title: RNA - shRNF8.rep3 [R3]

city: Toronto

first: Razq

last: Hakem

state: Ontario

address: TMDT, 101 College Street. Rm13-310

department: Princess Margaret Cancer Centre

institute: University Health Network

description: counts.txt

data_processing:
Raw reads were trimmed using trim_galore (v. 0.6.6)
Reads were aligned to the hg38 genome using Bowtie2 (v. 2.2.6; DRIP-seq) or STAR (v. 2.7.9a)
Low-quality reads and multimappers were removed using samtools (v. 1.14)
Duplicates were marked and removed using Picard (v. 2.10.9; DRIP-seq)
Peaks were called for DRIP-seq alignments using MACS2 (v. 2.2.7.1)
Bigwig files were generated using deeptools (v. 3.5.1) bamCompare normalizing sequencing depth and subtracting inputs. Averages of each condition were generated using bigwigCompare or wiggletools mean (v. 1.2.11).
RNA-seq reads were counted to exons features of hg38 using featureCounts (subread v. 2.0.1)
Assembly: hg38
Supplementary files format and content: Bigwig files of DRIP signal in 10bp bins normalized  to sequencing depth and subtracting inputs. Raw RNA-seq gene counts.

source_name: MDA MB 436

growth_protocol: MDA-MB-436 cells were cultured in high-glucose Dulbecco's Modified Eagle Medium containing HEPES buffer, penicillin, and streptomycin supplemented with 10% fetal bovine serum.

extract_protocol:
DNA-RNA hybrid was immunoprecipitated from sonicated chromatin using S9.6 antibody for DRIP-seq samples. Total RNA extraction was used for RNA-seq samples.
DRIP-seq samples were prepared and sequenced by Novogene using their ChIP-seq protocols (NEB Next Ultra II DNA Library preparation kit) and RNA-seq samples were prepared and sequenced by Novogene using their mRNA-seq protocols.

treatment_protocol: Dox-inducible lentiviral transduction of shScr or shRNF8 in MDA-MB-436 cells

value: MDA MB 436

tag: condition


title: 7-5M_F3-28_M28L_HOM_5xFAD_Ctx

status: Public on Sep 14 2023

type: SRA

city: Stanford

first: Andy

middle: P

last: Tsai

state: California

address: 290 Jane Stanford Way E365

country: USA

institute: Stanford University

description:
Bulk RNA-seq
RNAseq_STAR_featureCounts_matrix.tsv.gz

library_source: transcriptomic

data_processing:
FASTQ files were aligned to the mouse genome reference version gencode.vM26 by STAR 2.7.2b. Reads mapped to each gene were counted using featureCounts.
Assembly: gencode.vM26
Supplementary files format and content: tab-delimited text files include read counts for each Sample

molecule: total RNA

organism: Mus musculus

source_name: brain, cortex

extract_protocol:
RNA was isolated by chloroform extraction and purified using the Purelink RNA Mini Kit
RNA libraries for RNA-seq were prepared using KAPA mRNA HyperPrep kit following manufacturer's protocols.

tag: tissue

value: brain, cortex

tag: age

tag: genotype

tag: treatment

value: Transgenic mice


title: LPS+0-3

city: Shanghai

first: Sun

middle: Jia

last: Ming

address: No. 639, Zhi Zao Ju Road,

department: Department of Plastic & Reconstructive Surgery

country: China

institute: Shanghai Ninth People’s Hospital

data_processing:
Basecalls performed using  Solexa pipeline v1.8
The trimmed reads (trimmed 5’,3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.0.5)software
The transcript abundances for each sample was estimated with StringTie（1.3.1c）
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.6.0)
Genome_build: GRCm38
Supplementary_files_format_and_content: FPKM value for gene and transcript

extract_protocol:
fresh frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
The total RNA was processed by NEBNext® Poly(A) mRNA Magnetic Isolation Module (or rRNA removal by RiboZero Magnetic Gold Kit) to enrich mRNA, and the product RNA was used for construction Library, via KAPA Stranded RNA-Seq Library Prep Kit (Illumina). Sequencing libraries, denatured by 0.1 M NaOH to generate single-stranded DNA, as amplified in situ Illumina cBot (TruSeq SR Cluster Kit v3-cBot-HS (# GD-401-3001, Illumina)). The ends of the generated fragments was used to run 150 Cycles by the Illumina HiSeq 4000 Sequencer.
RNA libraries were prepared for sequencing using standard Illumina Hiseq protocols.

tag: group


title: 7-5M_F3-1190_WT_5xFAD_Ctx


title: KU087t

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

data_processing:
Raw cDNA reads are aligned to the reference genome (hg19) using the spliced gap aligner STAR, with count-based quantitation carried out via the Subread package featureCounts at the gene levels. The count data were normalized using “Relative Log Expression” normalization (RLE) implemented in the DESeq2 R package. Poor-quality transcriptome profiles were determined based on inter-sample correlation <0.7 and excluded from the subsequent analyses.
Assembly: hg19
Supplementary files format and content: .gct file format (tab-delimited text) including normalized gene expression levels normalized within 106 1st biopsy tissues (NAFLD.HUn106.gct) and within the 58 high-risk patients with paired biopsy tissues (NAFLD.HUn164.gct).

organism: Homo sapiens

source_name: Liver

extract_protocol:
RNA was isolated from 10 micron-thick FFPE tissue using High Pure RNA Paraffin kit (Roche) according to manufacturer’s protocol.
Truseq RNA Exome kit (Illumina, CA) following manufacturer’s protocol.
Exome-enriched RNA-seq

value: Liver

tag: Sex

value: Male

tag: recurrence

value: Yes


title: 7-5M_F2-24_P522R_HOM_5xFAD_Ctx


title: LPS+0-2


title: KU086t

value: No


title: RNA - shRNF8.rep2 [R2]

country: Canada

description: counts.txt

molecule: polyA RNA

tag: cell line


title: RNA - shRNF8.rep1 [R1]

description: counts.txt


title: NC-3

value: control


title: 7-5M_F2-1189_WT_5xFAD_Ctx


title: KU085t1


title: RNA - shScr.rep3 [C3]

description: counts.txt

value: WT


title: NC-2


title: KU081t


title: DRG2b

city: Chicago

first: Rachel

middle: E

last: Miller

address: 1735 W Harrison St

institute: Rush University Medical Center

description: Visium 10X Genomics

data_processing:
Fastq.gz files were generated and demultiplexed with Spaceranger 1.3.0
Raw sequencing data was processed through the Spaceranger (v1.3.0) pipeline. Loupe browser files and filtered matrices were generated.
Assembly: gencode v39
Supplementary files format and content: filtered_feature_bc_matrix.h5 (counts matrix from space ranger)
Supplementary files format and content: web_summary.html (metrics from space ranger)
Supplementary files format and content: .cloupe (cloupe file from space ranger)
Supplementary files format and content: image.png
Library strategy: Spatial Transcriptomics

source_name: Lumbar DRG

extract_protocol:
Human DRG was harvested and flash-frozen postmortem. Samples were embedded in OCT and sectioned at 16µm onto a 10x Visium expression slide (Serial numbers V11N01-301-A1 and V11N01-301-B1) and visualized with H&E. RNA within the tissue was hybridized to barcoded probes according to manufacturer’s protocol.
Libraries were prepared with the Visium Spatial Gene Expression FF kit V1 from 10X Genomics and sequenced on an SP 28x150nt lane in a NovaSeq 6000.

value: Female

value: Lumbar DRG

value: 96 years

tag: biol rep


title: RNA - shScr.rep2 [C2]

description: counts.txt


title: RNA - shScr.rep1 [C1]

description: counts.txt


title: KU079t


title: 7-5M_F1-106_P522R_HOM_5xFAD_Ctx


title: KU078t


title: 7-5M_F-8_P522R_HOM_5xFAD_Ctx


title: DRIP - shRNF8.Input.rep2 [RNF8_Input2]

library_source: genomic

molecule: genomic DNA


title: PolyA RNA ONS Rep 3

city: Cold Spring Harbor

first: Robert

middle: A

last: Martienssen

state: NY

address: 1 Bungtown Rd

department: Delbruck Bldg.

institute: Cold Spring Harbor Laboratory

data_processing:
Reads from each sample were mapped against the 21,830 predicted transcripts of the Lemna gibba draft genome v0.5.1 (www.lemna.org; genomevolution.org/coge/GenomeInfo.pl?gid=25249) using Bowtie (Langmead and Salzberg 2012).
Differential expression analysis for the two conditions (INS, ONS) was performed using the DESeq package (www.bioconductor.org, v1.20.0, (Anders and Huber 2010). This procedure included normalization of RNA-seq read count data (estimateSizeFactors, using default parameters) and the negative binominal test as implemented in DESeq. Significant differential expressed genes were defined for an adjusted p-value ≤ 5% (Benjamini-Hochberg anjustment for multiple testing) and a more than four-fold change in gene expression between conditions.
Genome_build: Lemna gibba 7742a draft v0.5.1
Supplementary_files_format_and_content: DESeq differential expression analysis full tabular output

organism: Lemna gibba

source_name: Frond tissue

growth_protocol: Axenic cultures of Lemna gibba G3 7742a were obtained from Rutgers University Duckweed Stock Cooperative (www.ruduckweed.org, ID 7742a/DWC131) and were cultured in SH medium (Sigma S6765, half as manufacturer’s recommended concentration, 1.6g/L)  (Schenk and Hildebrandt 1972) with 5 g/l glucose (pH 5.7). Fronds were cultured axenically in T-75 cell culture flask with vented caps filled with 100 ml of the culture medium, at 24°C, under continuous fluorescent light (100 µmol*m^-2*s^-1).

extract_protocol:
Fronds grown on inorganic nitrogen or on organic nitrogen medium were harvested and immediately frozen in liquid nitrogen. For each condition three biological replicates were analyzed. Total RNA was extracted by grinding 200 mg frozen tissue to a fine powder in liquid nitrogen with a mortar and pestle, followed by extraction with TRIzol Reagent (Invitrogen) and ethanol precipitation. Total RNA was resuspended and treated with RQ1 RNase-free DNase (Promega) on an RNA Clean & Concentrator-5 column (Zymo). The purity and concentration of RNA were determined by a NanoDrop Nd-1000 spectrophotometer (Thermo Scientific) and a Qubit fluorometer (Qiagen).
Polyadenylated RNA was enriched from total RNA with the Dynabeads mRNA Purification Kit (Life Technologies). Indexed, directional RNA-seq libraries were prepared with ScriptSeq v2 reagents (Epicentre) from 40-50 ng of polyA-selected RNA according to the manufacturer’s instructions. Libraries were sequenced on an Illumina HiSeq 2000 instrument generating 101bp paired-end reads.

treatment_protocol: The inorganic SH medium contains ammonium phosphate monobasic (1.3 mM) and potassium nitrate (12.4 mM) as nitrogen sources. For organic nitrogen growth medium these inorganic nitrogen containing salts were replaced by equal concentration of potassium phosphate monobasic and potassium chloride, respectively. Gln was added at 6.85 mM in order to provide nitrogen at the same concentration as in the SH medium.

