title: multiplexed sample set 03_09_2023. PVH nuclei, HTO

description:
Library name: MUX HTOs 03_09_2023
TotalSeq™-A anti-nuclear pore compelx proteins hashtag antibodies; read 1 (28nt) contains cell barcode and UMI (as per assoc. 10x library); read 2 (90nt) contains HTO (15nt) and noise

value: male

value: PB-projecting neuron


title: 16S rRNAseq of vaginal swab: 25587_Hnvaginal29

status: Public on Dec 16 2025

type: SRA

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

country: USA

institute: University of North Carolina at Chapel Hill

description: Library name: Hnvaginal29

library_source: genomic

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

molecule: genomic DNA

organism: metagenome

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.

tag: tissue

value: vaginal swab


title: PC3_oeCtrl H3K4me3

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: PV

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

organism: Homo sapiens

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).

tag: cell line

tag: cell type

value: Human prostate cancer


title: PVH nuclei, male, fed, sample 8, drop 3, RT-rxn B, lib. 1

city: Iowa City

first: Jon

last: Resch

state: Iowa

address: 51 Newton Rd

institute: University of Iowa

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

library_source: transcriptomic single cell

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)

molecule: polyA RNA

organism: Mus musculus

source_name: paraventricular nucleus of the hypothalamus

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

tag: Sex

tag: dietary condition/schedule

value: ad libitum feeding


title: PC3_oeDDC H3K4me3Q5ser#2

description: Library name: DQ-2


title: 16S rRNAseq of vaginal swab: 25466_Hnvaginal28

description: Library name: Hnvaginal28


title: PVH nuclei, male, fed, sample 8, drop 3, RT-rxn A, lib. 1

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

value: paraventricular nucleus of the hypothalamus


title: 16S rRNAseq of vaginal swab: 25367_Hnvaginal27

description: Library name: Hnvaginal27


title: multiplexed sample set 1, PVH nuclei, GEX

description:
Library name: MUX 01-1
10x Chromium universal 3′ gene expression (single-nucleus) v3.1; read 1 (28nt) contains cell barcode (16nt), then UMI (12nt); read 2 (55nt) contains transcript

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

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.

treatment_protocol: No treatment

value: mixed

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

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


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

city: Nanjing

first: Xi

last: Wang

address: Longmian Avenue 101, Jiangning District

country: China

institute: Nanjing Medical University

description: Library name: Male_KO

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

tag: genotype

value: Dgat1 knockout


title: PC3_oeSLC6A4 H3K4me3

description: Library name: PS


title: multiplexed sample set 03_09_2023. PVH nuclei, GEX

description:
Library name: MUX 03_09_2023
10x Chromium universal 3’ gene expression (single-nucleus) v3.1; read 1 (28nt) contains cell barcode (16nt), then UMI (12nt); read 2 (90nt) contains transcript


title: multiplexed sample set 04_14_2022, PVH nuclei, GEX

description:
Library name: MUX 04_14_2022
10x Chromium universal 3’ gene expression (single-nucleus) v3.1; read 1 (28nt) contains cell barcode (16nt), then UMI (12nt); read 2 (90nt) contains transcript

value: female

value: SC-projecting neuron


title: PC3_oeDDC H3K4me3Q5ser#1

description: Library name: DQ-1


title: 16S rRNAseq of vaginal swab: 25235_Hnvaginal26

description: Library name: Hnvaginal26


title: PVH nuclei, male, fed, sample 8, drop 2, RT-rxn B, lib. 1

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


title: PC3_oeDDC_TG2-IN-1 H3K4me3#2

description: Library name: DK-8


title: PC3_oeDDC_TG2-IN-1 H3K4me3#1

description: Library name: DK-7


title: 16S rRNAseq of vaginal swab: 25147_Hnvaginal25

description: Library name: Hnvaginal25


title: Input

city: Suwon-si

first: Minsuk

last: Cha

address: 2066, Seobu-ro, Jangan-gu

country: South Korea

institute: Sungkyunkwan University

description: Library name: SAMPLES 3

data_processing:
Illumina bcl2fastq v2.2.0 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence with Trimmomatic0.38.
The cleaned reads were aligned to the mouse genome (mm10) using Bowtie (version 1.1.2 parameter set --best --strata -m 1 -X 500) (Langmead et al., 2009). Mapped data (SAM file format) were performed sorting and indexing using SAMtools (version 1.9) (Li et al., 2009). Then, duplicate reads were excluded using a MarkDuplicates module in Picard (version 1.118).
Peaks were called in the aligned sequence data using a model-based analysis of ChIP-seq (MACS2 version 2.1.1.20160309) (Zhang et al., 2008). The following parameters were used: macs2 callpeak -t ChIP.bam -c Control.bam -g mm -q 0.05 --call-summits --keep-dup 1.
ChIPseeker (version 1.16.1) (Yu et al., 2015), a bioconductor package within the statistical programming environment R to facilitate batch annotation of enriched peaks identified from ChIP-seq data, was used to identify nearby genes and transcripts from the peaks obtained from MACS2.
Assembly: mm10
Supplementary files format and content: bw

source_name: spleen

extract_protocol:
CD24+ EPs from splenocytes of WT mice were sorted using the EZ-ChIPTM kit (Merck Millipore, 17-371), following the manufacturer's protocol.
ChIP-seq libraries were prepared using TruSeq ChIP Library Preparation kit (Illumina, USA)  according to the manufacture’s instructions.

treatment_protocol: Flt3L-Ig (10 μg) was intraperitoneally administered on days 0 and 3, and CD24⁺ EPs were sorted from the spleen on day 9.

value: spleen

value: WT

tag: treatment


title: PVH nuclei, male, fed, sample 8, drop 2, RT-rxn A, lib. 1

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


title: PVH nuclei, male, fed, sample 8, drop 1, RT-rxn A, lib. 1

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


title: PC3_oeDDC H3K4me3#2

description: Library name: DK-2


title: 24EP_TopBP1

description: Library name: SAMPLES 2


title: 16S rRNAseq of vaginal swab: 25092_Hnvaginal24

description: Library name: Hnvaginal24


title: PC3_oeDDC H3K4me3#1

description: Library name: DK-1


title: PVH nuclei, male, fasted, sample 8, drop 3, RT-rxn B, lib. 1

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

value: fasted


title: 16S rRNAseq of vaginal swab: 24344_Hnvaginal23

description: Library name: Hnvaginal23


title: multiplexed sample set 04_14_2022, PVH nuclei, HTO

description:
Library name: MUX HTOs 04_14_2022
TotalSeq™-A anti-nuclear pore compelx proteins hashtag antibodies; read 1 (28nt) contains cell barcode and UMI (as per assoc. 10x library); read 2 (90nt) contains HTO (15nt) and noise

library_source: other

molecule: other

tag: hto

value: see `feature_README.txt` for mapping


title: 4CC24_VKO_Input

city: Yuseong-gu, Daejeon-si

first: Taejun

last: Seol

address: 291, Daehak-ro

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

description:
Library name: 4CC24_VKO_Inp
Input;Vgll3 knockout;differentiation day 6

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: Vgll3 Knockout

value: Adipogenic cocktail


title: 3CC28_dWW_S51A_Input

description:
Library name: 3CC28_dWW_S51A_Inp
Input;differentiation day 6 with TAZ2SA/S51A/delWW activation

value: Dox-inducible TAZ2SA/S51A/delWW

value: Adipogenic cocktail + doxycycline


title: siTMEM19, pSiNP-C18-Eru, 4

city: La Jolla

first: Guoqin

last: Wei

state: CA

address: 10550 North Torrey Pines Rd, MB216

institute: The Scripps research institute

description: Library name: 16id16GW

library_source: transcriptomic

data_processing:
Quality control of raw sequencing data was performed using FastQC and MultiQC. Raw reads were aligned to the reference genome using RSubread. Gene expression levels were quantified using featureCounts. Post-alignment QC included assessing the distribution of reads across genomic features (e.g., exons, introns) and checking for potential batch effects using PCA. Differential expression analysis was carried out using the limma-voom pipeline. Data was filtered and normalisation was performed using the Trimmed Mean of M-values method. Linear modelling and empirical Bayes moderation were applied to identify differentially expressed genes. Genes with an FDR-adjusted p-value < 0.05 were considered significantly differentially expressed. Over-representation analysis and functional enrichment analysis were performed using the clusterProfiler package using Gene Ontology and KEGG to define biologically relevant pathways enrichment analysis was conducted.
Assembly: RSubread
Supplementary files format and content: Excel form of pocessed data in logCPMs

molecule: total RNA

source_name: Macrophage precursor cells  (MPCs)

growth_protocol: 12 weeks old iPSC-MPCs were plated into 6 well plate with mCSF at 90% confluencyand cultured for 1 days

extract_protocol:
Cells were collected in 500 μL of Trizol and total RNA was isolated using a PureLink RNA Mini Kit (Thermo Fisher Scientific) according to manufacturer's instructions.
NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina®

treatment_protocol: Cells were trasfected with scrmabled RNA or siTMEM19 at Day 2. Treated with eith pSiNP-C18 or pSiNP-C18-Erucamide at Day 3, RNA were harvested at Day 4.

