title: CRC_Collagen_plate3

city: Utrecht

first: Martijn

last: Gloerich

state: Utrecht

address: Universiteitsweg 100

department: Center for Molecular Medicine

institute: University Medical Center Utrecht

data_processing:
Single-cell mRNA-sequencing was performed by Single Cell Discoveries (Utrecht, the Netherlands) according to an adapted version of the Sort-seq protocol ((Muraro et al., 2016) with primers described in (Van Den Brink et al., 2017)).
The DNA library was paired-end sequenced on an Illumina Nextseq™ 500, high output, with a 1×75 bp Illumina kit (read 1: 26 cycles, index read: 6 cycles, read 2: 60 cycles).
Reads were mapped to the mm10 RefSeq genome.
Cells with at least 10.000 total transcripts were included in the analysis.
Assembly: mm10
Supplementary files format and content: Tab-seperated values files

source_name: CRC organoids

growth_protocol: Colorectal cancer organoids isolated from tumorigenic colons of VillinCre-ERT2; APCfl/fl; KRASLSL-G12D/+; TP53KO/KO; R26R-Confetti; Lgr5DTR-eGFP transgenic mice (Fumagalli et al., 2020) were cultured in Matrigel (Corning) drops in culture medium containing advanced DMEM/F12 advanced medium (Life Technologies), 10 mM HEPES (Life Technologies), 1x Glutamax (Life Technologies), 100 Units/mL Penicilin-Streptomycin (Westburg), 10% Noggin-conditioned medium, 2% B27 (Thermo Fisher), 1.25 mM N-Acetyl-L-Cysteine (Sigma) and 100 µg/mL Primocin (Bio-Connect), and passaged every 3 or 4 days.

extract_protocol:
Organoids cultured in Matrigel or Collagen I for 1 day were isolated from the gels using collagenase (Sigma) in PBS for 3 minutes at 37 °C, washed in PBS and dissociated into single cells by TrypLE treatment (Fisher Scientific) at 37 °C. Cells were washed in PBS containing 1% FCS and 1 mM EDTA, subsequently filtered through a Filcon 50 uM stainer (BD BioSciences), and plated as single cells in 384-well plates by FACS (FACS Aria III, BD Biosciences).
CEL-Seq2 (SORT-seq)

treatment_protocol: Intact organoids were isolated from Matrigel cultures 3 days after passaging using 1 mg/mL Dispase II (Cat# 17105041, Life Technologies) followed by 3 washes with DMEM/F12 media. Organoids were either embedded in Matrigel or in type I Collagen lattices consisting of non-pepsinized rat-tail Collagen at a final concentration of 1 mg/ml. The collagen mixture was prepared in buffer containing 10X phosphate buffer saline (PBS) (Gibco), NaOH and dH2O according to the manufacturer’s instructions and the collagen I gel was pre-polymerized on ice for 2-3 hours, after which organoids were embedded in the collagen I gel followed by incubation at room temperature for 5 minutes. The collagen I- and Matrigel gels were plated as 45 µL drops on a pre-warmed 24-well culture plate (Costar). The plate was incubated at 37 °C until polymerization of the gels was achieved, after which the culture medium was added.

value: CRC organoids

value: epithelial cells

value: VillinCre-ERT2; ApcFL/FL; KrasLSL-G12D/+; Tp53KO/KO; R26R-Confetti; Lgr5DTR-eGFP

value: embedded in Collagen I for 1 day


title: CrePos_3_12h

status: Public on Sep 23 2025

type: SRA

city: Singapore

first: Grace

last: Lim

address: 61 Biopolis Drive, Proteos

department: IMCB

country: Singapore

institute: A*STAR

library_source: transcriptomic

data_processing:
Reads were aligned using STAR (version 2.7.10a) using default setttings. Alignment was performed against the human genome version GRCh38, and a GTF file for Gencode annotation v41 was used to augment the alignment.
Quantification was performed using featureCounts (from the Subread suite, version 2.0.3) using default settings to obtain the counts matrix.
Assembly: GRCh38
Supplementary files format and content: The tab-delimited text file "featurecounts_output_matrix.txt"  contains the quantification output from featureCounts, which is essentially the raw count of reads mapped to each gene. The tab-delimited text file "MD5_checksums.txt" contains the MD5 checksums of the raw read files and the file "featurecounts_output_matrix.txt".

molecule: polyA RNA

organism: Homo sapiens

source_name: Human organoid tissue with cassette for conditional knockout of AQP5, with treatment, 12 hour timepoint, replicate 3

extract_protocol:
RNA was extracted using Qiagen RNeasy Micro Kit following manufacturer's instructions.
Library construction was performed using polyA enrichment method following manufacturer's instructions.

tag: tissue

value: Human organoid

tag: genotype

value: AQP5 knockout

tag: treatment

value: Treated to induce knockout of AQP5


title: DE_WT_1

city: WuHan

first: chenchao

last: yan

state: Hubei Province

address: Donghu Road, No. 115

country: China

institute: WuHan university

description:
Library name: Sample 4
Column name in featureCounts.txt: H8_rep1

data_processing:
Sequenced reads were trimmed for adaptor sequence, the clean data were mapped to human genome (hg38) using HISAT2 (v2.1.0)
Raw reads were counted using FeatureCounts (v1.6.4)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file include raw gene counts for each Sample

source_name: Human embryonic stem cells

extract_protocol:
The cells were washed by DPBS and harvested by buffer RL. The HiPure Total RNA Mini Kit (Magen, Cat# R4111-03) was used to extract total RNA following the manufacturer’s instructions and the RNA was quantitated with nanodrop 2000 (ThermoFisher).
RNA libraries were prepared using standard protocols, including mRNA enrichment, fragmentation, cDNA synthesis, adapter ligation, and PCR amplification.

value: Human embryonic stem cells

tag: cell line

tag: cell type

value: differentiated hESCs

value: WT of DVL2_kd

value: Definitive endoderm differentiation


title: CRC_Collagen_plate2

country: Netherlands

library_source: transcriptomic single cell

organism: Mus musculus


title: Control, organoids, 7 days, mouse 3

city: Groningen

first: Davide

last: Cinat

address: Hanzeplein 1

institute: University Medical Center Groningen

description:
Library name: Control 7 days 3
Lexogen

data_processing:
For the alignment of the fastq files the mouse genome GRCm39 was used. The gene counts per sample were detected with the QuantSeq 3' mRNA-seq Integrated Data Analysis Pipeline on the BlueBee Genomics Platform provided by Lexogen with default settings. Rstudion v4.1.3 was used for downstream analysis and for the generation of CPM files. The R package edgeR was used for normalization and identification of differentially expressed genes.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files including the raw counts from all replicates and conditions are provided.

source_name: Submandibular salivary gland

growth_protocol: Organoids from all animals and conditions were cultured in Matrigel in WRY medium (DMEM/F12, Pen/Strep antibiotics, glutamax 2 mM, EGF 20 ng/ml, FGF2 20 ng/mL, N2 1x, insulin 10 µg/mL, dexamethasone 1  µM, Y27632 10 µM, 10% R-spondin1-conditioned medium and 50% Wnt3a-conditioned medium). All conditions were kept in culture at 37°C and 5% CO2 until the day of the experiment.

extract_protocol:
For the cDNA library preparation, total RNA was extracted from organoids using Rneasy Mini Kit according to the manufacturer`s instructions and its quality was determined using High Sensitivity RNA ScreenTapes on an Agilent 2100 Bioanalyzer. 100 ng of RNA was used as an input for all samples.
100 ng of highly intact RNA (RIN values > 9) was processed for the cDNA library preparation using the Lexogen QuantSeq 3' mRNA-Seq Library Prep Kit following the manufacturers protocol.

treatment_protocol: Organoids are untreated

value: Submandibular salivary gland

value: Salivary gland cells derived from organoids

value: 8-12 weeks old mice, C57BL/6

value: Non-irradiated


title: DE_shC_2

description:
Library name: Sample 8
Column name in featureCounts.txt: H8_C_rep2

value: WT of LINC01612_ko


title: CRC_Collagen_plate1


title: CrePos_3_5d

source_name: Human organoid tissue with cassette for conditional knockout of AQP5, with treatment, 5 day timepoint, replicate 3


title: HFF uninfected, rep2

city: Rehovot

first: Noa

last: Aharon-Hefetz

address: 234 Herzl Street

country: Israel

institute: Weizmann Institute of Science

description:
Library name: Sample 2
HFF_uninf_Rep2_S9

data_processing:
tRNA-seq analysis is described in (DOI: 10.1073/pnas.2106556118)
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes read counts of mature tRNA genes for all samples
Supplementary files format and content: tab-delimited text file includes modification fraction per tRNA gene and modified residue for all samples

molecule: total RNA

source_name: HFF

growth_protocol: Human Foreskin Fibroblasts (ATCC) were grown in DMEM high glucose medium (Biological Industries) supplemented with 10% heat-inactivated FBS (Life Technologies), 1% penicillin/ streptomycin (P/S), and 1% L-Glutamine.

extract_protocol:
Samples were harvested with Tri-Reagent (Sigma-Aldrich). Total RNA was extracted according to the manufacturer’s protocol.
tRNA-seq libraries were constructed based on DM-TGIRT-seq protocol (DOI: 10.1038/nmeth.3478) with some modifications, as described in (DOI: 10.1073/pnas.2106556118)

treatment_protocol: HFF cells (passage 27) were grown to full confluence in 10 cm plates and then infected with the HCMV merlin UL32-GFP strain (Stanton et al., 2010) at a Multiplicity of infection (MOI) of 5. Cells were incubated with the virus for 1 hour, washed, and supplemented with fresh medium. Cells were harvested at 4 time points following infection- 5, 16, 24, and 72 hours post-infection. HFF treated with IFN were incubated with 550U/ml IFNα (PBL) and 700U/mL IFNβ (Peprotech) and harvested after 5 hours. Infected cells treated with ruxolitinib were supplemented with a medium containing 4uM ruxolitinib (InvivoGen) after 1-hour incubation with HCMV and harvested 24 hours post-infection.

value: HFF

value: WT


title: Control, organoids, 7 days, mouse 1

description:
Library name: Control 7 days 1
Lexogen


title: CRC_Matrigel_plate3

value: CRC organoids

value: epithelial cells

value: embedded in Matrigel for 1 day


title: Control, organoids, 7 days, mouse 2

description:
Library name: Control 7 days 2
Lexogen


title: DE_DVL2_KD3

description:
Library name: Sample 3
Column name in featureCounts.txt: DVL2_kd3

value: DVL2 knockdown


title: CrePos_3_2d

source_name: Human organoid tissue with cassette for conditional knockout of AQP5, with treatment, 2 day timepoint, replicate 3

value: Human organoid

value: AQP5 knockout


title: ChIPseq, Liver, KANSL3, rep4

city: Freiburg

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

library_source: genomic

data_processing:
Fastq files were aligned with snakePipes version 2 against the mm10 reference genome, using the DNA-mapping mode and the ChIP-seq mode.
Assembly: mm10
Supplementary files format and content: deepTools bamCompare (v3) was used to generate the log2 and subtract bigwig files.

molecule: genomic DNA

source_name: Liver

extract_protocol:
Cells and liver tissue cell suspensions were fixed with 1% PFA for 15 minutes at RT , Nuclei extraction, quantification and ChIP was performed using the published RELACS protocol (Arrigoni et al, 2018) Antibodies: KANSL3 ( Sigma HPA035018), H3K27ac (Diagenode C15410196), H3K4me3 (Diagenode C15410003), H3K9ac (Cell Signaling 9649), H4K16ac (abcam ab109463, Hepa1-6), H4K16ac (Milipore 07-329, liver tissue).
Libraries were prepared using a NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB, E7645)

value: Liver

value: AlbCre+


title: Control, organoids, 5 days, mouse 3

description:
Library name: Control 5 days 3
Lexogen


title: DE_DVL2_KD2

description:
Library name: Sample 2
Column name in featureCounts.txt: DVL2_kd2

value: Human embryonic stem cells

value: differentiated hESCs


title: CRC_Matrigel_plate1

value: VillinCre-ERT2; ApcFL/FL; KrasLSL-G12D/+; Tp53KO/KO; R26R-Confetti; Lgr5DTR-eGFP


title: CrePos_2_24h

source_name: Human organoid tissue with cassette for conditional knockout of AQP5, with treatment, 24 hour timepoint, replicate 2

value: Treated to induce knockout of AQP5


title: CrePos_2_5d

source_name: Human organoid tissue with cassette for conditional knockout of AQP5, with treatment, 5 day timepoint, replicate 2


title: Control, organoids, day11

description:
Library name: Control_day_11
10X Genomics

data_processing:
Processing and filtering was done using the CellRanger software v5
Assembly: mm10
Supplementary files format and content: For all conditions filtered features, barcodes sequences and matrix files are provided.

