title: 16S rRNAseq of stool: 31560_HNStool47

city: Chapel Hill

first: Office of Genomics Research

last: UNC Lineberger Comprehensive Cancer Center

state: NC

address: 125 Mason Farm Road, CB #7599 5105-5106 Marsico Hall

institute: University of North Carolina at Chapel Hill

description: Library name: HNStool47

data_processing:
Trimming: Trim Galore! - CutAdapt 3.7
Host Removal: Kraken2 2.1.2
ASV calling: DADA2 (QIIME2 2022.2.0)
Taxa Classification: QIIME 2 2022.2.0  - Silva 138
Assembly: Silva 138
Supplementary files format and content: ASV/OTU table: table.biom.txt (tab-separated text spreadsheet)
Supplementary files format and content: DNA sequences for ASV representatives: rep-seqs.fna (nucleotide fasta file)
Supplementary files format and content: Taxa classifications for each ASV: taxa-gg2.txt (tab-separated text spreadsheet)
Supplementary files format and content: Phylogenetic tree of ASV representative sequences: tree.nwk (Newick format)
Library strategy: 16S rRNA-seq

organism: metagenome

source_name: stool

extract_protocol:
Fecal samples were transferred to a 2 ml tube containing 200 mg of 106/500μm glass beads (Sigma, St. Louis, MO) and 0.5 ml of Qiagen PM1 buffer (Valencia, CA). Mechanical lysis was performed for 40 minutes on a Digital Vortex Mixer. After a 5 minute centrifugation, 0.45 ml of supernatants was aspirated and transferred to a new tube containing 0.15 ml of Qiagen IRS solution. The suspension was incubated at 4°C overnight. After a 5 minute centrifugation, supernatant was aspirated and transferred to deep well plates containing 0.45 ml of Qiagen binding buffer supplemented with Qiagen ClearMag Beads. DNA was purified using the automated KingFisher™ Flex Purification System and eluted in DNase free water.  12.5 ng of total DNA were amplified using universal primers targeting the V4 region of the bacterial 16S rRNA gene. Primer sequences contained overhang adapters appended to the 5’ end of each primer for compatibility with Illumina sequencing platform. The primers used were F515/R806. Master mixes contained 12.5 ng of total DNA, 0.5 µM of each primer and 2x KAPA HiFi HotStart ReadyMix (KAPA Biosystems, Wilmington, MA). The thermal profile for the amplification of each sample had an initial denaturing step at 95°C for 3 minutes, followed by a cycling of denaturing of 95°C for 30 seconds, annealing at 55°C for 30 seconds and a 30 second extension at 72°C (25 cycles), a 5 minute extension at 72°C and a final hold at 4°C. Each 16S amplicon was purified using the AMPure XP reagent (Beckman Coulter, Indianapolis, IN). In the next step each sample was amplified using a limited cycle PCR program, adding Illumina sequencing adapters and dual‐index barcodes (index 1(i7) and index 2(i5)) (Illumina, San Diego, CA) to the amplicon target. The thermal profile for the amplification of each sample had an initial denaturing step at 95°C for 3 minutes, followed by a denaturing cycle of 95°C for 30 seconds, annealing at 55°C for 30 seconds and a 30 second extension at 72°C (8 cycles), a 5 minute extension at 72°C and a final hold at 4°C. The final libraries were again purified using the AMPure XP reagent (Beckman Coulter), quantified and normalized prior to pooling. The DNA library pool was then denatured with NaOH, diluted with hybridization buffer and heat denatured.
Samples were transferred to a 2 ml tube containing 200 mg of 106/500μm glass beads (Sigma, St. Louis, MO) and 0.5 ml of Qiagen PM1 buffer (Valencia, CA). Mechanical lysis was performed for 40 minutes on a Digital Vortex Mixer. After a 5 minute centrifugation, 0.45 ml of supernatants was aspirated and transferred to a new tube containing 0.15 ml of Qiagen IRS solution. The suspension was incubated at 4°C overnight. After a 5 minute centrifugation, supernatant was aspirated and transferred to deep well plates containing 0.45 ml of Qiagen binding buffer supplemented with Qiagen ClearMag Beads. DNA was purified using the automated KingFisher™ Flex Purification System and eluted in DNase free water.  12.5 ng of total DNA were amplified using universal primers targeting the V4 region of the bacterial 16S rRNA gene. Primer sequences contained overhang adapters appended to the 5’ end of each primer for compatibility with Illumina sequencing platform. The primers used were F515/R806. Master mixes contained 12.5 ng of total DNA, 0.5 µM of each primer and 2x KAPA HiFi HotStart ReadyMix (KAPA Biosystems, Wilmington, MA). The thermal profile for the amplification of each sample had an initial denaturing step at 95°C for 3 minutes, followed by a cycling of denaturing of 95°C for 30 seconds, annealing at 55°C for 30 seconds and a 30 second extension at 72°C (25 cycles), a 5 minute extension at 72°C and a final hold at 4°C. Each 16S amplicon was purified using the AMPure XP reagent (Beckman Coulter, Indianapolis, IN).
In the next step each sample was amplified using a limited cycle PCR program, adding Illumina sequencing adapters and dual‐index barcodes (index 1(i7) and index 2(i5)) (Illumina, San Diego, CA) to the amplicon target. The thermal profile for the amplification of each sample had an initial denaturing step at 95°C for 3 minutes, followed by a denaturing cycle of 95°C for 30 seconds, annealing at 55°C for 30 seconds and a 30 second extension at 72°C (8 cycles), a 5 minute extension at 72°C and a final hold at 4°C. The final libraries were again purified using the AMPure XP reagent (Beckman Coulter), quantified and normalized prior to pooling. The DNA library pool was then denatured with NaOH, diluted with hybridization buffer and heat denatured.

value: stool


title: wound skin,wound model in healthy mice,  rep1

status: Public on Dec 16 2025

type: SRA

city: Hangzhou

first: Zhengtai

last: Chen

state: zhejiang

address: 88 Jie Fang Road, Hangzhou

country: China

institute: The Second Affiliated Hospital, Medical School, Zhejiang University

description:
Library name: sample6
Health1

library_source: transcriptomic

data_processing:
mRNA was isolated by Oligo(dT)-attached magnetic beads
mRNA was then randomly fragmented in fragmentation buffer.
First-strand cDNA was synthesized with fragmented mRNA as template and random hexamers as primers, followed by second-strand synthesis with addition of PCR buffer, dNTPs, RNase H and DNA polymerase I. Purification of cDNA was processed with AMPure XP beads.
Double-strand cDNA was subjected to end repair. Adenosine was added to the end and ligated to adapters. AMPure XP beads were applied here to select fragments within size range of 300-400 bp.
cDNA library was obtained by certain rounds of PCR on cDNA fragments generated from step 4.
Assembly: DEK, FDX1
Supplementary files format and content: xls file represent for gene expression level (FPKM) matrix file
Supplementary files format and content: gene-count file represent for comparison diagram of FPKM density distribution, the peak value of distribution curve represents the region with the highest concentration of gene expression in the whole sample.

molecule: total RNA

organism: Mus

source_name: skin metagenome

growth_protocol: Briefly, the wound tissues of type I diabetic mice, healthy mice, and normal skin were harvested, immediately frozen with liquid nitrogen, and stored at -80 °C. Total RNA was used as input material for RNA sample preparation. mRNA was purified from the total RNA using poly T oligo-attached magnetic beads.

extract_protocol:
Wound skin tissue were obtained from normal skin of healthy mice, wound skin of healthy mice and wound skin of diabetes mice, and then the TRIzol reagent (Invitrogen, 15596018) was used to extract the total RNA
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X）. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H . Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 240 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: There are three groups of mice in total, namely, the healthy mouse group, the healthy mouse wound model group, and the diabetes mouse wound model group

tag: tissue

value: wound skin

tag: treatment

value: wound surgery


title: Patient 21, plasma, healthy, female

city: Lodz

first: Urszula

last: Smyczynska

address: 15, Mazowiecka Street

department: Department of Biostatistics and Translational Medicine

country: Poland

institute: Medical University of Lodz

description: Library name: 31274-041

data_processing:
FASTQ files were generated using Illumina bcl2fastq. Sequencing reads were mapped to miRBase in version 22.1 using nf-core/smrnaseq in version 2.3.0. Contamination filtration was switched on with minor modification added to allow for detailed quantification of contaminants. Computational resources were limited to available server capacity, while other parameters were left at default values.
Assembly: miRBase version 22.1
Supplementary files format and content: Processed data are stored in two Excel (xlsx) files. First contains raw counts for all samples as generated by nf-core/smrnaseq pipeline. The second file stores filtered, normalized, and log-transformed counts. miRNAs present in at least 10 counts per million (CPM) in at least 50% of samples in either plasma or serum were kept. After removal of low-expression miRNAs, raw counts of remaining miRNAs were normalized to CPM with respect to sum of their counts and log2-transformed (after adding 0.5 to each value to avoid logarithms of 0), yielding log2(CPM) used in further analysis.

organism: Homo sapiens

source_name: Plasma

extract_protocol:
Total RNA was extracted from serum or plasma.
Libraries were prepared with QIAseq miRNA Library Kit (QIAGEN).

value: Plasma

tag: genotype

value: BRCA wild-type


title: 16S rRNAseq of stool: 31252_HNStool46

country: USA

description: Library name: HNStool46

library_source: genomic

molecule: genomic DNA


title: Chip-seq, H3K4Me3, PC3, OE C, rep#1

city: Chicago

first: Cheng-Wei

last: Ju

state: Illinois

address: 929 East 57th Street, GCIS, Room E313

institute: The University of Chicago

description:
Library name: PC3-C-1_H3K4Me3
combined.H3K4.final.narrowPeak
FeatureCounts.H3Q5region.txt

data_processing:
For RNA-seq, raw reads were trimmed with fastqc, then aligned to human genome and transcriptome (GRCh38.release108) using HISAT (version 2.1.0). Differentially expressed genes between the two groups were calculated in R using the DESeq2.
For Chip-seq, Raw sequencing reads were processed using FastQC for quality control and aligned to the human reference genome (GRCh38.release108) using Bowtie2. PCR duplicates have been removed. Peak calling was performed using MACS2, and annotation of binding sites was conducted using HOMER and in-house scripts.
Assembly: GRCh38.release108
Supplementary files format and content: csv files included Deseq2 normalized reads
Supplementary files format and content: BigWig files for ChIP-seq signal tracks of all samples.
Supplementary files format and content: NarrowPeak files for: H3K4me3 peaks; H3K4me3Q5ser peaks; H3K4me3Q5ser peaks overlapping with H3K4me3 peaks
Supplementary files format and content: FeatureCounts output for quantification within H3K4me3Q5ser peak regions

growth_protocol: The human prostate cancer cell lines PC3 (SCSP-532) was purchased from the Cell Bank, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences. Cells were cultured in RPMI-1640 (Gibco), supplemented with 10% fetal bovine serum (Invitrogen), 100 U/mL penicillin, and 100 μg/mL streptomycin (Gibco). Cells were incubated at 37°C in a humidified incubator with 5% CO2 and were routinely tested for mycoplasma contamination. The identity of the cell lines was verified through high-resolution short tandem repeat (STR) profiling.

extract_protocol:
RNA sequencing (RNA-seq) was performed on PC3 cells transduced with control (Ctrl), DDC, or SLC6A4 constructs. Total RNA was extracted using TRIzol Reagent (Invitrogen) and treated with DNase I to remove genomic DNA contamination.
mRNA was enriched using Oligo(dT)-modified magnetic beads and subsequently used for cDNA synthesis (Invitrogen). RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies). Libraries were prepared and quantified before sequencing on the Illumina NovaSeq 6000 platform (Illumina, San Diego, CA) in high-output mode.
ChIP assays were performed using the SimpleChIP Plus Enzymatic Chromatin IP Kit (9005, Cell Signaling Technology) following the manufacturer’s protocol. Briefly, cells were crosslinked with 1% formaldehyde and sonicated to obtain chromatin fragments averaging 250–1000 bp. Immunoprecipitated chromatin was subsequently reverse crosslinked.
For ChIP-seq, the immunoprecipitated DNA and input DNA were subjected to library preparation using the NEBNext Ultra II DNA Library Prep Kit (E7645, New England Biolabs) according to the manufacturer’s protocol.

