title: norrin and nutlin3 - replicate 2


title: Cardiomyocyte-Saline-WT-1

status: Public on Jun 30 2025

type: SRA

city: Charlottesville

first: Caitlin

last: Pavelec

state: VA

address: 1340 Jefferson Park Ave

department: Pharmacology

country: USA

institute: University of Virginia School of Medicine

library_source: transcriptomic

data_processing:
One hundred fifty-base paired-end sequencing was performed using an Illumina NovaSeq platform according to manufacture instructions. Fastq files were processed using in-house perl scripts from Novogene to obtain clean reads.  FeatureCounts was used to calculate read numbers for each gene and fragments of per kilobase of transcript sequence per millions base pairs sequenced (FPKM) were calculated.
Assembly: Clean reads were aligned to the mouse reference genome using Hisat2 v2.0.5.
Supplementary files format and content: all samples are included with fpkm values in a xlsx format

molecule: total RNA

organism: Mus musculus

source_name: Heart

extract_protocol:
For some experiments, isolated cardiomyocytes were suspended in 1mL of TRIzolTM (Invitrogen) and stored at -80oC for further analysis75. After chloroform incubation and centrifugation per manufacture instructions RNA-containing phase was diluted with 70% ethanol 1:1 and RNA isolation was performed using RNeasy Mini Kit (Qiagen). For tissues, Total RNA was isolated using RNeasy Mini Kit (Qiagen) after lysis in RLT buffer with bead homogenization. Total RNA quantity and quality were then assessed on a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific).
Library preparation including quality metrics, sequencing, and clustering were performed by Novogene (Sacramento, CA).

tag: tissue

value: Heart

tag: cell type

value: Cardiomyocyte

tag: genotype

tag: treatment

value: Saline


title: VAS9

city: Armilla

first: Bioinformatics Unit

last: IPBLN-CSIC

state: GRANADA

address: Avda. del Conocimiento, 17. Instituto de Parasitología y Biomedicina Lopez-Neyra. Bioinformática

country: Spain

institute: IPBLN-CSIC

data_processing:
The paired-end sequencing was conducted on a HiSeq sequencer (Illumina, CA, USA) producing 34.6x2 M raw paired reads sample on average.
We used miARma-Seq pipeline to process the data and perform the analyses.
Raw data were evaluated using FastQC software to analyse the quality of the reads, and afterwards, sequences were aligned to the GRCh38 reference genome with STAR.
Principal component analysis (PCA) and hierarchical clustering of normalized samples were performed to check the similarity of RNA-sequencing samples.
Samples identified as outliers were filtered out from further analyses as well as duplicated samples and those presenting gender discrepancies.
Differential expression analyses were conducted using the limma package11. First, we removed the low expressed genes (CPM< 1) and calculated reads per kilobase per million mapped reads (RPKM) for downstream analyses. Then, we performed a linear model using the limma voom function12 including sex as a covariate. Finally, we carried out an eBayes test in order to identify genes that are differentially expressed between the subgroups in our study. We considered statistically differentially expressed genes (DEGs) those with a false discovery rate (FDR) < 0.05. log2 fold changes (logFC) was used to assess expression changes among groups of comparison. We also calculated TMM (trimmed mean of M-values) values for graphical representations1
All genes with a FDR < 0.05 were statistically significant and designated as differentially expressed genes (DEGs).
Subsequently, we used the online tool Enrichr14 to perform enrichment analysis of DEGs based on the following databases: BioPlanet 2019 and gene ontology (GO) for biological processes, cellular component, and molecular function. Significant enrichments were considered when p < 0.05 and a minimum count of 3 genes. Finally, we performed TF binding motif enrichment analysis of DEGs by applying the DoRothEA v2 tool15. We restricted our analyses to the most reliable interactions (A, B and C levels), and a p < 0.05 and normalized enrichment score (NES) of ± 2 were considered significantly enriched.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TMM values for each Sample

organism: Homo sapiens

source_name: Whole blood

extract_protocol:
Peripheral blood mononuclear cells were acquired from whole blood by density gradient centrifugation using Ficoll-Paque (Rafer, Zaragoza, Spain). These cells were then incubated with CD4-APC conjugated antibodies (MiltenyiBiotec, Germany) in staining buffer (PBS with 2mM of EDTA and 4% FBS) for 20 minutes. Next, flow cytometry sorting was used to isolate CD4+ T cells through positive selection. Finally, both genomic DNA and total RNA were extracted from the same cell pellet by using AllPrep DNA/RNA/miRNA Universal kit (Qiagen, Hilden, Germany).  Total RNA quality was first determined by the 2100 Bioanalyzer System (Agilent, CA, USA),
1 ug of those samples with excellent quality RNA (RNA integrity number >7) was used for library synthesis with the TruSeq Stranded mRNA Library Prep Kit (Illumina, CA, USA) according to the manufacturer’s protocol

value: Whole blood

tag: cell line

value: CD4+ T cells

value: T cells

tag: clasification*

tag: Sex

value: F

tag: age

tag: sorter day


title: VAS88

value: M


title: norrin and nutlin3 - replicate 1

city: Minneapolis

first: Harald

middle: J

last: Junge

state: Minnesota

address: Room 310A LRB, 2001 6th Street SE

department: OVNS

institute: University of Minnesota

data_processing:
Data were processed using the DNASTAR Lasergene (version 15) Seqman NGen RNA-Seq module. Differential gene expression analysis, gene ontology analysis, and statistical tests were performed in the DNA STAR Lasergene (version 15) Arraystar module.
Assembly: human genome 38p12
Supplementary files format and content: Processed data were exported from the DNASTAR Arraystar module  in xlsm format. The exported table contains the number of reads per gene, RPKM values, and the RPKM fold change between groups.

source_name: primary human retinal microvascular endothelial cells

growth_protocol: Human retinal microvascular endothelial cells (ACBRI 181) were cultured and maintained in EBM2 medium (CC-3156, Lonza) supplemented with single-quot growth factors (CC-4176, Lonza). Approximately 325K cells were seeded per well into a gelatin coated 6-well plate.

extract_protocol:
Trizol (Invitrogen, 15596026) was used to extract total RNA. DNA was digested (Turbo DNAse free, Invitrogen™ AM1907), and RNA was ribodepleted (Ribozero RNA removal kit, Illumina). The samples RNA integrity values were >8.
Libraries were prepared using the Illumina TruSeq Stranded Total RNA Library Prep Kit (RS-122–2202), and 300 bp fragments were isolated. High output 150 bp paired-end sequencing was performed at Novogene, resulting in approximately 20 million reads per sample.

treatment_protocol: 24 hrs after seeding, cells were treated with R+D norrin (R+D Systems, 3014‐NR-025, 200 ng/ml), nutlin-3 (EMD Millipore, 444151-1MG, 10 µM), or their combination for 24 hr before harvest for RNA extraction. DMSO concentration in all samples was 0.1%.

value: HRMVECs represent a pooled population from multiple human donors

value: norrin 200 ng/ml plus nultin-3 10 µM


title: no treatment - replicate 2

value: primary human retinal microvascular endothelial cells

value: untreated


title: nutlin-3 - replicate 1

value: nultin-3 10 µM


title: VAS87


title: VAS90


title: VAS91


title: circRNA profile of case [30T]

type: RNA

city: Guangzhou

first: YUE NING

last: WANG

state: Guangdong

address: 651 Dongfeng Road East

country: China

institute: Sun Yat-Sen University Cancer Centre

description: The microarray was used to acquire circRNA expression profiles of 841 circRNAs.

hyb_protocol: The labeled cDNAs were hybridized to the array with a 1×hybridization solution (5× Denhart’s solution, 0.5% SDS, 5× SSC) in a Hybridization Chamber (Corning Inc, Corning, NY, USA) at 45°C for 12 to 16 hours.

scan_protocol: Scanned in a InnoScan 710 Microarray Scanner (Innopsys, France).

data_processing: Quantile normalization across multiple arrays,GPR normailization software, log 2 transformation of expression levels was used.

source_name: hepatocellular carcinoma

label_protocol: 2 μg of total RNA of hepatocellular carcinoma / adjacent noncancerous tissue was employed with 100 nmol/L of Cy5-dUTP (Enzo, New York USA) in reverse transcription.

extract_protocol: Total RNA was extracted using an acid phenol/chloroform extraction method followed by ethanol precipitation.

