title: P15

first: Jindan

last: Yu

address: E330, 1760 Haygood Dr NE

department: Urology

description:
Library name: M1488
PIP-Seq

data_processing:
10X Genomics raw sequencing files were processed and mapped using CellRanger 6.1.2. Pip-seq raw sequencing files were processed using Fluent BioSciences's PipSeeker 02.01.04 using results from sensitivity 5.
Assembly: mm10
Supplementary files format and content: Gene and fragment matrices from Cell Ranger and PipSeeker

source_name: Prostate

extract_protocol:
Fresh whole prostate tissues were dissected from genetically engineered mice and immediately processed for scRNA-seq analysis using the 10x Genomics Chromium Next GEM Single Cell 3' Kit v3.1 (Dual Index). In brief, whole prostate tissues were minced and dissociated into single cell suspensions using the Worthington-Biochem papain dissociation kit (according to manufacturer instructions), followed by incubation in TryPLE + 10uM Y-27632 at 37C for 15min and passage through a 40um strainer (Flowmi). Cell count and viability were measured by trypan blue staining using Cell Countess II to ensure single cell suspension and viability >80%. If doublets/multiplets remained, the TrypLE dissociation steps were repeated. Cells were resuspended in RPMI+10%FBS for loading into the 10x Chip G for GEM generation, with a targeted cell recovery of 4000-5000 cells. For PIP-seq analysis of CD45+ immune cells, prostates were collected and dissociated into single cell suspensions, as described above, then FACS-sorted for live CD45+ cells. In brief, cells were stained with Zombie Aqua Live/Dead stain (Biolegend Zombie Aqua™ Fixable Viability Kit # 423101) for 30min at 4C for live/dead staining. And for CD45 staining, Fc block (TruStain FcX™ PLUS Antibody # 156603) was applied for 5-10min, followed by CD45+ APC stain (Biolegend APC anti-mouse CD45 Antibody # 147707) for 30min. Cells were washed and resuspended in 2%FBS + 25mM HEPES PBS for cell sorting into 20%FBS collection media. Sorted live CD45+ cells were then washed with PIP-seq cell resuspension buffer.
10X genomics libraries were prepared using 10x Genomics Chromium Next GEM Single Cell 3' Kit v3.1 (Dual Index) per manufacturer’s protocol. Pip-seq libraries were prepared using the PIPseq™ T20 3ʹ Single Cell RNA Kit v3.0 per manufacturer’s protocol.

treatment_protocol: Prostate tissues were harvested from pairs of intact P vs PF mice at early (12wk) and late (18wk) timepoints (P12, PF12, P18, PF18), as well as a pair of P vs PF mice castrated at 18wk and harvested 12wk later (XP vs. XPF), for scRNA-seq analysis of whole prostate tissue. In addition, a pair of P vs PF mouse prostates were collected at 15wk and sorted for CD45+ cells for scRNA-seq analysis (P15 vs. PF15).

value: Prostate

value: Immune cells (live CD45+ cells)

value: PbCre4:Ptenf/f (P)

value: Intact


title: PF15

status: Public on Feb 21 2026

type: SRA

city: Atlanta

state: GA

country: USA

institute: Emory University

description:
Library name: M1489
PIP-Seq

library_source: transcriptomic single cell

molecule: polyA RNA

organism: Mus musculus

tag: tissue

tag: cell type

tag: genotype

value: PbCre4:Ptenf/fFoxa1f/f (PF)

tag: treatment


title: 028-CD68 [DSP-1001660009393-B-H08]

city: beijing

first: lu

last: z

state: - 选择 -

address: beijing

country: China

institute: institution of microbology

description:
Library name: DSP-1001660009393-B-H08
TB
NanoString GeoMx Digital Spatial Profiling (DSP)

library_source: transcriptomic

data_processing:
DSP sequencing data were processed with the GeoMx NGS Pipeline (DND). After sequencing, reads were trimmed, merged, and aligned to a list of indexing oligos to identify the source probe. The unique molecular identifier (UMI) region of each read was used to remove PCR duplicates and duplicate reads, thus converting reads into digital counts. The limit of quantitation (LOQ) was estimated as following: the geometric mean reads of the negative control probes plus 2 geometric standard deviations of the negative control probes. Targets that consistently fell below the LOQ were removed, and the datasets were normalized using upper quartile (Q3) normalization. Differentially expressed genes of each disease group were identified using Wald statistics test, with |fold change| > 1.5 and Benjamini–Hochberg (BH)-adjusted P-value < 0.05 as compared to HC group.
Assembly: GRCh38.p13
Supplementary files format and content: xlsx

molecule: total RNA

organism: Homo sapiens

source_name: Lung

extract_protocol:
For the NanoString GeoMx Digital Spatial Profiler (DSP) transcriptional assays, slides were prepared following the manufacturer’s instruction from GeoMx DSP Slide Preparation User Manual with some modifications (NanoString, MAN-10115-05 for software v2.3). Briefly, slides were baked at 60°C for 30 minutes. Deparaffinization and rehydration were performed in CitriSolv hybrid solvent, 100% ethanol, and 95% ethanol, sequentially. Target retrieval was performed in 1× Tris EDTA (TE) buffer (pH 9.0). Thereafter, tissue RNA targets were exposed by incubating the slides with 1 µg/mL proteinase K at 37°C. Slides were washed and then immediately placed in 10% neutral buffered formalin, followed by incubation in NBF stop buffer (100 mM Tris-HCl and 100 mM glycine). The Whole Transcriptome Atlas (WTA) probe reagent was diluted and added to each slide, which was covered with a HybriSlip cover (Grace Bio-Labs) and incubated for 15 hours at 37°C in a HybEZ II System (Advanced Cell Diagnostics, USA). Slides were washed and blocked in 200 μL Buffer W (NanoString) for 30 minutes. The optimal dilution solution of morphology markers and nuclear staining SYTO13 (Nanostring) were used for distinguishing various morphology. In detail, slides were covered with 200 μL morphology marker solution, and incubated at RT for 1 hours. Slides were blocked with Buffer W and covered with morphology marker and SYTO13 (1:10), subsequently incubated with HRP polymer and dye. After blocking with HRP blocker, slides were blocked and stained for the next staining cycle. Finally, Slides were then scanned with the NanoString DSP instrument for RNA probes collection. For spatial samples, slides were loaded into the slide holder of the GeoMx DSP machine and secured by closing the slide tray clamp. Each slide was covered with 2 mL of buffer S and the underside of the slides cleaned with 70% ethanol before loading the slide tray into the DSP. The scanning areas were set to only scan the tissues and the tissue boundaries were determined by adjusting the x and y scanning areas and the sensitivity. Each slide was scanned with a 20× objective. ROIs were placed per tissue based on the selection regions and assessment. After approval of the ROIs, the GeoMx DSP photocleaves the ultraviolet-cleavable barcoded linker of the bound RNA probes and collects the individual segmented areas into separate wells in the DSP collection plate. For each experimental group, n = 3–4 individual ROIs of 0.2–0.5 mm2 in area with each containing ~ 300 designated immune cells were collected for subsequent analysis.
DSP collection sample plates were dried down by sealing the plates with aeroseal and placed at RT overnight. The samples were then resuspended with diethyl pyrocarbonate (DEPC)-treated water. 96-well plates were prepared by mixing 2 μL polymerase chain reaction (PCR) mix (NanoString), 4 μL of index primer mix (NanoString), and 4 μL of DSP sample. The following PCR program was used to amplify the Illumina sequencing compatible libraries: 1) 37°C for 30 minutes, 50°C for 10 minutes, and 95°C for 3 minutes; 2) 18 cycles of 95°C for 15 seconds, 65°C for 1 minutes, and 68°C for 30 seconds; 3) 68°C for 5 minutes and a final hold at 4°C. The indexed libraries were pooled into 8-well strip tubes, and incubated with 58 μL AMPure XP beads (Beckman Coulter, Cat# A63880) in a 1:1.2 ratio. The 8-well strip was placed on a magnetic stand before removal of the supernatant. The beads were then washed twice with 80% ethanol and dried before being eluted with 10 μL elution buffer (10mM Tris-HCl pH 8, 0.05% Tween-20). The samples were combined into two pools of 40 μL each and incubated with 48 μL AMPure buffer (2.5 M NaCl, 20% PEG 8000) for 5 minutes. Following magnetic incubation for 5 minutes and removal of supernatants, the beads were washed twice with 80% ethanol and dried for 1 minute before elution with 17 μL elution buffer. The two pools were combined to a final elute of 34 μL. Sequencing library size was assessed with a DNA high sensitivity bioanalyzer assay (Agilent Technologies). Library concentration was assessed with Qubit dsDNA high sensitivity assay (Thermo Fisher Scientific). Total target counts per DSP collection plate for sequencing were calculated from the total sampled areas (μm2) reported in the DSP generated Lab Worksheet. All sequencing libraries were generated with unique indexes allowing pooled sequencing. WTA libraries for sequencing with an Illumina NovaSeq 6000 platform.

value: Lung

value: Macrophages

tag: group


title: 027-CD3 [DSP-1001660009393-B-H05]

description:
Library name: DSP-1001660009393-B-H05
TB
NanoString GeoMx Digital Spatial Profiling (DSP)

value: T cells


title: 030-CD3 [DSP-1001660009393-B-H11]

description:
Library name: DSP-1001660009393-B-H11
TB
NanoString GeoMx Digital Spatial Profiling (DSP)


title: genomic DNA from whole blood sample collected from episodic migraine subject 12 at timepoint T1

type: genomic

city: Bologna

first: Paolo

last: Garagnani

state: BO

address: Via San Giacomo 12

department: Department of Medical and Surgical Sciences (DIMEC)

country: Italy

institute: Univeristy of Bologna

description: bisulfite converted DNA from whole blood isolated from episodic migraine subject 12 at timepoint T1

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged on Illumina iScan scanner using iScan Control Software (ICS) with standard recommended Illumina scanner settings

data_processing:
R v3.6.3
*processed value definition: Average Beta (non normalized, not filtered).

label: Cy3 and Cy5

molecule: genomic DNA

source_name: genomic DNA from whole blood

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from whole blood samples using QIAamp DNA Blood Mini kit (Qiagen) according to manufacturer’s instructions.

value: whole blood

tag: Sex

value: female

tag: phenotype

value: episodic migraine

tag: timepoint


title: 028-CD3 [DSP-1001660009393-B-H07]

description:
Library name: DSP-1001660009393-B-H07
TB
NanoString GeoMx Digital Spatial Profiling (DSP)


title: 024-CD68 [DSP-1001660009393-B-H04]

description:
Library name: DSP-1001660009393-B-H04
TB
NanoString GeoMx Digital Spatial Profiling (DSP)


title: XPF

description:
Library name: M1475
10X Genomics

value: Surgical castration


title: 027-CD68 [DSP-1001660009393-B-H06]

description:
Library name: DSP-1001660009393-B-H06
TB
NanoString GeoMx Digital Spatial Profiling (DSP)


title: P18

description:
Library name: M1387
10X Genomics


title: PF18

description:
Library name: M1418
10X Genomics


title: XP

description:
Library name: M1415
10X Genomics


title: 001-CD3

description:
Library name: DSP-1001660018859-B-A02
001-CD3
NanoString GeoMx Digital Spatial Profiling (DSP)

data_processing:
DSP sequencing data were processed with the GeoMx NGS Pipeline (DND). After sequencing, reads were trimmed, merged, and aligned to a list of indexing oligos to identify the source probe. The unique molecular identifier (UMI) region of each read was used to remove PCR duplicates and duplicate reads, thus converting reads into digital counts. The limit of quantitation (LOQ) was estimated as following: the geometric mean reads of the negative control probes plus 2 geometric standard deviations of the negative control probes. Targets that consistently fell below the LOQ were removed, and the datasets were normalized using upper quartile (Q3) normalization. Differentially expressed genes of each disease group were identified using Wald statistics test, with |fold change| > 1.5 and Benjamini–Hochberg (BH)-adjusted P-value < 0.05 as compared to HC group.
Assembly: GRCm38 (mm10)
Supplementary files format and content: xlsx


title: 024-CD3 [DSP-1001660009393-B-H03]

description:
Library name: DSP-1001660009393-B-H03
TB
NanoString GeoMx Digital Spatial Profiling (DSP)


title: 029-CD3 [DSP-1001660009393-B-H09]

description:
Library name: DSP-1001660009393-B-H09
TB
NanoString GeoMx Digital Spatial Profiling (DSP)


title: PF12

description:
Library name: M1386
10X Genomics


title: P12

description:
Library name: M1385
10X Genomics


title: 023-CD3 [DSP-1001660009393-B-H01]

description:
Library name: DSP-1001660009393-B-H01
TB
NanoString GeoMx Digital Spatial Profiling (DSP)


title: PF18 [Visium]

description:
Library name: 554
FFPE Visium Spatial Sequencing

data_processing:
Raw sequences were processed and aligned to mm10 using Space Ranger 2.0.0 defaut options
Assembly: mm10
Supplementary files format and content: Gene expression, barcode and spatial output folder from Space Ranger
Library strategy: Spatial Transcriptomics

extract_protocol:
Mouse prostate tissues were harvested from a pair of P12 vs PF12 and P18 vs PF18 mice and formalin fixed for ~20-24h, followed by paraffin processing and embedding. Tissue blocks were scored for tissue region of interest, sectioned (5um thickness) and placed onto the 6.5 x 6.5 mm capture are
Visium slides were processed and libraries prepared using the 10x Genomics Visium Spatial Gene Expression Reagent Kits for FFPE per manufacturer’s protocol.

treatment_protocol: Prostate tissues from pairs of intact P vs. PF mice at an early 12-wk (P12 vs. PF12) and a late 18-wk (P18 vs. PF18) timepoint were harvested for spatial transcriptomics analysis.


title: 003-F4/80

description:
Library name: DSP-1001660018859-B-A07
003-F4/80
NanoString GeoMx Digital Spatial Profiling (DSP)


title: 022-CD3 [DSP-1001660009393-B-G11]

description:
Library name: DSP-1001660009393-B-G11
TB
NanoString GeoMx Digital Spatial Profiling (DSP)


title: JAR_rep2

city: Nagoya

first: Kosuke

last: Yoshida

state: Aichi

address: 65 Tsuruma-cho

country: Japan

institute: Nagoya University

description: Library name: 2

data_processing:
Expression levels for each gene were quantified from the sequencing data by Kallisto software.
The tximport package (ver. 1.18.0) was used to summarize the data.
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: a tsv file includes TPM counts of each sample

source_name: JAR

growth_protocol: Cells were maintained in RPMI-1640 medium (Nacalai Tesque, Kyoto, Japan) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin–streptomycin.