growth_protocol: Organoids derived from 4 different animals were cultured in Matrigel in WRY medium (DMEM/F12, Pen/Strep antibiotics, glutamax 2 mM, EGF 20 ng/ml, FGF2 20 ng/mL, N2 1x, insulin 10 µg/mL, dexamethasone 1  µM, Y27632 10 µM, 10% R-spondin1-conditioned medium and 50% Wnt3a-conditioned medium). All conditions were kept in culture under the same conditions (at 37°C and 5% CO2) until the day of the experiment. Day 11 organoids were collected from a different batch of animals and run in a separate run.

extract_protocol:
Organoids and tissue were collected and dissocited into single cells using 0.05% trypsin EDTA for 10 minutes. Cells were then washed with PBS/BSA 0.2% and resuspended with 500 µL PBS/BSA 0.2% and propidium iodide (PI). 45.000 PI negative cells/sample were sorted using a Moflo Astrios sorter and immediately leaded into the 10x Genomics chip.
For the GEM generation and barcoding, immediately after sorting samples were loaded on the Chromium Next GEM Chip G and ran in the Chromium Controller. The preparation of the library was performed by using the 10X Chromoum Next GEM Single Cell 3' kit T Set A following the manufacturer`s protocol step by step.

treatment_protocol: Organoids were irradiated with either 7 Gy photons or 7 Gy protons (plateau) at day 5. Organoid media of control, photon and proton irradiated samples was refreshed after irradiation. Organoids were collected at day 7. All experiments from all the conditions were carried out on the same day excepet for 11-day organoids.

value: Submandibular salivary gland

value: Salivary gland cells derived from organoids

tag: strain


title: DE_DVL2_KD1

description:
Library name: Sample 1
Column name in featureCounts.txt: DVL2_kd1

value: Definitive endoderm differentiation


title: CrePos_2_12h

source_name: Human organoid tissue with cassette for conditional knockout of AQP5, with treatment, 12 hour timepoint, replicate 2


title: ChIPseq, Liver, KANSL3, rep3


title: CrePos_2_2d

source_name: Human organoid tissue with cassette for conditional knockout of AQP5, with treatment, 2 day timepoint, replicate 2


title: ChIPseq, Liver, KANSL3, rep1


title: CRC_Matrigel_plate2


title: Organoids, Passage 2, 3-month-old mouse

description: Lexogen

data_processing:
For the analysis, alignment and peak calling were performed using the ENCODE ATAC-seq pipeline. All organoid samples were used to generate a consensus peak file (>41K peaks). HOMER function findMotifsGenome was used to perform motif enrichment analysis with default settings.
Assembly: GRCm39
Supplementary files format and content: Peak file

growth_protocol: Organoids from all animals were cultured in Matrigel in WRY medium (DMEM/F12, Pen/Strep antibiotics, glutamax 2 mM, EGF 20 ng/ml, FGF2 20 ng/mL, N2 1x, insulin 10 µg/mL, dexamethasone 1  µM, Y27632 10 µM, 10% R-spondin1-conditioned medium and 50% Wnt3a-conditioned medium). All conditions were kept in culture at 37°C and 5% CO2 until the day of the experiment.

extract_protocol:
ATAC-seq libraries were prepared using Nextera DNA Sample Preparation Kit following the manufacturer`s protocol. Following PCR amplification, DNA was purified using the Qiagen MinElute kit and run on a 2% E-gel agarose gel. The concentration of the libraries was determined using a Qubit and 2100 Bioanalyzer.
ATAC-seq libraries were prepared using Nextera DNA Sample Preparation Kit following the manufacturer`s protocol. Following PCR amplification, DNA was purified using the Qiagen MinElute kit and run on a 2% E-gel agarose gel. The concentration of the libraries was determined using a Qubit and 2100 Bioanalyzer. 1,6 pM of libraries with 5% PhiX was then loaded on a NextSeq 500 (Illumina) for a 75 bp paired-end sequencing run at the Research Sequencing Facility of ERIBA (UMCG).

treatment_protocol: Mice were housed under standard conditions with diet and water ad libitum. Submandibular salivary glands were harvested at the proper timepoint for sequencing.

tag: age

value: 3 months

value: Non-irradiated


title: 2CLC, dTAG, H3K9me2, rep3, input

city: New York

first: Christopher

middle: Mitsuo

last: Uyehara

state: NY

address: 413 E 69th St

department: Meyer Cancer Center

country: USA

institute: Weill Cornell Medicine

description: Library name: Sample 24

data_processing:
Technical replicates were merged using zcat
Trimmed reads were mapped to STAR v2.7.10 with parameters: --readFilesCommand zcat --runThreadN 10 --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 5000 --outSAMmultNmax 1 --outFilterMismatchNmax 3  --outMultimapperOrder Random --winAnchorMultimapNmax 5000 --alignEndsType EndToEnd --alignIntronMax 1 --alignMatesGapMax 350 --seedSearchStartLmax 30 --alignTranscriptsPerReadNmax 30000 --alignWindowsPerReadNmax 30000 --alignTranscriptsPerWindowNmax 300 --seedPerReadNmax 3000 --seedPerWindowNmax 300 --seedNoneLociPerWindow 1000 --alignSJoverhangMin 999 --alignSJDBoverhangMin 999
PCR duplicates were removed from mapped reads using picard v2.26.0 with parameters: VALIDATION_STRINGENCY=LENIENT REMOVE_DUPLICATES=true ASSUME_SORTED=true
After duplicate removal, reads that overlapped ranges annotated as "High Signal Region" from the ENCODE Blacklist (mm10 v2) were removed using samtools v1.14
Bam files were converted to bedpe files using bedtools v2.30.0 with parameters: -bedpe and then reformatting using: sort -k 1,1 -k 2,2n | cut -f 1,2,6,7
Bigwigs normalized to sequencing depth were made from bed files using deeptools v3.5.1 using parameters: --binSize 10 --ignoreForNormalization chrX chrM --normalizeUsing RPGC --effectiveGenomeSize 2652783500 --extendReads 200 --ignoreDuplicates --blackListFileName mm10-blacklist.v2_highSignalRegions.bed
Bigwigs were normalized at 10kb resolution with 5kb sliding steps using a custom R (v4.1.2, "Bird Hippie") script.
Bigwigs normalized to input [log2(ChIP/Input)] were generated using custom R (v4.1.2, "Bird Hippie") script from 10kb normalized bigwigs.
Assembly: mm10
Supplementary files format and content: bigwigs from individual replicates normalized to sequencing depth
Supplementary files format and content: bigwigs from merged replicates normalized to sequencing depth
Supplementary files format and content: bigwigs from individual replicates normalized as log2(chip/input)
Supplementary files format and content: bigwigs from merged replicates normalized as log2(chip/input)
Supplementary files format and content: bed files of H3K9me2 domains.

source_name: EHMT2-dTAG-mcherry MERV-GFP

growth_protocol: Cells were cultured in FBS/LIF conditions at 37C at 5%CO2.

extract_protocol:
Cells were collected in single cell suspension using trypsin and sorted to obtain ~100k cells based on MERVL-GFP to obtain MERVL- mESC and MERVL+ 2CLC.  ULI-NChIP was conducted according to the protocol published by Brind’Amour et al. (PMID 25607992). 1ug H3K9me2 antibody ab1220 was used.
ULI-NChIP libraries were prepared using the Thru-PLEX DNA-seq kit with adapters from Takara (cat. R400666). The quality of the libraries was checked using a DNA tape-station and sequencing conducted by the Weill Cornell Genomics core.

treatment_protocol: Cells were treated with DMSO or dTAG-13 for 72 hours (with TTNBP (TT; 0.2M) for 2 of the replicates to increase MERVL+ve cells)

value: EHMT2-dTAG-mcherry MERV-GFP

value: BL6/129 hybrid

value: dTAG 72hr

tag: antibody


title: 2CLC, dTAG, H3K9me2, rep2, input

description: Library name: Sample 23


title: Organoids, Passage 1, 12-week-old mouse

description: Lexogen

value: 12 weeks


title: ChIPseq, Liver, KANSL3, rep2


title: Organoids, Passage 1, 3-month-old mouse

description: Lexogen


title: Organoids, Passage 2, 12-week-old mouse

description: Lexogen


title: Fresh tissue

description: 10x Genomics

growth_protocol: Organoids derived from 4 different animals were cultured in Matrigel in WRY medium (DMEM/F12, Pen/Strep antibiotics, glutamax 2 mM, EGF 20 ng/ml, FGF2 20 ng/mL, N2 1x, insulin 10 µg/mL, dexamethasone 1  µM, Y27632 10 µM, 10% R-spondin1-conditioned medium and 50% Wnt3a-conditioned medium). All conditions were kept in culture under the same conditions (at 37°C and 5% CO2) until the day of the experiment.

treatment_protocol: Organoids were irradiated with either 7 Gy photons or 7 Gy protons (plateau) at day 5. Organoid media of control, photon and proton irradiated samples was refreshed after irradiation. Organoids were collected at day 7. All experiments from all the conditions were carried out on the same day.

value: 8-12 weeks old

value: Cells from freshly isolated submandibular salivary gland tissue


title: CrePos_1_2d

source_name: Human organoid tissue with cassette for conditional knockout of AQP5, with treatment, 2 day timepoint, replicate 1

value: Human organoid

value: AQP5 knockout


title: 2CLC, dTAG, H3K9me2, rep1, input

description: Library name: Sample 22


title: Proton, organoids, day 7

description: 10x Genomics

value: Proton irradiated (7 Gy)


title: 2CLC, dTAG, H3K9me2, rep3, chip

description: Library name: Sample 21


title: Photon, organoids, day 7

description: 10x Genomics

value: Photon irradiateed (7 Gy)


title: CreNeg_3_5d

source_name: Human organoid tissue with cassette for conditional knockout of AQP5, no treatment, 5 day timepoint, replicate 3

value: AQP5 wild-type

value: No treatment


title: CrePos_1_24h

source_name: Human organoid tissue with cassette for conditional knockout of AQP5, with treatment, 24 hour timepoint, replicate 1

value: Treated to induce knockout of AQP5


title: Control, organoids, day 7

description: 10x Genomics

value: Submandibular salivary gland

value: Salivary gland cells derived from organoids


title: 2CLC, dTAG, H3K9me2, rep2, chip

description: Library name: Sample 20


title: SD53 white adipose tissue

city: Cincinnati

first: Maria

middle: Eugenia

last: Fields

state: OH

address: 3430 Burnet Ave

department: Gastroeneterology Hepatology and Nutrition

institute: Cincinnati Children's Hospital Medical Center

description: Library name: SD53_S50

data_processing:
RNA-seq data were pseudo-aligned and quantified (transcript per million estimates) against the hg38 reference transcriptome using Kallisto via AltAnalyze version 2.1.4.4. (Emig, Salomonis et al. 2010).
AltAnalyze-normalized expression values between MH and MC was use for a two-tailed unpaired Welch’s t-test in Excel (Microsoft, USA). Fold change was calculated from the ratio of group means and expressed as log₂ fold change. Genes with |log₂FC| ≥ 1.5 and p < 0.05 were considered significant.
Note that processed expression data are merged for all samples, in accordance with AltAnalyze standard outputs
Assembly: hg38
Supplementary files format and content: tab delimited text file includes raw counts for each sample
Supplementary files format and content: txt file includes FPKM values for each sample

source_name: Omental white adipose tissue

growth_protocol: Omental adipose tissue from obese individuals undegoing bariatric surgery

extract_protocol:
RNA from adipose tissue was isolated using the mirVANA RNA isolation kit. To measure the library concentration, NEBNext Ultra II Directional RNA Library Prep kit  (New England BioLabs) was used.
Library construction was performed using the TruSeq RNA Library Prep Kit (Illumina) according to the manufacturer's protocols. RNA-seq was performed using the Illumina NextSeq 550 with the sequencing setting of paired ended read 101 bp to generate ∼50 M reads per sample.