tag: group

value: tumor

tag: disease

value: hepatocellular carcinoma


title: circRNA profile of case [2T]


title: circRNA profile of case [39T]


title: CETN_BAT_Ucp1ERCre_H3K9me3_3

city: Schwerzenbach

first: Laura

middle: Catharina

last: Hinte

address: Schorenstrasse 16

country: Switzerland

institute: ETH Zurich

library_source: genomic

data_processing:
*library strategy: Cut&Tag
TrimGalore v0.6.6 used for trimming low quality bases + adapter sequences
Bowtie2 v2.4.4 used for read mapping
samtools v1.13 used for sorting bam files
bedtools v2.30 used for converting sorted bam files into bedgraph files
SEACR v1.3 used for calling peaks
Assembly: mm10
Supplementary files format and content: tab delimited called peak regions for each sample

molecule: genomic DNA

source_name: Brown Adipose Tissue

extract_protocol:
Nuclei were isolated from snap frozen adipose tissue depots in ice cold Nuclei Extraction Buffer (Miltenyi, #130-128-024) supplemented with 10 mM sodium butyrate and 1x cOmpleteTM EDTA-free Protease Inhibitor (Roche, #5056489001) using the gentleMACSTM Octo Dissociator (Miltenyi, #130-096-427) using C-tubes (Miltenyi, #130-093-237). All centrifugation steps were carried out in a to 4˚C cooled swinging bucket centrifuge with settings at 500 xg for 5 minutes. Nuclei were subsequently filtered through a 50µm cell strainer (Sysmex, #04-0042-2317) and washed two times in PBS-BSA (1% w/v) containing protease inhibitor and sodium butyrate. Nuclei were centrifuged and subsequently bound to pre-blocked Dynabeads MyOne Streptavidin C1 beads (ThermoFisher, #65002) for 30 minutes at 4˚C followed by 3 washes with PBS-BSA (1% w/v) on a magnetic stand. CUT&Tag was performed as previously described with minor adjustments36,37. All buffers were supplemented with 1 x cOmplete EDTA-free Protease inhibitor and 10mM sodium butyrate. Briefly, nuclei bound to beads were aliquoted into 96-well LoBind plates (Eppendorf, #0030129547) and incubated with primary antibodies – anti-H3K4me3 (abcam, #ab8580), anti-H3K27me3 (Cell Signaling Technology, #C36B11), anti-H3K27ac (abcam, #ab4729), anti-H3K4me1 (abcam, #ab8895), anti-H3K9me3 (abcam, #ab8898) – overnight at 4˚C. All antibodies were diluted 1:100. With the plate on a magnet the primary antibody solution was removed, the beads were resuspended in secondary antibody solution (guinea pig anti-rabbit IgG (antibodies-online gmbh, #ABIN101961); 1:200 dilution) and incubated at room temperature for 30 minutes while rocking. pA-Tn5 was bound to antibodies, transposition performed at 37 ˚C and stopped using TAPS-Wash solution. Nuclei were lysed and pA-Tn5 decrosslinked using SDS-release solution.
PCR was performed using Kapa HiFi plus dNTPs (Roche Diagnostics, #07958846001) with the following PCR settings: 72˚C 5 minutes, 98˚C 30 seconds, X cycles of 98˚C 10 seconds, 63˚C 30 seconds, 72˚C final extension for 1 minute, hold at 4˚C. After 5 cycles the PCR was put on hold at 4˚C and 10% of the reaction was transferred into a 384 well plate and mixed with KAPA SYBR 2x (qPCR) and primers and qPCR was run for 20 cycles to determine the number of PCR cycles to be added38. Libraries were cleaned using SPRI beads using a 1.3 ratio, eluted in nuclease free water and pooled equimolecularily after library quantification using the KAPA library quantification kit (Roche Diagnostics, #079602).

treatment_protocol: control

value: Brown Adipose Tissue

value: Brown Adipocytes

tag: strain

value: Ucp1ERCre x NuTRAP on C57BL6 background

tag: histone

tag: replicate

value: biol rep 3

value: 17 week old at death, 1 week cold exposure at 8 degrees celsius at week 8; tamoxifen application during cold exposure; Then recovery at 30 degrees celsius for 8 weeks


title: CETN_ingAT_Ucp1ERCre_H3K9me3_1

source_name: Inguinal Adipose Tissue

value: Inguinal Adipose Tissue

value: Beige Adipocytes

value: biol rep 1


title: CETN_ingAT_Ucp1ERCre_H3K9me3_3


title: norrin - replicate 1

value: norrin 200 ng/ml


title: VAS86

value: Whole blood

value: CD4+ T cells

value: T cells

value: M


title: Cardiomyocyte-Saline-WT-2

value: Heart

value: Cardiomyocyte

value: Saline


title: CETN_BAT_Ucp1ERCre_H3K9me3_2

value: biol rep 2


title: VAS84

value: F


title: circRNA profile of case [27T]

value: tumor

value: hepatocellular carcinoma


title: no treatment - replicate 1

value: primary human retinal microvascular endothelial cells

value: HRMVECs represent a pooled population from multiple human donors

value: untreated


title: VAS89


title: VAS83


title: CERT_BAT_Ucp1ERCre_H3K4me3_1

value: Brown Adipose Tissue

value: Brown Adipocytes

value: Ucp1ERCre x NuTRAP on C57BL6 background

value: 17 week old at death, 1 week cold exposure at 8 degrees celsius at week 8; tamoxifen application during cold exposure; Then recovery at 22 degrees celsius for 8 weeks


title: shCald1 biol rep 3

city: Chongqing

first: Jie

last: Li

state: Chongqing

address: 426# Songshibei Road, Yubei District

department: College of Stomatology

institute: Chongqing Medical University

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Supplementary files format and content: mm8
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: periodontal ligament

extract_protocol:
RNA was harvested using TRIzol (Invitrogen). 1 ug of total RNA
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). The library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA).

value: periodontal ligament

value: primary cell

value: mesenchymal stem cells

value: Cald1 knockdown

value: Cald1 shRNA


title: circRNA profile of case [28T]


title: shCald1 biol rep 2


title: CETN_ingAT_Ucp1ERCre_H3K4me3_4

value: Inguinal Adipose Tissue

value: Beige Adipocytes

value: biol rep 4

value: 17 week old at death, 1 week cold exposure at 8 degrees celsius at week 8; tamoxifen application during cold exposure; Then recovery at 30 degrees celsius for 8 weeks


title: shCald1 biol rep 1


title: circRNA profile of case [24T]

value: tumor

value: hepatocellular carcinoma


title: circRNA profile of case [26T]


title: circRNA profile of case [2224T]


title: circRNA profile of case [2213T]


title: VAS8

value: Whole blood

value: CD4+ T cells

value: T cells

value: F


title: shNC biol rep 3

value: scrambled siRNA transfect

value: NC shRNA


title: CETN_ingAT_Ucp1ERCre_H3K4me3_2

value: Ucp1ERCre x NuTRAP on C57BL6 background

value: biol rep 2


title: VAS79

value: M


title: circRNA profile of case [2212T]


title: shNC biol rep 1

value: periodontal ligament

value: primary cell

value: mesenchymal stem cells


title: CETN_ingAT_Ucp1ERCre_H3K4me3_1

value: Inguinal Adipose Tissue

value: Beige Adipocytes

value: biol rep 1


title: circRNA profile of case [2210T]

value: tumor


title: CERT_BAT_Ucp1ERCre_H3K4me3_3

value: Brown Adipose Tissue

value: Brown Adipocytes

value: biol rep 3

value: 17 week old at death, 1 week cold exposure at 8 degrees celsius at week 8; tamoxifen application during cold exposure; Then recovery at 22 degrees celsius for 8 weeks


title: VAS78

value: Whole blood

value: CD4+ T cells

value: T cells

value: F


title: CETN_BAT_Ucp1ERCre_H3K4me3_3

value: Ucp1ERCre x NuTRAP on C57BL6 background

value: 17 week old at death, 1 week cold exposure at 8 degrees celsius at week 8; tamoxifen application during cold exposure; Then recovery at 30 degrees celsius for 8 weeks


title: VAS82


title: K562_WT_K_D9_Dox_IFN_R2

city: Nashville

first: Jason

middle: Ross

last: Schwartz

state: TN

address: 2220 Pierce Ave

department: Pediatrics, Ped Hematology/Oncology

institute: Vanderbilt University Medical Center

data_processing:
Reads were trimmed to remove adapter sequences using Cutadapt v2.10
Reads were aligned to the Gencode GRCh38.p13 genome using STAR v2.7.8a. Gencode v38 gene annotations were provided to STAR to improve the accuracy of mapping.
Quality control on both raw reads and adaptor-trimmed reads was performed using FastQC v0.11.9
featureCounts v2.0.2 was used to count the number of mapped reads to each gene.
Assembly: Gencode GRCh38.p13
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

growth_protocol: K562 cells were cultured and maintained in IMDM (Invitrogen 12440) with 10% FBS (Atlanta Biologicals S1155OH) and 1% pen/step (Invitrogen 15140122) in 5% CO2 and 37°C conditions.

extract_protocol:
Total RNA was obtain via extraction with the Zymo Research RNA Microprep Kit following manufacturer's protocol.
mRNA enrichment and cDNA library preparation was completed by the stranded mRNA (polyA-selected) library kit (Illumina) following manufacturer's protocol.

treatment_protocol: Doxycycline (Sigma Aldrich D9891) was used to induce the expression of dCas9-VPR or dCas9-KRAB by adding to the cell culture medium at a final concentration of 2ug/mL. Recombinant human IFN-alpha (Fisher Scientific cat.# 12100-1) was used to induce SAMD9 at a final concentration of 1000U/mL. Treatment duration was 24 hours for conditions treated with IFN.  K562[KRAB]-D9 cells were pre-treated with doxycycline for 24 hours before IFN was started.  Doxy was continued with IFN.