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini Kit (QIAGEN, Hilden, Germany).
The library construction and pair-end sequencing were conducted by Novogene. (Beijing, China.)

treatment_protocol: MTX-resistant JAR cells were established by continuous stepwise exposure to increasing concentrations of MTX. Cells were initially cultured in 10 nM MTX, and the concentration was gradually increased over several months.

tag: cell line

value: JAR

value: choriocarcinoma

value: No treatment

tag: batch


title: 022-CD68 [DSP-1001660009393-B-G12]

description:
Library name: DSP-1001660009393-B-G12
TB
NanoString GeoMx Digital Spatial Profiling (DSP)


title: 021-CD68 [DSP-1001660009393-B-G10]

description:
Library name: DSP-1001660009393-B-G10
TB
NanoString GeoMx Digital Spatial Profiling (DSP)


title: 023-CD68 [DSP-1001660009393-B-H02]

description:
Library name: DSP-1001660009393-B-H02
TB
NanoString GeoMx Digital Spatial Profiling (DSP)


title: PF12 [Visium]

description:
Library name: 551
FFPE Visium Spatial Sequencing


title: P18 [Visium]

description:
Library name: 187
FFPE Visium Spatial Sequencing


title: WT, Day28

city: Seoul

first: Suk-Kyung

last: Shin

address: 103 Daehak-ro, jongno-go

country: South Korea

institute: Seoul National University

description: 10x Genomics

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: mm10
Supplementary files format and content: mtx

source_name: pancreatic cancer tissue

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Chromium Single Cell 3' Reagent Kit v3.1 following manufacturer's protocols.

value: pancreatic cancer tissue

value: epithelial cell

value: WT

value: orthotopic inoculation of 5 x 10^5 Pan02 cells


title: 020-CD3 [DSP-1001660009393-B-G08]

description:
Library name: DSP-1001660009393-B-G08
TB
NanoString GeoMx Digital Spatial Profiling (DSP)


title: Vsir-/-, Day28

description: 10x Genomics

value: VISTA knockout


title: 019-CD3 [DSP-1001660009393-B-G07]

description:
Library name: DSP-1001660009393-B-G07
TB
NanoString GeoMx Digital Spatial Profiling (DSP)


title: 016-CD68 [DSP-1001660009393-B-G04]

description:
Library name: DSP-1001660009393-B-G04
TB
NanoString GeoMx Digital Spatial Profiling (DSP)


title: Mice-2717, prostate tissue Pten Single Knock Out, H3K27ac(ChIP)

description: Library name: M1667

library_source: genomic

data_processing:
Basecalls were performed using Bowtie2 v2.5.1 for Novaseq output
ChIP-seq reads were trimmed from 3' end untile the final base has a quality score > 30, using Trimmomatic v0.39, discarding reads left with < 36 bp
ChIP-seq reads were aligned to the mm10 genome using Bowtie2 v2.5.1. Duplicate reads were identified and removed using Picard v3.0.0.
Peaks were calling using HOMER v4.11 with default settings.
bigWig files were generating using deepTools v3.5.4 with binsize = 10bp
Assembly: mm10
Supplementary files format and content: bigWig, BED

source_name: Mice prostate tissue

extract_protocol:
Frozen tissues were ground using agate mortar and pestle and homogenized using the BeadBug benchtop homogenizer. Tissues were then double cross linked with 2mM DSG for 10min, followed by 1% formaldehyde for 10min, at room temperature. Crosslinking was quenched with 0.125 M glycine for 5min at room temperature. Chromatin was fragmented using an E220 focused ultrasonicator (Covaris), 50 ng of Drosophila chromatin was added to each sample as spike-in DNA, and samples were pre-cleared with protein A agarose beads (Millipore) for 1hr. Then samples were incubated with the following antibodies overnight at 4C with rotation: FOXA1 ab23738 (Abcam) and H3K27ac CST 8173S. 1 ug drosophila H3 antibody (Active motif Cat# 61686) was also added per sample. Then, protein A agarose beads were added and incubated for 2h at 4C, followed by washing the beads with 1×dialysis buffer (2mM EDTA, 50mM Tris-Cl, pH 8.0) twice, and IP wash buffer (100mM Tris-Cl, pH 9.0, 500mM LiCl, 1% NP40, 1% deoxycholate) four times. Finally, protein-DNA complexes were eluted (50mM NaHCO3, 1% SDS), crosslinks were reversed, and DNA was purified using DNA Clean & Concentrator-5 kit (ZYMO Research).
Total 10 ng ChIP DNA was used to prepare libraries using NEBNextUltra II DNA Library Prep Kit for Illumina (NEB E7645L) according to manufacturer’s instructions.

treatment_protocol: Prostate tissues were harvested from age-matched intact PbCre4:Ptenf/f (P) and PbCre4:Ptenf/fFoxa1f/f (PF) mice at 18-wk, in triplicate biological samples, and were flash frozen.

value: Mice prostate tissue

value: PbCre4:Ptenf/f (P)

value: Intact

tag: antibody

value: H3K27ac (CST 8173S), Spike-in antibody (Active motif Cat# 61686)


title: 021-CD3 [DSP-1001660009393-B-G09]

description:
Library name: DSP-1001660009393-B-G09
TB
NanoString GeoMx Digital Spatial Profiling (DSP)

value: Lung

value: T cells


title: Mice-2573, prostate tissue, Pten Single Knock Out, ,FOXA1(ChIP)

description: Library name: M1672

value: FOXA1 (abcam ab23738), Spike-in antibody (Active motif Cat# 61686)


title: Mice-2573, prostate tissue, Pten Single Knock Out, H3K27ac(ChIP)

description: Library name: M1673


title: Mice-1943, prostate tissue, Pten/Foxa1 Double Knock Out, H3K27ac(ChIP)

description: Library name: M1685

value: PbCre4:Ptenf/fFoxa1f/f (PF)


title: 017-CD3 [DSP-1001660009393-B-G05]

description:
Library name: DSP-1001660009393-B-G05
TB
NanoString GeoMx Digital Spatial Profiling (DSP)


title: Mice-2033, prostate tissue, Pten Single Knock Out, H3K27ac(ChIP)

description: Library name: M1662


title: 016-CD3 [DSP-1001660009393-B-G03]

description:
Library name: DSP-1001660009393-B-G03
TB
NanoString GeoMx Digital Spatial Profiling (DSP)


title: 018-CD3 [DSP-1001660009393-B-G06]

description:
Library name: DSP-1001660009393-B-G06
TB
NanoString GeoMx Digital Spatial Profiling (DSP)


title: 015-CD68 [DSP-1001660009393-B-G02]

description:
Library name: DSP-1001660009393-B-G02
TB
NanoString GeoMx Digital Spatial Profiling (DSP)

value: Macrophages


title: 015-CD3 [DSP-1001660009393-B-G01]

description:
Library name: DSP-1001660009393-B-G01
TB
NanoString GeoMx Digital Spatial Profiling (DSP)


title: Mice-2033, prostate tissue, Pten Single Knock Out, ,FOXA1(ChIP)

description: Library name: M1661


title: 014-CD68 [DSP-1001660009393-B-F12]

description:
Library name: DSP-1001660009393-B-F12
TB
NanoString GeoMx Digital Spatial Profiling (DSP)


title: Mice-2378, prostate tissue, Pten/Foxa1 Double Knock Out, H3K27ac(ChIP)

description: Library name: M1650


title: 013-CD68 [DSP-1001660009393-B-F10]

description:
Library name: DSP-1001660009393-B-F10
TB
NanoString GeoMx Digital Spatial Profiling (DSP)


title: Mice-2378, prostate tissue, Pten/Foxa1 Double Knock Out, ,FOXA1(ChIP)

description: Library name: M1649


title: Mice-1943, prostate tissue, Pten/Foxa1 Double Knock Out, ,FOXA1(ChIP)

description: Library name: M1684


title: Mouse, Lung,  Silica_2, scRNA

city: Chengdu

first: Bisen

last: Ding

address: Renmin South Road

institute: State Key Laboratory of Biotherapy

description: Library name: Silica_2

data_processing:
The cellranger pipeline (version 3.1.0, 10X Genomics) was used to process raw sequencing output.
Assembly: mm10
Supplementary files format and content: Cell Ranger software output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: lung

extract_protocol:
The homogenized lung tissues were suspended in DMEM medium (C11995500BT, GIBCO) containing 1 mg/mL type I collagenase (C8140，Solarbio), 1 mg/mL type IV collagenase (C8160，Solarbio), 1 mg/mL Dispase II (D6430，Solarbio), and 0.2 mg/mL DNAase (D8071, Solarbio) at 37°C for 30 min. The digested lung tissues were filtered through a 70 μm filter membrane (BS-70-XBS, biosharp), and the filtrate was centrifuged and treated with red blood cell lysis buffer (R1010, Solarbio) for 10 min, centrifuged again under the same conditions, the pellet was washed once with sterile PBS (C10010500BT, GIBCO), and centrifuged again under the same conditions. Cell pellet was resuspended again with MACS mixture (2 mM EDTA, 0.1% BSA, 1% penicillin/streptomycin/antimitotic in DPBS) to obtain lung single cell suspension.
Single-cell ATAC sequencing (scATAC-seq) was performed using the 10X Chromium 3′ v3 kit (10X Genomics, Pleasanton, CA) according to the manufacturer's instructions.

value: lung


title: Mice-2717, prostate tissue, Pten Single Knock Out, ,FOXA1(ChIP)

description: Library name: M1666


title: Mouse, Lung,  Silica_3, scRNA

description: Library name: Silica_3


title: 013-CD3 [DSP-1001660009393-B-F09]

description:
Library name: DSP-1001660009393-B-F09
TB
NanoString GeoMx Digital Spatial Profiling (DSP)


title: Mice-1751, prostate tissue, Pten/Foxa1 Double Knock Out, H3K27ac(ChIP)

description: Library name: M1644


title: Mouse, Lung,  Silica_1, scRNA

description: Library name: Silica_1


title: Mice-1751, prostate tissue, Pten/Foxa1 Double Knock Out, FOXA1(ChIP)

description: Library name: M1643


title: Whole gonad E12.5 XY WT Rep2

city: Ramat Gan

first: Isabelle

last: Stévant

address: Institute of Nanotechnology and Advanced Materials, Building 206

country: Israel

institute: University of Bar Ilan

description: Library name: E12.5_XY_WT_Rep2

data_processing:
FastQ files we mapped on the mm10 genome using the nf-core/rnaseq pipeline v3.12.0
Assembly: mm10
Supplementary files format and content: raw_counts.csv is a comma separated value file containing the number of read per gene
Supplementary files format and content: TPM_counts.csv is a comma separated value file containing normalized read counts using Transcript Per Million normalization

source_name: Whole gonad

extract_protocol:
RNA was extracted using Qiagen RNeasy Plus micro kit (Qiagen, 74034). 140ng of total RNA was taken from each sample for library preparation.
mRNA was transcribed to cDNA and prepared into libraries using Poly(A) mRNA Magnetic Isolation Module (NEB, E7490S), along with NEBNext UltraExpress RNA library prep kit (NEB, E3330S) and cleaned using AMPure beads (Beckman coulter, Bc-a63881) according to manufactures instruction. Unique indexes were added to each sample using ++NEBNext Multiplex Oligos for Illumina kit (NEB-E6440S) according to manufactures instruction and cleaned using AMPure beads.

value: Whole gonad

value: male


title: Mouse, Lung,  Bleomycin_2, scRNA

description: Library name: Bleomycin_2


title: 011-CD3 [DSP-1001660009393-B-F07]

description:
Library name: DSP-1001660009393-B-F07
TB
NanoString GeoMx Digital Spatial Profiling (DSP)


title: HBECs, Donor 4, PG/VG Control (40/60), Well 2

city: Chapel Hill

first: Ilona

last: Jaspers

state: NC

address: 125 Mason Farm Rd

department: Marsico Lung Institute

institute: University of North Carolina at Chapel Hill

description: Library name: DD021Rp1_VapedD8_H_Con_2

data_processing:
Sequence reads were trimmed and potential adapter sequences and nucleotides with poor quality were removed with Trimmomatic (v0.36). Reads were mapped to the reference genome using the STAR aligner (v2.5.2b). The Subread package (v1.5.2) was then used to calculate unique gene hit counts, where only unique reads falling within exon regions were counted.
Assembly: Homo sapiens GRCh38 with ERCC genes reference genome (ENSEMBL).
Supplementary files format and content: The processed data consists of raw read counts generated using the Subread package (v1.5.2). These counts were calculated by identifying only unique reads that mapped to exon regions of the Homo sapiens GRCh38 with ERCC genes reference genome (ENSEMBL). The data is provided in a tab-delimited text format containing the unique gene hit counts for each sample.