tag: cell line

tag: cell type

value: Prostate Cancer

value: Empty Vector OE


title: Patient 20, plasma, healthy, female

description: Library name: 31274-039

value: BRCA mutation


title: 16S rRNAseq of stool: 31054_HNStool45

description: Library name: HNStool45


title: Chip-seq, input, PC3, OE SLC6A4, rep#2

description: Library name: PC3-SLC6A4_OE-2_input

value: SLC6A4 OE


title: 16S rRNAseq of stool: 30933_HNStool44

description: Library name: HNStool44


title: Chip-seq, input, PC3, OE SLC6A4, rep#1

description: Library name: PC3-SLC6A4_OE-1_input


title: Patient 19, plasma, healthy, female

description: Library name: 31274-037


title: RPMI_8226_shN1_2_rep3

city: Wuerzburg

first: Carsten

middle: P

last: Ade

address: Am Hubland

department: Lehrstuhl Biochemie und Molekularbiologie

country: Germany

institute: University of Wuerzburg

description:
RPMI_8226_TPM_count_table
RPMI_8226_DESeq2_comparison_shN1_2_vs_shNTC

data_processing:
Following sequencing, base calling was done with Illumina’s FASTQ Generation software and high quality PF-clusters (according to the CASAVA filter) were selected for further analyses.
For RNA-seq, reads were mapped to the human genome using the STAR aligner (version 2.7.2b) with default parameters. The subsequent bioinformatics analysis of the aligned reads was done with the featureCounts tool (v1.6.4) followed by the DESeq2 package form Bioconductor.
Assembly: GRCh38.p13
Supplementary files format and content: For RNA-seq, a count-matrix with rawcounts, normalized to 1 million tags, and a count table with vst (variance stabilizing transformation) transformed counts are provided in text-format (*.csv). Furthermore, the DESeq2 calculated differential expressions for all analyzed genes for the relevant comparisons are provided for both cell-lines in text-format (*.csv).

growth_protocol: MM.1S and RPMI-8226 cells were grown and cultured in RPMI 1640 medium with GlutaMAX (Thermo Fisher Scientific, Darmstadt, Germany), supplemented with 10 % fetal calf serum (FCS) (Anprotec, Bruckberg, Germany), 1 % penicillin/streptomycin (10.000 U/ml, Thermo Fisher Scientific, Darmstadt, Germany), and 1 % sodium pyruvate (100 mM, Thermo Fisher Scientific, Darmstadt, Germany).

extract_protocol:
For RNA-seq, cells were harvested and total RNA was extracted from 1x10^7 cells using the Qiagen RNAeasy Plus Mini Kit (Qiagen, Hilden, Germany) following the manufacturer's protocol. To isolate protein coding messenger RNAs from the total RNA, the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Frankfurt, Germany) was used.
Library preparation was performed with the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs, Frankfurt, Germany) according to the manufacturer’s protocol. Libraries were size-selected using AMPure XP beads (Beckman Coulter, Beverly, USA). Samples were amplified and sample-specific indexes were introduced for the sequencing step using NEBNext Multiplex Oligos for Illumina (Dual Index Primer Set 1, Illumina, New England Biolabs, Frankfurt, Germany) in a 8-cycle PCR reaction. Determination of library size and concentration was performed with a 2100 Bioanalyzer System (Agilent Technologies, Santa Clara, CA, USA). Libraries were sequenced with a NextSeq 500 System (Illumina, San Diego, CA, USA) in a dual-index, single-read format.
RNA-sequencing (Illumina NextSeq 500)

treatment_protocol: For the RNA-seq experiment, MM.1S cells and RPMI-8226 cells were either transduced with a lentiviral shRNA vector that constitutively expresses a shRNA targeting Notch1 or Notch2 or a non-targeting shRNA. Transduced cells were then puromycin-selected by adding 0.75 µg per ml puromycin (Thermo Fisher Scientific)

tag: induction of shrna

value: constitutively expressed shRNA


title: Patient 18, plasma, healthy, female

description: Library name: 31274-035


title: RPMI_8226_shN2_1_rep2

description:
RPMI_8226_TPM_count_table
RPMI_8226_DESeq2_comparison_shN2_1_vs_shNTC


title: RPMI_8226_shN1_2_rep2


title: 16S rRNAseq of stool: 30845_HNStool43

description: Library name: HNStool43


title: Chip-seq, input, PC3, OE DDC, rep#3

description: Library name: PC3-DDC_OE-3_input

value: DDC OE


title: Chip-seq, input, PC3, OE SLC6A4, rep#3

description: Library name: PC3-SLC6A4_OE-3_input


title: Patient 17, plasma, healthy, female

description: Library name: 31274-033


title: 16S rRNAseq of stool: 29195_HNStool42

description: Library name: HNStool42


title: Patient 22, plasma, healthy, female

description: Library name: 31274-042


title: Chip-seq, input, PC3, OE DDC, rep#2

description: Library name: PC3-DDC_OE-2_input


title: RPMI_8226_shN2_1_rep3


title: RPMI_8226_shN1_1_rep3

description:
RPMI_8226_TPM_count_table
RPMI_8226_DESeq2_comparison_shN1_1_vs_shNTC


title: 16S rRNAseq of stool: 28953_HNStool41

description: Library name: HNStool41


title: Chip-seq, input, PC3, OE DDC, rep#1

description: Library name: PC3-DDC_OE-1_input


title: Patient 15, plasma, healthy, female

description: Library name: 31274-029


title: RPMI_8226_shN1_1_rep2


title: RPMI_8226_shN2_1_rep1


title: Chip-seq, input, PC3, OE C, rep#3

description: Library name: PC3-C-3_input


title: 16S rRNAseq of stool: 28579_HNStool39

description: Library name: HNStool39


title: Patient 14, plasma, healthy, female

description: Library name: 31274-027


title: 16S rRNAseq of stool: 28007_HNStool38

description: Library name: HNStool38


title: Chip-seq, input, PC3, OE C, rep#1

description: Library name: PC3-C-1_input


title: 16S rRNAseq of stool: 28766_HNStool40

description: Library name: HNStool40


title: RNA-seq, PC3, OE SLC6A4, rep#3

description:
Library name: PC3-SLC6A4_OE-3
Deseq2.SLC.anno.csv

molecule: polyA RNA


title: Patient 13, plasma, healthy, female

description: Library name: 31274-025


title: 16S rRNAseq of stool: 27204_HNStool36

description: Library name: HNStool36


title: RPMI_8226_shN1_2_rep1


title: 16S rRNAseq of stool: 27963_HNStool37

description: Library name: HNStool37


title: Patient 12, plasma, healthy, female

description: Library name: 31274-023


title: RPMI_8226_shNTC_rep3


title: RPMI_8226_shNTC_rep1


title: Patient 11, plasma, healthy, female

description: Library name: 31274-021


title: Patient 16, plasma, healthy, female

description: Library name: 31274-031


title: RNA-seq, PC3, OE SLC6A4, rep#2

description:
Library name: PC3-SLC6A4_OE-2
Deseq2.SLC.anno.csv


title: Patient 10, plasma, healthy, female

description: Library name: 31274-019


title: 16S rRNAseq of stool: 27171_HNStool35

description: Library name: HNStool35


title: RNA-seq, PC3, OE SLC6A4, rep#1

description:
Library name: PC3-SLC6A4_OE-1
Deseq2.SLC.anno.csv


title: Patient 9, plasma, healthy, female

description: Library name: 31274-017


title: 16S rRNAseq of stool: 27116_HNStool34

description: Library name: HNStool34


title: leaf,RNA-seq,WT-WL-3

city: Nanjing

first: Zexue

last: He

state: Jiangsu Province

address: Xuanwu District,1 Weigang

department: Agricultural College

institute: Nanjing Agricultural University

description:
Library name: WT-WL-3
RNA-seq

data_processing:
Raw data were filtered and quality-controlled using the Fastx-Toolkit software. Gene expression was quantified as reads per kilobase per million mapped reads (RPKM). Differential expression analysis was performed using Robinson and Smyth's exact test in the EdgeR package. Genes with FDR-corrected p-values 0.05 and fold changes > 2 were identified as differentially expressed.
Assembly: SolTub_3.0
Supplementary files format and content: FPKM

organism: Solanum tuberosum

source_name: leaf

growth_protocol: The experiment utilized 20-day-old potato plants (Solanum tuberosum L. cv. Atlantic) provided by the Agricultural Biotechnology Research Center, Ningxia Academy of Agriculture and Forestry Sciences. This cultivar was selected for its vigorous growth and broad adaptability. Virus-free plantlets were obtained through tissue culture and subcultured for three generations before experiment. Only plants with uniform growth were selected and transferred to soil, where they were acclimated for 14 days under a 16-h light/8-h dark cycle at 60% relative humidity. The growth environment simulated artificial shading conditions, with temperature maintained at 23-25°C. The experiment was conducted with six plants per treatment group. Light treatments were implemented using combinations of different LED light sources, including white light, blue light (400-499 nm), red light (600-699 nm), and far-red light (700-750 nm). To establish low R:FR conditions, far-red light (peak wavelength 730 nm) was supplemented to white light. For low blue light conditions, white light was passed through two layers of yellow filter (#101, Lee Filters, CA, USA). Light quality and intensity were measured using a HiPoint HR-350 spectrometer (wavelength range: 380-780 nm, accuracy: ±2 nm), and R:FR ratios were calculated according to the method described by Lyu et al [30]. Four light treatments were established to assess plant responses under varying light conditions. The white light treatment (WL) applied full-spectrum white LEDs with peak wavelengths at 450 nm and 570 nm, simulating a daylight-like spectrum. In the low blue light treatment (LBL), white light filtered through yellow filters, reducing blue light intensity to 1.5 μmol·m⁻²·s⁻¹.  For low R:FR treatment (WL+FR), far-red light was added to the white light, resulting in an R:FR ratio of 0.41. The fourth treatment combined WL+FR and LBL, and was referred to as LBL+FR. Photosynthetically active radiation (PAR) was maintained at 500 μmol m⁻²s⁻¹ to observe plant responses during the transition from etiolation to de-etiolation. Light quality parameters were monitored every 2 h throughout a 14-day treatment period， with detailed records of photon flux density (PPFD; 400-750 nm) under each treatment condition

extract_protocol:
Leaf samples were collected with three biological replicates per treatment. Total RNA was extracted from 100 mg of fresh tissue using TRIzol reagent (TransGen Biotech, Beijing, China). RNA integrity was assessed using an Agilent 2100 Bioanalyzer, and only samples with RNA integrity numbers (RINs) > 8.0 were used for library construction. RNA-seq libraries were prepared using 2-5 μg of total RNA, and the constructed libraries had fragment sizes ranging from 250 to 300 bp. Sequencing was performed on the Illumina HiSeq 2000 platform, with a minimum sequencing depth of 6 Gb per sample and paired-end sequencing of 150 bp read length.
Leaf samples were collected with three biological replicates per treatment. Total RNA was extracted from 100 mg of fresh tissue using TRIzol reagent (TransGen Biotech, Beijing, China). RNA integrity was assessed using an Agilent 2100 Bioanalyzer, and only samples with RNA integrity numbers (RINs) > 8.0 were used for library construction. RNA-seq libraries were prepared using 2-5 μg of total RNA, and the constructed libraries had fragment sizes ranging from 250 to 300 bp. Sequencing was performed on the Illumina HiSeq 2000 platform, with a minimum sequencing depth of 6 Gb per sample and paired-end sequencing of 150 bp read length.