value: IFN + Doxy


title: VAS81


title: VAS77


title: K562_WT_K_D9_Dox_IFN_R1


title: CETN_ingAT_Ucp1ERCre_H3K4me3_3


title: CETN_BAT_Ucp1ERCre_H3K4me3_1


title: VAS80


title: K562_WT_K_D9_Dox_NT_R2

value: Doxy alone


title: VAS76

value: M


title: shNC biol rep 2

value: periodontal ligament

value: primary cell

value: mesenchymal stem cells

value: scrambled siRNA transfect

value: NC shRNA


title: CERT_BAT_Ucp1ERCre_H3K4me1_3

value: Brown Adipose Tissue

value: Brown Adipocytes


title: K562_WT_K_D9_Dox_NT_R1


title: VAS75


title: VAS73


title: CERT_BAT_Ucp1ERCre_H3K4me1_2

value: biol rep 2

value: 17 week old at death, 1 week cold exposure at 8 degrees celsius at week 8; tamoxifen application during cold exposure; Then recovery at 22 degrees celsius for 8 weeks


title: K562_WT_K_D9_NT_IFN_R2

value: IFN alone


title: CERT_BAT_Ucp1ERCre_H3K4me1_1

value: biol rep 1


title: VAS72

value: Whole blood

value: CD4+ T cells

value: T cells

value: F


title: K562_WT_K_D9_NT_IFN_R1


title: CETN_BAT_Ucp1ERCre_H3K4me3_2

value: Ucp1ERCre x NuTRAP on C57BL6 background

value: 17 week old at death, 1 week cold exposure at 8 degrees celsius at week 8; tamoxifen application during cold exposure; Then recovery at 30 degrees celsius for 8 weeks


title: CETN_ingAT_Ucp1ERCre_H3K4me1_3

value: Inguinal Adipose Tissue

value: Beige Adipocytes

value: biol rep 3


title: circRNA profile of case [21T]

value: tumor

value: hepatocellular carcinoma


title: circRNA profile of case [2204T]


title: circRNA profile of case [2207T]


title: circRNA profile of case [2209T]


title: circRNA profile of case [2206T]


title: circRNA profile of case [2201T]


title: VAS71


title: K562_WT_K_D9_NT_NT_R2

value: No Treatment


title: CETN_ingAT_Ucp1ERCre_H3K4me1_2


title: circRNA profile of case [22T]


title: VAS70

value: M


title: K562_WT_K_D9_NT_NT_R1


title: CETN_ingAT_Ucp1ERCre_H3K4me1_1


title: circRNA profile of case [2196T]


title: circRNA profile of case [2199T]


title: K562_WT_V2_D9_D6_R2

value: Doxy alone


title: CETN_BAT_Ucp1ERCre_H3K4me1_2

value: Brown Adipose Tissue

value: Brown Adipocytes

value: biol rep 2


title: VAS69

value: Whole blood


title: K562_WT_V2_D9_D6_R1


title: VAS68

value: CD4+ T cells


title: CETN_BAT_Ucp1ERCre_H3K4me1_1

value: biol rep 1


title: K562_WT_V2_D9_D2000_R2


title: CERT_BAT_Ucp1ERCre_H3K27ac_1

value: 17 week old at death, 1 week cold exposure at 8 degrees celsius at week 8; tamoxifen application during cold exposure; Then recovery at 22 degrees celsius for 8 weeks


title: CERT_BAT_Ucp1ERCre_H3K27ac_2

value: Ucp1ERCre x NuTRAP on C57BL6 background


title: K562_WT_V2_D9_NT_R1


title: K562_WT_V2_D9_NT_R2


title: CERT_BAT_Ucp1ERCre_H3K27ac_3


title: VAS67

value: T cells

value: F


title: VAS66


title: K562_WT_V2_D9_D2000_R1


title: VAS65


title: VAS7


title: CETN_ingAT_Ucp1ERCre_H3K27ac_2

value: Inguinal Adipose Tissue

value: Beige Adipocytes

value: 17 week old at death, 1 week cold exposure at 8 degrees celsius at week 8; tamoxifen application during cold exposure; Then recovery at 30 degrees celsius for 8 weeks


title: CETN_ingAT_Ucp1ERCre_H3K27ac_3

value: biol rep 3


title: K562_iso_IFN_R2

value: IFN alone


title: K562_iso_IFN_R1


title: VAS63


title: CETN_ingAT_Ucp1ERCre_H3K27ac_1


title: VAS62


title: K562_iso_NT_R2

value: No Treatment


title: circRNA profile of case [2194T]

value: tumor

value: hepatocellular carcinoma


title: VAS6


title: CETN_BAT_Ucp1ERCre_H3K27ac_3

value: Brown Adipose Tissue

value: Brown Adipocytes


title: CETN_BAT_Ucp1ERCre_H3K27ac_2

value: biol rep 2


title: VAS64

value: Whole blood

value: CD4+ T cells

value: M


title: K562_iso_NT_R1


title: VAS59


title: VAS58


title: CETN_BAT_Ucp1ERCre_H3K27ac_1

value: Ucp1ERCre x NuTRAP on C57BL6 background

value: biol rep 1


title: CERT_BAT_Ucp1ERCre_H3K27me3_3

value: 17 week old at death, 1 week cold exposure at 8 degrees celsius at week 8; tamoxifen application during cold exposure; Then recovery at 22 degrees celsius for 8 weeks


title: PDC_D23

city: Salt Lake City

first: Makoto

last: Kondo

state: UT

department: Molecular Pharmaceutics

institute: University of Utah

data_processing:
The sequencing data were uploaded to the Galaxy web platform, and a public server at usegalaxy.org was used to analyze the data (Afgan et al., 2022).  After trimming of Illumina-specific sequences using Trimmomatic version 0.38 (Bolger et al., 2014), the sequence reads were aligned to the human genome reference sequence (hg38) using STAR version 2.7.5b (Dobin et al., 2013). Gene-level assignment was performed using featureCounts version 1.6.4 (Liao et al., 2014).  Acquired data quality was checked by MultiQC (Ewels et al., 2016).  The gene expression matrix with raw gene counts was used for differential gene expression analysis using the DESeq2 version 1.22.1 (Love et al., 2014).  Clustering analysis was performed with differentially expressed 1,554 genes of Padj <0.05, fold change > Abs(1). Gene ontology analysis was performed using Metascape platform at metascape.org (Zhou et al., 2019) with the differentially expressed gene list of Padj < 0.05, fold change >1 or fold change <-1.  Gene set enrichment analysis (GSEA) was performed by GSEA platform (version 4.3.2, Broad institute (https://www.gsea-msigdb.org/gsea/index.jsp)) (Subramanian et al., 2005) on normalized counts of each sequenced sample.  Pathway analysis was done using Ingenuity pathway analysis (IPA) (Qiagen) (Krämer et al., 2014).
Assembly: hg38
Supplementary files format and content: gene counts

source_name: cartilage

growth_protocol: DMEM-F12 with 20% FBS, 1% Anti-Anti.

extract_protocol:
RNA was extracted from harvested cell sheets using RNeasy mini kit (Qiagen, Hilden, Germany).
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor- ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: cartilage

value: primary chondrocytes

value: Cell sheet culture in chondrocyte medium


title: VAS57

value: T cells


title: PDC_D21


title: VAS56


title: CERT_BAT_Ucp1ERCre_H3K27me3_2


title: PDC_D25


title: PDC_D20


title: norrin - replicate 2

value: primary human retinal microvascular endothelial cells

value: HRMVECs represent a pooled population from multiple human donors

value: norrin 200 ng/ml


title: CERT_BAT_Ucp1ERCre_H3K27me3_1


title: VAS55


title: PDC_D19t


title: CETN_ingAT_Ucp1ERCre_H3K27me3_3

value: Inguinal Adipose Tissue

value: Beige Adipocytes

value: biol rep 3

value: 17 week old at death, 1 week cold exposure at 8 degrees celsius at week 8; tamoxifen application during cold exposure; Then recovery at 30 degrees celsius for 8 weeks


title: circRNA profile of case [13T]

value: tumor

value: hepatocellular carcinoma


title: VAS54

value: Whole blood

value: CD4+ T cells

value: F


title: circRNA profile of case [12T]


title: PDC_D18


title: CETN_ingAT_Ucp1ERCre_H3K27me3_2

value: Ucp1ERCre x NuTRAP on C57BL6 background

value: biol rep 2


title: VAS53

value: M


title: circRNA profile of case [18T]


title: circRNA profile of case [2035T]


title: circRNA profile of case [2050T]


title: circRNA profile of case [2042T]


title: circRNA profile of case [2164T]


title: circRNA profile of case [2044T]


title: circRNA profile of case [2169T]


title: PDC_D19f

value: cartilage

value: primary chondrocytes

value: Cell sheet culture in chondrocyte medium


title: circRNA profile of case [2170T]


title: circRNA profile of case [2193T]


title: circRNA profile of case [14T]


title: circRNA profile of case [1594T]


title: circRNA profile of case [2165T]


title: circRNA profile of case [2192T]


title: circRNA profile of case [11T]


title: CETN_ingAT_Ucp1ERCre_H3K27me3_1

value: biol rep 1


title: circRNA profile of case [10T]


title: PDC_D17


title: VAS5

value: T cells


title: VAS49


title: PDC_D16


title: VAS48


title: CETN_BAT_Ucp1ERCre_H3K27me3_1

value: Brown Adipose Tissue

value: Brown Adipocytes


title: PDC_D15


title: circRNA profile of case [9N]

value: non-tumor


title: PDC_D14


title: VAS43


title: NAC_D13

value: primary adult chondrocytes


title: VAS45


title: VAS46


title: VAS47


title: circRNA profile of case [94N]


