Pancreas, mouse 3

description:
Library name: Control_3
Column in normCounts_Pancreata_KPC_Controls.txt: Control_3


title: Replicate 1 UT-SCC-103 30 min

description:
Library name: UT-SCC-103_30min_1
Column name in normalizedData.csv: UT-SCC-103_30min_1


title: Control Pancreas, mouse 1

description:
Library name: Control_1
Column in normCounts_Pancreata_KPC_Controls.txt: Control_1

value: Cre-; Kras+/LSL-G12D; Trp53+/+


title: Control Pancreas, mouse 2

description:
Library name: Control_2
Column in normCounts_Pancreata_KPC_Controls.txt: Control_2

value: Cre-; Kras+/LSL-G12D; Trp53+/LSL-R172H


title: WT pCmrR, ATc 10, Rep 3

city: Chapel Hill

first: Anchal

last: Mehra

state: North Carolina

address: 125 Mason Farm Rd, 6th Floor, CB 7290, Marsico Hall

department: Department of Microbiology and Immunology

institute: University of North Carolina at Chapel Hill

description: Library name: Sample 22

data_processing:
Read quality assessed using FASTQC (v0.11.8).
Poor quality ends and Illumina adapter sequences were removed using Trimmomatic (v0.36) in PE mode with palindromic adapter trimming. Additional parameters as follows: SLIDINGWINDOW:5:25 MAXINFO:50:0.8 LEADING:30 TRAILING:25 MINLEN:40. Adapter file available from Trimmomatic GitHub page. Effectiveness of trimming was confirmed using FASTQC (v0.11.8)
Read mapping performed using Bowtie2 (v2.4.1) in global mode with --very-sensitive, --dovetail, --phred33, -t, and -q parameters.
Genomic feature counting performed using Feature Aggregate Depth Utility (FADU, v1.8), a prokaryotic-specific algorithm. This step generated the processed data files uploaded herein. Default parameters used.
More details on data processing and associated code are available from GitHub: https://github.com/klfurtado/2024_Cdiff_Mucus_Paper
Assembly: Genome was assembled with NCBI genome accession FN545816.1
Supplementary files format and content: Supplementary processed data files are provided as tab-delimted .txt as the direct output from FADU. One file is uploaded per sample. First column (featureID) provides CDR20291 locus tags from Accession ID FN545816.1, with "gene-" preceeding each locus tag. Second column (uniq_len) provides the number of bases that do not overlap with other features. Third column (num_alignments) provides the number of BAM records that align to non-overlapping bases for each feature. Fourth column (counts) provides fractionalized read counts for each feature; these values were used in differential expression analysis in the above study. Fifth column provides transcript per million values.

organism: Clostridioides difficile

source_name: bacterial cell

growth_protocol: Rough and smooth colony isolates of wildtype R20291, cmrΔ3-ON and cmrΔ3-OFF mutants, and the ΔcmrRΔcmrT mutant were spotted (10 µL) on BHIS-1.5% agar in triplicate. After 24-hours incubation at 37°C, the growth was collected in TRIzol for RNA extraction. Plasmid-bearing strains (pCmrR, pCmrT, or vector only) were grown from a single colony in TY-Tm10 broth overnight, then diluted 1:30 in BHIS-Tm broth. At an optical density at 600 nm (OD600) of ~ 0.3, expression was induced with anhydrotetracycline (ATc). C. difficile with pCmrR (RT2085) or the vector control (RT1615) were induced with 10 ng/mL ATc; because higher expression of cmrT is toxic to C. difficile, strains with pCmrT (RT2107) or the vector control (RT1615) were induced with 2 ng/mL ATc. Strains with pCmrR or pCmrT were grown in triplicate, and vector controls were grown in duplicate. At OD600 ~1, 2 mL of each culture was collected for RNA purification.

extract_protocol:
For RNA isolation, samples were pelleted at 4,000 x g for 10 minutes at 4°C, washed with 500 µL TE buffer, and pelleted again. Pellets were resuspended in 1 mL TRIzol (Invitrogen 15596026) and lysed by bead beating twice for 90 seconds, with 90 seconds on ice between rounds. Samples were vortexed upon the addition of 200 µL chloroform, incubated at room temperature for 5 minutes, then centrifuged at 14,000 x g for 10 minutes at 4°C. The aqueous phase was then added to 1 volume of isopropanol, incubated for 10 minutes at room temperature, and centrifuged again at 14,000 x g for 10 minutes. The pellet was washed with 75% ethanol then centrifuged again. The supernatant was removed and the pellet was air-dried for 10 minutes before RNA was suspended in 50 µL nuclease-free water.
Purified RNA was submitted to Genewiz (Azenta Life Sciences) for paired-end sequencing using the following pipeline, with kits used per manufacturer’s instructions. rRNA was depleted using the Ribo Zero rRNA Removal Kit (Illumina). RNA sequencing libraries were prepared with the NEBNext Ultra RNA library prep kit for Illumina (NEB) and checked using a Qubit 2.0 fluorometer. The libraries were multiplexed for sequencing using a 2 × 150 paired-end configuration on an Illumina HiSeq 2500 instrument. Image analysis and base calling were done using the HiSeq control software. The resulting raw sequence data files (.bcl) were converted to the FASTQ format and demultiplexed with bcl2fastq 2.17 software (Illumina). One mismatch was permitted for index sequence identification.

value: bacterial cell

value: WT pCmrR

value: BHIS broth, ATc 10


title: Replicate 1 UT-SCC-11 30 min

description:
Library name: UT_SCC11_30min_1
Column name in normalizedData.csv: UT_SCC11_30min_1


title: Control Pancreas, mouse 9

description:
Library name: Control_9
Column in normCounts_Pancreata_KPC_Controls.txt: Control_9


title: Replicate 1 Hacat 6h

description:
Library name: Hacat_6h_1
Column name in normalizedData.csv: Hacat_6h_1


title: Replicate 1 Hacat 30 min

description:
Library name: Hacat_30min_1
Column name in normalizedData.csv: Hacat_30min_1


title: WT pCmrR, ATc 10, Rep 2

description: Library name: Sample 21


title: Replicate 1 UT-SCC-11 CTRL

description:
Library name: UT_SCC11_CTRL_1
Column name in normalizedData.csv: UT_SCC11_CTRL_1


title: WT vector, ATc 10, Rep 2

description: Library name: Sample 19

value: WT vector


title: WT pCmrR, ATc 10, Rep 1

description: Library name: Sample 20


title: WT vector, ATc 10, Rep 1

description: Library name: Sample 18


title: Control Pancreas, mouse 7

description:
Library name: Control_7
Column in normCounts_Pancreata_KPC_Controls.txt: Control_7


title: Replicate 1 UT-SCC-103 CTRL

description:
Library name: UT-SCC-103_CTRL_1
Column name in normalizedData.csv: UT-SCC-103_CTRL_1

value: Vocal fold


title: WT pCmrT, ATc 2, Rep 3

description: Library name: Sample 17

value: WT pCmrT

value: BHIS broth, ATc 2


title: Control Pancreas, mouse 6

description:
Library name: Control_6
Column in normCounts_Pancreata_KPC_Controls.txt: Control_6


title: iHepatocyte from chr21-trisomic (T21) iPSC; Cell line 49bc3_ihep_T21_1; Differentiation replicate 1

city: Aurora

first: Matthew

middle: D

last: Galbraith

state: CO

department: Department of Pharmacology; Linda Crnic Institute for Down Syndrome

institute: University of Colorado Anschutz Medical Campus

description: Library name: 49bc3_ihep_T21_1

data_processing:
Signal processing, base-calling, and quality scoring was carried out automatically by the NovaSeq 6000 RTA3 software (Illumina).
Demultiplexing and conversion to FASTQ format was carried out using bcl2fastq (Illumina).
Data quality was assessed using FASTQC (v0.11.5) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and FastQ Screen (v0.11.0, https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/).
Trimming and filtering of low-quality reads was performed using bbduk from BBTools (v37.99) and fastq-mcf from ea-utils (v1.05, https://expressionanalysis.github.io/ea-utils/).
Alignment to the mouse reference genome (GRCh38) was carried out using HISAT2 (v2.1.0) in paired, spliced-alignment mode with a GRCh38 index with a Gencode v33 annotation GTF.
Alignments were sorted and filtered for mapping quality (MAPQ>10) using Samtools (v1.5).
Gene-level count data were quantified using HTSeq-count (v0.6.1) with the following options (--stranded=reverse –minaqual=10 –type=exon --mode=intersection-nonempty) using a Gencode v33 GTF annotation file.
Assembly: GRCm38
Supplementary files format and content: Counts: Tab-delimited text files containing per gene strand-specific fragment counts.
Supplementary files format and content: FPKMs: Tab-delimited text files containing per gene strand-specific normalized fragments-per-kilobase-per-million-mapped (FPKM).

source_name: LD 49BC-3

extract_protocol:
Total RNA was harvested using TRIzol reagent (Invitrogen) following the manufacturer protocol. RNA quality was assessed using an Agilent 2200 TapeStation and quantified by Qubit (Life Technologies).
Poly-A(+) RNA enrichment, and strand-specific library preparation were carried out using a Tecan/Nugen Universal Plus mRNA Kit. Paired-end 150 bp sequencing was carried out on an Illumina NovaSeq 6000 instrument by the University of Colorado Cancer Center Genomics Shared Resource.