value: leaf

value: WT

value: WL


title: RPMI_8226_shN1_1_rep1


title: Chip-seq, input, PC3, OE C, rep#2

description: Library name: PC3-C-2_input


title: leaf,RNA-seq,WT-WL-2

description:
Library name: WT-WL-2
RNA-seq


title: 16S rRNAseq of stool: 26676_HNStool33

description: Library name: HNStool33


title: RNA-seq, PC3, OE DDC, rep#3

description:
Library name: PC3-DDC_OE-3
Deseq2.DDC.anno.csv


title: Patient 8, plasma, healthy, female

description: Library name: 31274-015


title: RNA-seq, PC3, OE DDC, rep#2

description:
Library name: PC3-DDC_OE-2
Deseq2.DDC.anno.csv


title: leaf,RNA-seq,WT-WL-1

description:
Library name: WT-WL-1
RNA-seq


title: RPMI_8226_shNTC_rep2


title: 16S rRNAseq of stool: 26544_HNStool32

description: Library name: HNStool32


title: Patient 7, plasma, healthy, female

description: Library name: 31274-013


title: RNA-seq, PC3, OE DDC, rep#1

description:
Library name: PC3-DDC_OE-1
Deseq2.DDC.anno.csv


title: leaf,RNA-seq,WT-LBL-3

description:
Library name: WT-LBL-3
RNA-seq

value: LBL


title: Patient 6, plasma, healthy, female

description: Library name: 31274-011


title: RNA-seq, PC3, OE C, rep#3

description:
Library name: PC3-C-3
Deseq2.DDC.anno.csv
Deseq2.SLC.anno.csv


title: leaf,RNA-seq,WT-LBL-2

description:
Library name: WT-LBL-2
RNA-seq


title: Patient 5, plasma, healthy, female

description: Library name: 31274-009


title: 16S rRNAseq of stool: 26478_HNStool31

description: Library name: HNStool31


title: RNA-seq, PC3, OE C, rep#2

description:
Library name: PC3-C-2
Deseq2.DDC.anno.csv
Deseq2.SLC.anno.csv


title: leaf,RNA-seq,WT-LBL-1

description:
Library name: WT-LBL-1
RNA-seq


title: Patient 4, plasma, healthy, female

description: Library name: 31274-007


title: Patient 3, plasma, healthy, female

description: Library name: 31274-005


title: RNA-seq, PC3, OE C, rep#1

description:
Library name: PC3-C-1
Deseq2.DDC.anno.csv
Deseq2.SLC.anno.csv


title: 16S rRNAseq of stool: 25587_HNStool28

description: Library name: HNStool28


title: HUVEC (Input)

city: Pilani

first: Syamantak

last: Majumder

state: Rajasthan

address: Vidhya Vihar, 1264 MALVIYA BHAVAN

department: Biological Sciences

country: India

institute: BITS Pilani, Pilani Campus

description: Library name: HUVEC, Input

data_processing:
Raw sequencing data (FASTQ files) underwent quality control, assessing base quality score distribution and average base content per read.
Low-quality bases and reads were removed using Trimmomatic v0.39.
High-quality paired-end reads were aligned to the hg38 human reference genome using BWA-MEM v0.7.12.
Peaks were called using MACS2 v2.1.3 with the significance cut-off p-value < 0.05 to generate narrowPeak and bed files
narrow
Assembly: hg38
Supplementary files format and content: bed, narrowPeak (except for Input sample)
Library strategy: CUT&Run

source_name: Umbilical Vein

growth_protocol: Human Umbilical Vein Endothelial Cells (HUVEC; #CL002, HiMedia Laboratories) were cultured using the Endothelial Cell Expansion Medium (#AL517, HiMedia) supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin. Cells were maintained at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
HUVEC, either untreated (control) or treated with TNF-α (10 ng/ml) for 4 h, were subjected to Cleavage Under Targets & Release Using Nuclease (CUT&RUN) using the CUT&RUN Assay Kit (#86652, Cell Signaling Technology) following the manufacturer's instructions. Cells from three independent biological replicates were pooled and crosslinked before being bound to Concanavalin A-coated magnetic beads. The cells were then permeabilized with Digitonin and incubated overnight at 4°C with H3K79me3 Rabbit mAb (1:50; #74073, Cell Signaling Technology). Chromatin-bound antibodies were targeted by pAG-MNase, and enzymatic digestion was initiated with calcium chloride. The resulting DNA fragments were incubated at 37°C to release enriched chromatin. Input DNA was prepared in parallel. DNA from both input and CUT&RUN-enriched samples was purified using the DNA Purification Buffers and Spin Columns Kit (#14209, Cell Signaling Technology).
Input and H3K79me3-enriched DNA were processed using the NEBNext® Ultra™ II DNA Library Preparation Kit (#E7103, New England Biolabs) according to the manufacturer's protocol. Briefly, DNA samples were subjected to end repair and dA-tailing, followed by ligation with sequencing adapters. Adapter-ligated fragments were size-selected using SPRIselect magnetic beads (Beckman Coulter) to enrich for appropriate fragment lengths. Size-selected products were then amplified by limited-cycle PCR to incorporate unique index sequences and generate the final libraries. Library quality and quantity were assessed using a Bioanalyzer (Agilent Technologies) and Qubit Fluorometer (Thermo Fisher Scientific). High-throughput paired-end sequencing (2 x 150 bp) was performed on an Illumina NovaSeq 6000 platform (v1.5).

treatment_protocol: Serum-starved (1 h) HUVEC were treated with or without TNF-α (10 ng/ml) for 4 h.

value: Umbilical Vein

value: HUVEC

value: Endothelial Cell


title: leaf,RNA-seq,WT-FR-2

description:
Library name: WT-FR-2
RNA-seq

value: FR


title: Patient 2, plasma, healthy, female

description: Library name: 31274-003


title: HUVEC_TNF-4h, H3K79me3 (CUT&RUN)

description: Library name: HUVEC_TNF-4h, CUT_RUN

value: TNF-α


title: Patient 1, plasma, healthy, female

description: Library name: 31274-001

value: Plasma


title: 16S rRNAseq of stool: 25367_HNStool26

description: Library name: HNStool26

value: stool


title: leaf,RNA-seq,WT-FR-1

description:
Library name: WT-FR-1
RNA-seq


title: 16S rRNAseq of stool: 25466_HNStool27

description: Library name: HNStool27


title: HUVEC_Control, H3K79me3 (CUT&RUN)

description: Library name: HUVEC_Control, CUT_RUN


title: 16S rRNAseq of stool: 26082_HNStool30

description: Library name: HNStool30


title: leaf,RNA-seq,WT-FL-3

description:
Library name: WT-FL-3
RNA-seq

value: FL


title: H3K27me3 ChIP-seq of KO mouse

city: Toyama

first: Jun-Dal

last: Kim

state: Toyama

address: 2630 Sugitani

department: Department of Complex Biosystem Research (CBR), Institute of National Medicine (INM)

country: Japan

institute: University of Toyama

description: Library name: KO ChIP

data_processing:
Enrichment of H3K27me3 visualized by UCSC (University of California Santa Cruz) genomic browser track.
Assembly: GRCm38/mm10
Supplementary files format and content: Excel file includes raw read counts.

organism: Mus musculus

source_name: Gastrocnemius muscles

growth_protocol: C57BL/6N mice were obtained from Japan SLC Inc. (Shizuoka, Japan). NADS KO mice were obtained from the International Mouse Phenotyping Consortium (MMRRC:048728-UCD). MLC1f-Cre mice were described elsewhere (Genesis 26, 165-166 (2000)).

extract_protocol:
ChIP-sequencing was performed by Active motif (Carlsbad, CA, USA) using young WT and NADS KO gastrocnemius muscles. Muscles were mechanically homogenized and after fixation with 1% formaldehyde quenched with glycine. Lysis buffer was used to isolate the chromatin. Lysates were sonicated to sheared DNA with an average length of 300-500 bp with Active Motif’s PIXUL® Multi-Sample Sonicator. Isolated chromatin was treated with RNase, proteinase K, and heat for de-crosslinking to yield Genomic DNA. Quantification was performed by Qubit Flex Fluorometer (Thermo Fisher Scientific, Inc., MA, USA). Chromatin aliquot of 30 µg, spiked-in with 35 µl of Drosophila chromatin was precleared to remove nonspecific ligands and proteins via protein G coupled agarose beads (Invitrogen, MA, USA). Genomic DNA regions of interest were isolated using 4 µl of antibody against H3K27me3 (Active Motif). Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 °C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.
ChIP sequencing libraries were quantified and sequenced on Illumina’s NovaSeq 6000.

value: Gastrocnemius muscles

tag: chip antibody

value: H3K27me3 (Active Motif, #39155)


title: 16S rRNAseq of stool: 25147_HNStool24

description: Library name: HNStool24


title: HCC_CDX_DMSO_replicate3

city: Grand Rapids

first: Bin

state: Michigan

address: 400 Monroe Ave NW

department: Department of Pediatrics and Human Development

institute: MICHIGAN STATE UNIVERSITY

description: Library name: DMSO3

data_processing:
RNA-Seq reads were mapped on hg38  transcriptome using the ENSEMBL GRCh38  annotation with the STAR aligner and further processed using RSEM.
Assembly: hg38
Supplementary files format and content: comma-separated file includes Human ensembl_gene_id as rows and log2 transformed TPM values for each sample as columns.

source_name: Huh7 xenograft

growth_protocol: Subcutaneous Huh7 xenograft mouse model was constructed in 6 to 10 weeks old male NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ mice (Strain #:005557, RRID:IMSR_JAX:005557).

extract_protocol:
The tumor tissues were resected.  Total RNA was extracted from tumor tissues using RNeasy Plus Mini Kit (cat# 74136, Qiagen).
RNA libraries for RNA-seq were prepared using by the Genomics Core at the Van Andel Institute using  total RNA

treatment_protocol: 1 ug compound MSU45302 (dissolved in  DMSO, 20ug/ml) was administrated via intratumor injection every 3 days for two weeks.

tag: disease

value: HCC

value: Huh7 xenograft

value: DMSO


title: leaf,RNA-seq,WT-FL-2

description:
Library name: WT-FL-2
RNA-seq

value: leaf


title: 16S rRNAseq of stool: 25235_HNStool25

description: Library name: HNStool25


title: HCC_CDX_DMSO_replicate2

description: Library name: DMSO2


title: 16S rRNAseq of stool: 25092_HNStool23

description: Library name: HNStool23


title: HCC_CDX_DMSO_replicate1

description: Library name: DMSO1


title: leaf,RNA-seq,WT-FL-1

description:
Library name: WT-FL-1
RNA-seq

value: WT


title: leaf,RNA-seq,WT-FR-3

description:
Library name: WT-FR-3
RNA-seq


title: Pooled_Input

description: Library name: Input


title: D6TAZ_TEAD4_2

city: Yuseong-gu, Daejeon-si

first: Taejun

last: Seol

address: 291, Daehak-ro

country: South Korea

institute: Korea Advanced Institute of Science and Technology (KAIST)

description:
Library name: D6TAZ_TEAD4_2
TEAD4 ChIP-seq at differentiation day 6 with TAZ2SA activation

data_processing:
Prepared libraries were sequenced on a NovaSeq 6000 with paired-end method. (100bp reads)
ChIP-seq reads were trimmed using Trim Galore (v0.6.7) and aligned to the UCSC mm10 genome using Bowtie2 (v2.4.4)
Duplicates were removed using Picard MarkDuplicates (v2.26.3.)
Peaks were called using MACS3 (v3.0.0b1) with q-value cut-off 0.05 (PPARγ, TAZ) or 0.005 (H3K27ac).
BedGraph files were generated from -B parameter of MACS3 and local bias-substracted files were converted to bigWig files with bedGraphToBigwig (v4).
Assembly: mm10
Supplementary files format and content: BED(narrowPeak) files of ChIP-seq peaks or bigwig files of normalized coverage of input reads (generated using bamCoverage function of deeptools2 v3.5.1)

extract_protocol:
Cells were subjected to cross-linking with 1.5% formaldehyde for 10 min, and nuclear extracts were subjected to ultrasonic treatment followed by immunoprecipitation overnight at 4°C with antibodies to TAZ (560235, BD Biosciences), to PPARγ (2443S, Cell Signaling), or to H3K27ac (ab4729, Abcam) or with control mouse immunoglobulin G (sc-2025, Santa Cruz Biotechnology), of which had been prebound to Dynabeads Protein A (10001D, Thermo Fisher).
Antibody-bound chromatin fragments were subjected to Tn5 tagmentation with the use of TDE1 Tagment DNA Enzyme (20034197, Illumina), as described previously (Schmidl et al. Nature Methods 2015).

treatment_protocol: For induction of adipocyte differentiation, confluent C3H10T1/2 cells were stimulated for 2 days with an adipogenic cocktail consisting of 1 μM dexamethasone (D4902, Sigma), insulin at 5 µg/ml (I0516, Sigma), 500 μM isobutylmethylxanthine (I5879, Sigma), and 1 μM rosiglitazone (R2408, Sigma). After 2 days, adipogenic medium was then changed to a maintenance medium (culture medium supplemented with insulin at 5 µg/ml). For activation of ERT2-TAZ, Cells were treated with 1 µM 4-OHT (H6278, Sigma) for 24 h.

value: mesenchymal stem cells

value: Tamoxifen-inducible TAZ2SA

value: Adipogenic cocktail + 4-OHT


title: 16S rRNAseq of stool: 24344_HNStool22

description: Library name: HNStool22


title: H3K27me3 ChIP-seq of WT mouse

description: Library name: WT ChIP


title: D39_WB

city: Fujimino

first: Miyuki

last: Nakamura

state: Saitama

institute: KDDI research Inc

description: Library name: D39_WB

data_processing:
The raw data underwent quality filtering based on sequence quality using FastQC (v0.11.7). After trimming with Trimmomatic (v0.38), the remaining reads were mapped to a reference genome using Methylpy (v1.4.2). TDF files were generated using igvtools.
Assembly: CanFam3.1
Supplementary files format and content: TDF format for DNA methylation levels at base resolution.