value: Omental white adipose tissue

tag: disease state

value: MC

tag: disease

value: Obese


title: SD50 white adipose tissue

description: Library name: SD50_S47

value: MH


title: SD52 white adipose tissue

description: Library name: SD52_S49


title: CreNeg_3_2d

source_name: Human organoid tissue with cassette for conditional knockout of AQP5, no treatment, 2 day timepoint, replicate 3


title: SD46 white adipose tissue

description: Library name: SD46_S43


title: CrePos_1_5d

source_name: Human organoid tissue with cassette for conditional knockout of AQP5, with treatment, 5 day timepoint, replicate 1


title: CreNeg_3_24h

source_name: Human organoid tissue with cassette for conditional knockout of AQP5, no treatment, 24 hour timepoint, replicate 3


title: 2CLC, DMSO, H3K9me2, rep3, input

description: Library name: Sample 18

value: EHMT2-dTAG-mcherry MERV-GFP

value: BL6/129 hybrid

value: DMSO 72hr


title: SD49 white adipose tissue

description: Library name: SD49_S46


title: CreNeg_2_5d

source_name: Human organoid tissue with cassette for conditional knockout of AQP5, no treatment, 5 day timepoint, replicate 2


title: SD44 white adipose tissue

description: Library name: SD44_S41


title: SD39 white adipose tissue

description: Library name: SD39_S36


title: SD38 white adipose tissue

description: Library name: SD38_S35


title: 2CLC, DMSO, H3K9me2, rep2, input

description: Library name: Sample 17


title: CreNeg_2_2d

source_name: Human organoid tissue with cassette for conditional knockout of AQP5, no treatment, 2 day timepoint, replicate 2


title: SD34 white adipose tissue

description: Library name: SD34_S31


title: 2CLC, DMSO, H3K9me2, rep3, chip

description: Library name: Sample 15


title: 2CLC, DMSO, H3K9me2, rep1, input

description: Library name: Sample 16


title: CreNeg_2_24h

source_name: Human organoid tissue with cassette for conditional knockout of AQP5, no treatment, 24 hour timepoint, replicate 2


title: S_35_Plasma-derived extracellular vesicles, Non-severe asthma

city: Kansas City

first: Isaac Kirubakaran

last: Sundar

state: KS

address: University of Kansas Medical Center, Dept. of Internal Medicine/Pulmonary Critical Care and Sleep Medicine

department: Internal Medicine

institute: University of Kansas Medical Center

data_processing:
All samples passed quality control checks in FastQC and were aligned using miRDeep2 for miRNA analysis, using the hg38 genome as a reference.
The miRNA expression data was normalized and analyzed for differential expression using DESeq2 in R software.
Assembly: hg38
Supplementary files format and content: csv file includes normalized counts for each samples

source_name: Plasma

extract_protocol:
EV RNA was extracted using a commercial kit (Norgen Biotek Corp.) according to the manufacturer’s instructions.
100 ng of total RNA was then utilized for the QIAseq miRNA unique dual-indexed (UDI) library preparation (Qiagen 331505).

value: Plasma

value: Extracellular vesicles

tag: subject status

value: Non-severe asthma


title: SD36 white adipose tissue

description: Library name: SD36_S33


title: S_34_Plasma-derived extracellular vesicles, Severe asthma

value: Severe asthma


title: 2CLC, DMSO, H3K9me2, rep2, chip

description: Library name: Sample 14


title: S_33_Plasma-derived extracellular vesicles, Severe asthma


title: 2CLC, dTAG, H3K9me2, rep1, chip

description: Library name: Sample 19

value: dTAG 72hr


title: S_32_Plasma-derived extracellular vesicles, Severe asthma


title: CreNeg_2_12h

source_name: Human organoid tissue with cassette for conditional knockout of AQP5, no treatment, 12 hour timepoint, replicate 2

value: Human organoid

value: AQP5 wild-type


title: CreNeg_1_5d

source_name: Human organoid tissue with cassette for conditional knockout of AQP5, no treatment, 5 day timepoint, replicate 1

value: No treatment


title: S_31_Plasma-derived extracellular vesicles, Severe asthma


title: S_30_Plasma-derived extracellular vesicles, Non-severe asthma


title: 2CLC, DMSO, H3K9me2, rep1, chip

description: Library name: Sample 13


title: S_29_Plasma-derived extracellular vesicles, Non-severe asthma


title: CreNeg_3_12h

source_name: Human organoid tissue with cassette for conditional knockout of AQP5, no treatment, 12 hour timepoint, replicate 3


title: S_27_Plasma-derived extracellular vesicles, Severe asthma


title: mESC, dTAG, H3K9me2, rep2, input

description: Library name: Sample 11

value: ESC


title: S_25_Plasma-derived extracellular vesicles, Healthy control

value: Healthy control


title: mESC, dTAG, H3K9me2, rep3, input

description: Library name: Sample 12


title: CreNeg_1_12h

source_name: Human organoid tissue with cassette for conditional knockout of AQP5, no treatment, 12 hour timepoint, replicate 1


title: CreNeg_1_24h

source_name: Human organoid tissue with cassette for conditional knockout of AQP5, no treatment, 24 hour timepoint, replicate 1


title: S_24_Plasma-derived extracellular vesicles, Healthy control


title: S_23_Plasma-derived extracellular vesicles, Healthy control


title: S_22_Plasma-derived extracellular vesicles, Non-severe asthma


title: Treated mice_PF compound_Sample 2

city: La Jolla, CA 92093

first: Pradipta

last: Ghosh

state: CA

address: 9500 Gilman Drive (MC 0651)

department: Departments of Medicine and Cellular and Molecular Medicine

institute: University of California San Diego

data_processing:
RNASeq data was processed using kallisto (version 0.45.0). Gene-level TPM values and gene annotations were computed using a custom Perl Script.
Assembly: Homo sapiens genome build hsGRCh38_94
Supplementary files format and content: tab-delimited text file includes log2 of TPM values

growth_protocol: HCT-116 human colon cancer cells (1 x 10^6 cells) were injected subcutaneously into each flank of nude mice. The tumors were allowed to grow for 4 weeks or until 150 mm3 in size. Subcutaneous injection of HCT-116 cells (1 x 10^6) reconstituted in PBS and Matrigel Matrix (Corning, NY) was performed on the bilateral shoulders and flanks of nude mice. Tumors were allowed to grow until 50 mm3 in diameter. The tumors were then resected and divided into 1 mm3 pieces for subcutaneously implantation. Subcutaneous models were established by surgical implantation of 1 mm3 HCT-116 tumor fragment into the bilateral flank of nude mice. A small incision was made on the back of the mice and tumor fragment was directly implanted in the bilateral flank. The skin was closed with 6-0 nylon suture (Ethicon Inc., Sommerville. NJ). Tumors were allowed to grow until 150 mm3 in diameter

extract_protocol:
The tissues washed with PBS, homogenized, and then sujeted to RNA extraction using ZYMORESEARCH kit.
RNA sequencing libraries were generated using the Illumina TruSeq Stranded Total RNA Library Prep Gold with TruSeq Unique Dual Indexes (Illumina, San Diego, CA). Samples were processed following manufacturer’s instructions, except modifying RNA shear time to five minutes. Resulting libraries were multiplexed and sequenced with 100 basepair (bp) Paired End (PE100) to a depth of approximately 25-40 million reads per sample on an Illumina NovaSeq 6000. Samples were demuxltiplexed using bcl2fastq v2.20 Conversion Software (Illumina, San Diego, CA).

treatment_protocol: Mice were treated with either DMSO or PF compound (200 microgram/mouse)  through IV, two times weekly for six weeks

value: Colon

tag: behavior at diagnosis

value: PF-treated


title: S_20_Plasma-derived extracellular vesicles, Non-severe asthma


title: CreNeg_1_2d

source_name: Human organoid tissue with cassette for conditional knockout of AQP5, no treatment, 2 day timepoint, replicate 1


title: S_26_Plasma-derived extracellular vesicles, Healthy control


title: S_28_Plasma-derived extracellular vesicles, Healthy control


title: mESC, dTAG, H3K9me2, rep2, chip

description: Library name: Sample 8

source_name: EHMT2-dTAG-mcherry MERV-GFP


title: mESC, dTAG, H3K9me2, rep1, chip

description: Library name: Sample 7


title: S_21_Plasma-derived extracellular vesicles, Healthy control


title: Treated mice_PF compound_Sample 1


title: S_17_Plasma-derived extracellular vesicles, Healthy control


title: mESC, dTAG, H3K9me2, rep1, input

description: Library name: Sample 10


title: S_19_Plasma-derived extracellular vesicles, Severe asthma


title: mESC, DMSO, H3K9me2, rep2, input

description: Library name: Sample 5


title: S_18_Plasma-derived extracellular vesicles, Healthy control


title: Control mice_DMSO_Sample 3

value: Untreated


title: mESC, DMSO, H3K9me2, rep3, input

description: Library name: Sample 6


title: S_16_Plasma-derived extracellular vesicles, Severe asthma


title: S_15_Plasma-derived extracellular vesicles, Non-severe asthma


title: S_14_Plasma-derived extracellular vesicles, Non-severe asthma


title: Control mice_DMSO_Sample 2


title: S_13_Plasma-derived extracellular vesicles, Healthy control


title: mESC, DMSO, H3K9me2, rep1, input

description: Library name: Sample 4


title: Treated mice_PF compound_Sample 3


title: Control mice_DMSO_Sample 1


title: mESC, DMSO, H3K9me2, rep3, chip

description: Library name: Sample 3


title: mESC, dTAG, H3K9me2, rep3, chip

description: Library name: Sample 9


title: S_11_Plasma-derived extracellular vesicles, Healthy control


title: S_10_Plasma-derived extracellular vesicles, Healthy control


title: SW480_PF_20uL_D2_S34

description: cell lines

source_name: Colon

growth_protocol: HCT116 and SW480 cells were seeded in their suitable media containing  10% FBS for over night.

extract_protocol:
The cells washed with PBS and then sujeted to RNA extraction using ZYMORESEARCH kit.
RNA sequencing libraries were generated using the Illumina TruSeq Stranded Total RNA Library Prep Gold with TruSeq Unique Dual Indexes (Illumina, San Diego, CA). Samples were processed following manufacturer’s instructions, except modifying RNA shear time to five minutes. Resulting libraries were multiplexed and sequenced with 100 basepair (bp) Paired End (PE100) to a depth of approximately 25-40 million reads per sample on an Illumina NovaSeq 6000. Samples were demuxltiplexed using bcl2fastq v2.20 Conversion Software (Illumina, San Diego, CA).

treatment_protocol: Cells were treated with either DMSO or PF compound  for 16 hrs.

tag: group

value: PF compound for 16 hrs


title: S_8_Plasma-derived extracellular vesicles, Severe asthma


title: S_8_Plasma-derived extracellular vesicles, Healthy control


title: mESC, DMSO, H3K9me2, rep2, chip

description: Library name: Sample 2

value: EHMT2-dTAG-mcherry MERV-GFP


title: mESC, DMSO, H3K9me2, rep1, chip

description: Library name: Sample 1

value: BL6/129 hybrid


title: S_6_Plasma-derived extracellular vesicles, Severe asthma


title: S_7_Plasma-derived extracellular vesicles, Severe asthma


title: SW480_PF_20uL_B2_S36

description: cell lines


title: S_5_Plasma-derived extracellular vesicles, Non-severe asthma


title: SW480_DMSO_A2_S31

description: cell lines

value: DMSO for 16 hrs


title: S_4_Plasma-derived extracellular vesicles, Healthy control

value: Plasma


title: S_3_Plasma-derived extracellular vesicles, Healthy control

value: Extracellular vesicles


title: Model-2

city: Wuhan

first: Bin

last: Yang

address: jiefang Avenue,Qiaokou District

institute: Tongji Hospital

description: Library name: sample5

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality. The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. Hisat2 tools soft were used to map with reference genome.The StringTie Reference Annotation Based Transcript (RABT) assembly method was used to construct and identify both known and novel transcripts from Hisat2 alignment results Gene function was annotated based on the following databases:Nr (NCBI non-redundant protein sequences)； Pfam (Protein family)；KOG/COG (Clusters of Orthologous Groups of proteins)；Swiss-Prot (A manually annotated and reviewed protein sequence database)；KO (KEGG Ortholog database)；GO (Gene Ontology). Quantification of gene expression levelsGene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped. The formula is shown as follow:FPKM=cDNAFragmentsMappedFragments(Millions)∗TranscriptLength(kb). For the samples with biological replicates: Differential expression analysis of two conditions/groups was performed using the DESeq2. DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value < 0.01 & Fold Change≥2 found by DESeq2 were assigned as differentially expressed. For the samples without biological replicates: Differential expression analysis of two samples was performed using the edgeR.The FDR < 0.01 & Fold Change ≥2 was set as the threshold for significantly differential expression.
Assembly: GRCm38_release95
Supplementary files format and content: table-delimited text files include readcount values for each Samples

source_name: DN32.D3 derived from bone marrow

extract_protocol:
Suspended cells were collected, washed three times with PBS, subsequently resuspended in TRIZOL, and processed using the Illumina NovaSeq kit.
RNA libraries were prepared for sequencing using standard IIIumina protocols

value: DN32.D3 derived from bone marrow

value: iNKT cell

value: LPS+α-Galcer

tag: batch


title: SW480_DMSO_H1_S33

description: cell lines


title: Model-3

description: Library name: sample6


title: S_2_Plasma-derived extracellular vesicles, Non-severe asthma

value: Non-severe asthma


title: Model-1

description: Library name: sample4


title: S_1_Plasma-derived extracellular vesicles, Non-severe asthma


title: S_12_Plasma-derived extracellular vesicles, Healthy control


title: NC-3

description: Library name: sample3

value: PBS


title: nuRNA, DG, IE, rep3

city: San Juan de Alicante (Alicante)

first: Miguel

last: Fuentes-Ramos

address: Av. Santiago Ramón y Cajal s/n

country: Spain

institute: Instituto de Neurociencias (UMH/CSIC)

description: Library name: 18_nuRNA_DG_IE

data_processing:
Fastq files quality was analysed by FastQC, adapters were trimmed using TrimGalore (v0.39). The reads obtained were aligned to the mouse genome (mm10) using STAR (v2.7.9a). Mitochondrial reads and reads with mapq < 30 were eliminated using Samtools (v1.13). The data analysis was conducted with custom R scripts (v4.1.0, 2021) and Rsubreads (v2.6.4). To generate BigWigs, Deeptools (v3.5.1)  was used.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes raw counts for each Sample.