treatment_protocol: Hepatocyte-like cells (iHeps) were differentiated from a panel of 8 iPSC lines, four control lines and four lines trisomic for chromosome 21. The iPSCs were maintained on matrigel-coated plates (Corning, Cat. # 354277) in mTeSR Plus media (StemCell Technologies, Cat. # 100-0276), manually removing any spontaneously differentiating cells. Genomic integrity and retention of the triplicated chromosome 21 in the iPSCs were validated by g-banded karyotype analysis through the University of Colorado Cancer Center Pathology Shared Resource – Cytogenetics Section. IPSCs were differentiated into iHeps using previously described protocols with minor variations (REF). Briefly, iPSCs were singularized with accutase (Fisher Scientific, Cat. # NC9464543) and seeded into matrigel-coated six-well plates at 2e6 cells per well in mTeSR Plus media supplemented with 10uM Y-27632 (StemCell Technologies, Cat. # 72304). After 24 hours, when cells were 90-100% confluent, Y-27632 was removed, and the iPSCs were induced to form the definitive endoderm using the STEMDiff Definitive Endoderm Kit (StemCell, Cat. # 05110) according to the manufacturer’s instructions. Day 0 of iHep induction was considered when the definitive endoderm media was placed on the cells. On day 4 of differentiation, cells were singularized and plated 7.9e4 cells/cm2 in heptoblast media supplemented with 10 uM Y-27632. Hepatoblast media consisted of DMEM/F12 (Cytiva, Cat. # SH30023.01) supplemented with 10% KnockOut Serum Replacement (KOSR, Gibco, Cat. # 10828028), 1% GlutaMAX (Gibco, Cat. # 35050061), 1% Non-Essential Amino Acids (NEAA, Gibco, Cat. # 11140050), 1% Dimethyl-sulfoxide (DMSO, Sigma-Aldrich, Cat. # D2650), and 100 ng/ml of Hepatocyte Growth Factor (HGF, Peprotech, Cat. # 100-398H). After 24 hours Y-27632 was removed and the media was changed daily until day 12. From day 12 onward, cells were cultured in hepatocyte maturation media consisting of DMEM/F12, 10% KOSR, 1% NEAA, 1% GlutaMAX, and 100 nM dexamethasone (Sigma-Aldrich, Cat. # D4902). Media was changed daily until day 15.

value: Hepatocyte-like cells

value: LD 49BC-3

value: Male

value: hepatocyte differentiation

tag: sequencing batch

tag: differentiation replicate


title: iHepatocyte from chr21-trisomic (T21) iPSC; Cell line 232_ihep_T21_1; Differentiation replicate 1

description: Library name: 232_ihep_T21_1


title: WT pCmrT, ATc 2, Rep 1

description: Library name: Sample 15


title: iHepatocyte from euploid (D21) iPSC; Cell line 68bc5_ihep_D21_1; Differentiation replicate 1

description: Library name: 68bc5_ihep_D21_1

source_name: LC 68BC-5

value: LC 68BC-5


title: Replicate 1 UT-SCC-103 6h

description:
Library name: UT-SCC-103_6h_1
Column name in normalizedData.csv: UT-SCC-103_6h_1

value: laryngeal cancer cell

value: WT

value: 6h vibration


title: Replicate 1 Hacat CTRL

description:
Library name: Hacat_CTRL_1
Column name in normalizedData.csv: Hacat_CTRL_1

value: Skin

value: HaCat

value: epidermal keratinocyte

value: no vibration


title: iHepatocyte from euploid (D21) iPSC; Cell line 474_ihep_D21_1; Differentiation replicate 1

description: Library name: 474_ihep_D21_1


title: Replicate 1 UT-SCC-11 6h

description:
Library name: UT_SCC11_6h_1
Column name in normalizedData.csv: UT_SCC11_6h_1


title: iHepatocyte from chr21-trisomic (T21) iPSC; Cell line 194_ihep_T21_1; Differentiation replicate 1

description: Library name: 194_ihep_T21_1


title: WT vector, ATc 2, Rep 1

description: Library name: Sample 13

value: bacterial cell


title: WT vector, ATc 2, Rep 2

description: Library name: Sample 14

value: WT vector


title: cmr-locked-OFF, Rep 3

description: Library name: Sample 12

value: cmr-locked-OFF

value: BHIS-agar


title: iHepatocyte from chr21-trisomic (T21) iPSC; Cell line 76_ihep_T21_2; Differentiation replicate 2

description: Library name: 76_ihep_T21_2

source_name: iLD 7-6

value: iLD 7-6


title: cmr-locked-OFF, Rep 2

description: Library name: Sample 11


title: iHepatocyte from chr21-trisomic (T21) iPSC; Cell line 194_ihep_T21_2; Differentiation replicate 2

description: Library name: 194_ihep_T21_2

value: Hepatocyte-like cells


title: cmr-locked-OFF, Rep 1

description: Library name: Sample 10


title: iHepatocyte from chr21-trisomic (T21) iPSC; Cell line 76_ihep_T21_1; Differentiation replicate 1

description: Library name: 76_ihep_T21_1


title: iHepatocyte from chr21-trisomic (T21) iPSC; Cell line 23_ihep_T21_2; Differentiation replicate 2

description: Library name: 23_ihep_T21_2

source_name: iLD 2-3

value: iLD 2-3

value: Female


title: cmr-locked-ON, Rep 3

description: Library name: Sample 9

value: cmr-locked-ON


title: cmrR cmrT mutant, Rep 2

description: Library name: Sample 6

value: cmrR cmrT mutant


title: cmr-locked-ON, Rep 1

description: Library name: Sample 7


title: iHepatocyte from chr21-trisomic (T21) iPSC; Cell line 1121_ihep_T21_2; Differentiation replicate 2

description: Library name: 1121_ihep_T21_2

value: hepatocyte differentiation


title: WT pCmrT, ATc 2, Rep 2

description: Library name: Sample 16

value: WT pCmrT

value: BHIS broth, ATc 2


title: iHepatocyte from chr21-trisomic (T21) iPSC; Cell line 23_ihep_T21_1; Differentiation replicate 1

description: Library name: 23_ihep_T21_1


title: iHepatocyte from euploid (D21) iPSC; Cell line 423_ihep_D21_2; Differentiation replicate 2

description: Library name: 423_ihep_D21_2

value: Male


title: iHepatocyte from chr21-trisomic (T21) iPSC; Cell line 1121_ihep_T21_1; Differentiation replicate 1

description: Library name: 1121_ihep_T21_1


title: WT Smooth colony, Rep 2

description: Library name: Sample 4

value: WT Smooth


title: WT Smooth colony, Rep 1

description: Library name: Sample 3


title: iHepatocyte from euploid (D21) iPSC; Cell line 423_ihep_D21_1; Differentiation replicate 1

description: Library name: 423_ihep_D21_1


title: cmr-locked-ON, Rep 2

description: Library name: Sample 8


title: iHepatocyte from euploid (D21) iPSC; Cell line 626_ihep_D21_2; Differentiation replicate 2

description: Library name: 626_ihep_D21_2


title: iHepatocyte from euploid (D21) iPSC; Cell line 626_ihep_D21_1; Differentiation replicate 1

description: Library name: 626_ihep_D21_1


title: cmrR cmrT mutant, Rep 1

description: Library name: Sample 5


title: WT Rough colony, Rep 2

description: Library name: Sample 2

value: WT Rough


title: iHepatocyte from euploid (D21) iPSC; Cell line 113_ihep_D21_2; Differentiation replicate 2

description: Library name: 113_ihep_D21_2


title: WT Rough colony, Rep 1

description: Library name: Sample 1


title: iHepatocyte from euploid (D21) iPSC; Cell line 673_ihep_D21_1; Differentiation replicate 1

description: Library name: 673_ihep_D21_1


title: iHepatocyte from euploid (D21) iPSC; Cell line 113_ihep_D21_1; Differentiation replicate 1

description: Library name: 113_ihep_D21_1


title: iHepatocyte from euploid (D21) iPSC; Cell line 673_ihep_D21_2; Differentiation replicate 2

description: Library name: 673_ihep_D21_2


title: G793A, PLX5622, rep2

city: Irvine

first: Mathew

last: Blurton-Jones

state: CA

address: 845 Health Sciences Road

department: Neurobiology and Behavior

institute: University of California, Irvine

description:
Library name: G793A-PLX5622-2
Column name in rawcounts_analysis_all.tsv: G793A_484

data_processing:
FASTQ files were then preprocessed using BBDuk79 to filter out ribosomal RNA and PhiX reads, trim Illumina adapters, and to trim any base pairs below a PHRED score of 28.
The quality of sequencing files was then verified using FASTQC (version 0.11.9) and all files were determined to be of sufficient quality for downstream processing.
Reads were then aligned to the murine GRCm39 (Ensembl release 107) transcriptome using Kallisto (version 0.46.1), transcripts were summarized to the gene level through tximport (version 1.14.2), and differential gene expression analysis was performed using DESeq2 (version 1.26.0) after removing genes with summed counts <10.
Differentially expressed genes were calculated using DESeq2 by applying an FDR cutoff of 0.05 and a log2(fold-change) cutoff of ±1.
Assembly: murine GRCm39 (Ensembl release 107)
Supplementary files format and content: Tab-delimited text file containing raw gene-level counts for all FASTQ files.
Supplementary files format and content: Tab-delimited text file containing VST normalized counts for all sampels.

source_name: Brain

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen).
RNA libraries were made using the Illumina TruSeq Stranded mRNA kit which utilizes oligo-dT beads to select and amplify mRNA. cDNA was synthesized using nine rounds of PCR and quality and concentrations of the DNA libraries were assayed using the Agilent 2100 Bioanalyzer high sensitivity DNA assay and the DNA high sensitivity Qubit.The libraries were quantified by Kapa qPCR, normalized to 1.5nM and then multiplexed at equimolar concentrations for sequencing on the Illumina NovaSeq 6000 platform.