organism: Canis lupus familiaris

source_name: whole blood

extract_protocol:
Genomic DNA was extracted from whole blood using the DNeasy Blood and Tissue Kit (QIAGEN), according to the manufacturer’s protocol.
The bisulfite conversion process was performed using the Zymo Research EZ DNA Methylation Gold Kit. For library preparation, the ABclonal Scale Methyl-DNA Lib Prep Kit was utilized. The conversion process, library preparations, and sequencing were performed externally at Novogene.

value: whole blood

value: Shiba


title: D6TAZ_TEAD4_1

description:
Library name: D6TAZ_TEAD4_1
TEAD4 ChIP-seq at differentiation day 6 with TAZ2SA activation


title: HCC_CDX_S302_replicate3

description: Library name: S3023

value: Compound MSU45302


title: D40_WB

description: Library name: D40_WB

value: Poodle (Toy)


title: 16S rRNAseq of stool: 24267_HNStool21

description: Library name: HNStool21


title: HCC_CDX_S302_replicate2

description: Library name: S3022


title: 16S rRNAseq of stool: 24256_HNStool20

description: Library name: HNStool20


title: D37_WB

description: Library name: D37_WB

value: Pug


title: D38_WB

description: Library name: D38_WB

value: Norfolk Terrier


title: IPF297_DMSO

description: Library name: S297D5

source_name: Lung

extract_protocol:
Lung slices were homogenized in TRIzol™ Reagent (15596026, Invitrogen, Waltham, MA, USA) and treated with chloroform to extract RNA. The resulting aqueous phase was transferred to a clean tube, and an equal volume of 70% ethanol was added. The mixture was then loaded onto a column for RNA extraction and purification using the RNeasy Mini Kit (74104, QIAGEN, Hilden, Germany), following the manufacturer’s protocol. RNA concentration was measured using a NanoDrop™ OneC Microvolume UV-Vis Spectrophotometer (840274200, Thermo Scientific, Waltham, MA, USA). RNA samples were subsequently submitted to the Genomics Core at the Van Andel Institute for bulk RNA sequencing on an Illumina NovaSeq 6000.
RNA libraries for RNA-seq were prepared using by the Genomics Core at the Van Andel Institute using  total RNA

treatment_protocol: A piece of the left upper lobe, where active fibrosis occurs, of the IPF lung explants were inflated using an appropriate volume of liquified low melting point agarose solution in physiological DMEM+F-12 media (1:1) supplemented with 0.5 % FBS, 20 µg/ ml Gentamycin, and 0.5 µg/ ml and Amphotracin B, prepared as 2% W/V solution.  The inflated lungs were then cooled in ice to set the agarose and stiffen before slicing. PCLS were cut at a thickness of 400 µm with a vibrating tissue slicer (VF-510-0Z vibratome, Precisionary Instruments, San Jose, CA). The slices were treated with 10 µM concentrations of Pyrithyldione, in DMEM+F-12 media (1:1) supplemented with 0.5 % FBS, 20 µg/ ml Gentamycin, and 0.5 µg/ ml and Amphotracin B, with corresponding DMSO-treated groups serving as controls. Treatments were performed under standard culture conditions for 72 h, with fresh drug solutions changed daily over the 3 days. PCLS were harvested and stored at -80°C until analysis.

tag: donor id

value: IPF

tag: batch

value: Lung


title: D36_WB

description: Library name: D36_WB


title: 16S rRNAseq of stool: 23948_HNStool18

description: Library name: HNStool18

value: stool


title: IPF297_Drug

description: Library name: S2975

value: Pyrithyldione


title: 16S rRNAseq of stool: 24245_HNStool19

description: Library name: HNStool19


title: 16S rRNAseq of stool: 23882_HNStool17

description: Library name: HNStool17


title: IPF296_DMSO

description: Library name: S296D5


title: 16S rRNAseq of stool: 25851_HNStool29

description: Library name: HNStool29


title: 16S rRNAseq of stool: 23552_HNStool16

description: Library name: HNStool16


title: IPF296_Drug

description: Library name: S2965


title: PFC, sleep deprived male mice 3

city: Iowa City

first: Junko

last: Kasuya

state: IA

address: 169 Newton Rd

department: Neuroscience and Pharmacology

institute: University of Iowa

description:
Library name: PFC-SD3
10X Genomics

library_source: transcriptomic single cell

data_processing:
The fastq data were processed and analyzed using Illumina Partek Flow.
Assembly: mm39
Supplementary files format and content: Hierarchical Data Format 5 or h5 containing feature names and counts

molecule: nuclear RNA

source_name: prefrontal cortex

growth_protocol: Mice were maintained on a 12h light/12h dark cycle at 22-25 C. Food and water were available ad libitum.

extract_protocol:
Hippocampus or Prefrontal cortex were extracted immediately after the 5 hours of SD and flash-frozen in liquid nitrogen. Nuclei were extracted using 10x Genomics Chromium Nuclei Isolation with RNase Inhibitor Kit.  Extracted nuclei were further isolated by FANS.
The libraries were constructed by using Chromium GEM-X Single Cell 3’ Library Preparation Kit V3.1.

treatment_protocol: 11-12-week-old littermate males with one copy of the Aldh1l1-cre and the Sun1/sfGFP transgenes were single-housed for five days prior to the experiment day.  SD animals were subjected to an acute SD starting at ZT0 for 5 hours. NSD animals stayed in home cages.

value: prefrontal cortex

value: Sun1-sfGFP/+; Aldh1l1-cre/+

value: sleep deprived


title: PFC, sleep deprived male mice 2R

description:
Library name: PFC-SD2R
10X Genomics


title: PFC, non sleep deprived male mice 3

description:
Library name: PFC-NSD3
10X Genomics

value: non sleep deprived


title: PFC, sleep deprived male mice 1

description:
Library name: PFC-SD1
10X Genomics


title: PFC, sleep deprived male mice 2

description:
Library name: PFC-SD2
10X Genomics


title: D29_WB

description: Library name: D29_WB


title: 16S rRNAseq of stool: 23321_HNStool15

description: Library name: HNStool15


title: HCC_CDX_S302_replicate1

description: Library name: S3021

value: HCC

value: Huh7 xenograft


title: PFC, non sleep deprived male mice 1

description:
Library name: PFC-NSD1
10X Genomics


title: D31_WB

description: Library name: D31_WB

value: Yorkshire Terrier


title: D30_WB

description: Library name: D30_WB

value: whole blood

value: Shetland Sheepdog


title: IPF294_DMSO

description: Library name: S294D5

value: DMSO

value: WT


title: PFC, non sleep deprived male mice 2

description:
Library name: PFC-NSD2
10X Genomics


title: IPF294_Drug

description: Library name: S2945


title: 16S rRNAseq of stool: 22815_HNStool14

description: Library name: HNStool14


title: D28_WB

description: Library name: D28_WB

value: Shiba


title: 16S rRNAseq of stool: 22694_HNStool13

description: Library name: HNStool13


title: HPC, sleep deprived male mice 2

description:
Library name: HPC-SD2
10X Genomics

source_name: hippocampus

value: hippocampus


title: IPF322_DMSO

description: Library name: S322D5

value: IPF


title: D32_WB

description: Library name: D32_WB

value: Papillon


title: D25_WB

description: Library name: D25_WB

value: Poodle (Standard)


title: HPC, sleep deprived male mice 1

description:
Library name: HPC-SD1
10X Genomics


title: 16S rRNAseq of stool: 22595_HNStool12

description: Library name: HNStool12

value: stool


title: D24_WB

description: Library name: D24_WB

value: Boston Terrier


title: IPF322_Drug

description: Library name: S3225

value: Lung

value: Pyrithyldione


title: HPC, non sleep deprived male mice 2

description:
Library name: HPC-NSD2
10X Genomics

value: Sun1-sfGFP/+; Aldh1l1-cre/+

value: non sleep deprived


title: 16S rRNAseq of stool: 22485_HNStool11

description: Library name: HNStool11


title: IPF318_DMSO

description: Library name: S318D5


title: IPF318_Drug

description: Library name: S3185


title: D22_WB

description: Library name: D22_WB

value: Cavalier King Charles Spaniel


title: HPC, non sleep deprived male mice 1

description:
Library name: HPC-NSD1
10X Genomics


title: 16S rRNAseq of stool: 22078_HNStool10

description: Library name: HNStool10


title: D23_WB

description: Library name: D23_WB

value: Dachshund (Miniature)


title: 16S rRNAseq of stool: 22056_HNStool09

description: Library name: HNStool09


title: Patient 23, plasma, healthy, female

description: Library name: 31274-043

value: Plasma

value: BRCA wild-type


title: 16S rRNAseq of stool: 22001_HNStool08

description: Library name: HNStool08


title: Spinal cord nuclei, Sedentary and Trained, Timepoints PRE and 6h

city: Basel

first: Shivani

last: Mansingh

address: Spitalstrasse 41

country: Switzerland

institute: Biozentrum, University of Basel

description:
Library name: SED-TRAIN-PRE-6H
probe-based RNA profiling (10X Genomics Flex)

data_processing:
Demultiplexing and generation of feature-barcode matrix was done using the multi pipeline of CellRanger version 7.1.0 and the mouse reference genome GRCm39/mm10.
Assembly: Mouse mm10
Supplementary files format and content: Unfiltered feature-barcode matrices as h5-file

source_name: Spinal Cord

extract_protocol:
Spinal cords were dissected and snap-frozen in liquid nitrogen. Nuclei were isolated from frozen, lumar regions of the tissue in lysis buffer using a dounce-based homogenizer. The suspension was filtered before fixation for 1 h at room temperature with the 10X Genomics Fixation Kit. Fixed nuclei were stained for DAPI to enable FACS-based separation of single nuclei from debris and duplets. Sorted nuclei were cryopreserved until sequencing library preparation.
SnRNA-Seq libraries were generated with the Chromium Next GEM Fixed RNA Kit according to the manufacturer’s instructions (10X Genomics, User Guide Rev D, CG000522). 16 samples were multiplexed per run.

treatment_protocol: Training paradigm: 6 weeks of voluntary access to running wheels. Acute exercise bout: Forced running on a treadmill with increasing speed at 10° incline until exhaustion is reached.

value: Spinal Cord

value: all spinal cord nuclei

value: sedentary control and acute exercise

tag: age

value: 17 weeks

tag: Sex

value: male


title: Spinal cord nuclei, Sedentary and Trained, Timepoint 24h

description:
Library name: SED-TRAIN-24H
probe-based RNA profiling (10X Genomics Flex)


title: IPF295_Drug

description: Library name: S2955

value: IPF

value: WT


title: D20_WB

description: Library name: D20_WB

value: whole blood

value: Poodle (Toy)


title: 16S rRNAseq of stool: 21858_HNStool07

description: Library name: HNStool07

value: stool


title: D21_WB

description: Library name: D21_WB

value: French Bulldog


title: D19_WB

description: Library name: D19_WB

value: Chihuahua


title: PANC1_7.5_b

city: London

first: Eleni

last: Maniati

address: John Vane Science Centre, Charterhouse Square

department: Barts Cancer Institute

country: United Kingdom

institute: Queen Mary University of London

description: PANC1 GelMA 7.5% replicate 2

data_processing:
RNA-Seq reads were mapped to the human genome (hg38, Genome Reference Consortium GRCh38)  using using HISAT2 version 2.1.0
Number of reads aligned to the exonic region of each gene were counted using htseq-count based on the Ensembl annotation.
Genes that achieved at least one read count per million reads (CPM) in at least 25% of the samples were kept.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file includes log2 rpkm values for each sample

source_name: PDAC cell line

growth_protocol: BXPC3 (ATCC CRL-1687) and PANC1 (ATCC CRL-1469) cells were grown in high glucose Dulbecco’s Modified Eagle Medium (DMEM), supplemented with 10% foetal bovine serum (FBS) and 1% penicillin/streptomycin (P/S).

extract_protocol:
RNA extracted using a RNeasy mini kit. RNA Integrity Number (RIN) was measured using an Agilent high sensitivity D1000 screen tape system.
Extracted RNA samples were sent to the Oxford Genomics Centre for processing. Library preps were made using Poly-A capture.

