title: ATAC_Homeostasis_rep3

city: Kansas City

first: Shiyuan

middle: (Cynthia)

state: MO

department: Computational Biology

institute: Stowers Institute for Medical Research

description: Library name: ATAC_Homeostasis_rep3_L38874

data_processing:
Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq. Reads were aligned to UCSC genome danRer11 with bowtie2 aligner.
Assembly: danRer11
Supplementary files format and content: bigwig files for ATACseq

organism: Danio rerio

source_name: 5dpf FACS sorted zebrafish lateral line

extract_protocol:
600 each embryos of the Tg (she:H2A-mCherry)psi56Tg lateral line marker line were separately dissociated in 4.5ml 0.25% Trypsin-EDTA (Gibco) for 3.5 minutes on ice by triturating with a 1ml pipette repeatedly. Supernatant containing cells was filtered through a 70μm Cup Filcon (BD Biosciences) and cells were pelleted by centrifugation at 720g for five minutes at 4C. Cells were washed in cold PBST by resuspending the pellet and pelleted again at 720g for five minutes at 4C. Cells were filtered through a 35μm strainer (Falcon-Corning), and stained with Draq5 (BioStatus) at a dilution of 1:500. Cells were then sorted on a BD Influx Cell Sorter (BD Biosciences). mCherry and Draq5 double positive cells were sorted into DPBS.
Cells were pelleted by spinning in a microcentrifuge for 5 mins at 4°C and 1000g. Supernatant was removed carefully by pipette, and cells were resuspended in tagmentation reaction mix (22.5 μl H2O, 25μl TD Buffer (Illumina), and 2.5 μl TD Enzyme (Illumina)) and incubated in a ThermoMixer (Eppendorf) at 37°C for 30 minutes, 1000 RPM. 50 μl reverse crosslinking buffer (final concentration of 50mM TRIS pH 8, 1mM EDTA, 1% SDS, 200mM NaCl, 5ng/ml Proteinase K (Roche)) was added and mixture was incubated at 65°C overnight in a ThermoMixer. Tagmented DNA was purified with a DNA Clean & Concentrator 5 kit (Zymo Research) and eluted in 20 μl H2O. Library PCR amplification was performed with 20 μl eluted DNA, 25 μl NEBNext Ultra II Q5 Master Mix, 2.5ul forward primer Ad1 25M stock, 2.5ul reverse barcode primer115 Ad 2.x 25M stock. PCR conditions as follows: 72°C 5 mins, 98°C 30 seconds, 11 cycles of 98°C 10 seconds, 63°C 30 seconds, 72°C 1 minute, 4°C hold. Library was size selected with SPRIselect beads (Beckman Coulter) with the following conditions: 0.8x volume of beads first selection, the supernatant was retained and an additional 1.0x volume of beads was added (total volume 1.8x). The bead pellet was retained and rinsed with 85% EtOH, dried and DNA was eluted in 30ul H2O. Libraries were analyzed on a Bioanalyzer 2100 (Agilent) to evaluate tagmentation and quantified on a Qubit 3.0 (Thermo Fisher).

value: 5dpf FACS sorted zebrafish lateral line

value: Homeostasis

value: wild type

value: No


title: small EVs_15-370_CRC

status: Public on Jul 07 2025

type: RNA

city: Brno

first: Robin

last: Jugas

address: Kamenice 5

country: Czech Republic

institute: CEITEC MU

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then at 45°C for 5 minutes • Transfer 200 μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using R package oligo and custom made probe annotation. Background subtraction, normalization and summarization was done with RMA algorithm.
Clariom_D_Human.r1.pgf
Clariom_D_Human.r1.mps

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: blood serum small exctracellular vesicles

label_protocol: The fragmented cDNA was labeled by TdT using the proprietary DNA labeling reagent that is covalently linked to biotin according to the manufacturer's recommendations.

growth_protocol: not applicable

extract_protocol: Small EVs were isolated from 150 µl of sera. After the sample passed onto the column, 800 μl of 1X PBS was applied to the column. The fraction containing small EVs was eluted by applying 500 μl of 1X PBS to the column and collected. All samples were treated with proteinase K (20 mg/mL, 10 µl) and RNase Cocktail Enzyme Mix (20 000 U/mL, 5 µl) at 37 °C for 10 min. Finally, SUPERase·In RNase Inhibitor (20 U/μL, 4 µl) was added and mixed well. Total RNA including small RNAs was isolated from small EVs using Monarch® Total RNA Miniprep Kit (New England Biolabs) according to the manufacturer’s recommendations, treated with DNase I, and eluted with 50 μl of DEPC-treated water.

treatment_protocol: All samples were centrifuged at 1500 × g for 10 min at 4 °C and then at 10000 × g for 20 min at 4 °C.

tag: condition

value: CRC

tag: gender

value: female

tag: age

tag: diagnosis

tag: clinical stage

tag: localization

value: distal


title: ATAC_Homeostasis_rep2

type: SRA

last: Chen

country: USA

description: Library name: ATAC_Homeostasis_rep2_L37788

library_source: genomic

molecule: genomic DNA

tag: tissue

tag: cell type

tag: genotype

tag: treatment


title: induced pluripotent stem cell-derived fibroblasts grown in standard medium, replicate 1

city: Berlin

first: January

last: Weiner

address: Charitéplatz 1

department: CUBI

country: Germany

institute: Berlin Institute of Health, Charité Medical University of Berlin

description: Library name: A1

library_source: transcriptomic

data_processing:
Reads were mapped to human genome using the STAR aligner v. 2.7.3a. Raw counts were derived using the featureCounts program and GENCODE genome annotation v. 25.
Assembly: GRCh38 p7
Supplementary files format and content: TSV file with raw counts data

molecule: polyA RNA

growth_protocol: Human tissue material and maintenance The human iPSC lines used in this study were BIHi005-A, KCL-004, and KCL-011. The BIHi005-A line was obtained from the iPSC biobank maintained at the Berlin Institute of Health (Berlin, Germany), with detailed information regarding the donor, cell line derivation, ethical approval, and third-party availability accessible at the Human Pluripotent Stem Cell Registry (https://hpscreg.eu/cell-line/BIHi005-A). The derivation and use of KCL-004 and KCL-011 iPSC lines were approved by the UK National Health Service Research Ethics Committee under Reference 11/LO/0295. Informed consent was obtained from all donors, and all experiments adhered to the principles outlined in the WMA Declaration of Helsinki and the NIH Belmont Report. No financial inducements were offered for donation. Jejunal-organoids were obtained from Technische Universität Berlin who generated organoids from patient material with ethical approval from the University of Würzburg's ethics committee (Approval 37/16)29. ASC-jejunal cells were cultured in EIF medium as organoids for expansion and seeded on Matrigel-coated transwells (1:50) for monolayer formation for subsequent terminal differentiation. Normal Primary human keratinocytes and dermal fibroblasts were isolated from juvenile foreskin according to established standard procedures (with written, informed consent and ethical approval from Charité Ethics Board, approval #EA1/081/13). KCs were cultivated in EpiLife supplemented with Human Keratinocyte Growth Supplement (Thermo Scientific). human bronchial epithelial cells (NHBE) and lung fibroblasts were purchased from Epithelix. Normal human bronchial epithelial cells were cultured in PneumaCult Ex Plus (STEMCELL Technologies). Human intestinal fibroblasts were purchased from ScienCell. Cardiac fibroblasts were obtained as a gift from Prof. Sophie van Linthout. Primary fibroblasts were cultured in Fibroblast growth medium (FGM: DMEM (Sigma, D6546) supplemented with 10% FBS, 2mM L-glutamine and 400U/ml Penicillin/Streptomycin). iPSC maintenance and iFB generation The cells were cultured in E8 MDC-HomeBrew medium. Cells were passaged using TrypLE Express and plated in culture medium supplemented with iMatrix-511 (NP892-011, Reprocell) and 10µM Y-27632 (1254, Tocris). Medium was refreshed daily. iPSCs were differentiated into iFBs by adapting a previously published protocol 28 after being seeded at 2x104 cells/cm2 on iMatrix-511 in E8 medium with 10µM Y-27632. The next day, differentiation began in CnT-PR-F +10% FBS +25ng/mL BMP4, transitioning to Fibroblast Growth Medium (FGM) on Day 4. From Days 6–10, 10µM SB-43125 was added to prevent myofibroblast transition. Basic iFB characterisation is found in Fig. S1. Generation of iPSC-CMs At ~90% iPSC confluence, cardiac differentiation was initiated in RPMI + B27 (minus insulin) with CHIR99021 (8µM Day 0; 4µM Day 1), followed by 5µM IWR-1 on Day 3. On Day 7, cells were switched to RPMI + B27 (plus insulin). Spontaneous contractions typically began aroundDays 8–10. All media from Days 0–7 contained 30µM L-ascorbic acid.

extract_protocol:
Total RNA was extracted from iFBs. Briefly, models were lysed in PureLink RNA Mini Kit lysis buffer. RNA was isolated according to the manufacturer’s protocol. Total RNA was quantified, and cDNA was synthesised, using iScriptTM cDNA Synthesis Kit. The subsequent RT-qPCR was performed using SYBR Green I Master Mix (Bio-Rad Laboratories). 18S served as a Housekeeping gene control.
For library preparation, we used the Novogene NGS RNA Library Prep Set (PT042). Polyadenylated mRNA was enriched with oligo(dT)25 beads, randomly fragmented, and reverse-transcribed using random hexamers. The resulting double-stranded cDNA underwent purification, end-repair, A-tailing, and adapter ligation before PCR enrichment with indexed P5 and P7 primers. After quality checks via Qubit 2.0, real-time PCR, and Bioanalyzer 2100, libraries were pooled and sequenced on the Illumina Novaseq X platform (paired-end 150, PE150).

treatment_protocol: Co-culture of iFBs Setup Preparation of iFBs On day 10 post-differentiation initiation, iFBs were passaged using 0.25% trypsin-EDTA for 5minutes at 37°C. Following detachment, cells were collected, counted using a hemocytometer, and resuspended in culture medium. For co-culture experiments, iFBs were seeded at 3x104 cells/cm2 onto the Matrigel-coated basal side of inverted transwell inserts. Cells were allowed to adhere and settle for 45 minutes at 37°C in a humidified incubator with 5% CO₂. The inserts were then placed into standard culture wells containing FGM supplemented with 10 μM Y-27632 for submerged culture. Cells were maintained under these conditions for 24 hours prior to the introduction of organ-specific cell types. Direct Co-Culture Setup The following day, keratinocytes, NHBEs, iPSC-derived cardiomyocytes, or ASC-derived jejunal cells (Fig. S2) were seeded on the apical side of the transwell insert at a cell density of 3x104 cm2. This configuration allowed separation of iFBs and organ-specific cells by only the thin, permeable transwell membrane, thereby constituting a direct co-culture system. Direct co-cultures were maintained for 7 days in respective media (RPMI/B27 for cardiac, EpiLife for dermal, PneumaCult ExPlus for pulmonary, EIF for intestinal). iFBs were then collected for analysis; control iFBs were maintained separately but in the same media for direct comparison. Indirect Co-Culture Setup For indirect co-culture, iFBs were seeded on a Matrigel-coated plate; a transwell with organ-specific cells was placed above. After 7 days, some co-cultures were harvested, while others had the insert removed and were cultured for another 7 days to assess the persistence of co-culture effects.

