title: ChIP-seq of hpl2 in condition N2, rep5

description:
rep5
hpl2_N2.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
hpl2_N2_merged.bwa_aln.rmdup.bamCompare.bw


title: THP-1-derived macrophage cells,  siNC_3

status: Public on Jun 30 2026

type: SRA

city: Nanjing

first: Tao

last: Gui

state: Jiangsu

address: NO.100 Shizi Street, Hongshan Road

country: China

institute: Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine

description:
Library name: siNC_3
RNA-seq

library_source: transcriptomic

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software.
The mapped reads of each sample were assembled by StringTie in a reference-based approach.
All the alternative splice events that occurred in our sample were identified by using recently releases program rMATS. Only the isoforms that were similar to the reference or comprised novel splice junctions were considered, and the splicing differences were detected as exon inclusion, exclusion, alternative 5′, 3′, and intron retention events.
Assembly: GRCh38
Supplementary files format and content: gene.TPM.matrix.xlsx

molecule: total RNA

organism: Homo sapiens

source_name: cell line

growth_protocol: THP-1-derived macrophage cells were maintained in RPMI 1640 medium supplemented with FBS in humidified atmosphere wwith 5% CO2 at 37°C

extract_protocol:
Total RNA was extracted from cultured cells using TRIzol reagent (Invitrogen, USA).
RNA-seq transcriptome librariy was prepared following Illumina® Stranded mRNA Prep, Ligation (San Diego, CA) using 1μg of total RNA.

treatment_protocol: THP-1-derived macrophage cells were transfected with NC siRNA or DUSP6 siRNA, respectively.

tag: tissue

value: cell line

tag: cell line

value: THP-1-derived macrophage cells

tag: cell type

value: macrophage

tag: genotype

value: WT

tag: treatment

value: transfectIion with NC siRNA

tag: time


title: US-Stretched (+peristalsis)

city: Los Angeles

first: Shannon

last: Mumenthaler

state: California

address: 12414 Exposition Blvd

department: Translational Research

country: USA

institute: Ellison Medical Institute

description:
Library name: Sample 5
Column name in bulk_RNA_normalized_counts.csv: EITB.000US.Chip.Stretch

data_processing:
Fastp was used for read quality evaluation and STAR was used for read alignment against GENCODE v39 annotation (GRCh38).  MutliQC was used to summarize sample statistics.  High-quality samples were selected based on duplication and alignment rate as well as PCA and correlation to remove outliers.
Assembly: GRCh38
Supplementary files format and content: gene count matrix as a CSV file

source_name: Colon Epithelial Organoid

extract_protocol:
Cells were lysed directly on chip using Lysis Buffer and RNA was isolated using the PureLink RNA Mini Kit
Sequencing libraries were generated by SMARTer Stranded Total RNAseq Kit - Pico Input Mammalian V3 (Takara Bio)

value: Colon Epithelial Organoid

value: (+peristalsis)


title: (KT10434) BW3446TWS-119 5uM +pep-14

city: Seattle

first: Allen Institute

last: For Immunology

state: Washington

address: 615 Westlake Ave N, Seattle, WA

institute: Allen Institute

description:
Library name: FIX10434-029
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

library_source: transcriptomic single cell

data_processing:
Multiplexed sequencing data were prepared using a preprocessing pipeline based on 10x Genomics CellRanger software using the Fixed RNA Profiling capability (version 9.0.1), with the 10x Genomics GRCh38/hg38 Human Transcriptome Reference (refdata-cellranger-GRCh38-3.0.0; based on the GRCh38 genome reference and Ensembl v93 transcriptome annotations; Released Nov. 19, 2018) to generate cell x UMI count matrices for each sample
Data from individual samples assembled across all wells were given a first pass of cell type labels using Seurat label transfer with reference to the PBMC dataset provided by the Satija Lab (Stuart and Butler, et al. (2019); DOI: 10.1016/j.cell.2019.05.031) and provided online with the Seurat PBMC scATAC-seq vignette (v 3.0; Compiled June 6, 2019).
scRNA counts matrices were normalized and scaled using Seurat. Cell populations were manually re-labelled via clustering using a combination of selected reference markers for each cell type. Doublets were identified and removed using Scrublet.
Assembly: Ensembl GRCh38-3.0.0
Supplementary files format and content: h5 files, gene expression matrix

source_name: Blood

growth_protocol: VST culture and fixation: Culture was performed using GREX-10, 6 well plates (Wilson Wolf), largely following a previously published rapid expansion protocol (Lazarski 2021). Briefly, PBMC were thawed, pelleted at 400 xg and resuspended in 2% BSA/PBS for counting. Cells were pelleted once again and resuspended at 1.5x107 cells per mL in CTL culture media including 300ng/mL each of CMV derived pp65 and IE-1 peptide pools (Peptivator, Milltenyi) or vehicle control (water). CTL culture media contained 44% RPMI, 44% Clicks, 10% FBS, 1% PenStrep, 1x Glutamax. Cells were incubated/pulsed for 1h at 37C. Following peptide pulse, cells were distributed into GREX-10 6 well plates containing 30mL total volume CTL media. Media was supplemented with IL4 (400U/mL), IL7, and/or IL15 (10ng/mL) as indicated. On day 7 of culture, the upper 15mL of media was carefully removed from each well without disturbing cells and replaced with 15mL fresh CTL media including 2x cytokine addition. If applicable, treatment with metabolic inhibitors UK5099 (Sigma), TWS-119 (Selleck Chem.) or vehicle/DMSO, was initiated on day 1 of culture. Further addition of inhibitors was done at 1x concentration and occurred only during day 7 media exchange. Individual wells were harvested at indicated timepoints during VST culture. Upon harvest, cells were washed 1x with cold 0.4% BSA/PBS followed by 1x with cold PBS alone prior to pelleting and resuspension in cold 10x fixation buffer per the standard FLEX protocol. Cells were counted and fixed at a maximum of 1x107 per mL fixation buffer. Fixation occurred for 20-26 hours at 4C. After fixation, cells were pelleted at 850 xg and resuspended in 1mL ice cold quenching buffer per 10x FLEX guideline. 10x Enhancer and 50% glycerol were added, prior to storage at -80°C, per 10x FLEX guidelines.

extract_protocol:
Single cells were encapsulated in Gel-Beads-in emulsion (GEMs) using the 10X Controller with a Chromium Single Cell FLEX GEM Library and Gel Bead kit.
REFLEX (Library prep, pre-amp): Following GEM incubation, 125 μL of Recovery Agent was added to break the GEM emulsion. Mixtures were inverted 10x and incubated for 2 minutes at room temperature. 125 μL of recovery agent was then carefully removed from the bottom of each well. The remaining approximately 65 μL of recovered GEM sample was combined with a master mix containing 27 μL of Amp Mix (10X PN-2000047), 10 μL of Pre-Amp Primers B (10XPN-20000529), 1.5 μL of TruSeq1 [1 μM], and 3 μL of a pre-mixed TCR Variable Primer Pool (See Supplemental Note [REF]) [0.66 μM] for a total volume of 106.5 μL of master mix plus recovered GEM. Samples were inverted 10x to mix and placed in a thermal cycler with the following cycling conditions: 98C for 3 minutes; 8 cycles of 98C/20 seconds, 60C for 30 seconds, 72C for 2 minutes; 72C for 5 minutes, 4C infinite hold. Upon completion of the PCR, tubes were pulsed briefly on a minifuge to collect liquid. 90 μL was then transferred into a new 1.5 mL Eppendorf tube. A 1.8X SPRI bead cleanup was performed and sample was eluted into 100 μL of elution solution in accordance with 10X User Guide CG000673 Rev B.
REFLEX (library prep, re-amplification): Pre-amplified library eluates were split into two or three pools for preparation of gene expression libraries,TCR libraries, and ADT libraries (when applicable). Gene expression and ADT libraries were prepared using 20uL pre-amp product and following 10x guidelines for Multiplexed samples with Feature Barcode technology for Protein using Barcode Oligo Capture (CG000673, Rev B). Linear PCR master mix for TCR libraries consisted of 20 μL 1X KAPA HiFi HotStart (Roche, KK260), 10 uL molecular biology grade water (Fisher, BP2819100), and 0.5 μL TruSeq2 primer at 123.4 nM per reaction. TCR libraries utilized 40 μL of pre-amp product total, divided into 4, 10 μL aliquots. Each 10 μL aliquot was combined with 30.5 μL master mix in a PCR strip tube and incubated with the following PCR program: 95C/3min activation, [98C/20s denaturation, 62C/30s annealing, 72C/90s extension] repeat x4 for 5 total cycles, 72C/5min final extension, hold 4C. After the 5 cycle linear PCR was completed, 0.5 μL TruSeq1, at 123.4 nM per reaction, was spiked into each reaction and an exponential PCR was performed with the following conditions: 95C/3 min activation, [98C/20s denaturation, 62C/30s annealing, 72C/90s extension] repeated x7 for 8 total cycles, 72C/5min final extension, hold 4C. Following exponential PCR, each of the four 41 μL reactions per library condition were repooled for a total volume of 164 μL. Samples were SPRI cleaned at 0.8X ratio, eluted in 50 μL aforementioned “elution solution ”.
REFLEX (Indexing TCR Libraries): PCR indexing master mix was prepared with 50 μL 1X Kapa HiFi HotStart and 10 μL molecular biology grade water per reaction. Indexing reactions combined 20 μL cleaned re-amplified product, 60 μL master mix, and 20 μL Dual Index TT Set A (10X Genomics, PN-1000215). Each library used a unique TT index well enabling later identification via sequencing. Samples were inverted to mix and briefly spun down. Thermocycler conditions used were as follows: 98C/45s activation [98C/20s denaturation, 54C/30s annealing, 72C/90s] repeated x12-15 for 13-16 total cycles, 72C/60s final extension, hold 4C. Cycle number was adjusted to account for cell input during GEM generation. A final SPRIselect bead clean up was performed at a 0.7X ratio with cleaned product eluted into 40 μL Buffer EB (Qiagen, Cat No. 19086).
REFLEX (Indexing GEX libraries): GEX library preparation was performed separately per 10x User Guide CG000673 Rev B, Sample Index PCR guidelines, Section 4.1, using 20 μL pre-amplification product with 60 μL Sample Index PCR Mix (Amp Mix PN-2000103, Water) and 20 μL of a unique well of Dual Index TS Set A primers (PN-3000511). The combined solution was gently mixed and spun down. PCR performed per the following guidelines: 98C/45s activate, [98C/20s denature, 54C/30s anneal, 72C/20s elongate] repeat 7-14x for a total 8 to 15 cycles, 72C/60s final extension, hold 4C. Cycle number was adjusted to account for cell input during GEM generation. Indexed products were cleaned using a 1.0X SPRIselect bead cleanup and eluted in 40 μL Buffer EB.
REFLEX (Indexing ADT libraries): ADT library preparation was performed separately per 10x User Guide CG000673 Rev B, Sample Index PCR guidelines, Section 5.1, using 20 μL pre-amplification product with 60 μL Sample Index PCR Mix (Amp Mix PN-2000103, Water) and 20 μL of a unique well of Dual Index TN Set A primers for the ADT libraries (10X, PN 1000250). The combined solution was gently mixed and spun down. PCR performed per the following guidelines: 98C/45s activate, [98C/20s denature, 54C/30s anneal, 72C/20s elongate] repeat 7-14x for a total 8 to 15 cycles, 72C/60s final extension, hold 4C. Cycle number was adjusted to account for cell input during GEM generation. Indexed products were cleaned using a 1.0X SPRIselect bead cleanup and eluted in 40 μL Buffer EB.
Sequencing: Final scRNAseq libraries were sequenced using a NovaSeq X 25B PE300 or NextSeq2000 P4 300 cycle flow cell, Read1:80 Read2:200. A read depth of 5000 reads per cell for TCR libraries or 10,000 reads per cell for GEX libraries was targeted. ADT or CITEseq libraries were targeted at 5000 reads per cell.

treatment_protocol: Cell Lines: Parental Jurkat T cells were originally purchased from ATCC and were transduced with pMW39 lentivirus (CXCR4 sgRNA) + pMW5 lentivirus (dCas9 ) by our group for use in other studies. No modifications were made to the native Jurkat TCR. The Raji CCL-86 cell line was purchased from ATCC.

value: Blood

value: PBMC

tag: subject id

tag: age at_blood_drawn

tag: Sex

value: Male

tag: ethnicity/race

value: Asian/Non-Hispanic Origin

tag: cmv stats

value: CMV+

tag: treatment time

tag: batch id

tag: pool id

value: PB

tag: batch pool

tag: probe barcode_id


title: ChIP-seq of hpl2 in condition N2, rep2

city: Toulouse

first: Olivier

last: Cuvier

address: 118 route de Narbonne

department: LBME

country: France

institute: CNRS

description:
rep2
hpl2_N2.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
hpl2_N2_merged.bwa_aln.rmdup.bamCompare.bw