value: pancreatic cancer

tag: culture substrate

value: 7.5% GelMA


title: PANC1_7.5_a

description: PANC1 GelMA 7.5% replicate 1


title: 16S rRNAseq of stool: 21011_HNStool06

description: Library name: HNStool06


title: Taf5l_sgRNA1

city: Philadelphia

first: Michael

last: Haney

state: PA

address: 422 Curie Boulevard

institute: University of Pennsylvania, Perelman School of Medicine, Department of Pathology

description: Library name: Taf5l_sgRNA1

library_source: genomic single cell

data_processing:
Raw gene counts were obtained by aligning reads to the mouse genome using CellRanger software (v.4.0.0) (10x Genomics). For quality control, cells with unique feature counts over 2,500 or less than 200 were removed as well as cells that have >5% mitochondrial counts. Ambient cell free mRNA contamination was removed using SoupX for each individual sample. Multiplets were filtered out using DoubletFinder. The core statistical parameters of DoubletFinder (nExp and pK) used to build artificial doublets for true doublet classification were determined automatically using recommended settings. The SCTransform-based integration workflow of Seurat was used to align data, using default settings. In brief, the integration workflow searches for common gene modules (anchors) in cells with similar transcriptomes. Individual samples after undergoing quality control are integrated in a stepwise fashion, using cellular sequencing depth as a covariate to mitigate technical artifacts. After combining the samples into a single dataset or Seurat object, genes were projected into principal component space using the principal component analysis (RunPCA). The first 100 dimensions were used as inputs into the FindNeighbours, FindClusters and RunUMAP functions of Seurat. In brief, a shared-nearest-neighbor graph was constructed based on the Euclidean distance metric in principal component space, and cells were clustered using the Louvain method. RunUMAP functions with default settings were used to calculate 2D UMAP coordinates and search for distinct cell populations. Distinct cell populations were annotated based on conical marker genes. Monocle3 (v.0.2.1.) was used to generate the pseudotime trajectory analysis of HSCs. Cells were re-clustered as described in and used as input into Monocle to infer cluster and lineage relationships within a given cell type. Specifically, UMAP embeddings and cell subclusters generated from Seurat were converted to a cell_data_set object using SeuratWrappers (v.0.2.0) and then used as input to perform trajectory graph learning and pseudotime measurement through reversed graph embedding with Monocle. Cell cycle analysis was performed in Seurat using a list of cell cycle markers from Tirosh et al43. Differential gene expression was performed in Seurat using the MAST package under default conditions.
Assembly: mm10
Supplementary files format and content: barcodes.tsv.g,features.tsv.gz,

source_name: Bone marrow

extract_protocol:
At day-14 post-electroporation, control, Tada2b-KO, or Taf5l-KO HSC cultures were collected for RNA-seq analysis using a Gene Expression kit v3 (10x Genomics) according to the manufacturer’s protocol with libraries sequenced on a NovaSeq 6000 S4 (Illumina).
At day-14 post-electroporation, control, Tada2b-KO, or Taf5l-KO HSC cultures were collected for RNA-seq analysis using a Gene Expression kit v3 (10x Genomics) according to the manufacturer’s protocol with libraries sequenced on a NovaSeq 6000 S4 (Illumina).

value: Bone marrow

value: HSPC


title: PANC1_5_b

description: PANC1 GelMA 5% replicate 2

value: 5% GelMA


title: D18_WB

description: Library name: D18_WB

value: Golden Retriever


title: Tada2b_sgRNA3

description: Library name: Tada2b_sgRNA3


title: 16S rRNAseq of stool: 20670_HNStool05

description: Library name: HNStool05


title: Tada2b_sgRNA1

description: Library name: Tada2b_sgRNA1


title: IPF295_DMSO

description: Library name: S295D5

value: Lung

value: DMSO


title: PANC1_5_a

description: PANC1 GelMA 5% replicate 1


title: PANC1_COL_b

description: PANC1 collagen replicate 2

value: collagen


title: control2

description: Library name: control2


title: D15_WB

description: Library name: D15_WB

value: Bichon Frise


title: control1

description: Library name: control1


title: 16S rRNAseq of stool: 20285_HNStool03

description: Library name: HNStool03


title: 16S rRNAseq of stool: 20274_HNStool02

description: Library name: HNStool02


title: Taf5l_sgRNA3

description: Library name: Taf5l_sgRNA3


title: PANC1_COL_a

description: PANC1 collagen replicate 1


title: BxPC3_7.5_b

description: BXPC3 GelMA 7.5% replicate 2


title: 16S rRNAseq of vaginal swab: 31560_Hnvaginal48

description: Library name: Hnvaginal48

source_name: vaginal swab

extract_protocol:
Vaginal samples were transferred to a 2 ml tube containing 200 mg of 106/500μm glass beads (Sigma, St. Louis, MO) and 0.5 ml of Qiagen PM1 buffer (Valencia, CA). Mechanical lysis was performed for 40 minutes on a Digital Vortex Mixer. After a 5 minute centrifugation, 0.45 ml of supernatants was aspirated and transferred to a new tube containing 0.15 ml of Qiagen IRS solution. The suspension was incubated at 4°C overnight. After a 5 minute centrifugation, supernatant was aspirated and transferred to deep well plates containing 0.45 ml of Qiagen binding buffer supplemented with Qiagen ClearMag Beads. DNA was purified using the automated KingFisher™ Flex Purification System and eluted in DNase free water.  12.5 ng of total DNA were amplified using universal primers targeting the V4 region of the bacterial 16S rRNA gene. Primer sequences contained overhang adapters appended to the 5’ end of each primer for compatibility with Illumina sequencing platform. The primers used were F515/R806. Master mixes contained 12.5 ng of total DNA, 0.5 µM of each primer and 2x KAPA HiFi HotStart ReadyMix (KAPA Biosystems, Wilmington, MA). The thermal profile for the amplification of each sample had an initial denaturing step at 95°C for 3 minutes, followed by a cycling of denaturing of 95°C for 30 seconds, annealing at 55°C for 30 seconds and a 30 second extension at 72°C (25 cycles), a 5 minute extension at 72°C and a final hold at 4°C. Each 16S amplicon was purified using the AMPure XP reagent (Beckman Coulter, Indianapolis, IN). In the next step each sample was amplified using a limited cycle PCR program, adding Illumina sequencing adapters and dual‐index barcodes (index 1(i7) and index 2(i5)) (Illumina, San Diego, CA) to the amplicon target. The thermal profile for the amplification of each sample had an initial denaturing step at 95°C for 3 minutes, followed by a denaturing cycle of 95°C for 30 seconds, annealing at 55°C for 30 seconds and a 30 second extension at 72°C (8 cycles), a 5 minute extension at 72°C and a final hold at 4°C. The final libraries were again purified using the AMPure XP reagent (Beckman Coulter), quantified and normalized prior to pooling. The DNA library pool was then denatured with NaOH, diluted with hybridization buffer and heat denatured.
Samples were transferred to a 2 ml tube containing 200 mg of 106/500μm glass beads (Sigma, St. Louis, MO) and 0.5 ml of Qiagen PM1 buffer (Valencia, CA). Mechanical lysis was performed for 40 minutes on a Digital Vortex Mixer. After a 5 minute centrifugation, 0.45 ml of supernatants was aspirated and transferred to a new tube containing 0.15 ml of Qiagen IRS solution. The suspension was incubated at 4°C overnight. After a 5 minute centrifugation, supernatant was aspirated and transferred to deep well plates containing 0.45 ml of Qiagen binding buffer supplemented with Qiagen ClearMag Beads. DNA was purified using the automated KingFisher™ Flex Purification System and eluted in DNase free water.  12.5 ng of total DNA were amplified using universal primers targeting the V4 region of the bacterial 16S rRNA gene. Primer sequences contained overhang adapters appended to the 5’ end of each primer for compatibility with Illumina sequencing platform. The primers used were F515/R806. Master mixes contained 12.5 ng of total DNA, 0.5 µM of each primer and 2x KAPA HiFi HotStart ReadyMix (KAPA Biosystems, Wilmington, MA). The thermal profile for the amplification of each sample had an initial denaturing step at 95°C for 3 minutes, followed by a cycling of denaturing of 95°C for 30 seconds, annealing at 55°C for 30 seconds and a 30 second extension at 72°C (25 cycles), a 5 minute extension at 72°C and a final hold at 4°C. Each 16S amplicon was purified using the AMPure XP reagent (Beckman Coulter, Indianapolis, IN).
In the next step each sample was amplified using a limited cycle PCR program, adding Illumina sequencing adapters and dual‐index barcodes (index 1(i7) and index 2(i5)) (Illumina, San Diego, CA) to the amplicon target. The thermal profile for the amplification of each sample had an initial denaturing step at 95°C for 3 minutes, followed by a denaturing cycle of 95°C for 30 seconds, annealing at 55°C for 30 seconds and a 30 second extension at 72°C (8 cycles), a 5 minute extension at 72°C and a final hold at 4°C. The final libraries were again purified using the AMPure XP reagent (Beckman Coulter), quantified and normalized prior to pooling. The DNA library pool was then denatured with NaOH, diluted with hybridization buffer and heat denatured.

value: vaginal swab


title: BxPC3_7.5_a

description: BXPC3 GelMA 7.5% replicate 1


title: D16_WB

description: Library name: D16_WB

value: Shiba


title: 16S rRNAseq of vaginal swab: 31252_Hnvaginal47

description: Library name: Hnvaginal47


title: Mouse_Stomach_tissue_WT_scMultiome DNA

city: Daejeon

first: Bon-Kyoung

last: Koo

state: Yuseong-gu

address: Expo-ro 55

department: Center for genome engineering

institute: Institute for Basic Science

description: Library name: Mouse_Stomach_tissue_WT_scMultiome DNA

data_processing:
To generate count matrices consist of both gene expression and chromatin peaks for each organoid sample such as Rnf43/Znrf3 double knock-out (RZ), and Kras activated RZ-DKO (RZK), cellranger-ARC count (v2.1.0) was utilized with default option and mouse reference (‘refdata-cellranger-arc-mm10-2020-A-2.0.0’) provided in 10x Genomics. Based on both Signac (v1.8.0) and Seurat (v4.1.0) pipelines, we generated analytic objects from ‘filtered_feature_bc_matrix’ and ‘atac_fragments.tsv.gz’ of cellranger based on mouse genome which is output from ‘GetGRangesFromEnsDb’ with ‘EnsDb.Mmusculus.79’ for annotations. We filtered out poor-quality cell nuclei with unique molecular identifiers (UMIs) for RNA less than 1,000 and more than 25,000, and for ATAC less than 1,000 and more than 100,000, percent mitochondrial genes more than 15%, and nucleosome signal more than 3 for both samples. Using the selected nulei, we sequentially conducted NormalizeData (lognormalization) and FindVariableFeatures (‘vst’ method, 2,000 features) functions for RNA expression profiles. We also implemented FindTopFeatures with min.cutoff is ‘q0’, RunTFIDF, and RunSVD for both ATAC and macs2 assays for peak profiles from Signac package.
Stomach tissue snMultiome data were processed using the Seurat (v4.1.0) pipeline. Raw and filtered matrices were obtained from the Cell Ranger ARC (v2.1.0) output using ‘Read10X_h5’. Ambient RNA contamination was corrected using SoupX (v1.6.2), and the corrected RNA count matrix was used to construct the Seurat object for downstream analysis. We filtered out low-quality nuclei with nFeature_RNA less than 300 or greater than 3,000, total UMI counts exceeding 10,000, or mitochondrial RNA fraction above 5%. Using the selected nuclei, we sequentially conducted ‘NormalizeData’ (log-normalization), ‘FindVariableFeatures’ (‘vst’ method, 2,000 features), ‘ScaleData’, ‘RunPCA’ with 30 principal components (PCs), ‘RunUMAP’ using the PCA reduction, and ‘FindNeighbors’. Clustering was performed using the Louvain algorithm with a resolution of 0.9. Doublets were identified and removed using the DoubletFinder (v2.0.6)R package with default settings.
Assembly: mm10
Supplementary files format and content: hdf5: RNA+ATAC matrices
Supplementary files format and content: tsv: atac_fragments information

source_name: Stomach

extract_protocol:
Single-cell dissociation was carried out by incubating mechanically disrupted organoids and tissue with TrypLE for 30 min at 37 o C. Nuclei from single cells were extracted.
Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits scMultiome (RNA + ATAC)