tag: nitrogen source

value: organic

value: frond


title: PolyA RNA ONS Rep 1


title: KU077t2


title: PolyA RNA ONS Rep 2


title: PolyA RNA INS Rep 3

value: inorganic


title: DOCA-CRE_rep3

city: Wauwatosa

first: Ibrahim

last: Vazirabad

state: Wisconsin

address: 8915 W Connell Ave

department: Physiology

institute: Medical College of Wisconsin

data_processing:
Raw reads were demultiplexed and quality of pre-aligned data was computed by FastQC
Reads were aligned to the Gencode vM23 (GRCm38.p6) mouse reference genome with Star
Data was then further processed in the MAPRSeq3 workflow to obtain read counts at the gene and exon levels
Aligned data was inspected via RSeQC modules
Assembly: Gencode vM23 (GRCm38.p6)
Supplementary files format and content: tab-delimited text files with raw counts for each Sample.
Supplementary files format and content: tab-delimited text files with RPKM values for each Sample.

source_name: rostral ventrolateral nucleus

growth_protocol: This study was conducted using C57BL/6J mice (Jackson Laboratories, ME) and mice carrying floxed atp6ap2 encoding Pro-renin receptor. All mice were housed in a temperature and humidity-controlled facility with ad libitum access to Teklad diet and chlorinated water.

extract_protocol:
Total RNA was extracted using TRIzol (Thermo Fisher Scientific).
RNA libraries were prepared using Takara low-input, SMART-seq stranded preparation kit according to manufacturer protocol

treatment_protocol: Female PRRflox mice were divided into 4 groups: a)  PRRf/y + AAV-GFP (Baseline-WT), b)  PRRf/y + AAV-CRE-GFP (Baseline-CRE), c)  PRRf/f + AAV-GFP + DOCA-salt (DOCA- WT), and d)  PRRf/f + AAV-CRE-GFP +DOCA-salt (DOCA-CRE). At least 3 weeks were allowed to induce expression of Cre. Subsequently, groups c and d were subjected to DOCA-salt hypertension by a subcutaneous implant of 50 mg DOCA pellet (Deoxycorticosterone acetate), after which 0.15 M NaCl saline (dissolved in deionized water) was offered as the only source of drinking water. Tissues were collected after 13 days on DOCA-salt regimen.In Groups a and b, tissues were collected at 3 weeks post AAV injections.

value: rostral ventrolateral nucleus

value: KO of atp6ap2

value: DOCA-salt


title: DOCA-CRE_rep2


title: DRIP - shRNF8.Input.rep1 [RNF8_Input1]

value: MDA MB 436


title: DRIP - shRNF8.RNase.rep4 [RNF8RH_4]

tag: chip antibody


title: PolyA RNA INS Rep 2


title: DOCA-CRE_rep1


title: KU075t


title: PolyA RNA INS Rep 1


title: KU074t


title: 7-5M_F1-1180_WT_5xFAD_Ctx

value: brain, cortex

value: Transgenic mice


title: DRIP - shRNF8.RNase.rep2 [RNF8_RH2]


title: DOCA-WT_rep4

value: Wild Type


title: KU072t

value: Liver

value: Male

value: Yes


title: DOCA-WT_rep3


title: DRIP - shRNF8.RNase.rep1 [RNF8_RH1]


title: Macrophages from cattle infected with Mb534 and cocultured with autologous lymphocytes 3

city: CABA

first: Maria

middle: Mercedes

last: Bigi

address: Paraguay 2155 piso 5 M1

country: Argentina

institute: INSTITUTO DE INVESTIGACIONES BIOMEDICAS

data_processing:
All data analyses steps were carried out using the Galaxy server (usegalaxy.org) (Jalili et al., 2020).
Data from transcript sequencing was mapped to the bos Tau9 reference genome (GCF_002263795.1) using HISAT2 (Galaxy Version 2.2.1+galaxy1) (Kim et al., 2019).
Transcripts were assembled and merged from the mapped reads with StringTie (Galaxy Version 2.1.72.1.7+galaxy1) (Pertea et al., 2015).
FeatureCount (Galaxy Version 2.0.1+galaxy2) to determine gene expression
the NGS data was normalized and differential gene expression analysis bovine macrophages infected with Myocbacterium bovis strain Mb04-303 and the attenuated Mb534 strain was carried out using DESeq2 (Galaxy Version 2.11.40.2) (Love et al., 2014). Normalization method was based on the ‘median of ratios’ - the counts divided by sample-specific size factors determined by median ratio of gene counts relative to geometric mean per gene, to account for sequencing depth and RNA composition. Mean normalized counts, averaged over all samples from both conditions Logarithm (base 2) of the fold change. This allowed us to produce a table of gene expression which extracted genes with a significant change in gene expression (adjusted p-value less than 0.25 by Benjamini-Hochberg method).
Assembly: bosTau9
Supplementary files format and content: csv-comma-separated values-delimited text file include table of gene expression with a significant change in gene expression  (Logarithm base 2 of the fold change of Mb04-303 versus Mb534).
Supplementary files format and content: csv-comma-separated values-delimited text file include table rLog-Normalized feature counts

organism: Bos taurus

source_name: primary cells

growth_protocol: Heparinized whole blood samples (50mL) from three different animals were used for peripheral mononuclear cell (PBMC) isolation using Histopaque 1077 (Sigma-Aldrich, St. Louis, MO, USA) according to the manufacturer's protocol. PBMC were seeded in 12 well tissue culture plates using RPMI complete medium (Invitrogen, Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 10% autologous plasma and 1x Antibiotic-Antimycotic (Anti Anti) (Invitrogen, Thermo Fisher Scientific, Waltham, MA, USA). After 24 h of incubation, non-adherent cells were removed and cultured separately. Adherent cells were incubated with 10% autologous plasma for 4-5 days until macrophage differentiation.

extract_protocol:
Total RNA from infected co-cultures was obtained following the manufacturer's protocol with minor modifications. Briefly, cells lysed in 1 mL of Trizol were mixed with 0.2 mL of chloroform then centrifuged at 12000xg at 4°C for 15 min. The aqueous phase was transferred to a new tube and mixed again with 0.1 mL of chloroform and centrifuged  at 12000xg at 4°C for 5 min. Finally, RNA was precipitated from the aqueous phase adding 0.6mL of  isopropanol and 60 uL of Sodium Acetate (3M). After ON incubation at -70°C the tube was centrifuged at 12000xg at 4°C for 30 min. The pellet was washed with ethanol 70% and purified RNA was resuspended in 20 uL DEPC water.  Quality and quantity were determined using Fragment Analyser (preguntar detalles a Apu)
Quality and quantity of RNA samples were determined in the Bioanalyzer (Agilent, Santa Clara, CA, USA) instrument using Agilent RNA 6000 Nano Kit. The mean value for RNA integrity Number (RIN) of the six samples was 8.25, with high quality electropherograms. Libraries for RNA sequencing were constructed using the TruSeq Stranded mRNA kit (Illumina, San Diego, USA) following the manufacturer's protocol.
Libraries for RNA sequencing were constructed using the TruSeq Stranded mRNA kit (Illumina, San Diego, USA). ) and sequenced in the NextSeq500 (Illumina, San Diego, USA) equipment from the Hospital de Niños R. Gutierrez with a 75 cycles Single End kit and 20M readings per replicate.

treatment_protocol: Macrophages were infected in a multiplicity of infection of 1 (MOI=1) with Mb534 or Mb04-303. After 3 h of infection, macrophages were washed with PBS and co-cultivated with the autologous non adherent cells for 16 h. Non-adherent cells from the Infected co-cultures were pelleted and resuspended in 1 mL of Trizol (Invitrogen, Thermo Fisher Scientific, Waltham, MA, USA). Macrophages were detached using the same aliquot of Trizol and finally the samples were stored at -80°C until RNA purification.

value: primary cells

value: PBMC

tag: cell type

value: WT

value: infection with M. bovis 534

value: 24 hs


title: KU069t

value: No


title: DOCA-WT_rep2


title: KU076t

value: Female


title: DRIP - shRNF8.rep4 [RNF8_4]


title: DOCA-WT_rep1

value: rostral ventrolateral nucleus


title: Macrophages from cattle infected with Mb534 and cocultured with autologous lymphocytes 1


title: DRIP - shRNF8.rep3 [RNF8_3]


title: Macrophages from cattle infected with Mb04-303 and cocultured with autologous lymphocytes 3

value: infection with M. bovis 04-303


title: Macrophages from cattle infected with Mb04-303 and cocultured with autologous lymphocytes 2


title: Baseline-CRE_rep4

value: KO of atp6ap2


title: KU062t


title: KU061t


title: DRIP - shRNF8.rep2 [RNF8_2]

value: MDA MB 436


title: Macrophages from cattle infected with Mb04-303 and cocultured with autologous lymphocytes 1


title: Baseline-CRE_rep3


title: Baseline-CRE_rep2


title: DRIP - shRNF8.RNase.rep3 [RNF8RH_3]


title: KU039t


title: KU050t2


title: DRIP - shScr.Input [Control_Input]


title: Macrophages from cattle infected with Mb534 and cocultured with autologous lymphocytes 2


title: Baseline-WT_rep4


title: Baseline-CRE_rep1


title: DRIP - shRNF8.rep1 [RNF8_1]


title: KU020t


title: DRIP - shScr.RNase.rep2 [Control_RH2]


title: sci 3 dpi mpss replicate1 RNAseq_re-analyzed

city: Yiwu

first: jingjia

last: ye

state: zhejiang

address: chouzhoubeilu 1575

institute: zhejiang university

description:
10x Genomics
GSM5047192

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v.3.0.2
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

organism: Rattus norvegicus

source_name: spinal cord

extract_protocol:
Animals (5 animals for each condition) were anesthetized deeply with pentobarbital sodium, and from the center of the spinal cord injury site, a 5-mm section of the spinal cord was dissected. For extraction of RNA in cells, the tissue was cut and chopped into small pieces, then incubated in 2 ml of collagenase (1 mg/ml in PBS) for 30 min at 37°C and centrifuged at 300 g for 5 min at 4°C. Pelleted cells were collected in 2ml of 0.25% trypsin-EDTA solution and incubated at 37°C for 5 min. Then, digestion by trypsin was stopped by FBS (10%), and the pellet collected by centrifugation was dispersed in PBS with 0.5% BSA. The dispersed cell pellet was strained through a 40-µm cell strainer twice, ensuring there was no large cell cluster exist. To avoid the influence of blood cells, 10 ml of erythrocyte lysate was added to the cell for 10 min, and collect cell suspension by centrifuging. Finally, single-cell suspension was resuspended in PBS for counting.
Libraries were prepared according to 10X Genomics Chromium Single Cell 3′ Reagent Kit v3 (10X Genomics) and Single Cell 3’ Gel Bead Kit v2 instructions and an Agilent 2100 Expert High Sensitivity DNA Assay was used to assessing the quantity of cDNA. Finally, cDNA libraries were sequenced using an Illumina HiSeqTM 4000 system

treatment_protocol: After the animals were anesthetized with pentobarbital sodium (0.5 mL/100 g, injected intraperitoneally), a dorsal laminectomy was performed at the 10th thoracic vertebral level (T10-11) to expose the dorsal surface of the spinal cord. To perform a crush injury animal model, iridectomy scissors were used to transect the ventrally and laterally. After the injury, the muscles and skin were sutured. Bladder care was provided twice daily until spontaneous voiding resumed. Samples for analysis of distinct time points were collected at 1, and 3,7 dpi at the injury site. For drug injection, MPSS was dissolved in PBS solution at a concentration of 10mg/ml. The solution was loaded in the micropipette and injected at the rate of 200 nl/min at 5 sites (1 μL per site) and 2 different depths, 0.6 and 1.2 mm at 3dpi. For control animals, we performed an injection with PBS. Animals were sacrificed for analysis 2 weeks post-injury.