value: Macrophage precursor cells  (MPCs)

value: iPSC

value: TMEM19 konck down


title: PVH nuclei, male, fasted, sample 8, drop 3, RT-rxn A, lib. 1

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

value: male

value: paraventricular nucleus of the hypothalamus


title: siTMEM19, pSiNP-C18-Eru, 3

description: Library name: 15id15GW


title: 16S rRNAseq of vaginal swab: 24267_Hnvaginal22

description: Library name: Hnvaginal22

value: vaginal swab


title: 3CC27_dWW_Input

description:
Library name: 3CC27_dWW_Inp
Input;differentiation day 6 with TAZ2SAdelWW activation

value: Dox-inducible TAZ2SAdelWW


title: siTMEM19, pSiNP-C18-Eru, 2

description: Library name: 14id14GW


title: PVH nuclei, male, fasted, sample 8, drop 2, RT-rxn A, lib. 1

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


title: 16S rRNAseq of vaginal swab: 24245_Hnvaginal20

description: Library name: Hnvaginal20


title: siTMEM19, pSiNP-C18-Eru, 1

description: Library name: 13id13GW


title: 16S rRNAseq of vaginal swab: 23948_Hnvaginal19

description: Library name: Hnvaginal19


title: 3CC26_2SA_Input

description:
Library name: 3CC26_2SA_Inp
Input;differentiation day 6 with TAZ2SA activation

value: Dox-inducible TAZ2SA


title: 3CC25_Con_Input

description:
Library name: 3CC25_Con_Inp
Input;differentiation day 6


title: PVH nuclei, male, fasted, sample 8, drop 1, RT-rxn B, lib. 1

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


title: siTMEM19, pSiNP-C18, 4

description: Library name: 12id12GW


title: PVH nuclei, male, fasted, sample 8, drop 1, RT-rxn A, lib. 1

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


title: siTMEM19, pSiNP-C18, 3

description: Library name: 11id11GW


title: D6_Input

description:
Library name: CC29_D6_Input
Input;differentiation day 6

value: Tamoxifen-inducible TAZ2SA


title: 16S rRNAseq of vaginal swab: 23882_Hnvaginal18

description: Library name: Hnvaginal18


title: PVH-neuron nucleus, retrograde HSV, sample 200, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 200-1

data_processing:
Raw sequencing reads were demultiplexed to FASTQ format files using bcl2fastq (Illumina; version 2.20.0); read 1 was 75 bp, index read 1 was 8bp, and index read 2 was 8bp
Reads were aligned against the GRCm38 genome assembly for mouse using the STAR RNA alignment tool (version 2.6.1); transgeneic sequences for Cre and mCherry were included on-the-fly. Alignments were deduplicated using the Picard tool suite (version 2.18.21), specifically the “MarkDuplicates” tool with argument `REMOVE_DUPLICATES='TRUE'`.
Digital expression matrices were generated from the aligmment files using the Drop-Seq tools <https://github.com/broadinstitute/Drop-seq> pipeline (version 2.3.0). Gene counts were obtained, per-nucleus, by summarizing the unique read alignments across exons and introns (Drop-Seq tools “Digital Expression” option: “LOCUS_FUNCTION_LIST=INTRONIC”) in release 16 of the GENCODE mouse annotation. For lack of a “true” UMI sequence/barcode, deduplicated reads were assumed to be unique (pseudo-UMIs were generated based on the read name, as given by the demultiplexing process).
Assembly: GRCm38
Supplementary files format and content: Mm_PVH_LPBN-projecting.dge.tsv = a matrix of gene counts (gene-by-cell)

molecule: nuclear RNA

source_name: paraventricular nucleus of the hypothalamus -> (lateral) parabrachial nucleus

extract_protocol:
C57BL/6J or H2B-TRAP mice aged 6-12 weeks recieved bilateral stereotaxic injections of AAVDJ-hSyn-DIO-H2B-mCherry and/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 and treated with RNAlater (QIAGEN catalog #76106). The PVH was then microdissected under a fluorescent stereoscope and tissue was pooled and stored at -80. Each sample underwent nuclear dissociation and purification procedures and were incubated with NucBlue (Thermofisher scientific). After incubation, nuclei were flow sorted together into 96 well plates with each well containing sNuc-seq lysis buffer (Todd et al., 2020; Tao, et al., 2021) using a Beckman Coulter MoFlo Astrios EQ with a 70 μm nozzle.
Single nucleus samples were processed into cDNA libraries, and sequenced by Next-Seq 500 (SR75, high-output kit) as previously described (Todd et al., 2020). Reads were demultiplexed by bcl2fastq2 v2.20.0 (Illumina) and aligned to the mouse genome by STAR v2.6.1 (Dobin et al., 2013). Duplicates were removed with Picard Tools v2.18.21. Aligned reads were processed into a digital gene expression (DGE) file with Drop-Seq Tools v2.3.0 and tagged using “GENCODE_M16_PRI” annotation. The DGE file was input to the single-cell analysis R package, Seurat (Stuart et al., 2019), version 5, for further analysis, using default settings except where noted.

value: neuron

value: PB-projecting

tag: infection

value: retrograde HSV

tag: batch


title: D6TAZ_Input

description:
Library name: CC30_D6TZ_Input
Input;differentiation day 6 with TAZ2SA activation

value: mesenchymal stem cells

value: Adipogenic cocktail + 4-OHT


title: 16S rRNAseq of vaginal swab: 23321_Hnvaginal16

description: Library name: Hnvaginal16


title: siTMEM19, pSiNP-C18, 2

description: Library name: 10id10GW


title: siTMEM19, pSiNP-C18, 1

description: Library name: 09id09GW


title: PVH-neuron nucleus, retrograde HSV, sample 191, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 191-1

value: paraventricular nucleus of the hypothalamus -> (lateral) parabrachial nucleus


title: D6TAZ_TAZ2

description:
Library name: CC12_D6TAZ_TAZ2
TAZ ChIP-seq at differentiation day 6 with TAZ2SA activation


title: 16S rRNAseq of vaginal swab: 24256_Hnvaginal21

description: Library name: Hnvaginal21


title: PVH-neuron nucleus, retrograde HSV, sample 188, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 188-1


title: D0_Input

description:
Library name: CC28_D0_Input
Input;differentiation day 0


title: 16S rRNAseq of vaginal swab: 22694_Hnvaginal14

description: Library name: Hnvaginal14


title: D6TAZ_TAZ1

description:
Library name: CC3_D6TAZ_TAZ
TAZ ChIP-seq at differentiation day 6 with TAZ2SA activation


title: D6_TAZ2

description:
Library name: CC11_D6_TAZ2
TAZ ChIP-seq at differentiation day 6

value: Adipogenic cocktail


title: PVH-neuron nucleus, retrograde HSV, sample 186, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 186-1


title: 16S rRNAseq of vaginal swab: 22595_Hnvaginal13

description: Library name: Hnvaginal13


title: Scrambled, pSiNP-C18-Eru, 2

description: Library name: 06id06GW

value: WT


title: Scrambled, pSiNP-C18-Eru, 3

description: Library name: 07id07GW

value: Macrophage precursor cells  (MPCs)


title: PVH-neuron nucleus, retrograde HSV, sample 184, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 184-1


title: D6_TAZ1

description:
Library name: CC2_D6_TAZ
TAZ ChIP-seq at differentiation day 6


title: PVH nuclei, male, fasted, sample 8, drop 2, RT-rxn B, lib. 1

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

value: fasted


title: Scrambled, pSiNP-C18, 4

description: Library name: 04id04GW

value: iPSC


title: D0_TAZ2

description:
Library name: CC10_D0_TAZ2
TAZ ChIP-seq at differentiation day 0


title: PVH-neuron nucleus, retrograde HSV, sample 194, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 194-1


title: PVH-neuron nucleus, retrograde HSV, sample 183, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 183-1


title: PVH-neuron nucleus, retrograde HSV, sample 177, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 177-1


title: Scrambled, pSiNP-C18-Eru, 1

description: Library name: 05id05GW


title: 16S rRNAseq of vaginal swab: 23552_Hnvaginal17

description: Library name: Hnvaginal17


title: 16S rRNAseq of vaginal swab: 22078_Hnvaginal11

description: Library name: Hnvaginal11


title: D0_TAZ1

description:
Library name: CC1_D0_TAZ
TAZ ChIP-seq at differentiation day 0


title: 16S rRNAseq of vaginal swab: 22056_Hnvaginal10

description: Library name: Hnvaginal10


title: 16S rRNAseq of vaginal swab: 22485_Hnvaginal12

description: Library name: Hnvaginal12


title: PVH-neuron nucleus, retrograde HSV, sample 170, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 170-1


title: Scrambled, pSiNP-C18-Eru, 4

description: Library name: 08id08GW


title: Scrambled, pSiNP-C18, 3

description: Library name: 03id03GW


title: 16S rRNAseq of vaginal swab: 22815_Hnvaginal15

description: Library name: Hnvaginal15


title: Scrambled, pSiNP-C18, 2

description: Library name: 02id02GW


title: 16S rRNAseq of vaginal swab: 21858_Hnvaginal08

description: Library name: Hnvaginal08


title: 16S rRNAseq of vaginal swab: 22001_Hnvaginal09

description: Library name: Hnvaginal09


title: 4CC19R_VKOD6TAZ_Kac2

description:
Library name: 4CC19R_VKOTZ_Ac
Vgll3 knockout; H3K27ac ChIP-seq at differentiation day 6 with dox-induced TAZ2SA

value: Vgll3 Knockout; Dox-inducible TAZ2SA

value: Adipogenic cocktail + doxycycline


title: 16S rRNAseq of vaginal swab: 21704_Hnvaginal07

description: Library name: Hnvaginal07

value: vaginal swab


title: –10 timepoint of the second day of the transition from diurnal LL to HL, replicate 3

city: Berkeley

first: Sean

middle: D.

last: Gallaher

state: California

address: 176 Stanley Hall, room 408

department: California Institute for Quantitative Biosciences

institute: UC Berkeley

description: Library name: Cr077_BL_L2H_n2_m10h_B3

data_processing:
mapping to the C. reinhardtii reference assembly with STAR (v2.7.9a) with --alignIntronMax 3000 --outSAMtype BAM SortedByCoordinate --outMultimapperOrder Random --outSAMmultNmax 1 --limitBAMsortRAM 2000000000 --outSAMunmapped Within
reads assigned to genes with featureCounts() function in R using annot.ext=annotations, isGTFAnnotationFile="SAF", useMetaFeatures=TRUE, allowMultiOverlap=TRUE, fracOverlap=0.5, minOverlap=30, largestOverlap=TRUE, countMultiMappingReads=TRUE, fraction=TRUE, minMQS=0, primaryOnly=TRUE, ignoreDup=FALSE, strandSpecific=2, genome=genome, isLongRead=FALSE, isPairedEnd=FALSE, countReadPairs=TRUE, checkFragLength=TRUE, minFragLength=50, maxFragLength=3000, countChimericFragments=FALSE, autosort=TRUE
reads per transcript normalized with DESeq2 (v1.45.0) using dds <- DESeqDataSetFromMatrix(), dds <- DESeq(dds)
transcript lengths added with mcols(dds)$basepairs <- transcriptLengths
transcript abundances calculated as Fragments Per Kb per Million mapped reads (FPKMs) with DESeq2 using fpkm(dds, robust = TRUE)
Assembly: Chlamydomonas reinhardtii reference v6.1 (from phytozome-next.jgi.doe.gov)
Supplementary files format and content: Cr077.FPKMs_all.csv contains normalized expression values for all samples and for all nuclear genes in a comma-delimited text file

organism: Chlamydomonas reinhardtii

growth_protocol: Cultures were inoculated from TAP precultures at a starting optical density at 680 nm (OD680) of roughly 0.05 in HSM. Cultures were allowed to grow in turbidostat mode for at least 2 weeks prior to each experiment. The LL-acclimated population was first synchronized in diurnal ML (200 µmol photons m–2 s–1) for 1 week and then acclimated to diurnal LL for > 1 week. The HL-acclimated population was synchronized and acclimated in diurnal HL for > 1 week.