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the C. elegans WBcel235 reference genome using BWA with default parameters.
Fragment length and quality assessments were performed using PyMASC.
MACS2 was employed for peak calling using -q 0.5 to lower the threshold of reported peaks. Peak calling results from different replicates within a given IP and condition were then filtered using ChIP-R to assess the irreproducible discovery rate (IDR).
ChIP-seq samples were normalized using their respective input controls with bamCompare (deepTools), applying specific parameters including --minMappingQuality 20, --binSize 10, --smoothLength 30, --extendReads, --scaleFactorsMethod readCount, --operation log2, and --pseudocount 1.
Assembly: WBcel235/ce11
Supplementary files format and content: macs2 peak calling filtered by chipr
Supplementary files format and content: Input normalised bigwig
Supplementary files format and content: Differential zscore bigwig

molecule: genomic DNA

organism: Caenorhabditis elegans

source_name: embryos

growth_protocol: C. elegans were cultured on nematode growth medium (NGM) plates seeded with E. coli OP50-1 according to Lewis and Fleming (1995). NGM plates supplemented with ten times excess peptone were employed for growing worms destined for Hi-C and ChIP-seq experiments. The wild-type strain used was N2. The C. elegans strains utilized, along with their genotypes, are as follows: lin-61(tm2649) (Koester-Eiserfunke and Fischle, 2011), hpl-2(tm1489) (Schott et al., 2006), set-32(red11); met-2(n4256) set-25(n5021) (Kalinava et al., 2017), and cec-4(ok3124) (Gonzalez-Sandoval et al., 2015). The hpl-2(I158A) allele was created using a CRISPR/Cas9 approach; further details can be provided upon request. The genotypes of all C. elegans strains were routinely confirmed by single-worm PCR.

extract_protocol:
ChIP was conducted with slight adjustments following the method described by Ercan et al. (2007). Post-crosslinking, C. elegans embryos underwent a wash with 100 mM Tris-HCl, pH 7.5, followed by two washes with FA buffer (50 mM HEPES-KOH, pH 7.5; 1 mM EDTA; 1% (v/v) Triton X-100; 0.1% (w/v) sodium deoxycholate; 150 mM NaCl; 1x protease inhibitor (cOmplete™, Sigma, Germany)). Nuclei were sheared as for Hi-C and then centrifuged at 13,000 xg for 15 minutes at 4°C to gather extracts. Immunoprecipitations were arranged using extracts equivalent to 3 mg along with 3–5 μg of antibodies in a total volume of 500 μL FA buffer. Prior to antibody addition, 10% of the reactions were kept aside as input. After 16 hours of incubation at 65°C with agitation, complexes were recovered by adding 20 μL of Protein A/G beads (Pierce™ Protein A/G Magnetic Beads, USA) and washed twice with FA buffer supplemented to 1 M NaCl, followed by two washes with FA buffer supplemented to 500 mM NaCl. Beads were treated with 1% (w/v) SDS in TE containing 250 mM NaCl at 65°C for 30 minutes to elute the complexes. Samples and inputs were treated with 2 μL of 10 mg/mL Proteinase K for 1 hour at 55°C. Decrosslinking was carried out at 65°C overnight in a thermomixer. DNA purification was executed with a PCR clean-up kit (Macherey-Nagel™, Germany) and quantified using Qubit Fluorometric Quantification. Library preparation followed the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB, USA) protocol. Libraries were sequenced on Novaseq 6000 PE150 S4 flow cells. Various antibodies were employed for ChIP experiments: anti-HPL-2 (Novus Biologicals 38630002), anti-LIN-61 (Novus Biologicals 29590002), anti-LEM-2 (Novus Biologicals 48540002), anti-H3K9me2 (Abcam ab1220), anti-H3K9me3 (VWR 309M3-B), anti-H3K4me1 (Abcam ab8895), anti-H3K4me3 (Active Motif 39159), anti-H3K27me3 (Abcam ab6002), and anti-H3K27ac (Active Motif Ab39133). All ChIP-seq experiments were conducted as biological independent triplicates.
Immunoprecipitation of C. elegans nuclear extracts utilized anti-LIN-61 (Novus Biologicals 29590002), anti-HPL-2 (Novus Biologicals 38630002), and anti-T7 (Abcam ab9138) antibodies. The antibodies were crosslinked to dynabeads M-280 sheep anti-rabbit IgG (Pierce, USA) overnight at 4°C on a nutator, following the manufacturer’s instructions. Unbound antibodies were removed by washing the beads with 1xPBS three times. Beads were then resuspended in 1 mL 0.2 M triethanolamine, pH 8.2, 20 mM DMP at room temperature for 60 minutes. Cross-linking was halted by adding 1 mL 50 mM Tris-HCL, pH 7.5, at room temperature for 60 minutes. After three washes with 1xPBS, 5 mg of total protein C. elegans extracts in 500 μL were added to the beads and incubated for 30 minutes at room temperature. Subsequently, beads underwent six washes with buffer D (each wash involving incubation with 1 mL buffer D for 5 minutes followed by centrifugation at 2000 xg for 1 minute at room temperature). Bound proteins were released from the beads in SDS-PAGE sample buffer by incubating at 95°C for 10 minutes. The proteins were resolved on SDS-PAGE and subjected to analysis by western blotting following standard procedures.

treatment_protocol: Crosslinking of C. elegans embryos and nuclei preparation followed the protocol outlined by Crane et al. (2015). Gravid adult worms were harvested and bleached to yield a late-stage embryo pellet of at least 1 or 4 mL for ChIP-seq or Hi-C experiments, respectively. The embryos underwent two washes in 1xPBS, were flash-frozen in liquid nitrogen, and stored at -80 °C. Thawed on ice, the embryos were then crosslinked in 50 mL of 2% (v/v) formaldehyde in PBS for 30 minutes at room temperature on a nutator. Subsequent to crosslinking, they were sequentially washed in 100 mM Tris-HCl, pH 7.5, twice in 1xPBS, and once in lysis buffer (10 mM Tris-HCl, pH 8.0; 10 mM NaCl; 0.2% (v/v) Igepal CA-630 (Sigma, Germany); 5 mM DTT; 0.5 mM EGTA; 1x protease inhibitor (cOmplete™, Sigma, Germany)). The embryos were then dounced 25 times with pestle A and 25 times with pestle B (PYREX® 7 mL Dounce Tissue Grinder, Corning, USA) while kept on ice. The resulting extract was centrifuged at 100 xg at 4 °C, and the supernatant containing nuclei was collected. This extraction process was repeated up to six times, with each supernatant checked for the presence of DAPI-stained nuclei under a fluorescence microscope. Supernatants containing pure nuclei were combined and centrifuged for 5 minutes at 2000 xg at 4 °C to collect material for further experimentation.

value: embryos


title: (KT10434) BW3446TWS-119 10uM +pep-13

description:
Library name: FIX10434-028
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture


title: THP-1-derived macrophage cells,  siNC_2

description:
Library name: siNC_2
RNA-seq


title: THP-1-derived macrophage cells,  siNC_1

description:
Library name: siNC_1
RNA-seq


title: (KT10435) BW2164Day 0-na

description:
Library name: FIX10435-030
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

value: Female

value: Other/ Non-Hispanic Origin

value: PA


title: UP-Stretched (+peristalsis)

description:
Library name: Sample 3
Column name in bulk_RNA_normalized_counts.csv: EITB.000UP.Chip.Stretch


title: ChIP-seq of H3K9me3 in condition N2, rep1

description:
rep1
H3K9me3_N2.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
H3K9me3_N2_merged.bwa_aln.rmdup.bamCompare.bw


title: PanCK+, PDAC2, MGC WO-003

city: Rozzano

first: Anna Rita

last: Putignano

state: Milano

address: Via Alessandro Manzoni, 56

country: Italy

institute: IRCCS Humanitas Research Hospital

description:
Library name: DSP-1001660021509-A-D02
PanCK+ AOI from PDAC patient PDAC2, slide: Slide2_Panck, ROI: PDAC2-MGC_WO-003, area: 50029.01 um2, nuclei: 328

data_processing:
For each AOI, digital count conversion (.dcc) files were generated from fastqs using the GeoMx NGS Pipeline (version 3.1.1).
From each tissue under investigation DCC files were read into a NanoStringGeoMxSet object using the readNanoStringGeoMxSet function from GeomxTools R package (version 3.5, R version 4.3.3), and segments were assessed for sequence quality.
After generating gene-level counts, segments with high fraction of genes detected below the limit of quantification (LOQ) were removed. Count matrix, sample annotations, and feature annotations were read into a SpatialExperiment object and analyzed with standR package (version 1.6) workflow.
Genes with low expression levels were removed. Counts were normalized using the upper-quartile method from the edgeR package (version 4.0.16).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files containing raw expression values for each AOI/sample
Supplementary files format and content: DCC files containing raw probe read counts for each AOI/sample; RTS_IDs are interpretable using the accompanying PKC file

source_name: pancreas

extract_protocol:
After deparaffinization and target retrieval, slides were incubated with 0.1 μg/mL proteinase K for 15 minutes at 37°C and then post fixed for 5 minutes in 10% neutral buffered formalin followed by two washes in NBF stop buffer (24.5 g Tris base and 15 g Glycine in 2 L DEPC water). Slides were incubated with the Whole Transcriptome Atlas (WTA) RNA Probe set (121401102, NanoString), according to the manufacturer’s protocol.
Following probe incubation, slides were washed and incubated with the morphology marker solution: AlexaFluor™ 647 anti-human CD68 (BL13756, 375606 BioLegend, 1:400, RRID:AB_3097193) plus SYTO 13 (provided in GeoMx Nuclear Stain Morphology Kit, 121300303, NanoString) for 1 hour at RT and processed through the GeoMx® Digital Spatial Profiler instrument. Regions of interest (ROIs) with a circular shape and a diameter of 600 μm were selected, with an average of 3 ROIs without MGCs and 5 ROIs with MGCs per patient. For each ROI, the CD68+ area of interest (AOI) was selected to collect barcodes in a 96-well plate. Barcoded oligonucleotides were prepared for Illumina-based sequencing to generate target probe-specific count files, which were then saved in a digital count conversion format.

value: pancreas

value: tumor cells


title: U0-Not Stretched (-peristalsis)

description:
Library name: Sample 2
Column name in bulk_RNA_normalized_counts.csv: EITB.000U0.Chip.NoStretch

value: (-peristalsis)


title: (KT10434) BW3446UK5099 50uM late -p-20

description:
Library name: FIX10434-036
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture


title: ChIP-seq of H3K9me2 in condition N2, rep2

description:
rep2
H3K9me2_N2.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
H3K9me2_N2_merged.bwa_aln.rmdup.bamCompare.bw


title: U0-Stretched (+peristalsis)

description:
Library name: Sample 1
Column name in bulk_RNA_normalized_counts.csv: EITB.000U0.Chip.Stretch


title: ChIP-seq of H3K9me2 in condition N2, rep1

description:
rep1
H3K9me2_N2.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
H3K9me2_N2_merged.bwa_aln.rmdup.bamCompare.bw


title: (KT10434) BW3446UK5099 50uM late +p-19

description:
Library name: FIX10434-035
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture


title: I329T-2 organoid

city: Seoul

first: Eun-Ji

last: Kwon

address: 1, Gwanak-ro

country: South Korea

institute: Seoul National University

description: Library name: Sample 4

data_processing:
Briefly, the strand-specific protocol included the following steps: (1) strand cDNA synthesis, (2) strand synthesis using dUTPs instead of dTTPs, (3) end repair, A-tailing, and adaptor ligation, and (4) PCR amplification. Each library was then diluted to 8 pM for 76 cycles of paired-read sequencing (2 × 75 bp) on an Illumina NextSeq 500 following the manufacturer’s recommended protocol.
Read quality was assessed using FastQC (v) and poor-quality bases (Phred score < 20) were eliminated using TrimGalore (v0.6.6)
Trimmed reads were aligned to the mouse reference genome (GRCm38) using the STAR aligner (v2.7.9a) with default parameters
Gene-level expression values such as transcripts per million (TPM) and read counts were calculated using RSEM (v1.3.3.) with human gene annotation (GRCh38.84)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include read count values for each Sample

growth_protocol: The section “Generation of neuromuscular organoids from human pluripotent stem cells” in the Methods provides a detailed description.