value: Brain


title: G793A, PLX5622, rep4

description:
Library name: G793A-PLX5622-4
Column name in rawcounts_analysis_all.tsv: G793A_527


title: G793A, PLX5622, rep1

description:
Library name: G793A-PLX5622-1
Column name in rawcounts_analysis_all.tsv: G793A_439


title: G793A, PLX5622, rep3

description:
Library name: G793A-PLX5622-3
Column name in rawcounts_analysis_all.tsv: G793A_526


title: PDAC Tumor Sample PDAC17

description: Library name: PDAC17

library_source: transcriptomic single cell

data_processing:
Alignment of snRNA-seq data to the human reference genome (GRCh38-2020-A), cell filtering, and counting of barcodes and unique molecular identifiers was performed using the 10x Genomics Cell Ranger software v7.0.1 with intronic reads included.
Assembly: GRCh38-2020-A
Supplementary files format and content: Filtered Cell Ranger output for each sample separately: features.tsv; matrix.mtx; barcodes.tsv

extract_protocol:
For preparation of single-nucleus suspensions from banked frozen PDAC tumors,  30-60 mg of each tumor were first cut into small pieces at -80°C. Nuclei suspensions were generated using the Chromium Nuclei Isolation Kit with RNase Inhibitor (10x Genomics) according to the manufacturer’s instructions. Nuclei were assessed for singularization and integrity using trypan blue staining, quantified, and immediately used for snRNA-seq library preparation.
To prepare snRNA-seq libraries, the Chromium Next GEM Single Cell 3’ Kit v3.1 was used according to the manufacturer’s instructions. Per sample, nuclei were loaded on individual lanes of a 10x Chromium chip to generate gel beads in emulsion (GEMs). Complementary DNA and sequencing libraries were assessed for sample size and quality using the HS DNA Kit (Agilent) on an Agilent Bioanalyzer 2100. Gene expression libraries were sequenced on an Illumina NovaSeq 6000 (Novogene GmbH, PE150-S4; paired end, dual index) targeting 50,000 read pairs per nucleus.

treatment_protocol: All samples were derived from treatment-naive patients

value: Pancreas (tumor)

tag: age

value: female

tag: grade

value: treatment-naive


title: WT, PLX5622, rep3

description:
Library name: WT-PLX5622-3
Column name in rawcounts_analysis_all.tsv: WT_506

value: WT


title: WT, PLX5622, rep2

description:
Library name: WT-PLX5622-2
Column name in rawcounts_analysis_all.tsv: WT_431


title: G793A, PLX3397, rep4

description:
Library name: G793A-PLX3397-4
Column name in rawcounts_analysis_all.tsv: G793A_485


title: WT, PLX5622, rep1

description:
Library name: WT-PLX5622-1
Column name in rawcounts_analysis_all.tsv: WT_423


title: PDAC Tumor Sample PDAC12

description: Library name: PDAC12

value: male


title: PDAC Tumor Sample PDAC14

description: Library name: PDAC14


title: PDAC Tumor Sample PDAC13

description: Library name: PDAC13


title: PDAC Tumor Sample PDAC11

description: Library name: PDAC11


title: PDAC Tumor Sample PDAC15

description: Library name: PDAC15


title: G793A, PLX3397, rep3

description:
Library name: G793A-PLX3397-3
Column name in rawcounts_analysis_all.tsv: G793A_483


title: PDAC Tumor Sample PDAC10

description: Library name: PDAC10


title: G793A, PLX3397, rep1

description:
Library name: G793A-PLX3397-1
Column name in rawcounts_analysis_all.tsv: G793A_406


title: WT, PLX3397, rep4

description:
Library name: WT-PLX3397_4
Column name in rawcounts_analysis_all.tsv: WT_513


title: WT, PLX3397, rep3

description:
Library name: WT-PLX3397_3
Column name in rawcounts_analysis_all.tsv: WT_510


title: PDAC Tumor Sample PDAC9

description: Library name: PDAC9


title: PDAC Tumor Sample PDAC8

description: Library name: PDAC8


title: PDAC Tumor Sample PDAC5

description: Library name: PDAC5


title: WT, PLX3397, rep2

description:
Library name: WT-PLX3397_2
Column name in rawcounts_analysis_all.tsv: WT_433


title: G793A, control, rep4

description:
Library name: G793A-control-4
Column name in rawcounts_analysis_all.tsv: G793A_488

value: Control


title: PDAC Tumor Sample PDAC7

description: Library name: PDAC7


title: WT, PLX5622, rep4

description:
Library name: WT-PLX5622-4
Column name in rawcounts_analysis_all.tsv: WT_511


title: PDAC Tumor Sample PDAC16

description: Library name: PDAC16


title: WT, PLX3397, rep1

description:
Library name: WT-PLX3397_1
Column name in rawcounts_analysis_all.tsv: WT_430


title: PDAC Tumor Sample PDAC4

description: Library name: PDAC4


title: PDAC Tumor Sample PDAC6

description: Library name: PDAC6


title: G793A, control, rep2

description:
Library name: G793A-control-2
Column name in rawcounts_analysis_all.tsv: G793A_386


title: PDAC Tumor Sample PDAC3

description: Library name: PDAC3


title: G793A, control, rep3

description:
Library name: G793A-control-3
Column name in rawcounts_analysis_all.tsv: G793A_456


title: G793A, PLX3397, rep2

description:
Library name: G793A-PLX3397-2
Column name in rawcounts_analysis_all.tsv: G793A_450


title: PDAC Tumor Sample PDAC1

description: Library name: PDAC1


title: LNR_sgEZH2_c3

city: New York City

first: Richa

last: Singh

state: NY

address: 413 East, 69th street

department: Pathology and Laboratory Medicine

institute: Weill Cornell Medicine

description: Library name: Sample 12

data_processing:
Single-end bisulfite-converted reads were aligned using Bismark following trimming and adapter removal by TrimGalore. Methylkit was used for identifying differentially methylated sites (DMSs). Sites covered by at least 10 reads, at least 25% difference in methylation between conditions and 5% False Discovery Rate (FDR) were considered as significantly differentially methylated.
DMRcate was used to analyze differentially methylated regions (DMRs). CpG files generated by methylkit were normalized for coverage and sites covered by at least 10 reads were used for differential analysis. The comparison was made between two pairs of PRN NEPC Vs. PRN adeno tumors and between NEPC PDOs (n=3) Vs. CRPC PDOs (n=2). A minimum of 5 consecutive CpGs were used to define a DMR and 5% FDR was used to identify significant DMRs. Homer was used to annotating the significant DMRs to promoters/TSS (±2000 bp from TSS and TSS), gene body (exons, introns, 5’-UTR and 3’-UTR), intergenic regions and CpG islands.
Assembly: Genome_build: mm10 for mouse and hg38 for human data
Supplementary files format and content: CpG count files in tab-delimited txt

source_name: LNCaP cells with Rb1 knockdown and NMyc overexpression

growth_protocol: NEPC patient-derived organoids were grown in human organoid media as per published protocol. The cells were grown in RPMI 1640 medium (Gibco, 11875-093) supplemented with 10% fetal bovine serum (Gemini, 900–108) and 1% penicillin/streptomycin (Gibco, 15140-122).

extract_protocol:
DNA methylation profiling was performed on biopsy punched tumor tissues of histopathologically confirmed foci of adenocarcinomas and NEPC from mouse primary tumor. DNA was extracted using Nucleospin Tissue kit (Macherey Nagel, 740952). For DNA methylation profile from patient-derived organoids, DNA was extracted from cell pellets of each. For EZH2 knockout lines, DNA was extracted from cell pellets after 14 days of nucleofection and validating the knockout.
Library preparation for single-end 100 base-pairs(SE 100) RRBS libraries, sequencing, and post-processing of the raw data was performed at Epigenomics Core at Weill Cornell Medicine. The resulting libraries were normalized, pooled, multiplexed, and clustered on flow cells and sequenced for 100 cycles of single-end reads on an Illumina NovaSeq 6000 instrument.

treatment_protocol: NEPC patient-derived organoids were treated wth 5µM  of tazemetostat for 14 days followed by DNA extraction.