extract_protocol:
Roughly 17 mL of culture was collected by centrifugation at 2500 × g for 2 min at 4°C. Cell pellets were resuspended in 750 µL Zymo DNA/RNA Shield and transferred to ZR BashingBead Lysis Tubes containing 0.1 mm and 0.5 mm beads. Samples were subjected to bead beating for 2 min in a Mini-BeadBeater 16 Cell Disrupter in a 4°C room, and then were processed with the ZymoBIOMICS RNA Mini Kit according to the manufacturer's instructions.
Standard Illumina RNA-Seq kits.

treatment_protocol: At the start of the experiment (–12, t = 0 h), culture density was set to OD680 = 0.4 and medium flow was stopped. Then, the LL-acclimated populations were subjected to diurnal HL conditions, and the HL-acclimated populations were subjected to diurnal LL conditions. After the first 26 h (–10), experimental cultures were diluted back to OD680 = 0.4 and medium flow was stopped again before the second day of the experiment.

value: liquid culture

value: LL to HL


title: PVH-neuron nucleus, retrograde HSV, sample 165, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 165-1


title: PVH-neuron nucleus, retrograde HSV, sample 168, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 168-1


title: Scrambled, pSiNP-C18, 1

description: Library name: 01id01GW


title: 4CC18R_VKOD6_Kac2

description:
Library name: 4CC18R_VKO_Ac
Vgll3 knockout; H3K27ac ChIP-seq at differentiation day 6


title: –10 timepoint of the second day of the transition from diurnal LL to HL, replicate 2

description: Library name: Cr077_BL_L2H_n2_m10h_B2


title: PVH-neuron nucleus, retrograde HSV, sample 164, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 164-1


title: 16S rRNAseq of vaginal swab: 20670_Hnvaginal05

description: Library name: Hnvaginal05


title: PVH-neuron nucleus, retrograde HSV, sample 154, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 154-1


title: 16S rRNAseq of vaginal swab: 20648_Hnvaginal04

description: Library name: Hnvaginal04


title: +12 timepoint of the second day of the transition from diurnal LL to HL, replicate 3

description: Library name: Cr077_BK_L2H_d2_p12h_B3


title: –10 timepoint of the second day of the transition from diurnal LL to HL, replicate 1

description: Library name: Cr077_BL_L2H_n2_m10h_B1


title: 3CC5_dWW_Kac1

description: Library name: 3CC5_dWW_Ac1

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) 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) file of ChIP-seq peaks

value: Dox-inducible TAZ2SAdelWW


title: 3CC6_dWW_Kac2

description: Library name: 3CC6_dWW_Ac2


title: +12 timepoint of the second day of the transition from diurnal LL to HL, replicate 2

description: Library name: Cr077_BK_L2H_d2_p12h_B2


title: adult_HPD_DSS

city: Chengdu

first: Li

last: Zeng

state: China

address: Guoxuexiang 37, West China Hospital, Chengdu, Sichuan.

institute: West China Hospital, Sichuan University

description:
Library name: sample 8
all cell types
10x Genomics

data_processing:
Results from Illumina sequencing offline were converted to FASTQ format using bcl2fastq software (version 5.0.1). The scRNA-seq sequencing data were compared to reference genome using CellRanger software, and cellular and individual cellular 3' end transcripts were identified and counted in the sequenced samples. (https://support.10xgenomics.com/single-cell-geneexpression/software/pipelines/latest/what-is cell-ranger , version 7.0.0) The output CellRanger expression profile matrix was loaded into Seurat (version 4.1.0) for filtering of low quality cells from scRNA-seq data, and the filtered data was downscaled and clustered. Filtering low cell quality thresholds: number of genes expressed per cell >500, mitochondrial genes expressed in <25% of cells. Cells were projected into 2D space using t-SNE or UMAP.These steps include: 1. calculating gene expression values using the LogNormalize method of Seurat's "Normalization" function; 2. performing principal component analysis (PCA) using the normalized expression values, using the top 20 PCs for clustering, and Findcluster analysis. 3. analyze the marker genes of each cluster based on Findallmarker, and the marker genes were selected based on the following criteria: expressed in more than 10% of cells in each cluster, P value ≤ 0.01, gene expression ploidy logFC ≥ 0.26;
Assembly: Ensembl_v105_mus_musculus
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Peyer patches

extract_protocol:
The obtained tissues were transferred to a Petri dish (Petri dish was placed on wet ice) pre-spiked with 1×PBS (without RNase and Ca, Mg ions) and washed with 1XPBS to remove blood stains, grease and other adherents from the tissue surface. The tissue was then cut into 0.5 mm2 pieces and washed again with 1×PBS. The washed pieces were added with dissociation solvent (0.35% collagenase IV5, 2 mg/ml papain, 120 Units/ml DNase I) and reacted for 20 min at 37°C in a water bath shaker (100 rpm). PBS (containing 10% fetal bovine serum) was used to terminate the dissociation. The cells were repeatedly puffed 5-10 times with a pipette gun (gentle handling to prevent cell death due to shear force). The cell suspension was filtered through a 70-30um cell sieve and subsequently centrifuged at 300g for 5 min at 4°C. After centrifugation, the cell sediment was collected and the cells were resuspended by adding 100ul of 1× PBS (0.04% BSA) solution. To remove erythrocytes, 1 ml of 1X erythrocyte lysis solution (MACS 130-094-183, 10×) was added and reacted at room temperature or on wet ice for 2-10 min. After lysis, the cells were centrifuged at 300g for 5 min at 4°C, and the cell precipitate was collected after centrifugation. Add 100μl of Dead Cell Removal MicroBeads (MACS 130-090-101), mix well and incubate for 15min at room temperature. At the end of incubation, Binding Buffer was added, after MS Columns (130-042-201) to remove reagents, and dead cells.Cell precipitates were collected by centrifugation at 300g for 5min at 4°C. Subsequently 1×PBS (0.04% BSA) was used to resuspend the cell precipitate and centrifuged at 4°C 300g for 5min (repeated twice). The candidate cells were obtained after tissue dissociation, lysis of erythrocytes and removal of dead cells, and 100 μl of 1×PBS (0.04% BSA) was added to form a cell suspension. The cell activity was detected by trypan blue staining method, and the cell activity was required to be >85%. The number of cells was counted using a hemocytometer or Countess II Automated Cell Counter, and the cell concentration was 700-1200 cells/μl.
Single-cell suspension was added to the 10x Chromium chip according to the instructions for the 10X Genomics Chromium Single-Cell 3' kit (V3), with the expectation of capturing 8,000 cells. cDNA amplification and library construction were performed according to standard protocols. Libraries were sequenced on an Illumina NovaSeq 6000 sequencing system (double-end sequencing, 150 bp) at a minimum depth of 20,000 reads per cell.

tag: strain

tag: age

value: 11 weeks old

value: male

value: Peyer patches

value: B cells

value: Wild type

value: HPD+DSS


title: PVH-neuron nucleus, retrograde HSV, sample 152, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 152-1

value: paraventricular nucleus of the hypothalamus -> (lateral) parabrachial nucleus

value: neuron

value: PB-projecting

value: retrograde HSV


title: 4CC6R_D6VGLL3_Kac2

description:
Library name: 4CC6R_D6VG3_Ac
H3K27ac ChIP-seq at differentiation day 6 with dox-induced Vgll3

value: mesenchymal stem cells

value: Dox-inducible VGLL3


title: PVH-neuron nucleus, retrograde HSV, sample 169, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 169-1


title: PVH-neuron nucleus, retrograde HSV, sample 151, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 151-1


title: 4CC22R_ConD6_Kac2

description:
Library name: 4CC22R_ConD6_Ac
H3K27ac ChIP-seq at differentiation day 6 with dox-induced TAZ2SA

value: Dox-inducible TAZ2SA

value: Adipogenic cocktail


title: 4CC23R_ConD6TAZ_Kac2

description:
Library name: 4CC23R_D6TZ_Ac
H3K27ac ChIP-seq at differentiation day 6 with dox-induced TAZ2SA

value: Adipogenic cocktail + doxycycline


title: PVH-neuron nucleus, retrograde HSV, sample 150, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 150-1


title: 16S rRNAseq of vaginal swab: 20285_Hnvaginal03

description: Library name: Hnvaginal03

value: vaginal swab


title: 16S rRNAseq of vaginal swab: 20274_Hnvaginal02

description: Library name: Hnvaginal02


title: +10 timepoint of the second day of the transition from diurnal LL to HL, replicate 3

description: Library name: Cr077_BJ_L2H_d2_p10h_B3

value: liquid culture

value: WT

value: LL to HL


title: adult_SD_DSS

description:
Library name: sample 7
all cell types
10x Genomics

value: 11 weeks old

value: male

value: Peyer patches

value: SD+DSS


title: PVH-neuron nucleus, retrograde HSV, sample 148, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 148-1

value: paraventricular nucleus of the hypothalamus -> (lateral) parabrachial nucleus


title: 16S rRNAseq of vaginal swab: 20087_Hnvaginal01

description: Library name: Hnvaginal01


title: +10 timepoint of the second day of the transition from diurnal LL to HL, replicate 2

description: Library name: Cr077_BJ_L2H_d2_p10h_B2


title: 16S rRNAseq of vaginal swab: 21011_Hnvaginal06

description: Library name: Hnvaginal06


title: +10 timepoint of the second day of the transition from diurnal LL to HL, replicate 1

description: Library name: Cr077_BJ_L2H_d2_p10h_B1


title: Cerebellum nucleus mRNA, replicate 8 (Cseq)

city: Urbana

first: Boxuan

last: Zhao

state: IL

address: 505 S Goodwin Ave

institute: UIUC

description:
Library name: cseq33 CN_mRNA
polyA RNA
cseq33_CN_barcodes.tsv.gz
cseq33_CN_features.tsv.gz
cseq33_CN_matrix.mtx.gz