source_name: Primary human bronchial epithelial cells (HBECs)

growth_protocol: HBECs were obtained from the UNC Marsico Lung Institute Tissue Procurement and Cell Culture Core and donor information is available in Table E1. Culturing of HBECs was performed as described in detail previously 24,25. Briefly, HBECs were expanded in Pneumacult-Ex Plus on collagen-coated T-75 flasks, then seeded onto 12 mm transwells for differentiation at air–liquid interface in Pneumacult-ALI medium. Cultures were maintained at 37 °C with 5% CO₂ and 95% humidity, washed weekly, and differentiated for at least 28 days until fully ciliated.

extract_protocol:
After 10 puffs, the basolateral medium was removed, and cells were lysed in 300 µL RNA Lysis Buffer with 2-Mercaptoethanol (10%) (Invitrogen, Waltham, MA) and stored at -80 °C. RNA was isolated from 16HBE cells and HBEC lysates using a PureLink RNA Mini Kit (Invitrogen) and all manufacturer’s instructions were followed. Following preliminary quality assessment of RNA with a CLARIOstar and LVis plate (BMG LABTECH, Cary, NC), RNA was sent to GENEWIZ (Azenta Life Sciences, South Plainfield, NJ) where quality was further assessed with RNA ScreenTape Analysis and a TapeStation (Agilent, Santa Clara, CA).
HBEC samples were sequenced on an Illumina Novaseq X Plus (2x150bp). The sequencing strategy utilized a paired-end run. Reads were mapped to the Homo sapiens GRCh38 with ERCC genes reference genome (ENSEMBL) 60. Regarding sample quality, HBECs had 1,266,194,279 total reads and a 38.54 quality score.

treatment_protocol: Fully differentiated primary HBECs (n = 4 donors, Table E1) were exposed to the same 6 commercially available ∆8-THC vaping products (Table 1) used for chemical analysis or a 40/60 propylene glycol/vegetable glycerin (PG/VG) vaping control using the UNC Vaping Product Exposure System (VaPES) 28. Details of the devices used with each product can also be found in Table E1. For the Stiizy disposable product, a new 3D-printed mouthpiece and silicone insert were made to accommodate the different shape of the mouthpiece 28. We have previously shown deposition with VaPES to be 49.5 ± 2.75 µg/cm2 per puff on a 12 mm transwell 28. Two replicate wells per donor were exposed to each vaping product. HBECs were exposed to a total of 10 3-second puffs (2 L/min puffs with 10-minute rests to allow for complete sedimentation of the aerosol).

value: PG/VG Control (40/60)


title: 014-CD3 [DSP-1001660009393-B-F11]

description:
Library name: DSP-1001660009393-B-F11
TB
NanoString GeoMx Digital Spatial Profiling (DSP)


title: 009-CD3 [DSP-1001660009393-B-F05]

description:
Library name: DSP-1001660009393-B-F05
TB
NanoString GeoMx Digital Spatial Profiling (DSP)


title: Whole gonad E12.5 XY WT Rep1

description: Library name: E12.5_XY_WT_Rep1


title: 012-CD3 [DSP-1001660009393-B-F08]

description:
Library name: DSP-1001660009393-B-F08
TB
NanoString GeoMx Digital Spatial Profiling (DSP)


title: Mouse, Lung,  Bleomycin_1, scRNA

description: Library name: Bleomycin_1


title: Mouse, Lung,  Saline_3, scRNA

description: Library name: Saline_3


title: Mouse, Lung,  Saline_2, scRNA

description: Library name: Saline_2


title: HBECs, Donor 3, PG/VG Control (40/60), Well 2

description: Library name: DD008Rp1_VapedD8_H_Con_2

value: Primary human bronchial epithelial cells (HBECs)


title: HBECs, Donor 4, PG/VG Control (40/60), Well 1

description: Library name: DD021Rp1_VapedD8_H_Con_1

value: WT


title: Whole gonad E12.5 XY Enh13-3bp-del-hom Rep5

description: Library name: E12.5_XY_Enh13-3bp-del-hom_Rep5


title: 010-CD3 [DSP-1001660009393-B-F06]

description:
Library name: DSP-1001660009393-B-F06
TB
NanoString GeoMx Digital Spatial Profiling (DSP)


title: Whole gonad E12.5 XY Enh13-3bp-del-hom Rep4

description: Library name: E12.5_XY_Enh13-3bp-del-hom_Rep4


title: HBECs, Donor 2, PG/VG Control (40/60), Well 1

description: Library name: DD004Op1_VapedD8_H_Con_1


title: Whole gonad E12.5 XY Enh13-3bp-del-hom Rep3

description: Library name: E12.5_XY_Enh13-3bp-del-hom_Rep3


title: Whole gonad E12.5 XY WT Rep3

description: Library name: E12.5_XY_WT_Rep3


title: 008-CD3 [DSP-1001660009393-B-F03]

description:
Library name: DSP-1001660009393-B-F03
TB
NanoString GeoMx Digital Spatial Profiling (DSP)


title: Mouse, Lung,  Bleomycin_3, scRNA

description: Library name: Bleomycin_3


title: HBECs, Donor 1, PG/VG Control (40/60), Well 1

description: Library name: DD001Rp1_VapedD8_H_Con_1


title: 007-CD68 [DSP-1001660009393-B-F02]

description:
Library name: DSP-1001660009393-B-F02
TB
NanoString GeoMx Digital Spatial Profiling (DSP)


title: 008-CD68 [DSP-1001660009393-B-F04]

description:
Library name: DSP-1001660009393-B-F04
TB
NanoString GeoMx Digital Spatial Profiling (DSP)


title: HBECs, Donor 1, PG/VG Control (40/60), Well 2

description: Library name: DD001Rp1_VapedD8_H_Con_2


title: Whole gonad E12.5 XY Enh13-3bp-del-hom Rep2

description: Library name: E12.5_XY_Enh13-3bp-del-hom_Rep2


title: HBECs, Donor 4, Serene Tree Juice Green Apple, Well 1

description: Library name: DD021Rp1_VapedD8_G_Ju_1

value: Serene Tree Juice Green Apple


title: HBECs, Donor 3, Serene Tree Juice Green Apple, Well 2

description: Library name: DD008Rp1_VapedD8_G_Ju_2


title: HBECs, Donor 2, Serene Tree Juice Green Apple, Well 2

description: Library name: DD004Op1_VapedD8_G_Ju_2


title: HBECs, Donor 4, Serene Tree Juice Green Apple, Well 2

description: Library name: DD021Rp1_VapedD8_G_Ju_2


title: HBECs, Donor 1, Serene Tree Juice Green Apple, Well 2

description: Library name: DD001Rp1_VapedD8_G_Ju_2


title: 006-CD3 [DSP-1001660009393-B-E11]

description:
Library name: DSP-1001660009393-B-E11
TB
NanoString GeoMx Digital Spatial Profiling (DSP)


title: Whole gonad E12.5 XY Enh13-3bp-del-hom Rep1

description: Library name: E12.5_XY_Enh13-3bp-del-hom_Rep1


title: 007-CD3 [DSP-1001660009393-B-F01]

description:
Library name: DSP-1001660009393-B-F01
TB
NanoString GeoMx Digital Spatial Profiling (DSP)


title: HBECs, Donor 3, Serene Tree Juice Green Apple, Well 1

description: Library name: DD008Rp1_VapedD8_G_Ju_1


title: 006-CD68 [DSP-1001660009393-B-E12]

description:
Library name: DSP-1001660009393-B-E12
TB
NanoString GeoMx Digital Spatial Profiling (DSP)


title: Whole gonad E12.5 XY Enh13-3bp-del-het Rep2

description: Library name: E12.5_XY_Enh13-3bp-del-het_Rep2


title: HBECs, Donor 4, Serene Tree Juice Strawberry, Well 2

description: Library name: DD021Rp1_VapedD8_F_Ju_2

value: Serene Tree Juice Strawberry


title: HBECs, Donor 2, Serene Tree Juice Green Apple, Well 1

description: Library name: DD004Op1_VapedD8_G_Ju_1


title: 005-CD68 [DSP-1001660009393-B-E10]

description:
Library name: DSP-1001660009393-B-E10
TB
NanoString GeoMx Digital Spatial Profiling (DSP)


title: HBECs, Donor 1, Serene Tree Juice Green Apple, Well 1

description: Library name: DD001Rp1_VapedD8_G_Ju_1


title: Whole gonad E12.5 XY Enh13-3bp-del-het Rep3

description: Library name: E12.5_XY_Enh13-3bp-del-het_Rep3


title: HBECs, Donor 4, Serene Tree Juice Strawberry, Well 1

description: Library name: DD021Rp1_VapedD8_F_Ju_1


title: Whole gonad E12.5 XY Enh13-3bp-12bp-del-hom Rep3

description: Library name: E12.5_XY_Enh13-3bp-12bp-del-hom_Rep3


title: HBECs, Donor 3, Serene Tree Juice Strawberry, Well 2

description: Library name: DD008Rp1_VapedD8_F_Ju_2


title: HBECs, Donor 3, Serene Tree Juice Strawberry, Well 1

description: Library name: DD008Rp1_VapedD8_F_Ju_1


title: Whole gonad E12.5 XY Enh13-3bp-del-het Rep1

description: Library name: E12.5_XY_Enh13-3bp-del-het_Rep1


title: HBECs, Donor 2, Serene Tree Juice Strawberry, Well 2

description: Library name: DD004Op1_VapedD8_F_Ju_2


title: Whole gonad E12.5 XY Enh13-3bp-12bp-del-hom Rep2

description: Library name: E12.5_XY_Enh13-3bp-12bp-del-hom_Rep2


title: HBECs, Donor 1, Serene Tree Juice Strawberry, Well 2

description: Library name: DD001Rp1_VapedD8_F_Ju_2


title: Whole gonad E12.5 XY Enh13-3bp-12bp-del-hom Rep1

description: Library name: E12.5_XY_Enh13-3bp-12bp-del-hom_Rep1


title: HBECs, Donor 2, Serene Tree Juice Strawberry, Well 1

description: Library name: DD004Op1_VapedD8_F_Ju_1


title: HBECs, Donor 1, Serene Tree Juice Strawberry, Well 1

description: Library name: DD001Rp1_VapedD8_F_Ju_1


title: 004-CD68 [DSP-1001660009393-B-E08]

description:
Library name: DSP-1001660009393-B-E08
TB
NanoString GeoMx Digital Spatial Profiling (DSP)


title: m3_actB_ctrl RNA-seq

first: Chris

last: Scharer

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

description: Library name: m3_actB_ctrl

data_processing:
Raw sequencing reads were mapped to the mm10 version of the mouse genome using STAR and the GENCODE v27 reference transcriptome.
Reads mapping to exons were summarized for each unique ENTREZ gene using the GenomicRanges package in R/Bioconductor.
Assembly: mm10
Supplementary files format and content: csv file of RPKM normalized read counts for each detected gene

source_name: CD43- Splenic B cells

extract_protocol:
5,000 cells were FACS sorted into RLT + 1%BME and snap frozen using the indicated markers. Total RNA was purified using the Quick-RNA MicroPrep Kit (Zymo Research)
Purified RNA was used as input for the SMART-seq v4 cDNA synthesis kit (Takara) and used as an input for the NexteraXT kit with the NexteraXT indexing primers (Illumina).

treatment_protocol: Cells were derived from cultures of naïve B cells that were stimulated for 72 hours with 20 mg/ml LPS, 5 ng/ml IL-5, and 20 ng/ml IL-2

value: CD43- Splenic B cells

tag: mouse strain

tag: origin mouse

value: Activated B cell

value: ctrl

tag: sorting markers


title: Whole gonad E12.5 XY Enh13-1bp-ins-hom Rep5

description: Library name: E12.5_XY_Enh13-1bp-ins-hom_Rep5


title: HBECs, Donor 4, Stiiizy Disposable Skywalker OG, Well 2

description: Library name: DD021Rp1_VapedD8_E_Dis_2

value: Stiizy Disposable Skywalker OG


title: 003-CD3 [DSP-1001660009393-B-E05]

description:
Library name: DSP-1001660009393-B-E05
TB
NanoString GeoMx Digital Spatial Profiling (DSP)

value: Lung


title: 003-CD68 [DSP-1001660009393-B-E06]

description:
Library name: DSP-1001660009393-B-E06
TB
NanoString GeoMx Digital Spatial Profiling (DSP)


title: m2_actB_ctrl RNA-seq

description: Library name: m2_actB_ctrl


title: HBECs, Donor 4, Stiiizy Disposable Skywalker OG, Well 1

description: Library name: DD021Rp1_VapedD8_E_Dis_1


title: 002-CD68 [DSP-1001660009393-B-E04]

description:
Library name: DSP-1001660009393-B-E04
TB
NanoString GeoMx Digital Spatial Profiling (DSP)


title: m1_actB_ctrl RNA-seq

description: Library name: m1_actB_ctrl


title: Whole gonad E12.5 XY Enh13-1bp-ins-hom Rep4

description: Library name: E12.5_XY_Enh13-1bp-ins-hom_Rep4


title: 002-CD3 [DSP-1001660009393-B-E03]

description:
Library name: DSP-1001660009393-B-E03
TB
NanoString GeoMx Digital Spatial Profiling (DSP)

value: T cells


title: HBECs, Donor 3, Stiiizy Disposable Skywalker OG, Well 1

description: Library name: DD008Rp1_VapedD8_E_Dis_1


title: Whole gonad E12.5 XY Enh13-1bp-ins-hom Rep2

description: Library name: E12.5_XY_Enh13-1bp-ins-hom_Rep2


title: 004-CD3 [DSP-1001660009393-B-E07]