value: spinal cord

value: all cells

value: SD

value: crush injury and insitu injection of MPSS

value: 6-8 week


title: sci 3 dpi pbs replicate1 RNAseq_re-analyzed

description:
10x Genomics
GSM5047190

value: crush injury and insitu injection of PBS


title: DRIP - shScr.RNase.rep1 [Control_RH1]


title: Baseline-WT_rep3

value: Wild Type


title: KU012t

value: Liver

value: Male

value: Yes


title: DRIP - shScr.rep2 [Control_2]

description: Control.mean.bw

value: WT


title: sci 7dpi replicate1 RNAseq

description: 10x Genomics

value: spinal cord crush injury


title: sci 3dpi replicate1 RNAseq

description: 10x Genomics


title: DRIP - shScr.rep1 [Control_1]

description: Control.mean.bw


title: Baseline-WT_rep2


title: MB288, G3b, ATAC

city: La Jolla

first: Lukas

last: Chavez

state: CA

address: 10901 North Torrey Pines Road

department: Cancer Genome and Epigenetics Program, NCI-Designated Cancer Center

institute: Sanford Burnham Prebys Medical Discovery Institute

data_processing:
ATAC-seq reads were trimmed on both ends using Trimmomatic v0.38, LEADING:15 TRAILING:15
ATAC-seq reads were aligned to the GRCh38 genome using bowtie v2.2.5 and deduplicated using Picard MarkDuplicates v2.18.27. Only primary alignments were retained.
Peaks were called using MACS2 v2.1.2 with significance cutoff q<0.05.
Coverage tracks were generated by extending reads to 200bp and shifting by 100bp, then converting to bigwig format using deeptools v3.5.1 bamCoverage.
Assembly: GRCh38
Supplementary files format and content: bigWig, narrowPeak

source_name: medulloblastoma

extract_protocol:
Cells were cryopreserved in DMSO. Nuclei were thawed, lysed, stained (Trypan Blue), counted (Countess, Invitrogen), and tagmented (1X Tagment DNA Buffer, Illumina). DNA was purified using DNeasy Blood & Tissue Kit (Qiagen), and quantified using NanoDrop 2000 (Thermo Scientific), and purified using the Nextera DNA Library Preparation Kit (Illumina).
Between 50,000 and 100,000 nuclei were used in library construction. DNA was amplified by PCR (8 cycles), size-selected for nucleosome-free fragments (175-250bp) by gel electrophoresis (2% agarose gel, Invitrogen), and purified using the QIAquick Gel Extraction Kit (Qiagen). A second PCR amplification (4 cycles) and purification (Agencourt AMPure XP beads, Beckman Coulter) was performed on the size-selected fragments. The final library was validated using a Fragment Analyzer™ instrument (Advanced Analytical) and the KAPA Library Quantification Kit for Illumina Sequencing Platforms.

value: medulloblastoma


title: sci 1dpi replicate1 RNAseq

description: 10x Genomics


title: PVNS5

city: beijing

first: fei

last: wu

address: 49 North Garden Rd

institute: Peking university 3rd hospital

data_processing:
Basecalls performed using CASAVA version 1.8
Umi-tools was utilized to calculate the raw counts and cell whitelist by default parameter
We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:   MT% < 20%;    Cell Gene Number < Median Gene Number * 2;   Cell Gene Number > 200.  PCA and tSNE analysis was used for the single cell to cell relation description. Graphcluster and K-mean was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include normalized counts for each cell

source_name: Pigmented villonodular synovitis (PVNS)

extract_protocol:
Testicular immune cell were sorted CD45+ cells with BD FACS
Sequencing libraries were conducted using the BD Rhapsody Single-Cell Analysis System (BD Biosciences), following the manufacture's protocol.

treatment_protocol: sample of osteoarthritis or PVNS synovium receive no treatment before harvest during surgery

tag: tag

value: synovium


title: MB282, G4, ATAC


title: intact replicate1 RNAseq

description: 10x Genomics


title: Baseline-WT_rep1

value: rostral ventrolateral nucleus


title: MB281, G4, ATAC


title: KU022t1


title: PVNS3


title: MB278, G3b, ATAC


title: MB277, G3b, ATAC


title: BM, Spaceflight, Nrf2 KO, #FL12

city: Sendai-shi

first: IKUO

last: HIRANO

state: Miyagi

address: 2-1 Seiryou-machi, Aoba-ku

department: Graduate School of Medicine

country: Japan

institute: Tohoku university

data_processing:
The raw reads were mapped to the mouse GRCM38/mm10 genome using STAR (version 2.6.1).
Transcripts per million (TPM) values were obtained to measure gene expression using RSEM (version 1.3.1).
Assembly: mm10
Supplementary files format and content: csv file include TPM values for each sample

source_name: Bone marrow

extract_protocol:
RNA was harvested using ISOGEN-LS (NIPPON GENE). About 200 µg of total RNA used for cDNA library synthesis.
RNA library for RNA-seq were prepared using MGIEasy RNA Directional Library Prep Set (MGI).

value: Bone marrow

value: Nrf2 KO

value: Spaceflight


title: PVNS4

description:
PVNS4.cellBarcode.txt
5Sample.NormalizedCounts.txt
3Sample.NormalizedCounts.txt

data_processing:
Basecalls performed using CASAVA version 1.8.
Umi-tools was utilized to calculate the raw counts and cell whitelist by default parameter.
We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:
o MT% < 20%;
o Cell Gene Number < Median Gene Number * 2;
o Cell Gene Number > 200.
PCA and tSNE analysis was used for the single cell to cell relation description. Graphcluster and K-mean was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files include normalized counts for each cell.

source_name: synovium

extract_protocol: Sequencing libraries were conducted using the BD Rhapsody Single-Cell Analysis System (BD Biosciences), following the manufacturer's protocol.

treatment_protocol: Sample of osteoarthritis or PVNS synovium receive no treatment before harvest during surgery.

value: Synovium

tag: diagnosis

value: PVNS


title: BM, Spaceflight, Nrf2 KO, #FL11


title: BM, Spaceflight, Nrf2 KO, #FL09


title: PVNS2

description:
PVNS2.cellBarcode.txt
5Sample.NormalizedCounts.txt
3Sample.NormalizedCounts.txt


title: MB275, SHHa, ATAC


title: BM, Spaceflight, Nrf2 KO, #FL04


title: BM, Spaceflight, Nrf2 KO, #FL02


title: MB274, SHHa, ATAC


title: MB268, SHHa, ATAC


title: BM, Spaceflight, Nrf2 KO, #FL01


title: WES-14837T

city: 北京

first: YU

last: ZHANG

state: non-US Resident

address: XUEYUANLU No.38 Haidian District, PKUHSC Anatomy Building

institute: Peking Univ.

data_processing:
Not provided.
Assembly: mm10
Library strategy: WES-seq

source_name: PDAC

growth_protocol: cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C. C57BL mice in SPF grade were selected.

extract_protocol:
Genomic DNA for WES was extracted with TIANamp Genomic DNA Kit (TIANGEN, #DP304-02) as described by the manufacturer.1 ug of genomic DNA is used for the construction of sequencing libraries
WES Library preparation: The 200ng genomic DNA concentrations were sheared with Covaris LE220 Sonicator (Covaris) to target of 150-200bp average size.  DNA libraries were prepared using SureselectXT reagent kit (Agilent)/SureselectXT Low Input reagent kit (Agilent).  The fragments were repaired the 3’and 5’overhangs using End repair mix and purified using Agencourt AMPure XP Beads (Beckman).  The purified fragments were added with’A’ tail using A tailing Mix and then ligated with adapter using the DNA ligase.  The adapter-ligated DNA fragments were amplified with Herculase II Fusion DNA Polymerase (Agilent).  Finally, the pre-capture libraries containing exome sequences were captured using SureSelect Human All Exon V5 kit (Agilent).
WES Library QC: After library construction, Qubit 3.0 fluorometer dsDNA HS Assay (Thermo Fisher Scientific) was used to quantify concentration of the libraries, while the size distribution was analyzed by Agilent Bioanalyzer 4200 (Agilent).
Sequencing: Paired-end sequencing was performed using the NovaSeq 6000 S4 Reagent Kit v1.5 (300 cycles) on Illumina NovaSeq 6000 platform (Illumina, San Diego, USA).

value: PDAC

value: PDAC cells


title: BM, Spaceflight, Wild type, #FL10

value: Wild type


title: WES-15376T


title: Post natal day 15 mouse endometrium epithelium 3

city: Pullman

first: Kimberly

middle: M

last: Davenport

state: WA

address: 100 Dairy Rd

department: Animal Science

institute: Washington State University

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Endometrium

extract_protocol:
Nuclei were isolated from fresh tissue following the 10X Genomics protocol
Libraries were consructed according to the 10X Genomics manufacterer's instructions

value: Endometrium

value: post natal day 15


title: OA3

description:
OA3.cellBarcode.txt
5Sample.NormalizedCounts.txt

value: OA


title: OA

description:
OA.cellBarcode.txt
5Sample.NormalizedCounts.txt


title: PVNS1

description:
PVNS1.cellBarcode.txt
5Sample.NormalizedCounts.txt
3Sample.NormalizedCounts.txt


title: MB264, G4, ATAC


title: OA2

source_name: osteoarthritis synovium


title: P522R_5xFAD_M #31 (Glial)

type: RNA

description:
X7M.M7.31.P522R.5xFAD.Ctx
nCounter® Glial Panels

hyb_protocol: standard NanoString protocol

scan_protocol: standard NanoString protocol

data_processing:
Data were processed, normalized, and combined using NanoString nSolver 4.0 analysis software.
Processed data matrix represents normalized log2 values.