data_processing:
Raw sequencing data was processed using Cell Ranger (v7.1.0) with custom genome references including SynBar and Cre genes. Nuclear libraries were processed using force-cells parameter of actual loaded amount, while synaptosomal libraries used expect-cells parameter of actual loaded amount. Barcode sequences were extracted from filtered nuclear and unfiltered synaptosomal BAM files using custom Python scripts. Sequences were collapsed using Hamming distance 1 within samples to account for sequencing errors.
Assembly: mm10
Supplementary files format and content: CellRanger output files: *barcodes.tsv.gz, *features.tsv.gz, *matriz.mtx.gz (* represents different samples)

source_name: Cerebellum

extract_protocol:
After perfusion with ice-cold PBS, target brain regions (right one-third cerebellum or bilateral pons) were dissected, homogenized in SET buffer (sucrose, Tris-HCl, EDTA, protease and RNase inhibitors), and centrifuged to separate nuclear (P1) and synaptosomal (S1) fractions. Nuclei were isolated from P1 by brief rinsing and resuspension in nuclear lysis buffer, followed by homogenization (cerebellum) or gentle mixing (pons), dilution, incubation on ice, filtration, centrifugation, washing, and staining with SiR-DNA in washing and staining buffer prior to flow cytometry. Synaptosomes were isolated from S1 by centrifugation to obtain synaptosomal pellet (P2), which was resuspended in washing and staining buffer, blocked with Fc receptor blocker, stained with anti-V5-Alexa Fluor 647 and anti-HA-PE antibodies, washed, and incubated with CellBrite 405 membrane dye. Nuclei were sorted by DNA content (SiR-DNA) and GFP expression, while synaptosomes were sorted based on scatter profiles, membrane integrity (CellBrite 405), and double-positivity for V5 and HA, and all sorted samples were collected into tubes containing appropriate collection buffers for downstream processing.
Libraries were generated using the Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1, Chromium Next GEM Chip G, and 10x Chromium Controller (10x Genomics) according to manufacturer's protocol with modifications. For each experiment, approximately 20,000-30,000 individually sorted GFP-positive nuclei or double-positive synaptosomes were loaded into each channel of the chip. For nuclear libraries, cDNA was amplified, size-selected using SPRIselect beads to separate transcriptome and barcode components, and independently constructed into mRNA libraries and barcode libraries. Synaptosome libraries were constructed using barcode-specific amplification without template switching oligonucleotides.

value: Cerebellum

tag: library type

value: mRNA


title: +8 timepoint of the second day of the transition from diurnal LL to HL, replicate 3

description: Library name: Cr077_BI_L2H_d2_p08h_B3


title: PVH-neuron nucleus, retrograde HSV, sample 145, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 145-1

value: neuron

value: PB-projecting

value: retrograde HSV


title: adult_HPD

description:
Library name: sample 6
all cell types
10x Genomics

value: B cells

value: Wild type

value: HPD


title: Cerebellum synaptosome PostRNA, replicate 8 (Cseq)

description:
Library name: cseq35 Syn_4_Post_nb
Neuronal barcode (NB)
cseq35_S4post_barcodes.tsv.gz
cseq35_S4post_features.tsv.gz
cseq35_S4post_matrix.mtx.gz

value: NB


title: PVH-neuron nucleus, retrograde HSV, sample 141, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 141-1


title: young_HPD_DSS

description:
Library name: sample 4
all cell types
10x Genomics

value: 3 weeks old

value: HPD+DSS


title: +8 timepoint of the second day of the transition from diurnal LL to HL, replicate 2

description: Library name: Cr077_BI_L2H_d2_p08h_B2

value: liquid culture

value: WT

value: LL to HL


title: young_SD_DSS

description:
Library name: sample 3
all cell types
10x Genomics

value: male

value: Peyer patches


title: PVH-neuron nucleus, retrograde HSV, sample 138, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 138-1

value: paraventricular nucleus of the hypothalamus -> (lateral) parabrachial nucleus


title: Cerebellum synaptosome PostRNA, replicate 7 (Cseq)

description:
Library name: cseq35 Syn_3_Post_nb
Neuronal barcode (NB)
cseq35_S3post_barcodes.tsv.gz
cseq35_S3post_features.tsv.gz
cseq35_S3post_matrix.mtx.gz

value: Cerebellum


title: Cerebellum synaptosome PreRNA, replicate 8 (Cseq)

description:
Library name: cseq35 Syn_4_Pre_nb
Neuronal barcode (NB)
cseq35_S4pre_barcodes.tsv.gz
cseq35_S4pre_features.tsv.gz
cseq35_S4pre_matrix.mtx.gz


title: +8 timepoint of the second day of the transition from diurnal LL to HL, replicate 1

description: Library name: Cr077_BI_L2H_d2_p08h_B1


title: +6 timepoint of the second day of the transition from diurnal LL to HL, replicate 3

description: Library name: Cr077_BH_L2H_d2_p06h_B3


title: young_HPD

description:
Library name: sample 2
all cell types
10x Genomics


title: PVH-neuron nucleus, retrograde HSV, sample 134, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 134-1


title: young_SD

description:
Library name: sample 1
all cell types
10x Genomics

value: SD


title: +6 timepoint of the second day of the transition from diurnal LL to HL, replicate 2

description: Library name: Cr077_BH_L2H_d2_p06h_B2


title: Zcchc8 KO HSC rep3

city: Hangzhou

first: Aiwei

last: Wu

state: Zhejiang

address: 2318 Yuhangtang Road

department: School of Basic Medical Sciences

institute: Hangzhou Normal University

data_processing:
Raw reads were filtered by fastp and mapped to mouse genome (mm10) using Bowtie2.Number of reads mapped to each gene were evaluated by featureCounts, and normalized as FPKM.
Assembly: mm10
Supplementary files format and content: FPKM values

source_name: bone marrow

extract_protocol:
BM cells were harvested by crushing the bones (Femur, Tibia and Hip). Then, red blood cells were lysed with Ammonium-Chloride-Potassium (ACK) buffer and the remainning cells were washed twice with PBS, lineage depleted using the Lineage Cell Depletion Kit (Miltenyi),  and FACS sorted. Total RNA was extracted from 1500 FACS-sorted LT-HSCs using Quick-RNA Kits (ZYMO) and subjected to cDNA synthesis and amplification.
Sequencing libraries were generated from 500 pg cDNA using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD503) following the manufacturer’s instructions.

value: bone marrow

value: LT-HSC

value: ZCCHC8 KO


title: Cerebellum synaptosome PostRNA, replicate 6 (Cseq)

description:
Library name: cseq35 Syn_2_Post_nb
Neuronal barcode (NB)
cseq35_S2post_barcodes.tsv.gz
cseq35_S2post_features.tsv.gz
cseq35_S2post_matrix.mtx.gz


title: Cerebellum synaptosome PreRNA, replicate 7 (Cseq)

description:
Library name: cseq35 Syn_3_Pre_nb
Neuronal barcode (NB)
cseq35_S3pre_barcodes.tsv.gz
cseq35_S3pre_features.tsv.gz
cseq35_S3pre_matrix.mtx.gz


title: PVH-neuron nucleus, retrograde HSV, sample 132, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 132-1

value: neuron

value: PB-projecting

value: retrograde HSV


title: adult_SD

description:
Library name: sample 5
all cell types
10x Genomics

value: 11 weeks old

value: B cells

value: Wild type


title: Cerebellum synaptosome PreRNA, replicate 6 (Cseq)

description:
Library name: cseq35 Syn_2_Pre_nb
Neuronal barcode (NB)
cseq35_S2pre_barcodes.tsv.gz
cseq35_S2pre_features.tsv.gz
cseq35_S2pre_matrix.mtx.gz

value: NB


title: Zcchc8 KO HSC rep2


title: +6 timepoint of the second day of the transition from diurnal LL to HL, replicate 1

description: Library name: Cr077_BH_L2H_d2_p06h_B1

value: liquid culture

value: WT


title: PVH-neuron nucleus, retrograde HSV, sample 131, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 131-1


title: PVH-neuron nucleus, retrograde HSV, sample 130, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 130-1


title: Zcchc8 KO HSC rep1


title: +4 timepoint of the second day of the transition from diurnal LL to HL, replicate 2

description: Library name: Cr077_BG_L2H_d2_p04h_B2

value: LL to HL


title: Cerebellum synaptosome PreRNA, replicate 5 (Cseq)

description:
Library name: cseq35 Syn_1_Pre_nb
Neuronal barcode (NB)
cseq35_S1pre_barcodes.tsv.gz
cseq35_S1pre_features.tsv.gz
cseq35_S1pre_matrix.mtx.gz


title: WT HSC rep3

value: wild type


title: PVH-neuron nucleus, retrograde HSV, sample 128, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 128-1

value: paraventricular nucleus of the hypothalamus -> (lateral) parabrachial nucleus


title: PVH-neuron nucleus, retrograde HSV, sample 137, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 137-1


title: WT HSC rep2


title: +2 timepoint of the second day of the transition from diurnal LL to HL, replicate 3

description: Library name: Cr077_BF_L2H_d2_p02h_B3


title: PVH-neuron nucleus, retrograde HSV, sample 127, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 127-1


title: Cerebellum nucleus PostRNA, replicate 6 (Cseq)

description:
Library name: cseq35 CN_Post_nb
Neuronal barcode (NB)
cseq35_CN_barcodes.tsv.gz
cseq35_CN_features.tsv.gz
cseq35_CN_matrix.mtx.gz

value: Cerebellum


title: +4 timepoint of the second day of the transition from diurnal LL to HL, replicate 1

description: Library name: Cr077_BG_L2H_d2_p04h_B1


title: Cerebellum nucleus mRNA, replicate 6 (Cseq)

description:
Library name: cseq35 CN_mRNA
polyA RNA
cseq35_CN_barcodes.tsv.gz
cseq35_CN_features.tsv.gz
cseq35_CN_matrix.mtx.gz

value: mRNA


title: PVH-neuron nucleus, retrograde HSV, sample 124, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 124-1


title: WT HSC rep1

value: bone marrow


title: +2 timepoint of the second day of the transition from diurnal LL to HL, replicate 2

description: Library name: Cr077_BF_L2H_d2_p02h_B2


title: iWAT_snRNA_LAKO

data_processing:
Demultiplexed fastq files were mapped to optimized mm10 mouse transcriptome (Pool et al. Nature Methods 2023) with tdTomato-WPRE-bGHpA and Adipoq-Cre transcript sequences using Cell Ranger (v7.1.0). Count matrices from Cellranger were processed by CellBender(v0.2.2) with default parameters.
Assembly: mm10
Supplementary files format and content: Barcodes, features and matrix files after Cellbender cleanup