description:
Library name: DSP-1001660009393-B-E07
TB
NanoString GeoMx Digital Spatial Profiling (DSP)


title: Whole gonad E12.5 XY Enh13-1bp-ins-hom Rep3

description: Library name: E12.5_XY_Enh13-1bp-ins-hom_Rep3


title: m3_Pc_ctrl RNA-seq

description: Library name: m3_Pc_ctrl

value: plasmablast


title: 001-CD68 [DSP-1001660009393-B-E02]

description:
Library name: DSP-1001660009393-B-E02
TB
NanoString GeoMx Digital Spatial Profiling (DSP)


title: m2_Pc_ctrl RNA-seq

description: Library name: m2_Pc_ctrl


title: HBECs, Donor 3, Stiiizy Disposable Skywalker OG, Well 2

description: Library name: DD008Rp1_VapedD8_E_Dis_2


title: Whole gonad E12.5 XY Enh13-1bp-ins-hom Rep1

description: Library name: E12.5_XY_Enh13-1bp-ins-hom_Rep1


title: HBECs, Donor 2, Stiiizy Disposable Skywalker OG, Well 2

description: Library name: DD004Op1_VapedD8_E_Dis_2


title: m1_Pc_ctrl RNA-seq

description: Library name: m1_Pc_ctrl


title: 001-CD3 [DSP-1001660009393-B-E01]

description:
Library name: DSP-1001660009393-B-E01
TB
NanoString GeoMx Digital Spatial Profiling (DSP)


title: m3_actB_veh RNA-seq

description: Library name: m3_actB_veh

value: veh


title: HBECs, Donor 1, Stiiizy Disposable Skywalker OG, Well 2

description: Library name: DD001Rp1_VapedD8_E_Dis_2


title: Whole gonad E12.5 XY Enh13-1bp-ins-het Rep2

description: Library name: E12.5_XY_Enh13-1bp-ins-het_Rep2


title: Whole gonad E12.5 XY Enh13-1bp-ins-het Rep3

description: Library name: E12.5_XY_Enh13-1bp-ins-het_Rep3


title: HBECs, Donor 2, Stiiizy Disposable Skywalker OG, Well 1

description: Library name: DD004Op1_VapedD8_E_Dis_1


title: 030-CD68 [DSP-1001660009393-B-D12]

description:
Library name: DSP-1001660009393-B-D12
LUAD
NanoString GeoMx Digital Spatial Profiling (DSP)

value: Macrophages


title: m2_actB_veh RNA-seq

description: Library name: m2_actB_veh


title: HBECs, Donor 1, Stiiizy Disposable Skywalker OG, Well 1

description: Library name: DD001Rp1_VapedD8_E_Dis_1


title: 030-CD3 [DSP-1001660009393-B-D11]

description:
Library name: DSP-1001660009393-B-D11
LUAD
NanoString GeoMx Digital Spatial Profiling (DSP)


title: HBECs, Donor 4, Palmetto Disposable BubbaKush, Well 2

description: Library name: DD021Rp1_VapedD8_D_Dis_2

value: Palmetto Disposable BubbaKush


title: 029-CD68 [DSP-1001660009393-B-D10]

description:
Library name: DSP-1001660009393-B-D10
LUAD
NanoString GeoMx Digital Spatial Profiling (DSP)


title: Whole gonad E12.5 XX WT Rep3

description: Library name: E12.5_XX_WT_Rep3

value: Whole gonad

value: female


title: Whole gonad E12.5 XY Enh13-1bp-ins-het Rep1

description: Library name: E12.5_XY_Enh13-1bp-ins-het_Rep1

value: male


title: m3_Pc_veh RNA-seq

description: Library name: m3_Pc_veh


title: m1_actB_veh RNA-seq

description: Library name: m1_actB_veh


title: HBECs, Donor 4, Palmetto Disposable BubbaKush, Well 1

description: Library name: DD021Rp1_VapedD8_D_Dis_1

value: Primary human bronchial epithelial cells (HBECs)


title: HBECs, Donor 2, PG/VG Control (40/60), Well 2

description: Library name: DD004Op1_VapedD8_H_Con_2

value: WT

value: PG/VG Control (40/60)


title: HBECs, Donor 3, PG/VG Control (40/60), Well 1

description: Library name: DD008Rp1_VapedD8_H_Con_1


title: 028-CD68 [DSP-1001660009393-B-D08]

description:
Library name: DSP-1001660009393-B-D08
LUAD
NanoString GeoMx Digital Spatial Profiling (DSP)


title: 005-CD3 [DSP-1001660009393-B-E09]

description:
Library name: DSP-1001660009393-B-E09
TB
NanoString GeoMx Digital Spatial Profiling (DSP)


title: HBECs, Donor 3, Palmetto Disposable BubbaKush, Well 2

description: Library name: DD008Rp1_VapedD8_D_Dis_2


title: Whole gonad E12.5 XX WT Rep1

description: Library name: E12.5_XX_WT_Rep1


title: 028-CD3 [DSP-1001660009393-B-D07]

description:
Library name: DSP-1001660009393-B-D07
LUAD
NanoString GeoMx Digital Spatial Profiling (DSP)


title: 029-CD3 [DSP-1001660009393-B-D09]

description:
Library name: DSP-1001660009393-B-D09
LUAD
NanoString GeoMx Digital Spatial Profiling (DSP)


title: m2_Pc_veh RNA-seq

description: Library name: m2_Pc_veh


title: Whole gonad E12.5 XX WT Rep2

description: Library name: E12.5_XX_WT_Rep2


title: Whole gonad E12.5 XX Enh13-3bp-del-hom Rep5

description: Library name: E12.5_XX_Enh13-3bp-del-hom_Rep5


title: m1_Pc_veh RNA-seq

description: Library name: m1_Pc_veh


title: HBECs, Donor 3, Palmetto Disposable BubbaKush, Well 1

description: Library name: DD008Rp1_VapedD8_D_Dis_1


title: 027-CD68 [DSP-1001660009393-B-D06]

description:
Library name: DSP-1001660009393-B-D06
LUAD
NanoString GeoMx Digital Spatial Profiling (DSP)


title: Whole gonad E12.5 XX Enh13-3bp-del-hom Rep4

description: Library name: E12.5_XX_Enh13-3bp-del-hom_Rep4


title: 027-CD3 [DSP-1001660009393-B-D05]

description:
Library name: DSP-1001660009393-B-D05
LUAD
NanoString GeoMx Digital Spatial Profiling (DSP)


title: HBECs, Donor 2, Palmetto Disposable BubbaKush, Well 2

description: Library name: DD004Op1_VapedD8_D_Dis_2


title: Whole gonad E12.5 XX Enh13-3bp-del-hom Rep3

description: Library name: E12.5_XX_Enh13-3bp-del-hom_Rep3


title: HBECs, Donor 2, Palmetto Disposable BubbaKush, Well 1

description: Library name: DD004Op1_VapedD8_D_Dis_1


title: Whole gonad E12.5 XX Enh13-3bp-del-hom Rep2

description: Library name: E12.5_XX_Enh13-3bp-del-hom_Rep2


title: HBECs, Donor 1, Palmetto Disposable BubbaKush, Well 2

description: Library name: DD001Rp1_VapedD8_D_Dis_2


title: 026-CD68 [DSP-1001660009393-B-D04]

description:
Library name: DSP-1001660009393-B-D04
LUAD
NanoString GeoMx Digital Spatial Profiling (DSP)


title: 026-CD3 [DSP-1001660009393-B-D03]

description:
Library name: DSP-1001660009393-B-D03
LUAD
NanoString GeoMx Digital Spatial Profiling (DSP)


title: m1_actB_heme RNA-seq

description: Library name: m1_actB_heme

value: heme


title: HBECs, Donor 1, Palmetto Disposable BubbaKush, Well 1

description: Library name: DD001Rp1_VapedD8_D_Dis_1


title: m2_actB_heme RNA-seq

description: Library name: m2_actB_heme

value: CD43- Splenic B cells


title: m2_Pc_heme RNA-seq

description: Library name: m2_Pc_heme


title: Whole gonad E12.5 XX Enh13-3bp-del-hom Rep1

description: Library name: E12.5_XX_Enh13-3bp-del-hom_Rep1


title: m3_actB_heme RNA-seq

description: Library name: m3_actB_heme

value: Activated B cell


title: 025-CD68 [DSP-1001660009393-B-D02]

description:
Library name: DSP-1001660009393-B-D02
LUAD
NanoString GeoMx Digital Spatial Profiling (DSP)


title: HBECs, Donor 4, Not Ya Son's Weed Cartridge Grandaddy Purp, Well 2

description: Library name: DD021Rp1_VapedD8_C_Dis_2


title: 025-CD3 [DSP-1001660009393-B-D01]

description:
Library name: DSP-1001660009393-B-D01
LUAD
NanoString GeoMx Digital Spatial Profiling (DSP)


title: Whole gonad E12.5 XX Enh13-3bp-del-het Rep2

description: Library name: E12.5_XX_Enh13-3bp-del-het_Rep2


title: m3_Pc_heme RNA-seq

description: Library name: m3_Pc_heme


title: 024-CD68 [DSP-1001660009393-B-C12]

description:
Library name: DSP-1001660009393-B-C12
LUAD
NanoString GeoMx Digital Spatial Profiling (DSP)


title: m1_Pc_heme RNA-seq

description: Library name: m1_Pc_heme


title: HBECs, Donor 3, Not Ya Son's Weed Cartridge Grandaddy Purp, Well 2

description: Library name: DD008Rp1_VapedD8_C_Dis_2


title: HBECs, Donor 4, Not Ya Son's Weed Cartridge Grandaddy Purp, Well 1

description: Library name: DD021Rp1_VapedD8_C_Dis_1


title: Whole gonad E12.5 XX Enh13-3bp-del-het Rep3

description: Library name: E12.5_XX_Enh13-3bp-del-het_Rep3


title: Whole gonad E12.5 XX Enh13-3bp-12bp-del-hom Rep5

description: Library name: E12.5_XX_Enh13-3bp-12bp-del-hom_Rep5


title: m3_Pc_ctrl

description: Library name: m3_Pc_ctrl

data_processing:
Raw sequencing reads were mapped to the mm10 version of the mouse genome using Bowtie2
bigWig files were normalized to reads per million and generated using GenomicRanges and the bedGraphToBigWig function from the UCSC genome browser
Assembly: mm10
Supplementary files format and content: reads per million normalized bigWig files

extract_protocol:
10,000 cells were sorted into 40% FBS in complete media.
10,000 cells were centrifuged for 10 minutes at 500xg, and tagmentation was performed by resuspending cells in 25 ul of Tagmentation mix (1X TD buffer (10 mM TAPS-NaOH pH 8.1, 5 mM MgCl2, 10% DMF), 2.5 μl Tn5 transposase, 0.1% Tween 20 and 0.02% Digitonin) and then incubated for 1 h at 37°C. DNA was purified and amplified into a sequencing library with KAPA HiFi Polymerase and the Nextera Indexing Kit Primers (Illumina, Inc).

value: ctrl


title: Whole gonad E12.5 XX Enh13-3bp-del-het Rep1

description: Library name: E12.5_XX_Enh13-3bp-del-het_Rep1


title: 024-CD3 [DSP-1001660009393-B-C11]

description:
Library name: DSP-1001660009393-B-C11
LUAD
NanoString GeoMx Digital Spatial Profiling (DSP)


title: m2_Pc_ctrl

description: Library name: m2_Pc_ctrl


title: Whole gonad E12.5 XX Enh13-3bp-12bp-del-hom Rep4

description: Library name: E12.5_XX_Enh13-3bp-12bp-del-hom_Rep4


title: m1_Pc_ctrl

description: Library name: m1_Pc_ctrl


title: HBECs, Donor 3, Not Ya Son's Weed Cartridge Grandaddy Purp, Well 1

description: Library name: DD008Rp1_VapedD8_C_Dis_1


title: m3_actB_veh

description: Library name: m3_actB_veh


title: HBECs, Donor 2, Not Ya Son's Weed Cartridge Grandaddy Purp, Well 2

description: Library name: DD004Op1_VapedD8_C_Dis_2


title: 023-CD3 [DSP-1001660009393-B-C09]

description:
Library name: DSP-1001660009393-B-C09
LUAD
NanoString GeoMx Digital Spatial Profiling (DSP)


title: HBECs, Donor 2, Not Ya Son's Weed Cartridge Grandaddy Purp, Well 1

description: Library name: DD004Op1_VapedD8_C_Dis_1


title: Whole gonad E12.5 XX Enh13-3bp-12bp-del-hom Rep2

description: Library name: E12.5_XX_Enh13-3bp-12bp-del-hom_Rep2


title: HBECs, Donor 1, Not Ya Son's Weed Cartridge Grandaddy Purp, Well 2

description: Library name: DD001Rp1_VapedD8_C_Dis_2


title: 018-CD3 [DSP-1001660009393-B-C07]

description:
Library name: DSP-1001660009393-B-C07
LUAD
NanoString GeoMx Digital Spatial Profiling (DSP)


title: m2_actB_veh

description: Library name: m2_actB_veh


title: Whole gonad E12.5 XX Enh13-3bp-12bp-del-hom Rep3

description: Library name: E12.5_XX_Enh13-3bp-12bp-del-hom_Rep3


title: 023-CD68 [DSP-1001660009393-B-C10]

description:
Library name: DSP-1001660009393-B-C10
LUAD
NanoString GeoMx Digital Spatial Profiling (DSP)


title: 017-CD68 [DSP-1001660009393-B-C06]