label: NanoString

source_name: mouse cortex

label_protocol: standard NanoString protocol

extract_protocol: Total RNAs were prepared with Purelink RNA Mini Kit and subjected to NanoString analysis

value: Male

tag: disease state

value: 5xFAD P522R mice

value: brain cortex


title: MB248, G3a, ATAC

value: medulloblastoma


title: MB247, G3a, ATAC


title: Post natal day 15 mouse endometrium epithelium 2

description: 10X Genomics


title: P522R_5xFAD_M #30 (Glial)

description:
X7M.M6.30.P522R.5xFAD.Ctx
nCounter® Glial Panels


title: BM, Spaceflight, Wild type, #FL08


title: Post natal day 15 mouse endometrium epithelium 1

description: 10X Genomics


title: BM, Spaceflight, Wild type, #FL07


title: P522R_5xFAD_M #29 (Glial)

description:
X7M.M5.29.P522R.5xFAD.Ctx
nCounter® Glial Panels


title: BM, Spaceflight, Wild type, #FL06


title: WES-WT

source_name: tail

value: tail

value: tail tissue

value: WT


title: MB244, SHHa, ATAC


title: Post natal day 12 mouse endometrium epithelium 3

description: 10X Genomics

value: post natal day 12


title: MB234, SHHa, ATAC


title: Post natal day 12 mouse endometrium epithelium 2

description: 10X Genomics


title: BM, Spaceflight, Wild type, #FL05

value: Bone marrow

value: Spaceflight


title: BM, Spaceflight, Wild type, #FL03


title: P522R_5xFAD_M #21 (Glial)

description:
X7M.M2.21.P522R.5xFAD.Ctx
nCounter® Glial Panels


title: BM, Ground control, Nrf2 KO, #GC12

value: Nrf2 KO

value: Ground contol


title: P522R_5xFAD_F #8 (Glial)

description:
X7M.F.8.P522R.5xFAD.Ctx
nCounter® Glial Panels

value: Female


title: Post natal day 5 mouse endometrium epithelium 3

description: 10X Genomics

value: post natal day 5


title: BM, Ground control, Nrf2 KO, #GC11


title: MB164, G3b, ATAC


title: MB174, G4, ATAC


title: BM, Ground control, Nrf2 KO, #GC09


title: P522R_5xFAD_F #54 (Glial)

description:
X7M.F4.54.P522R.5xFAD.Ctx
nCounter® Glial Panels


title: Post natal day 5 mouse endometrium epithelium 1

description: 10X Genomics

value: Endometrium


title: P522R_5xFAD_F #49 (Glial)

description:
X7M.F3.49.P522R.5xFAD.Ctx
nCounter® Glial Panels


title: P522R_5xFAD_M #27 (Glial)

description:
X7M.M4.27.P522R.5xFAD.Ctx
nCounter® Glial Panels


title: Post natal day 5 mouse endometrium epithelium 2

description: 10X Genomics


title: MB106, G3a, ATAC


title: P522R_5xFAD_F #24 (Glial)

description:
X7M.F2.24.P522R.5xFAD.Ctx
nCounter® Glial Panels


title: Post natal day 1 mouse endometrium epithelium 3

description: 10X Genomics

value: post natal day 1


title: P522R_5xFAD_M #23 (Glial)

description:
X7M.M3.23.P522R.5xFAD.Ctx
nCounter® Glial Panels


title: Post natal day 1 mouse endometrium epithelium 2

description: 10X Genomics


title: MB136, SHHb, ATAC


title: BM, Ground control, Nrf2 KO, #GC02


title: BM, Ground control, Nrf2 KO, #GC01


title: MB227, G4, ATAC


title: BM, Ground control, Nrf2 KO, #GC04


title: Post natal day 12 mouse endometrium epithelium 1

description: 10X Genomics


title: MB199, G4, ATAC


title: Post natal day 1 mouse endometrium epithelium 1

description: 10X Genomics


title: MB102, SHHa, ATAC


title: P522R_5xFAD_F #106 (Glial)

description:
X7M.F1.106.P522R.5xFAD.Ctx
nCounter® Glial Panels


title: BM, Ground control, Wild type, #GC10

value: Wild type


title: Liver_Sen4

city: Pittsburgh

first: Jonathan

middle: K.

last: Alder

state: PA

address: 3459 Fifth Ave, NW 628

department: Medicine

institute: University of Pittsburgh

description:
Trf2LiverCounts.txt
Trf2_liver_normalized_counts.txt

data_processing:
Raw fastq files were aligned to mm10 using STAR
Count files were generated using FeatureCount (Novogene)
Normalized count files were generated using DeSeq2
Assembly: mm10
Supplementary files format and content: Matrix files containing the raw counts from Novogene using FeatureCount
Supplementary files format and content: Normalized count files were generated using DeSeq2

source_name: Terf2 deleted Liver, 6 weeks

growth_protocol: MEFs were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C. Deletion of Terf2 was initiated by addition of 4-hydroxytamoxifen to the media and cells were collected 7 days later. For Liver experiments, mice were treated with AAV8-Tbg-Cre via tail vein injection and primary liver samples were collected 6-7 weeks later.

extract_protocol:
RNAeasy mini protocol
QC and library construction was completed at Novogene

treatment_protocol: 4-hydroxy tamoxifen for MEFs and AAV8-Tbg-Cre for liver samples

value: Liver


title: M28L_5xFAD_M 9 (Glial)

description:
X7M.M7.9.M28L.5xFAD.Ctx
nCounter® Glial Panels

value: Male

value: 5xFAD M28L mice


title: P522R_5xFAD_F #60 (Glial)

description:
X7M.F6.60.P522R.5xFAD.Ctx
nCounter® Glial Panels

value: 5xFAD P522R mice

value: brain cortex


title: MB099, G4, ATAC

value: medulloblastoma


title: BM, Ground control, Wild type, #GC08


title: Liver_Sen3


title: M28L_5xFAD_M #21 (Glial)

description:
X7M.M3.21.M28L.5xFAD.Ctx
nCounter® Glial Panels


title: MB095, G3a, ATAC


title: M28L_5xFAD_M #17 (Glial)

description:
X7M.M9.17.M28L.5xFAD.Ctx
nCounter® Glial Panels


title: BM, Ground control, Wild type, #GC07


title: MB104, SHHa, ATAC


title: Liver_Sen1


title: M28L_5xFAD_M #15 (Glial)

description:
X7M.M2.15.M28L.5xFAD.Ctx
nCounter® Glial Panels


title: MB018, G3a, ATAC


title: BM, Ground control, Wild type, #GC06


title: BM, Ground control, Wild type, #GC05


title: M28L_5xFAD_M #11 (Glial)

description:
X7M.M1.11.M28L.5xFAD.Ctx
nCounter® Glial Panels


title: Liver_WT4

source_name: Control Liver

value: Rosa-mTmG


title: BM, Ground control, Wild type, #GC03


title: Liver_WT3


title: M28L_5xFAD_M #10 (Glial)

description:
X7M.M8.10.M28L.5xFAD.Ctx
nCounter® Glial Panels


title: M28L_5xFAD_F #28 (Glial)

description:
X7M.F3.28.M28L.5xFAD.Ctx
nCounter® Glial Panels


title: M28L_5xFAD_F #20 (Glial)

description:
X7M.F2.20.M28L.5xFAD.Ctx
nCounter® Glial Panels


title: Liver_WT2


title: MEF_Sen3

description:
MEF_RawReadCounts.txt
MEF_normalized_Mgi_symbol_counts.txt

source_name: Terf2 deleted MEFs, day 7

value: mouse embryonic fibroblast


title: Liver_Sen2


title: MB091, G4, ATAC


title: M28L_5xFAD_F #16 (Glial)

description:
X7M.F9.16.M28L.5xFAD.Ctx
nCounter® Glial Panels


title: MEF_Sen2


title: M28L_5xFAD_F8 #14 (Glial)

description:
X7M.F8.14.M28L.5xFAD.Ctx
nCounter® Glial Panels


title: M28L_5xFAD_F1 #14 (Glial)

description:
X7M.F1.14.M28L.5xFAD.Ctx
nCounter® Glial Panels


title: MEF_Con3

source_name: Control MEFs

value: vehicle


title: M28L_5xFAD_F #12 (Glial)

description:
X7M.F7.12.M28L.5xFAD.Ctx
nCounter® Glial Panels


title: MEF_Sen1


title: Kpn 43816 P13, replicate 3

city: Shenzhen

first: xing

last: shi

state: Guangdong

address: Luohu

department: Department of Respiratory and Critical Care Medicine

institute: Shenzhen Institute of Respiratory Disease

data_processing:
The raw reads underwent trimming using Trimmomatic to remove low-quality segments
Bowtie2 was used to map raw reads to reference genome
Gene counts were calculated using featureCounts
Differential expressed genes were identified using edgeR
Assembly: GCA_000742755.1
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files includes RPKM values for each Sample

organism: Klebsiella pneumoniae subsp. pneumoniae

growth_protocol: The K. pneumoniae isolate was grown from a single colony to the desired growth phase, then the precipitate was collected the by centrifugation at 11,000 g (2 min) for RNA extraction.

extract_protocol: RNA samples from three independent experiments were processed by Novogene Bioinformatics Technology Co., Ltd. (Beijing, China).

tag: strain


title: AdipoqCreMed1f/f BAT 10weeks rep2

city: New York

first: Keiichi

last: Ito

address: 1230 York Avenue

institute: The Rockefeller University

description: Gene expression data from interscapular BAT from AdipoqCreMed1f/f mice at 10weeks after birth

hyb_protocol: Hybridization was performed at 45 degrees celcius for 16 hours. The arrays were washed and stained in the GeneChip Fluidic Station 450 (Affymetrix) by using Hybridization, Wash and Stain kit (Affymetrix).

scan_protocol: The arrays were scanned by the GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The data expressed as CEL files were normalized using the Signal Space Transformation-Robust Multi-Chip Analysis (SST-RMA) algorithm with Transcriptome Analysis Console (TAC) 4.0 (Thermofisher)

label: biotin

source_name: Interscapular brown adipose tissue from AdipoqCreMed1f/f mouse at 10weeks after birth

label_protocol: RNA samples were processed and prepared for whole transcriptome expression analysis using the GeneChip WT PLUS Reagent Kit (Thermofisher 902280)

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

value: Adult brown adipose tissue:AdipoqCreMed1f/f


title: AdipoqCreMed1f/f BAT 10weeks rep1


title: Liver_WT1


title: MEF_Con2


title: RPMI_BMAL1-KD_2

city: San Giovanni Rotondo (FG)

first: Fabrizio

last: Bianchi

state: Outside U.S. & Canada

address: Viale Padre Pio 7

country: Italy

institute: Fondazione IRCCS Casa Sollievo della Sofferenza

hyb_protocol: Samples were then hybridized ON using using the Affymetrix GeneChip Hybridization Oven 640 (Thermo Fisher Scientific)

scan_protocol: Samples were whashed, stained, and scanned using a Fluidic Station 450 and Scanner 3000 7G (Thermo Fisher Scientific)

data_processing: Quality control and normalization of Affymetrix .CEL files were performed using TAC software (v4.0; Thermo Fisher Scientific) by performing “Gene level SST-RMA” summarization method with human genome version hg38 (NCBI-Genome Reference Consortium Human Build 38).

source_name: RPMI-8402 cell line, infected with shBMAL1, replica 2

label_protocol: RNA samples have been amplified, fragmented, and labeled for array hybridization according to the manufacturer’s instruction (Thermo Fisher Scientific).

growth_protocol: Cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS),1 mM sodium pyruvate, 2 mM L-glutamine, and antibiotics (Invitrogen)

extract_protocol: Total RNA was isolated by TRIzol™ (Invitrogen) following manufacturer's standard protocol (TRIzol™ Reagent; Invitrogen).

treatment_protocol: The RNAi Consortium (TRC) shRNAs targeting BMAL1 (shBMAL1_14, TRCN0000331014; shBMAL1_95, TRCN0000019095) or CLOCK (shCLOCK_76, TRCN0000018976; shCLOCK_77, TRCN0000018977) were cloned into a derivative of pLKO.1 vector (Addgene #8453) with the GFP or mCherry fluorescent marker. Lentiviruses were produced by transient co-transfection of 293T cells with pCMVΔR8.74 and pCMV-VSV-G packaging/envelope vectors.