title: PDC_D12f


title: CE_ingAT_Ucp1ERCre_H3K9me3_2

value: Inguinal Adipose Tissue

value: Beige Adipocytes

value: 9 week old at death, 1 week cold exposure at 8 degrees celsius at week 8; tamoxifen application during cold exposure


title: NAC_D12


title: CERT_ingAT_Ucp1ERCre_H3K9me3_6

value: biol rep 6

value: 17 week old at death, 1 week cold exposure at 8 degrees celsius at week 8; tamoxifen application during cold exposure; Then recovery at 22 degrees celsius for 8 weeks


title: PDC_D13


title: CE_ingAT_Ucp1ERCre_H3K9me3_3

value: Ucp1ERCre x NuTRAP on C57BL6 background

value: biol rep 3


title: circRNA profile of case [93N]

value: hepatocellular carcinoma


title: CE_ingAT_Ucp1ERCre_H3K9me3_1


title: CERT_ingAT_Ucp1ERCre_H3K4me3_6


title: CETN_BAT_Ucp1ERCre_H3K27me3_3

value: 17 week old at death, 1 week cold exposure at 8 degrees celsius at week 8; tamoxifen application during cold exposure; Then recovery at 30 degrees celsius for 8 weeks


title: circRNA profile of case [86N]


title: VAS42

value: Whole blood

value: CD4+ T cells

value: F


title: CERT_ingAT_Ucp1ERCre_H3K9me3_5

value: biol rep 5


title: VAS41

value: T cells

value: M


title: circRNA profile of case [102T]

value: tumor


title: circRNA profile of case [85N]

value: non-tumor


title: circRNA profile of case [82N]


title: NAC_D4

value: cartilage

value: primary adult chondrocytes

value: Cell sheet culture in chondrocyte medium


title: circRNA profile of case [90N]


title: CE_ingAT_Ucp1ERCre_H3K4me3_3

value: Inguinal Adipose Tissue

value: Beige Adipocytes

value: 9 week old at death, 1 week cold exposure at 8 degrees celsius at week 8; tamoxifen application during cold exposure


title: VAS40


title: NAC_D8


title: CE_ingAT_Ucp1ERCre_H3K4me3_2

value: Ucp1ERCre x NuTRAP on C57BL6 background

value: biol rep 2


title: circRNA profile of case [78N]

value: hepatocellular carcinoma


title: NAC_D7


title: NAC_D6


title: VAS38

value: Whole blood


title: VAS39

value: CD4+ T cells


title: NAC_D1


title: VAS4

value: F


title: CE_ingAT_Ucp1ERCre_H3K4me1_3

value: biol rep 3


title: NAC_D5


title: VAS37

value: T cells


title: CERT_ingAT_Ucp1ERCre_H3K4me1_6

value: biol rep 6

value: 17 week old at death, 1 week cold exposure at 8 degrees celsius at week 8; tamoxifen application during cold exposure; Then recovery at 22 degrees celsius for 8 weeks


title: circRNA profile of case [77N]

value: non-tumor


title: circRNA profile of case [67N]


title: circRNA profile of case [54N]


title: VAS35

value: M


title: circRNA profile of case [5N]


title: circRNA profile of case [71N]


title: VAS34


title: SUM159PT, siYES1, 48 hrs, rep 3

city: Cleveland

first: Ruth

last: Keri

state: Ohio

address: 9620 Carnegie Ave

institute: Cleveland Clinic Foundation

data_processing:
Library preparations were sequenced on Illumina platform and paired-end reads were generated.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. FPKM of each gene was calculated based on the length of the gene and reads count mapped to the gene.
Assembly: hg38
Supplementary files format and content: read counts, txt

source_name: breast cancer

growth_protocol: Cells were seeded into 6 mm dishes at 3 x 10^6 cells/plate in 4 mL complete RMPI (231) or Ham/F12 (SUM159) on day 0.

extract_protocol:
RNA was extracted using the RNAeasy Plus Minikit (Qiagen) per manufacturer's protocol
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.

treatment_protocol: On day 1, cells were transfected using Lipofectamine2000 in Optimem with siRNA that was targeted to fire-fly luciferase (siNS) or targeted to YES1 (siYES1). After 6 hrs, equal parts complete media (respective to cell line) was added to plates. At 24 hours, media was completely changed to media appropriate for cell line.

value: breast cancer

value: triple negative breast cancer cells

value: WT


title: CE_ingAT_Ucp1ERCre_H3K4me1_2

value: Inguinal Adipose Tissue

value: Beige Adipocytes


title: CE_ingAT_Ucp1ERCre_H3K4me1_1

value: Ucp1ERCre x NuTRAP on C57BL6 background

value: biol rep 1

value: 9 week old at death, 1 week cold exposure at 8 degrees celsius at week 8; tamoxifen application during cold exposure


title: SUM159PT, siYES1, 48 hrs, rep 4


title: circRNA profile of case [51N]

value: hepatocellular carcinoma


title: circRNA profile of case [52N]


title: SUM159PT, siYES1, 48 hrs, rep 2


title: CE_ingAT_Ucp1ERCre_H3K4me3_1


title: VAS33

value: Whole blood

value: CD4+ T cells


title: CERT_ingAT_Ucp1ERCre_H3K4me3_5

value: biol rep 5


title: RT_epiAT_AdipoCre_H3K9me3_3

source_name: Epididymal Adipose Tissue

value: Epididymal Adipose Tissue

value: Adipocytes

value: AdipoCre x NuTRAP on C57BL6 background

value: biol rep 3

value: 9 week old at death, born and kept at 22 degrees during whole life


title: SUM159PT, siYES1, 48 hrs, rep 1

value: breast cancer


title: VAS32

value: T cells

value: M


title: RT_epiAT_AdipoCre_H3K9me3_2

value: biol rep 2


title: circRNA profile of case [49N]

value: non-tumor


title: VAS31

value: F


title: RT_epiAT_AdipoCre_H3K9me3_1

value: biol rep 1


title: circRNA profile of case [48N]


title: SUM159PT, siNS, 48 hrs, rep 3

value: triple negative breast cancer cells

value: WT

value: siNS


title: VAS30

value: Whole blood

value: CD4+ T cells


title: VAS3


title: CE_BAT_Ucp1ERCre_H3K9me3_4

value: Brown Adipose Tissue

value: Brown Adipocytes

value: Ucp1ERCre x NuTRAP on C57BL6 background

value: biol rep 4

value: 9 week old at death, 1 week cold exposure at 8 degrees celsius at week 8; tamoxifen application during cold exposure


title: SUM159PT, siNS, 48 hrs, rep 4

value: breast cancer


title: CE_BAT_Ucp1ERCre_H3K9me3_3

value: biol rep 3


title: circRNA profile of case [47N]

value: hepatocellular carcinoma


title: SUM159PT, siNS, 48 hrs, rep 2


title: MDA-MB-231, siYES1, 48 hrs, rep 4


title: SUM159PT, siNS, 48 hrs, rep 1


title: VAS29

value: T cells


title: circRNA profile of case [46N]

value: non-tumor


title: CE_BAT_Ucp1ERCre_H3K9me3_2

value: biol rep 2


title: circRNA profile of case [43N]


title: circRNA profile of case [45N]


title: VAS28

value: F


title: CE_BAT_Ucp1ERCre_H3K9me3_1

value: biol rep 1


title: MDA-MB-231, siYES1, 48 hrs, rep 3

value: triple negative breast cancer cells

value: WT


title: RT_epiAT_AdipoCre_H3K4me3_3

value: Epididymal Adipose Tissue

value: Adipocytes

value: AdipoCre x NuTRAP on C57BL6 background

value: 9 week old at death, born and kept at 22 degrees during whole life


title: circRNA profile of case [39N]


title: VAS24

value: Whole blood

value: CD4+ T cells

value: M


title: MDA-MB-231, siYES1, 48 hrs, rep 2

value: breast cancer


title: MDA-MB-231, siYES1, 48 hrs, rep 1


title: VAS23


title: circRNA profile of case [30N]


title: CERT_ingAT_Ucp1ERCre_H3K27ac_6

value: Inguinal Adipose Tissue

value: Beige Adipocytes

value: Ucp1ERCre x NuTRAP on C57BL6 background

value: biol rep 6

value: 17 week old at death, 1 week cold exposure at 8 degrees celsius at week 8; tamoxifen application during cold exposure; Then recovery at 22 degrees celsius for 8 weeks


title: VAS22

value: T cells

value: F


title: MDA-MB-231, siNS, 48 hrs, rep 4

value: triple negative breast cancer cells

value: siNS


title: RT_epiAT_AdipoCre_H3K4me3_1

value: Epididymal Adipose Tissue

value: biol rep 1


title: VAS20


title: VAS27


title: circRNA profile of case [2N]

value: non-tumor

value: hepatocellular carcinoma


title: VAS21

value: Whole blood


title: VAS2

value: CD4+ T cells


title: CE_BAT_Ucp1ERCre_H3K4me3_3

value: Brown Adipose Tissue

value: Brown Adipocytes

value: biol rep 3

value: 9 week old at death, 1 week cold exposure at 8 degrees celsius at week 8; tamoxifen application during cold exposure