description:
Library name: DSP-1001660009393-B-C06
LUAD
NanoString GeoMx Digital Spatial Profiling (DSP)


title: Whole gonad E12.5 XX Enh13-3bp-12bp-del-hom Rep1

description: Library name: E12.5_XX_Enh13-3bp-12bp-del-hom_Rep1


title: HBECs, Donor 1, Not Ya Son's Weed Cartridge Grandaddy Purp, Well 1

description: Library name: DD001Rp1_VapedD8_C_Dis_1


title: Whole gonad E12.5 XX Enh13-1bp-ins-hom Rep5

description: Library name: E12.5_XX_Enh13-1bp-ins-hom_Rep5


title: m3_Pc_veh

description: Library name: m3_Pc_veh


title: 018-CD68 [DSP-1001660009393-B-C08]

description:
Library name: DSP-1001660009393-B-C08
LUAD
NanoString GeoMx Digital Spatial Profiling (DSP)


title: m1_actB_veh

description: Library name: m1_actB_veh


title: HBECs, Donor 4, Palmetto Cartridge Sour Lifter, Well 2

description: Library name: DD021Rp1_VapedD8_A_Dis_2

value: Palmetto Cartridge Sour Lifter


title: 017-CD3 [DSP-1001660009393-B-C05]

description:
Library name: DSP-1001660009393-B-C05
LUAD
NanoString GeoMx Digital Spatial Profiling (DSP)

value: Lung


title: m2_Pc_veh

description: Library name: m2_Pc_veh


title: HBECs, Donor 4, Palmetto Cartridge Sour Lifter, Well 1

description: Library name: DD021Rp1_VapedD8_A_Dis_1


title: 016-CD68 [DSP-1001660009393-B-C04]

description:
Library name: DSP-1001660009393-B-C04
LUAD
NanoString GeoMx Digital Spatial Profiling (DSP)


title: Whole gonad E12.5 XX Enh13-1bp-ins-hom Rep3

description: Library name: E12.5_XX_Enh13-1bp-ins-hom_Rep3


title: HBECs, Donor 3, Palmetto Cartridge Sour Lifter, Well 2

description: Library name: DD008Rp1_VapedD8_A_Dis_2


title: Whole gonad E12.5 XX Enh13-1bp-ins-hom Rep2

description: Library name: E12.5_XX_Enh13-1bp-ins-hom_Rep2


title: m3_actB_heme

description: Library name: m3_actB_heme


title: 016-CD3 [DSP-1001660009393-B-C03]

description:
Library name: DSP-1001660009393-B-C03
LUAD
NanoString GeoMx Digital Spatial Profiling (DSP)

value: T cells


title: 015-CD68 [DSP-1001660009393-B-C02]

description:
Library name: DSP-1001660009393-B-C02
LUAD
NanoString GeoMx Digital Spatial Profiling (DSP)


title: HBECs, Donor 3, Palmetto Cartridge Sour Lifter, Well 1

description: Library name: DD008Rp1_VapedD8_A_Dis_1


title: m2_actB_heme

description: Library name: m2_actB_heme


title: Whole gonad E12.5 XX Enh13-1bp-ins-hom Rep1

description: Library name: E12.5_XX_Enh13-1bp-ins-hom_Rep1


title: HBECs, Donor 2, Palmetto Cartridge Sour Lifter, Well 2

description: Library name: DD004Op1_VapedD8_A_Dis_2


title: Whole gonad E12.5 XX Enh13-1bp-ins-hom Rep4

description: Library name: E12.5_XX_Enh13-1bp-ins-hom_Rep4


title: m1_actB_heme

description: Library name: m1_actB_heme


title: Whole gonad E12.5 XX Enh13-1bp-ins-het Rep3

description: Library name: E12.5_XX_Enh13-1bp-ins-het_Rep3


title: m1_Pc_veh

description: Library name: m1_Pc_veh

value: plasmablast


title: HBECs, Donor 2, Palmetto Cartridge Sour Lifter, Well 1

description: Library name: DD004Op1_VapedD8_A_Dis_1


title: m2_Pc_heme

description: Library name: m2_Pc_heme


title: 015-CD3 [DSP-1001660009393-B-C01]

description:
Library name: DSP-1001660009393-B-C01
LUAD
NanoString GeoMx Digital Spatial Profiling (DSP)


title: Whole gonad E12.5 XX Enh13-1bp-ins-het Rep2

description: Library name: E12.5_XX_Enh13-1bp-ins-het_Rep2


title: HBECs, Donor 1, Palmetto Cartridge Sour Lifter, Well 2

description: Library name: DD001Rp1_VapedD8_A_Dis_2


title: m3_Pc_heme

description: Library name: m3_Pc_heme


title: Whole gonad E12.5 XX Enh13-1bp-ins-het Rep1

description: Library name: E12.5_XX_Enh13-1bp-ins-het_Rep1


title: Control [DSP-1001660009393-B-A01]

description:
Library name: DSP-1001660009393-B-A01
No Template Control
NanoString GeoMx Digital Spatial Profiling (DSP)

value: No Template Control


title: pcDNA3-Flag-hSOX9

type: protein

city: Rehovot

first: Ariel

last: Afek

address: Herzl st 234

institute: Weizmann Institute of Science

description: The protein was obtained by in vitro transcription translation using Promega TnT® Quick Coupled Transcription/Translation System. A standard protocol was followed with 1.5h of incubation at 30 degrees.

hyb_protocol: Commercial microarrays (Agilent Technologies) con-taining all possible 10-mer sequences were converted to double-stranded DNA via solid-phase primer extension using Thermo Sequenase DNA Polymerase (Cytiva, Catalog #: E79000Y)and a deoxynucleotide triphosphate (dNTP) mixture (dATP, dCTP, dGTP, dTTP).

scan_protocol: Slides were scanned immediately after washing on the GenePix® 4400A microarray scanner with 2.5um scan resolution. The dye channel is set to 635nm and 488nm, and PMT is adjusted according to the experiments.

data_processing: Signal intensities were extracted using GenePix Pro 7.0 software, and median pixel intensity was reported for each DNA probe. To identify DNA motifs recognized by the TF of interest, we analyzed all possible 8mers base sequences as previously described. In brief, DNA features were grouped into two sets—those containing the 8mer (foreground) and those without (background). We then compare the top half of signal intensities from both sets using a modified Wilcoxon-Mann-Whitney statistic, which helps identify the most enriched 8mer, termed the "seed" of the motif. Next, we assess the contribution of each nucleotide position within this seed by evaluating all possible nucleotide variants at each position, and the motif was further refined by including gaps at positions with high variability. Finally, we convert the derived motif into a position weight matrix (PWM), allowing for a quantitative representation of the TF's binding specificity. No features were flagged and excluded.

label: Flag

molecule: protein

source_name: Promega TnT® Quick Coupled Transcription/Translation System, in vitro translated protein

label_protocol: Flag tags were incorporated into the plasmids used for the in vitro TnT kits and expressed in the system fusing to the target protein.

extract_protocol: does not apply

value: SOX9 recombinant protein


title: m1_Pc_heme

description: Library name: m1_Pc_heme


title: ADPC/NEPC Patient 1

type: RNA

source_name: Prostate Cancer

extract_protocol: The FFPE tissue sample was sectioned (5um thickness) and mounted to a VWR Superfrost Plus Micro Slide. Sections were air-dried at room temperature for several hours or overnight, and shipped to NanoString for processing using the CosMx Human Universal Cell Characterization 1000-plex RNA Panel through the CosMx Technology Access Program (TAP).

treatment_protocol: Prostate cancer patient tissue was fixed in formalin and paraffin embedded (FFPE). The tissue sample contained normal adjacent, androgen-dependent prostate cancer (ADPC), and de-novo neuroendocrine prostate cancer (NEPC) regions.

value: prostate cancer


title: HBECs, Donor 1, Palmetto Cartridge Sour Lifter, Well 1

description: Library name: DD001Rp1_VapedD8_A_Dis_1


title: pcDNA3.1-Flag-Runx1-FL

value: Runx1 recombinant protein


title: P12 [Visium]

description:
Library name: 372
FFPE Visium Spatial Sequencing

value: Prostate

value: PbCre4:Ptenf/f (P)

value: Intact


title: Enriched CSTA-overexpressing FMC63 CAR T cells from production run 2

status: Public on Feb 20 2026

city: Baltimore

first: Carrie

last: McCracken

state: MD

address: 670 W. Baltimore St.

institute: Institute of Genome Sciences

description: Library name: FMC63_CSTA_Group_2

data_processing:
Reads were assessed for quality, trimmed if PHRED scores fell below 20, and any remaining adapter sequences were removed. Processed paired-end reads were aligned to human reference genome GRCh38 using HISAT2, and counts were generated using the HTseq analysis package. Reads that successfully mapped to the reference genome were used for downstream analyses
Assembly: hg38
Supplementary files format and content: htseq output with gene counts for each sample

source_name: T cells

growth_protocol: Cells were thawed and cultured in T-cell media + 40IU IL-2 for 48 hours. After 48 hours, CAR T cells were washed with FACS buffer, stained with anti-CD3, anti-HA, and DAPI, and sorted for CAR expression. Sorted CAR T cells were then pelleted and flash frozen.

extract_protocol:
RNA was extracted from cells using the Qiagen Rneasy Mini Kit.
Samples were prepped with the NEB polyA enrichment module followed by the NEB Ultra II library prep kit.


title: Enriched wildtype FMC63 CAR T cells from production run 1

description: Library name: FMC63_Group_1


title: Enriched wildtype FMC63 CAR T cells from production run 2

description: Library name: FMC63_Group_2


title: RNA_NSC69C_NT_1

city: Chuo-ku

first: Hideaki

last: Ogiwara

state: Tokyo

address: 5-1-1, Tsukiji

department: Division of Cancer Therapeutics

institute: National Cancer Center Research Institute

description: Library name: RNA_NSC69C_NT_1

data_processing:
Raw RNA-seq data were trimmed with fastp version 0.12.4 and mapped to the hg38 genome with HISAT2 version 2.2.1 (RRID: SCR_015530) (27). TPM values were calculated using Strand NGS ver 4.0 (TOMY).
Raw sequencing data from ATAC-seq were trimmed using fastp version 0.12.4 (RRID: SCR_016962) and mapped to the human reference genome (hg38) using Bowtie2 version 2.4.5 (RRID: SCR_016368), with parameters -k 1 --no-mixed --no-discordant -X 2000. Before all downstream analyses, duplicate reads were removed using the MarkDuplicates command in picard version 2.26.11 (RRID: SCR_006525) [http://broadinstitute.github.io/picard]. CPM values in the genome tracks were calculated from the ATAC-seq data.
Assembly: hg38
Supplementary files format and content: BigWig files for the ATAC-seq and RNA-seq data were generated using the bamCoverage command from deepTools version 3.5.1 (RRID: SCR_016366), with parameters --normalizeUsing CPM --binSize 10 --smoothLength 30.

source_name: diffuse gastric cancer

growth_protocol: RNA-seq: 5 × 10^5 cells were trypsinized, reseeded in 6-well plates for 24 h.

extract_protocol:
The cells were then washed with PBS, and RNA was isolated using the RNeasy Mini Kit (Qiagen)
Library preparation for RNA-seq samples was performed in the Rhelixa using the Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs).
ATAC-seq analysis was performed by DNAFORM. Cells (1 × 105) were lysed and the transposition reaction was performed with Tn5 Transposase (Illumina, FC121-1030) at 37°C for 30 min. The reaction liquid was purified using the MinElute PCR Purification Kit (Qiagen, 28004). Next, five cycles of PCR were conducted using custom Nextera PCR primers and NEBNext Q5 Hot Start HiFi PCR Master Mix (NEB, M0543S). The number of additional PCR cycles was determined by qPCR of the partly amplified products. The PCR products were purified using Agencourt AMPure XP beads (Beckman Coulter, A63881), using double size selection (left ratio: 1.4×; right ratio: 0.5×), according to the manufacturer’s protocol.

treatment_protocol: ATAC-seq: ARID1A-proficient NSC-29C cells (5 × 105) were cultured in 6-well plates and transfected for 72 h with siRNAs (10 nM) for non-targeting or ARID1A using Lipofectamine RNAiMAX (Thermo Fisher Scientific; 13778150).

value: diffuse gastric cancer

value: Patient-derived Cells

value: Non-treatment


title: RNA_NSC76C_NT_1

description: Library name: RNA_NSC76C_NT_1


title: RNA_NSC67C_NT_2

description: Library name: RNA_NSC67C_NT_2


title: RNA_NSC67C_NT_1

description: Library name: RNA_NSC67C_NT_1


title: RNA_NSC76C_NT_2

description: Library name: RNA_NSC76C_NT_2


title: Enriched CSTA-overexpressing FMC63 CAR T cells from production run 1

description: Library name: FMC63_CSTA_Group_1


title: RNA_NSC69C_NT_2

description: Library name: RNA_NSC69C_NT_2


title: OC3 cells 48 hours after LIUS (T1) treatment-Rep2

city: Zhunan Miaoli County

first: Chia

middle: Huei

last: Lee

address: 35, Keyan Rd.

department: National Institute of Cancer Research

country: Taiwan

institute: Taiwan National Health Research Institute

hyb_protocol: Samples were hybridized with Human Clariom S Array (Affymetrix) and scanned at the NHRI Microarray Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: The data were analyzed using Affymetrix Transcriptome Analysis Console (TAC) Software (version 4.0.2) default analysis settings and RMA (Robust Multi-Array) summarization and normalization options.

label: Biotin

source_name: LIUS (T1) treated OSCC OC3 cells

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT Plus cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: OC3 cells, an oral squamous cell carcinoma (OSCC) line, are typically cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin. The cells are maintained at 37°C in a humidified incubator with 5% CO₂.