source_name: DG granule neurons

extract_protocol:
After tissue dissociation, nuclei were extracted by mechanical homogenization using a 2 ml Dounce homogenizer (Sigma-Aldrich) containing 500 μl of Nuclei Extraction Buffer (NEB; Sucrose 250 mM, KCl 25 mM, MgCl2 5 mM, HEPES-KOH pH 7.8 20 mM, IGEPAL CA-630 0.5 %, spermine 0.2 mM, spermidine 0.5 mM, and 1X proteinase inhibitors (cOmplete EDTA-free, Roche)). Tissues from 3 mice were pooled in each sample, having a total volume of 1.5 ml NEB containing the nuclei for each hippocampal layer. Samples were filtered in a 35 μm mesh capped tube and incubated with 0.01 mM DAPI for 10 min in darkness in a rotator. Nuclei isolation was accomplished by the preparation of a gradient of different densities in which nuclei stay in the interphase. Nuclei were diluted in Optiprep density gradient medium (1114542, Proteogenix) to a final concentration of 22 % Optiprep. For the density gradient, 44 % Optiprep was added to a centrifuge tube followed by 22 % Optiprep containing the nuclei. Additional 22 % Optiprep was added until the tube was filled. After centrifugation at 7500 rpm for 23 min, the phase containing the nuclei was collected in a new tube containing Nuclei Incubation Buffer (NIB: sucrose 340 mM, KCl 25 mM, MgCl2 5 mM, HEPES-KOH pH 7.8 20 mM, spermine 0.2 mM, spermidine 0.5 mM, 1X proteinase inhibitors, newborn calf serum 5 %). Sorting of SUN1-GFP+ nuclei was performed in a flow-cytometer FACS Aria III (BD Bioscience). Sorted nuclei were pelleted by centrifugation (1000 g, 7 min, 4 °C). RNA extraction was performed using TRI-reagent (Merck) as recommended by the manufacturer. After treatment with RNase-free DNase I (Qiagen) for 30 min at 25 °C to eliminate genomic DNA, RNA was precipitated with phenol-chloroform-isoamyl alcohol. RNA concentration was measured using NanoDropOne (Themo Scientific). RNA was retrotranscribed to cDNA using the RevertAid First-Strand cDNA Synthesis kit (Thermo Scientific) and analysed by RT-qPCR with PyroTaq EvaGreen (Cultek) in a QuantStudio 3 thermocycler (Applied Biosystems).
TruSeq Stranded Total RNA, Illumina

value: DG granule neurons

tag: condition

value: IE


title: HCT116_PF_20uL_F1_S28

description: cell lines


title: nuRNA, DG, IE, rep2

description: Library name: 17_nuRNA_DG_IE


title: NC-2

description: Library name: sample2


title: nuRNA, DG, SC, rep3

description: Library name: 15_nuRNA_DG_SC

value: SC


title: SW480_PF_20uL_C2_S35

description: cell lines


title: nuRNA, DG, SC, rep2

description: Library name: 14_nuRNA_DG_SC


title: Lung tissue from TMAO-treated LPS-ALI mouse5

city: Guanghzou

first: Xilong

last: Wang

address: 253 Gongye Middle Avenue

institute: Zhujiang Hospital of the Southern Medical University

description:
Library name: Sample 9
TMAO-B167

data_processing:
Paired-end RNA sequencing reads were analyzed with open-source software tools such as fastp, HISAT2, SAMtools, and featureCounts.
Assembly: mm10
Supplementary files format and content: tsv files include fmpk values for each Sample

source_name: Lung

extract_protocol:
Total RNA was extracted from platelets using Trizol Reagent (Invitrogen, USA).To enrich for messenger RNA (mRNA), ribosomal RNA (rRNA) was depleted using the rRNA Depletion Kit v2 (E7400L, NEBNext, MA, USA).
RNA sequencing libraries were constructed using the NEBNext Ultra II RNA Library Prep Kit for Illumina Kit (E7770s, NEBNext, MA, USA) and quantified on an Agilent 4200 Bioanalyzer (Shanghai, China) following manufacturer's protocols.

value: Lung

tag: sample group

value: TMAO-treated LPS-ALI


title: NC-1

description: Library name: sample1


title: nuRNA, DG, SC, rep1

description: Library name: 13_nuRNA_DG_SC


title: HCT116_PF_20uL_D1_S30

description: cell lines


title: HCT116_DMSO_C1_S26

description: cell lines


title: Lung tissue from TMAO-treated LPS-ALI mouse4

description:
Library name: Sample 8
TMAO-B166


title: Lung tissue from TMAO-treated LPS-ALI mouse3

description:
Library name: Sample 7
TMAO-B165


title: nuRNA, DG, EE, rep3

description: Library name: 12_nuRNA_DG_EE

value: EE


title: Trp53_wildtype_MDM2_overexpression_replicate_3

city: Zurich

first: Jonas

last: Fullin

address: Rämistrasse 100

department: Department  of Medical Oncology and Hematology

country: Switzerland

institute: University of Zurich

description: Library name: monoallelic_GFP_neg_MDM2_3

data_processing:
Quality control, mapping and differential gene expression analysis was performed using the SUSHI bioinformatics pipeline. Gene set enrichment analysis was performed using the GSEA software developed jointly by UC San Diego and the Broad Institute.
Assembly: NCBI
Supplementary files format and content: excel, normalized counts

source_name: ER-Hoxb8 cell line

extract_protocol:
RNeasy Plus Mini Kit (Qiagen)
Illumina Stranded mRNA Prep, Ligation

value: ER-Hoxb8 cell line

value: Trp53_wt; SFFV-Mdm2-IRES-tRFP

value: etoposide


title: SW480_DMSO_G1_S32

description: cell lines

value: DMSO for 16 hrs


title: nuRNA, DG, EE, rep2

description: Library name: 11_nuRNA_DG_EE


title: Trp53_wildtype_MDM2_overexpression_replicate_4

description: Library name: monoallelic_GFP_neg_MDM2_4


title: HCT116_DMSO_A1_S25

description: cell lines


title: nuRNA, DG, EE, rep1

description: Library name: 10_nuRNA_DG_EE


title: Trp53_wildtype_MDM2_overexpression_replicate_1

description: Library name: monoallelic_GFP_neg_MDM2_1


title: nuRNA, DG, IE, rep1

description: Library name: 16_nuRNA_DG_IE


title: H20_PF_treated_S96_L002

description: mRNA Stranded

growth_protocol: Organoids were cultured in Matrigel in 12- or 24-well tissue culture plates incubated at 37ºC, 5% CO2. Organoids were provided 50% L-WRN-conditioned medium supplemented with differentiation inhibitors (complete medium) manufactured by the HUMANOID CoRE. Organoids were subcultured every 7-14 days, dissociated by non-enzymatic digestion in TrypLE and passaged to achieve the desired density.

extract_protocol:
To collect CRC PDM organoids for analysis of gene expression in response to PF-06409577, dissociated single cells were seeded in Matrigel in 24-well tissue culture plates. After 3 days in culture, organoids were administered complete medium or complete medium treated with 10 µM PF-06409577. Prior to treatment with PF-06409577 and after 2 days of treatment, whole organoids were collected in Dulbecco’s phosphate-buffered saline with 0.5 mM ethylenediaminetetraacetic acid (PBS-EDTA). Organoids were subsequently incubated in cell recovery solution, pelleted, and stored at -80ºC. Total RNA was extracted using the Quick-RNA Microprep Kit and concentration was measured using Nanodrop OneC Spectrophotometer. For qPCR, first-strand cDNA synthesis was performed using qScript cDNA SuperMix.
RNA sequencing libraries were generated using the Illumina TruSeq Stranded Total RNA Library Prep Gold with TruSeq Unique Dual Indexes (Illumina, San Diego, CA). Samples were processed following manufacturer’s instructions, except modifying RNA shear time to five minutes. Resulting libraries were multiplexed and sequenced with 100 basepair (bp) Paired End (PE100) to a depth of approximately 25-40 million reads per sample on an Illumina NovaSeq 6000. Samples were demuxltiplexed using bcl2fastq v2.20 Conversion Software (Illumina, San Diego, CA).

treatment_protocol: Organoids were treated with either DMSO or PF compound

value: treated

tag: type

value: Healthy


title: Lung tissue from TMAO-treated LPS-ALI mouse2

description:
Library name: Sample 6
TMAO-B164

tag: tissue


title: Trp53_wildtype_control_replicate_4

description: Library name: monoallelic_GFP_neg_ctrl_4

tag: genotype

value: Trp53_wt; SFFV-tRFP


title: nuRNA, CA1, IE, rep3

description: Library name: 9_nuRNA_CA1_IE

source_name: CA1 pyramidal neurons

value: CA1 pyramidal neurons


title: Lung tissue from LPS-ALI mouse4

description:
Library name: Sample 4
ALI-X85

value: LPS-ALI


title: HCT116_PF_20uL_E1_S29

description: cell lines

tag: treatment

value: PF compound for 16 hrs


title: H17_PF_treated_S78_L001

description: mRNA Stranded


title: Trp53_wildtype_control_replicate_3

description: Library name: monoallelic_GFP_neg_ctrl_3

tag: cell line


title: Lung tissue from LPS-ALI mouse3

description:
Library name: Sample 3
ALI-X84


title: nuRNA, CA1, IE, rep2

description: Library name: 8_nuRNA_CA1_IE

tag: cell type


title: H17_PF_treated_S95_L002

description: mRNA Stranded


title: nuRNA, CA1, IE, rep1

description: Library name: 7_nuRNA_CA1_IE

tag: strain


title: Trp53_wildtype_control_replicate_2

description: Library name: monoallelic_GFP_neg_ctrl_2


title: Lung tissue from LPS-ALI mouse2

description:
Library name: Sample 2
ALI-B220


title: H14_PF_treated_S94_L002

description: mRNA Stranded


title: nuRNA, CA1, SC, rep3

description: Library name: 6_nuRNA_CA1_SC


title: HCT116_DMSO_B1_S27

description: cell lines


title: Trp53_wildtype_control_replicate_1

description: Library name: monoallelic_GFP_neg_ctrl_1


title: Lung tissue from LPS-ALI mouse1

description:
Library name: Sample 1
ALI-B211


title: Trp53_wildtype_MDM2_overexpression_replicate_2

description: Library name: monoallelic_GFP_neg_MDM2_2


title: H14_PF_treated_S77_L001

description: mRNA Stranded


title: AdipoqF2KO mice sample 4

city: Chicago

first: Chioma

last: Nnyamah

state: Illinois

address: 840 South Wood Street, Suite 1020N, MC 787

institute: University of Illinois at Chicago

description:
Library name: Sample 7
Column name in FFA2adipoKO_featurecountstrimmo.txt: LAY013123-008_S24_L002Aligned

data_processing:
Raw sequencing reads were first trimmed to remove residual adapter sequences and low-quality bases. Adapter trimming was performed using Trimmomatic with the Illumina TruSeq adapter sequence CTGTCTCTTATACACATCT provided in Illumina Adapter Sequences v14 (Document #1000000002694).
Trimmed reads were then aligned to the mouse reference genome using the STAR aligner. Gene-level read quantification was performed using featureCounts, and differential expression analysis and normalization were conducted using DESeq2.
Assembly: Mouse genome GRCm38 (mm10), Ensembl annotation release [e.g., v98]
Supplementary files format and content: tab delimited text file includes raw counts for all samples
Supplementary files format and content: tab delimited text file includes raw counts for all samples

source_name: Adipose Tissue

growth_protocol: Male Adipoq-F2-KO mice were generated by crossing FFA2 floxed mice (FFA2^fl/fl) with Adiponectin-Cre transgenic mice (RRID: IMSR_JAX:028020). Littermate Adipoq-F2-KO and FFA2^fl/fl control mice were co-housed from birth under a 12-hour light/dark cycle at ambient temperature and given ad libitum access to Teklad LM-485 normal chow and water. Mice were euthanized at 20 weeks of age for tissue collection.