title: CE_BAT_Ucp1ERCre_H3K4me3_4

value: Ucp1ERCre x NuTRAP on C57BL6 background

value: biol rep 4


title: MDA-MB-231, siNS, 48 hrs, rep 3

value: breast cancer

value: WT


title: MDA-MB-231, siNS, 48 hrs, rep 2


title: MDA-MB-231, siNS, 48 hrs, rep 1


title: VAS19

value: T cells

value: F


title: circRNA profile of case [2224N]


title: CE_BAT_Ucp1ERCre_H3K4me3_2

value: biol rep 2


title: circRNA profile of case [2222N]


title: circRNA profile of case [28N]


title: circRNA profile of case [36N]


title: RT_epiAT_AdipoCre_H3K4me3_2

value: Epididymal Adipose Tissue

value: Adipocytes

value: AdipoCre x NuTRAP on C57BL6 background

value: 9 week old at death, born and kept at 22 degrees during whole life


title: VAS17

value: Whole blood

value: M


title: CE_BAT_Ucp1ERCre_H3K4me3_1

value: Brown Adipose Tissue

value: biol rep 1


title: RT_epiAT_AdipoCre_H3K4me1_2


title: VAS18

value: CD4+ T cells


title: circRNA profile of case [2212N]

value: non-tumor

value: hepatocellular carcinoma


title: circRNA profile of case [2218N]


title: VAS15


title: RT_epiAT_AdipoCre_H3K4me1_1


title: circRNA profile of case [2213N]


title: supine_study_Age_66_Surv_23_6_Rep1

city: Bethesda

first: Kory

middle: R

last: Johnson

state: MD

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

description: Library name: supine_study_Age_66_Surv_23_6_Rep1

data_processing:
RTA 1.13.48 and CASAVA 1.8.2. software used for basecalling and deplexing. Post deplexing, FASTQ files were quality inspected using the FastQC tool (available at: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and the MultiQC tool (Ewels et al., 2016). For reference mapping (BDGP6), the nf-core RNA-Seq Seq pipeline was used (version 3.10.1; available at https://nf-co.re/rnaseq) in conjunction with select parameters (--outFilterMultimapNmax 500, --winAnchorMultimapNmax 500, --clip_r1 10, --clip_r2 10). To enumerate counts for known genes, the featureCounts tool was used (Liao et al., 2014). To enumerate counts for transposable elements (TEs), the TEcount tool was used (Jin et al., 2015). Enumerated counts across known genes and TEs were then row concatted by sample and saved as tab-delimited text files.
Assembly: BDGP6
Supplementary files format and content: Tab-delimited text files describing expression in counts for known genes and TEs.

organism: Drosophila melanogaster

source_name: Whole Fly

growth_protocol: All experiments were performed on wild type adult male Drosophila melanogaster (Oregon R; y+ w+). Flies were maintained on Nutri-Fly Bloomington formulation food (Genesee Scientific, Raleigh/Durham NC) at 25°C and 50% humidity on a 12:12 hour light:dark cycle. For aging of flies, males and females were collected within 24 hours of eclosion by anesthetization with CO2 and transferred to fresh vials. After three days, males and females were separated on a CO2 pad and males only were placed into fresh vials, with 20 flies per vial. Any flies that died before separation of males and females were not included in either the aging or supine study. Aging male flies were flipped to fresh vials twice weekly, each time counting the number of dead and censored flies, until the population mortality reached ~20%. A fly was censored if it escaped, if it was stuck to the vial, if it was stuck to the food but still moving, or if it was removed for downstream analyses.   For the aging study, 3 flies (each from a separate vial) were gently removed each day without anaesthesia, using a mouth pipette once the population mortality reached ~20% (~day 50). Removed flies were frozen immediately in liquid nitrogen and stored at -80C for later RNA isolation. Daily removal of flies continued until the population mortality reached ~80 – 85 % (~day 70). After that, remaining flies were allowed to age until the entire population was dead. Additionally, when the population mortality reached ~50%, an additional 20 flies were collected, frozen in liquid nitrogen, and stored at -80C for later RNA isolation. The % mortality associated with the chronological age of each fly on its day of collection was interpolated from the survival curve of the entire population.  For the supine study, flies were checked three times daily for supine behavior once the population mortality reached ~20%. Supine behavior was defined as a fly remaining on its back for more than 10 seconds but still moving. Supine flies were gently removed from the vial using a mouth pipette. Half of these flies were immediately frozen in liquid nitrogen and stored at -80C for later RNA isolation. The other half of these flies were gently placed into a fresh vial for continued observation every few hours during the day, until they died. Note that there was a period of ~14 hours each night where no observations were made. Removal of supine flies continued daily until the population mortality reached ~80%, after which the remaining flies in the population were allowed to age until the entire population was dead. The % mortality associated with the chronological age of each fly on its day of collection was interpolated from the survival curve of the entire population.

extract_protocol:
Individual flies were homogenized in Lysis Binding Mix (from MagMAX mirVana Total RNA Isolation Kit; Thermo Fisher Scientific, Washington, DC; #A27828) using Navy Eppendorf RNA Lysis Kits (Next Advance, Troy, NY; #NAVYE5-RNA) and a Bullet Blender Storm 24 (Next Advance, Troy, NY; #4116-BBY24M). RNA was then isolated from these homogenates using the MagMAX mirVana Total RNA Isolation Kit as described in the manufacturer’s instructions, in conjunction with the KingFisher Apex Purification System with 96 Deep-Well head (Thermo Fisher Scientific, Washington, DC; #5400930).
RNA quality and quantity was first assessed by NanoDrop (Thermo Fisher Scientific, Washington, DC) and High Sensitivity RNA ScreenTape (Agilent Technologies, Santa Clara, CA). cDNA libraries were generated from 500 ng of total RNAusing NEBNext Ultra II Directional Poly-A RNA Library Prep Kit for Illumina (New EnglandBiolabs, Ipswich, MA; #E7760). cDNA library quality and quantity were assessed byTapeStation 2200 and Qubit (Thermo Fisher Scientific, Washington, DC). cDNA librarieswere sequenced on a NextSeq 2000 machine using NextSeq 2000 P3 reagents (Illumina,San Diego, CA).

value: Whole Fly

value: Oregon R; y+ w+

tag: study

value: supine

tag: replicate sample

tag: chronological age_(days)

tag: percent population_survival

value: Male

tag: supine death_phenotype

value: No


title: supine_study_Age_67_Surv_22_Rep1

description: Library name: supine_study_Age_67_Surv_22_Rep1

tag: tissue


title: supine_study_Age_63_Surv_22_5_Rep1

description: Library name: supine_study_Age_63_Surv_22_5_Rep1

value: Yes


title: supine_study_Age_69_Surv_17_7_Rep1

description: Library name: supine_study_Age_69_Surv_17_7_Rep1


title: RT_epiAT_AdipoCre_H3K4me1_3

value: Epididymal Adipose Tissue

tag: cell type

value: biol rep 3

tag: treatment


title: CE_BAT_Ucp1ERCre_H3K4me1_4

value: Brown Adipocytes

value: Ucp1ERCre x NuTRAP on C57BL6 background

value: biol rep 4

value: 9 week old at death, 1 week cold exposure at 8 degrees celsius at week 8; tamoxifen application during cold exposure


title: VAS16

value: Whole blood

tag: cell line

value: T cells

tag: clasification*

value: F


title: CE_ingAT_Ucp1ERCre_H3K27ac_4

value: Inguinal Adipose Tissue

value: Beige Adipocytes


title: VAS14

value: CD4+ T cells

tag: Sex

tag: age


title: circRNA profile of case [2209N]

tag: group

value: non-tumor

value: hepatocellular carcinoma


title: VAS12

tag: sorter day


title: supine_study_Age_62_Surv_25_7_Rep1

description: Library name: supine_study_Age_62_Surv_25_7_Rep1

value: Whole Fly

tag: strain

value: Oregon R; y+ w+

value: supine

value: Male


title: CE_BAT_Ucp1ERCre_H3K4me1_3

value: Brown Adipose Tissue

tag: histone

value: biol rep 3


title: circRNA profile of case [2206N]

tag: disease


title: circRNA profile of case [2204N]


title: circRNA profile of case [2210N]


title: supine_study_Age_65_Surv_29_Rep1

description: Library name: supine_study_Age_65_Surv_29_Rep1

tag: study

value: No


title: CE_BAT_Ucp1ERCre_H3K4me1_2

value: Brown Adipocytes

value: Ucp1ERCre x NuTRAP on C57BL6 background

tag: replicate

value: biol rep 2


title: supine_study_Age_61_Surv_29_2_Rep1

description: Library name: supine_study_Age_61_Surv_29_2_Rep1

tag: replicate sample

tag: chronological age_(days)

value: Yes


title: VAS115

value: Whole blood

value: T cells

value: M


title: CE_BAT_Ucp1ERCre_H3K4me1_1

value: biol rep 1

value: 9 week old at death, 1 week cold exposure at 8 degrees celsius at week 8; tamoxifen application during cold exposure


title: VAS113

value: CD4+ T cells


title: supine_study_Age_62_Surv_25_7_Rep2

description: Library name: supine_study_Age_62_Surv_25_7_Rep2

value: Whole Fly

tag: percent population_survival

tag: supine death_phenotype


title: supine_study_Age_62_Surv_37_6_Rep1

description: Library name: supine_study_Age_62_Surv_37_6_Rep1

tag: tissue

value: Oregon R; y+ w+


title: circRNA profile of case [2207N]