extract_protocol: Total RNA was isolated cultured cells with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.

treatment_protocol: With or without LIUS/T1 treatment before total RNA extraction

tag: gender

value: male

value: tumor of oral mucosa

tag: tumor stage


title: RNA_NSC29C_NT_1

description: Library name: RNA_NSC29C_NT_1


title: RNA_NSC60C_NT_2

description: Library name: RNA_NSC60C_NT_2


title: Periodontitis2_1

city: Beijing

first: yu

last: chenhao

state: Haidian District

address: 22 ZhongguancunNandajie, Haidian District, Beijing, China

department: School of  stomatology

institute: Peking University

description:
Library name: Periodontitis_3_1
Periodontitis_3

data_processing:
HISAT2 v2.0.5 was used to construct a reference genome index and align paired-end clean reads to the mouse reference genome.
Read counts for each gene were calculated using featureCounts (version 1.5.0-p3).
Differential gene expression analysis was performed using DESeq2 software with FDR < 0.05 as the threshold.
Enrichment analysis of DEGs was conducted via ClusterProfiler package for GO Biological Process, Reactome, and KEGG databases.
Gene Set Enrichment Analysis (GSEA) was applied to explore gene set enrichment related to Th17 cell differentiation.
Assembly: mm10 (Mus musculus genome assembly)
Supplementary files format and content: Tab-delimited text files include raw read counts for each sample.
Supplementary files format and content: Text files include differentially expressed genes (DEGs) with adjusted p-values and fold changes.

source_name: spleen

growth_protocol: Th17 cells were sorted from spleens of IL-17GFP/+ transgenic mice (control/periodontitis groups) via flow cytometry (Beckman CytoFLEX) based on GFP expression, following red blood cell lysis and cell suspension preparation.

extract_protocol:
Total RNA was isolated from sorted Th17 cells using TRIzol reagent. RNA integrity was assessed with the RNA Nano 6000 Assay Kit on the Agilent Bioanalyzer 2100 system.
RNA libraries for RNA-seq were prepared using high-quality RNA (after removing adapters, poly-N sequences, and low-quality reads) and sequenced on the Illumina NovaSeq platform.

treatment_protocol: Periodontitis was induced in mice via ligature of bilateral mandibular first molars with 5-0 sterile silk thread; control mice received no ligature.

value: spleen

value: T helper cell


title: Untreated OC3 cells-Rep2

description: Untreated OC3 cells

source_name: Untreated OSCC OC3 cells


title: Seq_HTO_23

city: Rochester

first: Ruoqiao

last: Wang

state: NY

address: 601 Elmwood Avenue

department: Biomedical Genetics and Genomics

institute: University of Rochester Medical Center

description:
Library name: Seq_HTO_23
10x Genomics

data_processing:
Demultiplexing FASTQ files, feature barcode analysis, and alignment to the GRCh38 reference genome were processed using Cell Ranger (v7.1.0), followed by downstream analysis in Seurat (5.3.0) under R version 4.3.3. Cells that express <200 genes, >7500 genes, and >25% mitochondrial genes were filtered out for initial quality control. Gene counts were followed by normalization using SCTransform while regressing out mito- chondrial percentage. Antibody-derived tag (ADT) counts were normalized using CLR and demultiplexed with a positive quantile threshold of 0.99. Anchor-based reciprocal PCA (RPCA) integration method was used for batch correction.
Assembly: GRCh38
Supplementary files format and content: Single-cell RNA-seq data were analyzed using Seurat (v5.3.0) in R (v4.3.3), and saved in rds format. Cells with <200 genes, >7,500 genes, or >25% mitochondrial expression were removed during quality control. RNA counts were normalized using SCTransform with mitochondrial percentage regressed out. ADT counts were normalized using CLR and demultiplexed using a 0.99 positive quantile threshold. Datasets were integrated using anchor-based RPCA integration for batch correction.
Library strategy: CITE-seq

source_name: PBMCs

extract_protocol:
Cell sorting and monocyte isolation Monocytes were isolated from cryopreserved PBMCs or from whole blood. For whole blood, 6 mL of 1:1 RPMI-diluted blood was thawed at 37◦C and transferred into 44 mL of 2 mM EDTA + 2% FBS in 1X DPBS, followed by centrifugation at 500 ×g for 5 minutes. The supernatant was removed, cells were washed with 800 μL staining buffer (0.5% BSA in 1X DPBS), and centrifuged again at 500 ×g for 5 minutes. After discarding the supernatant, cells were resuspended in 1 mL 1X DPBS. Then, cell suspensions were stained with titrated antibodies against CD14, CD16, CD56 (NK cells), CD20, CD19 (B cells), and CD3 (T cells), scaled to the number of cells per million. Samples were barcoded with 2 μL TotalSeq-B anti-human hashtag antibodies (BioLegend), and Zombie Red viability dye was added at 1:1000. Samples were incubated for 25 minutes at room temperature in the dark, diluted in 1 mL staining buffer, and centrifuged at 500 ×g for 5 minutes. After removing the supernatant, cells were resuspended in 300 μL of staining buffer and passed through a 40 μm strainer to obtain a single-cell suspension.  Monocytes were sorted on a BD FACSAria II flow cytometer using the following gating strategy: SSC-A/FSC-A profile → FSC-H/FSC-W (Singlets) → SSC-H/SSC-W (Singlets) → Zombie Red- (Live cells) → Lineage- (Exclusion of B, T, and NK cells)→ CD14+ and/or CD16+ (Monocytes). Flow-sorted cells were evaluated for viability and concentration using a Bio-Rad TC20 automated cell counter with Trypan Blue staining and then pooled based on cell counts. The pooled cell suspension was loaded into the Chromium Controller (10X Genomics, Pleasanton, CA, USA) to generate single-cell Gel Bead-in-Emulsions (GEMs) following the manufacturer’s protocol.
Prior to flow sorting, cells were labeled with TotalSeq-B anti-human hashtag antibodies, anti-CD298 and anti-beta2-microglobulin, (BioLegend) for cell. Flow sorted cells were evaluated for viability and concentration on a BioRad TC20 automated cell counter with trypan and pooled based on cell counts. The pooled cell suspension was loaded into the Chromium Controller (10x Genomics, Pleasanton, CA, USA) to generate single-cell Gel Bead-in-Emulsions (GEMs), per manufacturer’s protocol. Single-cell RNA-Seq libraries were prepared using Next GEM Single Cell 3′ GEM, Library and Gel Bead Kit v3.1 (10x Genomics). Briefly, GEM reverse transcription (GEM-RT) was performed to produce a barcoded, full-length cDNA from poly-adenylated mRNA. Following cDNA synthesis, GEMs were broken and the pooled cDNA was purified with silane magnetic beads (DynaBeads MyOne Silane Beads, ThermoFisher). The purified cDNA product was then amplified by limited PCR to generate a 3’ cDNA library. Enzymatic fragmentation and size selection is used to optimize the cDNA amplicon size and indexed Illumina sequencing libraries were constructed via end-repair, A-tailing, adaptor ligation, and PCR.  Hashtag library amplification was performed following SPRI bead purification of amplified hashtag and cell surface protein amplicons from above using the 10X Genomics Feature Barcoding library prep kit. Amplified libraries were purified using AMPure XP (Beckman Coulter, Indianapolis, IN) beads and quantified by Qubit dsDNA assay (ThermoFisher, Waltham, MA) and Bioanalyzer HSDNA (Agilent, Santa Clara, CA) analysis.  Hashtag libraries were pooled with 10x Genomics 3’ gene expression libraries for sequencing on Illumina’s NovaSeq 6000.

value: PBMCs

value: monocytes


title: Seq_HTO_24

description:
Library name: Seq_HTO_24
10x Genomics


title: OC3 cells 48 hours after LIUS (T1) treatment-Rep1


title: Health4_1

description:
Library name: Health_4_1
Health_4


title: RNA_NSC29C_NT_2

description: Library name: RNA_NSC29C_NT_2


title: RNA_NSC64C_NT_2

description: Library name: RNA_NSC64C_NT_2


title: Periodontitis1_1

description:
Library name: Periodontitis_2_1
Periodontitis_2


title: RNA_NSC60C_NT_1

description: Library name: RNA_NSC60C_NT_1


title: RNA_NSC64C_NT_1

description: Library name: RNA_NSC64C_NT_1


title: Health2_1

description:
Library name: Health_2_1
Health_2


title: Untreated OC3 cells-Rep1

description: Untreated OC3 cells


title: Health3_1

description:
Library name: Health_3_1
Health_3


title: Periodontitis3_1

description:
Library name: Periodontitis_4_1
Periodontitis_4


title: Health1_1

description:
Library name: Health_1_1
Health_1


title: db-sham2

city: Guangzhou

first: Fang

last: Tan

address: Dongfengdong Road 567

institute: Sun Yat-sen University Cancer Center

description: Library name: Sample 6

data_processing:
Raw data (raw reads) of fastq format were firstly processed using fastp(version 0.20.0) softeware with default parameters in single end mode.
The clean data were obtained for downstream analyses by removing reads containing adapter, reads containing ploy-N and low-quality reads from raw data.
The clean reads were mapped to reference of mouse mRNAs and lncRNAs using bowtie2(version 2.3.1) with parameters -q -L 16 --phred64 -p 6
TPM value and read counts of each transcript were obtained by eXpress(version 1.5.1) with parameters --no-update-check --rf-stranded.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include TPM values for each Sample.
Supplementary files format and content: Tab-delimited text files include raw gene counts for each Sample.

source_name: Intestine

extract_protocol:
Total RNA of intestine samples was extracted respectively using the TRIzol (Thermo Scientific, USA) reagent according to the manufacturer’s protocol. RNA purity and quantification were evaluated using a NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). A total amount of 1 µg RNA per sample was used as initial material for the RNA sample preparations. Ribosomal RNA was removed using Ribo-off™ rRNA Depletion Kit (Human/Mouse/Rat) (Vazyme, China).
The sequencing libraries were generated following manufacturer recommendations with varied index label by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (NEB, USA). The libraries were sequenced on an BGISEQ-500 platform.

value: Intestine

tag: disease state

value: db

value: Sham Operation


title: Seq_HTO_20

description:
Library name: Seq_HTO_20
10x Genomics

tag: tissue


title: Seq_HTO_19

description:
Library name: Seq_HTO_19
10x Genomics

tag: cell type


title: db-sham1

description: Library name: Sample 5


title: Seq_HTO_21

description:
Library name: Seq_HTO_21
10x Genomics


title: Seq_HTO_22

description:
Library name: Seq_HTO_22
10x Genomics


title: Seq_HTO_18

description:
Library name: Seq_HTO_18
10x Genomics


title: db-CLP1

description: Library name: Sample 3

value: CLP


title: Seq_HTO_17

description:
Library name: Seq_HTO_17
10x Genomics


title: db-CLP2

description: Library name: Sample 4


title: Seq_HTO_16

description:
Library name: Seq_HTO_16
10x Genomics


title: Seq_HTO_15

description:
Library name: Seq_HTO_15
10x Genomics


title: wt-CLP1

description: Library name: Sample 1

value: wt


title: Lung airway epithelium, IPF9

city: London

first: Probir

last: Chakravarty

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

description: IPF, Sex: M, Age 50

data_processing:
Library generation for 10x Genomics analysis were performed following the Chromium Single Cell 3′ Reagents Kits (10x Genomics) and sequenced on an Hiseq4000 (Illumina)
Raw reads were initially processed by the Cell Ranger v.3.0.2 pipeline, aligning to the GRChg38 transcriptome
All subsequent analyses were performed in R v.3.6.0  using the Seurat (v3) package
Assembly: GRCh38
Supplementary files format and content: Tab-separated barcodes ID's, features files and count files

source_name: Lung airway epithelium

growth_protocol: Not applicable

extract_protocol:
Enzymatic dissociation with collagenase D from Clostridium histolyticum (Roche) and 0.1mg/ml DNase I from bovine pancreas (Roche). Incubation for 1 hour at 37oC. Dissociated cells passed through passed through a 70μm filter, centrifuged (1200rpm, 5mins, 4oC) and the resulting cell pellet resuspended in HBSS with 0.04% UltraPure BSA (Invitrogen).
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics).