extract_protocol:
Mature adipocytes were isolated from perigonadal adipose tissue via collagenase digestion. Total RNA was extracted from isolated adipocytes using TRIzol Reagent (Life Technologies) following the manufacturer's instructions. Phase separation was performed using chloroform, and the aqueous RNA phase was recovered for downstream processing.
RNA libraries were constructed using the Illumina TruSeq Stranded mRNA Library Prep Kit, which includes poly-A selection to enrich for mRNA. Libraries were sequenced on an Illumina NovaSeq X Plus system using paired-end 150 bp reads according to manufacturer protocols.

treatment_protocol: No experimental treatment was applied; mice remained on a standard chow diet throughout the study.

value: Adipose Tissue

value: White Adipocytes

value: Normal Chow diet for 20 weeks


title: PDM363_PF_treated_S93_L002

description: mRNA Stranded

value: Resistant


title: 1574

city: Omaha

first: Saraswathi

last: Viswanathan

state: NE

address: 4101 Woolworth Ave

institute: University of Nebraska Medical Center

data_processing:
The original FASTQ format reads were trimmed by fqtrim tool (https://ccb.jhu.edu/software/fqtrim) to remove adapters, terminal unknown bases (Ns) and low quality 3’ regions (Phred score < 30).
For quality control (QC), the low quality 3’ regions were trimmed and only high quality reads with Phred score >=30 were retained.
The QC passed trimmed fastq files were mapped to reference genome using STAR 2.7.0f aligner and RSEM 1.2.31 for reads quantification and normaliation into FPKM and TPM values
Assembly: mm10
Supplementary files format and content: tab-delimited text files include normalized FPKM and TPM values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: ET

growth_protocol: C57BL/6 wildtype mice were purchased from Jackson lab.

extract_protocol:
9 h after oral gavage. Mice were euthanized, and left ventricles were collected.
Libraries were generated using 1000 ng of total RNA from each sample and the NuGEN Universal mRNA Plus kit (TECAN GENOMICS, 900 Chesapeake Drive, Redwood City, CA 94063) following the recommended procedure. Libraries were multiplexed and sequenced on the NextSeq550 DNA Analyzer (Illumina) in the UNMC Genomics Core to generate a total of approximately 15 million 75 bp paired reads for each sample.

treatment_protocol: 8-week Mice were fed with 5% Ethanol diet or isocaloric control diet for 10 days followed by one binge of ethanol or maltose-dextrin by oral gavage (followed by the NIAAA model).

value: left ventricle

value: Ethanol diet

value: Alcoholic cardiomyopathy


title: nuRNA, CA1, SC, rep2

description: Library name: 5_nuRNA_CA1_SC

value: SC


title: Lung tissue from TMAO-treated LPS-ALI mouse1

description:
Library name: Sample 5
TMAO-B163

value: Lung

value: TMAO-treated LPS-ALI


title: nuRNA, CA1, SC, rep1

description: Library name: 4_nuRNA_CA1_SC


title: AdipoqF2KO mice sample 3

description:
Library name: Sample 6
Column name in FFA2adipoKO_featurecountstrimmo.txt: LAY013123-007_S23_L002Aligned


title: AdipoqF2KO mice sample 2

description:
Library name: Sample 5
Column name in FFA2adipoKO_featurecountstrimmo.txt: LAY013123-006_S22_L002Aligned


title: PDM359_PF_treated_S92_L002

description: mRNA Stranded


title: 1560


title: 1561


title: nuRNA, CA1, EE, rep3

description: Library name: 3_nuRNA_CA1_EE

value: EE


title: AdipoqF2KO mice sample 1

description:
Library name: Sample 4
Column name in FFA2adipoKO_featurecountstrimmo.txt: LAY013123-005_S21_L002Aligned


title: PDM277_PF_treated_S76_L001

description: mRNA Stranded

value: treated


title: FFA2 fl/fl control mice sample 3

description:
Library name: Sample 3
Column name in FFA2adipoKO_featurecountstrimmo.txt: LAY013123-004_S20_L002Aligned

value: FFA2 fl/fl


title: nuRNA, CA1, EE, rep2

description: Library name: 2_nuRNA_CA1_EE


title: 1552

source_name: CONT

value: Control diet


title: 1548


title: PDM185_PF_treated_S90_L002

description: mRNA Stranded


title: PDM277_PF_treated_S91_L002

description: mRNA Stranded


title: 1547


title: PDM95_PF_treated_S75_L001

description: mRNA Stranded

value: Sensetive


title: CyT, CA1, SC, IgG

description: Library name: 18_CyT_CA1_SC_IgG

data_processing:
Fastq files were quality checked using FastQC (v0.11.9). Paired-end reads were aligned using Bowtie2 (v2.3.4.3) and were filtered to eliminate duplicates using Picard (v2.26.2). Reads with mapq < 2 were eliminated with Samtools (v1.13). Significant peaks of H3K27ac were called from these aligned files using SEACR. To generate BigWigs, Deeptools (v3.5.1) was used to normalize reads by reads per kilobase million.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

extract_protocol:
After tissue dissociation, nuclei were extracted by mechanical homogenization using a 2 ml Dounce homogenizer (Sigma-Aldrich) containing 500 μl of Nuclei Extraction Buffer (NEB; Sucrose 250 mM, KCl 25 mM, MgCl2 5 mM, HEPES-KOH pH 7.8 20 mM, IGEPAL CA-630 0.5 %, spermine 0.2 mM, spermidine 0.5 mM, and 1X proteinase inhibitors (cOmplete EDTA-free, Roche)). Tissues from 3 mice were pooled in each sample, having a total volume of 1.5 ml NEB containing the nuclei for each hippocampal layer. Samples were filtered in a 35 μm mesh capped tube and incubated with 0.01 mM DAPI for 10 min in darkness in a rotator. Nuclei isolation was accomplished by the preparation of a gradient of different densities in which nuclei stay in the interphase. Nuclei were diluted in Optiprep density gradient medium (1114542, Proteogenix) to a final concentration of 22 % Optiprep. For the density gradient, 44 % Optiprep was added to a centrifuge tube followed by 22 % Optiprep containing the nuclei. Additional 22 % Optiprep was added until the tube was filled. After centrifugation at 7500 rpm for 23 min, the phase containing the nuclei was collected in a new tube containing Nuclei Incubation Buffer (NIB: sucrose 340 mM, KCl 25 mM, MgCl2 5 mM, HEPES-KOH pH 7.8 20 mM, spermine 0.2 mM, spermidine 0.5 mM, 1X proteinase inhibitors, newborn calf serum 5 %). Sorting of SUN1-GFP+ nuclei was performed in a flow-cytometer FACS Aria III (BD Bioscience). Sorted nuclei were pelleted by centrifugation (1000 g, 7 min, 4 °C). H3K27ac CUT&TAG on sorted SUN1-GFP+ neurons from IE, NC and EE mice was conducted as described in (Kaya-Okur et al., 2019) using the anti-H3K27ac antibody from Abcam (ab4729).
CUT&Tag

value: CA1 pyramidal neurons

value: IgG


title: FFA2 fl/fl control mice sample 2

description:
Library name: Sample 2
Column name in FFA2adipoKO_featurecountstrimmo.txt: LAY013123-003_S19_L002Aligned

value: Adipose Tissue


title: nuRNA, CA1, EE, rep1

description: Library name: 1_nuRNA_CA1_EE


title: CyT, DG, IE, rep3

description: Library name: 17_CyT_DG_IE

value: DG granule neurons

value: IE


title: FFA2 fl/fl control mice sample 1

description:
Library name: Sample 1
Column name in FFA2adipoKO_featurecountstrimmo.txt: LAY013123-002_S18_L002Aligned

value: White Adipocytes

value: Normal Chow diet for 20 weeks


title: PDM95_PF_treated_S89_L002

description: mRNA Stranded


title: CyT, DG, IE, rep2

description: Library name: 16_CyT_DG_IE


title: PDM50_PF_treated_S88_L002

description: mRNA Stranded


title: Knockout hippocampus, postnatal day 19, snRNAseq

city: Edmotnotn

first: Qiumin

last: Tan

state: Alberta

address: 114 St and 87 Ave

department: Cell Biology

country: Canada

institute: University of Alberta

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v8.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm39
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: Hippocampus

extract_protocol:
Nuclei were isolated using 10x Genomics Chromium Nuclei Isolation Kit (10x Genomics, Cat# 1000493) lysis buffer and the debris was removed using Miltenyi Anti-Nucleus beads (Miltenyi Biotec, Cat# 130-132-997). Frozen tissue pieces were pooled, weighed and chopped into small pieces on dry ice, before adding Lysis Reagent (10x Genomics, Cat# 2000558), Reducing Agent B (10x Genomics, Cat# 2000087), and Surfactant A (10x Genomics, Cat# 2000559). The tissue was homogenized using a glass douncer (MilliporeSigma, Cat# D9063) and lysed for 5 min on ice. A total of 500 µL of lysate was transferred to the Nuclei Isolation Column (10x Genomics, Cat# 2000562) to remove leftover tissue. The sample was then spun at 500 xg for 3 min at 4ºC, and the nuclei pellet was resuspended in Nuclei Separation buffer composed of Nuclei Extraction buffer (Miltenyi Biotec, Cat# 130-128-024), PBS, 10% BSA and RNase Inhibitor (MilliporeSigma, Cat# 3335402001). Miltenyi anti-nucleus beads (Cat# 130-132-997) were then added to the sample (50 µL per million nuclei) and incubated for 15 min on ice followed by an additional 2 mL of the Nuclei Separation buffer. Then the sample was purified using an LS column (Miltenyi Biotec, Cat#130-042-401) attached to the MACS MultiStand (Miltenyi Biotec, Cat# 130-042-303) with a QuadroMACS separator (Miltenyi Biotec, Cat# 130-042-302). The purified nuclei were spun at 500 xg for 5 min, and the nuclei pellet was washed with wash buffer comprised of PBS, 10% BSA and RNase Inhibitor. The nuclei suspension was centrifuged at 4ºC for 5 min at 500 xg again and the nuclei pellet was resuspended in wash buffer. Nuclei counting was done using a 1:1 dilution with acridine orange and propidium iodide on a haemocytometer (Thermo Fisher, Cat# 22-600-100).
Following counting, the appropriate volume for each sample was calculated for a target capture of 20,000 nuclei and then the nuclei were loaded onto 10x 3’ GEM X chip. cDNA libraries were prepared as outlined by the Chromium GEM-X Single Cell 3’ Reagent Kits v4 user guide with modifications to the PCR cycles based on the calculated cDNA concentration. The molarity of each library was calculated based on library size as measured bioanalyzer (Agilent Technologies) and qPCR amplification data (Roche, Cat# 07960140001). Gene Expression libraries were sequenced on Illumina’s NovaSeqX with the following run parameters: read 1 – 28 cycles, read 2 – 90 cycles, index 1 – 10 cycles and index 2 – 10 cycles.

value: Hippocampus

value: postnatal day 19

value: Neurons, glia, other brain parenchymal cells

value: Emx1-Cre; Cicflox/flox

value: 2 males and 1 female


title: Control hippocampus, postnatal day 19, snRNAseq

description: 10X Genomics

source_name: Hippocampus,

value: Hippocampus,

value: Cicflox/flox


title: PDM50_PF_treated_S74_L001

description: mRNA Stranded

value: treated


title: CyT, DG, IE, rep1

description: Library name: 15_CyT_DG_IE


title: E. coli ATCC25922 grown in M9 media with glucose added for 40 minutes

city: Columbus

first: Justin

last: North

address: 484 W 12th Ave

department: Department of Microbiology

institute: Ohio State University

description: Library name: PluGlu-40

data_processing:
Sequences reads were trimmed of adapter sequences/ low-quality sequences
Sequence reads were aligned with reference genome of E. coli ATCC 25922
Sequence reads were aligned to an annotated genome and a counts table was generated
Conducted differential expression analysis
Assembly: E. coli ASM1735750
Supplementary files format and content: tab-deliminated text file including number of reads assigned to each gene

organism: Escherichia coli

growth_protocol: E. coli cultures were incubated at aerobically at 37 C in M9 media supplemented with specific carbon sources until mid-exponential growth was reached. At which point, cells were harvested and prepped for extraction using RNAprotect from RNeasy Kit.