tag: medium

value: standard medium

value: grown in standard medium

tag: replicate


title: induced pluripotent stem cell-derived fibroblasts grown in bronchial epithelial cell medium, replicate 2

description: Library name: A14

value: bronchial epithelial cell medium


title: small EVs_15-157_CRC

value: male


title: small EVs_15-351_CRC


title: Uninfected_rep3

city: Hangzhou

first: Ming

last: Zeng

address: 866 Yuhangtang Road

country: China

institute: Zhejiang university

description: Library name: Uninfected_rep3

data_processing:
For CLIP-seq, The clean reads were mapped to the reference genome of O. sativa L. japonica at the NCBI (https://www.ncbi.nlm.nih.gov/) using the STAR software (version 2.5.3a) with default parameters. The R package exomePeak software was then used to find peak callings and the peaks were presented using the Integrative Genomics Viewer (IGV) software (https://www.igv.org/).
For RNA-seq,  Adaptor and low-quality reads were removed by using Trimmomatic software (version 0.38). The clean reads were mapped to reference genome of O. sativa L. japonica (https://www.ncbi.nlm.nih.gov/) using Tophat (version 1.4.6). Gene expression levels were calculated as fragments per kilobase per million reads (FPKM) and DEseq2 was used to analyzed differentially expressed genes.
Supplementary files format and content: csv files include FPKM values for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

organism: Oryza sativa

source_name: 30-day rice plants

extract_protocol:
For RNA-seq, Total RNA samples were collected from WT, P6-OE, uninfected and SRBSDV-infected rice plants by using TRIzol Reagent. For CLIP-seq, RNA samples were IP from uninfected and SRBSDV-infected rice and extracted using TRI-Reagent®.
For RNA-seq, The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. For CLIP-seq, RNA sequencing library was constructed using the KC-Digital Stranded mRNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: leaves and shoots

value: Wildtype

value: none-virus-innoculation


title: induced pluripotent stem cell-derived fibroblasts grown in intestinal cell medium, replicate 1

description: Library name: A7

value: intestinal cell medium

value: grown in intestinal cell medium


city: Los Angeles

first: Riki

last: Kawaguchi

state: CA

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

description:
Library name: hisat_12p
mouse cerebral white matter EC stroke 12

data_processing:
Basecalls/demultiplexing performed using Illumina Bcl2fastq2 v 2.20
Alignment to mouse genome using STAR spliced read aligner
Counting reads using HTSeq with homo sapiens  genome GRCm38 as reference
Normalization using trimmed mean of M values method, and differential expression analysis using Biocoductor packages.
Assembly: GRCm38
Supplementary files format and content: counts

organism: Mus musculus

source_name: mouse cerebral white matter

extract_protocol:
NucleoSpin® RNA XS (Macherey-Nagel)
Takara SMART-Seq v4 Ultra low Input RNA kit

value: EC

value: mouse cerebral white matter

value: stroke


title: induced pluripotent stem cell-derived fibroblasts co-cultured with keratinocytes, replicate 1

description: Library name: A18

value: keratinocyte medium

value: co-cultured with keratinocytes


description:
Library name: hisat_N12p
mouse cerebral white matter OPC control 12

value: OPC

value: control


description:
Library name: hisat_T9p
mouse cerebral white matter pericyte control 9

value: pericyte


title: Intramuscular fat 3

city: BLACKSBURG

first: Zhendong

last: Tan

state: VA

address: 175 West Campus Drive

institute: Virginia Tech

description:
Library name: sample 3
bIF4

data_processing:
The raw RNA-seq reads were filtered using Trimmomatic v0.39 to remove low-quality reads and reads containing adapters
Clean reads were aligned to the bovine reference genome ARS-UCD 2.0 using STAR v2.7.11a
Gffread v0.12.18 was used to convert the genomic annotation files from gff to gtf format
FeatureCounts (v2.0.2) was used to estimate the read counts
Differential expression analysis was performed using the DESeq2 (v1.42.0) R package
Genes with Benjamini–Hochberg approach adjusted P value < 0.05 and |log2fold change| ≥ 1 were designated as differentially expressed genes (DEGs)
Assembly: ARS-UCD 2.0
Supplementary files format and content: comma separated file contains gene expression profile that includes list of all genes that are differentially expressed

organism: Bos taurus

source_name: Adipose tissue

extract_protocol:
Total RNA was extracted using TRIzol reagent (Zymo Research, Irvine, CA) and the Direct-zol RNA MiniPrep Plus Kit (Zymo Research)
Total RNA was extracted and fragmented, followed by first-strand cDNA synthesis using random hexamer primers. Second-strand cDNA synthesis was performed using a dUTP mix. The resulting double-stranded cDNA was purified using the AMPure XP system. After end repair and adaptor ligation, the adaptor-linked cDNA was again purified with the AMPure XP system and enriched through 10 cycles of PCR. The final cDNA library was purified using the AMPure XP system, pooled, and paired-end sequenced on an Illumina platform.

treatment_protocol: Intramuscular and subcutaneous adipose tissue was collected from five adult Heifers, all of which were angus cross breed.

value: Adipose tissue

tag: tissue type

value: Intramuscular fat

tag: Sex

value: Female

tag: Stage

value: Adult


title: small EVs_15-117_CRC

value: CRC

value: male

value: distal


title: small EVs_15-26_CRC


title: Intramuscular fat 2

description:
Library name: sample 2
bIF3


title: induced pluripotent stem cell-derived fibroblasts grown in standard medium, replicate 3

description: Library name: A3

value: standard medium

value: grown in standard medium


title: Uninfected_rep2

description: Library name: Uninfected_rep2

value: leaves and shoots

value: Wildtype

value: none-virus-innoculation


description:
Library name: hisat_T5p
mouse cerebral white matter pericyte control 5

value: mouse cerebral white matter


description:
Library name: hisat_14p
mouse cerebral white matter EC stroke 14

value: EC

value: stroke


description:
Library name: hisat_T8p
mouse cerebral white matter pericyte control 8

value: control


title: Uninfected_rep1

description: Library name: Uninfected_rep1


title: mouse cerebral white matter EC stroke 8

description:
Library name: hisat_8p
mouse cerebral white matter EC stroke 8


title: small EVs_15-217_CRC

value: female

value: proximal


title: small EVs_14-488_CRC


title: Intramuscular fat 1

description:
Library name: sample 1
bIF2

value: Adipose tissue

value: Intramuscular fat


title: small EVs_14-469_CRC


title: mouse cerebral white matter EC stroke 6

description:
Library name: hisat_6p
mouse cerebral white matter EC stroke 6


title: ATAC_Homeostasis_rep1

description: Library name: ATAC_Homeostasis_rep1_L37082

value: 5dpf FACS sorted zebrafish lateral line

value: Homeostasis

value: wild type

value: No


description:
Library name: hisat_10p
mouse cerebral white matter EC stroke 10


title: LC_3_1

city: Changchun

first: Hang

last: Cheng

state: Jilin

address: Xin Min Street

institute: Jilin University

data_processing:
Illumina Casava1.7 software used for basecalling.
After reads filtering, we map clean reads to reference genome using HISAT.
After genome mapping, we use StringTie  to reconstruct transcripts, and with genome annotation information we identify novel transcripts by using Cuffcompare(a tool of Cufflinks) and predict the coding ability of those new transcripts using CPC.
After genome mapping, we use GATK to call SNP and INDEL variant for each sample.
map clean reads to it using Bowtie2,then calculate gene expression level for each sample with RSEM.
Genome_build: use StringTie to reconstruct transcripts, and use Cuffcompare（Cufflinks tools） to compare reconstructed transcripts to reference annotation, after that, we select 'u','i','o','j' class code types as novel transcripts. And then, we use CPC  to predict coding potential of novel transcripts, then we merge coding novel transcripts with reference transcripts to get a complete reference, and downstream analysis will base on this reference.
Supplementary_files_format_and_content: FPKM values (calculated by RSEM software) for each Sample

source_name: lung cancer diseased region NKp44-ILC3s

extract_protocol:
NKp44- ILC3s and  NKp44+ ILC3s  were sorted,  RNA was harvested using Trizol reagent. Illumina HiSeq RNA Sample Prep Kit  was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: lung cancer

value: NKp44- ILC3s


title: small EVs_14-203_CRC

value: CRC

value: distal


title: LC_2_1


title: SRBSDV_infected_rep2

description: Library name: SRBSDV_infected_rep2

value: leaves and shoots

value: Wildtype

value: virus-innoculation


title: P6_OE_rep3

description: Library name: P6_OE_rep3


title: mouse cerebral white matter EC stroke 4

description:
Library name: hisat_4p
mouse cerebral white matter EC stroke 4

value: EC

value: mouse cerebral white matter

value: stroke


title: LC_1_2

source_name: lung cancer diseased region NKp44+ILC3s

value: NKp44+ ILC3s


title: LC_3_2


title: LC_2_2


title: P6_OE_rep2

description: Library name: P6_OE_rep2


title: SRBSDV_infected_rep1

description: Library name: SRBSDV_infected_rep1


title: small EVs_14-160_CRC

value: female

value: proximal


title: mouse cerebral white matter EC stroke 2

description:
Library name: hisat_2p
mouse cerebral white matter EC stroke 2


description:
Library name: hisat_9p
mouse cerebral white matter EC control 9

value: control


title: small EVs_13-246_CRC

value: male


description:
Library name: hisat_11p
mouse cerebral white matter EC control 11


title: SRBSDV_infected_rep3

description: Library name: SRBSDV_infected_rep3


title: small EVs_14-159_CRC


description:
Library name: hisat_7p
mouse cerebral white matter EC control 7


title: LC_1_1


title: RNA-Seq of Cranberry Hybrids: V. oxycoccos, baseline, replicate 4

city: Encinitas

first: Audrey

last: Dickinson

state: California

address: 300 Quail Gardens Dr

department: Science and Conservation

institute: San Diego Botanic Garden

description: Library name: Vhyb_Voxy_NJ96_57

data_processing:
Sequencing runs were basecalled using the Dorado v5.0.0 super-high accuracy model with a quality threshold of Q9 and a 200 base pair cutoff.
Reads were aligned using minimap2 v2.28-r1209 against Helixer-generated (v0.3.2) coding sequences (CDS) from either V. macrocarpon, V. oxycoccos, or a concatenated hybrid reference, as appropriate. Only primary alignments were retained.
Transcript abundance was quantified using Salmon v1.6.0.
Assembly: V. macrocarpon, V. oxycoccos (Kawash et al., 2022)
Supplementary files format and content: Quantification table output from Salmon. Rows represent genes in each sample. Columns represent length, effective length, TPM, and the number of reads mapping to each transcript.

organism: Vaccinium oxycoccos

source_name: Leaf

growth_protocol: All plants were maintained in a greenhouse in Chatsworth, New Jersey, USA, prior to the temperature stress experiments. Each F1 hybrid with the same genotype identifier were clonally propagated from seedling progeny by cuttings. Experimental material consisted of V. macrocarpon, V. oxycoccos, and their F1 hybrids. Experiments were conducted in mid to late September during the growing season, prior to cold acclimation.

extract_protocol:
Approximately 50 mg of leaf tissue was processed per sample. Total nucleic acids were isolated using a CTAB-based method (Daverdin et al., 2017). RNA was precipitated from total nucleic acid using 10M LiCl overnight, pelleted, and resuspended in nuclease-free water. Samples were treated with DNase (Optizyme, Fisherbrand #BP81071), followed by chloroform treatment, sodium acetate precipitation, ethanol washing, and final resuspension in nuclease-free water.
Full-length cDNA was synthesized from 200 ng of total RNA per sample using the Oxford Nanopore cDNA-PCR Sequencing Kit (SQK-PCB111.24). PCR amplification used barcoded primers (16 cycles), and barcoded cDNA from nine samples was pooled per run. ONT Rapid Adapter Kit (EXP-RAA114) was used to prepare libraries for sequencing with R10.4.1 flow cells and V14 chemistry. Sequencing was performed on the PromethION platform for 72 hours.

treatment_protocol: For temperature stress experiments, plants were acclimated for three days at 21 °C under a 12 h day/night cycle. For heat stress, incubators were pre-set to 45 °C and samples were harvested at 0 min (T0), 15 min (T1, 39.7 °C), and 30 min (T2, 47 °C). For cold stress, incubators were set to 2 °C and samples were harvested at T0, 60 min (T1, 10.5 °C), and 95 min (T2, 3 °C). Whole leaves were collected and snap frozen in liquid nitrogen, then stored in RNAlater ICE.