treatment_protocol: Not applicable

value: Lung airway epithelium

value: IPF

value: Epithelial cells, immune cells

value: M

tag: age


title: Lung airway epithelium, IPF8

description: IPF, Sex: M, Age 74


title: Seq_HTO_13

description:
Library name: Seq_HTO_13
10x Genomics


title: Seq_HTO_9

description:
Library name: Seq_HTO_9
10x Genomics


title: Seq_HTO_14

description:
Library name: Seq_HTO_14
10x Genomics


title: Seq_HTO_12

description:
Library name: Seq_HTO_12
10x Genomics


title: Lung airway epithelium, IPF6

description: IPF, Sex: M, Age 79


title: Lung airway epithelium, IPF3

description: IPF, Sex: M, Age 71


title: Lung airway epithelium, IPF5

description: IPF, Sex: M, Age 65


title: Lung airway epithelium, IPF4

description: IPF, Sex: M, Age 84


title: Seq_HTO_6

description:
Library name: Seq_HTO_6
10x Genomics


title: Seq_HTO_5

description:
Library name: Seq_HTO_5
10x Genomics


title: Lung airway epithelium, IPF2

description: IPF, Sex: M, Age 61


title: Seq_HTO_8

description:
Library name: Seq_HTO_8
10x Genomics


title: Lung airway epithelium, H7

description: Healthy, Sex: M, Age: 44

value: Healthy


title: wt-CLP2

description: Library name: Sample 2

tag: treatment


title: Lung airway epithelium, IPF7

description: IPF, Sex: M, Age 66


title: Seq_HTO_10

description:
Library name: Seq_HTO_10
10x Genomics


title: Seq_HTO_11

description:
Library name: Seq_HTO_11
10x Genomics


title: Lung airway epithelium, IPF1

description: IPF, Sex: M, Age 73


title: Seq_HTO_4

description:
Library name: Seq_HTO_4
10x Genomics


title: Seq_HTO_7

description:
Library name: Seq_HTO_7
10x Genomics


title: Lung airway epithelium, H6

description: Healthy, Sex: F, Age: 55

value: F


title: Seq_HTO_3

description:
Library name: Seq_HTO_3
10x Genomics


title: Lung airway epithelium, H5

description: Healthy, Sex: F, Age: 50


title: Lung airway epithelium, H3

description: Healthy, Sex: M, Age: 51


title: Seq_HTO_1

description:
Library name: Seq_HTO_1
10x Genomics


title: Lung airway epithelium, H2

description: Healthy, Sex: F, Age: 26


title: Seq_HTO_2

description:
Library name: Seq_HTO_2
10x Genomics


title: Seq_GEX_24

description:
Library name: Seq_GEX_24
10x Genomics


title: Lung airway epithelium, H1

description: Healthy, Sex: M, Age: 47


title: Seq_GEX_23

description:
Library name: Seq_GEX_23
10x Genomics


title: Seq_GEX_21

description:
Library name: Seq_GEX_21
10x Genomics


title: Seq_GEX_20

description:
Library name: Seq_GEX_20
10x Genomics


title: Lung airway epithelium, H4

description: Healthy, Sex: F, Age: 47


title: Seq_GEX_18

description:
Library name: Seq_GEX_18
10x Genomics


title: Seq_GEX_16

description:
Library name: Seq_GEX_16
10x Genomics


title: Seq_GEX_22

description:
Library name: Seq_GEX_22
10x Genomics


title: Seq_GEX_17

description:
Library name: Seq_GEX_17
10x Genomics


title: SW620_INVITRO_PARENT_SENEXIN-B_C

city: Sutton

first: Konstantinos

last: Mitsopoulos

state: London

address: 15 Cotswold Road

department: Cancer Therapeutics Unit

institute: The Institute of Cancer Research

description: Replicate 2 of 3

hyb_protocol: standard protocol

scan_protocol: standard protocol

data_processing:
# 1.Initialisation
library(limma)
# 2. Read in tab-delimited targets file
sw620_in_vitro_targets <- readTargets(sw620_in_vitro_sample_annotation.txt)
# 3. Use LIMMA's read.maimages function to load data into an RGList object
sw620_in_vitro_RG <- read.maimages(sw620_in_vitro_targets, source=agilent)
# 4. Subtract the background (optional, but recommended)
sw620_in_vitro_RG.b <- backgroundCorrect(sw620_in_vitro_RG, method=normexp, offset=50)
# 5. Normalize within and between the arrays - remove controls
sw620_in_vitro_MA.p <- normalizeWithinArrays(sw620_in_vitro_RG.b, method=loess)
sw620_in_vitro_MA.pAq <- normalizeBetweenArrays(sw620_in_vitro_MA.p, method=Aquantile)
sw620_in_vitro_MA2.pAq <- sw620_in_vitro_MA.pAq[sw620_in_vitro_MA.pAq$genes$ControlType==0,]
# 6. Use the avereps function to average replicate spots
sw620_in_vitro_MA2.ave <- avereps(sw620_in_vitro_MA2.pAq, ID=sw620_in_vitro_MA2.pAq$genes$ProbeName)
# 7. Whole spot contrasts (to use for deriving average expression):
write.table(sw620_in_vitro_MA2.ave$A, file = sw620_in_vitro_MA2_ave_A_expression_matrix.txt, sep=\t)
# 8. Within spot contrasts (to use for log2FC calculations)
write.table(sw620_in_vitro_MA2.ave$M, file = sw620_in_vitro_MA2_ave_M_expression_matrix.txt, sep=\t)

label_protocol: Cy5 (red): human reference standard (Stratagene), Cy3 (green): experimental samples

extract_protocol: standard protocol

tag: condition

value: in vitro

tag: cell line background

value: colorectal cell line

tag: clone

value: PARENT

tag: compound

source_name: human reference standard

value: reference


title: SW620_INVITRO_PARENT_SEL120-34A_D

description: Replicate 3 of 3


title: SW620_INVITRO_PARENT_SENEXIN-B_B

description: Replicate 1 of 3


title: Seq_GEX_15

description:
Library name: Seq_GEX_15
10x Genomics

value: PBMCs


title: SW620_INVITRO_PARENT_SEL120-34A_B

description: Replicate 1 of 3


title: Seq_GEX_19

description:
Library name: Seq_GEX_19
10x Genomics

value: monocytes


title: SW620_INVITRO_PARENT_MSC2530818_D

description: Replicate 3 of 3


title: Seq_GEX_14

description:
Library name: Seq_GEX_14
10x Genomics


title: SW620_INVITRO_PARENT_SEL120-34A_C

description: Replicate 2 of 3


title: Seq_GEX_13

description:
Library name: Seq_GEX_13
10x Genomics


title: SW620_INVITRO_PARENT_MSC2530818_B

description: Replicate 1 of 3


title: SW620_INVITRO_PARENT_MSC2530818_C

description: Replicate 2 of 3


title: Seq_GEX_12

description:
Library name: Seq_GEX_12
10x Genomics


title: SW620_INVITRO_PARENT_SENEXIN-B_D

description: Replicate 3 of 3


title: SW620_INVITRO_PARENT_DMSO_D

description: Replicate 3 of 3

value: DMSO


title: Seq_GEX_11

description:
Library name: Seq_GEX_11
10x Genomics


title: Seq_GEX_9

description:
Library name: Seq_GEX_9
10x Genomics


title: Seq_GEX_8

description:
Library name: Seq_GEX_8
10x Genomics


title: SW620_INVITRO_PARENT_DMSO_C

description: Replicate 2 of 3


title: Seq_GEX_7

description:
Library name: Seq_GEX_7
10x Genomics


title: SW620_INVITRO_PARENT_DMSO_B

description: Replicate 1 of 3


title: Seq_GEX_6

description:
Library name: Seq_GEX_6
10x Genomics


title: Seq_GEX_10

description:
Library name: Seq_GEX_10
10x Genomics


title: SW620_INVITRO_PARENT_CCT251921_D

description: Replicate 3 of 3


title: SW620_INVITRO_PARENT_CCT251921_C

description: Replicate 2 of 3


title: Seq_GEX_2

description:
Library name: Seq_GEX_2
10x Genomics


title: SW620_INVITRO_PARENT_CCT251545_B

description: Replicate 1 of 3


title: SW620_INVITRO_PARENT_CCT251545_C

description: Replicate 2 of 3


title: Seq_GEX_3

description:
Library name: Seq_GEX_3
10x Genomics


title: SW620_INVITRO_PARENT_CCT251921_B

description: Replicate 1 of 3


title: SW620_INVITRO_PARENT_CCT251545_D

description: Replicate 3 of 3


title: SW620_INVITRO_CDK8_CL1_DMSO_D

description: Replicate 3 of 3

value: CDK8 KO, clone1


title: SW620_INVITRO_CDK8_CL1_DMSO_C

description: Replicate 2 of 3


title: con-8

first: Fengna

last: Yan

address: No. 8 Jingshun East Street, Chaoyang District

department: Beijing Ditan Hospital

institute: Capital Medical University

description:
Library name: con-8
health blood

data_processing:
Raw reads were trimmed of adapters and low-quality bases using Fastp (v0.20.1) and processed with the SeekSoul Tools pipeline to generate a gene-expression matrix. Downstream analyses were performed in Seurat v3: nuclei or cells of high or low quality were filtered based on gene counts, UMI counts, and mitochondrial gene proportions; after normalization, PCA was applied for dimensionality reduction followed by graph-based clustering. Intestinal mucosal cell subpopulations were extracted, and differentially expressed genes (DEGs) between conditions were identified using the Wilcoxon rank-sum test (adjusted p < 0.05). Finally, GO and KEGG pathway enrichment analyses of these DEGs were conducted using ClusterProfiler to elucidate the molecular mechanisms underlying PEDV-induced changes in intestinal mucosal cells.
Assembly: hg38
Supplementary files format and content: tab-separated values files and matrix files

source_name: blood

extract_protocol:
An appropriate number of cells were loaded into the flow channel of the MM chip and allowed to settle into microwells by gravity. Unsettled cells were removed, and cell-barcoded magnetic beads (CBBs) were pipetted into the flow channel and allowed to settle into microwells under a magnetic field. Excess CBBs were rinsed away, and cells on the MM chip were lysed to release and capture RNA.
Reverse transcription was carried out at 37 °C for 30 min. The barcoded cDNA on CBBs was hybridized with a random primer containing read-2 SeqPrimer sequences at the 5′ end, enabling extension to form the second strand with a 3′ cell barcode. The resulting second-strand DNA was denatured off the CBBs, purified, and amplified by PCR. The cDNA product was cleaned, ligated to adapters and sample indices, and the indexed sequencing libraries were purified with SPRI beads, quantified, and sequenced on an Illumina NovaSeq.

value: blood


title: T-5

description:
Library name: T-5
health blood

source_name: liver

value: liver


title: SW620_INVITRO_CDK8_CL1_CCT251545_D

description: Replicate 3 of 3


title: SW620_INVITRO_CDK8_CL1_CCT251545_C

description: Replicate 2 of 3


title: SW620_INVITRO_CDK8_CL1_DMSO_B

description: Replicate 1 of 3


title: SW620_INVITRO_CDK8_CL1_CCT251545_B

description: Replicate 1 of 3


title: SW620_INVITRO_CDK8_CL2_DMSO_D

description: Replicate 3 of 3

value: CDK8 KO, clone2


title: con-7

description:
Library name: con-7
health blood


title: T-4

description:
Library name: T-4
tumor


title: con-6

description:
Library name: con-6
health blood


title: PT-5

description:
Library name: PT-5
Adjacent Non-tumor Liver Tissue


title: SW620_INVITRO_CDK8_CL2_DMSO_C

description: Replicate 2 of 3


title: PT-4

description:
Library name: PT-4
Adjacent Non-tumor Liver Tissue


title: SW620_INVITRO_CDK8_CL2_CCT251545_C

description: Replicate 2 of 3


title: con-5

description:
Library name: con-5
health blood


title: con-4

description:
Library name: con-4
health blood


title: SW620_INVITRO_CDK8_CL2_DMSO_B

description: Replicate 1 of 3


title: PT-3

description:
Library name: PT-3
Adjacent Non-tumor Liver Tissue


title: T-3

description:
Library name: T-3
tumor


title: SW620_INVITRO_CDK8CDK19_CL1_DMSO_D

description: Replicate 3 of 3

value: CDK8 and CDK19 KO, clone1


title: con-3

description:
Library name: con-3
health blood


title: SW620_INVITRO_CDK8CDK19_CL1_DMSO_B

description: Replicate 1 of 3


title: T-2

description:
Library name: T-2
tumor


title: SW620_INVITRO_CDK8_CL2_CCT251545_B

description: Replicate 1 of 3


title: SW620_INVITRO_CDK8_CL2_CCT251545_D

description: Replicate 3 of 3


title: PT-2

description:
Library name: PT-2
Adjacent Non-tumor Liver Tissue


title: Seq_GEX_4

description:
Library name: Seq_GEX_4
10x Genomics


title: SW620_INVITRO_CDK8CDK19_CL1_DMSO_C

description: Replicate 2 of 3


title: SW620_INVITRO_CDK8CDK19_CL1_CCT251545_D

description: Replicate 3 of 3


title: con-1

description:
Library name: con-1
health blood


title: SW620_INVITRO_CDK8CDK19_CL2_DMSO_D

description: Replicate 3 of 3

value: CDK8 and CDK19 KO, clone2


title: SW620_INVITRO_CDK8CDK19_CL1_CCT251545_B

description: Replicate 1 of 3


title: SW620_INVITRO_CDK8CDK19_CL1_CCT251545_C

description: Replicate 2 of 3


title: PT-1

description:
Library name: PT-1
Adjacent Non-tumor Liver Tissue


title: SW620_INVITRO_CDK8CDK19_CL2_CCT251545_D

description: Replicate 3 of 3


title: SW620_INVITRO_CDK8CDK19_CL2_DMSO_B

description: Replicate 1 of 3


title: WTC11 hiPSC, Passage 81, high purity hPSM-CM differentiation, D6

city: Madison

first: Sean

middle: P.