extract_protocol:
RNA was extracted using the Qiagen RNeasy kit (Qiagen)
Libraries were constructed using the Illumina Stranted Total RNA Prep, Ligation with Ribo-Zero Plus

treatment_protocol: WT ATCC 25922 and DmtnR were grown in M9 media containing either glucose, 5dR, or lacking any carbon supplementation

value: Wildtype

value: M9 with glucose added


title: CUT&Tag, protoplast, ADA2-KRH/A, anti-H3K9ac, rep2

first: Xiaoyuan

last: Guo

state: Hubei

address: No.1 Shizishan Street, Hongshan District

institute: Huazhong Agricultural University

description: Library name: XGSZ018

data_processing:
RNA-seq: Raw RNA-seq reads were quality-filtered using FastP (v 0.23.4) to remove adapter sequences and low-quality reads. Clean reads were aligned to the rice reference genome (MSU v7.0) using HISAT2 (v2.2.0). Differential gene expression analysis was performed with Cufflinks (v2.2.1). Genes with p value< 0.05 and fold change >2 (1.5 for acla2) in mutants relative to wild type were considered as differentially expressed genes.The root tip specifically expressed genes were identified by generating cuffnorm data by comparing root tips with other tissues. The FPKM (Fragments Per Kilobase of transcript per Million mapped reads) value of gene expression in root tips must be more than five times the average FPKM value of the same gene in other tissues. Additionally, the FPKM value in root tips must be at least 2 units higher than the maximum FPKM value observed in any of the other tissues. The enrichment of root specifically expressed genes compared to the genomic background was calculated by Fisher’s exactly test. CUT&Tag: Raw reads were filtered using FastP (v0.23.4) to eliminate adapter sequences and low-quality reads. Clean reads were aligned to the rice reference genome (MSU v7.0) using Bowtie2 (v2.5.2). Then, duplicated reads were discarded using samtools (v1.9). SICER2 software (version 1.0.2) was used to call histone modification peaks with “-w 200 -g 600 -f 150 -egf 0.74 -fdr 0.01” parameters. BigWig files generated by deepTools software with RPKM normalization were used for data visualization by IGV (version 2.3.88).
Assembly: RGAP version 7.0
Supplementary files format and content: RNA-seq:The diff file containing information of differential expression analysis between transcriptomes; CUT&Tag:The bigwig file incorporating data on chromosomal regions, signal intensity, and coverage.
Library strategy: CUT&Tag

organism: Oryza sativa Japonica Group

source_name: shoot

growth_protocol: In this study, the rice variety Zhonghua11 (Oryza sativa ssp. Japonica) was used to produce the transgenic plants. For in vitro cultures, seeds were surface-sterilized and germinated in media containing 0.3% phytagel supplemented with 2% (w/v) sucrose at 28 °C (in light) and 24 °C (in dark) with a 14 h light/10 h dark cycle.

extract_protocol:
RNA-seq: Total RNA was isolated from either 1 cm rice root tips of 7-day-old post-germination seedlings and 0.1 cm inflorescence meristems using the RNeasy Plus Micro Kit (Qiagen, 74034). First-strand cDNA was synthesized from 100 ng of total RNA using a reverse transcription kit (Vazyme, N712). Sequencing libraries were then prepared with the Vazyme TD502 kit and sequenced on an Illumina HiSeq 3000 system. CUT&Tag: Root tips from 7-day-old germinated rice seedlings were harvested to isolate nuclei. The nuclei were washed with wash buffer (Vazyme, TD903), followed by incubation with ConA Beads (Vazyme, TD903) at room temperature for 10 minutes.CUT&Tag experiment and DNA libraries were performed according to the instruction of Hyperactive Universal CUT&Tag Assay Kit (Vazyme, TD903).The PCR-amplified library was purified using VAHTS DNA Clean Beads (Vazyme, N411-01) and sequenced on the Illumina NovaSeq X Plus  platform.
RNA libraries for RNA-seq were prepared using TruePrep DNA Library Prep Kit V2 for Illumina following manufacturer's protocols. DNA libraries for CUT&Tag were prepared using Hyperactive Universal CUT&Tag Assay Kit for Illumina following manufacturer's protocols.

value: shoot

tag: cut&tag antibody


title: PDM5_PF_treated_S73_L001

description: mRNA Stranded

value: Sensetive


title: CyT, DG, SC, rep4

description: Library name: 14_CyT_DG_SC

value: SC


title: E. coli ATCC25922 grown in M9 media with glucose added for 20 minutes

description: Library name: PluGlu-20


title: CyT, DG, SC, rep3

description: Library name: 13_CyT_DG_SC

value: DG granule neurons


title: CUT&Tag, protoplast, ADA2-KRH/A, anti-H3K9ac, rep1

description: Library name: XGSZ017


title: PDM5_PF_treated_S87_L002

description: mRNA Stranded


title: CyT, DG, SC, IgG

description: Library name: 19_CyT_DG_SC_IgG

value: IgG


title: PDM2_PF_treated_S86_L002

description: mRNA Stranded


title: CUT&Tag, protoplast, ADA2, anti-H3K9ac, rep2

description: Library name: XGSZ016


title: CyT, DG, SC, rep2

description: Library name: 12_CyT_DG_SC


title: A.thaliana XVE_mTCP3 ER vs DMSO Replicate 1

type: RNA

city: Tsukuba

first: Nobutaka

last: Mitsuda

state: Ibaraki

address: Central 6 Higashi 1-1-1

department: Bioproduction Research Institute

country: Japan

institute: National Institute of Advanced Industrial Science and Technology

description: Biological replicate 1 of 3

hyb_protocol: Fragmented 0.825µg-each labeled cRNAs with hybridization buffer (Agilent GE hybridization buffer HI-PRM) were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed.

scan_protocol: Scanned on an Agilent G2505B scanner.

data_processing:
Images were quantified using Agilent Feature Extraction Software (version 9.1.3.1).
Agilent Feature Extraction Software (v 9.1.3.1) was used for background subtraction and LOWESS normalization.

organism: Arabidopsis thaliana

source_name: A.thaliana XVE_mTCP3 seedling ER treated

label_protocol: 1 µg of total RNA were used for reverse transcription at 40°C for 2 h, and labeled cRNA were prepared using T7 RNA polymerase with Cy3/5-labeled CTP at 40°C for 2 h following manufacture's instructions (Agilent Quick Amp Labeling kit).

growth_protocol: On a plate containing half strength MS salts under a cycle of 16-h-light (photosynthetic photon flux density of 50 μmol m−2 s−1)/8-h-dark at 22 °C

extract_protocol: Total RNA was extracted using Trizol (Thermo Fisher Scientific Inc.) following manufacturer's instructions

treatment_protocol: 10-d-old seedlings were transferred into a liquid medium that contained half-strength MS salts, 5 g/L sucrose, and 0.5 g/L MES for 36 h with gentle agitation under continuous light conditions and then chemicals that included DMSO and 5 µM estradiol (Wako) were added to the liquid medium

tag: age

value: day 10

value: whole seedling

value: estrogen (ER)

source_name: A.thaliana XVE_mTCP3 seedling DMSO treated


title: CUT&Tag, protoplast, ADA2, anti-H3K9ac, rep1

description: Library name: XGSZ015


title: A.thaliana XVE_mTCP3 ER vs DMSO Replicate 3

description: Biological replicate 3 of 3


title: A.thaliana XVE_mTCP3 ER vs DMSO Replicate 2

description: Biological replicate 2 of 3


title: CUT&Tag, ACLA2, anti-FLAG, rep2

description: Library name: XGSZ014

source_name: root

value: root

value: FLAG


title: E. coli ATCC25922 grown in M9 media without glucose added for 20 minutes

description: Library name: MinGlu-20

value: M9 without glucose added


title: H20_control_S72_L001

description: mRNA Stranded

value: cntrl

value: Healthy


title: CyT, DG, EE, rep2

description: Library name: 10_CyT_DG_EE

value: EE


title: CyT, DG, SC, rep1

description: Library name: 11_CyT_DG_SC


title: H20_control_S85_L002

description: mRNA Stranded


title: CyT, DG, EE, rep1

description: Library name: 9_CyT_DG_EE


title: E. coli ATCC25922 grown in M9 media with glucose replicate 3

description: Library name: WT-g-3

value: M9 with glucose


title: H17_control_S84_L002

description: mRNA Stranded


title: CUT&Tag, GCN5, anti-mcherry, rep1

description: Library name: XGSZ011

value: mcherry


title: E. coli ATCC25922 grown in M9 media with 5-deoxyribose replicate 4

description: Library name: WT-5dr-4

value: Wildtype

value: M9 with 5dR


title: H14_control_S83_L002

description: mRNA Stranded


title: H17_control_S71_L001

description: mRNA Stranded


title: E. coli ATCC25922 grown in M9 media with glucose replicate 1

description: Library name: WT-g-1


title: CUT&Tag, ADA2, anti-GFP, rep2

description: Library name: XGSZ010

value: GFP


title: CyT, CA1, IE, rep3

description: Library name: 8_CyT_CA1_IE

value: CA1 pyramidal neurons

value: IE


title: H14_control_S70_L001

description: mRNA Stranded


title: E. coli ATCC25922 grown in M9 media without glucose added for 40 minutes

description: Library name: MinGlu-40


title: CyT, CA1, IE, rep2

description: Library name: 7_CyT_CA1_IE


title: E. coli ATCC25922 grown in M9 media with 5-deoxyribose replicate 3

description: Library name: WT-5dr-3


title: PDM363_control_S82_L002

description: mRNA Stranded

value: Resistant


title: CyT, CA1, SC, rep3

description: Library name: 5_CyT_CA1_SC

value: SC


title: CUT&Tag, GCN5 RNAi, anti-H3K9ac, rep2

description: Library name: XGSZ008

value: GCN5 RNAi


title: E. coli DmtnR grown in M9 media with glucose replicate 4

description: Library name: TF-g-4

value: dmtnR


title: E. coli ATCC25922 grown in M9 media with glucose replicate 4

description: Library name: WT-g-4


title: PDM363_control_S69_L001

description: mRNA Stranded


title: CUT&Tag, ACLA2, anti-FLAG, rep1

description: Library name: XGSZ013

value: root


title: CyT, CA1, SC, rep2

description: Library name: 4_CyT_CA1_SC


title: CUT&Tag, GCN5, anti-mcherry, rep2

description: Library name: XGSZ012


title: CUT&Tag, GCN5 RNAi, anti-H3K9ac, rep1

description: Library name: XGSZ007


title: E. coli DmtnR grown in M9 media with glucose replicate 2

description: Library name: TF-g-2


title: CyT, CA1, SC, rep1

description: Library name: 3_CyT_CA1_SC


title: E. coli DmtnR grown in M9 media with glucose replicate 1

description: Library name: TF-g-1


title: CUT&Tag, acla2, anti-H3K9ac, rep2

description: Library name: XGSZ006


title: PDM359_control_S68_L001

description: mRNA Stranded


title: CyT, CA1, IE, rep1

description: Library name: 6_CyT_CA1_IE


title: CUT&Tag, ada2, anti-H3K9ac, rep2

description: Library name: XGSZ004


title: E. coli DmtnR grown in M9 media with 5-deoxyribose replicate 4

description: Library name: TF-5dr-4


title: CUT&Tag, ADA2, anti-GFP, rep1

description: Library name: XGSZ009


title: E. coli ATCC25922 grown in M9 media with 5-deoxyribose replicate 2

description: Library name: WT-5dr-2


title: CUT&Tag, acla2, anti-H3K9ac, rep1

description: Library name: XGSZ005


title: PDM277_control_S80_L002

description: mRNA Stranded


title: ATAC, DG, IE, rep3

description: Library name: 18_ATAC_DG_IE

data_processing:
Fastq files quality was analysed by FastQC (v0.11.9) and TrimGalore (v0.39) was used to trim the adapters. Reads obtained were aligned to the mouse genome (mm10) using Bowtie2 (v 2.4.2) and filtered to eliminate PCR duplicates using Picard (v2.26.2). Mitochondrial reads and reads with mapq < 30 were eliminated using Samtools (v1.13). Peakcalling was conducted using MACS2 (v2.2.7.1)
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
After tissue dissociation, nuclei were extracted by mechanical homogenization using a 2 ml Dounce homogenizer (Sigma-Aldrich) containing 500 μl of Nuclei Extraction Buffer (NEB; Sucrose 250 mM, KCl 25 mM, MgCl2 5 mM, HEPES-KOH pH 7.8 20 mM, IGEPAL CA-630 0.5 %, spermine 0.2 mM, spermidine 0.5 mM, and 1X proteinase inhibitors (cOmplete EDTA-free, Roche)). Tissues from 3 mice were pooled in each sample, having a total volume of 1.5 ml NEB containing the nuclei for each hippocampal layer. Samples were filtered in a 35 μm mesh capped tube and incubated with 0.01 mM DAPI for 10 min in darkness in a rotator. Nuclei isolation was accomplished by the preparation of a gradient of different densities in which nuclei stay in the interphase. Nuclei were diluted in Optiprep density gradient medium (1114542, Proteogenix) to a final concentration of 22 % Optiprep. For the density gradient, 44 % Optiprep was added to a centrifuge tube followed by 22 % Optiprep containing the nuclei. Additional 22 % Optiprep was added until the tube was filled. After centrifugation at 7500 rpm for 23 min, the phase containing the nuclei was collected in a new tube containing Nuclei Incubation Buffer (NIB: sucrose 340 mM, KCl 25 mM, MgCl2 5 mM, HEPES-KOH pH 7.8 20 mM, spermine 0.2 mM, spermidine 0.5 mM, 1X proteinase inhibitors, newborn calf serum 5 %). Sorting of SUN1-GFP+ nuclei was performed in a flow-cytometer FACS Aria III (BD Bioscience). 75,000 SUN1-GFP+ sorted neuronal nuclei were subjected to centrifugation, resuspended in the transposase reaction mixture (TD buffer and Tn5 transposase, Illumina) and incubated at 37 °C for 30 min. DNA extraction was immediately performed (MinElute PCR Purification Kit, Qiagen) and samples were stored at -20 °C. Once all samples had been collected, DNA libraries were generated using Custom Nextera PCR primers.
ATAC-seq