value: Leaf

tag: time

tag: temperature


title: small EVs_11-417_CRC

tag: condition


title: RNA-Seq of Cranberry Hybrids: V. oxycoccos, baseline, replicate 3

description: Library name: Vhyb_Voxy_NJ96_25


description:
Library name: hisat_5p
mouse cerebral white matter EC control 5


title: Wildtype_rep2

description: Library name: Wildtype_rep2


title: SMAC mimetic single arm

city: Vienna

first: Martin

last: Aichinger

address: Dr. Boehringer-Gasse 5-11

country: Austria

institute: Boehringer-Ingelheim

data_processing:
Sequence alignment was performed by SevenBridges platform 1.9.1(workflow reversion 13).
Single-cell datasets were analyzed with Seurat package (version 4.2.0) in R in a standard way: first 30 principal components were used for the UMAP embedding, Leiden clustering was performed with the resolution of 0.8. Scrublet (version 0.2.3) was used to detect potential doublet, cells with scrublet score smaller than 0.15 were excluded from the analysis. Automated annotation of the cell types was performed with SingleR package (version 2.0.0). With Seurat, differentially expressed genes were discovered within cell types between treatments.
Assembly: mm10 / custom reference
Supplementary files format and content: Seurat object with the counts of RNA-seq reads and barcodes
Supplementary files format and content: seurat.rds contains a Seurat object with single cell RNA-seq and antibody barcode counts, as well as the cell type annotation.
Supplementary files format and content: reference_rna.fasta containst a custome reference of the transcripts of the genes included in the gene panel. Alternatively, the reads can be mapped on mm10 genome.
Supplementary files format and content: reference_adt.fasta contains the sequences of the antibody barcodes for the proteomics analysis
Supplementary files format and content: feature_reference.csv contains the mapping of cell hashing barodes (SampleTag) to the samples and the mapping of antibody barcodes to the proteins they bind to.
Library strategy: CITE-seq

source_name: subcutaneous tumor

growth_protocol: Subcutaneously transplanted syngeneic tumor PDAC tumor model.

extract_protocol:
15 days post treatment start, explanted Pan02 tumors were minced into small ~1mm³ pieces and single cell suspensions were prepared using the Tumor Dissociation Kit, mouse (Miltenyi, 130-096-730) and the gentleMACS Octo Dissociator (Miltenyi, 130-096-427) following manufacturer’s protocol using the programs “37_m_TDK_2” and “m_impTumor_01”. Red blood cells were lysed by incubating resuspended pellets for 1-2 min on ice in 1 ml ACK lysing buffer (Thermo Fisher, A10492-01). 7 dissociated tumors per group were used for analysis by flow cytometry and 3/group were additionally enriched for tumor infiltrating leukocytes with CD45 (TIL) MicroBeads, mouse (Miltenyi, 130-110-618) using the MultiMACS X Separator (Miltenyi) followed by single cell labelling for CITE-seq analysis.Single cell libraries were generated using the BD Rhapsody system. Enriched CD45+ TILs from 3 tumors/group were stained for multiplexing and with AbSeq Ab-Oligos according to manufacturer’s protocol (BD Doc ID: 214419 Rev 2.0) with slight modifications. In detail, cells were labelled with the Mouse Immune Single-Cell Multiplexing Kit, (BD, 633793), followed by equal pooling of 3 samples each (resulting in 4 pooled samples), Fc blocking with TruStain FcX PLUS antibody (Biolegend, 156604) and staining with oligo-conjugated Ab-Seq antibody mix. Single cell capture and cDNA synthesis was performed with the BD Rhapsody Single-Cell Analysis System and the Cartridge Reagent Kit (BD, 633731), the Cartridge Kit (BD, 33733) and the cDNA Kit (BD, 633773) according to manufacturer’s protocol (BD Doc ID: 210966 Rev. 1.0).
Libraries were generated with the Targeted Amplification Kit (BD, 633774) and the Mouse Immune Response Panel (BD, 633753) according to manufacturer’s protocol (Doc ID: 214508 Rev. 3.0). Pooling of libraries of each cartridge was calculated following instructions given in BDs’ “SEQ Calculator v1.2.xlsm” and libraries were sequenced (paired-end) on the Illumina platform.

treatment_protocol: Syngenetic PAN02 subcutaneous model were treated with SMAC mimetic (50mg/kg, BET inhibitor (2mg/kg) and the combination.

value: subcutaneous tumor

tag: cell line

value: tumor infiltrating lymphocytes

value: SMAC mimetic


title: RNA-Seq of Cranberry Hybrids: V. oxycoccos, baseline, replicate 2

description: Library name: Vhyb_Voxy_NJ96_21


title: small EVs_13-254_CRC

value: CRC

tag: gender

tag: age


description:
Library name: hisat_3p
mouse cerebral white matter EC control 3


title: small EVs_14-328_CRC

tag: diagnosis

tag: clinical stage

value: distal


title: control

tag: tissue

value: vehicle


title: Brain Cortical Endothelial cells from MCAO-Ezh2 ECKO mice (Ipsilateral  side)-2

status: Public on Jul 06 2025

city: Houston

first: Peeyush Kumar

last: Thankamani Pandit

state: TEXAS

address: 6431 Fannin St,

department: Neurosurgery

institute: University of Texas Health Science Center Houston

description: Library name: Sample 17

data_processing:
mRNA-seq reads were quality checked using FastQC [www.bioinformatics.babraham.ac.uk/projects/fastqc/] after removing adaptors with cutadapt. .
Raw reads were mapped with STAR read aligner and default parameters against build mm10 of the mouse reference genome and the latest annotation of mouse genome from the mouse GENCODE repository
We used featureCounts to count reads on each gene for gene expression quantification.
Differentially expressed genes were detected and ranked using DESeq2
Assembly: mm10
Supplementary files format and content: tab limited file contain normalised counts for each samples

source_name: Brain

extract_protocol:
The FACS sorted cells were suspended in solution as suggested by SMART-Seq v4 PLUS Kit User Manual (Takara Bio, Japan). The sorted cells were frozen on dry ice as soon as the sorting was done at The University of Texas Health Science Center in Houston (CPRIT RP180734).
Libraries were prepared with SMART-Seq V4 PLUS Kit (R400752, Takara Bio, Japan) following the manufacturer’s instructions. Agilent High Sensitive DNA Kit (#5067-4626) by Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, USA) was used to check the quality of the final libraries and the library concentrations were determined by qPCR using Collibri Library Quantification kit (#A38524500, Thermo Fisher Scientific, Texas, USA). The libraries were pooled evenly and went for the paired-end 150-cycle sequencing on an Illumina NovaSeq X plus System (Illumina, Inc., USA).

treatment_protocol: Endothelial cells were isolated on day 7 from ipsilateral and contralateral sides of mice brain  by FACS sorting from  sham, MCAO, MCAO-Hdac2 ECKO and MCAO-Ezh2 ECKO mice.

value: Brain

tag: cell type

value: Endothelial cells

value: Ezh2 ECKO

value: Tamoxifen (75mg/Kg)


title: Wildtype_rep1

description: Library name: Wildtype_rep1

value: leaves and shoots

tag: genotype

value: Wildtype


title: RNA-Seq of Cranberry Hybrids: V. oxycoccos, baseline, replicate 1

description: Library name: Vhyb_Voxy_NJ96_112

tag: treatment


title: Brain Cortical Endothelial cells from MCAO-Ezh2 ECKO mice (Ipsilateral  side)-3

description: Library name: Sample 18


title: Brain Cortical Endothelial cells from MCAO-Hdac2 ECKO mice (Ipsilateral  side)-3

description: Library name: Sample 15

value: Hdac2 ECKO


title: BETi single arm

value: BET inhibitor


title: SMAC mimetic plus BET inhibitor combination

value: SMAC mimetic and BET inhibitor


title: Brain Cortical Endothelial cells from MCAO-Ezh2  ECKO mice (Ipsilateral  side)-1

description: Library name: Sample 16


title: Brain Cortical Endothelial cells from MCAO-Hdac2 ECKO mice (Ipsilateral  side)-2

description: Library name: Sample 14


title: Brain Cortical Endothelial cells from MCAO mice (Contralateral  side)-3

description: Library name: Sample 12

value: WT


title: P6_OE_rep1

description: Library name: P6_OE_rep1


title: Brain Cortical Endothelial cells from MCAO mice (Contralateral  side)-2

description: Library name: Sample 11


title: Brain Cortical Endothelial cells from MCAO-Hdac2 ECKO mice (Ipsilateral  side)-1

description: Library name: Sample 13


title: Brain Cortical Endothelial cells from MCAO mice (Contralateral  side)-1

description: Library name: Sample 10


title: Brain Cortical Endothelial cells from MCAO mice (Ipsilateral  side)-3

description: Library name: Sample 9


title: Brain Cortical Endothelial cells from MCAO mice (Ipsilateral  side)-2

description: Library name: Sample 8


title: Brain Cortical Endothelial cells from MCAO mice (Ipsilateral  side)-1

description: Library name: Sample 7


title: Wildtype_rep3

description: Library name: Wildtype_rep3


title: Brain Cortical Endothelial cells from Sham mice (Contralateral  side)-3

description: Library name: Sample 6


title: Brain Cortical Endothelial cells from Sham mice (Contralateral  side)-2

description: Library name: Sample 5


title: Brain Cortical Endothelial cells from Sham mice (Ipsilateral side)-2

description: Library name: Sample 2


title: Brain Cortical Endothelial cells from Sham mice (Ipsilateral side)-3

description: Library name: Sample 3


title: Brain Cortical Endothelial cells from Sham mice (Ipsilateral side)-1

description: Library name: Sample 1


title: Brain Cortical Endothelial cells from Sham mice (Contralateral  side)-1

description: Library name: Sample 4


title: Mouse_RA_treatment_15dpi_ear_pinna_scRNA-seq_10x

city: Beijing

first: Weifeng

last: Lin

state: Beijing

address: 7 Science Park Road ZGC Life Science Park

institute: National Institute of Biological Sciences

description:
Library name: Mouse_RA_treatment_15dpi
Note: because the file1 is larger than 100G, the file 1 was split into two files(part1, part2)

library_source: transcriptomic single cell

data_processing:
Raw reads were aligned to the mouse and rabbit reference genomes to produce the single-cell gene expression matrixes using Cell Ranger (Version 7.0), respectively.
The file 1 was split into two files(part1, part2) with linux command 'split' because it's more than 100G.
Assembly: GRCm39 and oryCun2
Supplementary files format and content: Cell Ranger software output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: ear-pinna

extract_protocol:
The ear hole tissues were collected using biopsy punches and washed with ice-cold PBS. Subsequently, the tissues were dissected into small pieces quickly and transferred into tubes with Collagenase dissociation buffer containing 2mg/ml Collagenase type I (Sigma, C2674) and 100ug/ml DNase I (Roche, 10104159001). After incubating at 37 ℃, the dissociated cell suspension was filtered through a 70 μm filter. The remaining incompletely digested tissue pellets were further dissociated with TrypLE (Gibco, 12605010) and then filtered and mixed with dissociated cells digested with collagenase. For separate living cells, the dissociated cell mixtures were resuspended with ice-cold PBS containing 5% fetal bovine serum (FBS) and incubated with Propidium Iodide (PI) to stain dead cells. The PI-negative cells were sorted using BD FACSAria II Flow cytometry. To ensure single-cell sample quality, the proportion of living cells was evaluated by Trypan blue staining before library preparation with the 10X Genomics platform.
The scRNA library construction were performed according to the manufacturer’s protocol

treatment_protocol: For RA treatment, RA solutions were intraperitoneally injected into mice every two days upon injury at the dose of 20 μg/g until 15 dpi, equal volume DMSO solution were used as control

value: ear-pinna

value: RA treatment


title: Mouse_5dpi_scRNA-seq_10x

description:
Library name: Mouse_5dpi_scRNA-seq
Note: because the file1 is larger than 100G, the file 1 was split into two files(part1, part2)