value: Stomach

value: multiple

value: WT


title: Mouse_Stomach_tissue_WT_scMultiome RNA

description: Library name: Mouse_Stomach_tissue_WT_scMultiome RNA


title: 16S rRNAseq of stool: 20648_HNStool04

description: Library name: HNStool04

extract_protocol:
Fecal samples were transferred to a 2 ml tube containing 200 mg of 106/500μm glass beads (Sigma, St. Louis, MO) and 0.5 ml of Qiagen PM1 buffer (Valencia, CA). Mechanical lysis was performed for 40 minutes on a Digital Vortex Mixer. After a 5 minute centrifugation, 0.45 ml of supernatants was aspirated and transferred to a new tube containing 0.15 ml of Qiagen IRS solution. The suspension was incubated at 4°C overnight. After a 5 minute centrifugation, supernatant was aspirated and transferred to deep well plates containing 0.45 ml of Qiagen binding buffer supplemented with Qiagen ClearMag Beads. DNA was purified using the automated KingFisher™ Flex Purification System and eluted in DNase free water.  12.5 ng of total DNA were amplified using universal primers targeting the V4 region of the bacterial 16S rRNA gene. Primer sequences contained overhang adapters appended to the 5’ end of each primer for compatibility with Illumina sequencing platform. The primers used were F515/R806. Master mixes contained 12.5 ng of total DNA, 0.5 µM of each primer and 2x KAPA HiFi HotStart ReadyMix (KAPA Biosystems, Wilmington, MA). The thermal profile for the amplification of each sample had an initial denaturing step at 95°C for 3 minutes, followed by a cycling of denaturing of 95°C for 30 seconds, annealing at 55°C for 30 seconds and a 30 second extension at 72°C (25 cycles), a 5 minute extension at 72°C and a final hold at 4°C. Each 16S amplicon was purified using the AMPure XP reagent (Beckman Coulter, Indianapolis, IN). In the next step each sample was amplified using a limited cycle PCR program, adding Illumina sequencing adapters and dual‐index barcodes (index 1(i7) and index 2(i5)) (Illumina, San Diego, CA) to the amplicon target. The thermal profile for the amplification of each sample had an initial denaturing step at 95°C for 3 minutes, followed by a denaturing cycle of 95°C for 30 seconds, annealing at 55°C for 30 seconds and a 30 second extension at 72°C (8 cycles), a 5 minute extension at 72°C and a final hold at 4°C. The final libraries were again purified using the AMPure XP reagent (Beckman Coulter), quantified and normalized prior to pooling. The DNA library pool was then denatured with NaOH, diluted with hybridization buffer and heat denatured.
Samples were transferred to a 2 ml tube containing 200 mg of 106/500μm glass beads (Sigma, St. Louis, MO) and 0.5 ml of Qiagen PM1 buffer (Valencia, CA). Mechanical lysis was performed for 40 minutes on a Digital Vortex Mixer. After a 5 minute centrifugation, 0.45 ml of supernatants was aspirated and transferred to a new tube containing 0.15 ml of Qiagen IRS solution. The suspension was incubated at 4°C overnight. After a 5 minute centrifugation, supernatant was aspirated and transferred to deep well plates containing 0.45 ml of Qiagen binding buffer supplemented with Qiagen ClearMag Beads. DNA was purified using the automated KingFisher™ Flex Purification System and eluted in DNase free water.  12.5 ng of total DNA were amplified using universal primers targeting the V4 region of the bacterial 16S rRNA gene. Primer sequences contained overhang adapters appended to the 5’ end of each primer for compatibility with Illumina sequencing platform. The primers used were F515/R806. Master mixes contained 12.5 ng of total DNA, 0.5 µM of each primer and 2x KAPA HiFi HotStart ReadyMix (KAPA Biosystems, Wilmington, MA). The thermal profile for the amplification of each sample had an initial denaturing step at 95°C for 3 minutes, followed by a cycling of denaturing of 95°C for 30 seconds, annealing at 55°C for 30 seconds and a 30 second extension at 72°C (25 cycles), a 5 minute extension at 72°C and a final hold at 4°C. Each 16S amplicon was purified using the AMPure XP reagent (Beckman Coulter, Indianapolis, IN).
In the next step each sample was amplified using a limited cycle PCR program, adding Illumina sequencing adapters and dual‐index barcodes (index 1(i7) and index 2(i5)) (Illumina, San Diego, CA) to the amplicon target. The thermal profile for the amplification of each sample had an initial denaturing step at 95°C for 3 minutes, followed by a denaturing cycle of 95°C for 30 seconds, annealing at 55°C for 30 seconds and a 30 second extension at 72°C (8 cycles), a 5 minute extension at 72°C and a final hold at 4°C. The final libraries were again purified using the AMPure XP reagent (Beckman Coulter), quantified and normalized prior to pooling. The DNA library pool was then denatured with NaOH, diluted with hybridization buffer and heat denatured.

value: stool


description: Library name: Mouse_Stomach_organoid_WT_scMultiome DNA

source_name: Stomach organoid

value: Stomach organoid


title: Control_2_ATAC_Seq

description: Library name: Control_2_ATAC_Seq

data_processing:
The supernatants were discarded and pellets gently resuspenSequencing was carried out using an Illumina NexSeq 550, paired-end, 2× 100 bp.  Reads were mapped to the mm10 genome using Bowtie2, and SAM files were converted to BAM format with Samtools. The BAM files were sorted and indexed using Samtools, and mapping statistics were generated. PCR duplicates were removed with Samtools, and BED files were created using bedtools bamtobed. Reads mapping to chrM and regions in the ENCODE mm10 blacklist were removed from the BED files. Genome coverage was calculated using bedtools genomecov to produce bedGraph files. A scale factor was calculated by dividing 5,000,000 by the number of regions in each BED file, and applied to the bedGraph files. BigWig files were generated using bedGraphToBigWig. Peaks were called with MACS2 in broad mode.ded in 50 μl of transposition reaction mix (25 μl of tagment DNA buffer (Nextera, Illumina), 2.5 μl of tagment DNA enzyme (Nextera, Illumina), 22.5 μl of nuclease free water) and incubated at 37 °C for 30 min. Tagmented DNA was purified using MinElute PCR purification kit (Qiagen) and size selected for 70–500 base pairs (bp) using AmpureXP beads (Beckman Coulter). Libraries were constructed and amplified using 1.25 μM Nextera index primers and NEBNext High-Fidelity 2× PCR Master Mix (New England BioLabs). A quantitative PCR was run to determine the optimal number of cycles. Libraries were gel size selected for 165–300 bp fragments.
Assembly: mm10
Supplementary files format and content: .bam, .bw, .broadPeak

extract_protocol:
HSPCs were pelleted at 400g and 4 °C. Next, pellets were gently resuspended in ice-cold 50 μl of lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and spun down at 500g for 10 min and 4 °C.
The supernatants were discarded and pellets gently resuspended in 50 μl of transposition reaction mix (25 μl of tagment DNA buffer (Nextera, Illumina), 2.5 μl of tagment DNA enzyme (Nextera, Illumina), 22.5 μl of nuclease free water) and incubated at 37 °C for 30 min. Tagmented DNA was purified using MinElute PCR purification kit (Qiagen) and size selected for 70–500 base pairs (bp) using AmpureXP beads (Beckman Coulter). Libraries were constructed and amplified using 1.25 μM Nextera index primers and NEBNext High-Fidelity 2× PCR Master Mix (New England BioLabs). A quantitative PCR was run to determine the optimal number of cycles. Libraries were gel size selected for 165–300 bp fragments.


title: 16S rRNAseq of vaginal swab: 31054_Hnvaginal46

description: Library name: Hnvaginal46

data_processing:
Trimming: Trim Galore! - CutAdapt 3.7
Host Removal: Kraken2 2.1.2
ASV calling: DADA2 (QIIME2 2022.2.0)
Taxa Classification: QIIME 2 2022.2.0  - Silva 138
Assembly: Silva 138
Supplementary files format and content: ASV/OTU table: table.biom.txt (tab-separated text spreadsheet)
Supplementary files format and content: DNA sequences for ASV representatives: rep-seqs.fna (nucleotide fasta file)
Supplementary files format and content: Taxa classifications for each ASV: taxa-gg2.txt (tab-separated text spreadsheet)
Supplementary files format and content: Phylogenetic tree of ASV representative sequences: tree.nwk (Newick format)
Library strategy: 16S rRNA-seq


description: Library name: Mouse_Stomach_organoid_WT_scMultiome RNA


title: Control_1_ATAC_Seq

description: Library name: Control_1_ATAC_Seq


title: 63-PT

type: RNA

city: Beijing

first: He

last: Luyun

address: 15 DaTun Road, Chaoyang District

institute: IBP

description: This is peri-tumor tissue

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Data was extracted using Agilent Feature Extraction software.

source_name: Human HCC peri-tumor tissues

label_protocol: Total RNA from each sample was amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Freshly drawn tissues from HCC patients was cut into suitable size for RNA extract.

value: liver

tag: penotype

value: peri-tumor


title: 63-T

description: This is tumor tissue

source_name: Human HCC tumor tissues

value: tumor


title: 16S rRNAseq of vaginal swab: 30933_Hnvaginal45

city: Chapel Hill

first: Office of Genomics Research

institute: University of North Carolina at Chapel Hill

description: Library name: Hnvaginal45


title: Tada2b_SgRNA_2_ATAC_Seq

description: Library name: Tada2b_SgRNA_2_ATAC_Seq

value: Bone marrow

value: HSPC

value: Tada2b KO


title: Sample 1 of P-PTEN WT Vagus nerve 2 weeks after HFD

city: Toronto

first: Minna

last: Woo

state: Ontario

address: 10-601D, College Street

department: Department of Medicine

country: Canada

institute: University of Toronto

description:
Library name: Sample 3
10x Genomics

data_processing:
The molarity of the obtained library was calculated based on library size as measured bioanalyzer and qPCR amplification data . snRNA sequencing. Each sample was sequenced using 100 bp pair-ended protocol and multiplexed to obtain ~40 million reads/sample with reads mapped to GRCh38.
Assembly: mm10
Supplementary files format and content: fastq raw counts and tab delimited text files are provided along with the filtered feature bc matrix files for each specific sample.

source_name: Vagus Nerve

extract_protocol:
Animals were euthanized with CO2 prior to vagus nerve dissection to obtain left and right cervical vagus nerves that contain the nodose ganglion. Vagus nerve samples were immediately flash frozen into 1.5 mL eppendorf tubes containing dry ice. The nerve tissue was then homogenized in nuclei extraction buffer using glass douncers.  The nuclei was then ultracentrifuged at 1000xG for ~2 hrs and then resuspended with the process repeated for 3 cycles. Samples were then filtered and washed with a sucrose column and placed in nuclei suspension buffer. Nuclei is then sorted with FACS with trypan blue to sort for cell viability.
The appropriate amount of volume was used for ~7500 reads. Library preparation was performed per manafacturers instructions using 10x Genomics 3' v3 Reagent Kit and 10x Cell Ranger software Version 3.  Samples were loaded into a 10x Transportation reaction and incubated into  a 10x chip to generate a collection of gel beads in emulsions. The sample is then processed through a reverse transcription reaction to generate a shared 10x barcode containing the cDNA and all the nuclei which is then subjected to illumina sequencing.