value: DG granule neurons


title: E. coli DmtnR grown in M9 media with 5-deoxyribose replicate 2

description: Library name: TF-5dr-2


title: PDM185_control_S79_L002

description: mRNA Stranded


title: PDM95_control_S67_L001

description: mRNA Stranded

value: Sensetive


title: CUT&Tag, ada2, anti-H3K9ac, rep1

description: Library name: XGSZ003


title: ATAC, DG, IE, rep2

description: Library name: 17_ATAC_DG_IE


title: ATAC, DG, IE, rep1

description: Library name: 16_ATAC_DG_IE


title: PDM95_control_S78_L002

description: mRNA Stranded

value: cntrl


title: CUT&Tag, WT, anti-H3K9ac, rep2

description: Library name: XGSZ002

value: WT


title: PDM359_control_S81_L002

description: mRNA Stranded


title: CUT&Tag, WT, anti-H3K9ac, rep1

description: Library name: XGSZ001


title: PDM50_control_S66_L001

description: mRNA Stranded


title: ATAC, DG, SC, rep3

description: Library name: 15_ATAC_DG_SC


title: CyT, CA1, EE, rep2

description: Library name: 2_CyT_CA1_EE

value: EE


title: CyT, CA1, EE, rep1

description: Library name: 1_CyT_CA1_EE


title: ATAC, DG, SC, rep2

description: Library name: 14_ATAC_DG_SC


title: AgNPs-treated, 30 minutes, biological replicate 3

city: Perugia

first: Benedetta

last: Orfei

address: Borgo XX Giugno 74

country: Italy

institute: University of Perugia

description: Library name: T30_3

data_processing:
Raw sequencing reads were assessed using FastQC
Reads were aligned to the reference genome using Bowtie2
SAM files were converted to sorted BAM format using SAMtools
Gene-level raw read counts were obtained using featureCounts
Assembly: GCF_949769235.1
Supplementary files format and content: tab-delimited text file containing raw read counts per gene for each sample

organism: Pseudomonas syringae pv. tomato

source_name: bacterial culture

extract_protocol:
RNA was extracted from the frozen cell pellets with the RNeasy® Plus Micro Kit (Qiagen Europe) according to the manufacturer instructions.
Performed by Novogene Europe. After ensuring rRNA removal, a directional mRNA library was prepared and tested for its quality. The Illumina NovaSeq 6000 Sequencing System was used to perform a paired-end 150 bp sequencing of the samples.

value: bacterial

value: silver nanoparticles (AgNPs) 0.125 ppm

tag: time

value: 30 minutes

value: Treated


title: AgNPs-treated, 30 minutes, biological replicate 2

description: Library name: T30_2


title: AgNPs-treated, 30 minutes, biological replicate 1

description: Library name: T30_1


title: PDM5_control_S76_L002

description: mRNA Stranded


title: E. coli DmtnR grown in M9 media with 5-deoxyribose replicate 1

description: Library name: TF-5dr-1

value: M9 with 5dR


title: ATAC, DG, EE, rep3

description: Library name: 12_ATAC_DG_EE


title: ATAC, DG, SC, rep1

description: Library name: 13_ATAC_DG_SC


title: AgNPs-treated, 10 minutes, biological replicate 3

description: Library name: T10_3

value: 10 minutes


title: PDM2_control_S75_L002

description: mRNA Stranded


title: PDM5_control_S65_L001

description: mRNA Stranded


title: ATAC, DG, EE, rep2

description: Library name: 11_ATAC_DG_EE


title: AgNPs-treated, 10 minutes, biological replicate 2

description: Library name: T10_2


title: PDM2_control_S64_L001

description: mRNA Stranded


title: ATAC, DG, EE, rep1

description: Library name: 10_ATAC_DG_EE


title: AgNPs-treated, 10 minutes, biological replicate 1

description: Library name: T10_1


title: ATAC, CA1, IE, rep3

description: Library name: 9_ATAC_CA1_IE

value: CA1 pyramidal neurons

value: IE


title: Control, 30 minutes, biological replicate 3

description: Library name: C30_3

value: ultra-pure sterile water

value: Control


title: ATAC, CA1, IE, rep2

description: Library name: 8_ATAC_CA1_IE


title: H14-colon_S29_L002

description: mRNA Stranded

value: Healthy


title: Liver DNA from High fat + methyl donor diet mice  [MET3]

type: other

city: guadalajara

first: angel

middle: omar

last: vazquez

address: SIERRA MOJADA 950

country: Mexico

institute: IBMMTG

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium MouseMethylation array (MouseMethylation-12v1-0_A2) using estándar Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader (Iscan) And standard recommended Illumina scanner setting

data_processing: SeSame package in R evironment (v4.3.1)

label: Cy3 and Cy5

molecule: other

source_name: Liver

label_protocol: Standard Ilumina protocol

extract_protocol: Liver DNA was extracted using DNA QIAamp (Qiagen cat. P-1030)

value: Liver

value: High fat + methyl donor diet mice


title: H14-colon_S22_L001

description: mRNA Stranded

source_name: Colon


title: Liver DNA from High fat diet mice  [HF2]

value: High fat diet mice


title: PDM50_control_S77_L002

description: mRNA Stranded

value: cntrl

value: Sensetive


title: Ventricular Myocyte, 50µM Senexin, Rep3

city: Iowa City

first: Chad

middle: E

last: Grueter

state: IA

address: 169 Newton Rd, 4332 PBDB

institute: University of Iowa

description: Library name: S50-3

data_processing:
Illumina basespace used for analysis
Base trimming to 125 bp was performed using Fastq toolkit (V2.2.0)  10 bases were trimmed from the 5' end, and 16 bases were trimmed from the 3' end
Alignment was performed using RNAseq Alignment (v1.1.0) and Bowtie2 to align to Rattus norvegicus (UCSC rn5)
Transcripts were assembled and differential gene expression was performed using Cufflinks Assembly and DE (Version 2.1.0)
Assembly: UCSC rn5
Supplementary files format and content: FPKM Values in txt format

organism: Rattus norvegicus

source_name: Ventricular myocytes

extract_protocol:
Neonatal rat cardiomyocytes were scraped from plates in Trizol and RNA was extracted using RNA miniprep kit (Zymo)
RNA libraries were prepared for sequencing using TruSeq RNA Library prep kit  V2

treatment_protocol: NRCM were isolated using Neonatal dissociation kit (Miltenyi Biotec.) and treated with AraC for 48 h.  Cells were then serum starved for 24 hours and treated for 48 hours with PE in the presence or absence of Senexin A for 48 hours.  Media treatments were replaced at 24 hours.

value: Ventricular myocytes

value: Wistar rats (Charles River 003)

value: 50 µm Senexin A


title: Control, 30 minutes, biological replicate 1

description: Library name: C30_1

value: bacterial

value: WT

value: 30 minutes


title: Control, 10 minutes, biological replicate 3

description: Library name: C10_3

value: 10 minutes


title: Ventricular Myocyte, 50µM Senexin, Rep2

description: Library name: S50-2


title: Control, 30 minutes, biological replicate 2

description: Library name: C30_2


title: ATAC, CA1, IE, rep1

description: Library name: 7_ATAC_CA1_IE

value: CA1 pyramidal neurons


title: ATAC, CA1, SC, rep3

description: Library name: 6_ATAC_CA1_SC

value: SC


title: Control, 10 minutes, biological replicate 2

description: Library name: C10_2

value: ultra-pure sterile water


title: Ventricular Myocyte, 10µM Senexin, Rep3

description: Library name: S10-3

value: 10 µm Senexin A


title: Control, 10 minutes, biological replicate 1

description: Library name: C10_1

value: Control


title: Liver DNA from High fat + methyl donor diet mice  [MET2]

value: Liver


title: Liver DNA from High fat diet mice  [HF3]


title: Liver DNA from High fat + methyl donor diet mice  [MET1]

value: High fat + methyl donor diet mice


title: Ventricular Myocyte, 10µM Senexin, Rep2

description: Library name: S10-2


title: ATAC, CA1, SC, rep2

description: Library name: 5_ATAC_CA1_SC


title: Ventricular Myocyte, 50µM Senexin, Rep1

description: Library name: S50-1


title: ATAC, CA1, SC, rep1

description: Library name: 4_ATAC_CA1_SC


title: Ventricular Myocyte, 10µM Senexin, Rep1

description: Library name: S10-1


title: Liver DNA from Normo Diet mice  [ND1]

value: Normo Diet mice


title: ATAC, CA1, EE, rep1

description: Library name: 1_ATAC_CA1_EE

value: EE


title: Liver DNA from High fat diet mice  [HF1]

value: High fat diet mice


title: Liver DNA from Normo Diet mice  [ND2]


title: Liver DNA from Normo Diet mice  [ND3]


title: ATAC, CA1, EE, rep2

description: Library name: 2_ATAC_CA1_EE


title: ATAC, CA1, EE, rep3

description: Library name: 3_ATAC_CA1_EE


title: Flowers, ES-Lim

city: Chuncheon

first: Prakash

last: Basnet

state: Gangwon-do

address: Department of Agriculture and Life Industry, Kangwon National University, Bldg. Asangwan Rm.424, 1 K

department: Agriculture and Life Industries

country: South Korea

institute: Kangwon National University

description: Library name: ES-Lim

data_processing:
Trimmomatic v0.36
Trimmomatic sliding window (4:20)
HITSAT2 v2.1.0
String Tie v1.3.4d
DESeq V1.36.0 (for DEGs analysis)
Assembly: Cannabis. sativa L
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

organism: Cannabis sativa

source_name: Flowers

growth_protocol: Hemp plants were grown in greenhouse under normal condition

extract_protocol:
Kit using Genall Hybrid plant
RNA-Seq and cDNA library

treatment_protocol: No treatments

value: Flowers

tag: Stage

value: ES

tag: cultivar

value: Lim


title: Flowers, LS-Lim

description: Library name: LS-Lim

value: LS


title: hUCMSC-EVs_rep2

city: Xinxiang

first: JIE

last: LIAN

state: Henan

address: Jinsui Road

department: Henan Joint International Research Laboratory of Stem Cell Medicine

institute: Xinxiang Medical University

description: miRNAs expression of EVs isolated from conditioned medium of hUCMSCs culture over 48 hrs

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Normalized signal intensity by quantile method.

source_name: hUCMSC-EVs, 48 hrs, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: EVs were isolated from the cell-free conditioned medium of hUCMSCs culture over 48 hr by differential ultracentrifugation.

extract_protocol: Total RNA was extracted with TRIZOL reagent, quantified spectrophotometrically (NanoDrop ND-2000, Thermo Scientific), and assessed for integrity using an Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: Primary hUCMSCs were isolated from fresh Wharton’s jelly tissue obtained from healthy donors. Cells were cultured in DMEM supplemented with 10% FBS and maintained at 37 °C in a humidified atmosphere of 5% CO₂. Upon reaching 70–80% confluence, hUCMSCs at passage 3 were used for EVs production. EVs were isolated from cell-free conditioned medium collected after 48 hrs of culture in DMEM containing 10% EV-depleted FBS using differential ultracentrifugation.