value: EZH2 knockout

value: nucleofected with  EZH2 targeting guide RNAs


title: WT, control, rep2

description:
Library name: WT-control-2
Column name in rawcounts_analysis_all.tsv: WT_429


title: LNR_sgEZH2_c2

description: Library name: Sample 11

value: LNCaP cells with Rb1 knockdown and NMyc overexpression


title: WT, control, rep1

description:
Library name: WT-control-1
Column name in rawcounts_analysis_all.tsv: WT_419


title: LNR_sgEZH2_c1

description: Library name: Sample 10


title: LNR_sgNT2

description: Library name: Sample 9

value: non-targeting control

value: nucleofected with non-targeting guide RNAs


title: LNR_sgNT1

description: Library name: Sample 8


title: MSK-PCa10_Taze2

description: Library name: Sample 7

source_name: NEPC patient-derived organoid cells

value: NEPC patient-derived organoid cells

value: Treated

value: 5uM tazemetostat for 14 days


title: Old_mHSC_Ex_Vivo

city: New York

first: Saghi

last: Ghaffari

state: , New York

address: 1468 Madison Ave

institute: Icahn  School of Medicine at Mount Sinai

description:
Library name: Sample 6
10x genomics

data_processing:
Demultiplexing, barcoding, gene counting and aggregation were done using Cell Ranger (10X Genomics)
Assembly: mouse mm10
Supplementary files format and content: raw counts for each sample

source_name: bone marrow

extract_protocol:
Bone marrow (BM) cells were flushed out of the femur and tibia bones in ice-cold IMDM and 2% FBS. Flow cytometry and FACS (fluorescence-activated cell sorting) were performed as previously described (Rimmele et al., 2015; Yalcin et al., 2010). In brief, total BM cells were immune-stained with fluorochrome-labeled antibodies for surface markers, such as lineage markers (CD5, B220, CD11b, Gr-1, 7-4, and Ter-119) using a lineage cocktail consisted of biotinylated hematopoietic multilineage monoclonal antibodies (StemCell Technology), CD45.1, CD45.2, stem and progenitor markers (c-Kit, Sca-1, CD48, CD150) for 15 min. followed by incubation with APC/CY7–streptavidin to identify progenitors (Lin- Sca1- c-Kit+) and LT-HSCs (LSK CD48- CD150+).  All samples were stained with DAPI for live cells. FACS isolation was performed using FACS Aria-II.
Freshly sorted, viable HSCs (12000 -16000) from pooled young or old mice, or old HSCs cultured with ConA (40 nM), ddC (40 µM), or DMSO for 16 hrs were washed and re-suspended in 50µl 0.04% BSA/PBS, and proceeded to single cell RNA-Seq on 10X genomics platform from Genomics Core Facility at the Icahn School of Medicine at Mount Sinai. Briefly, single cells were partitioned, barcoded, and Gel Beads-in-emulsion (GEM) were generated using Chromium Next GEM Chip J Single Cell kit. Libraries were then prepared using Chromium Next GEM Single Cell 3′ Kits v3.1 (10x Genomics) and were sequenced using NovaSeq S4 200 cycle v1.5.

treatment_protocol: For non "ex-vivo" samples, HSC were ex-vivo cultured in presence of ConA (40 nM) or ddc (40uM).

value: bone marrow

value: HSC

tag: strain


title: Young_mHSC_Ex_Vivo

description:
Library name: Sample 5
10x genomics

tag: tissue


title: MSK-PCa10_Taze1

description: Library name: Sample 6


title: Old-like_mHSC_Cultured

description:
Library name: Sample 1
10x genomics

value: DMSO


title: Old_mHSC_Cultured_ddC

description:
Library name: Sample 4
10x genomics

value: ddC


title: Vehicle_PDX61_H3K4me3

description:
Library name: Sample 20
H3K4me3 IP

data_processing:
Quality of raw sequencing reads was assessed by FastQC (Babraham Bioinformatics). Adapters and low-quality reads (Phred score <20) were removed using TrimGalore. Good quality reads were aligned to mm10 or hg38 genome using Bowtie2. Reads with mapping quality score <20 was removed from downstream analysis. PCR duplicates were removed using Picard MarkDuplicates. Peak calling was performed using the sonicated input DNA as control by MACS2 algorithm with a q-value of <0.05. For H3K27me3, broad peak module of MACS2 was used. Enriched ChIP-seq peak regions were annotated to mm10/hg38 genomic features using HOMER annotatePeak.pl. Known or de novo transcription factor motifs were identified using HOMER findMotifs.pl +/−100 bp from each peak. Unique and overlapping peaks between conditions were defined using BEDTools, keeping atleast 1bp overlap for overlapping peaks. For each condition, two replicates were used and normalized to its input control before merging. The combined signal from both replicates were used to generate enrichment profile plots and heatmap using deepTools.
Assembly: Genome_build: mm10 for mouse and hg38 for human data
Supplementary files format and content: Bedgraph files

source_name: NEPC patient-derived xenograft tumor

growth_protocol: NEPC patient-derived organoid cells (1 × 106 cells diluted in 100ul of 1:1 PBS and Matrigel) were injected subcutaneously in the flanks of nude (NU/J) mice (Jackson Laboratories, #002019, RRID: IMSR_JAX:002019). Treatment was started after the tumor reached 150mm3.

extract_protocol:
Adenocarcinoma and NEPC foci were identified from hematoxylin-eosin stained slides of OCT blocks of primary tumors, reviewed by pathologist. The corresponding foci in OCT blocks were cored using 2mm biopsy punch and tissues were dissociated using pestle and motor homogenizer, followed by syringes in cold PBS.  Cryosections of xenograft tumors were homogenized in a similar protocol. Dissociated cells were crosslinked in 1% methanol-free formaldehyde (Thermo Scientific, 28908) for 15 min at 37 °C. Crosslinking was quenched with 2.5 M glycine for 5 min at room temperature. Washed cell pellets were resuspended in 1 mL of lysis buffer (50 mM Tris HCl pH 8, 0.5% SDS, 10 mM EDTA with protease and phosphatase inhibitors; Thermo Fisher Scientific, 78428/78430) and lysed for 20 minutes at 4°C. Collected nuclei were resuspended in a second lysis buffer (10 mM Tris HCl pH 7.5, 150 mM NaCl, 0.1% SDS, 1 mM EDTA, 1% NP-40, 1% sodium deoxycholate, with protease and phosphatase inhibitors; Thermo Fisher Scientific, 78428/78430) and sonicated in Bioruptor Pico, Diagenode for 12mins. To the sheared chromatin, equal volumes of specific antibody and respective IgG control antibody was added and incubated overnight at 4°C. The immunoprecipitated chromatin was washed with several buffers and eluted in 300 µL of fresh elution buffer (100 mM NaHCO3 and 1% SDS). Reverse crosslinking was performed with 45 mM Tris pH 7, 170 mM NaCl at 65°C overnight, followed by RNase and proteinase K treatment and DNA was purified using the NucleoSpin Gel and PCR Clean-up Kit (Macherey-Nagel, 740609) as per manufacturer’s recommendation.
Libraries with purified immunoprecipitated DNA fragments were generated using the Hyper Prep Kit (Kapa Biosystems, KK8502). Library quality and fragment size distribution was checked in DNA High Sensitivity Bioanalyzer (Agilent, 5067-4626). Equimolar concentration of immunoprecipitated and input DNA fragments were pooled and sequenced in Illumina NovaSeq 6000 instrument at Weill Cornell Medicine Genomics core facility.

treatment_protocol: Decitabine (0.8mg/kg) was administered to mice in treated group by intraperitoneal injection once daily for 7 days. Equal volume of PBS was injected to mice in vehicle groups.

value: NEPC patient-derived xenograft tumor

value: Vehicle

value: Vehicle for 7 days

value: Intact mice


title: Vehicle_PDX61_H3K4me3-Input

description:
Library name: Sample 19
Input


title: Old_mHSC_Cultured

description:
Library name: Sample 2
10x genomics


title: PDAC Tumor Sample PDAC2

description: Library name: PDAC2

value: Pancreas (tumor)

value: male

value: treatment-naive


title: G793A, control, rep1

description:
Library name: G793A-control-1
Column name in rawcounts_analysis_all.tsv: G793A_290

value: Brain

value: Control


title: Vehicle_PDX55_H3K4me3

description:
Library name: Sample 18
H3K4me3 IP


title: Vehicle_PDX55_H3K4me3-Input

description:
Library name: Sample 17
Input


title: Liv_KO_Fast_73

first: Artem

last: Khan

address: 1230 York Ave

institute: Rockefeller University

description: Library name: 73

data_processing:
Quality control of the sequencing data was conducted with Rfastp.52  Transcript expression was computed using Salmon (73), followed by processing with DESeq2 (74).
Assembly: The reads alignment was performed according to the reference genome (Mus_musculus.GRCm39.cdna.all.fa.gz), and gene models were based on Mus_musculus.GRCm39.107.gtf.gz.
Supplementary files format and content: Salmon obtained counts in .sf format that can be read as a table

source_name: Liver

extract_protocol:
Total RNA was extracted from the livers harvested as described above from Slc25a45-/- vs. Slc25a45+/-, Slc25a45+/+ mice using the RNeasy Mini Kit (Qiagen #74104) in accordance with the manufacturer's protocol.
Library preparation and RNA-sequencing was performed by Genewiz.

value: Liver

value: KO

value: Fasting


title: Liv_WT_Fast_8

description: Library name: 8

value: WT


title: Decitabine_PDX53_H3K4me3

description:
Library name: Sample 16
H3K4me3 IP

value: Treated

value: Decitabine for 7 days


title: Neutrophils, iEC-Erg-/- , Basal

city: Chicago

first: Vijay Avin

last: Balaji Ragunathrao

state: IL

address: 835 S Wolcott Ave

department: Pharmacology and Regenerative Medicine

institute: University of Illinois at Chicago

description: Library name: Sample 2

data_processing:
Adaptor trimming using ‘cutadapt’.  Genome alignment using ‘HISAT2’. Feature counting using ‘featurecount’. Differential analysis using ‘edgeR’. Pathway analysis using ‘metascape’.
Assembly: mm10
Supplementary files format and content: tab-delimited csv file incudes normalized count for each sample and differential expression.