treatment_protocol: Animals were fed 2 weeks of HFD for both P-PTEN WT and P-PTEN KO cohort

value: Vagus Nerve

value: PTEN WT

value: High Fat Diet


title: 50-T

description: This is tumor tissue


title: Sample 2 of P-PTEN WT Vagus nerve 2 weeks after HFD

description:
Library name: Sample 4
10x Genomics


title: 50-PT

description: This is peri-tumor tissue


title: 16S rRNAseq of vaginal swab: 30845_Hnvaginal44

last: UNC Lineberger Comprehensive Cancer Center

address: 125 Mason Farm Road, CB #7599 5105-5106 Marsico Hall

description: Library name: Hnvaginal44


title: 16S rRNAseq of stool: 20087_HNStool01

description: Library name: HNStool01

source_name: stool


title: BXPC3_COL_a

description: BXPC3 collagen replicate 1

value: pancreatic cancer

value: collagen


title: Tada2b_SgRNA_1_ATAC_Seq

description: Library name: Tada2b_SgRNA_1_ATAC_Seq


title: Sample 2 of P-PTEN KO Vagus nerve 2 weeks after HFD

description:
Library name: Sample 2
10x Genomics

value: PTEN KO


title: 16S rRNAseq of vaginal swab: 29195_Hnvaginal43

description: Library name: Hnvaginal43

value: vaginal swab


title: Mouse ENS 49

city: New York

first: Robert

last: Lovelett

state: New York

address: 430 E 29th Street, 10th Floor

institute: Kallyope

description:
Library name: K_10X_mENS049
10X Genomics

data_processing:
Demultiplexed and counted using CellRanger 6.1 with the --include_introns flag set to True
Assembly: A modified mm10 where each gene was extended in the 3' direction up to 5000 bp, unless it conflicted with another gene on either strand
Supplementary files format and content: Raw and filtered count matrices output from CellRanger Count as h5 files

source_name: Myenteric layer of Mid Colon

extract_protocol:
Snap frozen myenteric tissue was pulverized and then dounce homogenized with in CST buffer, filtered through a 40µm filter, spun down at 800g for 8 minutes at 4°C, and blocked in ST-SB buffer for 10 minutes. Nuclei were inubated in directly conjugated HuC/D antibody (1:200) for 30 minutes at 4°C in the dark. Homogenates were then washed with additional ST buffer, spun at 800g for 8 min at 4°C, supernatant was removed, and nuclei were resuspended in ST-SB and filtered through a 40µm Flowmi filter. Single nuclei were sorted on a Sony SH800 as AF488+ directly into a tube with 10X Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 reverse transcription master mix without RT Enzyme C. RT Enzyme C was added when sorting was complete and the nuclei in master mix was then loaded into a 10X Chip G for barcoding and droplet generation. The sample protocol was done for submucosal tissue but some buffers were changed. TSP was used in the dounce homogenization step, blocking and staining was performed in SP-SB buffer, and washes were done in SPMB buffer.
Used 10x Genomics 3' v3.1 kit. Enzyme C was added to the RT reaction after sorting and before GEM generation. Manufacturer instructions were followed for reverse transcription, cDNA amplification, fragmentation, ligation and sample single indexing PCR.

value: Myenteric layer of Mid Colon


title: BxPC3_5_b

description: BXPC3 GelMA 5% replicate 2

value: 5% GelMA


title: Sample 1 of P-PTEN KO Vagus nerve 2 weeks after HFD

description:
Library name: Sample 1
10x Genomics


title: smg2_3

city: riverside

first: Shameerudeen

last: Athavudeen

address: 900 university ave

department: Biochemistry

institute: UC Riverside

description: Library name: Sample 9

data_processing:
.fastqs reconstructed from .bam files using bamtofastq (bedtools)
Assembly: caenorhabditis_elegans.PRJNA13758.WBPS18.canonical_geneset.gtf
Supplementary files format and content: xlsx file containing splice junction information and Percent Spliced In values

organism: Caenorhabditis elegans

source_name: whole-animal

extract_protocol:
RNA extraction via NEBNext polyA kit
RNA extraction via NEBNext polyA kit

value: whole-animal

tag: strain


title: smg2_2

description: Library name: Sample 8


title: BxPC3_5_a

description: BXPC3 GelMA 5% replicate 1


title: 16S rRNAseq of vaginal swab: 28953_Hnvaginal42

description: Library name: Hnvaginal42


title: Mouse ENS 47

description:
Library name: K_10X_mENS047
10X Genomics

source_name: Myenteric layer of Antrum

value: Myenteric layer of Antrum


title: shDis3l2, - Doxycycline, D4

city: Frederick

first: Sandra

middle: L

last: Wolin

state: MD

address: FDC 560 BG RM 11-82C / 560 CHANDLER STREET

institute: NCI

description: Library name: shDis3l2 no Doxy

data_processing:
Illumina adapter sequences were trimmed with CutAdapt. After trimming, reads < 35 nt were discarded.
Transcript quantification was performed using RSEM tools
Transcripts were mapped to the mouse reference genome (GRCm38) with STAR 2.7.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

growth_protocol: Cells were cultured at 37°C with 5% CO2 and maintained in Dulbecco’s modified Eagle’s medium (DMEM, Gibco) supplemented with 10% fetal bovine serum (FBS), 100 U/mL penicillin-streptomycin, and 2 mM L-glutamine.

extract_protocol:
Total cell RNA was extracted from Trizol and treated with Turbo DNase prior to library construction.
Total RNA-seq libraries were prepared from total cell RNA from shNS- and shDis3l2-expressing cells by the NCI CCR sequencing facility using the Illumina Stranded Total RNA Library Prep Kit with Ribo-Zero-Plus (20040525) according to the manufacturer’s instructions. Samples were sequenced on an Illumina NovaSeq 6000 SP cell, obtaining 150 nt paired end reads.

treatment_protocol: Cells were seeded at 2 x 105 cells/well in 6 well dishes. Cells were grown in DMEM +/- 1 μg/mL doxycycline. Media and drug treatment were replaced daily. RNA was extracted after 4 days of treatment, at which time cells were 75-85% confluent.

value: macrophage

value: no treatment


title: smg2_1

description: Library name: Sample 7


title: 16S rRNAseq of vaginal swab: 28766_Hnvaginal41

description: Library name: Hnvaginal41


title: BXPC3_COL_b

description: BXPC3 collagen replicate 2


title: Mouse ENS 46

description:
Library name: K_10X_mENS046
10X Genomics

source_name: Myenteric layer of Colon

value: Myenteric layer of Colon


title: shNS, - Doxycycline, D4

description: Library name: shNS no Doxy

value: shNS


title: 16S rRNAseq of vaginal swab: 28007_Hnvaginal39

description: Library name: Hnvaginal39


title: shDis3l2, + Doxycycline, Replicate 3

description: Library name: shDis3l2 Rep3

value: Doxycycline


title: 16S rRNAseq of vaginal swab: 28579_Hnvaginal40

description: Library name: Hnvaginal40


title: shDis3l2, + Doxycycline, Replicate 2

description: Library name: shDis3l2 Rep2


title: smg1_2

description: Library name: Sample 5


title: 16S rRNAseq of vaginal swab: 27963_Hnvaginal38

description: Library name: Hnvaginal38


title: shDis3l2, + Doxycycline, Replicate 1

description: Library name: shDis3l2 Rep1


title: smg1_1

description: Library name: Sample 4


title: Mouse ENS 40

description:
Library name: K_10X_mENS040
10X Genomics

source_name: Myenteric layer of Proximal Colon

value: Myenteric layer of Proximal Colon


title: WT_3

description: Library name: Sample 3

value: WT


title: Mouse ENS 41

description:
Library name: K_10X_mENS041
10X Genomics

source_name: Submucosal layer of Proximal Colon

value: Submucosal layer of Proximal Colon


title: 16S rRNAseq of vaginal swab: 27204_Hnvaginal37

description: Library name: Hnvaginal37


title: WT_2

description: Library name: Sample 2


title: Mouse ENS 39

description:
Library name: K_10X_mENS039
10X Genomics

source_name: Myenteric layer of Ileum

value: Myenteric layer of Ileum


title: shNS, + Doxycycline, D4, Replicate 2

description: Library name: shNS Rep2


title: 16S rRNAseq of vaginal swab: 27116_Hnvaginal35

description: Library name: Hnvaginal35


title: shNS, + Doxycycline, D4, Replicate 3

description: Library name: shNS Rep3


title: WT_1

description: Library name: Sample 1


title: 16S rRNAseq of vaginal swab: 26676_Hnvaginal34

description: Library name: Hnvaginal34


title: 16S rRNAseq of vaginal swab: 27171_Hnvaginal36

description: Library name: Hnvaginal36


title: PVH nuclei, female, sample 10, 10x SC3Pv3

first: Jon

last: Resch

state: Iowa

address: 51 Newton Rd

description:
Library name: Mm PVH 10F-1
10x Chromium universal 3′ gene expression (single-nucleus) v3; read 1 (28nt) contains cell barcode (16nt), then UMI (12nt); read 2 (55nt) contains transcript

data_processing:
Raw sequencing reads were demultiplexed to FASTQ format files using bcl2fastq (Illumina; version 2.20.0).
Digital expression matrices were generated from the FASTQ files using a slightly modified version of the Drop-Seq tools <https://github.com/broadinstitute/Drop-seq> pipeline (version 2.3.0) to account for the difference in read structure in 10x libraries (as opposed to “native” Drop/DroNc seq libraries) --- “BASE_RANGE=1-16” and “BASE_RANGE=17-28”. Additionally, the TSO adapter used to identify and trim contaminated reads was altered to reflect the slight differences between the 10x TSO from the default in Drop-seq tools (“SEQUENCE=AAGCAGTGGTATCAACGCAGAGTACATGGG”). Reads from were aligned with STAR (version 2.7.7) against the GRCm38 mouse genome assembly. Gene counts were obtained, per-droplet, by summarizing the unique read alignments across exons and introns (Drop-Seq tools “Digital Expression” option: “LOCUS_FUNCTION_LIST=INTRONIC”) in release 24 of the GENCODE mouse annotation.
CellBender (Fleming, et. al 2019) version 0.2.0 was used to remove background/ambient signal from the mouse gene count matrices.
Assembly: GRCm38
Supplementary files format and content: Cell Ranger output files: *.counts.h5 (same as raw_feature_bc_matrix.h5)
Supplementary files format and content: CellBender output files *.cellbender.tsv.gz

source_name: paraventricular nucleus of the hypothalamus

extract_protocol:
C57BL/6J  mice aged 6-12 weeks were sacrificed between 9 am – 12 pm by rapid decapitation immediately after removal from the home cage. Brains were rapidly extracted and chilled in DMEM/F12 media slush. Next, brains were placed ventral side up in a chilled stainless steel brain matrix (Roboz Surgical Instrument Co.: SA-2165) and 1 mm coronal sections of the hypothalamus were collected. The PVH was then microdissected under a fluorescent stereoscope and tissue from each mouse was pooled.
The pooled sample was kept frozen until immediately before nuclei isolation, and all sample handling steps were performed on ice. The frozen tissue sample was placed into a gentleMACS C tube (Miltenyi Biotec) with 2 mL freshly prepared TST buffer (0.03% Tween 20 [Bio-Rad], 0.01% Molecular Grade BSA [New England Biolabs], 146 mM NaCl [ThermoFisher Scientific], 1 mM CaCl2 [VWR International], 21 mM MgCl2 [Sigma Aldrich], and 10 mM Tris-Hcl pH 7.5 [ThermoFisher Scientific] in Ultrapure water [ThermoFisher Scientific]) with or without 0.2 U/ µL of Protector RNase Inhibitor (Sigma Aldrich). The gentleMACS Dissociator (Miltenyi Biotec) was used for tissue dissociation and samples were then incubated on ice for 10 minutes. Lysate was passed through a 40 µm nylon filter (CellTreat) and collected into a 50 mL conical tube (Corning). Filter was rinsed with 3 mL of freshly prepared ST buffer buffer (146 mM NaCl, 1 mM CaCl2, 21 mM MgCl2; 10 mM Tris-Hcl pH 7.5) with or without 0.2 U/µL RNase Inhibitor, and collected into the same tube. Flow-through was centrifuged at 500 x g for 5 minutes at 4ºC with brake set to low. Following centrifugation, supernatant was removed, and the nuclear pellet was resuspended in 50 - 200 µl PBS pH 7.4 (ThermoFisher Scientific) with 0.02% BSA, with or without 0.2U/µL RNase Inhibitor. In order to reduce ambient mRNA, the nuclear pellets of some samples were washed 1-3 times with 5 mL of PBS-0.02% BSA before final resuspension. An aliquot of nuclei from each sample was stained with NucBlue (Thermofisher Scientific), counted in a hemocytometer using fluorescence to identify intact nuclei, and then immediately loaded on the 10x Chromium controller (10x Genomics) according to the manufacturer’s protocol. 15,000 nuclei were loaded in one channel of a Chromium Chip (10x Genomics). The Single Cell 3’ v3.1 chemistry was used to generate the cDNA library, in accordance with manufacturer's instructions (10x Genomics). cDNA and gene expression library fragment sizes were assessed with a DNA High Sensitivity Bioanalyzer Chip (Agilent). cDNA and gene expression libraries were quantified using the Qubit dsDNA High Sensitivity assay kit (ThermoFisher Scientific). Gene expression libraries were multiplexed and sequenced on a NextSeq 500 (Illumina) with a 75-cycle kit and the following read structure: Read 1 =  28 cycles,  Index Read 1 = 8 cycles, Read 2 = 55 cycles.