extract_protocol:
RNA was harvested using Easy-BLUETM RNA isolation kit (iNtRON Biotechnology) . 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA)

value: lymphoblast

value: I329T base editing


title: PanCK+, PDAC2, MGC W-005

description:
Library name: DSP-1001660021509-A-C11
PanCK+ AOI from PDAC patient PDAC2, slide: Slide2_Panck, ROI: PDAC2-MGC_W-005, area: 39689.34 um2, nuclei: 275


title: ChIP-seq of H3K4me3 in condition N2, rep2

description:
rep2
H3K4me3_N2.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
H3K4me3_N2_merged.bwa_aln.rmdup.bamCompare.bw


title: I329T-1 organoid

description: Library name: Sample 3


title: (KT10434) BW3446UK5099 25uM -pep-11

description:
Library name: FIX10434-026
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture


title: H9-2 organoid

description: Library name: Sample 2

value: WT


title: ChIP-seq of H3K27me3 in condition N2, rep2

description:
rep2
H3K27me3_N2.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
H3K27me3_N2_merged.bwa_aln.rmdup.bamCompare.bw


title: PanCK+, PDAC2, MGC W-003

description:
Library name: DSP-1001660021509-A-C09
PanCK+ AOI from PDAC patient PDAC2, slide: Slide2_Panck, ROI: PDAC2-MGC_W-003, area: 34064.87 um2, nuclei: 241


title: H9-1 organoid

description: Library name: Sample 1


title: ChIP-seq of H3K4me3 in condition N2, rep1

description:
rep1
H3K4me3_N2.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
H3K4me3_N2_merged.bwa_aln.rmdup.bamCompare.bw


title: PanCK+, PDAC2, MGC W-004

description:
Library name: DSP-1001660021509-A-C10
PanCK+ AOI from PDAC patient PDAC2, slide: Slide2_Panck, ROI: PDAC2-MGC_W-004, area: 42548.96 um2, nuclei: 303


title: PanCK+, PDAC2, MGC W-002

description:
Library name: DSP-1001660021509-A-C08
PanCK+ AOI from PDAC patient PDAC2, slide: Slide2_Panck, ROI: PDAC2-MGC_W-002, area: 45058.32 um2, nuclei: 238


title: (KT10434) BW3446UK5099 12.5uM +pep-9

description:
Library name: FIX10434-024
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture


title: HTR16/SVneo cells, pAKK+H/R

city: Beijing

first: Di

last: Liu

address: No. 45 West Street, Beijing

institute: Xuanwu Hospital, Capital Medical University

description: Library name: Sample 9

data_processing:
Fastqc was used to assess the quality of the reads. Fastp was used to trim low-quality bases and remove adapters.
Bowtie2 was used to map the reads to the hg19 reference genome.
SAMTools was used to convert, sort, and index the BAM files.
HTSeq was used to count the number of reads mapping to each gene.
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Trophoblast

growth_protocol: HTR-8/SVneo cells were cultured in RPMI 1640 medium (Procell, Wuhan, China), enriched with 10% FBS and antibiotics. The cultures were maintained in a humidified incubator at 37°C, 5% CO2.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qjagen),. 1.3 ug of total RNA w as used for the construction of sequencing libraries
RNA libraries for RNA-seg w ere prepared using SMARTER mRNA-Seg Library Prep Kifollow ing manufacturer's protocols

treatment_protocol: For the induction of a trophoblast cell model of PE, HTR-8/SVneo cells were subjected to hypoxic conditions (2% O2) at 37°C for 8 h, followed by a 16 h reoxygenation period with 5% CO2/air (H/R). To test the impact of pAKK, cells were pretreated with 1 × 108 CFU/mL pAKK in a fresh culture medium for 24 h, and then co-treat with 1 × 108 CFU/mL pAKK and H/R for 24 h.

value: Trophoblast

value: Human Villous Trophoblasts

value: pAKK+H/R


title: ChIP-seq of lin61 in condition met2-set25-set32, rep2

description:
rep2
lin61_met2-set25-set32.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
lin61_met2-set25-set32_merged.bwa_aln.rmdup.bamCompare.bw
lin61_met2-set25-set32_vs_N2_zscore.bwa_aln.rmdup.bamCompare.bw


title: PanCK+, PDAC2, MGC W-001

description:
Library name: DSP-1001660021509-A-C07
PanCK+ AOI from PDAC patient PDAC2, slide: Slide2_Panck, ROI: PDAC2-MGC_W-001, area: 38132.97 um2, nuclei: 150


title: (KT10434) BW3446UK5099 25uM +pep-8

description:
Library name: FIX10434-023
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

value: Blood

value: PBMC

value: Male


title: ChIP-seq of lin61 in condition met2-set25-set32, rep1

description:
rep1
lin61_met2-set25-set32.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
lin61_met2-set25-set32_merged.bwa_aln.rmdup.bamCompare.bw
lin61_met2-set25-set32_vs_N2_zscore.bwa_aln.rmdup.bamCompare.bw


title: PanCK+, PDAC5, MGC WO-003

description:
Library name: DSP-1001660021509-A-C06
PanCK+ AOI from PDAC patient PDAC5, slide: Slide4_Panck, ROI: PDAC5-MGC_WO-003, area: 40320.92 um2, nuclei: 271


title: HTR14/SVneo cells, pAKK+H/R

description: Library name: Sample 7


title: ChIP-seq of hpl2 in condition met2-set25-set32, rep3

description:
rep3
hpl2_met2-set25-set32.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
hpl2_met2-set25-set32_merged.bwa_aln.rmdup.bamCompare.bw
hpl2_met2-set25-set32_vs_N2_zscore.bwa_aln.rmdup.bamCompare.bw


title: PanCK+, PDAC5, MGC WO-002

description:
Library name: DSP-1001660021509-A-C05
PanCK+ AOI from PDAC patient PDAC5, slide: Slide4_Panck, ROI: PDAC5-MGC_WO-002, area: 21068.44 um2, nuclei: 92


title: (KT10434) BW3446DMSO -pep-6

description:
Library name: FIX10434-021
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

value: Asian/Non-Hispanic Origin

value: CMV+


title: HTR13/SVneo cells, H/R

description: Library name: Sample 6

value: H/R


title: ChIP-seq of hpl2 in condition met2-set25-set32, rep2

description:
rep2
hpl2_met2-set25-set32.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
hpl2_met2-set25-set32_merged.bwa_aln.rmdup.bamCompare.bw
hpl2_met2-set25-set32_vs_N2_zscore.bwa_aln.rmdup.bamCompare.bw

value: embryos


title: LPA4-KO, SNI, rep3

city: izunokuni mifuku

first: takahisa

last: shimoda

state: Shizuoka

country: Japan

institute: Asahi Kasei Pharma

description: Library name: sample15

data_processing:
Sequencing was conducted on the Illumina NovaSeq platform in paired-end mode (150 bp × 2) (performed by Takara Bio, Shiga, Japan).
Raw sequencing reads were subjected to quality control using fastp (v0.22.0).
High-quality reads were aligned to the rat reference genome (mRatBN7.2) using STAR aligner (v2.7.9a).
Gene-level counts and transcripts per million (TPM) were calculated using RSEM (v1.3.1).
Assembly: mRatBN7.2
Supplementary files format and content: CSV (Comma-Separated Values) file includes raw counts for each sample

molecule: polyA RNA

organism: Rattus norvegicus

source_name: spinal dorsal horn

extract_protocol:
Total RNA was purified using the Monarch Total RNA Miniprep Kit (Catalog # NEB #T2110, New England Biolabs, Ipswich, MA, USA) .
Total RNA was processed for sequencing using the TruSeq Stranded mRNA Sample Preparation Kit (Illumina, San Diego, CA, USA).

value: spinal dorsal horn


title: PanCK+, PDAC5, MGC WO-001

description:
Library name: DSP-1001660021509-A-C04
PanCK+ AOI from PDAC patient PDAC5, slide: Slide4_Panck, ROI: PDAC5-MGC_WO-001, area: 10091.64 um2, nuclei: 14

value: pancreas


title: ChIP-seq of H3K9me3 in condition N2, rep2

description:
rep2
H3K9me3_N2.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
H3K9me3_N2_merged.bwa_aln.rmdup.bamCompare.bw


title: UP-Not Stretched (-peristalsis)

description:
Library name: Sample 4
Column name in bulk_RNA_normalized_counts.csv: EITB.000UP.Chip.NoStretch

value: Colon Epithelial Organoid


title: (KT10434) BW3446Std -pep-5

description:
Library name: FIX10434-020
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

value: PA


title: ChIP-seq of H3K9me3 in condition met2-set25-set32, rep3

description:
rep3
H3K9me3_met2-set25-set32.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
H3K9me3_met2-set25-set32_merged.bwa_aln.rmdup.bamCompare.bw
H3K9me3_met2-set25-set32_vs_N2_zscore.bwa_aln.rmdup.bamCompare.bw


title: HTR12/SVneo cells, H/R

description: Library name: Sample 5


title: neurons,WT,week18,male,rep3 (9771_H3K4me2)

city: Philadelphia

first: Matthew

last: Edwards

state: PA

address: 450 Clinical Research Building

department: Genetics

institute: University of Pennsylvania School of Medicine

description: Library name: 9771_H3K4me2

data_processing:
CUT&Tag profiles for all four histone marks were trimmed using Cutadapt and aligned to the mm10 using bowtie2.  Reads were then centered and extended to represent the full DNA fragment, and were normalized using base-pair normalization with the Deeptools BamCoverage function.
Assembly: mm10
Supplementary files format and content: Bigwig tracks of histone modifications after BPM normalization
Library strategy: CUT&Tag

organism: Mus musculus

source_name: Cortex

extract_protocol:
Cut&Tag was used to profile H3K4me3, H3K4me2, H3K4me1 and H3K27ac in eighteen-week-old cortical neurons. The CUT&Tag-direct V.3 protocol31,32 were performed with minor modifications. For each sample, 50,000 GFP⁺/NeuN⁺ excitatory neuron nuclei were bound to Concanavalin-A beads (3.5 µL bead slurry per reaction) and incubated with primary antibodies (1:50 dilution) overnight at 4°C: H3K4me1 (EpiCypher #13-0057), H3K4me2 (EpiCypher #13-0027), H3K4me3 (Active Motif #39159), or H3K27ac (Active Motif #39133). After washing, bead-bound nuclei were incubated with guinea pig anti-rabbit secondary antibody for 30 min at room temperature. Protein A–Tn5 transposome (pAG-Tn5; EpiCypher #15-1117) was added (2.5 µL per reaction) and incubated for 1 hr at room temperature, followed by tagmentation at 37°C for 1 hour.Tagmented chromatin was released by incubation with 0.1% SDS at 58°C for 1 hr and neutralized with 0.67% Triton-X100.
Libraries were amplified using NEBNext High-Fidelity 2× PCR Master Mix (non-hot-start) (NEBNext #M0541L) with unique dual indexes (Buenrostro-style i7/i5 indexing) for 11–12 cycles depending on mark abundance. PCR products were cleaned with 1.3× SPRI bead purification, eluted in 13.2 µL, and assessed by Qubit and Bioanalyzer.

value: Cortex

value: In vivo

value: Excitatory neurons

value: wild-type

tag: batch


title: PanCK+, PDAC5, MGC W-005

description:
Library name: DSP-1001660021509-A-C03
PanCK+ AOI from PDAC patient PDAC5, slide: Slide4_Panck, ROI: PDAC5-MGC_W-005, area: 23551.81 um2, nuclei: 64

tag: tissue

value: tumor cells


title: (KT10434) BW3446Std -pep-4

description:
Library name: FIX10434-019
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture


title: (KT10434) BW3446Day 0-na

description:
Library name: FIX10434-038
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture


title: HTR11/SVneo cells, H/R

description: Library name: Sample 4

value: Trophoblast

tag: cell line

value: Human Villous Trophoblasts

value: WT


title: ChIP-seq of H3K9me3 in condition met2-set25-set32, rep2

description:
rep2
H3K9me3_met2-set25-set32.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
H3K9me3_met2-set25-set32_merged.bwa_aln.rmdup.bamCompare.bw
H3K9me3_met2-set25-set32_vs_N2_zscore.bwa_aln.rmdup.bamCompare.bw


title: LPA4-KO, WT, rep2

description: Library name: sample10


title: (KT10434) BW3446DMSO +pep-3

description:
Library name: FIX10434-018
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

value: Blood

tag: cell type

value: PBMC

value: Male


title: PanCK+, PDAC2, MGC WO-001

description:
Library name: DSP-1001660021509-A-C12
PanCK+ AOI from PDAC patient PDAC2, slide: Slide2_Panck, ROI: PDAC2-MGC_WO-001, area: 25267.77 um2, nuclei: 221


title: PanCK+, PDAC5, MGC W-004

description:
Library name: DSP-1001660021509-A-C02
PanCK+ AOI from PDAC patient PDAC5, slide: Slide4_Panck, ROI: PDAC5-MGC_W-004, area: 6094.23 um2, nuclei: 17


title: PanCK+, PDAC2, MGC WO-002

description:
Library name: DSP-1001660021509-A-D01
PanCK+ AOI from PDAC patient PDAC2, slide: Slide2_Panck, ROI: PDAC2-MGC_WO-002, area: 112900.09 um2, nuclei: 825