source_name: adipose (iWAT)

extract_protocol:
Frozen iWAT (pooled from 10 mice per group) was homogenized, and nuclei were counted with the use of a LUNA-FL Automated Fluorescence Cell Counter. the nuclei were isolated by flow cytometry.
Barcoded cDNA libraries were constructed from the sorted nuclei with a 10X Genomics Chromium Instrument and cDNA synthesis kit (1000268 and 1000127, 10X genomics)

value: adipose (iWAT)

value: Lats1fl/fl; Lats2fl/fl; Rosa-LSL-tdTomato; Adipoq-Cre


title: Pons nucleus PreRNA, replicate 6 (Cseq)

description:
Library name: cseq35 PN_Pre_nb
Neuronal barcode (NB)
cseq35_PN_barcodes.tsv.gz
cseq35_PN_features.tsv.gz
cseq35_PN_matrix.mtx.gz

source_name: Pons

value: Pons


title: PVH-neuron nucleus, retrograde HSV, sample 122, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 122-1

value: neuron

value: PB-projecting


title: Pons nucleus mRNA, replicate 6 (Cseq)

description:
Library name: cseq35 PN_mRNA
polyA RNA
cseq35_PN_barcodes.tsv.gz
cseq35_PN_features.tsv.gz
cseq35_PN_matrix.mtx.gz


title: +4 timepoint of the second day of the transition from diurnal LL to HL, replicate 3

description: Library name: Cr077_BG_L2H_d2_p04h_B3


title: +2 timepoint of the second day of the transition from diurnal LL to HL, replicate 1

description: Library name: Cr077_BF_L2H_d2_p02h_B1


title: Cerebellum synaptosome PostRNA, replicate 4 (Cseq)

description:
Library name: cseq34 Syn_Post_nb
Neuronal barcode (NB)
cseq34_Spost_barcodes.tsv.gz
cseq34_Spost_features.tsv.gz
cseq34_Spost_matrix.mtx.gz


title: +1 timepoint of the second day of the transition from diurnal LL to HL, replicate 3

description: Library name: Cr077_BE_L2H_d2_p01h_B3


title: iWAT_snRNA_Control


title: PVH-neuron nucleus, retrograde HSV, sample 118, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 118-1

value: retrograde HSV


title: Cerebellum synaptosome PreRNA, replicate 4 (Cseq)

description:
Library name: cseq34 Syn_Pre_nb
Neuronal barcode (NB)
cseq34_Spre_barcodes.tsv.gz
cseq34_Spre_features.tsv.gz
cseq34_Spre_matrix.mtx.gz


title: +1 timepoint of the second day of the transition from diurnal LL to HL, replicate 2

description: Library name: Cr077_BE_L2H_d2_p01h_B2


title: PVH-neuron nucleus, retrograde HSV, sample 129, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 129-1


title: iWAT_snATAC_LAKO

library_source: genomic single cell

data_processing:
Demultiplexed fastq files were mapped to mm10 mouse genome using Cellranger-ATAC (v2.0.0). Mapped fragment files and peak files of control and mutant data were independently imported and processed with the R package Signac (v1.10.0).
Assembly: mm10
Supplementary files format and content: Filtered peak matrix, fragments, fragment index and cell matrix file from Cellrange-ATAC

extract_protocol:
Frozen iWAT (pooled from 10 mice per group) was homogenized, and nuclei were counted with the use of a LUNA-FL Automated Fluorescence Cell Counter. The nuclei were isolated with a Chromium Nuclei Isolation Kit (1000493, 10X Genomics)
Tagmentation of accessible DNA regions with sequencing adaptors was performed with a 10X Genomics Chromium Instrument and ATAC kit (1000390 and 1000162, 10X Genomics). The quality of each library was determined with an Agilent Bioanalyzer, and the libraries were sequenced with a NovaSeq 6000 system (Illumina).


title: PVH-neuron nucleus, retrograde HSV, sample 116, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 116-1


title: Pons nucleus PreRNA, replicate 5 (Cseq)

description:
Library name: cseq34.2 PN_Pre_nb
Neuronal barcode (NB)
cseq34_PN2_barcodes.tsv.gz
cseq34_PN2_features.tsv.gz
cseq34_PN2_matrix.mtx.gz


title: iWAT_snATAC_Control


title: +1 timepoint of the second day of the transition from diurnal LL to HL, replicate 1

description: Library name: Cr077_BE_L2H_d2_p01h_B1


title: PVH-neuron nucleus, retrograde HSV, sample 114, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 114-1


title: Pons nucleus mRNA, replicate 5 (Cseq)

description:
Library name: cseq34.2 PN_mRNA
polyA RNA
cseq34_PN2_barcodes.tsv.gz
cseq34_PN2_features.tsv.gz
cseq34_PN2_matrix.mtx.gz


title: 4CC19_VKOD6TAZ_Kac1

description: Vgll3 knockout; H3K27ac ChIP-seq at differentiation day 6 with dox-induced TAZ2SA

value: mesenchymal stem cells

value: Vgll3 Knockout; Dox-inducible TAZ2SA (Dox+)

value: Adipogenic cocktail + doxycycline


title: +0.5 timepoint of the second day of the transition from diurnal LL to HL, replicate 3

description: Library name: Cr077_BD_L2H_d2_p30m_B3

value: liquid culture


title: Cerebellum synaptosome PostRNA, replicate 5 (Cseq)

description:
Library name: cseq35 Syn_1_Post_nb
Neuronal barcode (NB)
cseq35_S1post_barcodes.tsv.gz
cseq35_S1post_features.tsv.gz
cseq35_S1post_matrix.mtx.gz

value: NB


title: PVH-neuron nucleus, retrograde HSV, sample 110, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 110-1


title: PVH-neuron nucleus, retrograde HSV, sample 104, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 104-1


title: Cerebellum nucleus mRNA, replicate 5 (Cseq)

description:
Library name: cseq34.2 CN_mRNA
polyA RNA
cseq34_CN2_barcodes.tsv.gz
cseq34_CN2_features.tsv.gz
cseq34_CN2_matrix.mtx.gz


title: Cerebellum nucleus PostRNA, replicate 5 (Cseq)

description:
Library name: cseq34.2 CN_Post_nb
Neuronal barcode (NB)
cseq34_CN2_barcodes.tsv.gz
cseq34_CN2_features.tsv.gz
cseq34_CN2_matrix.mtx.gz


title: 4CC23_ConD6TAZ_KAc1

description: H3K27ac ChIP-seq at differentiation day 6 with dox-induced TAZ2SA

value: Dox-inducible TAZ2SA (Dox+)


title: +0.5 timepoint of the second day of the transition from diurnal LL to HL, replicate 2

description: Library name: Cr077_BD_L2H_d2_p30m_B2

value: WT

value: LL to HL


title: 4CC22_ConD6_Kac1

value: Dox-inducible TAZ2SA (Dox-)

value: Adipogenic cocktail


title: PVH-neuron nucleus, retrograde HSV, sample 102, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 102-1

value: paraventricular nucleus of the hypothalamus -> (lateral) parabrachial nucleus


title: Pons nucleus PreRNA, replicate 4 (Cseq)

description:
Library name: cseq34.1 PN_Pre_nb
Neuronal barcode (NB)
cseq34_PN1_barcodes.tsv.gz
cseq34_PN1_features.tsv.gz
cseq34_PN1_matrix.mtx.gz


title: Pons nucleus mRNA, replicate 4 (Cseq)

description:
Library name: cseq34.1 PN_mRNA
polyA RNA
cseq34_PN1_barcodes.tsv.gz
cseq34_PN1_features.tsv.gz
cseq34_PN1_matrix.mtx.gz

value: mRNA


title: 4CC6_D6VGLL3_Kac1

description: H3K27ac ChIP-seq at differentiation day 6 with dox-induced Vgll3

value: Dox-inducible VGLL3(Dox+)


title: –2 timepoint of the second day of the transition from diurnal LL to HL, replicate 3

description: Library name: Cr077_BC_L2H_n2_m02h_B3


title: –2 timepoint of the second day of the transition from diurnal LL to HL, replicate 2

description: Library name: Cr077_BC_L2H_n2_m02h_B2


title: PVH-neuron nucleus, retrograde HSV, sample 99, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 099-1


title: 3CC8_dWW_S51A_Kac2

description: H3K27ac ChIP-seq at differentiation day 6 with dox-induced TAZ2SA/S51AΔWW


title: 3CC7_dWW_S51A_Kac1


title: PVH-neuron nucleus, retrograde HSV, sample 98, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 098-1


title: Cerebellum nucleus mRNA, replicate 4 (Cseq)

description:
Library name: cseq34.1 CN_mRNA
polyA RNA
cseq34_CN1_barcodes.tsv.gz
cseq34_CN1_features.tsv.gz
cseq34_CN1_matrix.mtx.gz

value: Cerebellum


title: Cerebellum nucleus PostRNA, replicate 4 (Cseq)

description:
Library name: cseq34.1 CN_Post_nb
Neuronal barcode (NB)
cseq34_CN1_barcodes.tsv.gz
cseq34_CN1_features.tsv.gz
cseq34_CN1_matrix.mtx.gz


title: PVH-neuron nucleus, retrograde HSV, sample 100, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 100-1

value: neuron


title: –10 timepoint of the first day of the transition from diurnal LL to HL, replicate 3

description: Library name: Cr077_BB_L2H_n1_m10h_B3


title: –2 timepoint of the second day of the transition from diurnal LL to HL, replicate 1

description: Library name: Cr077_BC_L2H_n2_m02h_B1


title: PVH-neuron nucleus, retrograde HSV, sample 96, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 096-1

value: PB-projecting


title: 3CC4_TAZ2SA_Kac2


title: –10 timepoint of the first day of the transition from diurnal LL to HL, replicate 2

description: Library name: Cr077_BB_L2H_n1_m10h_B2


title: Cerebellum synaptosome PostRNA, replicate 3 (Cseq)

description:
Library name: cseq31 Syn_Post_nb
Neuronal barcode (NB)
cseq31_Spost_barcodes.tsv.gz
cseq31_Spost_features.tsv.gz
cseq31_Spost_matrix.mtx.gz


title: 4CC18_VKOD6_Kac1

description: Vgll3 knockout; H3K27ac ChIP-seq at differentiation day 6

value: Vgll3 Knockout; Dox-inducible TAZ2SA (Dox-)