value: injury, 5dpi


title: Mouse_DMSO_control_15dpi_ear_pinna_scRNA-seq_10x

description:
Library name: Mouse_DMSO_control_15dpi
Note: because the file1 is larger than 100G, the file 1 was split into two files(part1, part2)

value: DMSO treatment


title: Mouse_10dpi_ear_pinna_scRNA-seq_10x

description:
Library name: Mouse_10dpi_ear_pinna_scRNA-seq
Note: because the file1 is larger than 100G, the file 1 was split into two files(part1, part2)

value: injury, 10dpi


title: STAMP_166

city: Memphis

first: Jasmine

last: Plummer

state: TN

address: 262 Danny Thomas Pl

department: Developmental Neurobiology

institute: St. Jude Children's Research Hospital

hyb_protocol: The Imaging based platforms used in this study are the CosMX SMI (Nanostring) and the Xenium Analyzer (10X Genomics) with all specifications required for this study outlined in the CosMX SMI was used for both RNA and protein assays. All sections were also stained after data acquisition on their respective imaging platform. The specifics for each assay is outlined in the proceeding sections and found in STSOP. All methods were used across the three institutions: site #1 (UoA), site #2 (St. Jude Children’s Research Hospital), and site #3 (Weill-Cornell Medicine).  CosMx RNA Slide Preparation: Samples were processed following the guidelines outlined in the CosMx slide preparation manual MAN-10159-02 for prostate cancer processed in Adelaide and MAN-10184-01-1 for all other tissues. In summary, 5-μm sections were placed onto the 15 mm x 22 mm scannable area of a Superfrost Plus Micro Slide (VWR, 48311-703) and dried in an oven at 37°C for 2 hours then kept at room temperature with desiccant overnight before storage at 4°C. The slides were then incubated overnight at 60°C for 17–18 hours and then brought to room temperature for 3–5 minutes. This was followed by two xylene washes for 5 minutes each, and two washes in 100% ethanol for 2 minutes each. For normal tissues, CitroSolv workflow was used in place of xylene. The slides were then dried in an oven at 60°C for 5 minutes. The slides were immersed in pre-heated 1X Target Retrieval solution (CosMx FFPE slide preparation kit, RNA) in a pressure cooker (or steamer) at 100°C for 15 minutes, timing started once the retrieval solution reached 100°C. The slides were immediately transferred to water for 15 seconds, then washed in 100% ethanol for 3 minutes, and air-dried at room temperature for 30 minutes to 1 hour. Incubation frames were attached to each slide, and a pre-warmed digestion buffer containing 3 ug/mL Proteinase K (CosMx FFPE slide preparation kit, RNA) and 1X PBS (AM9922, AM9625 was applied and incubated in a hybridization chamber for 30 minutes. The slides were then rinsed twice in water, and fiducials were applied at 0.001%, followed by a 5-minute incubation at room temperature, shielded from light. The slides underwent a 1X PBS wash for 1 minute, were fixed in 10% NBF for 1 minute, immediately followed by two washes in NBF stop buffer for 5 minutes each, and then a 5-minute wash in 1X PBS. A 100 mM NHS-acetate solution was applied to the tissue for 15 minutes at room temperature, followed by two washes in 2X SSC for 5 minutes each. The CosMx Human Universal Cell Characterization RNA Panel (CMX-H-USCP-1KP-R) targeting 950 human genes and a 50-target add-on panel set, were denatured at 95°C for 2 minutes and then cooled on ice for 1 minute. A probe mix containing RNase inhibitor, buffer R, and nuclease free water was applied to the slide and incubated for 17 hours in the hybridization chamber at 37°C. Post-incubation, the slides were washed twice in a final concentration of 50% deionized formamide and 2X SSC mix for 25 minutes each, followed by two washes in 2X SSC for 2 minutes each. DAPI stock was diluted to 1:40 and applied to the slides for 15 minutes at room temperature, protected from light. The slides were then washed in 1X PBS for 5 minutes and stained for 1 hour with a cocktail of CD298/B2M, PanCK, CD45, and CD68 antibodies (Item # 121500020, 121500021, 121500022). Colon, HCC TMA, pancreas, and prostate cancer samples were stained with 4 uL of the CD298/B2M antibody, following the guidelines in MAN-10184-01-1. In contrast, appendix, ileum, and prostate cancer samples received a staining of 8 uL of the CD298/B2M antibody, as specified in MAN-10159-01-1.The slides were washed three times in 1X PBS for 5 minutes each and then stored in 2X SSC. The pre-bleaching profile followed configuration C, while the cell segmentation profile adhered to configuration A, except for the HCC TMA, which used configuration E. These procedures were consistently applied across all sites: St. Jude Children's Research Hospital, Weill Cornell Medical Center, and the University of Adelaide, with FOVs remaining uniform across all three locations.  CosMx Protein Slide Preparation: Samples were processed according to the guidelines provided in the CosMx SMI slide preparation manual MAN-10185-01-1 (NanoString). In summary, 5-μm FFPE sections were placed onto the 15 mm x 22 mm scannable area of a Superfrost Plus Micro Slide and dried in an oven at 37°C for 12 hours, sealed with desiccant and dried for a further 12 hours at room temperature before storage at 4°C. The slides were baked at 65°C for 2 hours and then equilibrated to room temperature for 3–5 minutes, and then washed twice in xylene (or CitriSolv) for 5 minutes each at room temperature. The slides were then washed twice in 100% ethanol for 10 minutes each, twice in 95% ethanol for 5 minutes each, and once in 70% ethanol for 5 minutes, followed by two washes in 1X PBS for 5 minutes each. The slides were immersed in pre-heated 1X Target Retrieval solution and heated in a pressure cooker at 100°C with the valve closed for 15 minutes, then allowed to equilibrate to room temperature in the same solution. Afterward, the slides were washed three times in 1X PBS for 5 minutes each, and incubation frames were attached. Tissue sections were then covered with Buffer W and incubated at room temperature for 1 hour in the dark. The NanoString 64-plex human protein antibody panel was combined with CD298/B2M and PanCK/CD45 segmentation markers in Buffer W. Samples from the appendix, ileum, and pancreas were also incubated with the CD68 segmentation marker. The primary antibody mix was incubated at 4°C for 17 hours, followed by three washes with 1X TBS-T buffer for 10 minutes each and once with 1X PBS for 2 minutes. Fiducials, prepared at the recommended concentration of 0.00005%, were applied to the slides at room temperature for 5 minutes, protected from light. Slides were then washed once with 1X PBS for 5 minutes and fixed with 4% PFA for 15 minutes. This was followed by three washes in 1X PBS for 5 minutes each. Sections were stained with nuclei stain for 10 minutes, washed twice with 1X PBS for 5 minutes, and incubated with 100 mM NHS acetate for 5 minutes, before a final wash in 1X PBS for 5 minutes. The selected pre-bleaching profile was configuration C, and the cell segmentation profile was configuration A. These procedures were uniformly followed at St. Jude Children's Research Hospital, Weill Cornell Medical Center, and the UoA, ensuring consistency in the FOVs across all three locations. Breast cancer, normal appendix, and normal ileum samples processed as part of the NanoString’s Technology Access Program followed the methods previously described (He et al,. Nat Biotechnol, 2022).  Xenium Slide Preparation: Sections for Xenium were prepared according to the Xenium In Situ for FFPE-Tissue Preparation Guide (CG000578 Rev C, 10X Genomics) protocol. Briefly, 5-μm sections were cut, floated in an RNAse-free water bath, and carefully placed onto the 10.45 mm x 22.45 mm sample area of Xenium slides (PN-3000941, 10X Genomics). The slides were then placed on a drying rack at room temperature for 30 minutes to remove excess water. This was followed by a 3-hour incubation at 42 ̊C on a Xenium Thermocycler Adapter plate, positioned atop the 96-well block of a C1000 Touch Thermal Cycler (BioRad) with the lid open. Subsequently, the slides were stored overnight at room temperature with a desiccant to facilitate further drying. The slides were then processed following the Xenium In Situ for FFPE Deparaffinization and Decrosslinking protocol (CG000580 Rev C, 10X Genomics). The slides were placed again on a Xenium Thermocycler Adapter plate atop the 96-well block of a thermocycler with the lid open and incubated at 60 ̊C for 2 hours. They were then equilibrated to room temperature for 7 minutes, deparaffinized, and rehydrated by immersion twice in xylene for 10 minutes each, twice in 100% ethanol for 3 minutes each, twice in 96% ethanol for 3 minutes each, once in 70% ethanol for 3 minutes, and once in water for 20 seconds. Subsequently, the Xenium slides were assembled into Xenium cassettes and hydrated with 1X PBS. The tissue sections were reverse crosslinked using a decrosslinking buffer containing tissue enhancer, urea, and perm enzyme B, at 80 ̊C for 30 minutes, followed by three washes with PBS-T. Slides were then immediately processed following the Xenium In Situ Gene Expression user guide (CG000582 Rev E, 10X Genomics) for the remaining slide preparation steps. Briefly, the pre-designed gene expression probe set, Xenium Human Multi-Tissue and Cancer Panel (10X-1000626, 10X Genomics) targeting 377 human genes, was utilized for prostate cancer, ileum, appendix, pancreas, and colon samples. For breast cancer samples, the Xenium Human Breast Panel (10X-1000463, 10X Genomics) targeting 380 human genes was used. Panels were denatured at 95 ̊C for 2 minutes, crash-cooled on ice for 1 minute, and then equilibrated to room temperature before being added to the probe hybridization buffer and TE buffer to make the probe hybridization mix. The slides were incubated with the hybridization mix at 50 ̊C for 17 hours. Slides were washed three times with PBS-T for 1 minute each then incubated with a post-hybridisation wash buffer for 30 minutes at 37 ̊C. Slides were washed three times with PBS-T for 1 minute each and incubated with ligation mix for 2 hours at 37 ̊C. Three 1-minute PBS-T washes were followed by a 2-hour incubation at 30 ̊C with an amplification mix. Slides were then washed three times with TE buffer then three washes with 1X PBS for 1 minute each followed by incubation with reducing agent B for 10 minutes, washed once in 70% ethanol for 1 minute, twice in 100% ethanol then treated with autofluorescence solution for 10 minutes in the dark. Slides were washed three times with 100% ethanol for 2 minutes each then dried for 5 minutes at 37 ̊C before rehydrating with 1X PBS then PBS-T for 2 minutes. Slides were stained with a nuclei staining buffer for 1 minute at room temperature followed by three washes with PBS-T for 1 minute each in the dark. The slides were then assembled into Xenium Cassettes and loaded into the Xenium Analyzer for imaging and decoding. These procedures were uniformly followed at St. Jude Children's Research Hospital, Weill Cornell Medical Center, 10x Genomics, and the UoA, ensuring consistency in theFOVs across all four locations. Breast cancer samples processed as part of the 10x Genomics’ Catalyst Program followed the methods previously described (19); these experiments were carried out at 10X Genomics headquarters (Pleasanton, CA, USA). Sections from the prostate cancer samples were also subjected to Xenium Multimodal segmentation through an early access program and processed at the 10X Genomics headquarters (Pleasanton, CA). In brief, the procedure for in situ gene expression with cell segmentation staining was conducted following the Demonstrated Protocol for Xenium In Situ for FFPE - Tissue Preparation Guide (CG000578 Rev C, 10X Genomics), the Xenium In Situ Gene Expression User Guide (CG000582 Rev F, 10X Genomics), and the Xenium In Situ Gene Expression Cell Segmentation User Guide (CG000749 Rev A, 10X Genomics). The combined protocol utilized the Xenium Human Multi-Tissue and Cancer Panel for in situ gene expression and the Xenium Cell Segmentation Staining Reagents add-on (PN-1000661, 10X Genomics) for segmentation staining. This add-on kit contains a single cocktail of Xenium Multi-Tissue Stain Mix (PN-2000991, 10X Genomics), which contains a cocktail of antibodies labeling the membranes (anti-ATP1A1/CD45/E-cadherin), antibodies labeling the cell interior (anti-alphaSMA/Vimentin) and a universal interior label against Ribosomal RNA (18S rRNA). Stain was then enhanced by the addition of Xenium Staining Enhancer reagent, followed by treatment of the sections with Xenium Autofluorescence Mix (PN-2000753, 10X Genomics) to diminish unwanted autofluorescence and enhance the signal-to-noise ratio in the tissue sections. Subsequently, Xenium Nuclei Staining Buffer (PN-2000762, 10x Genomics) was used to help the identification of tissues or regions of interest during the instrument's overview scan.  Xenium RNA to CosMx Protein slide preparation: Following completion of the Xenium RNA run, slides were removed from the instrument and stored in the Xenium cassette with PBS-T at 4C. After storage for up to 3 days, slides were washed three times in PBS-T for 1 minute each as recommended in Technical Note: Post-Xenium In Situ Applications: Immunofluorescence, H&E, and Visium CytAssist Spatial Gene Expression (CG000709 Rev A, 10X Genomics), removed from the Xenium cassette and placed into a wash jar of 1X PBS for 5 minutes as described in CosMx SMI Manual Slide Preparation for Protein Assays (MAN-10185-01-1, NanoString), incubation frames were attached to the Xenium slide and tissue sections were covered with Buffer W and incubated at room temperature for 1 hour in the dark. Afterwards, MAN-10185-01-1 and MAN-10161-03-2 were followed as previously described in CosMx Protein slide preparation and CosMx SMI setup and data acquisition.