value: human umbilical cord

tag: gender

value: female


title: Ventricular Myocyte, PE + 50µM Senexin, Rep1

description: Library name: PS50-1

value: Ventricular myocytes

value: Wistar rats (Charles River 003)

value: 10 µm Phenylephrine + 50 µm Senexin A


title: Ventricular Myocyte, PE + 50µM Senexin, Rep2

description: Library name: PS50-2


title: Flowers, LS-Amb

description: Library name: LS-Amb

value: Amb


title: Ventricular Myocyte, PE + 10µM Senexin, Rep3

description: Library name: PS10-3

value: 10 µm Phenylephrine + 10 µm Senexin A


title: Ventricular Myocyte, PE + 50µM Senexin, Rep3

description: Library name: PS50-3


title: hUCMSC-EVs_rep1

source_name: hUCMSC-EVs, 48 hrs, replicate 1


title: Ventricular Myocyte, PE + 10µM Senexin, Rep2

description: Library name: PS10-2


title: Flowers, ES-Amb

description: Library name: ES-Amb


title: Phenylephrine + µ50M Senexin A, NRVM, RNA Pol II

description: Library name: Zr_2406_7

data_processing:
Zymo Research utilized Fastp v0.19.7 and aligned using Bowtie2 v2.3.5.
MACS2 v2.2.3 was using to identify transcription factor binding sites.
ChIPQC v1.18.2 calculated quality metrics.
Assembly: rn6
Supplementary files format and content: bedwig

source_name: Ventricular Cardiomyocytes

extract_protocol:
NRCM were scraped from plates in trizol. Genomic DNA was extracted using the Zymo-Spin ChIP kit according to manufacturer's directions.
libraries were prepared by Zymo Research using ThruPLEX_DNA_Seq.

value: Ventricular Cardiomyocytes

tag: chip antibody

value: RNA Pol II


title: #113 ,CCR2high

city: Kumamoto

first: Naofumi

last: Takahashi

address: 2-2-1 Honjo, Chuo-ku

institute: Kumamoto University

description: Library name: PM-06

data_processing:
Making FASTQ were performed using Local Run Manager v2.4.0 for NextSeq 500 output
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim galore! v0.6.6
Trimmed sequence reads were mapped to UCSC hg19 using STAR v2.7.9a
Read count extraction and normalization were performed using RSEM v1.3.3
Assembly: UCSC hg19
Supplementary files format and content: TPM values for each sample are included in a matrix file

source_name: Ascites

extract_protocol:
Total RNA was isolated using RNeasy micro kit (QIAGEN). 1ng of total RNA was used for the construction of sequencing libraries. Agilent 2100 Bioanalyzer was used for QC.
RNA libraries were prepared using NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina (New England Biolabs).

value: Ascites

value: peritoneal macrophages

tag: subset


title: Ventricular Myocyte, PE + 10µM Senexin, Rep1

description: Library name: PS10-1


title: Phenylephrine + µ50M Senexin A, NRVM, H3K27ac

description: Library name: Zr_2406_4


title: #113, CCR2low

description: Library name: PM-05


title: Phenylephrine, NRVM, RNA Pol II

description: Library name: Zr_2406_6

value: 10 µm Phenylephrine


title: #107, CCR2high

description: Library name: PM-02


title: Vehicle, NRVM, H3K27ac

description: Library name: Zr_2406_2

value: Vehicle


title: Phenylephrine, NRVM, H3K27ac

description: Library name: Zr_2406_3


title: poly I:C_GD10, LPS_P11

city: Tsu

first: Takeshi

last: Ohkawara

department: Developmental and Regenerative Medicine

institute: Mie University

hyb_protocol: Hybridization to Agilent Rat 8x60 K Ver. 2.0 microarray and wash were performed using Gene Expression wash pack (Agilent) according to the manufacturer's instruction.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G4900DA)  using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters (protocol GE1_1105_Oct12 and Grid: 074036_D_F_20150914) to obtain background subtracted and spatially detrended Processed Signal intensities. Data were normalized by percentile shift method (percentile target 75 %) using GeneSpring software (Agilent, CA).

source_name: pons and medulla, poly I:C_LPS

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from100 ng RNA using the Low Input Quick Amp Labeling kit (One-Color) (Agilent) according to the manufacturer's instructions, followed by RNAeasy mini kit (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop Spectrophotometer.

extract_protocol: RNA was prepared using Trizol Reagent (Thermo Fisher SCIENTIFIC, CA) following the manufacturer's instruction. RNA was quantified using a NanoDrop one spectrophotometer and quality was monitored with the Agilent Bioanalyzer RNA600 Nano (Agilent Technologies, Santa Clara, CA).

tag: tisuue

value: pons and medulla

value: male

value: Wistar


title: #111, CCR2low

description: Library name: PM-03


title: Venticular Myocyte, Vehicle, Rep3

description: Library name: Veh3


title: Venticular Myocyte, PE, Rep3

description: Library name: PE3


title: Venticular Myocyte, PE, Rep1

description: Library name: PE1


title: #111, CCR2high

description: Library name: PM-04


title: Venticular Myocyte, PE, Rep2

description: Library name: PE2


title: PBS_GD10, PBS_P11

source_name: pons and medulla, PBS_PBS


title: Vehicle, NRVM, RNA Pol II

description: Library name: Zr_2406_5


title: Combined ChIP Input

description: Library name: Zr_2406_1


title: PBS_GD10, LPS_P11

source_name: pons and medulla, PBS_LPS


title: Tag, Subjects UNC0232 and UNC0233

status: Public on Sep 22 2025

city: Chapel Hill

first: Austin

last: Hepperla

state: NC

address: 7018B Mary Ellen Jones Building

institute: UNC Chapel Hill

description:
Library name: TAG232A233C
Hashtag-derived oligonucleotide (HTO)

library_source: other

data_processing:
CITE-Seq and multiplexed files were demultiplexed using the Lex plug-in in SeqGeq.
The Seurat plug-in in SeqGeq was used for multimodal analysis.
Assembly: Human
Supplementary files format and content: CSV file containing DBEC moleculers per cell.
Supplementary files format and content: CSV file containing sample tag call
Library strategy: CITE-seq

molecule: protein

source_name: PBMCs

extract_protocol:
Peripheral blood mononuclear cell preparations were enriched for B cells from the same patient and sequentially labeled with sample tags using the BD Human Single-Cell Multiplexing Kit and BD AbSeq oligo-conjugated antibodies.
Single cells were captured, and cDNA was synthesized on beads, followed by targeted amplification of transcripts using the Human Immune Response Panel primers (399 genes) and a custom supplemental panel set (20 targets), as well as amplification of cDNA of sample Tag and AbSeq. Final RNA-seq libraries were prepared by performing the index PCR using a combination of 3 forward index primers (TreSeq D501-D503) and 12 reverse index primers (TrueSeq D701-D712).

value: PBMCs

value: Mixed samples (Control, AGS)

tag: library type

value: HTO


title: Tag, Subjects UNC0234and UNC0235

description:
Library name: TAG234A235A
Hashtag-derived oligonucleotide (HTO)

value: AGS


title: Tag, Subjects UNC0239 and UNC0240

description:
Library name: TAG239C240C
Hashtag-derived oligonucleotide (HTO)

value: Control


title: poly I:C_GD10, PBS_P11

source_name: pons and medulla, poly I:C_PBS


title: Venticular Myocyte, Vehicle, Rep1

description: Library name: Veh1

value: Ventricular myocytes

value: Wistar rats (Charles River 003)


title: Tag, Subjects UNC0230 and UNC0231

description:
Library name: TAG230A231A
Hashtag-derived oligonucleotide (HTO)


title: Venticular Myocyte, Vehicle, Rep2

description: Library name: Veh2


title: Tag, Subjects UNC0236 and UNC0237

description:
Library name: TAG236A237A
Hashtag-derived oligonucleotide (HTO)


title: Tag, Subjects UNC0224 and UNC0225

description:
Library name: TAG224A225A
Hashtag-derived oligonucleotide (HTO)


title: Tag, Subjects UNC0218 and UNC0219

description:
Library name: TAG218A219A
Hashtag-derived oligonucleotide (HTO)


title: Tag, Subjects UNC0221 and UNC0222

description:
Library name: TAG221A222A
Hashtag-derived oligonucleotide (HTO)


title: #107, CCR2low

description: Library name: PM-01


title: Tag, Subjects UNC0211 and UNC0212

description:
Library name: TAG211A212A
Hashtag-derived oligonucleotide (HTO)


title: Tag, Subjects UNC0142 and UNC0229

description:
Library name: TAG142C229C
Hashtag-derived oligonucleotide (HTO)


title: mRNA, Subjects UNC0239 and UNC0240

description:
Library name: MRNA239C240C
polyA RNA

data_processing:
CITE-Seq and multiplexed files were demultiplexed using the Lex plug-in in SeqGeq.
The Seurat plug-in in SeqGeq was used for multimodal analysis.
Assembly: Human
Supplementary files format and content: CSV file containing DBEC moleculers per cell.
Supplementary files format and content: CSV file containing sample tag call

value: mRNA


title: Tag, Subjects UNC0039 and UNC0085

description:
Library name: TAG039C095C
Hashtag-derived oligonucleotide (HTO)


title: AbSeq, Subjects UNC0209 and UNC0210

description:
Library name: ABSEQ209A210A
Antibody-derived oligonucleotide (ADT)

value: ADT


title: mRNA, Subjects UNC0236 and UNC0237

description:
Library name: MRNA236A237A
polyA RNA


title: mRNA, Subjects UNC0026 and UNC0029

description:
Library name: MRNA026C029C
PolyA RNA


title: mRNA, Subjects UNC0234and UNC0235

description:
Library name: MRNA234A235A
polyA RNA


title: mRNA, Subjects UNC0224 and UNC0225

description:
Library name: MRNA224A225A
polyA RNA


title: mRNA, Subjects UNC0230 and UNC0231

description:
Library name: MRNA230A231A
polyA RNA


title: mRNA, Subjects UNC0221 and UNC0222

description:
Library name: MRNA221A222A
polyA RNA


title: mRNA, Subjects UNC0218 and UNC0219

description:
Library name: MRNA218A219A
polyA RNA


title: mRNA, Subjects UNC0142 and UNC0229

description:
Library name: MRNA142C229C
polyA RNA


title: mRNA, Subjects UNC0039 and UNC0085

description:
Library name: MRNA039C095C
polyA RNA


title: AbSeq, Subjects UNC0026 and UNC0029

description:
Library name: ABSEQ026C029C
Antibody-derived oligonucleotide (ADT)


title: mRNA, Subjects UNC0119 and UNC0223

description:
Library name: MRNA119A223A
polyA RNA


title: mRNA, Subjects UNC0216 and UNC0217

description:
Library name: MRNA216C217A
polyA RNA


title: mRNA, Subjects UNC0211 and UNC0212

description:
Library name: MRNA211A212A
polyA RNA


title: AbSeq, Subjects UNC0239 and UNC0240

description:
Library name: ABSEQ239C240C
Antibody-derived oligonucleotide (ADT)


title: AbSeq, Subjects UNC0236 and UNC0237

description:
Library name: ABSEQ236A237A
Antibody-derived oligonucleotide (ADT)


title: mRNA, Subjects UNC0232 and UNC0233

description:
Library name: MRNA232A233C
polyA RNA


title: AbSeq, Subjects UNC0234and UNC0235

description:
Library name: ABSEQ234A235A
Antibody-derived oligonucleotide (ADT)


title: Tag, Subjects UNC0216 and UNC0217

description:
Library name: TAG216C217A
Hashtag-derived oligonucleotide (HTO)


title: AbSeq, Subjects UNC0230 and UNC0231

description:
Library name: ABSEQ230A231A
Antibody-derived oligonucleotide (ADT)


title: AbSeq, Subjects UNC0218 and UNC0219

description:
Library name: ABSEQ218A219A
Antibody-derived oligonucleotide (ADT)


title: AbSeq, Subjects UNC0232 and UNC0233

description:
Library name: ABSEQ232A233C
Antibody-derived oligonucleotide (ADT)


title: AbSeq, Subjects UNC0224 and UNC0225

description:
Library name: ABSEQ224A225A
Antibody-derived oligonucleotide (ADT)


title: mRNA, Subjects UNC0209 and UNC0210

description:
Library name: MRNA209A210A
PolyA RNA


title: AbSeq, Subjects UNC0216 and UNC0217

description:
Library name: ABSEQ216C217A
Antibody-derived oligonucleotide (ADT)