title: HTR10/SVneo cells, PBS

description: Library name: Sample 3

tag: genotype

value: PBS


title: (KT10434) BW3446Std +pep-2

description:
Library name: FIX10434-017
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

tag: treatment

value: Asian/Non-Hispanic Origin

value: CMV+


title: (KT10434) BW3446UK5099 12.5uM -pep-12

description:
Library name: FIX10434-027
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture


title: ChIP-seq of H3K9me2 in condition met2-set25-set32, rep3

description:
rep3
H3K9me2_met2-set25-set32.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
H3K9me2_met2-set25-set32_merged.bwa_aln.rmdup.bamCompare.bw
H3K9me2_met2-set25-set32_vs_N2_zscore.bwa_aln.rmdup.bamCompare.bw

value: embryos


title: PanCK+, PDAC5, MGC W-003

description:
Library name: DSP-1001660021509-A-C01
PanCK+ AOI from PDAC patient PDAC5, slide: Slide4_Panck, ROI: PDAC5-MGC_W-003, area: 5696.58 um2, nuclei: 8

value: pancreas


title: HTR9/SVneo cells, PBS

description: Library name: Sample 2


title: ChIP-seq of H3K9me2 in condition met2-set25-set32, rep2

description:
rep2
H3K9me2_met2-set25-set32.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
H3K9me2_met2-set25-set32_merged.bwa_aln.rmdup.bamCompare.bw
H3K9me2_met2-set25-set32_vs_N2_zscore.bwa_aln.rmdup.bamCompare.bw


title: PanCK+, PDAC5, MGC W-002

description:
Library name: DSP-1001660021509-A-B12
PanCK+ AOI from PDAC patient PDAC5, slide: Slide4_Panck, ROI: PDAC5-MGC_W-002, area: 6240.19 um2, nuclei: 32


title: (KT10434) BW3446Std +pep-1

description:
Library name: FIX10434-016
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

value: PA


title: HTR8/SVneo cells, PBS

description: Library name: Sample 1


title: BW2164- Day 10-IL15/7-Pep-

description:
Library name: FIX10435-015
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

value: Female

value: Other/ Non-Hispanic Origin

value: PC


title: PanCK+, PDAC5, MGC W-001

description:
Library name: DSP-1001660021509-A-B11
PanCK+ AOI from PDAC patient PDAC5, slide: Slide4_Panck, ROI: PDAC5-MGC_W-001, area: 7790.69 um2, nuclei: 61


title: Sample 22_bdd 7 b

city: Bonn

first: Muhammad Ahmer

last: Jamil

state: NRW

address: Sigmund-Freud Str. 25

department: Institute of experimental haematology and transfusion medicine

country: Germany

institute: University Clinic Bonn

data_processing:
Fastqc was used for quality analysis of the sequences. Cutadapt was used to remove the illumina universal adapter sequence in the reads. miARma-seq pipeline was used for further analysis. Tophat2 with bowtie algorithm was used as a mapper whereas gtf file of genome build HG38 from ensemble was used as annotation file. Read counts were generated from miARma-seq and Qlucore omics explorer 3.6 was used to convert read counts into expression value. Trimmed mean of M-values (TMM) normalization was performed using Qlucore Omics explorer 3.5, where the same gtf file was used to annotate genes. Gene with less than five read counts per sample were removed.
Assembly: hg38
Supplementary files format and content: tab delimited text file included TMM normalized values for each sample with ensemble gene id with chromosome and external gene names

source_name: Embryonic Kidney

growth_protocol: HEK28 specialized cell line with B-Domain Deleted Factor VIII and Full length Factor VIII were cultured until about 70% confluency in six well plates

extract_protocol:
RNA was purified using the PureLink™ RNA mini kit according to manufacturer’s instructions (Invitrogen 12183018A) from the collected cell pellets.
The concentration of the RNA was determined by measuring absorbance at 260 nm using NanoDrop One (ThermoFisher Scientific).
RNA samples of different cell clones were then sequenced on ILLUMINA sequencer. Raw reads files of different cell clones were generated using Illumina Hi-Seq 4000 as fastq files

treatment_protocol: No treatment

value: Embryonic Kidney

value: human embryonic kidney 293 cells

value: B-domain deleted FVIII


title: neurons,WT,week18,male,rep2 (9768_H3K4me3)

description: Library name: 9768_H3K4me3

value: Cortex

value: In vivo

value: Excitatory neurons

value: wild-type


title: ChIP-seq of lin61 in condition lin61, rep2

description:
rep2
lin61_lin61.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
lin61_lin61_merged.bwa_aln.rmdup.bamCompare.bw
lin61_lin61_vs_N2_zscore.bwa_aln.rmdup.bamCompare.bw


title: PanCK+, PDAC4, MGC WO-005

description:
Library name: DSP-1001660021509-A-B10
PanCK+ AOI from PDAC patient PDAC4, slide: Slide1_Panck, ROI: PDAC4-MGC_WO-005, area: 29363.29 um2, nuclei: 304

value: tumor cells


title: ChIP-seq of LEM2 in condition lin61, rep2

description:
rep2
LEM2_lin61.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
LEM2_lin61_merged.bwa_aln.rmdup.bamCompare.bw
LEM2_lin61_vs_N2_zscore.bwa_aln.rmdup.bamCompare.bw


title: (KT10434) BW3446UK5099 50uM -pep-10

description:
Library name: FIX10434-025
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

value: Blood

value: PBMC

value: Male


title: Sample 21_FL 9  a

value: Full length FVIII


title: PanCK+, PDAC4, MGC WO-004

description:
Library name: DSP-1001660021509-A-B09
PanCK+ AOI from PDAC patient PDAC4, slide: Slide1_Panck, ROI: PDAC4-MGC_WO-004, area: 17186.41 um2, nuclei: 75

value: pancreas


title: BW2164- Day 10-IL15/7-Pep+

description:
Library name: FIX10435-014
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

value: CMV+


title: ChIP-seq of lin61 in condition lin61, rep1

description:
rep1
lin61_lin61.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
lin61_lin61_merged.bwa_aln.rmdup.bamCompare.bw
lin61_lin61_vs_N2_zscore.bwa_aln.rmdup.bamCompare.bw

value: embryos


title: BW2164- Day 10-IL4/7--Pep-

description:
Library name: FIX10435-013
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

value: Female

value: Other/ Non-Hispanic Origin


title: ChIP-seq of H3K27me3 in condition N2, rep1

description:
rep1
H3K27me3_N2.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
H3K27me3_N2_merged.bwa_aln.rmdup.bamCompare.bw


title: Sample 20_bdd 13 b

value: Embryonic Kidney


title: ChIP-seq of LEM2 in condition lin61, rep1

description:
rep1
LEM2_lin61.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
LEM2_lin61_merged.bwa_aln.rmdup.bamCompare.bw
LEM2_lin61_vs_N2_zscore.bwa_aln.rmdup.bamCompare.bw


title: PanCK+, PDAC4, MGC WO-003

description:
Library name: DSP-1001660021509-A-B08
PanCK+ AOI from PDAC patient PDAC4, slide: Slide1_Panck, ROI: PDAC4-MGC_WO-003, area: 29357.27 um2, nuclei: 285


title: BW2164- Day 10-IL4/7--Pep+

description:
Library name: FIX10435-012
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

value: PC


title: Sample 19_bdd 1 a

value: human embryonic kidney 293 cells

value: B-domain deleted FVIII


title: PanCK+, PDAC4, MGC WO-002

description:
Library name: DSP-1001660021509-A-B07
PanCK+ AOI from PDAC patient PDAC4, slide: Slide1_Panck, ROI: PDAC4-MGC_WO-002, area: 38036.14 um2, nuclei: 323


title: ChIP-seq of hpl2 in condition lin61, rep2

description:
rep2
hpl2_lin61.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
hpl2_lin61_merged.bwa_aln.rmdup.bamCompare.bw
hpl2_lin61_vs_N2_zscore.bwa_aln.rmdup.bamCompare.bw


title: ChIP-seq of hpl2 in condition lin61, rep1

description:
rep1
hpl2_lin61.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
hpl2_lin61_merged.bwa_aln.rmdup.bamCompare.bw
hpl2_lin61_vs_N2_zscore.bwa_aln.rmdup.bamCompare.bw


title: BW2164-Day 7-IL15/7-Pep+

description:
Library name: FIX10435-010
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture


title: Sample 17_oldbdd 2 b


title: ChIP-seq of H3K9me3 in condition lin61, rep2

description:
rep2
H3K9me3_lin61.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
H3K9me3_lin61_merged.bwa_aln.rmdup.bamCompare.bw
H3K9me3_lin61_vs_N2_zscore.bwa_aln.rmdup.bamCompare.bw


title: Sample 18_FL 4 b


title: PanCK+, PDAC4, MGC W-008

description:
Library name: DSP-1001660021509-A-B05
PanCK+ AOI from PDAC patient PDAC4, slide: Slide1_Panck, ROI: PDAC4-MGC_W-008, area: 39532.75 um2, nuclei: 469


title: ChIP-seq of H3K9me3 in condition lin61, rep1

description:
rep1
H3K9me3_lin61.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
H3K9me3_lin61_merged.bwa_aln.rmdup.bamCompare.bw
H3K9me3_lin61_vs_N2_zscore.bwa_aln.rmdup.bamCompare.bw


title: Sample 16_bdd 12 a


title: PanCK+, PDAC4, MGC W-007

description:
Library name: DSP-1001660021509-A-B04
PanCK+ AOI from PDAC patient PDAC4, slide: Slide1_Panck, ROI: PDAC4-MGC_W-007, area: 27985.39 um2, nuclei: 200


title: BW2164-Day 7-IL4/7--Pep+

description:
Library name: FIX10435-008
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture


title: Sample 15_FL 9 b


title: Sample 14_HEK 28 a


title: PanCK+, PDAC4, MGC W-006

description:
Library name: DSP-1001660021509-A-B03
PanCK+ AOI from PDAC patient PDAC4, slide: Slide1_Panck, ROI: PDAC4-MGC_W-006, area: 31953.48 um2, nuclei: 237


title: BW2164-Day 4-IL15/7-Pep+

description:
Library name: FIX10435-006
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture


title: Sample 13_bdd 27 a


title: PanCK+, PDAC4, MGC W-005

description:
Library name: DSP-1001660021509-A-B02
PanCK+ AOI from PDAC patient PDAC4, slide: Slide1_Panck, ROI: PDAC4-MGC_W-005, area: 48767.28 um2, nuclei: 282


title: ChIP-seq of lin61 in condition I158A, rep2

description:
rep2
lin61_I158A.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
lin61_I158A_merged.bwa_aln.rmdup.bamCompare.bw
lin61_I158A_vs_N2_zscore.bwa_aln.rmdup.bamCompare.bw


title: PanCK+, PDAC4, MGC W-004

description:
Library name: DSP-1001660021509-A-B01
PanCK+ AOI from PDAC patient PDAC4, slide: Slide1_Panck, ROI: PDAC4-MGC_W-004, area: 21500.96 um2, nuclei: 96


title: ChIP-seq of H3K9me2 in condition lin61, rep1

description:
rep1
H3K9me2_lin61.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
H3K9me2_lin61_merged.bwa_aln.rmdup.bamCompare.bw
H3K9me2_lin61_vs_N2_zscore.bwa_aln.rmdup.bamCompare.bw


title: Sample 12_bdd 1 b


title: ChIP-seq of lin61 in condition I158A, rep1

description:
rep1
lin61_I158A.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
lin61_I158A_merged.bwa_aln.rmdup.bamCompare.bw
lin61_I158A_vs_N2_zscore.bwa_aln.rmdup.bamCompare.bw


title: BW2164-Day 4-IL4/7--Pep-

description:
Library name: FIX10435-005
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture


title: PanCK+, PDAC4, MGC W-003

description:
Library name: DSP-1001660021509-A-A12
PanCK+ AOI from PDAC patient PDAC4, slide: Slide1_Panck, ROI: PDAC4-MGC_W-003, area: 26516.98 um2, nuclei: 150


title: Sample 11_FL 7 a


title: BW2164-Day 4-IL4/7--Pep+

description:
Library name: FIX10435-004
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture


title: ChIP-seq of LEM2 in condition I158A, rep2

description:
rep2
LEM2_I158A.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
LEM2_I158A_merged.bwa_aln.rmdup.bamCompare.bw
LEM2_I158A_vs_N2_zscore.bwa_aln.rmdup.bamCompare.bw


title: BW2164-Day 0

description:
Library name: FIX10435-003
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture


title: Sample 10_bdd 12 b


title: ChIP-seq of LEM2 in condition I158A, rep1

description:
rep1
LEM2_I158A.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
LEM2_I158A_merged.bwa_aln.rmdup.bamCompare.bw
LEM2_I158A_vs_N2_zscore.bwa_aln.rmdup.bamCompare.bw