scan_protocol: CosMx SMI Setup and Data Acquisition: The setup and scan acquisition for the CosMx SMI instrument were carried out as detailed in the CosMx SMI Instrument User Manual   (MAN-10161-02-1 or MAN-10161-03-2, Software Version 1.1, NanoString). A new acquisition process was initiated through the CosMx SMI Control Center web interface. Prior to insertion into the CosMx Flow Cell Assembly Tool, the slides were carefully dried in the areas surrounding the imaging region. The process involved lowering the tailgate, placing the slide, and then securing it by raising the tailgate. After removing the adhesive backing, a new flow cell coverslip was precisely aligned above the slide's imaging area. The Assembly Tool's lid was closed securely to affix the coverslip to the slide, thus creating a functional CosMx flow cell. Following the assembly, 2X SSC was gently introduced through one of the flow cell ports to hydrate the tissue section. Subsequent steps included entering the flow cell configuration data into the Control Center interface, which comprised the flow cell's barcode and the slide's ID number. The prostate sections underwent scanning with Configuration C for the pre-bleaching profile and Configuration A for the cell segmentation profile. Further details regarding the probe panel, cell segmentation, and supplemental markers were entered into the flow cell configuration data for each section. Assembled flow cells/slides, along with Buffer Bottles 1–4, were then loaded into the instrument. Before positioning Bottle 4, catalase and pyranose oxidase enzymes were added. The Control Center configuration was verified and following a period of equilibration to room temperature and the addition of an RNase inhibitor to a designated well in the CosMx imaging tray, the tray was placed in the instrument. A pre-run check and a tissue find scan for each tissue section were performed by the instrument. After the completion of tissue find scans, rectangular scan areas were delineated around each tissue section for the preview scan. The preview scan images facilitated the selection of a contiguous region of FOVs using the grid FOV placement tool, thoroughly covering the tissue areas on each slide. FOV selections for each slide were confirmed before initiating the cycling process. CosMx scan data were automatically uploaded to NanoString’s cloud-based AtoMx Spatial Analysis Platform during the run, as detailed in the CosMx Data Analysis manual (MAN-10162-02, Software Version 1.1, NanoString). Briefly, upon the completion of the run and the full upload of scan data to AtoMx, a study was created for each CosMx scan. Within AtoMx, pipelines were executed for each study, facilitating the export of data in various formats, such as TileDB arrays and Seurat objects, for in-house analysis.     Xenium Analyzer Setup and Data Acquisition: Xenium slides, assembled within Xenium cassettes, were imaged using the Xenium Analyzer, in accordance with the guidelines specified in the Xenium Analyzer User Guide (CG000584 Rev D and Rev E for Multi-modal Segmentation-stained slides, 10X Genomics). The Xenium Decoding Consumables Kit, (PN-1000487, 10X Genomics) was used for instrument loading. Briefly, Xenium slide ID numbers and information on pre-designed gene expression probes—were input into the Analyzer. The necessary consumables and reagents were loaded into the instrument: reagent module B, thawed at 4 ̊C overnight and equilibrated to room temp for 30 minutes prior to loading into the instrument, reagent module A, stored at 4 ̊C until loading in the instrument, instrument wash buffer (100% Milli-Q water), sample wash buffer A (1X PBS, 0.05% Tween-20), sample wash buffer B (100% Milli-Q water), and probe removal buffer (50% DMSO, 50 mM KCl, 0.1% Tween-20) were mixed prior to loading into the instrument with buffer caps along with, pipette tip rack, extraction tip, objective wetting consumable. After loading, the sample was scanned to generate images of the fluorescently labeled nuclei in each section which was used for FOV selection prior scanning. For the prostate cancer sample, the entire section was included in the full scan as 4 regions were selected for the appendix. After the run, the instrument was cleared of consumables, and the Xenium slides were carefully removed. Fresh PBS-T was applied to each slide/cassette, which were then   covered and stored in the dark at 4°C until post-run H&E staining. All procedures were standardized across three sites. The data were then acquired using the Xenium In Situ software suite (v1.9, 10X Genomics), which is a set of software applications for analyzing and visualizing in situ gene expression data produced by the Xenium Analyzer. For prostate samples stained with Multi-Modal Cell Segmentation reagents (10X Genomics Headquarters), both in situ gene expression and segmentation data were simultaneously collected and processed using v2.0 of the Xenium In Situ software suite.

data_processing: To ensure a fair comparison, cells without detected transcripts were excluded from the analysis following the Xenium Onboard Analysis or the AtoMx processing workflow. Subsequent analyses, including cell type annotation, were conducted using raw transcript counts

source_name: KELLY

label_protocol: CosMx and Xenium barcoded probes for RNA and protein assays.

extract_protocol: To confirm the RNA quality of all the samples included in this study three consecutive 10-μm scrolls for the isolation and purification of total RNA using the Norgen Biotek FFPE RNA Purification Kit (Product ID 25300). RNA material (5 ng) was analyzed using a 5200 Fragment Analyzer with the High Sensitivity RNA Assay kit (DNF-472, Agilent Technologies). DV200 values across all samples ranged between 50%–70%. Single Nucleus RNA sequencing was performed following the snPATHO-Seq protocol (Wang et al. BioRxiv, 2023). Briefly, two 30- to 50-μm-thick scrolls from each sample, adjacent to sections for CosMx, Xenium, and H&E staining, were cut and placed into 1.5-mL Eppendorf tubes and stored at 4°C inside Ziplock bags with desiccants to control moisture. Scrolls were stored for up to 1 week. For the preparation of nuclei suspensions, scrolls sections underwent a triple wash in 1 mL of xylene (214736, Millipore Sigma) for 10 minutes each to dewax, followed by rehydration through sequential ethanol (E7023, Millipore Sigma) immersions of decreasing concentrations (100% twice, then 70%, 50%, and 30% once each), each for a duration of 1 minute. Of note, the initial xylene wash was performed at 55°C for 10 minutes to enhance paraffin removal. Subsequent to rehydration, a single wash was performed using 1 mL of wash RPMI 1640 media (11875093, Gibco). After removing the RPMI1640 wash, 50–100 uL of digestion mix [RPMI1640 supplemented with 1 mg/mL of Liberase TH (5401151001, Millipore-Sigma), along with 1 U/uL RNAse Inhibitor (RiboLock RNase Inhibitor, EO0382, Thermo Fisher Scientific)] was added to the tissue scrolls breaking them to smaller pieces with a 1.5-mL pellet pestle before topping up to 1 mL with the same digestion media. Digestion was carried out in a Thermomixer at 800 rpm. After digestion, 400 uL of Ez Lysis Buffer (NUC-101, Sigma-Aldrich) was added, mixed by inversion five times, and centrifuged at 850xRCF for 5 minutes at 4°C. The pellet, consisting of released nuclei and undigested tissue, was resuspended in 250 uL of Ez Lysis buffer with 2% BSA (130-091-376,  MACS BSA Stock Solution, Miltenyi) and 1 U/uL RNAse Inhibitor, followed by homogenization using a 1.5-mL pellet pestle. This was supplemented with an additional 750 uL of the same lysis mix, with further disaggregation achieved through pipetting. The sample was then filtered through a 70-μm strainer (pluriStrainer Mini 70um, 43-10070-50, pluriSelect) and centrifuged, with the flow-through washed again with 800 uL of the lysis mix. Nuclei pellet was washed three times in 1x PBS (70011044, Gibco) with 1% BSA, followed by two washes in 0.5x PBS (70011044, Gibco) with 0.02% BSA. Nuclei was finally resuspended in a volume of 500-1000 uL of the same buffer, dependent on pellet size, and filtered through a 40-μm strainer (pluriStrainer Mini 40um, 43-10040-50, pluriSelect. Nuclei were counted using a Luna-FX7 using Acridine Orange/Propidium Iodide Stain (Logos). For immediate analysis, the suspension was kept on wet ice until processing using the Chromium X controller and the Chromium Fixed RNA Profiling Reagent Kits for multiplexed samples (Chromium Fixed RNA Kit, Human Transcriptome, PN1000475; Chromium Next GEM Chip Q Single Cell Kit, PN-1000418; Dual Index Kit TS Set A, PN-1000251, 10x Genomics) and the User guide CG000527, Rev E. For storage, the pre- or post-hybridized nuclei suspensions were supplemented with 10% Glycerol and 0.1X Enhancer (PN-2000482, 10x Genomics), rested on ice for 10 minutes, and then cryopreserved at −80°C. For the hybridization step, between 500,000 and 1.5 million nuclei were used; hybridization was conducted for 20 hours at 42°C across all samples. BC1-4 were used in all samples used in this study. Post-hybridization washes were carried out in a pool-wash setting as per User guide, with an additional wash included. Approximately 10,000 nuclei/sample were aimed for capture. An extra cycle was introduced for the Pre-Amplification PCR step. Indexing PCR conditions were tailored to attain the target library concentration of 50–200 nM. Libraries were checked for quality control and quantified using a Fragment Analyzer 5200 (Agilent) and a Qbit Flex Fluorometer (Thermo Fisher Scientific), respectively. The indexed libraries were sequenced using the Illumina NovaSeq 6000 system. The read configuration was Read 1: 28, i7: 10, i5: 10, and Read 2: 90. Libraries were sequenced to aim for 20,000–30,000 read pairs/nuclei.

treatment_protocol: Normal and cencerous samples used for RNA and/or protein profiling (Xenium and CosMx platforms) as well as for tissue staining (Hematoxylin and Eosin, H&E) and single nuclei RNA-seq (snPATHO-Seq, using Chromium platform) were fixed in 10% neutral buffered formalin (NBF) and parafin embedeed (FFPE). To confirm the RNA quality of all the samples included in this study three consecutive 10-μm scrolls for the isolation and purification of total RNA (DV200 was used as measure of RNA intgrity post BioAnalyzer, TapeStation or Fragment Analyzer run). for snRNA-Seq from FFPE (snPATHO-Seq).