value: non-tumor

value: hepatocellular carcinoma


title: VAS13

tag: cell type


title: circRNA profile of case [2202N]


title: RT_epiAT_AdipoCre_H3K27ac_2

value: Epididymal Adipose Tissue

value: Adipocytes

value: AdipoCre x NuTRAP on C57BL6 background

tag: treatment

value: 9 week old at death, born and kept at 22 degrees during whole life


title: RT_epiAT_AdipoCre_H3K27ac_3

value: biol rep 3


title: VAS112

tag: cell line

tag: clasification*


title: supine_study_Age_60_Surv_47_Rep1

description: Library name: supine_study_Age_60_Surv_47_Rep1

value: supine

tag: Sex

value: Male

value: No


title: VAS110

value: Whole blood

value: T cells

value: F

tag: age


title: supine_study_Age_60_Surv_33_Rep2

description: Library name: supine_study_Age_60_Surv_33_Rep2

value: Yes


title: CE_ingAT_Ucp1ERCre_H3K27ac_3

value: Inguinal Adipose Tissue

value: Beige Adipocytes

value: Ucp1ERCre x NuTRAP on C57BL6 background

value: 9 week old at death, 1 week cold exposure at 8 degrees celsius at week 8; tamoxifen application during cold exposure


title: circRNA profile of case [2201N]

tag: group

value: non-tumor

value: hepatocellular carcinoma


title: supine_study_Age_60_Surv_33_Rep3

description: Library name: supine_study_Age_60_Surv_33_Rep3

value: Whole Fly

tag: strain

value: Oregon R; y+ w+


title: circRNA profile of case [2199N]


title: supine_study_Age_60_Surv_33_Rep1

description: Library name: supine_study_Age_60_Surv_33_Rep1


title: circRNA profile of case [2194N]


title: VAS11

value: CD4+ T cells

tag: sorter day


title: circRNA profile of case [2193N]

tag: disease


title: RT_epiAT_AdipoCre_H3K27ac_1

value: Epididymal Adipose Tissue

value: Adipocytes

value: AdipoCre x NuTRAP on C57BL6 background

tag: histone

value: biol rep 1

value: 9 week old at death, born and kept at 22 degrees during whole life


title: VAS107

value: Whole blood

value: T cells


title: supine_study_Age_59_Surv_37_1_Rep1

description: Library name: supine_study_Age_59_Surv_37_1_Rep1

tag: study

value: supine

value: Male

value: Yes


title: circRNA profile of case [2192N]


title: VAS106

value: M


title: CE_BAT_Ucp1ERCre_H3K27ac_4

value: Brown Adipose Tissue

value: Brown Adipocytes

value: Ucp1ERCre x NuTRAP on C57BL6 background

tag: replicate

value: biol rep 4

value: 9 week old at death, 1 week cold exposure at 8 degrees celsius at week 8; tamoxifen application during cold exposure


title: supine_study_Age_58_Surv_55_Rep1

description: Library name: supine_study_Age_58_Surv_55_Rep1

value: Whole Fly

value: Oregon R; y+ w+

tag: replicate sample

tag: chronological age_(days)

value: No


title: CE_BAT_Ucp1ERCre_H3K27ac_3

value: biol rep 3


title: circRNA profile of case [2170N]

value: non-tumor

value: hepatocellular carcinoma


title: VAS105

value: Whole blood

value: CD4+ T cells

value: F


title: supine_study_Age_58_Surv_41_2_Rep2

description: Library name: supine_study_Age_58_Surv_41_2_Rep2

value: supine

tag: percent population_survival

value: Male

tag: supine death_phenotype


title: CE_BAT_Ucp1ERCre_H3K27ac_2

tag: tissue

tag: cell type

value: biol rep 2


title: VAS104

tag: cell line

value: T cells

value: M


title: circRNA profile of case [2166N]

description: The microarray was used to acquire circRNA expression profiles of 841 circRNAs.


title: supine_study_Age_58_Surv_41_2_Rep1

description: Library name: supine_study_Age_58_Surv_41_2_Rep1

value: Yes


title: supine_study_Age_57_Surv_59_Rep1

description: Library name: supine_study_Age_57_Surv_59_Rep1


title: CE_BAT_Ucp1ERCre_H3K27ac_1

value: Brown Adipose Tissue

value: Brown Adipocytes

value: Ucp1ERCre x NuTRAP on C57BL6 background

value: biol rep 1

tag: treatment


title: VAS102

tag: clasification*

tag: Sex


title: VAS101

tag: age


title: supine_study_Age_57_Surv_45_3_Rep1

description: Library name: supine_study_Age_57_Surv_45_3_Rep1

value: Whole Fly

tag: strain

value: Oregon R; y+ w+


title: CE_ingAT_Ucp1ERCre_H3K27ac_2

value: Inguinal Adipose Tissue

value: Beige Adipocytes

value: 9 week old at death, 1 week cold exposure at 8 degrees celsius at week 8; tamoxifen application during cold exposure


title: RT_epiAT_AdipoCre_H3K27me3_2

value: Epididymal Adipose Tissue

value: Adipocytes

value: AdipoCre x NuTRAP on C57BL6 background

value: 9 week old at death, born and kept at 22 degrees during whole life


title: circRNA profile of case [2164N]

tag: group

value: non-tumor

value: hepatocellular carcinoma


title: supine_study_Age_56_Surv_49_6_Rep2

description: Library name: supine_study_Age_56_Surv_49_6_Rep2

value: supine

value: Male


title: circRNA profile of case [2044N]

tag: disease


title: circRNA profile of case [2042N]


title: VAS10

value: Whole blood

value: CD4+ T cells

value: T cells

value: F

tag: sorter day


title: supine_study_Age_56_Surv_49_6_Rep1

description: Library name: supine_study_Age_56_Surv_49_6_Rep1

value: Whole Fly

tag: study

value: Yes


title: RT_epiAT_AdipoCre_H3K27me3_1

tag: histone

tag: replicate

value: biol rep 1


title: VAS1


title: VAS103


title: CE_BAT_Ucp1ERCre_H3K27me3_4

value: Brown Adipose Tissue

value: Brown Adipocytes

value: Ucp1ERCre x NuTRAP on C57BL6 background

value: biol rep 4


title: RT_epiAT_AdipoCre_H3K27me3_3

value: Epididymal Adipose Tissue

value: Adipocytes

value: AdipoCre x NuTRAP on C57BL6 background

value: biol rep 3


title: circRNA profile of case [2035N]

value: non-tumor

value: hepatocellular carcinoma


title: supine_study_Age_57_Surv_45_3_Rep2

description: Library name: supine_study_Age_57_Surv_45_3_Rep2

value: Oregon R; y+ w+

value: supine

tag: replicate sample

tag: chronological age_(days)

value: Male


title: supine_study_Age_55_Surv_53_8_Rep2

description: Library name: supine_study_Age_55_Surv_53_8_Rep2

tag: percent population_survival

tag: supine death_phenotype


title: Tecaudatus, endometrial stromal cells, Te135, primary isolate, bulk RNA-seq, replicate 1

city: New Haven

first: Gunter

middle: P

last: Wagner

state: CT

address: 165 Prospect Street

department: Ecology & Evolutionary Biology

institute: Yale University

description: Library name: Te135-T25

data_processing:
Reads were mapped to the tenrec genome with a draft annotation informed by long-read sequencing using kallisto (0.48.0)
Assembly: Draft genome by Michael Hiller lab
Supplementary files format and content: abundance.tsv files from kallisto containing estimated counts and TPM values from pseudoalignment

molecule: polyA RNA

organism: Tenrec ecaudatus

source_name: uterus

growth_protocol: Cells were expanded in T25 flasks in a growth medium consisting of 15.5 g/L Dulbecco’s modified eagle medium (30-2002, ATCC), 1.2 g/L sodium bicarbonate, 10 mL/L sodium pyruvate (11360, Thermo Fisher), and 1 mL/L ITS supplement (354350, VWR) in 10% charcoal-stripped fetal bovine serum (100-199, Gemini).

extract_protocol:
Bulk RNA was isolated using a Qiagen RNeasy Micro Kit (74004).
Libraries were prepared by the Yale Center for Genomic Analysis and sequenced using an Illumina NovaSeq.

treatment_protocol: Samples were treated with either base medium (Base), 1 μM medroxyprogesterone acetate (MPA; M1629, Sigma-Aldrich), or 1 μM MPA and 0.5 mM 8-bromoadenosine 3’,5’-cyclic adenosine monophosphate (cAMP; B7880, Sigma-Aldrich) for 6 days, with replenishment on day 3 (n=4 for each condition, total n=12).