title: PanCK+, PDAC4, MGC W-002

description:
Library name: DSP-1001660021509-A-A11
PanCK+ AOI from PDAC patient PDAC4, slide: Slide1_Panck, ROI: PDAC4-MGC_W-002, area: 16035.78 um2, nuclei: 155


title: PanCK+, PDAC4, MGC W-001

description:
Library name: DSP-1001660021509-A-A10
PanCK+ AOI from PDAC patient PDAC4, slide: Slide1_Panck, ROI: PDAC4-MGC_W-001, area: 18860.37 um2, nuclei: 123


title: BW2164-Day 7-IL7/15--Pep-

description:
Library name: FIX10435-002
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture


title: Sample 9_FL 10 a


title: ChIP-seq of hpl2 in condition I158A, rep3

description:
rep3
hpl2_I158A.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
hpl2_I158A_merged.bwa_aln.rmdup.bamCompare.bw
hpl2_I158A_vs_N2_zscore.bwa_aln.rmdup.bamCompare.bw


title: BW2164 - Day 7-IL7/15--Pep+

description:
Library name: FIX10435-001
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture


title: Sample 8_HEK 28 b


title: ChIP-seq of hpl2 in condition I158A, rep2

description:
rep2
hpl2_I158A.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
hpl2_I158A_merged.bwa_aln.rmdup.bamCompare.bw
hpl2_I158A_vs_N2_zscore.bwa_aln.rmdup.bamCompare.bw


title: Foxa1_Input_rep1

city: Basel

first: Prisca

last: Liberali

address: Klingelbergstrasse 48

department: D-BSSE

country: Switzerland

institute: ETHZ

description: Library name: Foxa1_Input_rep1

data_processing:
Illumina RTA 3.4.4 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing. All analyses, unless stated otherwise, were performed within R (version 4.3.2) and Bioconductor (version 3.18) (14). ChIP-seq read pairs were aligned to the GRCm38/mm10 mouse genome assembly using the qAlign function from the QuasR package (Gaidatzis et al., Bioinformatics 2015) with default parameters.
BigWig files with alignment fragment coverage along the genome were generated from the bam files using bedtools version 2.30, by first extracting a bed file with fragment coordinates (bedtools bamtobed), calculating genome coverage in a bedGraph file (bedtools genomecov) and then converting it to BigWig format using bedGraphToBigWig from KentTools version 442.
Assembly: GRCm38/mm10
Supplementary files format and content: bigwig files with alignment fragment coverage along the genome

source_name: mouse small intestinal organoids

growth_protocol: Organoids were generated from isolated crypts of mice, as previously described (Sato et al.,Nature 2009). Maintenance of organoid cultures was performed in ENR medium (advanced DMEM/F-12 with 15mM HEPES (STEM CELL Technologies) supplemented with 100 μg/ml Penicillin and Streptomycin, 1×Glutamax (Thermo Fisher Scientific), 1×B27 (Thermo Fisher Scientific), 1xN2 (Thermo Fisher Scientific), 1mM N-acetylcysteine (Sigma), 500ng/ml R-Spondin (kind gift from Novartis), 100 ng/ml Noggin (PeproTech) and 100 ng/ml murine EGF (R&D Systems)).

extract_protocol:
A total of 10⁷ cells were crosslinked for 8 minutes at room temperature in 10 mL PBS supplemented with 1% formaldehyde (Sigma, F8775). The reaction was quenched by adding glycine to a final concentration of 0.125 mM. Cells were pelleted by centrifugation at 500 × g for 3 minutes at 4°C, washed once with PBS, pelleted again, flash-frozen in liquid nitrogen, and stored until further processing.
30µL of a 1:1 mixture of Protein A/G Dynabeads (Invitrogen, 10002D and 10004D) was pre-coupled with 3 µL of FOXA1 antibody (ab170933) for 1 hour at room temperature, followed by three washes with 1× ChIP buffer and stored on ice until use. The cells were lysed in 10 mL of buffer A (50 mM HEPES pH 8.0, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100) on ice for 10 minutes. After centrifugation, the pellet was resuspended in 5 mL of buffer B (10 mM Tris pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 200 mM NaCl) and incubated on ice for 5 minutes. Nuclei were pelleted by centrifugation at 500 × g for 3 minutes at 4°C, resuspended in 150 µL of buffer C (50 mM Tris pH 8.0, 5 mM EDTA, 1% SDS, 100 mM NaCl), and incubated on ice for 10 minutes. TE buffer (1.3 mL) was then added, and chromatin was sheared in 15 mL tubes using a Bioruptor Pico device for two sessions of 10 cycles (30 seconds ON / 30 seconds OFF). After shearing, 160 µL of 10× ChIP buffer (0.1% SDS, 10% Triton X-100, 12 mM EDTA, 167 mM Tris-HCl pH 8.0, 1.67 M NaCl) was added. The chromatin was transferred to fresh tubes and centrifuged at 13,000 × g for 10 minutes at 4°C. Per sample, 30 µL of 1:1 pre-coupled beads were added to the chromatin, and the mixture was incubated with rotation for 4 hours at 4°C. The ChIP samples were washed four times with LSB (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate), twice with HSB (same as LSB but with 500 mM NaCl), twice with LiSB (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 250 mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate), and once with TE+ buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 50 mM NaCl). During the final wash, beads were transferred to fresh tubes, and the wash buffer was completely removed. DNA was eluted twice from the beads using 75 µL of elution buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 150 mM NaCl, 1% SDS) by incubation at 65˚C with shaking. The eluates were pooled, and 2 µL of RNase A (20 µg/µL) was added, followed by incubation for 1 hour at 37°C. Input samples were adjusted to a total volume of 150 µL with elution buffer and processed in the same manner as ChIP samples. Proteinase K (2 µL, 20 mg/mL) was added, and samples were incubated for 2 hours at 55°C and then for 6 hours at 65°C. Afterward, 9 µL of 5 M NaCl, 30 µL of AMPure XP beads, and 190 µL of isopropanol were added. Samples were vigorously mixed, incubated at room temperature for 10 minutes, and the beads were collected on a magnetic rack. The beads were washed twice with 80% ethanol, and DNA was eluted in 30 µL of 10 mM Tris-HCl pH 8.0 for 5 minutes at 37°C. For library preparation, 25 µL of ChIP DNA or 50 ng of input DNA was used with the NEBNext Ultra II Library Prep Kit for Illumina (NEB), following the manufacturer’s protocol but with reactions scaled down to half-volume. Libraries were sequenced on the NovaSeq 6000 platform (Illumina) with paired-end reads (2x 56 bp).

value: mouse small intestinal organoids

tag: strain

value: intestinal epithelial cells

value: Lgr5::DTR-EGFP (Genentech, de Sauvage laboratory)

tag: chip antibody


title: PanCK+, PDAC3, MGC WO-002

description:
Library name: DSP-1001660021509-A-A08
PanCK+ AOI from PDAC patient PDAC3, slide: Slide3_Panck, ROI: PDAC3-MGC_WO-002, area: 20093.74 um2, nuclei: 404

value: tumor cells


title: BW3446- Day 10-IL15/7-Pep-

description:
Library name: FIX10434-015
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

value: Blood

tag: subject id

tag: age at_blood_drawn

value: Asian/Non-Hispanic Origin

value: PB


title: ChIP-seq of H3K9me3 in condition I158A, rep2

description:
rep2
H3K9me3_I158A.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
H3K9me3_I158A_merged.bwa_aln.rmdup.bamCompare.bw
H3K9me3_I158A_vs_N2_zscore.bwa_aln.rmdup.bamCompare.bw


title: Sample 7_bdd 27 b


title: BW3446- Day 10-IL15/7-Pep+

description:
Library name: FIX10434-014
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

value: PBMC

tag: Sex

value: Male

tag: ethnicity/race


title: Sample 6_bdd 7 a


title: PanCK+, PDAC3, MGC WO-001

description:
Library name: DSP-1001660021509-A-A07
PanCK+ AOI from PDAC patient PDAC3, slide: Slide3_Panck, ROI: PDAC3-MGC_WO-001, area: 41274.86 um2, nuclei: 343

value: pancreas


title: ChIP-seq of H3K9me3 in condition I158A, rep1

description:
rep1
H3K9me3_I158A.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
H3K9me3_I158A_merged.bwa_aln.rmdup.bamCompare.bw
H3K9me3_I158A_vs_N2_zscore.bwa_aln.rmdup.bamCompare.bw

value: embryos


title: BW3446- Day 10-IL4/7--Pep-

description:
Library name: FIX10434-013
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

tag: cmv stats

value: CMV+

tag: treatment time


title: ChIP-seq of H3K9me2 in condition I158A, rep2

description:
rep2
H3K9me2_I158A.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
H3K9me2_I158A_merged.bwa_aln.rmdup.bamCompare.bw
H3K9me2_I158A_vs_N2_zscore.bwa_aln.rmdup.bamCompare.bw


title: BW3446- Day 10-IL4/7--Pep+

description:
Library name: FIX10434-012
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

tag: batch id

tag: pool id


title: Sample 4_bdd 13 a


title: ChIP-seq of LEM2 in condition hpl2-lin61, rep2

description:
rep2
LEM2_hpl2-lin61.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
LEM2_hpl2-lin61_merged.bwa_aln.rmdup.bamCompare.bw
LEM2_hpl2-lin61_vs_N2_zscore.bwa_aln.rmdup.bamCompare.bw


title: PanCK+, PDAC3, MGC W-003

description:
Library name: DSP-1001660021509-A-A04
PanCK+ AOI from PDAC patient PDAC3, slide: Slide3_Panck, ROI: PDAC3-MGC_W-003, area: 33679.75 um2, nuclei: 302


title: BW3446-Day 7-IL15/7-Pep-

description:
Library name: FIX10434-011
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

tag: batch pool

tag: probe barcode_id


title: Sample 3_FL 10 b

tag: tissue

value: Full length FVIII


title: ChIP-seq of LEM2 in condition hpl2-lin61, rep1

description:
rep1
LEM2_hpl2-lin61.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
LEM2_hpl2-lin61_merged.bwa_aln.rmdup.bamCompare.bw
LEM2_hpl2-lin61_vs_N2_zscore.bwa_aln.rmdup.bamCompare.bw


title: PanCK+, PDAC3, MGC W-002

description:
Library name: DSP-1001660021509-A-A03
PanCK+ AOI from PDAC patient PDAC3, slide: Slide3_Panck, ROI: PDAC3-MGC_W-002, area: 11145.91 um2, nuclei: 95


title: BW3446-Day 7-IL15/7-Pep+

description:
Library name: FIX10434-010
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture


title: Sample 2_FL 4 a

value: Embryonic Kidney

tag: cell line


title: ChIP-seq of hpl2 in condition hpl2-lin61, rep2

description:
rep2
hpl2_hpl2-lin61.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
hpl2_hpl2-lin61_merged.bwa_aln.rmdup.bamCompare.bw
hpl2_hpl2-lin61_vs_N2_zscore.bwa_aln.rmdup.bamCompare.bw


title: PanCK+, PDAC3, MGC W-001

description:
Library name: DSP-1001660021509-A-A02
PanCK+ AOI from PDAC patient PDAC3, slide: Slide3_Panck, ROI: PDAC3-MGC_W-001, area: 14624.75 um2, nuclei: 103

tag: cell type


title: BW3446-Day 7-IL4/7--Pep-

description:
Library name: FIX10434-009
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture


title: Sample 30_HEK par #3

data_processing:
Fastqc was used for quality analysis of the sequences. Cutadapt was used to remove the illumina universal adapter sequence in the reads. miARma-seq pipeline as used for further analysis, tophat2 with bowtie algorithm was used as a mapper whereas gtf file of genome build HG38 from ensemble was used as annotation file. Read counts were generated from miARma-seq and Qlucore omics explorer 3.6 was used to convert read counts into expression value. Trimmed mean of M-values (TMM) normalization was performed using Qlucore Omics explorer 3.5, same gtf file was used to annotate genes. Gene with less than 5 read counts in a sample were removed, also if gene is not expressed in both replicates of a sample were also removed.
Assembly: hg38
Supplementary files format and content: tab delimited text file included TMM normalized values for each sample and have ensembl gene Ids and gene symbols

growth_protocol: Different cell line with specific knockouts where cultured until about 70% confluency in six well plates

extract_protocol:
RNA was purified using the PureLink™ RNA mini kit according to manufacturer’s instructions (Invitrogen 12183018A) from the collected cell pellets
The concentration of the RNA was determined by measuring absorbance at 260 nm using NanoDrop One (ThermoFisher Scientific). The RNA and subjected to the Illumina sequencing protocol
3' RNA-seq (Illumina HiSeq 2500 V4 platform)