source_name: Lung

extract_protocol:
Total RNA was extracted using the RNeasy mini kit (Qiagen USA), and ribosomal RNA was depleted using the RiboMinus™ Eukaryote kit v2 (Thermo Fisher Scientific).
RNA libraries were then constructed with the TruSeq RNA library prep kit v2 (Illumina)

value: Lung

value: Neutrophils

value: iEC-ERG Knockout

value: Basal


title: Decitabine_PDX53_H3K4me3-Input

description:
Library name: Sample 15
Input

value: NEPC patient-derived xenograft tumor


title: Neutrophils, ERGfl/fl,  Basal

description: Library name: Sample 1

value: ERG Flox


title: Liv_KO_Fed_7

description: Library name: 7

value: Ad libitum


title: Decitabine_PDX48_H3K4me3

description:
Library name: Sample 14
H3K4me3 IP

value: Intact mice


title: Decitabine_PDX48_H3K4me3-Input

description:
Library name: Sample 13
Input


title: WT, control, rep3

description:
Library name: WT-control-3
Column name in rawcounts_analysis_all.tsv: WT_432


title: Liv_KO_Fed_64

description: Library name: 64


title: Liv_KO_Fast_59

description: Library name: 59


title: MSK-PCa10_Cont

description: Library name: Sample 5

value: NEPC patient-derived organoid cells


title: Old_mHSC_Cultured_ConA

description:
Library name: Sample 3
10x genomics

value: bone marrow

value: HSC

value: ConA


title: Vehicle_PDX61_H3K27me3-Input

description:
Library name: Sample 11
Input

value: Vehicle

value: Vehicle for 7 days


title: Liv_HET_Fast_45

description: Library name: 45

value: Liver

value: HET

value: Fasting


title: 60 min conjugation F plasmid, replicate 1

city: Gif sur Yvette

first: Elena

last: ESPINOSA

address: 1, Avenue de la Terrasse

country: France

institute: CNRS

description: Library name: p60m1_F

data_processing:
Sequence reads were mapped to references genomes and pESBL using Bowtie2.
.bam fileswere used to measure the read counts of each gene with featureCounts, followed by differential gene expression (DGE) analysis done by DESeq2 package in SARTools.
Assembly: E. coli chromosome (NC_000913.2)
Supplementary files format and content: tab-delimited text file containing raw count per sample, Padj and log2 fold change (I2FC) of fragments per kilobase of gene per million reads  (FPKM)

organism: Escherichia coli

source_name: prokaryotic cell

growth_protocol: Cells were grown in LB media with agitation (180 rpm) at 37 ᵒC and 30 ᵒC for E. coli and S. meliloti, respectively.

extract_protocol:
Total RNA was extracted with Monarch Total RNA Miniprep Kit (New England Biolabs, NEB), following manufacturer’s protocol.
Library construction was performed by Novogene.

treatment_protocol: Donor and recipient growing cells were mixed and placed in a filter membrane in a LB plate supplemented with 1 mM MgCl2. Cells were incubated at 37 ᵒC for 30 and 60 minutes.  After incubation, cells were recovered and washed twice with 2 mM Ethylenediaminetetraacetic acid solution (EDTA). Pellet was resuspended in 1 ml of EDTA.

value: prokaryotic cell


title: 60 min conjugation F plasmid, replicate 2

description: Library name: p60m2_F


title: Vehicle_PDX55_H3K27me3

description:
Library name: Sample 10
H3K27me3 IP


title: Mock conjutagion F plasmid, replicate 1

description: Library name: mock1_F


title: 15 min conjugation, replicate 2

description: Library name: p15m2


title: Small RNA-sequencing of U4.4 cells infected with BZL mosquitoes

city: BOSTON

first: NELSON

middle: C

last: LAU

state: MA

address: 72 E Concord St K219, Dept of Biochemistry

department: Biochemistry and Cell Biology

institute: Boston University Chobanian & Avedisian School of Medicine

description: Library name: AeAlb_U44_BZL_sRNA

library_source: other

data_processing:
The Mosquioto Small RNA Genomics (MSRG)  pipeline published in PMIDs: 33419731 and 35796973. Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt and Trimmomator. Total RNA reads were also further trimmed by length to 35 nt to be compatable for processing with the MSRG pipeline
Assembly: AaegL5
Supplementary files format and content: tab-delimited text file with Excel extension includes processed counts for each Sample for microRNA genes or protein-coding genes. csv files include RPM values for each Sample mapped to viruses

molecule: other

organism: Aedes albopictus

extract_protocol:
RNA was harvested using the NEB Monarch Total RNA extration kit.  0.5 to 1.0ug of total RNA was used for the construction of sequencing libraries.
Total RNA libraries for RNA-seq were prepared using Zymo RiboFree Zymo-Seq Library Prep Kit following manufacturer's protocols.  Small RNA libraries for microRNA-seq were prepared with the NEBNext Small RNA Library prep kit according to the manufacturer's protocols.

value: BZL mosquito virus-infected


title: Liv_HET_Fast_43

description: Library name: 43


title: Vehicle_PDX55_H3K27me3-Input

description:
Library name: Sample 9
Input


title: 15 min conjugation, replicate 1

description: Library name: p15m1


title: Small RNA-sequencing of U4.4 cells infected with AWK mosquitoes

description: Library name: AeAlb_U44_AWK_sRNA

value: AWK mosquito virus-infected


title: Liv_KO_Fast_65

description: Library name: 65

value: KO


title: Small RNA-sequencing of U4.4 cells uninfected

description: Library name: AeAlb_U44_Mock_sRNA

value: mock


title: Liv_KO_Fast_36

description: Library name: 36


title: Vehicle_PDX51_H3K27me3-Input

description:
Library name: Sample 7
Input

value: NEPC patient-derived xenograft tumor


title: Liv_KO_Fed_62

description: Library name: 62

value: Ad libitum


title: MDA-MB-231 cells,shAKAP2,dox,03

city: Seattle

first: John

last: Scott

state: WA

address: 1959 NE Pacific St

institute: University of Waqshington

description:
Library name: shAKAP2 dox biol rep 3
AKAP2shRNAdox03 in raw_counts.csv file

data_processing:
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality.
The trimmed reads were mapped to the reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step.
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
Assembly: GRCh38
Supplementary files format and content: tab delimited text file includes raw counts for each sample

source_name: Breast; Mammary gland

extract_protocol:
RNA was extracted at Genewiz/Azent and Total RNA samples were quantified using Qubit 3.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA).
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94°C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 3.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).

value: Breast; Mammary gland

value: epithelial cell

value: doxycycline


title: Vehicle_PDX61_H3K27me3

description:
Library name: Sample 12
H3K27me3 IP

value: Intact mice


title: MDA-MB-231 cells,shAKAP2,dox,02

description:
Library name: shAKAP2 dox biol rep 2
AKAP2shRNAdox02 in raw_counts.csv file


title: Liv_KO_Fed_31

description: Library name: 31


title: Decitabine_PDX58_H3K27me3

description:
Library name: Sample 6
H3K27me3 IP

value: Treated

value: Decitabine for 7 days


title: MDA-MB-231 cells,shAKAP2,dox,04

description:
Library name: shAKAP2 dox biol rep 4
AKAP2shRNAdox04 in raw_counts.csv file


title: MDA-MB-231 cells,shAKAP2,dox,01

description:
Library name: shAKAP2 dox biol rep 1
AKAP2shRNAdox01 in raw_counts.csv file


title: Decitabine_PDX58_H3K27me3-Input

description:
Library name: Sample 5
Input


title: Mock conjugation F plasmid, replicate 2

description: Library name: mock2_F


title: MDA-MB-231 cells,shAKAP2,no dox,03

description:
Library name: shAKAP2 no dox biol rep 3
AKAP2shRNAnodox03 in raw_counts.csv file


title: MDA-MB-231 cells,shAKAP2,no dox,04

description:
Library name: shAKAP2 no dox biol rep 4
AKAP2shRNAnodox04 in raw_counts.csv file


title: MDA-MB-231 cells,shAKAP2,no dox,02

description:
Library name: shAKAP2 no dox biol rep 2
AKAP2shRNAnodox02 in raw_counts.csv file


title: Decitabine_PDX50_H3K27me3

description:
Library name: Sample 4
H3K27me3 IP


title: Liv_KO_Fed_23

description: Library name: 23


title: Liv_HET_Fast_42

description: Library name: 42


title: Vehicle_PDX51_H3K27me3

description:
Library name: Sample 8
H3K27me3 IP

value: Vehicle

value: Vehicle for 7 days


title: Decitabine_PDX50_H3K27me3-Input

description:
Library name: Sample 3
Input


title: MDA-MB-231 cells,shAKAP2,no dox,01

description:
Library name: shAKAP2 no dox biol rep 1
AKAP2shRNAnodox01 in raw_counts.csv file


title: MDA-MB-231 cells, shScramble,dox,04

description:
Library name: scramble dox biol rep 4
scrambledox04 in raw_counts.csv


title: Liv_KO_Fast_40

description: Library name: 40

value: Liver


title: Liv_HET_Fed_26

description: Library name: 26

value: HET


title: MDA-MB-231 cells, shScramble,dox,03

description:
Library name: scramble dox biol rep 3
scrambledox03 in raw_counts.csv


title: Decitabine_PDX48_H3K27me3

description:
Library name: Sample 2
H3K27me3 IP


title: MDA-MB-231 cells, shScramble,dox,01

description:
Library name: scramble dox biol rep 1
scrambledox01 in raw_counts.csv


title: Liv_HET_Fed_21

description: Library name: 21


title: Decitabine_PDX48_H3K27me3-Input

description:
Library name: Sample 1
Input


title: MDA-MB-231 cells, shScramble,no dox,04

description:
Library name: scramble no dox biol rep 4
scramblenodox04 in raw_counts.csv


title: MDA-MB-231 cells, shScramble,dox,02

description:
Library name: scramble dox biol rep 2
scrambledox02 in raw_counts.csv


title: Liv_WT_Fast_12

description: Library name: 12

value: WT

value: Fasting


title: Liv_WT_Fed_22

description: Library name: 22


title: TLSCs_DUX4-OE_OTX2-KO-2 [RNA-Seq]