tag: tumor type

value: T-cell acute lymphoblastic leukemia (T-ALL)

value: Blood


title: RPMI_CLOCK-KD_2

source_name: RPMI-8402 cell line, infected with shCLOCK, replica 2

tag: tissue


title: 5xFAD_M #1270 (Glial)

city: Stanford

first: Andy

last: Tsai

address: 290 Jane Stanford Way E365

institute: Stanford University

description:
X7M.M6.1270.WT.5xFAD.Ctx
nCounter® Glial Panels

value: 5xFAD mice


title: Med1f/f BAT 10weeks rep2

description: Gene expression data from interscapular BAT from Med1f/f mice at 10weeks after birth

source_name: Interscapular brown adipose tissue from Med1f/f mouse at 10weeks after birth

value: Adult brown adipose tissue:Med1f/f


title: Kpn 43816 P13, replicate 2


title: MEF_Con1


title: Myf5CreMed1f/f  BAT E17.5 rep4

description: Gene expression data from interscapular BAT from Myf5CreMed1f/f mice at E17.5

source_name: Interscapular brown adipose tissue from Myf5CreMed1f/f mouse embryo at E17.5

value: E17.5 Brown adipose tissue:Myf5CreMed1f/f


title: Myf5CreMed1f/f  BAT E17.5 rep3


title: 5xFAD_M #1269 (Glial)

description:
X7M.M5.1269.WT.5xFAD.Ctx
nCounter® Glial Panels


title: RPMI_control_2

source_name: RPMI-8402 cell line, infected with a scamble oligo, replica 2


title: Kpn 43816 P13, replicate 1


title: RPMI_control_1

source_name: RPMI-8402 cell line, infected with a scamble oligo, replica 1


title: 6 month old Ts65Dn mouse model for down syndrome, biological rep 3 (snATAC-seq)

city: Boston

first: Brian

last: Kalish

state: MA

address: 220 Longwood Ave

department: Neurobiology

institute: Boston Children's Hospital

description: ATAC-seq

library_source: genomic single cell

data_processing:
For snRNA-seq, fastQ files were processed using Cell Ranger (10X Genomics, cellranger-6.1.2)using standard pipeline. Briefly, reads were aligned to Mouse mm10 genome, and quantified with Cell Ranger count function using default settings. Data was futhered filtered, normalized and log transformed using default parameters in Seurat v4.0.6. The snATAC-seq data was processed using standard pipline of 10X Genomics, cellrangerATAC-2.0.0. Peaks were analyzed using Signac v1.9.0 pipeline with default parameters.
Assembly: mm10
Supplementary files format and content: snRNA-seq files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: snATAC-seq files: filtered_peak_bc_matrix.h5, fragments.tsv.gz, fragments.tsv.gz.tbi

extract_protocol:
Frozen tissue was thawed in 500 uL Buffer HB (0.25M sucrose, 25mM KCl, 5mM MgCl2, 20mM Tricine-KOH pH 7.8, 0.15mM spermine tetrahydrochloride, 0.5mM spermidine trihydrochloride, 1mM DTT). The tissue was transferred to a 2 mL dounce. 500ul 5% IGEPAL CA-630 (Sigma) and 1 mL HB were added to the tissue and the tissue was homogenized with a tight pestle 10-15 times. The sample was transferred to a 15 mL tube and total solution brought to 9 mL with HB. In a ultra-clear centrifuge tubes (Beckman Coulter), 1 mL 30% iodixanol layered on top of 1 mL 40% iodixanol. The 9 mL sample was layered on top of the iodixanol cushion. The sample was spun at 10,000 xg for 18 minutes. 1 mL of sample at the 30-40% iodixanol interface was collected for subsequent nuclei processing.
The snRNAseq and snATACseq libraries were constructed and sequenced as described in the 10X Genomics protocol.

value: Cortex

tag: age

value: 6 month old

tag: condition

value: Down syndrome model


title: Kpn 43816 P2, replicate 3

tag: genotype


title: Med1f/f BAT 10weeks rep1


title: RPMI_CLOCK-KD_1

source_name: RPMI-8402 cell line, infected with shCLOCK, replica 1


title: 6 month old Ts65Dn mouse model for down syndrome, biological rep 2 (snATAC-seq)

description: ATAC-seq


title: 5xFAD_M #1182 (Glial)

description:
X7M.M3.1182.WT.5xFAD.Ctx
nCounter® Glial Panels

value: Male


title: Myf5CreMed1f/w BAT E17.5 rep2

description: Gene expression data from interscapular BAT from Myf5CreMed1f/w mice at E17.5

source_name: Interscapular brown adipose tissue from Myf5CreMed1f/w mouse embryo at E17.5

value: E17.5 Brown adipose tissue:Myf5CreMed1f/w


title: Kpn 43816 P2, replicate 2


title: Myf5CreMed1f/f  BAT E17.5 rep1


title: Myf5CreMed1f/w BAT E17.5 rep1


title: Myf5CreMed1f/f  BAT E17.5 rep2


title: Kpn 43816 P2, replicate 1


title: 6 month old control mice, biological rep 3 (snATAC-seq)

description: ATAC-seq

source_name: 6 month old control mice

value: control


title: 6 month old Ts65Dn mouse model for down syndrome, biological rep1 (snATAC-seq)

description: ATAC-seq


title: 5xFAD_M #1177 (Glial)

description:
X7M.M1.1177.WT.5xFAD.Ctx
nCounter® Glial Panels

value: brain cortex


title: Kpn 43816 CP6, replicate 3


title: RPMI_BMAL1-KD_1

source_name: RPMI-8402 cell line, infected with shBMAL1, replica 1


title: 5xFAD_M #1181 (Glial)

description:
X7M.M2.1181.WT.5xFAD.Ctx
nCounter® Glial Panels

source_name: mouse cortex


title: Myf5CreMed1f/w BAT E17.5 rep3


title: Kpn 43816 CP6, replicate 2


title: 5xFAD_F #1253 (Glial)

description:
X7M.F6.1253.WT.5xFAD.Ctx
nCounter® Glial Panels

value: Female


title: 6 month old control mice, biological rep1 (snATAC-seq)

description: ATAC-seq


title: MED1-KO 3T3-L1 Day0 pool rep2

description: Gene expression data from differentiating MED1-KO 3T3-L1 at day2

source_name: MED1-KO 3T3-L1 cells 2 days after hormonal stimulation

value: Cell line:MED1-KO 3T3-L1


title: 5xFAD_M #1268 (Glial)

description:
X7M.M4.1268.WT.5xFAD.Ctx
nCounter® Glial Panels


title: 5xFAD_F #1249 (Glial)

description:
X7M.F5.1249.WT.5xFAD.Ctx
nCounter® Glial Panels


title: Kpn 43816 CP6, replicate 1


title: MED1-KO 3T3-L1 Day2 pool rep2


title: WT 3T3-L1 Day2 rep2

description: Gene expression data from differentiating WT 3T3-L1 at day2

source_name: WT 3T3-L1 cells 2 days after hormonal stimulation

value: Cell line:WT 3T3-L1


title: 6 month old Ts65Dn mouse model for down syndrome, biological rep 3 (snRNA-seq)

description: RNA-seq


title: 5xFAD_F #1248 (Glial)

description:
X7M.F4.1248.WT.5xFAD.Ctx
nCounter® Glial Panels


title: 5xFAD_F #1190 (Glial)

description:
X7M.F3.1190.WT.5xFAD.Ctx
nCounter® Glial Panels


title: Kpn 43816 CP17, replicate 2


title: Kpn 43816 CP17, replicate 3


title: 6 month old Ts65Dn mouse model for down syndrome, biological rep 2 (snRNA-seq)

description: RNA-seq


title: WT 3T3-L1 Day0 rep2


title: 6 month old Ts65Dn mouse model for down syndrome, biological rep1 (snRNA-seq)

description: RNA-seq


title: Kpn 43816 CP17, replicate 1


title: 5xFAD_F #1180 (Glial)

description:
X7M.F1.1180.WT.5xFAD.Ctx
nCounter® Glial Panels


title: 6 month old control mice, biological rep 2 (snATAC-seq)

description: ATAC-seq


title: 6 month old control mice, biological rep 3 (snRNA-seq)

description: RNA-seq


title: Kpn 43816 WT, replicate 3

value: WT


title: 6 month old control mice, biological rep 2 (snRNA-seq)

description: RNA-seq


title: E125-SMC3-WT

city: shanghai

first: bowen

last: zhang

state: shanghai

address: dongan road

institute: Fudan university

description:
barcodes.tsv
features.tsv.gz
matrix.mtx

data_processing:
Illumina Casava1.7 software used for basecalling.
Pair-wise chromatin interactions for 3C-HTGTS data processing. Paired-end Illumina sequencing fastq data were filtered by removing adapters and low-quality reads with using fastp (v0.20.0). Trimmed reads again were extracted from the sequence file after quality control with Cutadapt (v1.18). Paired-end reads containing nested primer or adapter primer were merged manually using restriction enzyme recognition sequences into single reads with Pear (v0.9.6), then the first digested fragment behind the bait was obtained through spliting the single reads into fragments according to restriction enzyme recognition sequences. The remaining single-end reads were aligned to the enzyme-digested mm10 reference genome with Bowtie2 (v2.4.5, parameter: -p 8 --sensitive), and mouse genome sequence (mm10) was retrieved from the UCSC and we extracted concordantly exactly alignments using SAMtools (v1.9). Self-ligation reads and off-targeted reads were filtered after mapping. For visualization, we converted the final bam files into bedGraph file using Bedtools (v2.29.2). The signal peak bedGraph file was obtained by post-comparison filtering, signal statistics, and standardization. We normalized bedGraph file using CPM (Counts Per Million in cis) normalization method, and visualized on IGV genome browser. Differential pair-wise interactions were identified by the R package R.4Cker (v1.0.0, k=30) with the function nearBaitAnalysis called to define domains of interaction with the bait and DESeq2 (v1.34.0, p < 0.05). Finally, we organized the results report and visualized it with the Bioconductor package ggplot2 (v3.3.6). The analysis of the correlation for experimental repetition used the R package corrplot(v.0.92).
For snRNA-seq data analysis, the cleaned data were generated by Cell Ranger (v3.0.2) (https://github.com/10XGenomics/cellranger) and filtered for the low-quality reads. The data were aligned to mouse mm10 reference genome. 10× Genomics‐derived data were collected. The downstream analysis using the Seurat (v4.0.5) (https://satijalab.org/seurat) program screened out Cells with gene numbers greater than 200, and mitochondrial gene ratios less than 25% and 2000 genes with highly variable expression in 3 or more cells. Principal component analysis was then runned using significantly variable genes, and Uniform Manifold Approximation and Projection (UMAP) was performed to visualize data. Cells were represented in a two-dimensional UMAP plane, and clusters were identified and annotated according to the previously published cardiac cell markers. The significance of differential expression was calculated using the bimod test. Functional enrichment of differentially expressed genes was then processed by Gene Ontology (GO) (http://www.geneontology.org/) analysis. The pseudotime trajectory was determined with the Monocle2 package with the default settings. Specifically, the DDRTree method was used for dimension reduction with max_components set at 2, and the cells were ordered using the orderCells function.
Bulk RNA-sequencing (RNA-seq) of mouse embryo hearts and HL-1 cells was carried on by the LC-Bio Technology, Hangzhou, China. The detailed operations were as follows: total RNA was isolated and purified using TRIzol reagent (Invitrogen, CA, USA). The RNA samples which passed quality control were fragmented into small pieces at 94℃ for 5-7min and reverse-transcribed to create the cDNA. The average insert size for the final cDNA library was 300±50 bp. The FASTQ data of sequencing reads were trimmed using paired-end sequencing. Consecutively, the trimmed reads were mapped to the mouse genome reference (mm10) by HISAT2 software (https://ccb.jhu.edu/software/hisat2). The mRNA expression abundance was analyzed using StringTie software and represented by FPKM. The differentially expressed mRNAs were selected with FC >1.5 and a parametric F-test comparing nested linear models (p value < 0.05) by the R package edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html). Gene set enrichment analysis was run on all expressed genes which were ranked by log2FC value. Functional enrichment of differentially expressed genes was then processed by GO (http://www.geneontology.org/) analysis.
For ChIP-seq, ChIP products were end repaired, dA-tailing and linker ligation were performed, and barcoding and Illumina adapter addition were performed by PCR amplification. Libraries were purified using QiaQuick PCR purification reagents (Qiagen, Hilden, Germany) and size selected by 0.7×and 0.2×Ampure XP beads (Beckman, California, USA).
Assembly: mm10
Supplementary files format and content: bedGraph files were generated using Bedtools (v2.29.2) with normalized values for each sample. we used the custom script to get bedpe files for interaction loops identified by using raw contact frequencies.  The custom utility was used to convert the raw contact frequencies into sparse .matrix format, and  these interaction counts were normalized for a total of 1,000,000 interactions at the same resolutions.