tag: genotype

value: WT-HEKpar

value: WT


title: PanCK+, PDAC4, MGC WO-001

description:
Library name: DSP-1001660021509-A-B06
PanCK+ AOI from PDAC patient PDAC4, slide: Slide1_Panck, ROI: PDAC4-MGC_WO-001, area: 27887.76 um2, nuclei: 391


title: ChIP-seq of hpl2 in condition hpl2-lin61, rep1

description:
rep1
hpl2_hpl2-lin61.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
hpl2_hpl2-lin61_merged.bwa_aln.rmdup.bamCompare.bw
hpl2_hpl2-lin61_vs_N2_zscore.bwa_aln.rmdup.bamCompare.bw

tag: treatment


title: No Template Control, run_3

description:
Library name: DSP-1001660021509-A-A01
No Template Control (NTC) , run: run_3

source_name: No Template Control

value: No Template Control


title: BW2164-Day 7-IL4/7--Pep-

description:
Library name: FIX10435-009
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

value: Female

value: Other/ Non-Hispanic Origin

value: PC


title: Sample 29_HEK par #2

value: human embryonic kidney 293 cells


title: ChIP-seq of H3K9me3 in condition hpl2-lin61, rep2

description:
rep2
H3K9me3_hpl2-lin61.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
H3K9me3_hpl2-lin61_merged.bwa_aln.rmdup.bamCompare.bw
H3K9me3_hpl2-lin61_vs_N2_zscore.bwa_aln.rmdup.bamCompare.bw


title: BW3446-Day 7-IL4/7--Pep+

description:
Library name: FIX10434-008
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

value: Blood


title: ChIP-seq of H3K9me2 in condition lin61, rep2

description:
rep2
H3K9me2_lin61.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
H3K9me2_lin61_merged.bwa_aln.rmdup.bamCompare.bw
H3K9me2_lin61_vs_N2_zscore.bwa_aln.rmdup.bamCompare.bw


title: CD68+, PDAC2, MGC W-009

description:
Library name: DSP-1001660035205-B-C09
CD68+ AOI from PDAC patient PDAC2, slide: CD68_Slide10, ROI: PDAC2-MGC_W-009, area: 53740.67 um2, nuclei: 207

value: macrophages


title: BW3446-Day 4-IL15/7-Pep-

description:
Library name: FIX10434-007
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

value: Asian/Non-Hispanic Origin

value: PB


title: ChIP-seq of H3K9me3 in condition hpl2-lin61, rep1

description:
rep1
H3K9me3_hpl2-lin61.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
H3K9me3_hpl2-lin61_merged.bwa_aln.rmdup.bamCompare.bw
H3K9me3_hpl2-lin61_vs_N2_zscore.bwa_aln.rmdup.bamCompare.bw


title: BW3446-Day 4-IL15/7-Pep+

description:
Library name: FIX10434-006
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

value: PBMC

value: Male


title: Sample 28_HEK par #1


title: CD68+, PDAC2, MGC W-008

description:
Library name: DSP-1001660035205-B-C08
CD68+ AOI from PDAC patient PDAC2, slide: CD68_Slide10, ROI: PDAC2-MGC_W-008, area: 58380.6 um2, nuclei: 307

value: pancreas


title: Sample 27_HEK 28 #3


title: BW3446-Day 4-IL4/7--Pep-

description:
Library name: FIX10434-005
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

value: CMV+


title: CD68+, PDAC2, MGC W-007

description:
Library name: DSP-1001660035205-B-C07
CD68+ AOI from PDAC patient PDAC2, slide: CD68_Slide10, ROI: PDAC2-MGC_W-007, area: 55183.56 um2, nuclei: 187


title: BW2164-Day 4-IL15/7-Pep-

description:
Library name: FIX10435-007
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture


title: Sample 26_HEK 28 #2


title: ChIP-seq of H3K9me2 in condition hpl2-lin61, rep2

description:
rep2
H3K9me2_hpl2-lin61.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
H3K9me2_hpl2-lin61_merged.bwa_aln.rmdup.bamCompare.bw
H3K9me2_hpl2-lin61_vs_N2_zscore.bwa_aln.rmdup.bamCompare.bw

value: embryos


title: ChIP-seq of H3K9me2 in condition hpl2-lin61, rep1

description:
rep1
H3K9me2_hpl2-lin61.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
H3K9me2_hpl2-lin61_merged.bwa_aln.rmdup.bamCompare.bw
H3K9me2_hpl2-lin61_vs_N2_zscore.bwa_aln.rmdup.bamCompare.bw


title: BW3446-Day 4-IL4/7--Pep+

description:
Library name: FIX10434-004
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture


title: CD68+, PDAC2, MGC W-006

description:
Library name: DSP-1001660035205-B-C06
CD68+ AOI from PDAC patient PDAC2, slide: CD68_Slide10, ROI: PDAC2-MGC_W-006, area: 51131.31 um2, nuclei: 176


title: Sample 25_HEK 28 #1

value: Embryonic Kidney


title: ChIP-seq of lin61 in condition hpl2, rep2

description:
rep2
lin61_hpl2.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
lin61_hpl2_merged.bwa_aln.rmdup.bamCompare.bw
lin61_hpl2_vs_N2_zscore.bwa_aln.rmdup.bamCompare.bw


title: CD68+, PDAC2, MGC W-005

description:
Library name: DSP-1001660035205-B-C05
CD68+ AOI from PDAC patient PDAC2, slide: CD68_Slide10, ROI: PDAC2-MGC_W-005, area: 75579.69 um2, nuclei: 379


title: stomach, day7, GEX, rep2

city: TORONTO

first: Adrian

middle: Kwan Ho

last: Loe

state: ON

address: 686 Bay Street

country: Canada

institute: The Hospital for Sick Children

description: 10x Genomics

data_processing:
cellranger-arc-2.0.1
Assembly: GRCm39/mm39
Supplementary files format and content: CellRanger output files: mRNA_barcodes.tsv.gz, mRNA_features.tsv.gz, mRNA_matrix.mtx.gz
Supplementary files format and content: CellRanger output file: ATAC_fragment.tsv.gz
Supplementary files format and content: Text files include UMAP embedding
Supplementary files format and content: Text files include metadata

molecule: nuclear RNA

source_name: stomach

extract_protocol:
Single cells were encapsulated in GEMS using the 10X Chromium controller with the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle, 4 rxns PN-1000285
Chromium Next GEM Single Cell Multiome ATAC + Gene Expression (CG000338 Rev C)

value: stomach

value: wildtype

value: High dose tamoxifen, 7 days

tag: library type

value: mRNA


title: Sample 24_#96 GABA SKO - #3

value: KO-GABA

value: CRISPR-KO


title: ChIP-seq of lin61 in condition hpl2, rep1

description:
rep1
lin61_hpl2.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
lin61_hpl2_merged.bwa_aln.rmdup.bamCompare.bw
lin61_hpl2_vs_N2_zscore.bwa_aln.rmdup.bamCompare.bw


title: CD68+, PDAC2, MGC W-004

description:
Library name: DSP-1001660035205-B-C04
CD68+ AOI from PDAC patient PDAC2, slide: CD68_Slide10, ROI: PDAC2-MGC_W-004, area: 63048.9 um2, nuclei: 297


title: BW3446-Day 0

description:
Library name: FIX10434-003
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture


title: BW3446-Day 7-IL7/15--Pep-

description:
Library name: FIX10434-002
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture


title: Sample 23_#96 GABA SKO - #2

value: human embryonic kidney 293 cells


title: ChIP-seq of LEM2 in condition hpl2, rep2

description:
rep2
LEM2_hpl2.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
LEM2_hpl2_merged.bwa_aln.rmdup.bamCompare.bw
LEM2_hpl2_vs_N2_zscore.bwa_aln.rmdup.bamCompare.bw


title: CD68+, PDAC2, MGC W-003

description:
Library name: DSP-1001660035205-B-C03
CD68+ AOI from PDAC patient PDAC2, slide: CD68_Slide10, ROI: PDAC2-MGC_W-003, area: 65577.28 um2, nuclei: 265


title: BW3446 - Day 7-IL7/15--Pep+

description:
Library name: FIX10434-001
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

value: Blood


title: PanCK+, PDAC3, MGC WO-003

description:
Library name: DSP-1001660021509-A-A09
PanCK+ AOI from PDAC patient PDAC3, slide: Slide3_Panck, ROI: PDAC3-MGC_WO-003, area: 60781.87 um2, nuclei: 414

value: tumor cells


title: Sample 22_#96 GABA SKO - #1


title: ChIP-seq of LEM2 in condition hpl2, rep1

description:
rep1
LEM2_hpl2.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
LEM2_hpl2_merged.bwa_aln.rmdup.bamCompare.bw
LEM2_hpl2_vs_N2_zscore.bwa_aln.rmdup.bamCompare.bw


title: CD68+, PDAC2, MGC W-002

description:
Library name: DSP-1001660035205-B-C02
CD68+ AOI from PDAC patient PDAC2, slide: CD68_Slide10, ROI: PDAC2-MGC_W-002, area: 63586.02 um2, nuclei: 204

value: macrophages


title: KT08836- Day 10-IL15/7-Pep-

description:
Library name: FIX08836-018
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

value: Asian/Non-Hispanic Origin

value: PA


title: neurons,WT,week18,female,rep2 (504_H3K4me3)

description: Library name: 504_H3K4me3

value: Cortex

value: In vivo

value: Excitatory neurons

value: wild-type

tag: batch


title: Sample 21_#89 MCFD2 SKO - #3

value: Embryonic Kidney


title: stomach, day7, GEX, rep1

description: 10x Genomics

value: stomach


title: ChIP-seq of H3K9me3 in condition hpl2, rep2

description:
rep2
H3K9me3_hpl2.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
H3K9me3_hpl2_merged.bwa_aln.rmdup.bamCompare.bw
H3K9me3_hpl2_vs_N2_zscore.bwa_aln.rmdup.bamCompare.bw

value: embryos


title: CD68+, PDAC2, MGC W-010

description:
Library name: DSP-1001660035205-B-C01
CD68+ AOI from PDAC patient PDAC2, slide: CD68_Slide10, ROI: PDAC2-MGC_W-010, area: 56569.55 um2, nuclei: 195

value: pancreas


title: KT08836- Day 10-IL15/7-Pep+

description:
Library name: FIX08836-017
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

value: PBMC

tag: subject id

value: Male

value: CMV+


title: ChIP-seq of H3K9me3 in condition hpl2, rep1

description:
rep1
H3K9me3_hpl2.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
H3K9me3_hpl2_merged.bwa_aln.rmdup.bamCompare.bw
H3K9me3_hpl2_vs_N2_zscore.bwa_aln.rmdup.bamCompare.bw


title: KT08836- Day 10-IL4/7--Pep-

description:
Library name: FIX08836-016
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

tag: age at_blood_drawn


title: Sample 19_#89 MCFD2 SKO - #1

value: human embryonic kidney 293 cells

value: CRISPR-KO


title: ChIP-seq of H3K9me2 in condition hpl2, rep2

description:
rep2
H3K9me2_hpl2.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
H3K9me2_hpl2_merged.bwa_aln.rmdup.bamCompare.bw
H3K9me2_hpl2_vs_N2_zscore.bwa_aln.rmdup.bamCompare.bw


title: CD68+, PDAC2, MGC W-001

description:
Library name: DSP-1001660035205-B-B12
CD68+ AOI from PDAC patient PDAC2, slide: CD68_Slide10, ROI: PDAC2-MGC_W-001, area: 58693.3 um2, nuclei: 217


title: KT08836- Day 10-IL4/7--Pep+

description:
Library name: FIX08836-015
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

value: Blood

tag: Sex


title: CD68+, PDAC2, MGC WO-006

description:
Library name: DSP-1001660035205-B-B11
CD68+ AOI from PDAC patient PDAC2, slide: CD68_Slide10, ROI: PDAC2-MGC_WO-006, area: 14775.31 um2, nuclei: 78

value: macrophages


title: Sample 18_#83 CALR SKO - #3

value: KO-CALR


title: CD68+, PDAC2, MGC WO-005

description:
Library name: DSP-1001660035205-B-B10
CD68+ AOI from PDAC patient PDAC2, slide: CD68_Slide10, ROI: PDAC2-MGC_WO-005, area: 13492.66 um2, nuclei: 66


title: KT08836-Day 7-IL15/7-Pep-

description:
Library name: FIX08836-014
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

tag: ethnicity/race

value: Asian/Non-Hispanic Origin

value: PA


title: ChIP-seq of H3K9me2 in condition hpl2, rep1

description:
rep1
H3K9me2_hpl2.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
H3K9me2_hpl2_merged.bwa_aln.rmdup.bamCompare.bw
H3K9me2_hpl2_vs_N2_zscore.bwa_aln.rmdup.bamCompare.bw


title: CD68+, PDAC2, MGC WO-004

description:
Library name: DSP-1001660035205-B-B09
CD68+ AOI from PDAC patient PDAC2, slide: CD68_Slide10, ROI: PDAC2-MGC_WO-004, area: 35556.89 um2, nuclei: 171