description: Library name: KO-dux-toti2

source_name: TLSCs

value: TLSCs

value: totipotent


title: Liv_HET_Fed_10

description: Library name: 10


title: MDA-MB-231 cells, shScramble,no dox,02

description:
Library name: scramble no dox biol rep 2
scramblenodox02 in raw_counts.csv


title: MDA-MB-231 cells, shScramble,no dox,01

description:
Library name: scramble no dox biol rep 1
scramblenodox01 in raw_counts.csv


title: TLSCs_DUX4-OE_OTX2-KO-1 [RNA-Seq]

description: Library name: KO-dux-toti1


title: TLSCs_OTX2-KO-4 [RNA-Seq]

description: Library name: KO-toti2


title: MIA PaCa-2/shCWC22, Dox(+), rep2

city: Kyoto

first: Ryuzaburo

last: Yuki

address: 5 Misasagi-Nakauchi-cho, Yamashina-ku

country: Japan

institute: Kyoto Pharmaceutical Univeristy

description:
Library name: Sample 4
Column name in FeatureCounts.txt: KD_rep2

data_processing:
After trimming of the adapters using trim_galore, the reads were mapped with STAR (version 2.7.10a) with default parameters to ENSEMBL genome assembly GRCh37.87, indexed with SAMtools and features counted with featureCounts.
Assembly: GRCh37.87
Supplementary files format and content: tab-delimited text file includes featureCounts for each Sample

source_name: pancreas

growth_protocol: MIA PaCa-2/shCWC22#2 cells were cultured in DMEM containing 10% FBS with 20 mM HEPES–NaOH (pH 7.4) at 37℃ in 5% CO2.

extract_protocol:
Total RNA was purified using NucleoSpin RNA Plus (740984; Takara bio, Shiga, Japan).
Purified RNA was subjected to RNA-seq by Rhelixa Inc. (Tokyo, Japan). In brief, mRNA was isolated using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Ipswich, MA), and a cDNA library for sequencing was prepared using NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs). Finally, samples were subjected to sequencing at 150 bp x2 by Illumina NovaSeq X Plus (Illumina, San Diego, CA, USA).

treatment_protocol: MIA PaCa-2/shCWC22#2 cells were treated with or without 4 µg/mL Dox for 40 h and then treated with 5 μM STLC plus 5 µM proTAME for 16 h. Mitotic cells were collected by mitotic shake-off and analyzed by RNA-seq.

value: pancreas

value: MIA PaCa-2

value: pancreatic adenocarcinoma

value: Dox(+)

value: Dox


title: MIA PaCa-2/shCWC22, Dox(+), rep1

description:
Library name: Sample 3
Column name in FeatureCounts.txt: KD_rep1


title: TLSCs_OTX2-KO-3 [RNA-Seq]

description: Library name: KO-toti1


title: MIA PaCa-2/shCWC22, Dox(-), rep2

description:
Library name: Sample 2
Column name in FeatureCounts.txt: Ctrl_rep2

value: Dox(-)


title: KPfrt Slc4a11-MCD/+ Rosa26-mTmG/+ tumors treated and harvested at 17 weeks PTI after 3 weeks of tracing, HTO, rep2

first: Jason

middle: Earl

last: Chan

address: 1275 York Ave, Box 20

department: Medicine

institute: Memorial Sloan Kettering Cancer Center

description:
Library name: IGO16562_HTO
10x genomics

data_processing:
FASTQ files of single-cell RNA-sequencing data generated on the 10X Chromium platform were processed using the standard CellRanger pipeline (version >=6.0.0). Reads were aligned to a custom GRCm38 / mm10 reference containing additional transgenes used in the study. The generated cell-gene count matrices were analyzed using a combination of published packages and custom scripts in either the scanpy (v> 1.9.0) / AnnData (v. 0.10.5, Python)
Assembly: GRCm38/mm10
Supplementary files format and content: h5: raw counts
Supplementary files format and content: h5ad: processed file
Supplementary files format and content: csv: featureref for Total Seq B Hash antibodies

source_name: lung

growth_protocol: Cells were isolated from animals. No additional growth was involved.

extract_protocol:
Encapsulation and library preparation were performed using the 10X Genomics Chromium Single Cell 3’ Library & Gel bead Kit V3 (10X Genomics, PN-1000121) according to the manufacturer’s protocol. Libraries were sequenced using the Nova-Seq 6000 platform (Illumina).
Single cell suspensions were stained with Trypan blue and Countess II Automated Cell Counter (ThermoFisher) was used to assess both cell number and viability. Following QC, the samples were loaded onto Next GEM Chip G (14143, 15123, 15342, 15488, 15600, 15601, 15771) or GEM-X Single Cell Chip (16235, 16318, 16562, 16686, 17402, 17483, 17543) (10X Genomics PN 1000690 & 2000060) and GEM generation, cDNA synthesis, cDNA amplification, and library preparation of ~4-50,000 cells proceeded using the Chromium Next GEM Single Cell 3’ Kit v3.1 or GEM-X Single Cell 3’ Kit v4 (10X Genomics PN 1000268 & 1000691) according to the manufacturer’s protocol. cDNA amplification included 11-12 cycles and 78-863 ng of the material was used to prepare sequencing libraries with 8-14 cycles of PCR. Indexed libraries were pooled and sequenced on a NovaSeq 6000 (14143, 16235, 16562) or X (15123, 15342, 15488, 15600, 15601, 15771, 16235, 16318, 16562, 16686, 17402, 17483, 17543) in a PE28/88 run using the NovaSeq 6000 S4 (200 Cycles) or X 10B (100 Cycles) or 25B (300 cycles) Reagent Kit (Illumina).  An average of 38 thousand paired reads was generated per cell.

treatment_protocol: KP mice with either Slc4a11-FSF-MCD/+ or Hopx-FSF-MACD/+ alleles with either Hipp11-FSF-GGCB/+ or Rosa26-FSF-mTmG/+ reporter alleles were infected by adenoviral CMV-FlpO or lentiviral PGK-FlpO recombinase. Mice bearing tumors were treated with either Tamoxifen, Diphtheria toxin, or saline with or without Cisplatin and MRTX1133 as indicated, and tumor cells were isolated, hashed using TotalSeq-B antibodies, and processed for single-cell mRNA sequencing after FACS purification. One dataset contains KP Rosa26-tdTomato/+ tumors used in this study.

value: lung

value: Primary tumor cells

value: Tumor cells

value: Kras-G12D/+ Trp53-delta/delta Slc4a11-MCD/+ Rosa26-mTmG/+

value: Tamoxifen, cisplatin, MRTX1133, Diptheria toxin


title: KPfrt Slc4a11-MCD/+ Rosa26-mTmG/+ tumors treated and harvested at 17 weeks PTI after 3 weeks of tracing, GEX rep2

description:
Library name: IGO16562_GEX
10x genomics

value: Tamoxifen, cisplatin, MRTX1133, Diphtheria toxin


title: Dp16; High fat diet; Sample_T1_534139

description: Library name: T1_534139

data_processing:
Signal processing, base-calling, and quality scoring was carried out automatically by the NovaSeq 6000 RTA3 software (Illumina).
Demultiplexing and conversion to FASTQ format was carried out using bcl2fastq (Illumina).
Data quality was assessed using FASTQC (v0.11.5) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and FastQ Screen (v0.11.0, https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/).
Trimming and filtering of low-quality reads was performed using bbduk from BBTools (v37.99) and fastq-mcf from ea-utils (v1.05, https://expressionanalysis.github.io/ea-utils/).
Alignment to the mouse reference genome (GRCm38) was carried out using HISAT2 (v2.1.0) in paired, spliced-alignment mode with a GRCm38 index with a Gencode M24 annotation GTF.
Alignments were sorted and filtered for mapping quality (MAPQ>10) using Samtools (v1.5).
Gene-level count data were quantified using HTSeq-count (v0.6.1) with the following options (--stranded=reverse –minaqual=10 –type=exon --mode=intersection-nonempty) using a Gencode M24 GTF annotation file.
Assembly: GRCm38
Supplementary files format and content: Counts: Tab-delimited text files containing per gene strand-specific fragment counts.
Supplementary files format and content: FPKMs: Tab-delimited text files containing per gene strand-specific normalized fragments-per-kilobase-per-million-mapped (FPKM).

source_name: liver

extract_protocol:
Total RNA from tissue samples was extracted using TRIzol reagent (Invitrogen) following the manufacturer protocol. RNA quality was assessed using an Agilent 2200 TapeStation and quantified by Qubit (Life Technologies).
Poly-A(+) RNA enrichment, and strand-specific library preparation were carried out using a Tecan/Nugen Universal Plus mRNA Kit. Paired-end 150 bp sequencing was carried out on an Illumina NovaSeq 6000 instrument by the University of Colorado Cancer Center Genomics Shared Resource.

value: liver

value: Male

value: High fat diet


title: MIA PaCa2 cells, TIMP1 KO 2, biol rep 3

description:
Library name: MiaPaCa2_KO2_3
column name in MiaPaCa2_normCounts.txt: MiaPaCa2_KO2_3

data_processing:
All data processing steps were performed using the Galaxy platform (http://usegalaxy.org and https://usegalaxy.eu)
FastQC tool was used to evaluate read quality, GC content, sequence duplication levels, and adapter contamination
Poor-quality reads and adapter sequences were removed using Cutadapt with parameters set to trim bases ≤20 bp
Quality reports were aggregated using MultiQC
DESeq2 was used to nornalize read counts and extract DEGs
Assembly: Reads were mapped to the reference genome (Homo sapiens, GRCh38) using STAR
Supplementary files format and content: tab-delimited text file including normalized counts for each sample

source_name: MIA PaCa-2

growth_protocol: MIA PaCa-2 cells were grown in RPMI 1640 supplemented with 10% FCS and 1% P/S at 37°C and 5% CO2.