title: 3CC3_TAZ2SA_Kac1

value: mesenchymal stem cells


title: +0.5 timepoint of the second day of the transition from diurnal LL to HL, replicate 1

description: Library name: Cr077_BD_L2H_d2_p30m_B1


title: –10 timepoint of the first day of the transition from diurnal LL to HL, replicate 1

description: Library name: Cr077_BB_L2H_n1_m10h_B1


title: Pons nucleus PreRNA, replicate 3 (Cseq)

description:
Library name: cseq31 PN_Pre_nb
Neuronal barcode (NB)
cseq31_PN_barcodes.tsv.gz
cseq31_PN_features.tsv.gz
cseq31_PN_matrix.mtx.gz

value: Pons


title: PVH-neuron nucleus, retrograde HSV, sample 93, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 093-1

value: retrograde HSV


title: 3CC2_Con_Kac2

description: H3K27ac ChIP-seq at differentiation day 6


title: PVH-neuron nucleus, retrograde HSV, sample 94, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 094-1


title: 3CC1_Con_Kac1


title: +12 timepoint of the first day of the transition from diurnal LL to HL, replicate 2

description: Library name: Cr077_BA_L2H_d1_p12h_B2

value: liquid culture


title: Pons nucleus mRNA, replicate 3 (Cseq)

description:
Library name: cseq31 PN_mRNA
polyA RNA
cseq31_PN_barcodes.tsv.gz
cseq31_PN_features.tsv.gz
cseq31_PN_matrix.mtx.gz


title: PVH-neuron nucleus, retrograde HSV, sample 92, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 092-1


title: D6TAZ_Kac1

description: H3K27ac ChIP-seq at differentiation day 6 with TAZ2SA activation

value: Tamoxifen-inducible TAZ4SA(4OHT+)

value: Adipogenic cocktail + 4-OHT


title: +12 timepoint of the first day of the transition from diurnal LL to HL, replicate 3

description: Library name: Cr077_BA_L2H_d1_p12h_B3

value: WT


title: Cerebellum nucleus PostRNA, replicate 3 (Cseq)

description:
Library name: cseq31 CN_Post_nb
Neuronal barcode (NB)
cseq31_CN_barcodes.tsv.gz
cseq31_CN_features.tsv.gz
cseq31_CN_matrix.mtx.gz

value: NB


title: D6TAZ_Kac2


title: Cerebellum synaptosome PostRNA, replicate 2 (Cseq)

description:
Library name: cseq25 Syn_Post_nb
Neuronal barcode (NB)
cseq25_Spost_barcodes.tsv.gz
cseq25_Spost_features.tsv.gz
cseq25_Spost_matrix.mtx.gz


title: PVH-neuron nucleus, retrograde HSV, sample 91, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 091-1


title: +10 timepoint of the first day of the transition from diurnal LL to HL, replicate 2

description: Library name: Cr077_AZ_L2H_d1_p10h_B2

value: LL to HL


title: Cerebellum nucleus mRNA, replicate 3 (Cseq)

description:
Library name: cseq31 CN_mRNA
polyA RNA
cseq31_CN_barcodes.tsv.gz
cseq31_CN_features.tsv.gz
cseq31_CN_matrix.mtx.gz


title: +10 timepoint of the first day of the transition from diurnal LL to HL, replicate 3

description: Library name: Cr077_AZ_L2H_d1_p10h_B3


title: D6_Kac1

value: Tamoxifen-inducible TAZ4SA(4OHT-)

value: Adipogenic cocktail


title: Cerebellum synaptosome PreRNA, replicate 3 (Cseq)

description:
Library name: cseq31 Syn_Pre_nb
Neuronal barcode (NB)
cseq31_Spre_barcodes.tsv.gz
cseq31_Spre_features.tsv.gz
cseq31_Spre_matrix.mtx.gz


title: PVH-neuron nucleus, retrograde HSV, sample 88, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 088-1

value: paraventricular nucleus of the hypothalamus -> (lateral) parabrachial nucleus


title: Cerebellum synaptosome PreRNA, replicate 2 (Cseq)

description:
Library name: cseq25 Syn_Pre_nb
Neuronal barcode (NB)
cseq25_Spre_barcodes.tsv.gz
cseq25_Spre_features.tsv.gz
cseq25_Spre_matrix.mtx.gz


title: D0_Kac2

description: H3K27ac ChIP-seq at differentiation day 0


title: PVH-neuron nucleus, retrograde HSV, sample 95, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 095-1


title: Pons nucleus PreRNA, replicate 2 (Cseq)

description:
Library name: cseq25 PN_Pre_nb
Neuronal barcode (NB)
cseq25_PN_barcodes.tsv.gz
cseq25_PN_features.tsv.gz
cseq25_PN_matrix.mtx.gz


title: PVH-neuron nucleus, retrograde HSV, sample 90, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 090-1


title: PVH-neuron nucleus, retrograde HSV, sample 87, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 087-1


title: +8 timepoint of the first day of the transition from diurnal LL to HL, replicate 2

description: Library name: Cr077_AY_L2H_d1_p08h_B2


title: D0_Kac1


title: PVH-neuron nucleus, retrograde HSV, sample 86, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 086-1


title: Pons nucleus mRNA, replicate 2 (Cseq)

description:
Library name: cseq25 PN_mRNA
polyA RNA
cseq25_PN_barcodes.tsv.gz
cseq25_PN_features.tsv.gz
cseq25_PN_matrix.mtx.gz

value: mRNA


title: +8 timepoint of the first day of the transition from diurnal LL to HL, replicate 3

description: Library name: Cr077_AY_L2H_d1_p08h_B3


title: Cerebellum nucleus PostRNA, replicate 2 (Cseq)

description:
Library name: cseq25 CN_Post_nb
Neuronal barcode (NB)
cseq25_CN_barcodes.tsv.gz
cseq25_CN_features.tsv.gz
cseq25_CN_matrix.mtx.gz

value: Cerebellum


title: D6TAZ_PPARg2

description: PPARγ ChIP-seq at differentiation day 6 with TAZ4SA activation


title: D6_Kac2

description: H3K27ac ChIP-seq at differentiation day 6


title: +12 timepoint of the first day of the transition from diurnal LL to HL, replicate 1

description: Library name: Cr077_BA_L2H_d1_p12h_B1


title: +6 timepoint of the first day of the transition from diurnal LL to HL, replicate 3

description: Library name: Cr077_AX_L2H_d1_p06h_B3


title: Cerebellum nucleus mRNA, replicate 2 (Cseq)

description:
Library name: cseq25 CN_mRNA
polyA RNA
cseq25_CN_barcodes.tsv.gz
cseq25_CN_features.tsv.gz
cseq25_CN_matrix.mtx.gz


title: +6 timepoint of the first day of the transition from diurnal LL to HL, replicate 2

description: Library name: Cr077_AX_L2H_d1_p06h_B2


title: PVH-neuron nucleus, retrograde HSV, sample 89, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 089-1

value: neuron


title: D6TAZ_PPARg1


title: PVH-neuron nucleus, retrograde HSV, sample 82, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 082-1

value: PB-projecting


title: +6 timepoint of the first day of the transition from diurnal LL to HL, replicate 1

description: Library name: Cr077_AX_L2H_d1_p06h_B1


title: Cerebellum synaptosome PostRNA, replicate 1 (Cseq)

description:
Library name: cseq1 Syn_Post_nb
Neuronal barcode (NB)
cseq1_Spost_barcodes.tsv.gz
cseq1_Spost_features.tsv.gz
cseq1_Spost_matrix.mtx.gz


title: PVH-neuron nucleus, retrograde HSV, sample 79, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 079-1


title: D6_PPARg2

description: PPARγ ChIP-seq at differentiation day 6


title: +10 timepoint of the first day of the transition from diurnal LL to HL, replicate 1

description: Library name: Cr077_AZ_L2H_d1_p10h_B1


title: PVH-neuron nucleus, retrograde HSV, sample 81, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 081-1


title: +4 timepoint of the first day of the transition from diurnal LL to HL, replicate 3

description: Library name: Cr077_AW_L2H_d1_p04h_B3


title: PVH-neuron nucleus, retrograde HSV, sample 78, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 078-1


title: D0_PRg2

description: PPARγ ChIP-seq at differentiation day 0


title: Pons nucleus PreRNA, replicate 1 (Cseq)

description:
Library name: cseq1 PN_Pre_nb
Neuronal barcode (NB)
cseq1_PN_barcodes.tsv.gz
cseq1_PN_features.tsv.gz
cseq1_PN_matrix.mtx.gz


title: Cerebellum synaptosome PreRNA, replicate 1 (Cseq)

description:
Library name: cseq1 Syn_Pre_nb
Neuronal barcode (NB)
cseq1_Spre_barcodes.tsv.gz
cseq1_Spre_features.tsv.gz
cseq1_Spre_matrix.mtx.gz


title: +4 timepoint of the first day of the transition from diurnal LL to HL, replicate 2

description: Library name: Cr077_AW_L2H_d1_p04h_B2


title: D0_PRg1

description: PPARγ ChIP-seq at differentiation day 0


title: Cerebellum nucleus PostRNA, replicate 1 (Cseq)

description:
Library name: cseq1 CN_Post_nb
Neuronal barcode (NB)
cseq1_CN_barcodes.tsv.gz
cseq1_CN_features.tsv.gz
cseq1_CN_matrix.mtx.gz


title: PVH-neuron nucleus, retrograde HSV, sample 76, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 076-1


title: +4 timepoint of the first day of the transition from diurnal LL to HL, replicate 1

description: Library name: Cr077_AW_L2H_d1_p04h_B1


title: Pons nucleus mRNA, replicate 1 (Cseq)

description:
Library name: cseq1 PN_mRNA
polyA RNA
cseq1_PN_barcodes.tsv.gz
cseq1_PN_features.tsv.gz
cseq1_PN_matrix.mtx.gz


title: 3FC10_LAKO_Ac2

data_processing:
Prepared libraries were sequenced on a NovaSeq 6000 with paired-end method. (100bp reads)
CUT&Tag 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 0.005 (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) file of CUT&Tag peaks
Library strategy: CUT&Tag

extract_protocol:
Freshly dissected iWAT was snap-frozen in liquid nitrogen. Nuclei were isolated by Dounce homogenization and centrifugation, and were counted after trypan blue staining.
The library for CUT&Tag was prepared with the use of a CUT&Tag-IT Assay Kit (AT53160, Active Motif).