title: ChIP-seq of lin61 in condition CEC4, rep2

description:
rep2
lin61_CEC4.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
lin61_CEC4_merged.bwa_aln.rmdup.bamCompare.bw
lin61_CEC4_vs_N2_zscore.bwa_aln.rmdup.bamCompare.bw


title: KT08836-Day 7-IL15/7-Pep+

description:
Library name: FIX08836-013
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

tag: cmv stats


title: Sample 16_#83 CALR SKO - #1


title: CD68+, PDAC2, MGC WO-003

description:
Library name: DSP-1001660035205-B-B08
CD68+ AOI from PDAC patient PDAC2, slide: CD68_Slide10, ROI: PDAC2-MGC_WO-003, area: 16228.5 um2, nuclei: 68


title: ChIP-seq of lin61 in condition CEC4, rep1

description:
rep1
lin61_CEC4.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
lin61_CEC4_merged.bwa_aln.rmdup.bamCompare.bw
lin61_CEC4_vs_N2_zscore.bwa_aln.rmdup.bamCompare.bw


title: KT08836-Day 7-IL4/7--Pep-

description:
Library name: FIX08836-012
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

tag: treatment time


title: ChIP-seq of hpl2 in condition CEC4, rep3

description:
rep3
hpl2_CEC4.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
hpl2_CEC4_merged.bwa_aln.rmdup.bamCompare.bw
hpl2_CEC4_vs_N2_zscore.bwa_aln.rmdup.bamCompare.bw


title: KT08836-Day 7-IL4/7--Pep+

description:
Library name: FIX08836-011
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

tag: batch id


title: CD68+, PDAC2, MGC WO-002

description:
Library name: DSP-1001660035205-B-B07
CD68+ AOI from PDAC patient PDAC2, slide: CD68_Slide10, ROI: PDAC2-MGC_WO-002, area: 19406.37 um2, nuclei: 53


title: Sample 15_#60 ATG 7 SKO - #3


title: Sample 13_#60 ATG 7 SKO - #1


title: KT08836-Day 4-IL15/7-Pep-

description:
Library name: FIX08836-010
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

tag: pool id


title: CD68+, PDAC3, MGC W-005

description:
Library name: DSP-1001660035205-B-B05
CD68+ AOI from PDAC patient PDAC3, slide: CD68_Slide12, ROI: PDAC3-MGC_W-005, area: 11039.72 um2, nuclei: 22


title: CD68+, PDAC2, MGC WO-001

description:
Library name: DSP-1001660035205-B-B06
CD68+ AOI from PDAC patient PDAC2, slide: CD68_Slide10, ROI: PDAC2-MGC_WO-001, area: 32686.02 um2, nuclei: 100


title: Sample 12_#36 GABA L1 SKO -#3


title: ChIP-seq of H3K9me3 in condition CEC4, rep1

description:
rep1
H3K9me3_CEC4.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
H3K9me3_CEC4_merged.bwa_aln.rmdup.bamCompare.bw
H3K9me3_CEC4_vs_N2_zscore.bwa_aln.rmdup.bamCompare.bw


title: KT08836-Day 4-IL15/7-Pep+

description:
Library name: FIX08836-009
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

tag: batch pool


title: Sample 11_#36 GABA L1 SKO -#2


title: ChIP-seq of H3K9me2 in condition CEC4, rep2

description:
rep2
H3K9me2_CEC4.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
H3K9me2_CEC4_merged.bwa_aln.rmdup.bamCompare.bw
H3K9me2_CEC4_vs_N2_zscore.bwa_aln.rmdup.bamCompare.bw


title: CD68+, PDAC3, MGC W-003

description:
Library name: DSP-1001660035205-B-B03
CD68+ AOI from PDAC patient PDAC3, slide: CD68_Slide12, ROI: PDAC3-MGC_W-003, area: 30281.26 um2, nuclei: 91


title: KT08836-Day 4-IL4/7--Pep-

description:
Library name: FIX08836-008
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

tag: probe barcode_id


title: ChIP-seq of H3K9me2 in condition CEC4, rep1

description:
rep1
H3K9me2_CEC4.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
H3K9me2_CEC4_merged.bwa_aln.rmdup.bamCompare.bw
H3K9me2_CEC4_vs_N2_zscore.bwa_aln.rmdup.bamCompare.bw

tag: tissue


title: KT08836-Day 4-IL4/7--Pep+

description:
Library name: FIX08836-007
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture


title: Sample 14_#60 ATG 7 SKO - #2

tag: cell line


title: CD68+, PDAC3, MGC W-002

description:
Library name: DSP-1001660035205-B-B02
CD68+ AOI from PDAC patient PDAC3, slide: CD68_Slide12, ROI: PDAC3-MGC_W-002, area: 26650.75 um2, nuclei: 109

tag: cell type


title: KT08836-Day 0

description:
Library name: FIX08836-006
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture


title: Sample 9_#29 LMAN1 SKO - #3

tag: genotype


title: CD68+, PDAC3, MGC W-001

description:
Library name: DSP-1001660035205-B-B01
CD68+ AOI from PDAC patient PDAC3, slide: CD68_Slide12, ROI: PDAC3-MGC_W-001, area: 50520.81 um2, nuclei: 176


title: KT08836 -Day 7-IL7/15--Pep-

description:
Library name: FIX08836-005
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

tag: treatment


title: met-2 set-25 set-32 Celegans late stage embryos-replicate2

data_processing:
RNA-seq reads were aligned to the Caenorhabditis elegans reference genome (WBcel235/ce11) using the STAR aligner with default parameters
featureCounts was utilized to generate raw count matrices from aligned reads.
Within the DESeq2 framework, size factors were estimated to account for differences in library depth and sequencing run variations.
Low count genes (<10 in each samples) were filtered out to improve the robustness and accuracy of the statistical analysis.
DE gene were filtered out using pval <= 0.005 and qval <= 0.1
Assembly: ce11/WBcel235
Supplementary files format and content: bigwig and DESeq2 results

source_name: late stage embryos

extract_protocol:
C. elegans RNA was extracted as described (Green and Sambrook, 2020). Briefly, late stage embryos were collected from worms grown on five NGM plates and flash frozen in liquid N2. The frozen pellet was grinded to a fine powder and dissolved in ten volumes of TRIzol™ (Invitrogen, USA). Total RNA was isolated according to the manufacturer’s protocol, flash frozen in liquid N2 and stored at -80 °C. For RNA-seq, library preparation and sequencing were performed by Novogene (Novogene Co, Hong Kong).
Poly-T oligo-attached magnetic beads (NEB Oligo d(T)25 Magnetic Beads, S1419S) were used to purify mRNA from total RNA. Random hexamer primers were used to synthesize first-strand cDNA (included in the library preparation kit), followed by second-strand cDNA synthesis using dUTP for strand-specific libraries. NEBNext® Ultra™II Directional RNA Library Prep Kit(Cat No. E7760) was used for library preparation. Qubit (Thermo fisher scientific) and real-time PCR were used for quantification and quality control. The size distribution of the library was analyzed using Agilent bioanalyzer (2100). Quantified libraries were pooled and sequenced on Illumina NovaSeq 6000 PE150 platform.

value: late stage embryos


title: Sample 8_#29 LMAN1 SKO - #2


title: KT08836 - Day 7-IL7/15--Pep+

description:
Library name: FIX08836-004
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture


title: Sample 7_#29 LMAN1 SKO - #1


title: lin-61 hpl-2 Celegans late stage embryos-replicate2


title: CD68+, PDAC3, MGC WO-002

description:
Library name: DSP-1001660035205-B-A11
CD68+ AOI from PDAC patient PDAC3, slide: CD68_Slide12, ROI: PDAC3-MGC_WO-002, area: 13735.15 um2, nuclei: 98


title: Long-Bridge RT Probe Test BC016

description:
Library name: FIX08824-016
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

value: Female

value: Caucasian/Non-Hispanic

value: Unknown


title: Sample 6_#108 GABA L2 SKO - #3

value: Embryonic Kidney


title: lin-61 Celegans late stage embryos-replicate2


title: CD68+, PDAC3, MGC WO-001

description:
Library name: DSP-1001660035205-B-A10
CD68+ AOI from PDAC patient PDAC3, slide: CD68_Slide12, ROI: PDAC3-MGC_WO-001, area: 16203.14 um2, nuclei: 113


title: Long-Bridge RT Probe Test BC015

description:
Library name: FIX08824-015
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture


title: Sample 5_#108 GABA L2 SKO - #2


title: hpl-2I158A Celegans late stage embryos-replicate2


title: CD68+, PDAC1, MGC W-005

description:
Library name: DSP-1001660035205-B-A09
CD68+ AOI from PDAC patient PDAC1, slide: CD68_Slide9, ROI: PDAC1-MGC_W-005, area: 36756.65 um2, nuclei: 111


title: Long-Bridge RT Probe Test BC014

description:
Library name: FIX08824-014
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture


title: Sample 4_#108 GABA L2 SKO - #1


title: CD68+, PDAC1, MGC W-004

description:
Library name: DSP-1001660035205-B-A08
CD68+ AOI from PDAC patient PDAC1, slide: CD68_Slide9, ROI: PDAC1-MGC_W-004, area: 59613.81 um2, nuclei: 287


title: Long-Bridge RT Probe Test BC013

description:
Library name: FIX08824-013
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture


title: hpl-2 Celegans late stage embryos-replicate2


title: CD68+, PDAC1, MGC W-003

description:
Library name: DSP-1001660035205-B-A07
CD68+ AOI from PDAC patient PDAC1, slide: CD68_Slide9, ROI: PDAC1-MGC_W-003, area: 59047.68 um2, nuclei: 218


title: N2 Celegans late stage embryos-replicate1


title: Long-Bridge RT Probe Test BC012

description:
Library name: FIX08824-012
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture


title: met-2 set-25 set-32 Celegans late stage embryos-replicate1


title: CD68+, PDAC1, MGC W-002

description:
Library name: DSP-1001660035205-B-A06
CD68+ AOI from PDAC patient PDAC1, slide: CD68_Slide9, ROI: PDAC1-MGC_W-002, area: 38239.48 um2, nuclei: 134


title: Long-Bridge RT Probe Test BC011

description:
Library name: FIX08824-011
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture


title: lin-61 hpl-2 Celegans late stage embryos-replicate1


title: Sample 1_#105 CANX SKO - #1

value: KO-CANX


title: Long-Bridge RT Probe Test BC010

description:
Library name: FIX08824-010
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture


title: CD68+, PDAC1, MGC W-001

description:
Library name: DSP-1001660035205-B-A05
CD68+ AOI from PDAC patient PDAC1, slide: CD68_Slide9, ROI: PDAC1-MGC_W-001, area: 42738.51 um2, nuclei: 246

value: pancreas


title: Yeast, no drug, no MTX, time0

city: Montreal

middle: W R

last: Serohijos

state: QC

address: 5155 Chem. de la Rampe

department: Department of Biochemistry

institute: University of Montreal

data_processing:
*library strategy: DNA barcode sequencing
Demultiplexing: Using AdapterRemoval (version 2.3.2), we allowed at most 2 mismatches within the inner-adapters (--barcode-mm-r1 = 2 and --barcode-mm-r2 = 2) to account for mutations that could arise from PCR and/or NGS.
Barcode extracting: Extracting the strains barcodes from the reads using the command bartender_extractor_com of Bartender (version 1.1)
Barcode mapping: we mapped extracted barcodes to the 361 unique strains using in-house Python scripts (https://github.com/ladyson1806/SerohijosLab-piQTL).
Assembly: not applicable
Supplementary files format and content: comma-separated files contain the read numbers of the barcoded strains under the specified conditions.

organism: Saccharomyces cerevisiae

source_name: in house yeast library

growth_protocol: 40 μL of frozen cells (~4 x 10^5 cells) were inoculated into 760 μL SD media (minimal synthetic defined bases, 2% glucose, 120 mg/L Leucine) in 96 deep-well plates. The cells were grown at 30°C for 96 hours and passaged every 24 hours at a ratio of 1:8 (100 μL of cultured cells were added into 700 μL of fresh media).