source_name: Muscle

growth_protocol: All mouse procedures were approved and monitored by the Research Ethics Committee of the School of Basic Medical Sciences, Fudan University, China. Mice were on a C57Bl/6 genetic background . Animals were housed and bred in a specific pathogen-free animal facility.

extract_protocol: For 3C-HTGTS, mouse thymus and liver were removed, cells were filtered through nylon mech.10 million cells were cross-linked with 1% formaldehyde. Cell were lysed and digest with 200U MboI overnight at 37°C. The sample was ligated with T4 DNA ligase overnight at 16°C. Crosslinks were reversed by Proteinase K and RNase A prior to DNA extraction with 1:1 phenol-chloroform and precipitation with ethanol. The 10ug 3C DNA was sonicated to 300-500bp and was linearly amplified with a biotinylated primer. The biotin-labeled single-stranded DNA products were enriched with streptavidin C1 beads, and followed by 3’ ends ligation with the bridge adaptor. The adaptor-ligated products were amplified via nested PCR using a nested primer and an adaptor-complementary primer. And a final PCR for another 5-10 cycles with P5 and P7 was performed. After purification of the PCR products, the final libraries were sequenced on an Illumina NovaSeq 6000 platform to obtain 150 bp or 250 bp paired-end reads. For SnRNA-seq, the E12.5 mouse embryos were microdissected in PBS solution using a Leica M205C microscope, and the heart tissues were extracted. The whole heart samples from different embryos, including six Smc3fl/fl, seven Smc3fl/+; Nkx2.5-Cre, and seven Smc3fl/fl; Nkx2.5-Cre, subjected to mechanical trituration, were made into the cell suspension. Cell counts and viability were determined for the resulting suspension, and the cell concentration was adjusted to the ideal 300-600 cells / μL. The prepared single-cell suspension was combined with a mixture of gel beads containing barcode information and enzymes and then encapsulated by oil droplets to form Gel Bead-In-EMulsions (GEMs). After the reverse transcription reaction, the GEMs were fragmented to complete the amplification of nuclear cDNA, and the quality-checked amplification products were constructed as sequencing libraries. Briefly, the cDNA was broken into fragments of 200-300 bp, end-repaired, ligated into the P7 Adapter, and finally amplified by PCR for introduction into the indexes of samples.

value: Cardiac muscle tissue


title: E125-SMC3-HET

description:
barcodes.tsv
features.tsv.gz
matrix.mtx

value: Smc3fl/+; Nkx2.5-Cre


title: WT 3T3-L1 Day2 rep1

description: Gene expression data from undifferenriated WT 3T3-L1

source_name: WT 3T3-L1 cells before hormonal stimulation


title: Kpn 43816 WT, replicate 2


title: E125-SMC3-HOMO

description:
barcodes.tsv
features.tsv.gz
matrix.mtx

value: Smc3fl/fl; Nkx2.5-Cre


title: Kpn 43816 WT, replicate 1


title: MED1-KO 3T3-L1 Day2 pool rep1

description: Gene expression data from undifferenriated MED1-KO 3T3-L1

source_name: MED1-KO 3T3-L1 cells before hormonal stimulation


title: WT 3T3-L1 Day0 rep1


title: MED1-KO 3T3-L1 Day0 pool rep1


title: BB-X2-72h

city: Clayton

first: Tom

last: Dierschke

state: VIc

address: Wellington Road

country: Australia

institute: Monash University

data_processing:
Mapping of FastQC reads to the published Marchantia polymorpha genome v3.1 (Marchantia.info) was done using STAR on the omicsbox platform (BioBam Bioinformatics (Version 3.0.30). March 3, 2019. www. biobam.com/omicsbox)
gene level quantification was performed based in the HTseq package on the omicsbox platform using published (Marchantia.info) genomic features (Mpolymorphav3.1.primaryTrs.gff3).
A pairwise differential expression analysis (without replicates) based on NOIseq was used to analyse both time points without replicates using the omicsbox platform
Assembly: Marchantia polymorpha genome v3.1
Supplementary files format and content: tab-delimited test file including normalized counts (normalized_counts)
Supplementary files format and content: Excel file of pairwise comparison (BELL1-KNOX2-72h_vs_BELL1-KNOX2-mock)

organism: Marchantia polymorpha

source_name: gametophytic thallus

growth_protocol: gemmae were grown under normal growth conditions (23°C, 24h white light) on ½ B5 Gamborg’s media for 10 days

extract_protocol:
RNA was extracted from ~ 100mg plant tissue using the RNeasy plant kit (Quiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: gemmae were transferred to plates containing 5μM 17-β-estradiol or mock and snap frozen in liquid nitrogen after72h

value: gametophytic thallus

value: proEF1:MpKNOX2; proEF1:XVE>>MpBELL1

tag: treatment


title: BB-X2-mock

data_processing:
Mapping of FastQC reads to the published Marchantia polymorpha genome v3.1 (Marchantia.info) was done using STAR on the omicsbox platform (BioBam Bioinformatics (Version 3.0.30). March 3, 2019. www. biobam.com/omicsbox)
gene level quantification was performed based in the HTseq package on the omicsbox platform using published (Marchantia.info) genomic features (Mpolymorphav3.1.primaryTrs.gff3).
A pairwise differential expression analysis (without replicates) based on NOIseq was used to analyse both time points without replicates using the omicsbox platform
Assembly: Marchantia polymorpha genome v3.1
Supplementary files format and content: tab-delimited test file including normalized counts (normalized_counts)
Excel file of pairwise comparison (BELL1-KNOX2-72h_vs_BELL1-KNOX2-mock)

value: mock


title: Bacillus circulans, treatment,rep1

status: Public on Sep 13 2023

city: guangzhou

first: Wu

last: Shuo

address: wushan

institute: South China Agricultural University

data_processing:
The library  was  sequenced on Illumina sequencing platform.
Low quality reads were trimmed by using Trimmomatic (version 0.38)(parameter settings :HEADCROP:8 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36).
Quality control of raw reads was performed using FastQC (version 0.11.5).
Assembly: GCF_013267435.1,GCF_000002545.3,GCA_001576635.1
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Niallia circulans

source_name: Bacillus circulans

growth_protocol: Bacterial suspension culture at 37℃;Fungus suspension culture at 28℃

extract_protocol:
RNA was extracted using Invitrogen TRIzol® Reagent. 1 ug of total RNA was used for the construction of sequencing libraries.
The fragmented mRNA was reverse transcripted with SuperScript II and then converted to double-stranded cDNA using RNaseH and DNA Pol I by random priming. After purification, the double-stranded cDNA was subjected to blunt-ending, dA addition to 3’-end and adapter ligation. Finally, PCR was carried out to enrich the adapter ligated cDNA and the libraries were analyzed by Agilent Bioanalyzer 2100 and quantified by qPCR before sequenced by the Illumina sequencing platform.

treatment_protocol: Microorganisms in logarithmic growth phase were cultured for 4 hours after adding MIC values essential oil or not.

value: Bacillus circulans

value: treated with Neolamarckia cadamba essential oil for four hours


title: Bacillus circulans, treatment,rep2


title: 5xFAD_F #1189 (Glial)

description:
X7M.F2.1189.WT.5xFAD.Ctx
nCounter® Glial Panels

tag: Sex

value: 5xFAD mice


title: Bacillus circulans, treatment,rep3


title: Bacillus circulans, control,rep3


title: Bacillus circulans, control,rep2


title: WT NK cells, unstimulated, biol rep 3

first: Hyunu

last: Kim

address: 417 E 68th St

department: Immunology

institute: Memorial Sloan Kettering Cancer Center

description:
WT_polySTAT4_unstim_3
The Illumina NovaSeq X was used as the sequencing instrument.

data_processing:
Paired reads were trimmed for adaptors and removal of low-quality reads by using Trimmomatic (v0.39) and aligned to the mm10 reference genome using Bowtie2 (v2.4.1).
Upon alignment, peaks were called using MACS2 (v2.2.7.1) with input samples as control using narrow peak parameters --cutoff-analysis -p 1e-5 --keep-dup all -B --SPMR.
For each sample groups, irreproducible discovery rate (IDR) calculations using scripts provided by the ENCODE project (https://www.encodeproject.org/software/idr/; v.2.0.4.2). Reproducible peaks showing an IDR value of 0.05 or less in each conditions were aggregated across the experiment and merged via union to the peak atlas, annotated with UCSC Known Gene model.
Assembly: mm10
Supplementary files format and content: bigwig files are unscaled pileups of reads aligned to the reference genome.
Supplementary files format and content: tsv file is tab delimited table of peak atlas with normalized counts (1 count per pair of reads, normalized by spike-in DNA) calculated using the summarizeOverlaps function from the GenomicAlignments R package (v10.10.1)
Library strategy: CUT&RUN

source_name: Cultured NK

extract_protocol:
250,000 (or 50,000 for input) sorted cells were washed thrice with PBS, resuspended in Buffer 1 (1X eBioscience Perm/Wash Buffer, 1X Roche cOmplete EDTA-free Protease Inhibitor, 0.5 uM Spermidine in H2O) and incubated with STAT4 (Invitrogen 71-4500) antibodies at 1/100 dilution in Antibody Buffer (Buffer 1 + 2uM EDTA) in 96 well V-bottom plate at 4C overnight. Upon antibody incubation, cells were washed twice with Buffer 1 and resuspended in 50ul of Buffer 1 + 1X pA/G-MNase (Cell Signaling #57813) and incubated on ice for 1 hr and washed with Buffer 2 (0.05% w/v Saponin, 1X Roche cOmplete EDTA-free Protease Inhibitor, 0.5 uM Spermidine in 1X PBS) three times. After washing, Calcium Buffer (Buffer 2 + 2uM of CaCl2) was used to resuspend the cells for 30 mins on ice to activate the pA/G-MNase reaction, and equal volume of 2X STOP Buffer (Buffer 2 + 20uM EDTA + 4uM EGTA) was added along with 1pg of Saccharomyces cerevisiae spike-in DNA (Cell Signaling #29987). Samples were incubated for 15 mins at 37C and DNA was isolated and purified using Qiagen MinElute Kit according to manufacturer’s protocol
Immunoprecipitated DNA was quantified by PicoGreen and the size was evaluated by Agilent BioAnalyzer. When possible, fragments between 100 and 600 bp were size selected using aMPure XP beads (Beckman Coulter catalog # A63882) and Illumina sequencing libraries were prepared using the KAPA HTP Library Preparation Kit (Kapa Biosystems KK8234) according to the manufacturer’s instructions with 0.001-0.5ng input DNA and 14 cycles of PCR. Barcoded libraries were run on the NovaSeq X in a PE100 run using 10B reagent kit (200 Cycles) (Illumina). An average of 23 million paired reads were generated per sample.