value: adipose (iWAT)

value: Lats1fl/fl; Lats2fl/fl; Rosa-LSL-tdTomato; Adipoq-Cre


title: PVH-neuron nucleus, retrograde HSV, sample 75, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 075-1


title: 3FC9_LAKO_Ac1


title: D6_PPARg1

description: PPARγ ChIP-seq at differentiation day 6

value: mesenchymal stem cells


title: Cerebellum nucleus mRNA, replicate 1 (Cseq)

description:
Library name: cseq1 CN_mRNA
polyA RNA
cseq1_CN_barcodes.tsv.gz
cseq1_CN_features.tsv.gz
cseq1_CN_matrix.mtx.gz


title: PVH-neuron nucleus, retrograde HSV, sample 74, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 074-1

value: retrograde HSV


title: +2 timepoint of the first day of the transition from diurnal LL to HL, replicate 2

description: Library name: Cr077_AV_L2H_d1_p02h_B2

value: liquid culture


title: PVH-neuron nucleus, retrograde HSV, sample 73, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 073-1


title: +2 timepoint of the first day of the transition from diurnal LL to HL, replicate 1

description: Library name: Cr077_AV_L2H_d1_p02h_B1


title: +1 timepoint of the first day of the transition from diurnal LL to HL, replicate 3

description: Library name: Cr077_AU_L2H_d1_p01h_B3


title: PVH-neuron nucleus, retrograde HSV, sample 71, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 071-1


title: 10/2-Trikine +PD1 TILs, scRNA-seq

city: Stanford

first: Yang

address: Beckman B169B, 279 Campus Drive

department: MCP

institute: Stanford University

description: Library name: Combo

data_processing:
The fastq files were generated and demultiplexed by cellranger mkfastq from 10x Genomics, and primary data analysis was performed with Cell Ranger
Assembly: mm10
Supplementary files format and content: Tab-seperated values files and matrix files

source_name: primary cells

growth_protocol: tumor infiltrating T cells

extract_protocol:
F1 mice were inoculated s.c. with 5 × 10⁵ KP1 cells and received i.p. administration of mono-IL-10 or IL-10/2-Trikine (3 μg functional cytokine per dose) every other day from day 7 to day 19, along with anti-PD-1 antibody (BioXcell, 200 μg per dose, clone RMP1-14) on days 7, 11, 15, and 19. On day 19, mice were sacrificed and tumors were collected. Tumor-infiltrating leukocytes were enriched by density gradient centrifugation using Ficoll-Paque PLUS (Cytiva), followed by surface marker and DAPI staining (Thermo Fisher Scientific). Live CD45⁺ leukocytes were sorted using a Sony SH800 Cell Sorter (Sony Biotechnology) for Single cell RNA sequencing.
10x 3' Gene Expression v3.1

treatment_protocol: cytokines

value: tumor

value: Mouse T cells

value: Wild-type

value: 10/2-Trikine + PD1


title: 10/2-Trikine TILs, scRNA-seq

description: Library name: Trikine


title: +2 timepoint of the first day of the transition from diurnal LL to HL, replicate 3

description: Library name: Cr077_AV_L2H_d1_p02h_B3

value: WT

value: LL to HL


title: Supermono10 TILs, scRNA-seq

description: Library name: 10


title: +1 timepoint of the first day of the transition from diurnal LL to HL, replicate 2

description: Library name: Cr077_AU_L2H_d1_p01h_B2


title: PVH-neuron nucleus, retrograde HSV, sample 70, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 070-1


title: PVH-neuron nucleus, retrograde HSV, sample 77, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 077-1


title: OK_3

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

data_processing:
Reads were mapped on GRCm38/mm10 mouse reference genome and quantified using CLC Genomics Workbench version 12.0 (Qiagen).
Read counts were normalized by calculating number of reads per kilobase per million (RPKM) for each transcript in individual samples using the CLC Genomic Workbench software version 12.0 (Qiagen).
Filtering characteristics of fold-change and false discovery rate (FDR) were used to identify the DEGs.
Assembly: GRCm38/mm10
Supplementary files format and content: Excel file includes raw read counts and RPKM normalized values for all genes from each sample.

source_name: Skeletal muscle

extract_protocol:
NADS knockout mice were obtained from the International Mouse Phenotyping Consortium (MMRRC:048728-UCD). RNA extraction from murine muscle tissue was performed by using TRI reagent (Molecular Research Center, Inc., Cincinnati, OH, USA) according to the supplier’s protocol. Total RNAs were purified by using a Qiagen RNeasy® mini kit. RNA concentrations were measured by Thermo Scientific NanoDrop One.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: skeletal muscle

tag: strain background

value: NADS knockout mice

value: male

tag: time


title: OK_4


title: sIL-2 + IL-21 TILs, scRNA-seq

description: Library name: 2Pos21

extract_protocol:
For the low dose regimen of sIL-2, sIL-2 + IL-21, or IL-2/21-treatment in the B16F10 +pmel ACT model, tumors from mice were harvested on day 18 following tumor injection. Tumorswere minced and dissociated using a gentleMACS Octo Dissociator. TILs were collected forsequencing by sorting for live, single cell, Thy1.1+CD8+ cells on a Sony Cell Sorter SH800S.
10x 3' Gene Expression v3.1

value: TCR transgenic


title: +1 timepoint of the first day of the transition from diurnal LL to HL, replicate 1

description: Library name: Cr077_AU_L2H_d1_p01h_B1


title: 3FC8_Control_Ac2


title: OK_2


title: PVH-neuron nucleus, retrograde HSV, sample 68, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 068-1

value: paraventricular nucleus of the hypothalamus -> (lateral) parabrachial nucleus

value: neuron


title: OK_1


title: PVH-neuron nucleus, retrograde HSV, sample 69, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 069-1

value: PB-projecting


title: PVH-neuron nucleus, retrograde HSV, sample 65, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 065-1


title: +0.5 timepoint of the first day of the transition from diurnal LL to HL, replicate 2

description: Library name: Cr077_AT_L2H_d1_p30m_B2


title: YK_4


title: 3FC7_Control_Ac1

value: adipose (iWAT)


title: YK_2


title: Bird 20, PR, pineal gland

city: Tromsø

first: Jana

last: Kalinova

address: Postboks 6050 Stakkevollan

country: Norway

institute: UiT The Arctic University of Norway

description: Library name: 20_P

data_processing:
Long-read RNA-seq: Raw circular consensus sequences (CCS) were deconcatenated at segmentation adapter positions using skera split generating segmented reads (S-reads). Demultiplexing and primer removal were performed using lima (submited raw files have undergone these pre-processing steps). Isoseq refine was used to obtain full-length non-concatemer reads (FLNC-reads) and to trim poly(A) tails. FLNC-reads were clustered at the isoform level to generate high-quality transcript sequences using isoseq cluster2. Isoforms were aligned to a reference genome using minimap2. Identification and quantification of known and novel isoforms was performed using TALON.
Short-read RNA-seq: Raw sequences in fastq format were mapped to the Rock ptarmigan genome using STAR aligner. Reads for each exons were summarized via featureCounts using the Rock ptarmigan gff annotation file, manually modified to account for newly discovered VA opn exons. Raw exon counts were analyzed with edgeR separately for each tissue (hypothalamus, retina, pineal gland).
snRNAseq: Raw bcl files from each flow cell directory were demultiplexed into fastq files using cellranger mkfastq. Custom reference was created via cellranger mkref. The gtf file was filtered via cellranger mkgtf prior to creating the reference as per 10x Genomics instructions.  Furthermore, the gtf file was manually modified to (a) include newly discovered VA opn exons and (b) allow for counting of individual exons of the VA opn gene. The sequencing reads in fastq format were aligned to the reference via the cellranger count pipeline. Each library (n=4) was processed in a separate run of cellranger count. Subsequently, 2 libraries originating from the same sample (i.e., 1A+1B and 2A+2B) were combined via cellranger aggr. As a result, this pipeline outputted two filtered feature-barcode matrices (Sample1, Sample2).
Assembly: GCF_023343835.1
Supplementary files format and content: long-read RNA-seq: gtf file - annotation from the TALON database, tsv file - read counts for TALON isoforms
Supplementary files format and content: short-read RNA-seq: csv file - raw counts per exon for each sample
Supplementary files format and content: snRNAseq: tsv and mtx files

organism: Lagopus muta hyperborea

source_name: pineal gland

extract_protocol:
RNA extraction: From hypothalamus and retina, total RNA was extracted using TRI Reagent (Invitrogen™). From the pineal gland, total RNA was extracted using RNeasy Plus Micro Kit (Qiagen™). Nuclei isolation was performed as described in Ayhan et al. (2021) with minor adjustmets.
long-read RNA-seq: Kinnex Full-Length RNA Kit; short-read RNA-seq: DNBSEQ Eukaryotic Strand-specific mRNA library; snRNAseq: 10x Chromium Single Cell 3’ Reagents Kit

value: pineal gland


title: Bird 22, PR, pineal gland

description: Library name: 22_P


title: –10 timepoint of the second day of the transition from diurnal HL to LL, replicate 3

description: Library name: Cr077_AS_H2L_n2_m10h_B3

value: HL to LL


title: +12 timepoint of the second day of the transition from diurnal HL to LL, replicate 3

description: Library name: Cr077_AR_H2L_d2_p12h_B3

value: liquid culture


title: Bird 19, PR, pineal gland

description: Library name: 19_P


title: 2/21-trikine TILs, scRNA-seq

description: Library name: 2-trikine

value: tumor


title: YK_1


title: PVH-neuron nucleus, retrograde HSV, sample 64, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 064-1

value: retrograde HSV


title: OW_4

value: Wild type control


title: Bird 18, PR, pineal gland

description: Library name: 18_P


title: +12 timepoint of the second day of the transition from diurnal HL to LL, replicate 2

description: Library name: Cr077_AR_H2L_d2_p12h_B2


title: YK_3


title: PVH-neuron nucleus, retrograde HSV, sample 57, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 057-1


title: OW_3


title: sIL-2 TILs, scRNA-seq

description: Library name: 2

value: Mouse T cells


title: Bird 21, PR, pineal gland

description: Library name: 21_P


title: +12 timepoint of the second day of the transition from diurnal HL to LL, replicate 1

description: Library name: Cr077_AR_H2L_d2_p12h_B1

value: WT


title: –10 timepoint of the second day of the transition from diurnal HL to LL, replicate 1

description: Library name: Cr077_AS_H2L_n2_m10h_B1


title: PVH-neuron nucleus, retrograde HSV, sample 54, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 054-1