last: Palecek

state: Wisconsin

address: 1415 Engineering Drive

department: Chemical and Biological Engineering

institute: University of Wisconsin-Madison

description:
Library name: W81g_D6
column name in both processed data files: WTC11_High_D6

data_processing:
Raw FASTQ files were mapped to the human genome (hg38+decoy) using STAR v2.5.3a
Gene-level transcript abundances were calculated using featureCounts v2.0.3
Assembly: Assembly: hg38+decoy
Supplementary files format and content: csv files starting with featureCounts include gene-level counts for each sample and gene, csv files starting with TPM include transcipts per million values for each sample and gene

source_name: WTC11 hiPSC line

growth_protocol: hPSCs were differentiated using the GiWi protocol as described previously. On Day -2, hPSCs were detached and singularized with Accutase (Innovative Cell Technology AT104) for 5 min prior to quenching 1:1 v/v in DMEM/F12 (ThermoFisher 11330032). Subsequently, hPSCs were counted and resuspended at cell densities optimized for cardiomyocyte differentiation for each hPSC line. hPSCs were resuspended in mTeSR1 with 5 μM Y-27632 (Tocris 1254) and seeded onto Matrigel-coated 12-well plates in 2 mL of media. To facilitate even cell attachment on Day -2, plates were left at room temperature for 30 min prior to maintenance in a cell culture incubator. On Day -1, medium was replaced with mTeSR1. On Day 0, differentiation was induced with CHIR99021 (Selleckchem S1263) at a concentration between 6-12 μM, optimized for cardiomyocyte differentiation for each hPSC line. CHIR99021 was added to RPMI1640 medium (Life Technologies 11875119) with 2% v/v B27 minus insulin (B27-). After Day 0, protocol timing is dependent on hPSC line as previously established. For WTC11 hiPSCs, media was replaced with B27- and 5 μM IWP2 (Tocris 3533) on Day 2 and on Day 4 with B27-. On Days 6, 8, 10, and 13, media was replaced with RPMI1640 with 2% v/v B27 with insulin (B27+, Life Technologies 17504044) until collection on Day 16. In GiWi hPSCs (IMR90-4 hiPSCs and H9 hESCs), media was replaced on Days 1 and 5 with B27- and on Day 3 with 1:1 v/v B27-:conditioned medium with 5 μM IWP2. On Days 7, 10, and 13, media was replaced with B27+ until collection on Day 16.

extract_protocol:
For both the multi-omic collection experiment and the RNA sequencing only collection, RNA was harvested from Trizol-collected samples by tri-phasic extraction followed by purification and concentration with Zymo Direct-zol MiniPrep Plus columns (including on-column DNAase treatment). 500ng of total RNA per sample was used for the construction of sequencing libraries.
For the multi-omic collection experiment, mRNA libraries for RNA sequencing were constructed using the Illumina TruSeq Stranded mRNA kit and sequenced on an Illumina NovaSeq6000. For the RNA sequencing only collection experiment, total RNA libraries for RNA sequencing were constructed using the Takara SMARTer Stranded Total RNA Kit - HI Mammalian and sequenced on an Illumina NovaSeq 6000.

treatment_protocol: After hPSC-CM differentiation was completed and flow cytometry was performed to quantify hPSC-CM differentiation purity (%cTnT+ cells), differentiations were classified as either high or low purity. Subsequently, temporally trizol-collected high and low purity hPSC-CM differentiation samples were further processed for RNA sequencing.

tag: cell line

value: WTC11 hiPSC line

tag: time

value: high purity hPSC-CM differentiation

value: RNAseq from RNA-only experiment


title: SW620_INVITRO_CDK8CDK19_CL2_DMSO_C

description: Replicate 2 of 3


title: WTC11 hiPSC, Passage 81, high purity hPSM-CM differentiation, D2

description:
Library name: W81g_D2
column name in both processed data files: WTC11_High_D2

tag: batch


title: WTC11 hiPSC, Passage 81, high purity hPSM-CM differentiation, D0

description:
Library name: W81g_D0
column name in both processed data files: WTC11_High_D0


title: T-1

description:
Library name: T-1
tumor


title: SW620_INVITRO_CDK8CDK19_CL2_CCT251545_B

description: Replicate 1 of 3


title: con-2

description:
Library name: con-2
health blood


title: SW620_INVITRO_CDK19_CL2_DMSO_D

description: Replicate 3 of 3

value: CDK19 KO, clone2


title: WTC11 hiPSC, Passage 69, low purity hPSM-CM differentiation, D2

description:
Library name: W69b_D2
column name in both processed data files: WTC11_Low_D2

value: low purity hPSC-CM differentiaiton


title: SW620_INVITRO_CDK19_CL2_DMSO_C

description: Replicate 2 of 3

value: in vitro

value: colorectal cell line


title: WTC11 hiPSC, Passage 69, low purity hPSM-CM differentiation, D4

description:
Library name: W69b_D4
column name in both processed data files: WTC11_Low_D4


title: SW620_INVITRO_CDK19_CL2_CCT251545_D

description: Replicate 3 of 3

value: reference


title: WTC11 hiPSC, Passage 81, high purity hPSM-CM differentiation, D4

description:
Library name: W81g_D4
column name in both processed data files: WTC11_High_D4


title: WTC11 hiPSC, Passage 69, low purity hPSM-CM differentiation, D0

description:
Library name: W69b_D0
column name in both processed data files: WTC11_Low_D0


title: WTC11 hiPSC, Passage 69, low purity hPSM-CM differentiation, D6

description:
Library name: W69b_D6
column name in both processed data files: WTC11_Low_D6


title: IMR90-4 hiPSC, Passage 75, low purity hPSC-CM differentiation, D7

description:
Library name: I75b_D7
column name in both processed data files: IMR90_Low_D7

source_name: IMR90-4 hiPSC line

value: IMR90-4 hiPSC line


title: SW620_INVITRO_CDK19_CL2_DMSO_B

description: Replicate 1 of 3


title: SW620_INVITRO_CDK19_CL1_DMSO_D

description: Replicate 3 of 3

value: CDK19 KO, clone1


title: IMR90-4 hiPSC, Passage 75, low purity hPSC-CM differentiation, D5

description:
Library name: I75b_D5
column name in both processed data files: IMR90_Low_D5


title: IMR90-4 hiPSC, Passage 75, low purity hPSC-CM differentiation, D3

description:
Library name: I75b_D3
column name in both processed data files: IMR90_Low_D3


title: SW620_INVITRO_CDK19_CL2_CCT251545_C

description: Replicate 2 of 3


title: IMR90-4 hiPSC, Passage 55, high purity hPSC-CM differentiation, D7

description:
Library name: I55g_D7
column name in both processed data files: IMR90_High_D7


title: IMR90-4 hiPSC, Passage 75, low purity hPSC-CM differentiation, D0

description:
Library name: I75b_D0
column name in both processed data files: IMR90_Low_D0


title: SW620_INVITRO_CDK19_CL1_DMSO_C

description: Replicate 2 of 3

value: DMSO


title: IMR90-4 hiPSC, Passage 55, high purity hPSC-CM differentiation, D5

description:
Library name: I55g_D5
column name in both processed data files: IMR90_High_D5


title: SW620_INVITRO_CDK19_CL1_CCT251545_D

description: Replicate 3 of 3


title: IMR90-4 hiPSC, Passage 55, high purity hPSC-CM differentiation, D0

description:
Library name: I55g_D0
column name in both processed data files: IMR90_High_D0


title: Pcbp1cKO_4

city: Los Angeles

first: Yao Wei

last: Lu

state: CA

address: 2011 Zonal Ave

department: Department of Medicine

institute: University of Southern California

data_processing:
FASTQ files were extracted and sequencing adapters and low-quality reads were removed by Cutadapt (v.2.3)
Quality of the processed FASTQ files were checked by FastQC (Babraham Bioinformatics), then aligned to the mouse genome (Esembl GRCm38 genome obtained from GENCODE) using HISAT2 (v.2.1.0)
EdgeR (v.3.26.1) was used to identify differentially expressed genes.
Assembly: Assembly: Esembl GRCm38.102
Supplementary files format and content: Supplementary files format and content: CSV, raw counts of sequencing reads on the gene level

source_name: heart ventricle

growth_protocol: All animal experiments were approved by the Institutional Animal Care and Use Committees.

extract_protocol:
Total RNA from the embryonic heart ventricles was isolated using TRIzol (Invitrogen) from tissues using standard protocol. rRNA-depleted libraries were generated with the TruSeq RNA Library Preparation Kit (Illumina) RNA-sequencing was processed by GENEWIZ using Illumina platform (paired-ended, 150bp read-length)
rRNA-depletion library

value: heart ventricle

tag: developmental stage

tag: genotype


title: IMR90-4 hiPSC, Passage 55, high purity hPSC-CM differentiation, D3

description:
Library name: I55g_D3
column name in both processed data files: IMR90_High_D3


title: H9 hESC, Passage 58, high purity hPSC-CM differentiation, D7

description:
Library name: H58g_D7
column name in both processed data files: H9_High_D7

source_name: H9 hESC line

value: H9 hESC line


title: H9 hESC, Passage 58, high purity hPSC-CM differentiation, D3

description:
Library name: H58g_D3
column name in both processed data files: H9_High_D3


title: SW620_INVITRO_CDK19_CL1_CCT251545_C

description: Replicate 2 of 3


title: Control 5


title: Pcbp1cKO_5


title: SW620_INVITRO_CDK19_CL2_CCT251545_B

description: Replicate 1 of 3


title: Control 4


title: SW620_INVITRO_CDK19_CL1_DMSO_B

description: Replicate 1 of 3


title: Control 3


title: SW620_INVITRO_CDK19_CL1_CCT251545_B

description: Replicate 1 of 3


title: H9 hESC, Passage 58, high purity hPSC-CM differentiation, D0

description:
Library name: H58g_D0
column name in both processed data files: H9_High_D0


title: Control 2


title: H9 hESC, Passage 58, high purity hPSC-CM differentiation, D5

description:
Library name: H58g_D5
column name in both processed data files: H9_High_D5


title: Pcbp1cKO_2


title: H9 hESC, Passage 55, low purity hPSC-CM differentiation, D7

description:
Library name: H55b_D7
column name in both processed data files: H9_Low_D7


title: H9 hESC, Passage 55, low purity hPSC-CM differentiation, D3

description:
Library name: H55b_D3
column name in both processed data files: H9_Low_D3


title: Pcbp1cKO_3


title: H9 hESC, Passage 55, low purity hPSC-CM differentiation, D5

description:
Library name: H55b_D5
column name in both processed data files: H9_Low_D5


title: Control 1


title: AKOm6_P21_6

source_name: Heart ventricle

value: Heart ventricle

tag: Sex

value: Male


title: WTC11 hiPSC, Passage 69, low purity hPSM-CM differentiation, D16, Well Replicate 3

description:
Library name: W69D16-3
column name in both processed data files: Low_D16_3

value: RNAseq from multi-omics experiment


title: H9 hESC, Passage 55, low purity hPSC-CM differentiation, D0

description:
Library name: H55b_D0
column name in both processed data files: H9_Low_D0


title: Pcbp1cKO_1


title: AWT_P21_4


title: AKOm6_P21_4


title: AWT_P21_5


title: WTC11 hiPSC, Passage 69, low purity hPSM-CM differentiation, D16, Well Replicate 1

description:
Library name: W69D16-1
column name in both processed data files: Low_D16_1


title: WTC11 hiPSC, Passage 69, low purity hPSM-CM differentiation, D16, Well Replicate 2

description:
Library name: W69D16-2
column name in both processed data files: Low_D16_2


title: WTC11 hiPSC, Passage 69, low purity hPSM-CM differentiation, D13, Well Replicate 4

description:
Library name: W69D13-4
column name in both processed data files: Low_D13_4


title: WTC11 hiPSC, Passage 69, low purity hPSM-CM differentiation, D13, Well Replicate 3

description:
Library name: W69D13-3
column name in both processed data files: Low_D13_3


title: AWT_P21_3


title: WTC11 hiPSC, Passage 69, low purity hPSM-CM differentiation, D13, Well Replicate 2

description:
Library name: W69D13-2
column name in both processed data files: Low_D13_2


title: AKOm6_P21_3


title: Seq_GEX_5

description:
Library name: Seq_GEX_5
10x Genomics

value: PBMCs

value: monocytes


title: AKOm6_P21_5


title: AKOm6_P21_2


title: AHet_P21_1


title: AWT_P21_2


title: WTC11 hiPSC, Passage 69, low purity hPSM-CM differentiation, D8, Well Replicate 4

description:
Library name: W69D8-4
column name in both processed data files: Low_D8_4

value: WTC11 hiPSC line


title: WTC11 hiPSC, Passage 69, low purity hPSM-CM differentiation, D10, Well Replicate 3

description:
Library name: W69D10-3
column name in both processed data files: Low_D10_3


title: WTC11 hiPSC, Passage 69, low purity hPSM-CM differentiation, D10, Well Replicate 1

description:
Library name: W69D10-1
column name in both processed data files: Low_D10_1


title: WTC11 hiPSC, Passage 69, low purity hPSM-CM differentiation, D8, Well Replicate 3

description:
Library name: W69D8-3
column name in both processed data files: Low_D8_3


title: WTC11 hiPSC, Passage 69, low purity hPSM-CM differentiation, D10, Well Replicate 2

description:
Library name: W69D10-2
column name in both processed data files: Low_D10_2


title: WTC11 hiPSC, Passage 69, low purity hPSM-CM differentiation, D10, Well Replicate 4

description:
Library name: W69D10-4
column name in both processed data files: Low_D10_4


title: WTC11 hiPSC, Passage 69, low purity hPSM-CM differentiation, D6, Well Replicate 4

description:
Library name: W69D6-4
column name in both processed data files: Low_D6_4


title: AKOm6_P21_1


title: Control_5


title: AcKO_3


title: WTC11 hiPSC, Passage 69, low purity hPSM-CM differentiation, D8, Well Replicate 2

description:
Library name: W69D8-2
column name in both processed data files: Low_D8_2


title: Control_4


title: AWT_P21_1


title: WTC11 hiPSC, Passage 69, low purity hPSM-CM differentiation, D13, Well Replicate 1

description:
Library name: W69D13-1
column name in both processed data files: Low_D13_1


title: AcKO_5


title: WTC11 hiPSC, Passage 69, low purity hPSM-CM differentiation, D8, Well Replicate 1

description:
Library name: W69D8-1
column name in both processed data files: Low_D8_1


title: AcKO_4


title: WTC11 hiPSC, Passage 69, low purity hPSM-CM differentiation, D6, Well Replicate 3

description:
Library name: W69D6-3
column name in both processed data files: Low_D6_3