extract_protocol:
To extract the gDNA, the cell pellets were resuspended in 300 μL of 50 mM EDTA containing 1 unit of Zymolyase (US Biological Life Sciences). We centrifuged the mixtures at 1,900 x g for 10 minutes after incubating them for 30 to 60 minutes at 37°C. By aspirating the supernatant, we removed the excess liquid. Next, we added 200 μL of lysis buffer (2% Triton X-100, 1% SDS, 100 mM NaCl, 10% Tris-HCl, 1 mM EDTA, pH 8), 2 μL of RNaseA, and 2 μL of protease K, and incubated for 10 minutes at 55 °C. The samples were vortexed, centrifuged at 1,900 x g for 10 minutes, and 200 μL of the supernatant was then transferred to fresh deep-well plates with 600 μL of 100% ethanol in each well. The samples were kept at room temperature for 15 minutes, then centrifuged at 1,900 x g for 10 minutes at 4°C, discarding the supernatant. We next obtained the isolated genome pellets, washed them using 150 liters of 70% ethanol, and centrifuged them at 1,900 x g for 10 minutes at 4°C. We removed the supernatant and let the pellet air dry at 60 °C for 5-10 minutes. The pellets were rehydrated for an hour at 65°C after being dissolved in 40 μL of TE.
Strain barcodes were amplified from the extracted genomic DNA in a two-step PCR. The first PCR was performed using PrimeSTAR GXL polymerase and 1:2000 SYBR Green I (20 μL/reaction) with 2 μL of extracted genomic DNA per reaction as a template. Because the concentrations of extracted genomic DNA varied, the number of PCR cycles was first determined by qPCR; the number of PCR cycles was chosen such that the amplification curve reached the mid to late log-linear phase (typically ~24 cycles). The PCR amplification conditions were one cycle of 98°C for 3 min (initiation), followed by amplification cycles of 98°C for 10 sec, 55°C for 15 sec, and 68°C for 30 sec, repeated until the amplification curve reached the mid to late log-linear phase. The PCR products were pooled per growth media condition and purified with DNA Clean & Concentrator (Zymo Research). The second PCR was performed using PrimeSTAR GXL polymerase with 5 ng of purified product from the previous PCR was used as a template (50 μL/reaction). Primers were unique pairs of index primers (i5 and i7) from the Nextera XT DNA library preparation kit (Illumina). The PCR amplification conditions were one cycle of 98°C for 45 sec, then 12 cycles each of 98°C for 10 s, 55°C for 15 s, and 68°C for 30 s. The second PCR products were purified using Agencourt AMPure XP PCR purification kit (Beckman Coulter). We performed pair-end sequencing on Illumina NextSeq platforms with 30% balanced DNA (phiX).

treatment_protocol: For drug treatments, the following concentrations of drugs were added to the growth medium: 10 μg/mL methotrexate (MTX), 0.2 μM 5-FC, 100 μM fluconazole, 50 mM metformin, and 17.5 μM trifluoperazine.

value: in house yeast library

value: no stimulation

tag: time

value: 0 h


title: lin-61 Celegans late stage embryos-replicate1


title: CD68+, PDAC1, MGC WO-003

description:
Library name: DSP-1001660035205-B-A04
CD68+ AOI from PDAC patient PDAC1, slide: CD68_Slide9, ROI: PDAC1-MGC_WO-003, area: 34280.42 um2, nuclei: 135


title: Long-Bridge RT Probe Test BC009

description:
Library name: FIX08824-009
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

value: PBMC


title: Hep3B_NAT10-WT_rep1_Mock

city: Chicago

first: Daniel

last: Arango

state: IL

address: 303 E Superior St, Office 7-119

institute: Northwestern University

description: Library name: M4

data_processing:
Raw reads were pre-processed to remove low quality bases, adapter sequences, and a stretch of at least 10 consecutive guanine nucleotides at the 3’ end using cutadapt/4.2.
The UMI was extracted using UMI-tools/1.1.5.
Reads were aligned to the human genome using STAR/2.7.9a in local alignment mode.
All alignments were deduplicated using UMI-tools and nucleotide counts of aligned reads were extracted via samtools/1.6 mpileup. Read counts were extracted with https://github.com/IARCbioinfo/mpileup2readcounts.
We appended strand information to each site. We then filtered: 1) read depth per position must be >=30 2) dominant mismatch nucleotide per position must have at least 5 reads and a mismatch frequency of 0.001 or 0.01. We then identified significantly decreased sites in each sample vs NAT10-WT. Statistics and plots were performed in R/.
Assembly: GRCh38
Supplementary files format and content: BED files containing raw nucleotide counts per position

source_name: Liver

growth_protocol: HEP3B cells were maintained in DMEM supplemented with 10% fetal bovine albumin (FBS) and 1% Penicillin/Streptomycin. All cells were grown in an incubator condition of 37oC and 5% CO2 and passaged every 3 days.

extract_protocol:
Total RNA isolation was performed using Trizol Reagent (ThermoFisher Scientific) according to the manufacturer's protocol. Total RNA was then DNase treated with DNase I (NEB) and reconstituted in nuclease-free water.
Total RNA was dephosphorylated followed by a 3' adapter ligation. The 3' adapter contains a spacer that impedes the self-ligation of RNA. The ligated RNA was fragmented, treated with NaCNBH3, dephosphorylated, and repurified. Reverse transcription was performed using the Induro enzyme in a dNTP cocktail contianing 2-amino-dATP. cDNA was then ligated to an adapter containing unique molecular identifiers (UMI) of ten randomized nucleotides.Final libraries were PCR amplified using Q5® High-Fidelity 2X Master Mix (NEB) and NEBNext® Multiplex Oligos for Illumina®. The primers aligned perfectly to the 5’ adapter and the second 3’ adapter. Each sample was assigned a different indexed primer.

treatment_protocol: NAT10-FKBP cells were transduced with single mutants in the Helicase domain (E389L. K290A) or the acetyltransferase domain (G641E, H537A), NAT10-WT, or a control plasmid for 24 h, released from transduction by replacing with fresh DMEM for 24 h, and then selected using 5 µg/ml Blasticidin-S HCl for 5 days. Blasticidin selected transduced cells with parental control and NAT10-FKBP cells were then treated with 100 nM dTAGV1 for 24 hrs.

value: Liver

value: Hepatocellular carcinoma

value: Mock

tag: batch


title: Hep3B_G641E_rep1_Mock

description: Library name: M5


title: H69, DMSO, control3

city: Yiwu

first: Yixuan

last: Yu

address: 1575 Chouzhou North Road, Futian Street

institute: The Fourth Affiliated Hospital of School of Medicine, and International School of Medicine

description: Library name: 3-H69-DMSO

data_processing:
RNA-seq data processing typically involves quality control, adapter trimming, alignment to a reference genome, quantification of gene expression, and differential expression analysis.
Assembly: hg38
Supplementary files format and content: txt file include count value for each samples

extract_protocol:
Total RNA was isolated using the TRIzol reagent.
Using Hieff NGS® Ultima Dual-mode mRNA Library Prep Kit for Illumina

value: cell line

value: Small Cell Lung Carcinoma (SCLC), classic type

value: DMSO


title: hpl-2I158A Celegans late stage embryos-replicate1

value: late stage embryos


title: Yeast, Trifluoperazine, no MTX, replicate B

value: Trifluoperazine


title: Long-Bridge RT Probe Test BC008

description:
Library name: FIX08824-008
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

value: Blood

tag: subject id

value: Female

value: Caucasian/Non-Hispanic

value: PA


title: Yeast, no drug, no MTX, replicate B


title: hpl-2 Celegans late stage embryos-replicate1


title: CD68+, PDAC1, MGC WO-001

description:
Library name: DSP-1001660035205-B-A02
CD68+ AOI from PDAC patient PDAC1, slide: CD68_Slide9, ROI: PDAC1-MGC_WO-001, area: 19507.17 um2, nuclei: 78

value: pancreas

value: macrophages


title: kd-2

city: 咸阳市

first: YouJie

last: Cui

state: 陕西省

address: 西北农林科技大学北校西南区

institute: 西北农林科技大学动物科技学院

data_processing:
The original sequencing data contains adapter sequences, low-quality bases, and undetermined bases (denoted as N), which can significantly interfere with subsequent data analysis. To remove these interfering elements and obtain reliable data, a thorough filtering process is performed, resulting in clean data or clean reads. The format of the clean data file is identical to that of the raw data.  The filtering process is conducted using SOAPnuke software (v2.1.0) [1]. The main parameters used are: --lowQual=20, --nRate=0.005, --qualRate=0.5, with other parameters set to default values. The steps involved in data processing are as follows:  Filtering out paired reads that contain adapter sequences. Removing paired reads with an N content (representing undetermined bases) exceeding 0.5%. Discarding low-quality paired reads, where the number of bases with a Qphred score less than or equal to 20 constitutes more than 50% of the total read length.
Assembly: Genome assembly Sscrofa11.1
Supplementary files format and content: Gene expression information for each sample

organism: Sus scrofa

source_name: Pigtesticles

extract_protocol:
Aspirate the culture medium from the culture dish and wash once with 1 mL of PBS. Aspirate the PBS (removing as much as possible) and add 1 mL of TRIzol. Incubate for 5 minutes, gently pipette against the bottom of the dish, then aspirate the TRIzol and transfer it to a 1.5 mL centrifuge tube. Allow it to stand at room temperature for 5 minutes. Add 250 µL of chloroform, vortex for 30 seconds. Allow it to stand at room temperature for 5 minutes. Centrifuge at 12,000 rpm for 5 minutes; carefully transfer the aqueous phase to another 1.5 mL centrifuge tube using a pipette. Add 500 µL of isopropanol to the aqueous phase, mix gently, and incubate at 4°C overnight. Centrifuge at maximum speed (12,000 rpm) for 20 minutes. Discard the isopropanol, wash the pellet with 1 mL of 75% ethanol. Centrifuge at 12,000 rpm for 5 minutes. Discard the ethanol and air-dry the pellet. Dissolve the RNA pellet in approximately 30 µL of DEPC-treated water and store at -80°C.
1Two biological RNA samples from two independent experiments were sent to Frasergen (Wuhan, China) for mRNA sequencing library construction.Briefly, these libraries were sequenced using the MGI high-throughput sequencing platform. Raw reads were filtered using SOAPnuke (v2.1.0) software to obtain clean reads, which were then aligned to the pig genome (Sscrofa 11.1) using HISAT2 (v2.2.1). The quality-controlled second-generation sequences were subsequently mapped to the reference transcriptome sequences using bowtie2 (v2.3.5) software. RSEM (v1.3.3) was used to count the number of reads mapped to each transcript in each sample and convert them to FPKM (Fragments Per Kilobase of transcript per Million mapped reads), thereby obtaining the expression levels of genes and transcripts. Finally, the DESeq2 algorithm was employed with a moderate cutoff value (Pvalue < 0.05) to filter differentially expressed genes (DEGs).

value: Pigtesticles

value: Immature spermatogonia from the porcine

value: ZBTB16 knockdown


title: Yeast, Metformin, no MTX, replicate B

value: in house yeast library

value: Metformin


title: No Template Control, run_2

description:
Library name: DSP-1001660035205-B-A01
No Template Control (NTC) , run: run_2

value: No Template Control


title: Yeast, Fluconazole, no MTX, replicate B

value: Fluconazole


title: Long-Bridge RT Probe Test BC006

description:
Library name: FIX08824-006
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

value: PBMC

tag: age at_blood_drawn

value: Unknown


title: kd-1

address: 西北农林科技大学北校西南区

institute: 西北农林科技大学动物科技学院


title: CD68+, Scar4, MGC W-003

description:
Library name: DSP-1001660036826-A-G08
CD68+ AOI from skin lesion, secondary intention healing patient Scar4, slide: CD68_Slide6, ROI: Scar4-MGC_W-003, area: 15059.64 um2, nuclei: 75

source_name: skin

value: skin


title: Long-Bridge RT Probe Test BC005

description:
Library name: FIX08824-005
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

tag: Sex


title: Yeast, 5-FC, no MTX, replicate B


title: CD68+, Scar4, MGC W-002

description:
Library name: DSP-1001660036826-A-G07
CD68+ AOI from skin lesion, secondary intention healing patient Scar4, slide: CD68_Slide6, ROI: Scar4-MGC_W-002, area: 25293.13 um2, nuclei: 96


title: Yeast, Trifluoperazine, MTX, replicate B

value: Trifluoperazine, MTX


title: con-1

address: 西北农林科技大学北校西南区

institute: 西北农林科技大学动物科技学院

value: WT


title: H69, DMSO, control1

description: Library name: 1-H69-DMSO

source_name: cell line

value: cell line

value: Small Cell Lung Carcinoma (SCLC), classic type

value: DMSO


title: CD68+, Scar4, MGC W-001

description:
Library name: DSP-1001660036826-A-G06
CD68+ AOI from skin lesion, secondary intention healing patient Scar4, slide: CD68_Slide6, ROI: Scar4-MGC_W-001, area: 29372.48 um2, nuclei: 144


title: Long-Bridge RT Probe Test BC003

description:
Library name: FIX08824-003
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

value: Blood

value: Female

tag: ethnicity/race

value: Caucasian/Non-Hispanic

value: PA


title: Hep3B_NAT10(-)_rep1_Mock

description: Library name: M3

value: Liver

value: Hepatocellular carcinoma

value: Mock


title: Yeast, no drug, MTX, replicate B

value: in house yeast library

value: MTX