value: Human neuroblastoma cell line

tag: sample source

value: Goodall Lab (University of South Australia)

tag: sample processed

value: Martelotto Lab (Adelaide Centre for Epigenetics, The University of Adelaide)

tag: sample type

value: Fixed cells

tag: technology

value: MERFISH

tag: panel size

value: PanCancer Pathways 500-gene Panel:500

tag: panel size custom


title: Mouse_0dpi_ear_pinna_scRNA-seq_10x

description:
Library name: Mouse_0dpi_ear_pinna_scRNA-seq
Note: because the file1 is larger than 100G, the file 1 was split into two files(part1, part2)

value: injury, 0dpi


title: STAMP_163

source_name: LNCaP, SK-BR-3, MCF-7

tag: tissue type

value: Breast and prostate cancer cell lines mix

value: Butler lab (South Australian Health and Medical Research Institute)

tag: replicate


title: STAMP_164

source_name: SK-N-DZ


title: STAMP_165

source_name: SK-N-SH


title: STAMP_160

source_name: Tongue cancer CAFs

value: Cancer-associated fibroblasts (CAFs) isolated from tongue squamous cell carcinoma

value: Dr. Marina Kochetkova (University of South Australia)


title: STAMP_162

value: Castration-resistant prostate cancer cell line derived from LNCaP cells


title: STAMP_158

value: Human erythroleukemia cell line

value: Dr. Winnie Kan (University of South Australia)


title: STAMP_159

value: Human glioblastoma-astrocytoma cell line


title: Homo sapiens, uterine myometrial tissue, Scar uterus disease group, biol repl1

city: Chongqing

first: Siqi

last: Zhang

address: No. 1, Youyi Road

department: Department of Pharmaceutics

institute: Third Military Medical University

description: Library name: Scar1

data_processing:
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 and other parameters set as a default.
Assembly: hg38; mm39
Supplementary files format and content: Excel reads count values of genes for each sample across human and mouse group

source_name: uterine tissue

growth_protocol: HUVECs (Accession number: PCS-100-013; ATCC) were cultured in DMEM/Low Glucose medium supplemented with 10% fetal bovine serum (FBS; Invitrogen, Carlsbad, CA, USA), penicillin (100U/mL; Invitrogen) and streptomycin (100 U/mL; Invitrogen). Cells were maintained at 37°C with 21% O2 and 5% CO2. HUVECs were transfected with indicated siRNAs using Lipofectamine 3000 (Invitrogen).

extract_protocol:
RNA extraction library construction and sequencing Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library. After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA).
An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol

value: uterine tissue

value: experiment


title: STAMP_157

source_name: LNCaP

value: Prostate cancer cell line


title: Homo sapiens, uterine myometrial tissue, control, biol repl2

description: Library name: NC2

value: Control blank


title: STAMP_156

value: Breast cancer cell line

value: Swarbrick Lab (The Garvan Institute)

value: Martelotto Lab (Adelaide Centre for Epigenetics, The University of Adelaide)


title: STAMP_155

value: Fixed cells

value: MERFISH

value: PanCancer Pathways 500-gene Panel:500


title: WT_6_S2_L008_

city: Aurora

first: Raul

last: Torres

state: CO

address: 12800 East 19th Avenue,

department: Immunology and Microbiology

institute: The University of Colorado Anschutz Medical Campus

description:
Library name: Sample 10
Column name in 20241018_rnaseq1_final_counts.txt

data_processing:
Raw sequencing reads in FASTQ format were trimmed using Cutadapt (v4.2) to remove adapter sequences and low-quality bases
Read quality was assessed using FastQC (v0.11.9). High-quality reads were aligned to the mm10 (GRCm38) mouse genome using the STAR aligner (v2.7.10b)
Gene-level quantification was performed using featureCounts (v2.0.3) from the Rsubread package (v4.4.1), with annotation from Gencode vM10. Genes were retained if they were present in at least 80% of samples, one condition, and had a minimum of 30 total reads across all samples
Differential expression analysis was performed using DESeq2 (v1.40.2). A Principal Component Analysis (PCA) was performed on variance-stabilized transformed (VST) counts to assess sample clustering. limma::removeBatchEffect() was used to adjust the VST-transformed counts, allowing for improved PCA interpretation and heatmap visualization. To enhance effect size estimation, log fold change shrinkage was applied using lfcShrink() with the “ashr” (Adaptive Shrinkage) method. Genes were considered significantly differentially expressed if they had an adjusted p-value < 0.05 and a log2 fold change (LFC) threshold of |LFC| > 1.
To account for unwanted variation, DESeq2 analysis was repeated with PC1 included as a covariate. To reduce the impact of PC1-driven variation,
Assembly: mm10
Supplementary files format and content: text final with raw counts for each gene in each sample

source_name: spleen

growth_protocol: Isolated P14 CD8 T cells

extract_protocol:
Sorted into Trizol
The Universal Plus mRNA-Seq library preparation kit with NuQuant was used with an input of 500ng of total RNA to generate RNA-Seq libraries.

treatment_protocol: P14 cells isolated from D6 post-infection with LCMV Clone 13

value: spleen

value: CD8 T cell

value: CD45.1/2 [wild-type]

value: D6 LCMV Clone 13

tag: batch


title: Homo sapiens, uterine myometrial tissue, control, biol repl1

description: Library name: NC1


title: wHS_Squamous_Cell_PC_MLF

city: Boston

first: Karl

last: Semaan

state: MA

address: Brookline Ave 450

institute: Dana-Farber Cancer Institute

description:
Library name: wHS_Squamous_Cell_PC_MLF
LPWGS

data_processing:
ChIP-seq reads were aligned to the hg19 human genome build using Burrows–Wheeler Aligner version 0.7.1740. Non-uniquely mapping and redundant reads were discarded. MACS version 2.1.1.2014061641 was used for ChIP-seq peak calling with a q value (false discovery rate (FDR)) threshold of 0.01. Fragment locations were converted to BED files using BEDTools (version 2.29.2) bamtobed with the -bedpe flag set. For analyses involving overlap with genomic regions, fragments were imported as GRanges objects and collapsed to 1 bp at the center of the fragment location to ensure that a fragment can map to only one site. LPWGS data were used to estimate ctDNA using ichorCNA with default settings.
Assembly: hg19
Supplementary files format and content: bigWig, narrowPeak

source_name: Plasma

extract_protocol:
No extraction
ChIP-seq libraries were generated from purified input and IP sample DNA using the ThruPLEX DNA-seq Kit from TakaraBio.
Libraries were sequenced using 150-base paired-end reads on an Illumina platform.

value: Plasma


title: wHS_RGENP4611_Squamous

description:
Library name: wHS_RGENP4611_Squamous
LPWGS


title: WT_5_S2_L008_

description:
Library name: Sample 9
Column name in 20241018_rnaseq1_final_counts.txt


title: WT_4_S2_L008_

description:
Library name: Sample 8
Column name in 20241018_rnaseq1_final_counts.txt


title: STAMP_161

source_name: Oral cancer cell line (UM-SCC-1)

value: Human squamous cell carcinoma cell line

value: Dr. Marina Kochetkova (University of South Australia)


title: Homo sapiens, uterine myometrial tissue, Scar uterus disease group, biol repl3

description: Library name: Scar3

value: uterine tissue


title: WT_3_S2_L008_

description:
Library name: Sample 7
Column name in 20241018_rnaseq1_final_counts.txt


title: wHS_RGENP3649_Squamous

description:
Library name: wHS_RGENP3649_Squamous
LPWGS


title: WT_2_S2_L008_

description:
Library name: Sample 6
Column name in 20241018_rnaseq1_final_counts.txt


title: JC_K4_SquamousPC_FL

description:
Library name: JC_K4_SquamousPC_FL
H3K4me3 ChIP-seq


title: Homo sapiens, uterine myometrial tissue, Scar uterus disease group, biol repl2

description: Library name: Scar2

value: experiment


title: KO_5_S2_L008_

description:
Library name: Sample 4
Column name in 20241018_rnaseq1_final_counts.txt

value: CD45.1/1 [Lpar5 knockout]


title: KO_3_S2_L008_

description:
Library name: Sample 2
Column name in 20241018_rnaseq1_final_counts.txt


title: JC_K27_SCPC_RGENP4611

description:
Library name: JC_K27_SCPC_RGENP4611
H3K27ac ChIP-seq


title: JC_K4_SCPC_GENP8956

description:
Library name: JC_K4_SCPC_GENP8956
H3K4me3 ChIP-seq


title: JC_K4_reSCPC_RGENP4611

description:
Library name: JC_K4_reSCPC_RGENP4611
H3K4me3 ChIP-seq


title: KO_6_S2_L008_

description:
Library name: Sample 5
Column name in 20241018_rnaseq1_final_counts.txt


title: KO_4_S2_L008_

description:
Library name: Sample 3
Column name in 20241018_rnaseq1_final_counts.txt


title: KO_2_S2_L008_

description:
Library name: Sample 1
Column name in 20241018_rnaseq1_final_counts.txt


title: Homo sapiens, uterine myometrial tissue, control, biol repl3

description: Library name: NC3

value: Control blank


title: JC_K4_reSCPC_RGENP3649

description:
Library name: JC_K4_reSCPC_RGENP3649
H3K4me3 ChIP-seq


title: JC_K27_SCPC_RGENP3649

description:
Library name: JC_K27_SCPC_RGENP3649
H3K27ac ChIP-seq


title: JC_K27_SCPC_GENP8956

description:
Library name: JC_K27_SCPC_GENP8956
H3K27ac ChIP-seq


title: human microglia treated with APOE4 ACM (Aβ-treated)_3

city: Seoul

first: Jinsoo

last: Seo

address: 50 Yonsei-ro

department: Department of Systems Biology

country: South Korea

institute: Yonsei University

data_processing:
The raw fastq data were aligned to human hg38 assembly using STAR 2.4.0 RNA-seq aligner
Gene raw counts were generated from the mapped data using featureCounts tool
The mapped reads were also processed by Cufflinks 2.2 to estimate transcript abundances.
Gene differential expression test between sample groups was performed using Cuffdiff module with adjusted q-value < 0.05 for statistical significance
Assembly: Human hg38
Supplementary files format and content: text file includes raw counts for each Sample
Supplementary files format and content: text file includes FPKM values for each Sample

source_name: Immortalized human microglia (hTERT)

growth_protocol: human microglia cell lines cultured in Prigrow III media (ABM)

extract_protocol:
Cells were lysed using Ambion Trizol Reagent (Invitrogen) under RNase-free conditions for RNA extraction. The lysate was separated into an aqueous RNA phase using chloroform and centrifugation. The RNA pellet was washed with RNase-free 75% ethanol, air-dried, and resuspended in RNase-free water.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit following manufacturer's protocols

tag: cell line

value: Immortalized human microglia (hTERT)

value: Microglia

value: Control (APOE3)

value: Aβ-treated


title: wHS_GENP8956_Squamous

description:
Library name: wHS_GENP8956_Squamous
LPWGS


title: human microglia treated with APOE4 ACM (Aβ-treated)_2


title: human microglia treated with APOE4 ACM (Aβ-treated)_1


title: JC_K27_SquamousPC_FL

description:
Library name: JC_K27_SquamousPC_FL
H3K27ac ChIP-seq


title: human microglia treated with APOE4 ACM (non-treated)_3

value: non-treated


title: human microglia treated with APOE3 ACM (Aβ-treated)_3


title: human microglia treated with APOE4 ACM (non-treated)_2


title: human microglia treated with APOE4 ACM (non-treated)_1


title: human microglia treated with APOE3 ACM (non-treated)_1


title: human microglia treated with APOE3 ACM (Aβ-treated)_2


title: 5752I

city: Durham

first: Staci

last: Bilbo

state: North Carolina

address: 207 Research Dr, GSRB2

department: Psychology and Neuroscience

institute: Duke University

description:
Library name: Sample3
PIP-Seq

data_processing:
Raw data were pre-processed using pipseeker v3.3.0
Assembly: GRCm39 vM29 2022.04
Supplementary files format and content: tab separated values files and matrix files