tag: cell number

value: Cultured NK

tag: antibody

value: unstim

tag: replicate


title: STAT4KO NK cells, stimulated with IL12 + IL18, biol rep 2

description:
STAT4KO_polySTAT4_stim_2
The Illumina NovaSeq X was used as the sequencing instrument.


title: STAT4KO NK cells, unstimulated, non enriched input

description:
STAT4KO_input_unstim_1
The Illumina NovaSeq X was used as the sequencing instrument.

value: input


title: 6 month old control mice, biological rep1 (snRNA-seq)

description: RNA-seq

value: Cortex

value: 6 month old

value: control


title: WT NK cells, unstimulated, non enriched input

description:
WT_input_unstim_1
The Illumina NovaSeq X was used as the sequencing instrument.


title: WT NK cells, unstimulated, biol rep 1

description:
WT_polySTAT4_unstim_1
The Illumina NovaSeq X was used as the sequencing instrument.


title: WT NK cells, stimulated with IL12 + IL18, biol rep 3

description:
WT_polySTAT4_stim_3
The Illumina NovaSeq X was used as the sequencing instrument.


title: WT NK cells, stimulated with IL12 + IL18, biol rep 2

description:
WT_polySTAT4_stim_2
The Illumina NovaSeq X was used as the sequencing instrument.


title: WT NK cells, stimulated with IL12 + IL18, biol rep 1

description:
WT_polySTAT4_stim_1
The Illumina NovaSeq X was used as the sequencing instrument.


title: NK cells, stimulated with IL12 + IL18, biol rep 2

extract_protocol:
500,000 sorted cells (50,000 for input) were washed thrice with PBS, resuspended in Buffer 1 (1X eBioscience Perm/Wash Buffer, 1X Roche cOmplete EDTA-free Protease Inhibitor, 0.5 uM Spermidine in H2O) and incubated with BHLHE40 (anti-DEC1, Novus NB100-1800) antibodies at 1/100 dilution in Antibody Buffer (Buffer 1 + 2uM EDTA) in 96 well V-bottom plate at 4C overnight. Upon antibody incubation, cells were washed twice with Buffer 1 and resuspended in 50ul of Buffer 1 + 1X pA/G-MNase (Cell Signaling #57813) and incubated on ice for 1 hr and washed with Buffer 2 (0.05% w/v Saponin, 1X Roche cOmplete EDTA-free Protease Inhibitor, 0.5 uM Spermidine in 1X PBS) three times. After washing, Calcium Buffer (Buffer 2 + 2uM of CaCl2) was used to resuspend the cells for 30 mins on ice to activate the pA/G-MNase reaction, and equal volume of 2X STOP Buffer (Buffer 2 + 20uM EDTA + 4uM EGTA) was added along with 1pg of Saccharomyces cerevisiae spike-in DNA (Cell Signaling #29987). Samples were incubated for 15 mins at 37C and DNA was isolated and purified using Qiagen MinElute Kit according to manufacturer’s protocol
Immunoprecipitated DNA was quantified by PicoGreen and the size was evaluated by Agilent BioAnalyzer. When possible, fragments between 100 and 600 bp were size selected using aMPure XP beads (Beckman Coulter catalog # A63882) and Illumina sequencing libraries were prepared using the KAPA HTP Library Preparation Kit (Kapa Biosystems KK8234) according to the manufacturer’s instructions with 0.001-0.5ng input DNA and 14 cycles of PCR. Barcoded libraries were run on the NovaSeq 6000 in a PE100 run, using S4 kit v1.5 with XP mode or NovaSeq X in a PE100 run using 10B reagent kit (200 Cycles) (Illumina). An average of 23 million paired reads were generated per sample.

tag: seq date


title: NK cells, unstimulated, non enriched input


title: NK cells, unstimulated, biol rep 3


title: NK cells, stimulated with IL12 + IL18, non enriched input


title: NK cells, unstimulated, biol rep 1


title: NK cells, stimulated with IL12 + IL18, biol rep 3


title: NK cells, unstimulated, biol rep 2


title: NK cells, stimulated with IL12 + IL18, biol rep 1


title: Bacillus circulans, control,rep1


title: WT NK cells, unstimulated, biol rep 2

description:
WT_polySTAT4_unstim_2
The Illumina NovaSeq X was used as the sequencing instrument.


title: KO Section 1

first: Elizaveta

last: Bashkirova

address: 3227 Broadway

department: Biochemistry

institute: Columbia University

description: 10X slide ID: V11U15-123 Area C1

data_processing:
Data were demultiplexed and processed using SpaceRanger's default settings
Reads were aligned to the mm10 2020-A reference mouse transcriptome (10X Genomics) and the OR transcriptome generated by Ibarra-Soria et al
Assembly: mm10
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_positions_list.csv: spatial barcodes and position of spatial spots
Supplementary files format and content: cloupe.cloupe: 10X Loupe browser file for visualizing spatial gene expression
Supplementary files format and content: filtered_feature_bc_matrix.h5: filtered count matrtices in Hierarchical Data Format
Library strategy: spatial transcriptomics

source_name: olfactory epithelium

growth_protocol: Adult mice were injected 3x IP with tamoxifen (24 hours apart), 10 days following the first injection olfactory epithelium was ablated with an IP injection of methimazole. Then olfactory epithelium was regenerated for 40 days.

extract_protocol:
14µm cryosections of tissue were mounted onto Visium Spatial Gene Expression slides (10X Genomics)
Barcoded cDNA libraries of tissue sections were generated using the Spatial Gene Expression Reagent Kit (10X Genomics) according to the manufacture’s protocols.

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The olfactory epithelium  was dissected , embedded in OCT and frozen on dry ice.

value: olfactory epithelium

value: NfiAfl/fl; NfiBfl/fl; NfiXfl/fl;  K5CreER*/+;  Rosa-CAG-tdtomfl/fl


title: KO Section 2

description: 10X slide ID: V11U15-123 Area A1


title: MIN6 cells, sh2 3

city: Wuhan

first: Zhengwei

last: Zhang

address: 169 Donghu Road

institute: Zhongnan Hospital of Wuhan University

description:
treatment
gene_fpkm.txt

data_processing:
CLC Genomics Workbench v 11.0.1
Sequenced reads were trimmed for adaptor sequence/low-quality sequence using CLC genomics benchwork (parameter-Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomics benchwork (parameter-mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomics benchwork
Assembly: mm 10
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

extract_protocol:
Tissues were flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: Pancreatic beta-cells (endocrine cells)

value: PP2Ac knockdown


title: MIN6 cells, sh2 1

description:
treatment
gene_fpkm.txt

tag: cell type


title: WT Section 1

description: 10X slide ID: V11U15-119 Area D1

value: K5CreER*/+;  Rosa-CAG-tdtomfl/fl


title: MIN6 cells, sh2 2

description:
treatment
gene_fpkm.txt


title: MIN6 cells, shc 2

description:
control
gene_fpkm.txt


title: MIN6 cells, shc 1

description:
control
gene_fpkm.txt


title: STAT4KO NK cells, stimulated with IL12 + IL18, biol rep 1

description:
STAT4KO_polySTAT4_stim_1
The Illumina NovaSeq X was used as the sequencing instrument.


title: WT Section 2

description: 10X slide ID: V11U15-119 Area B1


title: MIN6 cells, shc 3

description:
control
gene_fpkm.txt


title: CT_GC-SAL_rep3

city: Loma Linda

first: Isaac

middle: Jacob

last: Kremsky

address: 11175 Campus St., Chan Shun Pavilion, Room A1022

department: Basic Sciences

institute: Loma Linda University

description:
DSP-1001460001002-B-E01
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

data_processing:
dcc-metadata = true
save-interim-files = false
quality-trim-score = 20
2color-trimming = True
adapter1 = AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
adapter2 = AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
adapter-trim-match-length = 10
adapter-trim-max-mismatch = 3
barcode-max-mismatch = 1
stitching-max-mismatch = 2
dedup-hd = 1
threads = 4
Assembly: NA
Supplementary files format and content: Digital count conversion (DCC) files produced by Nanostring's GeoMx NGS pipeline
Supplementary files format and content: Files ending in "GeneExpression_Q3norm.txt" give Q3-normalized gene expression of the indicated brain region. TX=BuOE treatment; SAL=Saline treatment; FLT=spaceflight mice; GC=Grounded Control mice.
Supplementary files format and content: Files ending in "DEanalysis.txt" are thre results of the differential expression analysis output by the GeoMx DSP Control Center. GCvsFLT-SAL=GC-SAL vs. FLT-SAL; SALvsBuOE-FLT=FLT-BuOE vs. FLT-SAL; SALvsBuOE-GC=GC-BuOE vs. GS-SAL;  BuOE=BuOE treatment; SAL=Saline treatment; FLT=spaceflight mice; GC=Grounded Control mice.
Library strategy: GeoMx-Seq

source_name: Cortex

growth_protocol: Ten-week-old C57BL/6 male mice.

extract_protocol:
After sacrifice, mouse brains were then removed and prepared as follows. The left hemibrains were fixed in 4% paraformaldehyde in phosphate-buffered saline (PBS) for 24 hours and then rinsed and washed with PBS for immunohistochemistry (IHC) assays or spatial genomics profiling. The right brains were flash-frozen and stored at −80 °C for further analysis. The study was approved by the Institutional Animal Care and Use Committee (IACUC) of Loma Linda University (LLU), Roskamp Institute, and The National Aeronautics and Space Administration (NASA).
Each collection of oligo tags from one well (representing an ROI from the tissue section) was indexed with i7xi5 unique dual indexes using GeoMx SeqCode primers with 18 cycles of PCR.  After PCR, indexed AOIs were pooled and purified in two rounds of AMPure XP PCR purification using 1.2x bead:sample ratio.

treatment_protocol: Mice were launched at the Kennedy Space Center (KSC) and spent 35 days aboard the international space station (ISS). All mice were maintained at an ambient temperature of 26–28 °C with a 12-hour light/dark cycle during the flight. All mice were provided NASA Nutrient-upgraded Rodent Food Bar (NuRFB) and autoclaved deionized water ad libitum. MnTnBuOE-2-PyP5+ (BuOE) at 1 mg/kg (0.2 mL) was administrated subcutaneously 7 days prior to the flight launch and weekly aboard the ISS. All mice were subdivided into saline or BuOE treated groups. Upon return to the Earth, spaceflight mice were transported to the research laboratory at Roskamp Institute, Sarasota, Florida within 20 hours of splashdown. Mice were exsanguinated by closed-cardiac blood collection under deep Ketamine/Xylazine (150/45 mg/kg) anesthesia, followed by cervical dislocation as a secondary euthanasia method to ensure death. Ground control mice were maintained on Earth for 35 days in flight hardware cages under similar environmental conditions as the flight groups, including the same food, light/dark, temperature, treatment (SAL or BuOE), and euthanasia regimens. The protocol for GC mice commenced three days subsequent to the commencement of the protocol for spaceflight mice.