extract_protocol:
Total RNA was isolated using RNeasy Plus Mini Kit (Qiagen)
Libraries were prepared using the NGS RNA Library Prep Set (PT042; Novogene GmbH)

value: TIMP1 KO (exon4)


title: TLSCs_DUX4-OE-2 [RNA-Seq]

description: Library name: WT-dux-toti2

data_processing:
RNAseqv1
Adapter of sequence reads were trimmed and poor quality reads  were removed by TrimGalore(quality <20 or length <30),
Paired-end RNA-seq reads were trimmed and then mapped to hg38 genome by STAR (v.2.7.4a)
Raw count tables of genes were computed using featureCounts (v2.0.1)
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

extract_protocol:
Total RNA was isolated using RNA isolater Total RNA Extraction Reagent (Vazyme, R401) according to the manufacturer’s instructions.
TRIzol was used to extract total RNA, and libraries were constructed using the VAHTS Universal V8 RNA-seq Library Prep Kit (Vazyme, NR605) according to the manufacturer’s instructions. 500 ng total RNA was used to construct libraries. Library samples were subjected to the Illumina NovaSeq 6000 sequencing system.

value: TLSCs

value: totipotent


title: BMAL1-2

city: 武汉市

first: Shaowei

last: Zeng

state: 湖北省

address: 水果湖街道

institute: wuhan university

description: Library name: BMAL1-2

data_processing:
The CUT&Tag-seq data were processed by trimming adapters and low-quality bases with Trimmomatic, assessing read quality with FastQC, and mapping clean reads to the reference genome using Bowtie2. Low-quality alignments, duplicates, and organelle reads were removed with Samtools and Picard, and valid pairs were used for peak calling with MACS3. Replicate consistency was checked, signal enrichment analyzed with deepTools, peaks annotated with ChIPseeker, and visualized with Gviz. For differential analysis, consensus peaksets were generated, peaks annotated to genes, and GO/KEGG enrichment performed with clusterProfiler. Differential peaks were identified using DiffBind, with motif analysis carried out by MEME.  In short: reads were cleaned, mapped, filtered, peaks called and annotated, then differential peaks identified and analyzed for functional enrichment and motifs.
Assembly: hg38
Supplementary files format and content: xls(BAMPE),peaks
Library strategy: CUT&Tag

source_name: cerebral organoids

extract_protocol:
Cerebral organoids were digested into single cells using Cell Recovery Solution for Organoids (Yeasen, 41421ES60), and approximately 2.5 × 105 cells were collected. The dissociated cells were cross-linked with Enhancer buffer and then combined with activated ConA beads and incubated overnight with BMAL1 antibodies. Following incubation, the supernatant was removed, and the samples were incubated with a secondary antibody (Vazyme, Ab207) for 1 hour at room temperature with rotation. Subsequently, the supernatant was discarded, and the ConA beads were incubated with pA/G-Tnp Pro and TTBL, each for 1 hour at both room temperature and 37°C. After TTBL incubation, 2 mL of 10% SDS was added to each sample and incubated at 55°C for 10 min. The fragmented DNA in the supernatant was enriched using activated DNA Extract Beads Pro
next-generation sequencing library was constructed according to the manufacturer’s protocol (Vazyme, TD202).In brief, mix DNA Extract Beads Pro, 2×CAM Master Mix, index primers N506 and N702, and DNA sample to a total volume of 100 ?l. Run PCR with 15 cycles following standard thermal conditions. After amplification, purify the product using VAHTS DNA Clean Beads: bind beads to the PCR product, wash twice with 80% ethanol, air dry, elute with ddH?O, and recover 20 ?l of purified DNA for storage at ?30 to ?15°C.

value: cerebral organoids

value: WT

value: synchronized with 100 nM hydrocortisone


title: Single Cell Gene Expression Flex Fixed RNA Profiling (10x Genomics); Multiplexed mouse liver samples

description: Library name: Multiplexed mouse liver samples

data_processing:
Signal processing, base-calling, and quality scoring was carried out automatically by the NovaSeq 6000 RTA3 software (Illumina).
Conversion to FASTQ format was carried out using bcl2fastq (Illumina).
Multiplexed reads in FASTQ format were processed using Cellranger-8.0.1 in 'multi' mode with the mm10-2020-A transcriptome reference and Chromium Mouse Transcriptome Probe Set v1.0.1.
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of droplet barcodes; raw or filtered by Cellranger
Supplementary files format and content: features.tsv.gz: list of gene IDs; raw or filtered by Cellranger
Supplementary files format and content: matrix.mtx.gz: sparse matrix of gene expression count data in Matrix Market exchange format; raw or filtered by Cellranger

extract_protocol:
Preparation of fixed single cells from mouse liver: Upon euthanasia and cardiac puncture, mouse livers were perfused with cold 1x Dulbecco’s PBS (DPBS), then removed. Livers were minced manually with a scalpel, suspended in DMEM (Corning) with 2 mg/mL Collagenase P (Roche) and 0.2 mg/mL Deoxyribonuclease I (Worthington Biochemical), and incubated with shaking at 37ºC for 15 minutes. Next, the suspension was filtered through a 70 micron cell strainer to remove debris, and centrifuged at 100g for 8 minutes at 4ºC to separate primary mouse hepatocytes (pelleted) from the nonparenchymal cells of the liver (supernatant). Nonparenchymal cells were pelleted by centrifugation at 400g for 7 minutes at 4ºC, resuspended in red blood cell lysis buffer (BD Biosciences) and incubated 1 min at room temperature to remove red blood cells, filtered through a 40 micron filter, pelleted again by centrifugation at 400g for 7 minutes at 4ºC, and resuspended in 50 µL DPBS with 1% (w/v) BSA. The hepatocyte pellet was resuspended in red blood cell lysis buffer and incubated 1 min at room temperature, filtered through a 40 micron filter, pelleted again by centrifugation at 100g for 8 minutes at 4ºC, and resuspended in 50 µL DPBS with 1% (w/v) BSA. Viability and cell counts for both hepatocyte and nonparenchymal cell fractions were determined using tryphan blue and a Countess 2 cell counter (Thermo Fisher Scientific). Per animal, each fraction was then combined at a 1:1 ratio, pelleted by centrifugation, and fixed by resuspending in a 4% (w/v) formaldehyde fixative solution from a Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit (10X Genomics).
Mouse liver fixed single cell library construction: The 10X Genomics Single Cell Gene Expression Flex Fixed RNA Profiling (FRP) workflow measures RNA levels in fixed samples using probes targeting the whole transcriptome. Fixed liver single cell suspensions were hybridized with a mouse transcriptome probe panel (10X Genomics), according to manufacturer instructions, and loaded into a Chromium X (10X Genomics) microfluidics instrument to generate an oil emulsion with partitioned nanoliter-scale droplets, each ideally containing a barcoded gel bead and a single cell, along with enzyme Master Mix (10X Genomics) for probe pair ligation and gel bead primer barcode extension. The resulting Illumina-compatible sequencing library was subjected to paired-end 150 bp sequencing on a Novaseq 6000 instrument (Illumina) by the Genomics Shared Resource at the University of Colorado Anschutz Medical Campus.


title: MIA PaCa2 cells, TIMP1 KO 2, biol rep 1

description:
Library name: MiaPaCa2_KO2_1
column name in MiaPaCa2_normCounts.txt: MiaPaCa2_KO2_1

value: MIA PaCa-2


title: MDA-MB-231 cells, shScramble,no dox,03

description:
Library name: scramble no dox biol rep 3
scramblenodox03 in raw_counts.csv

value: Breast; Mammary gland

value: epithelial cell


title: TLSCs_WT-6 [RNA-Seq]

description: Library name: WT-toti2


title: Dp16; High fat diet; Sample_T2_534134

description: Library name: T2_534134


title: Dp16; High fat diet; Sample_T3_534139

description: Library name: T3_534139


title: MIA PaCa2 cells, TIMP1 KO 1, biol rep 3

description:
Library name: MiaPaCa2_KO1_3
column name in MiaPaCa2_normCounts.txt: MiaPaCa2_KO1_3


title: MIA PaCa2 cells, TIMP1 KO 1, biol rep 1

description:
Library name: MiaPaCa2_KO1_1
column name in MiaPaCa2_normCounts.txt: MiaPaCa2_KO1_1


title: MIA PaCa2 cells, TIMP1 KO 1, biol rep 2

description:
Library name: MiaPaCa2_KO1_2
column name in MiaPaCa2_normCounts.txt: MiaPaCa2_KO1_2


title: TLSCs_WT-5 [RNA-Seq]

description: Library name: WT-toti1


title: MIA PaCa2 cells, CRISPR Control, biol rep 3

description:
Library name: MiaPaCa2_CRISPRCtrl_3
column name in MiaPaCa2_normCounts.txt: MiaPaCa2_CRISPRCtrl_3

value: WT (silent point mutation)


title: MIA PaCa2 cells, CRISPR Control, biol rep 2

description:
Library name: MiaPaCa2_CRISPRCtrl_2
column name in MiaPaCa2_normCounts.txt: MiaPaCa2_CRISPRCtrl_2


title: naive_hPSCs_OTX2-OE-2 [RNA-Seq]

description: Library name: iOTX2-OE-4CL2

source_name: naive hPSCs

value: naive hPSCs

value: naive


title: Dp16; High fat diet; Sample_T1_534134

description: Library name: T1_534134


title: MIA PaCa2 cells, CRISPR Control, biol rep 1

description:
Library name: MiaPaCa2_CRISPRCtrl_1
column name in MiaPaCa2_normCounts.txt: MiaPaCa2_CRISPRCtrl_1