treatment_protocol: No treatment

value: female

tag: dietary condition/schedule

value: ad libitum feeding


title: shNS, + Doxycycline, D4, Replicate 1

description: Library name: shNS Rep1


title: 16S rRNAseq of vaginal swab: 26544_Hnvaginal33

description: Library name: Hnvaginal33


title: Cd8+ TILs, Male mice, wildtype

city: Nanjing

first: Xi

last: Wang

address: Longmian Avenue 101, Jiangning District

institute: Nanjing Medical University

description: Library name: Male_WT

data_processing:
Seeksoultools (version 1.2.2, available at https://github.com/seekgenebio/seeksoultools) used with the prebuilt reference transcriptome data (mm10, Ensembl 102).
Assembly: mm10
Supplementary files format and content: tar of seeksoultools output files, gene-by-cell count matrix

source_name: CD8+T cell

extract_protocol:
Cells were loaded onto sample wells of SeekOne chip S3 and processed with SeekOne Digital Droplet Single Cell 3' library preparation kit.
Libraries  were prepared with SeekOne Digital Droplet Single Cell 3' library preparation kit.

value: CD8+T cell

value: Male

value: wildtype


title: Mouse ENS 44

description:
Library name: K_10X_mENS044
10X Genomics


title: multiplexed sample set 1, PVH nuclei, HTO

description:
Library name: MUX HTOs 01-1
TotalSeq™-A anti-nuclear pore compelx proteins hashtag antibodies; read 1 contains cell barcode and UMI (as per assoc. 10x library); read 2 (55nt) contains HTO (15nt) and noise

library_source: other

data_processing:
Raw sequencing reads were processed into count matrices using Cell Ranger (10x Genomics; version 6.1.2 or version 7.0.1) and using the GRCm38 mouse assembly. Mouse samples that were part of the multiplexed sample MUX_01-1 were sequenced together with barnyard test data and hence Cell Ranger was run with a combined mouse & human genome reference (GRCh38). Gene annotations were obtained from GENCODE --- release m24 for the mouse assembly (release 33 for the human assembly).
For sample MUX HTOs 01-1, HTO sequencing reads were processed into corresponding count matrices using the Cumulus Tool on Feature Barcoding (https://github.com/lilab-bcb/cumulus_feature_barcoding), while kallisto | bustools (https://www.kallistobus.tools/) was used to process HTO sequencing reads into corresponding count matrices for samples MUX HTOs 04_14_2022 and MUX HTOs 03_09_2023
For sample MUX 01-1 DemuxEM (version 0.1.6) was used to sort cells into individual samples based on their antibody hashtags.
Ambient RNA was removed from the Cell Ranger counts matrices using CellBender (version 0.2.0)
Assembly: GRCm38
Supplementary files format and content: Cell Ranger output files: *.counts.h5 (same as raw_feature_bc_matrix.h5)
Supplementary files format and content: CellBender output files *.counts_cellbender.h5
Supplementary files format and content: Cumulus Tool on Feature Barcoding output or kalisto | bustools counts matrix: *.htos.csv.gz

molecule: other

extract_protocol:
Sim1-Cre and H2B-TRAP mice aged 6-12 weeks recieved bilateral stereotaxic injections of AAVDJ-hSyn-DIO-H2B-mCherry or AAVrg-hSyn-Cre, respectively. After 2-3 weeks of recovery, mice were sacrificed between 9 am – 12 pm by rapid decapitation immediately after removal from the home cage. Brains were extracted and chilled in DMEM/F12 media slush. Next, brains were placed ventral side up in a chilled stainless steel brain matrix (Roboz Surgical Instrument Co.: SA-2165) and 1 mm coronal sections of the hypothalamus were collected. The PVH was then microdissected under a fluorescent stereoscope and tissue was pooled by experiment (Sim1-Cre or projection-specific labeling). Each sample underwent nuclear dissociation and purification procedures and were incubated with NucBlue (Thermofisher scientific) as well as an individual hashtag antibody (BioLegend). After incubation, nuclei were flow sorted together into RT Reagent B (10x Genomics) using a Beckman Coulter MoFlo Astrios EQ or Cytek Aurora CS cell sorter with a 70 μm nozzle to remove poor quality nuclei and count the number of nuclei per sample.
Sorted nuclei were immediately loaded on the 10x Chromium controller (10x Genomics) according to the manufacturer’s protocol. Single Cell 3’ v3.1 chemistry was used to process all samples and cDNA and gene expression libraries were generated according to the manufacturer's instructions (10x Genomics). HTO libraries were constructed according to the manufacturer's instructions (BioLegend). Gene expression libraries were multiplexed and sequenced on either the Nextseq 500 (Illumina) using a 75 cycle kit or the NovaSeq 6000 (Illumina) using a 100 cycle kit with the following read struture: Read 1 = 28 cycles, Index (1) = 8cycles, followed by Read 2 = 55 cycles.

value: mixed

value: paraventricular nucleus of the hypothalamus

value: Sim1-pos neuron, SC-projecting neuron, PB-projecting neuron

value: mixed (3x ad libitum feeding, 1x fasted, 1x refed)

tag: hto

value: see `feature_README.txt` for mapping


title: PC3_oeSLC6A4_shTGM2 H3K4me3

city: Chicago

first: Cheng-Wei

last: Ju

address: 929 East 57th Street, GCIS, Room E313

institute: The University of Chicago

description: Library name: PSS

data_processing:
Raw sequencing reads were processed using FastQC for quality control and aligned to the human reference genome (GRCh38.release108) using Bowtie2. PCR duplicates have been removed. Peak calling was performed using MACS2, and annotation of binding sites was conducted using HOMER and in-house scripts.
Assembly: GRCh38.release108
Supplementary files format and content: bw files.
Supplementary files format and content: peak information
Library strategy: CUT&Tag

extract_protocol:
CUT&Tag was performed in human prostate cancer cells using the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme, TD903), followed by paired-end sequencing on Novaseq X.
Following the protocol of Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme, TD903).

value: Human prostate cancer


title: Mouse ENS 42

description:
Library name: K_10X_mENS042
10X Genomics

source_name: Myenteric layer of Duodenum

tag: tissue

value: Myenteric layer of Duodenum


title: 16S rRNAseq of vaginal swab: 26478_Hnvaginal32

description: Library name: Hnvaginal32

source_name: vaginal swab

value: vaginal swab


title: smg1_3

description: Library name: Sample 6

value: whole-animal


title: PVH nuclei, female, sample 9, drop 3, RT-rxn A&B, lib. 1

description:
Library name: Mm PVH 9F-3AB-1
DroNc-seq; read 1 (20nt) contains cell barcode (12nt) then UMI (8nt); read 2 (60nt) contains contains transcript

data_processing:
Raw sequencing reads were demultiplexed to FASTQ format files using bcl2fastq (Illumina; version 2.20.0). Read 1 was 20 bp (bases 1–12 cell barcode, bases 13–20 UMI), read 2 (paired end) was 60 bp, and index primer was 8bp.
Digital expression matrices were generated from the FASTQ files using the Drop-Seq tools <https://github.com/broadinstitute/Drop-seq> pipeline (version 2.3.0). Reads from were aligned with STAR (version 2.7.7) against the GRCm38 mouse genome assembly. Gene counts were obtained, per-droplet, by summarizing the unique read alignments across exons and introns (Drop-Seq tools “Digital Expression” option: “LOCUS_FUNCTION_LIST=INTRONIC”) in release 24 of the GENCODE mouse annotation.
CellBender (Fleming, et. al 2019) version 0.2.0 was used to remove background/ambient signal from the mouse gene count matrices.
Assembly: GRCm38
Supplementary files format and content: *.dge.tsv: tab-separated-values tables of gene x cell digital gene expression counts (DGEs)
Supplementary files format and content: *.dge_cellbender.tsv.gz: same as the DGEs, with specific gene counts reduced by CellBender (see data processing, above)

extract_protocol:
C57BL/6J or Sim1-Cre::R26-LSL-EGFP-L10a mice aged 6-12 weeks were sacrificed between 9 am – 12 pm by rapid decapitation immediately after removal from the home cage. Brains were rapidly extracted and chilled in DMEM/F12 media slush. Next, brains were placed ventral side up in a chilled stainless steel brain matrix (Roboz Surgical Instrument Co.: SA-2165) and 1 mm coronal sections of the hypothalamus were collected. The PVH was then microdissected under a fluorescent stereoscope and frozen. For each sample preparation, 4-6 male or female mice were pooled. 4-6 tissue dissections were placed in a dounce homogenizer with 1 mL cold (4C) Lysis Buffer containing 10 mM trisHCl pH 8 (Sigma-Aldrich), 250 mM Sucrose (Sigma-Aldrich), 25 mM KCl, 5mM MgCl2 (Sigma-Aldrich), 0.1% Triton x100 (Sigma-Aldrich), 0.5% RNasin Plus RNase Inhibitor (Promega), 0.1 mM Dithiothreitol (DTT) (Sigma-Aldrich) in UltraPure™ DNase/RNase-Free Distilled Water (Thermo Fisher Scientific). After douncing for 20 times, the solution was filtered through a sterile 20 µm Cell Strainer (pluriSelect), collected in 1.5 mL DNA LoBind® Tubes (Eppendorf), and centrifuged for 10 min at 900 g (rcf) at 4 C. The "slow sedimenting" component (debris and membranes) was aspirated and discarded while the "fast sedimenting" component (nuclear fraction) was gently resuspended in a 1 mL of Working Solution containing 1X pH 7.4 RNase free PBS (Thermo Fisher Scientific), 0.01% Albumin Bovine Serum (BSA) (Sigma-Aldrich), 0.5% RNasin Plus RNase inhibitor (Promega) in UltraPure™ DNase/RNase-Free Distilled Water (Thermo Fisher Scientific). Nuclei were kept on ice while transferred to the BNORC Functional Genomics and Bioinformatics (FGB) Core for DroNc-seq assay.
DroNc-seq was performed as per Habib et al. 2017, with minor modifications. Briefly, nuclei stained with Hoechst 33342 (ThermoFisher, cat. R37605) were counted on a hemocytometer and diluted in NSB to ~250,000 nuclei/ml. Barcoded beads (Chemgenes, Cat # Macosko-2011-10) were size-selected using a 40 μm strainer, diluted to 350,000 per ml, and loaded onto 70 μm wide and 75 μm deep microfluidic device (Nanoshift). The nuclei and barcoded bead suspensions were loaded and run at 35 ml/hr each, along with carrier oil (BioRad Sciences, Cat # 186-4006) at 200 ul/min, to co-encapsulate single nuclei and beads in ~75 μm drops (vol. ~ 200 pl) at 4,500 drops/sec and double Poisson loading concentrations. The microfluidic emulsion was collected into 50 ml Falcon tubes for 10-25 min each and placed on ice 2h before droplet disruption. Individual 200µl reverse transcription (RT) reactions were performed on up to 90K beads. After further exonuclease digestion, aliquots of 800-5K beads were PCR amplified for 10 cycles, and PCR products were pooled in batches of 4 wells or 16 wells for library construction. Purified cDNA was quantified, and 550 pg of each sample was fragmented, tagged, and amplified in each Nextera reaction. Libraries were sequenced on the Illumina NextSeq 500 using between 1.6–1.7 pM and 0.3 μM Read1CustSeqB (GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC).

treatment_protocol: Ad libitum fed or fasted overnight


title: Cd8+ TILs, Female mice, wildtype

description: Library name: Female_WT

value: Female


title: 16S rRNAseq of vaginal swab: 26082_Hnvaginal31

description: Library name: Hnvaginal31


title: PC3_oeDDC_TG2-IN-1 H3K4me3Q5ser#2

description: Library name: DQ-8


title: PVH nuclei, female, sample 9, drop 2, RT-rxn A&B, lib. 1

description:
Library name: Mm PVH 9F-2AB-1
DroNc-seq; read 1 (20nt) contains cell barcode (12nt) then UMI (8nt); read 2 (60nt) contains contains transcript


title: Cd8+ TILs, Female mice with T cell specific deletion of Dgat1

description: Library name: Female_KO

value: Dgat1 knockout


title: PC3_oeDDC_TG2-IN-1 H3K4me3Q5ser#1

description: Library name: DQ-7


title: 16S rRNAseq of vaginal swab: 25851_Hnvaginal30

description: Library name: Hnvaginal30


title: PVH nuclei, female, sample 9, drop 1, RT-rxn A&B, lib. 1

description:
Library name: Mm PVH 9F-1AB-1
DroNc-seq; read 1 (20nt) contains cell barcode (12nt) then UMI (8nt); read 2 (60nt) contains contains transcript