value: male

value: ground control

value: Saline

tag: slide id

tag: roi number

tag: segment type

value: Full

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: CA_GC-SAL_rep3

description:
DSP-1001460001002-B-D11
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

source_name: Cornu Ammonis 1

tag: strain

tag: Sex

tag: tissue

value: Cornu Ammonis 1

tag: treatment


title: DG_GC-SAL_rep3

description:
DSP-1001460001002-B-D12
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

source_name: Dentate Gyrus

value: Dentate Gyrus


title: DG_GC-SAL_rep2

description:
DSP-1001460001002-B-D08
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.


title: FCT_GC-SAL_rep3

description:
DSP-1001460001002-B-D10
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

source_name: Frontal Cortex

value: Frontal Cortex


title: CA_GC-SAL_rep2

description:
DSP-1001460001002-B-D07
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.


title: FCT_GC-SAL_rep2

description:
DSP-1001460001002-B-D06
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.


title: CT_GC-SAL_rep1

description:
DSP-1001460001002-B-D05
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.


title: FCT_GC-SAL_rep1

description:
DSP-1001460001002-B-D02
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.


title: DG_FLT-SAL_rep3

description:
DSP-1001460001002-B-C11
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

value: spaceflight


title: CT_FLT-SAL_rep3

description:
DSP-1001460001002-B-D01
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.


title: CA_FLT-SAL_rep3

description:
DSP-1001460001002-B-C10
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.


title: DG_GC-SAL_rep1

description:
DSP-1001460001002-B-D04
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.


title: CA_GC-SAL_rep1

description:
DSP-1001460001002-B-D03
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.


title: CA_FLT-SAL_rep2

description:
DSP-1001460001002-B-C06
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.


title: DG_FLT-SAL_rep2

description:
DSP-1001460001002-B-C07
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.


title: CT_FLT-SAL_rep2

description:
DSP-1001460001002-B-C09
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.


title: FCT_FLT-SAL_rep2

description:
DSP-1001460001002-B-C08
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.


title: CT_FLT-SAL_rep1

description:
DSP-1001460001002-B-C05
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.


title: FCT_FLT-SAL_rep3

description:
DSP-1001460001002-B-C12
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.


title: DG_FLT-SAL_rep1

description:
DSP-1001460001002-B-C03
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.


title: FCT_FLT-SAL_rep1

description:
DSP-1001460001002-B-C04
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.


title: CA_GC-BuOE_rep3

description:
DSP-1001460001002-B-B11
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

value: BuOE


title: CT_GC-BuOE_rep3

description:
DSP-1001460001002-B-C01
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

value: Cortex


title: FCT_GC-BuOE_rep2

description:
DSP-1001460001002-B-B08
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.


title: CA_FLT-SAL_rep1

description:
DSP-1001460001002-B-C02
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.


title: DG_GC-BuOE_rep3

description:
DSP-1001460001002-B-B10
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.


title: CT_GC-BuOE_rep2

description:
DSP-1001460001002-B-B09
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.


title: FCT_GC-BuOE_rep3

description:
DSP-1001460001002-B-B12
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.


title: CT_GC-BuOE_rep1

description:
DSP-1001460001002-B-B05
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.


title: CT_GC-SAL_rep2

description:
DSP-1001460001002-B-D09
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.


title: DG_GC-BuOE_rep2

description:
DSP-1001460001002-B-B06
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.


title: CA_GC-BuOE_rep2

description:
DSP-1001460001002-B-B07
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.


title: FCT_GC-BuOE_rep1

description:
DSP-1001460001002-B-B04
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.


title: DG_GC-BuOE_rep1

description:
DSP-1001460001002-B-B02
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.


title: CT_FLT-BuOE_rep3

description:
DSP-1001460001002-B-B01
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.


title: CA_GC-BuOE_rep1

description:
DSP-1001460001002-B-B03
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.


title: FCT_FLT-BuOE_rep3

description:
DSP-1001460001002-B-A12
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.


title: CA_FLT-BuOE_rep3

description:
DSP-1001460001002-B-A11
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.


title: DG_FLT-BuOE_rep3

description:
DSP-1001460001002-B-A10
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.


title: CT_FLT-BuOE_rep2

description:
DSP-1001460001002-B-A09
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.


title: DG_FLT-BuOE_rep2

description:
DSP-1001460001002-B-A06
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.


title: CT_FLT-BuOE_rep1

description:
DSP-1001460001002-B-A05
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.


title: FCT_FLT-BuOE_rep2

description:
DSP-1001460001002-B-A08
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.


title: CA_FLT-BuOE_rep2

description:
DSP-1001460001002-B-A07
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.


title: FCT_FLT-BuOE_rep1

description:
DSP-1001460001002-B-A04
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.


title: Colon_Infected_D10_rep4

city: Blacksburg

first: Raquel

last: Hontecillas

address: 1800 Kraft dr suite 100

institute: NIMML

data_processing:
Raw sequence reads were trimmed for adapter sequences/low-quality bases using cutadapt.
Clean sequence reads were aligned to Mouse reference transcriptome GRCm28 using salmon.
Assembly: GRCm28
Supplementary files format and content: tab-delimited text file includes counts for each sample.

source_name: Colon

extract_protocol:
RNA was extracted using the Rneasy mini kit (Qiagen). TapeStation RNA Sample QC was conducted.
RNA libraries for RNA-seq were prepared using the SeqMatic TailorMix Directional mRNA library preparation kit.

value: Colon

tag: infection

value: Infected

tag: time


title: DG_FLT-BuOE_rep1

description:
DSP-1001460001002-B-A02
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

tag: slide id

tag: roi number


title: Colon_Infected_D10_rep2


title: Colon_Infected_D10_rep5


title: Colon_Infected_D10_rep3


title: CA_FLT-BuOE_rep1

description:
DSP-1001460001002-B-A03
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

tag: segment type

tag: area


title: Colon_Infected_D10_rep1


title: Colon_Infected_D8_rep5


title: Colon_Infected_D8_rep4


title: Colon_Infected_D8_rep3


title: Colon_Infected_D8_rep2


title: Colon_Infected_D8_rep1


title: Colon_Infected_D5_rep3


title: Colon_Infected_D5_rep2


title: Colon_Infected_D4_rep4


title: Colon_Infected_D5_rep1


title: Colon_Infected_D4_rep3


title: Colon_Infected_D4_rep2


title: Colon_Infected_D3_rep3


title: Colon_Infected_D3_rep4


title: Colon_Infected_D4_rep1


title: Colon_Infected_D3_rep1


title: Colon_Uninfected_D10_rep3

value: Uninfected


title: Colon_Uninfected_D10_rep1


title: Colon_Uninfected_D10_rep2


title: Colon_Uninfected_D8_rep3


title: Colon_Uninfected_D8_rep4


title: Colon_Uninfected_D5_rep2


title: Colon_Uninfected_D5_rep1


title: Colon_Uninfected_D8_rep2


title: Colon_Uninfected_D8_rep1


title: Colon_Uninfected_D5_rep3


title: Colon_Uninfected_D4_rep4


title: Colon_Uninfected_D5_rep4


title: Colon_Uninfected_D4_rep2


title: Colon_Infected_D5_rep4


title: Colon_Uninfected_D4_rep1


title: Colon_Uninfected_D3_rep3


title: Colon_Uninfected_D3_rep1


title: Colon_Uninfected_D3_rep2


title: Colon_Uninfected_D3_rep4


title: Colon_Uninfected_D0_rep3


title: Colon_Uninfected_D0_rep2


title: Colon_Uninfected_D0_rep4


title: Colon_Infected_D3_rep2


title: Colon_Uninfected_D0_rep1


title: Colon_Uninfected_D10_rep4


title: 748_Pb-PRL_ATT

city: Paris

first: Mickael

middle: Mathieu

last: Menager

address: 24 Boulevard du Montparnasse

country: France

institute: Institut Imagine

data_processing:
Sequencing reads were demultiplexed and aligned to the mouse reference genome (mm10-2020-A), using the CellRanger Pipeline v5.0.1
Unfiltered RNA UMI counts were loaded into Seurat v4.0.1 (Stuart et al., 2019) for quality control, data integration and downstream analyses. Apoptotic cells and empty sequencing capsules were excluded by filtering out cells with fewer than 500 features or a mitochondrial content higher than 20%.
Data from each sample were log normalisedand scaled, before batch correction using Seurat’s FindIntegratedAnchors.
On this integrated dataset, we computed the principal component analysis on the 3000 most variable genes. UMAP was carried out using the 30 most significant PCs, and community detection was performed using the graph-based modularity-optimization Louvain algorithm from Seurat’s FindClusters function.
Cell types labels were assigned to resulting clusters based on a manually curated list of marker genes as well as previously defined signatures of the known Prostate subtypes.
Assembly: mm10-2020-A
Supplementary files format and content: h5 file containes the raw counts for each sample

source_name: Prostate

extract_protocol:
The prostates were dissected and minced, then digested for one and a half hours with 1mg collagenase at 37°C in 10 ml DMEM + 10% SVF. The cells were then dissociated with trypsin and sieved using a 40µM cell sieve, then cleared of debris using histopaque centrifugation. Live ter119-negative cells were then isolated by flow cytometry.
The scRNA-seq libraries were generated using Chromium Single Cell Next GEM 3′ Library & Gel Bead Kit v.3.1 (10x Genomics) according to the manufacturer’s protocol. Briefly, cells were counted, diluted at 1,000 cells/µL in PBS+0,04% and 20,000 viable cells were loaded in the 10x Chromium Controller to generate single-cell gel-beads in emulsion. After reverse transcription, gel-beads in emulsion were disrupted. Barcoded complementary DNA was isolated and amplified by PCR. Following fragmentation, end repair and A-tailing, sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq (Illumina) with 28 cycles of read 1, 8 cycles of i7 index and 91 cycles of read 2.

treatment_protocol: daily gavage for 30 days with a dose of 60mg/kg/day of Anethole tritione or vehicle (coconut oil).

value: Prostate

tag: genotype

value: Pb-PRL

value: anethole tritione


title: 756_Pb-PRL_Vehicle

value: coconut oil


title: 506_Pb-PRL_ATT


title: RNA PDS rep1

city: Riverside

first: Yinsheng

last: Wang

address: 501 Big Springs Road

institute: University of California Riverside

data_processing:
The sequencing reads were aligned to GRCh38 assembly using STAR (v.2.7.0) with default parameters. Transcript quantification was conducted using featureCounts (v.2.0.3). Differential gene expression analysis was performed with DESeq2 (v.1.36.0)
Assembly: GRCh38
Supplementary files format and content: xlsx files were generated with gene expression transcripts per million (TPM) data included.

growth_protocol: Cells were cultured at 37 degrees in a humidified incubator with 5% CO2

extract_protocol:
Total RNA was extracted from cells with Omega Total RNA Kit I.
Poly(A) RNA enrichment was conducted using NEBNext Poly(A) mRNA Magnetic Isolation Module following the manufacturer's instructions, and the sequencing library was constructed by using the NEBNext Ultra II RNA Library Prep Kit.

treatment_protocol: Mock treatment or 20uM PDS treatment for 24hrs

tag: cell line

tag: cell type

value: Human hepatocellular carcinoma

value: wild type

value: 20uM PDS, 24hrs


title: Colon_Uninfected_D4_rep3