title: OW_2


title: +0.5 timepoint of the first day of the transition from diurnal LL to HL, replicate 1

description: Library name: Cr077_AT_L2H_d1_p30m_B1

value: LL to HL


title: PVH-neuron nucleus, retrograde HSV, sample 58, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 058-1


title: Bird 16, BR, pineal gland

description: Library name: 16_P


title: –10 timepoint of the second day of the transition from diurnal HL to LL, replicate 2

description: Library name: Cr077_AS_H2L_n2_m10h_B2


title: PVH-neuron nucleus, retrograde HSV, sample 62, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 062-1


title: PVH-neuron nucleus, retrograde HSV, sample 61, lib. 1

description: Library name: Mm PVH LPBN-projecting HSV 061-1


title: Bird 15, BR, pineal gland

description: Library name: 15_P


title: +10 timepoint of the second day of the transition from diurnal HL to LL, replicate 3

description: Library name: Cr077_AQ_H2L_d2_p10h_B3


title: PVH-neuron nucleus, retrograde AAV, sample 223, lib. 1

description: Library name: Mm PVH LPBN-projecting AAV 223-1

value: retrograde AAV


title: OW_1

value: skeletal muscle


title: YW_4

value: male


title: +10 timepoint of the second day of the transition from diurnal HL to LL, replicate 2

description: Library name: Cr077_AQ_H2L_d2_p10h_B2


title: PVH-neuron nucleus, retrograde AAV, sample 203, lib. 1

description: Library name: Mm PVH LPBN-projecting AAV 203-1


title: YW_3


title: PVH-neuron nucleus, retrograde AAV, sample 201, lib. 1

description: Library name: Mm PVH LPBN-projecting AAV 201-1


title: Bird 13, PI, pineal gland

description: Library name: 13_P


title: PVH-neuron nucleus, retrograde AAV, sample 214, lib. 1

description: Library name: Mm PVH LPBN-projecting AAV 214-1


title: +8 timepoint of the second day of the transition from diurnal HL to LL, replicate 2

description: Library name: Cr077_AP_H2L_d2_p08h_B2


title: PVH-neuron nucleus, retrograde AAV, sample 199, lib. 1

description: Library name: Mm PVH LPBN-projecting AAV 199-1


title: Bird 14, BR, pineal gland

description: Library name: 14_P


title: +8 timepoint of the second day of the transition from diurnal HL to LL, replicate 3

description: Library name: Cr077_AP_H2L_d2_p08h_B3


title: YW_2


title: YW_1


title: Bird 12, PI, pineal gland

description: Library name: 12_P


title: Bird 11, PI, pineal gland

description: Library name: 11_P


title: Bird 10, PI, pineal gland

description: Library name: 10_P


title: +10 timepoint of the second day of the transition from diurnal HL to LL, replicate 1

description: Library name: Cr077_AQ_H2L_d2_p10h_B1


title: PVH-neuron nucleus, retrograde AAV, sample 197, lib. 1

description: Library name: Mm PVH LPBN-projecting AAV 197-1


title: Bird 6, SP, pineal gland

description: Library name: 6_P


title: 12-week old male KPC, scRNA-seq replicate 2

city: NAGOYA

first: XINGXING

last: WANG

state: 愛知県

address: 65 Tsurumai-cho, Showa-ku

department: cancer biology

institute: Nagoya University

data_processing:
The read count was quantified using the Cell Ranger version 6.0.0 count pipeline (10x Genomics) with default parameters.
The Seurat v4.0.5 was used for downstream analysis.
Assembly: mm10
Supplementary files format and content: tab-separated values files and matrix files

source_name: pancreas

extract_protocol:
pancreatic tissue were dissociated into single cells using a MACS Tumor Dissociation Kit
The scRNA-seq libraries were prepared using  using Chromium Single Cell 3′ Reagent Kits v3.1 (10x Genomics).

value: pancreas

value: 12-week old

value: Unfractionated live cell mixtures

value: KPC (Pdx1cre/+; LSL-KrasG12D/+; LSL-Trp53+/R172H)


title: +6 timepoint of the second day of the transition from diurnal HL to LL, replicate 2

description: Library name: Cr077_AO_H2L_d2_p06h_B2


title: +6 timepoint of the second day of the transition from diurnal HL to LL, replicate 1

description: Library name: Cr077_AO_H2L_d2_p06h_B1


title: PVH-neuron nucleus, retrograde AAV, sample 145, lib. 1

description: Library name: Mm PVH LPBN-projecting AAV 145-1

value: paraventricular nucleus of the hypothalamus -> (lateral) parabrachial nucleus

value: neuron

value: PB-projecting


title: Bird 5, SP, pineal gland

description: Library name: 5_P

value: pineal gland


title: 12-week old male KPC, scRNA-seq replicate 1


title: 12-week old male WT, scRNA-seq replicate 2

value: Wild type


title: PVH-neuron nucleus, retrograde AAV, sample 120, lib. 1

description: Library name: Mm PVH LPBN-projecting AAV 120-1


title: +4 timepoint of the second day of the transition from diurnal HL to LL, replicate 3

description: Library name: Cr077_AN_H2L_d2_p04h_B3

value: liquid culture

value: HL to LL


title: PVH-neuron nucleus, retrograde AAV, sample 34, lib. 1

description: Library name: Mm PVH LPBN-projecting AAV 034-1


title: Bird 4, SP, pineal gland

description: Library name: 4_P


title: Bird 22, PR, retina

description: Library name: 22_R

source_name: retina

value: retina


title: +8 timepoint of the second day of the transition from diurnal HL to LL, replicate 1

description: Library name: Cr077_AP_H2L_d2_p08h_B1

value: WT


title: D6 biol rep2

data_processing:
Prepared libraries were sequenced on a NovaSeq 6000 with paired-end method. (100bp reads)
ATAC-seq reads were trimmed using Trim Galore version 0.6.7 and aligned to the UCSC mm10 genome using Bowtie2 version 2.4.4
Duplicates were removed using Picard MarkDuplicates version 2.26.3.
Peaks were called using MACS3 version 3.0.0b1 with q-value cut-off 0.05.
BedGraph files were generated from -B parameter of MACS3 and loca bias-substracted files were converted to bigWig files.
Assembly: mm10
Supplementary files format and content: BED(narrowPeak) file of ATAC-seq peaks

extract_protocol:
Nuclear suspensions obtained from 100,000 cells were treated with assembled Tn5 transposase for 30 min at 37°C. Tagmented DNA was cleaned up with a MinElute PCR Purification Kit (28006, Qiagen) before library preparation.
Library preparation for ATAC-seq was performed with the use of an ATAC-seq kit (AT53150, Active Motif) and the Omni-ATAC protocol (Corces et al. 2017)

value: mesenchymal stem cells

tag: condition

value: Adipogenic cocktail + 4-OHT


title: Bird 2, SP, pineal gland

description: Library name: 2_P


title: +4 timepoint of the second day of the transition from diurnal HL to LL, replicate 2

description: Library name: Cr077_AN_H2L_d2_p04h_B2


title: Bird 21, PR, retina

description: Library name: 21_R


title: D6TAZ biol rep1


title: D6TAZ biol rep2


title: PVH cells, female, sample 7, drop 1, RT-rxn B, lib. 2

description:
Library name: Mm PVH 7F-1B-2
Drop-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. For each sample preparation, 4-6 male or female mice were pooled.
Pooled tissue samples were digested in papain solution with DNAse for 1hr at 37C with gentle agitation, according to a published protocol (Saxena A, et al.) except that an entire vial of papain was used in a 1.6mL final reaction volume. Digestion was stopped by dilution with “EBSS #2” 56, with 10% fetal bovine serum used in place of the ovomucoid protease inhibitor. Tissue was centrifuged at 300×g for 5 min, re-suspended in the modified EBSS #2, then gently triturated using a series of 5 Pasteur pipettes with tips fire-polished to incrementally smaller openings. The resulting cell suspension was divided between two microfuge tubes, diluted with Drop-seq buffer (Macosko et al., 2015) to a volume of 1.5mL per tube. Cells were then washed twice by centrifugation at 300×g for 5 min, followed by re-suspension in Drop-seq buffer. Drop-seq buffer consisted of: 5% weight/volume trehalose; 1x Hank’s Buffered Salt Solution (magnesium- and calcium-free); 2.13mM MgCl2; 2mM MgSO4; 1.26mM CaCl2; 1mM glucose; 0.01% bovine serum albumin (molecular biology grade). Cells were filtered through a 20um mesh, diluted to 220 cells/uL based on cell concentration estimates from a hemacytometer, and then kept on ice until use. Drop-seq was performed as in the reference (Macosko et al., 2015) but with the following modifications: first, flow rates of 2.1 mL/hr were used for each aqueous suspension, and 12 mL/hr for the oil. Second, libraries were sequenced on the Illumina NextSeq 500, using 1.7 pM in a volume of 1.2 mL HT1 and 3 mL of 0.3 μM Read1CustSeqB.

value: female

value: paraventricular nucleus of the hypothalamus

value: ad libitum feeding


title: D6 biol rep1


title: PVH-neuron nucleus, retrograde AAV, sample 27, lib. 1

description: Library name: Mm PVH LPBN-projecting AAV 027-1

value: retrograde AAV


title: 12-week old male WT, scRNA-seq replicate 1

value: pancreas

value: 12-week old

value: male

value: Unfractionated live cell mixtures


title: PVH cells, female, sample 7, drop 1, RT-rxn A, lib. 1

description:
Library name: Mm PVH 7F-1A-1
Drop-seq; read 1 (20nt) contains cell barcode (12nt) then UMI (8nt); read 2 (60nt) contains contains transcript


title: PVH cells, female, sample 6, drop 2, RT-rxn A, lib. 1

description:
Library name: Mm PVH 6F-2A-1
Drop-seq; read 1 (20nt) contains cell barcode (12nt) then UMI (8nt); read 2 (60nt) contains contains transcript


title: Bird 20, PR, retina

description: Library name: 20_R


title: PVH cells, female, sample 7, drop 1, RT-rxn A, lib. 2

description:
Library name: Mm PVH 7F-1A-2
Drop-seq; read 1 (20nt) contains cell barcode (12nt) then UMI (8nt); read 2 (60nt) contains contains transcript


title: +1 timepoint of the second day of the transition from diurnal HL to LL, replicate 3

description: Library name: Cr077_AL_H2L_d2_p01h_B3


title: Bird 19, PR, retina

description: Library name: 19_R