source_name: Intestine

extract_protocol:
The jejunum and ileum of a P6 male and female mouse of was isolated and rinsed with HBSS. The tissue was segmented into ~2 cm fragments and opened longitudinally to expose the epithelium. The tissue was incubated in 30 mM EDTA in HBSS without calcium and magnesium at 37˚C for 20 min. The tissue was vigorously shaken to release epithelium. The epithelium was collected, incubated on ice, and allowed to settle via gravity. The epithelium was washed twice in HBSS, then transferred to 1 mg/ml dispase II in HBSS and triturated for 10 passes. Cell suspension was incubated on macs dissociator for 12 mins at 200 rom at 37C.  Cells were strained and washed with HBSS +10% FBS and centrifuged at 300 G for 5 mins. Cells were centrifuged and washed in cell suspension buffer (PIPSeq kit) and cells were resuspended at a concentration of ~4000 cells/uL.
Single cell libraries were prepared using PIP-Seq V T20 kit

value: Intestine

tag: tissue region

value: Ileum

tag: age

tag: Sex

value: Female

value: WT


title: 5442J

description:
Library name: Sample2
PIP-Seq

tag: tissue

value: Jejunum

value: Male


title: human microglia treated with APOE3 ACM (non-treated)_2

tag: cell type


title: 5442I

description:
Library name: Sample1
PIP-Seq

tag: genotype


title: APOE4 primed + Aβ treated_3

source_name: hiPSC-derived astrocytes

growth_protocol: hiPSC-astrocytes were cultured in astrocyte media (ScienCell)

treatment_protocol: 10 μM PolyI:C or 10 μM Aβ42 oligomer for 6 hours

value: hiPSC-derived astrocytes

value: Astrocytes

tag: treatment

value: PolyI:C, recovery, Aβ


title: APOE4 primed + Aβ treated_2


title: Mus musculus, uterine myometrial tissue, Scar uterus disease group, biol repl3

description: Library name: SCAR_3

value: uterine tissue

value: experiment


title: APOE4 primed + PolyI:C treated_3

value: PolyI:C, recovery, PolyI:C


title: Mus musculus, uterine myometrial tissue, Scar uterus disease group, biol repl1

description: Library name: SCAR_1


title: APOE4 primed + PolyI:C treated_2


title: 5752J

description:
Library name: Sample4
PIP-Seq


title: PLK1-overexpressed tumor 0001

city: Lexington

first: Xiaoqi

last: Liu

state: KY

address: 760 Press Avenue, Research Building 2, Room 330

institute: University of Kentucky

description:
Library name: KI_0001
column name in readcount_genename.xls: KI_0001

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Paired-end clean reads were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software.
Assembly: mm10
Supplementary files format and content: tab-delimited xls file include readcount for each sample

source_name: melanoma

growth_protocol: The mice with indicated genotype was treated with 4-OHT to induce the melanoma. After 40 days, the mouse melanoma tissues were harvested.

extract_protocol:
The total mRNA was extacted by Qiagen RNeasy mini kit.
1ug of total RNA was used to generate the library. The library was generated using NEBNex Ultra RNA library Prep Kit fo Illumina following the manufacturer's manual.

value: melanoma

value: BrafCA/+ / Ptenloxp/loxp / Plk1


title: PLK1-overexpressed tumor 4975

description:
Library name: KI_4975
column name in readcount_genename.xls: KI_4975


title: PLK1 wt tumor 4958

description:
Library name: WT_4958
column name in readcount_genename.xls: WT_4958

value: BrafCA/+ / Ptenloxp/loxp


title: PLK1 wt tumor 4957

description:
Library name: WT_4957
column name in readcount_genename.xls: WT_4957


title: PLK1-overexpressed tumor 4976

description:
Library name: KI_4976
column name in readcount_genename.xls: KI_4976


title: PLK1-overexpressed tumor 0006

description:
Library name: KI_0006
column name in readcount_genename.xls: KI_0006


title: PLK1 wt tumor 4949

description:
Library name: WT_4949
column name in readcount_genename.xls: WT_4949


title: PLK1 wt tumor 4971

description:
Library name: WT_4971
column name in readcount_genename.xls: WT_4971


title: PLK1 wt tumor 0002

description:
Library name: WT_0002
column name in readcount_genename.xls: WT_0002


title: PLK1-overexpressed tumor 4980

description:
Library name: KI_4980
column name in readcount_genename.xls: KI_4980


title: PLK1 wt tumor 0007

description:
Library name: WT_0007
column name in readcount_genename.xls: WT_0007


title: human microglia treated with APOE3 ACM (non-treated)_3

value: Immortalized human microglia (hTERT)

value: Microglia

value: Control (APOE3)


title: human microglia treated with APOE3 ACM (Aβ-treated)_1

value: Aβ-treated


title: Mus musculus, uterine myometrial tissue, Scar uterus disease group, biol repl2

description: Library name: SCAR_2


title: Mus musculus, uterine myometrial tissue, control, biol repl3

description: Library name: NC_3

value: Control blank


title: APOE4 primed + PolyI:C treated_1


title: Mus musculus, uterine myometrial tissue, control, biol repl2

description: Library name: NC_2


title: Mus musculus, uterine myometrial tissue, control, biol repl1

description: Library name: NC_1


title: APOE4 primed_2

value: PolyI:C then recovered for 72 hours


title: APOE4 primed_3


title: APOE4 Aβ treated_3

value: Aβ


title: APOE4 primed + Aβ treated_1


title: SostPB/-, liver, MCD diet, biol rep 2

city: Shanghai

first: Guangxing

last: Lu

address: 上海市淞沪路2005号

institute: Fudan University

data_processing:
The raw data were aligned using HISAT2 and quantified by Stringtie
Differentially expressed genes were determined by DESeq2
Assembly: mm10
Supplementary files format and content: comma-separated values file includes raw counts for each sample
Supplementary files format and content: comma-separated values file includes normalized counts (using DESeq2) for each sample

source_name: Liver

extract_protocol:
Total RNA was extracted from the liver using RNAiso Plus reagent (Takara)
The RNA with poly-A in eukaryotic total RNA was enriched by TIANSeq mRNA Capture Kit (TIANGEN). Then, using the captured RNA as the starting sample, TIANSeq Fast RNA Library Kit (Illumina) was used to construct the transcriptome sequencing libraries

value: Liver

value: SostPB/-

value: MCD diet


title: SostPB/-, liver, MCD diet, biol rep 4


title: APOE4 Aβ treated_2

value: hiPSC-derived astrocytes

value: Astrocytes


title: SostPB/-, liver, MCD diet, biol rep 1


title: SostPB/-, liver, MCD diet, biol rep 3


title: Sost-/-, liver, MCD diet, biol rep 3

value: Sost-/-


title: APOE4 PolyI:C treated_3


title: APOE4 Aβ treated_1


title: Sost-/-, liver, MCD diet, biol rep 2


title: APOE4 PolyI:C treated_2


title: APOE4 control_1


title: APOE3 primed + Aβ treated_3

value: PolyI:C, recovery, Aβ


title: Sost-/-, liver, MCD diet, biol rep 4


title: APOE3 primed + Aβ treated_1


title: Sost-/-, liver, MCD diet, biol rep 1


title: APOE3 primed + PolyI:C treated_3

value: PolyI:C, recovery, PolyI:C


title: APOE4 control_3


title: APOE4 PolyI:C treated_1


title: N_RPM_1

city: Innsbruck

first: Johannes

last: Woelk

address: Peter-Mayr-Str. 1a

department: Cell Genetics

institute: Medical University of Innsbruck

data_processing:
Clean reads were obtained by filtering raw reads to remove those containing adapters, reads with more than 10% undetermined bases, and low-quality reads (quality value of over 50% bases of the read is <=5) using the fastp software. Paired-end clean reads were aligned to the mouse genome (mm10) using HISAT2 (V.2.0.5) (Mortazavi et al., 2008). Gene counts were derived based on the number of reads mapped to each gene using featureCounts (v1.5.0-p3). Differentially expression (DE) analysis was performed using the DESeq2 R package (1.20.0). The resulting p-values were adjusted using Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value <=0.05 were considered as differentially expressed.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes DESeq2 normalized values for each Sample

extract_protocol:
RNA from sorted cells was extracted using the RNeasy mini Kit as per manufacturer instructions. DNA was removed using DNA-removal columns (Quiagen). RNA quantity and integrity were determined by Agilent 5400, and only samples with > 100 ng RNA and RNA integrity number > 4 were used.
mRNA was isolated from total RNA using poly-T oligo-attached magnetic beads. The isolated mRNA was subjected to fragmentation, followed by the synthesis of first-strand cDNA employing random hexamer primers. Subsequently, second-strand cDNA synthesis was performed with dTTP to create a non-directional library. The prepared library underwent a series of steps, including end repair, poly-A enrichment, adapter ligation, size selection, amplification, and purification. The library quality and quantity were assessed using Quibit and real-time PCR for quantification and a bioanalyzer for size distribution analysis. Quantified libraries were pooled and subjected to next-generation Illumina sequencing, generating paired-end reads.

value: spleen

tag: strain background

value: Red pulp macrophages


title: large intestine, 9w, scRNA-seq, lane2

city: Fukuoka

first: Shinichiro

last: Sawa

address: 3-1-1 Maidashi, Higashiku

country: Japan

institute: Kyushu University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting were performed using the Cell Ranger software v7.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: colon

extract_protocol:
Intestines were collected, cut into 1cm pieces, and then washed with EDTA-free cold PBS. Gut tissue was incubated in 30mM EDTA-containing PBS for 13 minutes at room temperature then immediately washed with EDTA-free cold PBS to remove epithelium.  Washed gut specimens were incubated in DMEM containing 1 mg/mL Collagenase P , 0.2 mg/mL Liberase TH and 0.33 mg/mL DNase I  at 37ºC. Dissociated cells were collected every 30 min and strained with a 100 μm nylon mesh, and then were subjected to density gradient centrifugation using 40%/80% Percoll system (Cyvita). The cells at the intermediate layer were collected by centrifuge and resuspended in 2% FBS/2 mM EDTA/PBS. The isolated cells were stained with antibodies against PDPN, CD45 and CD31. Fixable viability dye (eBioscience) was used to stain dead cells. Alive PDPN+CD45-CD31- cells were sorted for single cell 3' gene expression library construction.
Library construction was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics) with slight modification.  Cells up to 10,000 were directly sorted into the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). .

value: colon

tag: strain

value: wild type


title: WT_RPM_3

value: wild-type


title: WT_RPM_1


title: APOE4 control_2


title: N_RPM_2


title: APOE3 primed + Aβ treated_2

value: Control (APOE3)


title: APOE3 primed_3


title: APOE4 primed_1


title: APOE3 primed + PolyI:C treated_1


title: APOE3 primed + PolyI:C treated_2


title: RNA_KO_WM2

city: Incheon

first: Ik Soo

last: Kim

address: Gaetbeol-ro, Yeonsu-gu

institute: Gachon University college of Medicine

data_processing:
RNA-Seq : The reads were pre-processed to remove adaptors and bases with low quality by Trimmomatic (v0.36). Next, STAR (v2.5.3) was used to align the reads, and Transcripts Per Million (TPM) was calculated with RSEM (v1.3.0).
Assembly: mm10
Supplementary files format and content: *.gtf : Output of StringTie mediated assembly of RNA-Seq alignments into potential transcripts.
Supplementary files format and content: *.txt : Combined output of StringTie mediated assembly of transcripts into genes (counts, FPKM, TPM)

growth_protocol: Mouse crypts were isolated and resuspended in DMEM/F-12 (Hyclone Laboratories).  Single intestinal organoid cells which were incubated by 1× TrypLE™ Express (Gibco) were subcultured with Matrigel matrix (Corning) in 24well plates. Each well was supplemented with 600µl of IntestiCult Organoid Growth Medium (OGM). Organoids were grown at 37 °C in a humidified incubator with 5% CO2.