tag: tissue

value: uterus

value: primary

tag: cell type

value: endometrial stromal cell

value: base media


title: CE_BAT_Ucp1ERCre_H3K27me3_2

value: Brown Adipose Tissue

value: biol rep 2

tag: treatment

value: 9 week old at death, 1 week cold exposure at 8 degrees celsius at week 8; tamoxifen application during cold exposure


title: CE_BAT_Ucp1ERCre_H3K27me3_3

value: Brown Adipocytes

value: Ucp1ERCre x NuTRAP on C57BL6 background


title: supine_study_Age_55_Surv_53_8_Rep1

description: Library name: supine_study_Age_55_Surv_53_8_Rep1

value: Whole Fly

value: Yes


title: circRNA profile of case [2029N]


title: VAS100

value: Whole blood

tag: cell line

value: CD4+ T cells

value: T cells

tag: clasification*

value: F


title: circRNA profile of case [2050N]

value: non-tumor

value: hepatocellular carcinoma


title: circRNA profile of case [20N]


title: supine_study_Age_53_Surv_72_Rep1

description: Library name: supine_study_Age_53_Surv_72_Rep1

value: Oregon R; y+ w+

value: supine

tag: Sex

value: Male

value: No


title: circRNA profile of case [19N]


title: CE_BAT_Ucp1ERCre_H3K27me3_1

value: Brown Adipose Tissue

tag: strain

value: biol rep 1


title: circRNA profile of case [1594N]

tag: group


title: circRNA profile of case [11N]

tag: disease


title: supine_study_Age_53_Surv_70_6_Rep1

description: Library name: supine_study_Age_53_Surv_70_6_Rep1


title: CERT_BAT_Ucp1ERCre_H3K9me3_1

value: 17 week old at death, 1 week cold exposure at 8 degrees celsius at week 8; tamoxifen application during cold exposure; Then recovery at 22 degrees celsius for 8 weeks


title: CERT_BAT_Ucp1ERCre_H3K9me3_3

value: Brown Adipocytes

value: biol rep 3


title: supine_study_Age_53_Surv_62_3_Rep4

description: Library name: supine_study_Age_53_Surv_62_3_Rep4

value: Whole Fly


title: Tecaudatus, endometrial stromal cells, Te132, 6 days, 1 uM MPA + 500 uM cAMP, bulk RNA-seq, replicate 10

description: Library name: Te132-10-DIFF

value: uterus

value: primary

value: endometrial stromal cell

value: 1 um MPA + 500 uM 8-Br-cAMP

tag: batch


title: circRNA profile of case [2031N]


title: emf1-12DAP-1

city: Beijing

first: Zhijia

last: Yang

address: No.2 Yuanmingyuan West Road, Haidian

department: College of Agronomy and Biotechnology

institute: China Agricultural University

description:
Library name: emf1-12DAP-1
emf1-12DAP-1

data_processing:
RNA-seq:methods from"High Temporal-Resolution Transcriptome Landscape of Early Maize Seed Development."
Assembly: B73 (AGPv4)
Supplementary files format and content: RNA-seq:GTF

organism: Zea mays

source_name: endosperm

extract_protocol: RNA-seq:Total RNA was extracted from mn8 and B73 endosperms obtained from the same F2 ears at 12 DAP (30 endosperms per replicate). Three biological replicates were collected from the kernels of three independent ears. Total RNA was extracted with TRIzol reagent (Ambion), and DNA was digested with RNase free DNase I (NEB). cDNA libraries were constructed using a VAHTS mRNA-seq Library Prep Kit (Vazyme) and sequenced using an Illumina NovaSeq 6000 (BerryGenomics).

value: endosperm


title: Tecaudatus, endometrial stromal cells, Te132, 6 days, 1 uM MPA + 500 uM cAMP, bulk RNA-seq, replicate 11

description: Library name: Te132-11-DIFF


title: supine_study_Age_53_Surv_62_3_Rep2

description: Library name: supine_study_Age_53_Surv_62_3_Rep2

tag: study

value: Yes


title: CERT_ingAT_Ucp1ERCre_H3K27ac_5

value: Inguinal Adipose Tissue

value: Beige Adipocytes

value: Ucp1ERCre x NuTRAP on C57BL6 background

tag: histone

value: biol rep 5


title: Tecaudatus, endometrial stromal cells, Te132, 6 days, 1 uM MPA + 500 uM cAMP, bulk RNA-seq, replicate 9

description: Library name: Te132-9-DIFF


title: emf1-12DAP-2

description:
Library name: emf1-12DAP-2
emf1-12DAP-2


title: B73-12DAP-1

description:
Library name: B73-12DAP-1
B73-12DAP-1


title: emf1-H3K27 (ChIP)

description:
Library name: emf1-H3K27
emf1-H3K27

data_processing:
Chip-seq:The detailed steps for ChIP-seq data analysis have been uploaded to GitHub (https://github.com/YZJ-cau/Chip-seq-code).
Assembly: B73 (AGPv4)
Supplementary files format and content: Chip-seq:bigWig

extract_protocol: Chip-seq:Nuclei (from 2.0 g of fresh tissue per sample) were lysed with nuclear lysis buffer (50 mM Tris-HCl [pH 7.5], 10 mM EDTA [pH 8.0], 1% SDS, protease inhibitor and phosphatase inhibitor) and subjected to high-speed sonication at 200-600 bp using a Bioruptor instrument. Anti-H2Aub (Abcam,) and anti-H3K27me3 (Abcam,) antibodies were used for chromatinimmunoprecipitation. The chromatin solutions were pre-cleared with 50 μL ChIP-grade protein A/G beads (Millipore) for 2 h at 4°C. The mixture was then incubated overnight with 5 μg antibody at 4°C, followed by incubation with 20 μL ChIP-grade protein A/G beads for 2 h at 4°C on a rotating tube shaker. The beads were washed four times using wash buffer (20 mM Tris-HCl [pH 7.5], 2 mM EDTA [pH 8.0], 1% Triton X-100, 0.1% SDS and 500 mM NaCl) and eluted with elution buffer (50 mM Tris-HCl [pH 8.0], 10 mM EDTA [pH 8.0], 1% SDS, 10 μg RNase A). The prepared DNA was then recovered using a QIAquick PCR purification kit (Qiagen), and quality was checked using the Qubit (Thermo Fisher). The DNA libraries were constructed using a VAHTS DNA Library Prep Kit (Vazyme) and sequenced on the NovaSeq 6000 platform with 150-bp paired-end reads (BerryGenomics).


title: Tecaudatus, endometrial stromal cells, Te132, 6 days, 1 uM MPA, bulk RNA-seq, replicate 9

description: Library name: Te132-8-MPA

value: 1 uM MPA 6 days


title: B73-12DAP-2

description:
Library name: B73-12DAP-2
B73-12DAP-2


title: Tecaudatus, endometrial stromal cells, Te132, 6 days, 1 uM MPA, bulk RNA-seq, replicate 8

description: Library name: Te132-7-MPA


title: supine_study_Age_53_Surv_62_3_Rep1

description: Library name: supine_study_Age_53_Surv_62_3_Rep1

value: Oregon R; y+ w+

value: supine

value: Male


title: CE_ingAT_Ucp1ERCre_H3K27me3_3

tag: replicate

value: 9 week old at death, 1 week cold exposure at 8 degrees celsius at week 8; tamoxifen application during cold exposure


title: CERT_ingAT_Ucp1ERCre_H3K27me3_6

value: biol rep 6

value: 17 week old at death, 1 week cold exposure at 8 degrees celsius at week 8; tamoxifen application during cold exposure; Then recovery at 22 degrees celsius for 8 weeks


title: Tecaudatus, endometrial stromal cells, Te132, 6 days, 1 uM MPA, bulk RNA-seq, replicate 6

description: Library name: Te132-6-MPA

value: uterus


title: supine_study_Age_54_Surv_58_1_Rep1

description: Library name: supine_study_Age_54_Surv_58_1_Rep1

value: Whole Fly

tag: replicate sample


title: emf1-H2A (ChIP)

description:
Library name: emf1-H2A
emf1-H2A


title: CE_ingAT_Ucp1ERCre_H3K27me3_2

value: biol rep 2


title: Tecaudatus, endometrial stromal cells, Te132, 6 days, 1 uM MPA, bulk RNA-seq, replicate 5

description: Library name: Te132-5-MPA

value: primary

value: endometrial stromal cell


title: Tecaudatus, endometrial stromal cells, Te132, 6 days, 1 uM MPA + 500 uM cAMP, bulk RNA-seq, replicate 12

description: Library name: Te132-12-DIFF

value: 1 um MPA + 500 uM 8-Br-cAMP


title: Tecaudatus, endometrial stromal cells, Te132, primary isolate, bulk RNA-seq, replicate 1

description: Library name: Te132-T25

value: base media


title: CE_ingAT_Ucp1ERCre_H3K27ac_1

value: Inguinal Adipose Tissue

value: Beige Adipocytes

value: biol rep 1


title: supine_study_Age_53_Surv_62_3_Rep3

description: Library name: supine_study_Age_53_Surv_62_3_Rep3

tag: chronological age_(days)

value: Yes


title: supine_study_Age_52_Surv_66_1_Rep1

description: Library name: supine_study_Age_52_Surv_66_1_Rep1

value: Oregon R; y+ w+

tag: percent population_survival


title: B73-H3K27 (ChIP)

description:
Library name: B73-H3K27
B73-H3K27

value: endosperm


title: CE_ingAT_Ucp1ERCre_H3K27me3_1

value: Ucp1ERCre x NuTRAP on C57BL6 background


title: Tecaudatus, endometrial stromal cells, Te132, 6 days, base media, bulk RNA-seq, replicate 4

description: Library name: Te132-4-Base

value: base media 6 days


title: supine_study_Age_52_Surv_73_6_Rep1

description: Library name: supine_study_Age_52_Surv_73_6_Rep1

value: supine

value: Male

tag: supine death_phenotype

value: No


title: supine_study_Age_51_Surv_78_9_Rep1

description: Library name: supine_study_Age_51_Surv_78_9_Rep1

tag: tissue

value: Whole Fly


title: Tecaudatus, endometrial stromal cells, Te132, 6 days, base media, bulk RNA-seq, replicate 3