title: MIA PaCa-2/shCWC22, Dox(-), rep1

description:
Library name: Sample 1
Column name in FeatureCounts.txt: Ctrl_rep1

value: pancreas

value: pancreatic adenocarcinoma

value: Dox(-)


title: MIA PaCa2 cells, TIMP1 KO 2, biol rep 2

description:
Library name: MiaPaCa2_KO2_2
column name in MiaPaCa2_normCounts.txt: MiaPaCa2_KO2_2


title: MIA PaCa2 cells, WT, biol rep 3

description:
Library name: MiaPaCa2_WT_3
column name in MiaPaCa2_normCounts.txt: MiaPaCa2_WT_3


title: Dp16; High fat diet; Sample_T0_534134

description: Library name: T0_534134

value: liver

value: Male


title: BMAL1-1

description: Library name: BMAL1-1


title: naive_hPSCs_OTX2-OE-1 [RNA-Seq]

description: Library name: iOTX2-OE-4CL1


title: MIA PaCa2 cells, WT, biol rep 1

description:
Library name: MiaPaCa2_WT_1
column name in MiaPaCa2_normCounts.txt: MiaPaCa2_WT_1


title: Dp16; High fat diet; Sample_T5_531358

description: Library name: T5_531358

value: High fat diet


title: naive_hPSCs_WT-4 [RNA-Seq]

description: Library name: iOTX2-WT-4CL2


title: naive_hPSCs_WT-3 [RNA-Seq]

description: Library name: iOTX2-WT-4CL1


title: BM Ebf1+/-Pax5+/- proB CD25+, RNA-seq, rep4

city: Linköping

first: Mikael

last: Sigvardsson

address: Lab1, Level 13

department: Department of Biomedical and Clinical Sciences

institute: Linköping University

description: Library name: RNAseq_TH_BM_proB_CD25pos_rep4

data_processing:
RNA-seq data were preprocessed by trimming with TrimGalore (v0.6.4) –clip_R1/R2 15 –thre_prime_clip_R1/R2 3 (except for reanalysis of GSE122597 data: --length 20), followed by alignment to the mm10 mouse reference genome (GRCm38.p5.vM15) with STAR (v2.7.3) using the following options: --quantMode TranscriptomeSAM --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMstrandField intronMotif. Transcript levels were generated with rsem-calculate-expression in RSEM (v1.3.0), with the following options: --paired-end --alignments --output-genome-bam --sampling-for-bam --estimate-rspd --calc-ci (--paired-end omitted for single-end data).
Assembly: mm10
Supplementary files format and content: *Aligned.toTranscriptome.rsem.out.genes.results

source_name: BM proB CD25+

extract_protocol:
Up to 50.000 ex vivo sorted WT, Ebf1+/-, Pax5+/- and Ebf1+/-Pax5+/- (CD25-, CD25+ and total proB cell population) and sorted cells were spun down (800 x g, 5 min, 4 °C). Pellets were resuspended in 350 µl RLT (Qiagen, 74004) supplemented with 3.5 µl β-mercaptoethanol (ThermoFischer Scientific, 35602BID) and snap frozen on dry ice. RNA purification was performed with RNAeasy micro kit (Qiagen, 74004) and samples were eluted in 14 µl RNase-free water. 1 µl of each sample was used for quality control on Agilent 2100 Bioanalyser using the RNA 6000 Pico kit (Agilent, 5067-1513). SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (Takara Bio) was used for cDNA synthesis, followed by DNA purification with Ampure XP (Beckman-Coulter, A63881) and concentration measurement using Qubit® dsDNA HS Assay Kit & assay tubes (ThermoFisher Scientific, Q32854/Q32856). Quality of amplified cDNA were evaluated by running 1 µl of each sample on Agilent 2100 Bioanalyser with the High Sensitivity DNA Kit (Agilent, 5067-4626).
Libraries for sequencing were generated with Nextera XT DNA Library Preparation Kit (Illumina, FC-131-1024) using the Nextera XT Index Kit (Illumina, FC-131-1001) for indexing. Library quantification and quality control was performed with Qubit® dsDNA HS Assay Kit & assay tubes ThermoFisher Scientific, Q32854/Q32856) and Agilent 2100 Bioanalyser with the High Sensitivity DNA Kit (Agilent, 5067-4626). SMART-seq libraries were subject to 2x150 cycles of paired-end sequencing on a Nextseq2000 (Illumina) using NextSeq 2000 P3 Reagents (Illumina, 20040561).

value: BM proB CD25+


title: BM Ebf1+/-Pax5+/- proB CD25-, RNA-seq, rep4

description: Library name: RNAseq_TH_BM_proB_CD25neg_rep4

source_name: BM proB CD25-

value: BM proB CD25-


title: Dp16; High fat diet; Sample_T0_531084

description: Library name: T0_531084


title: Dp16; High fat diet; Sample_T1_531084

description: Library name: T1_531084


title: Dp16; High fat diet; Sample_T6_534140

description: Library name: T6_534140

value: Female


title: TLSCs_OTX2-OE-1 [RNA-Seq]

description: Library name: iOTX2-OE1

value: TLSCs

value: totipotent


title: TLSCs_OTX2-OE-2 [RNA-Seq]

description: Library name: iOTX2-OE2


title: BM Ebf1+/-Pax5+/- proB CD25-, RNA-seq, rep1

description: Library name: RNAseq_TH_BM_proB_CD25neg_rep1


title: BM Ebf1+/-Pax5+/- proB CD25-, RNA-seq, rep2

description: Library name: RNAseq_TH_BM_proB_CD25neg_rep2


title: BM Ebf1+/-Pax5+/- proB CD25-, RNA-seq, rep3

description: Library name: RNAseq_TH_BM_proB_CD25neg_rep3


title: TLSCs_DUX4-OE-1 [RNA-Seq]

description: Library name: WT-dux-toti1


title: BM Ebf1+/-Pax5+/- proB total, RNA-seq, rep2

description: Library name: RNAseq_TH_BM_proB_total_rep2

source_name: BM proB Total

value: BM proB Total


title: TLSCs_WT-4 [RNA-Seq]

description: Library name: iOTX2-WT2


title: BM Ebf1+/-Pax5+/- proB total, RNA-seq, rep4

description: Library name: RNAseq_TH_BM_proB_total_rep4


title: TLSCs_WT-3 [RNA-Seq]

description: Library name: iOTX2-WT1


title: BM Ebf1+/-Pax5+/- proB total, RNA-seq, rep3

description: Library name: RNAseq_TH_BM_proB_total_rep3


title: MIA PaCa2 cells, WT, biol rep 2

last: Frädrich

institute: TUM School of Medicine and Health

description:
Library name: MiaPaCa2_WT_2
column name in MiaPaCa2_normCounts.txt: MiaPaCa2_WT_2

value: MIA PaCa-2

value: WT


title: BM Ebf1+/-Pax5+/- proB total, RNA-seq, rep1

description: Library name: RNAseq_TH_BM_proB_total_rep1


title: Dp16; High fat diet; Sample_T9_534138

description: Library name: T9_534138


title: hPSCs_WT-4 [RNA-Seq]

last: Jiang

institute: southwest medical university

description: Library name: ndox-prime2

source_name: hPSCs

value: hPSCs

value: prime


title: Dp16; High fat diet; Sample_T4_531085

description: Library name: T4_531085


title: BM Pax5+/- proB, RNA-seq, rep3

description: Library name: RNAseq_Pax5het_BM_proB_rep3


title: BM Ebf1+/-Pax5+/- proB CD25+, RNA-seq, rep3

description: Library name: RNAseq_TH_BM_proB_CD25pos_rep3


title: Dp16; High fat diet; Sample_T4_531358

description: Library name: T4_531358


title: BM Pax5+/- proB, RNA-seq, rep2

description: Library name: RNAseq_Pax5het_BM_proB_rep2


title: hPSCs_WT-3 [RNA-Seq]

description: Library name: ndox-prime1


title: BM Ebf1+/- proB, RNA-seq, rep3

description: Library name: RNAseq_Ebf1het_BM_proB_rep3


title: BM Pax5+/- proB, RNA-seq, rep1

description: Library name: RNAseq_Pax5het_BM_proB_rep1


title: BM Ebf1+/- proB, RNA-seq, rep2

description: Library name: RNAseq_Ebf1het_BM_proB_rep2


title: hPSCs_OTX2-OE-2 [RNA-Seq]

description: Library name: pdox-prime2


title: Dp16; High fat diet; Sample_T5_534140

description: Library name: T5_534140


title: BM WT proB, RNA-seq, rep2

description: Library name: RNAseq_WT_BM_proB_rep2


title: BM Ebf1+/- proB, RNA-seq, rep1

description: Library name: RNAseq_Ebf1het_BM_proB_rep1


title: Dp16; Control diet; Sample_T1_532053

description: Library name: T1_532053

value: Control diet


title: BM WT proB, RNA-seq, rep3

description: Library name: RNAseq_WT_BM_proB_rep3


title: Dp16; Control diet; Sample_T2_531357

description: Library name: T2_531357


title: BM WT proB, RNA-seq, rep1

description: Library name: RNAseq_WT_BM_proB_rep1


title: Dp16; Control diet; Sample_T1_531357

description: Library name: T1_531357


title: TLSCs_OTX2-KO-2 [RNA-Seq]

description: Library name: OTX2-KO-toti2


title: TLSCs_OTX2-KO-1 [RNA-Seq]

description: Library name: OTX2-KO-toti1