extract_protocol:
RNA: Total RNAs were extracted from WT and Phf16-/Y intestinal organoid cells on day1, with or without WM3835 treatment. Then, the stranded mRNA-seq library was prepared following Illumina's TruSeq protocol.
RNA-seq library was prepared following Illumina's TruSeq protocol

value: Intestinal epithelium


title: large intestine, 9w, scRNA-seq, lane1

description: 10x Genomics


title: RNA_KO1


title: APOE3 Aβ treated_2


title: RNA_WT2

value: WT


title: RNA_WT_WM1


title: APOE3 Aβ treated_3

value: Aβ


title: WT_RPM_2


title: APOE3 Aβ treated_1


title: APOE3 PolyI:C treated_3


title: Crypt_organoids_RNA_seq_KO_day3_rep2

data_processing:
ATAC-Seq: After trimming adapter sequences by Trim Galore (V0.5.0), paired-end reads were aligned onto mm10 using Bowtie2 (v2.3.5.1)51 and peak calling was conducted by Model-based Analysis for ChIP-Seq (MACS) (v2.1.2) General analysis of chromatin accessibility including annotation of genomic coordinates, peak counts, and normalization was performed using ChrAccR (v.0.9.17).
RNA-Seq : The reads were pre-processed to remove adaptors and bases with low quality by Trimmomatic (v0.36). Next, STAR (v2.5.3) was used to align the reads, and Transcripts Per Million (TPM) was calculated with RSEM (v1.3.0).
Assembly: mm10
Supplementary files format and content: *.bw : The bigWig format is for display of dense, continuous data that will be displayed as a graph in IGV or UCSC browser.
Supplementary files format and content: *.gtf : Output of StringTie mediated assembly of RNA-Seq alignments into potential transcripts.
Supplementary files format and content: *.txt : Combined output of StringTie mediated assembly of transcripts into genes (counts, FPKM, TPM)

extract_protocol:
DNA: ATAC-seq libraries were prepared for sequencing using Illumina Tagment DNA TDE1 Enzyme and Buffer Kits (#20034197, Illumina) and paired-end sequencing was performed by Illumina platform
ATAC-seq libraries were prepared for sequencing using Illumina Tagment DNA TDE1 Enzyme and Buffer Kits (#20034197, Illumina)
RNA: Total RNAs were extracted from WT and Phf16-/Y intestinal organoid cells on days1-3. Then, the stranded mRNA-seq library was prepared following Illumina's TruSeq protocol.
RNA-seq library was prepared following Illumina's TruSeq protocol

tag: time


title: APOE3 PolyI:C treated_2


title: APOE3 PolyI:C treated_1


title: Crypt_organoids_RNA_seq_KO_day3_rep1


title: APOE3 control_2


title: RNA_WT1


title: Crypt_organoids_RNA_seq_KO_day2_rep2


title: APOE3 control_3


title: RNA_KO_WM1


title: APOE3 primed_2

value: PolyI:C then recovered for 72 hours


title: Crypt_organoids_RNA_seq_KO_day1_rep2


title: Crypt_organoids_RNA_seq_WT_day3_rep2


title: hiPSCs KO day 20 biol rep 3

city: Rome

first: Alessandro

last: Palma

address: Piazzale Aldo Moro 5

department: Biology and Biotechnologies "Charles Darwin"

country: Italy

institute: Sapienza University of Rome

data_processing:
Q30-filtered raw reads were obtained from Illumina BaseSpace Reads and aligned to GRCh38 assembly using STAR aligner software, using a customized hg38 annotation file
Read counts of “reverse” configuration files were combined into a count matrix file, that was given as input to DESeq2 (Love et al., 2014) R package for normalization and differential expression analysis, after removing genes with less than 10 counts in at least two samples
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include DESeq2-normalized counts for each sample

source_name: human induced pluripotent stem cells (hiPSC)-derived cardiomyocytes

extract_protocol:
Total RNA was harvested from cultured cells using Direct-zolTM RNA MiniPrep (Zymo Research). 500 ng of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using Illumina Stranded mRNA Prep following manufacturer's protocols

value: HSCHARME KO

value: cardiomyocyte differentiation


title: APOE3 control_1

value: hiPSC-derived astrocytes


title: Crypt_organoids_RNA_seq_KO_day1_rep1


title: RNA_KO2


title: hiPSCs KO day 20 biol rep 2

value: human induced pluripotent stem cells (hiPSC)-derived cardiomyocytes


title: Crypt_organoids_RNA_seq_WT_day3_rep1


title: hiPSCs KO day 20 biol rep 1


title: APOE3 primed_1

value: Astrocytes


title: RNA_WT_WM2


title: hiPSCs KO day 10 biol rep 3


title: hiPSCs KO day 10 biol rep 1


title: Crypt_organoids_RNA_seq_WT_day2_rep2


title: Crypt_organoids_RNA_seq_WT_day2_rep1


title: hiPSCs KO day 10 biol rep 2


title: Crypt_organoids_RNA_seq_WT_day1_rep2


title: Crypt_organoids_RNA_seq_WT_day1_rep1


title: hiPSCs WT day 20 biol rep 3

value: HSCHARME WT


title: Retina, 5xFAD, 6M, rep3

first: Jung-Woong

address: 84 Heuksuk-ro Dongjak-ku

department: Life Science

institute: Chung-Ang University

data_processing:
The low quality and TruSeq adapter sequence in mRNA-seq reads were trimmed by TrimGalore (v.0.6.6).
The alignment of sequences to the reference genome was performed using STAR (v.2.7.1a) with the ENCODE v3 parameters.
The alignment sequences were applied for transcript assembly and estimation of their abundances using RSEM (v.1.3.3).
The statistics for differentially expressed transcripts (or genes) and FPKM were calculated by DESeq2 (v.1.32.0).
Assembly: GRCm38.p6.101
Supplementary files format and content: tab-delimited text file include raw counts for each sample

source_name: whole retina

extract_protocol:
Total RNA was extracted from 100 mg of mouse retina using TRIzol solution (15596018, Invitrogen, CA, USA), according to the manufacturer’s specifications. Contaminated genomic DNA was removed from 10 μg of total RNA by the incubation with 20 units of RNase-free DNase I (New England Biolabs) and 4 units of RNase inhibitor (New England Biolabs) in DEPC-treated water. The reaction mixture was incubated for 1 h at 37 °C and then for 10 min at 60 °C. The RNA samples quantified spectrophotometrically at 260 nm and all RNA extracts had an OD260:OD280 between 1.8 and 2.0, demonstrating that RNA was suitable for subsequent analyses. Oligo‐dT (6110A, Takara) was used as the primer in the first step of cDNA synthesis. Total RNA (1 μg) was combined with 1 μl of oligo dT, and H2O and then preheated at 70 °C for 10 min to denature the secondary structures of RNA. The mix was then cooled off quickly to 4 °C, subsequent to which 10 mM DTT, 2 μl of 10X reverse-transcriptase buffer, and 200 units of reverse transcriptase (18064022, Invitrogen, CA, USA) was added to make a total volume of 20 μl. The reverse-transcriptase mixture was incubated at 40 °C for 60 min, after which it was stopped by heating at 94 °C for 20 sec.
The construction of RNA-sequencing library was performed using TruSeq RNA Sample preparation kit v2 (Illumina, Inc., San Diego, CA, cat. no. RS-122–2002). In briefly, 100 ng of total RNA from each sample was exposed to poly-T oligo-attached magnetic beads to isolate poly-A mRNA following mRNA fragmentation. The cleaved RNA fragments were constructed onto a double-stranded cDNA.  After degradation of the RNA template, second strand synthesis was initiated by a random primer containing an Illumina-compatible linker sequence at its 5’ end. Then, the double-stranded library was purified using AMPure XP beads (A63881, Beckman coulter, CA, USA) to remove all reaction components. The library was amplified to add the complete adapter sequences required for cluster generation. The finished library is purified from PCR components. Libraries were analyzed by an Agilent 2100 Bioanalyzer using the High-Sensitivity DNA Chip (Agilent Technologies, Santa Clara, CA). Then, the cDNA libraries were used for paired-end 75 sequencing using an Illumina NextSeq 500 (Illumina, Inc., San Diego, CA).

value: whole retina


title: Crypt_organoids_RNA_seq_KO_day2_rep1


title: hiPSCs WT day 20 biol rep 2


title: Retina, 5xFAD, 6M, rep2


title: Crypt_organoids_ATAC_seq_KO_day3_rep1


title: Retina, 5xFAD, 6M, rep1


title: Retina, B6J WT, 6M, rep3


title: hiPSCs WT day 10 biol rep 2


title: Crypt_organoids_ATAC_seq_KO_day2_rep1


title: Retina, B6J WT, 6M, rep1


title: hiPSCs WT day 10 biol rep 3


title: Crypt_organoids_ATAC_seq_KO_day1_rep2


title: Crypt_organoids_ATAC_seq_KO_day2_rep2


title: Retina, B6J WT, 6M, rep2


title: hiPSCs WT day 20 biol rep 1


title: Retina, 5xFAD, 1M, rep2


title: Retina, 5xFAD, 1M, rep1


title: Retina, 5xFAD, 1M, rep3


title: hiPSCs WT day 10 biol rep 1


title: Crypt_organoids_ATAC_seq_KO_day1_rep1


title: Retina, B6J WT, 1M, rep1


title: Crypt_organoids_ATAC_seq_KO_day3_rep2


title: Retina, B6J WT, 1M, rep3


title: Retina, B6J WT, 1M, rep2


title: SK-N-SH cells, DA+,rep3

first: Yang

last: Yaqi

address: No.1678 Dongfang Road, Pudong, Shanghai, China

institute: Shanghai Children Medical Centre

data_processing:
For quality control of the raw sequencing data, FastQ Screen (version 0.13.0) and FastQC (version 0.11.9) were utilized.
The STAR software (version 2.7.1a) was employed for mapping the reads to the human genome (hg19) or hybrid human(hg19)-ERCC genome. Read counts within each gene were computed using HTSeq count (version 0.11.2).
Gene transcription was quantified by calculating Fragments Per Kilobase of exon per Million mapped reads (FPKM). Statistical significance was assessed using DESeq2 (version 1.40.2)
Assembly: hg19
Supplementary files format and content: 6h_DA+_DA-.fpkm_all_fpkm.txt

growth_protocol: EMEM/F12 medium supplemented with 10% FBS. cells were cultured in an incubator at 37°C with 5% CO2.

extract_protocol:
Lyse cells directly in a culture dish by adding 1 mL TRIzol reagent and mix thoroughly. add 200μL chloroform, vortex mix for 15 seconds. incubate the mix for 5 minutes at room temperature and two layer should form. centrifuge at 12000 g at 4 °C for 10 minutes. Carefully transfer the top layer into the new tubes.add 1:1V of isopropanol to each tube and mix by inversion. Centrifuge at 12000 g at 4 °C for 15 minutes. Discard the supernatant and wash the pellet with 1 mL 75%  ethanol. Centrifuge at 12000g at 4 °C for 10 minutes. Remove all of residential ethanol with a pipet and air dry for 5 min. redissolve RNA in 30-50 μL  DEPC treated water.
The rRNA-depleted sequencing libraries from total RNA were prepared using Illumina TruSeq® Stranded Total RNA Gold preparation Kit. About 1 μg total RNA was used as input material, and Ribo-Zero Gold kit was used to remove both cytoplasmic and mitochondrial rRNA. Purified RNA was then fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers, followed by second strand cDNA synthesis. These cDNA fragments were then subjected to end-repair, phosphorylation and 'A' base addition according to Illumina's library construction protocol.

treatment_protocol: SK-N-SH cells were cultured for 24 hours in standard medium, and then cells were treated with medium (control) or DA at 40 M for 6 h.

value: SK-N-SH

value: neuroblastoma cells

value: Wild Type

value: dopamine


title: Rabbit_0dpi_replicate_2_scRNA-seq_10x

description:
Library name: Rabbit_0dpi_replicate_2_scRNA-seq
Note: because the file1 is larger than 100G, the file 1 was split into two files(part1, part2)

organism: Oryctolagus cuniculus

source_name: ear-pinna

value: ear-pinna

value: injury, 0dpi


title: Crypt_organoids_ATAC_seq_WT_day2_rep2

value: Intestinal epithelium