description: Library name: Te132-3-Base

value: uterus

tag: cell type


title: CERT_ingAT_Ucp1ERCre_H3K27me3_5

value: biol rep 5

tag: treatment

value: 17 week old at death, 1 week cold exposure at 8 degrees celsius at week 8; tamoxifen application during cold exposure; Then recovery at 22 degrees celsius for 8 weeks


title: CE_DT_ingAT_AdipoCre_H3K9me3_1

value: Adipocytes

value: AdipoCre x NuTRAP x Ucp1DTRGfp on C57BL6 background

value: 10 week old at death, 1 week cold exposure at 8 degrees celsius at week 8, then diphtheria toxin injections and euthanasia


title: supine_study_Age_51_Surv_69_8_Rep2

description: Library name: supine_study_Age_51_Surv_69_8_Rep2


title: B73-H2A (ChIP)

description:
Library name: B73-H2A
B73-H2A

tag: cell line


title: CE_DT_ingAT_AdipoCre_H3K9me3_2

value: Inguinal Adipose Tissue

value: biol rep 2


title: supine_study_Age_50_Surv_73_1_Rep1

description: Library name: supine_study_Age_50_Surv_73_1_Rep1

value: Yes


title: supine_study_Age_51_Surv_69_8_Rep1

description: Library name: supine_study_Age_51_Surv_69_8_Rep1

value: Oregon R; y+ w+


title: Tecaudatus, endometrial stromal cells, Te132, 6 days, base media, bulk RNA-seq, replicate 1

description: Library name: Te132-1-Base

value: primary

value: endometrial stromal cell


title: iCM, MΔGΔT3

city: Tsukuba

first: SEIICHIRO

last: HONDA

address: 2-1-1 Amakubo

department: Cardiology

country: Japan

institute: University of Tsukuba

description: Library name: Mutant TCA_012_13

data_processing:
FASTQ files were imported to CLC Genomics Workbench (Ver 10.1.1, Qiagen).
Reads were mapped to mouse reference genome (mm10).
CLC Main Workbench(Ver 21.0.4, Qiagen) was used for the downstream analysis.
Total counts were normalized by scaling method. Transformed values (log2-converted after adding 1 to the normalized expression value) were used for Heatmap creation.
Low-expression genes (normalized expression value did not exceed 10 in any sample) were excluded before DGE analysis.
Assembly: Differentially expressed genes were identified using Empirical Analysis of DGE tool.
Supplementary files format and content: Microsoft Excel file  with raw counts, normalized expression values and transformed values for every gene

source_name: mouse embryonic fibroblast

extract_protocol:
RNA was extracted using the ReliaPrep RNA Cell Miniprep System (Promega, Z6012).
500 ng total RNA is used for rRNA-depletion (NEB, E6310), followed by directional library synthesis (NEB, E7420).

value: mouse embryonic fibroblast

tag: genotype

value: ICR

value: MΔGΔT transdused MEFs


title: iCM, MΔGΔT4

description: Library name: Mutant TCA_012_14


title: CE_saline_ingAT_AdipoCre_H3K9me3_1

value: biol rep 1

value: 10 week old at death, 1 week cold exposure at 8 degrees celsius at week 8, then saline injections and euthanasia


title: iCM, MΔGΔT2

description: Library name: Mutant TCA_012_12


title: CE_DT_ingAT_AdipoCre_H3K4me3_3

value: biol rep 3


title: Te, fmi, 28dpme, Te134

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
CellRanger v7.0.0-v8.0.0
Assembly: GRCm39 (M. musculus); cavPor3 (C. porcellus); ASM229v1 (M. domestica); Draft Genome (T. ecaudatus)
Supplementary files format and content: CellRanger tab-separated features and cell barcodes and matrix expression files.
Supplementary files format and content: Raw counts in annotated h5 format with hierarchical cell type annotations, and gene annotations according to ENSEMBL and BLAST to human.

source_name: uterus + placenta

extract_protocol:
All tissue was processed as follows, with small species-specific modifications as noted. Tissue was minced with a scalpel into ~1 mm3 cubes in 2 mL of digestive solution containing 0.2 mg/mL Liberase TL (05401020001, Sigma). Tissue suspensions were heated at 37°C for 15 minutes and then passed 10 times through a 16-gauge needle attached to a 3-mL syringe. This incubation and needle passage process was repeated two more times, with the substitution of an 18-gauge needle. Finally, 2 mL of charcoal-stripped fetal bovine serum (100-199, Gemini) was added and the suspension was immediately passed through a 70-μm cell strainer then a 40-μm cell strainer. The flowthrough was pelleted by centrifugation at 500 g for 5 minutes and cells were resuspended in 1x ACK red blood cell lysis buffer (A1049201, Thermo-Fisher), incubated at room temperature for 5 minutes, centrifuged again and resuspended in PBS containing 0.04% bovine serum albumen (A9647, Sigma). At this point, cells were examined on a hemocytometer to gauge concentration and check for debris and cell death using trypan blue stain (15250061, ThermoFisher). Mouse tissue was processed as above with the addition of Accumax (Stem Cell Technologies) to the final 0.04% bovine serum albumen solution. Guinea pig tissue was processed as with the mouse with the following modifications: a wide-bore 1 mL pipette tip was substituted for the 16-gauge needle, and 0.2 mg/mL collagenase I (17018029, Thermo-Fisher) was added to the digestion solution. As tenrec and guinea pig tissue showed higher cell death, a fractionated protocol was adopted to reduce exposure of cells to digestive enzymes. For these species, cells which had dislodged following each passage step were separated from intact tissue and immediately passed through a 70-μm cell strainer into 2 mL of charcoal-stripped fetal bovine serum (100-199, Gemini), while remaining intact tissue was allowed to continue with further digestion. Each fraction was centrifuged at 300 rpm for 5 minutes and resuspended in 500 μL ACK red blood cell lysis buffer (A1049201, Thermo-Fisher) for 5 minutes, then centrifuged at 500 rpm for 2 minutes and resuspended in 0.04% bovine serum albumen (A9647, Sigma) and kept on ice until dissociation was complete. Cells were counted on a hemocytometer and recombined in a proportional manner before sequencing. Cells were captured using the 10X Chromium platform (3’ chemistry, version 3)
Libraries were generated according to manufacturer protocols (CG000315: 10x Genomics 3’ chemistry, version 3).

value: uterus + placenta

tag: Sex

value: Female

tag: developmental stage

value: 28 days post male exposure


title: supine_study_Age_48_Surv_79_3_Rep2

description: Library name: supine_study_Age_48_Surv_79_3_Rep2

value: Whole Fly

tag: strain

value: supine

value: Male


title: CE_DT_ingAT_AdipoCre_H3K4me3_2

value: Inguinal Adipose Tissue

value: Adipocytes

value: AdipoCre x NuTRAP x Ucp1DTRGfp on C57BL6 background

value: biol rep 2

value: 10 week old at death, 1 week cold exposure at 8 degrees celsius at week 8, then diphtheria toxin injections and euthanasia


title: iCM, MΔGΔT1

description: Library name: Mutant TCA_012_11

value: mouse embryonic fibroblast


title: supine_study_Age_49_Surv_76_4_Rep1

description: Library name: supine_study_Age_49_Surv_76_4_Rep1

value: Oregon R; y+ w+

value: Yes


title: Te, fmi, 28dpme, Te132

description: 10x Genomics


title: iCM, MGT5

description: Library name: MGT TCA_012_10

value: ICR

value: MGT transdused MEFs


title: supine_study_Age_48_Surv_79_3_Rep1

description: Library name: supine_study_Age_48_Surv_79_3_Rep1


title: iCM, MΔGΔT5

description: Library name: Mutant TCA_012_15

value: MΔGΔT transdused MEFs


title: Tecaudatus, endometrial stromal cells, Te132, 6 days, base media, bulk RNA-seq, replicate 2

description: Library name: Te132-2-Base

value: uterus

value: primary

value: endometrial stromal cell

value: base media 6 days


title: CE_DT_ingAT_AdipoCre_H3K4me3_1

value: biol rep 1


title: aging_study_Age_70_Surv_14_Rep1

description: Library name: aging_study_Age_70_Surv_14_Rep1

value: Whole Fly

value: aging

value: Male


title: iCM, MGT4

description: Library name: MGT TCA_012_09


title: dsFactin rep3

city: changsha

first: Huilin

middle: huilin

state: huannan

address: Donghu Street

institute: Hunan Agricultural University

description: Library name: sample6

data_processing:
Illumina Novaseq platform were used for basecalling.
The clustering of the index-coded samples was performed on acBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS(Illumia) according to the manufacturer’s instructions.
After cluster generation, thelibrary preparations were sequenced on an Illumina Novaseq platformand150bp paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed throughin-house perl scripts. In this step, clean data (clean reads) were obtainedbyremoving reads containing adapter, reads containing N base and lowqualityreads from raw data. At the same time, Q20, Q30 and GC content thecleandata were calculated. All the downstream analyses were based on thecleandata with high quality.
The left files (read1 files) from all libraries_x0014__x001D_mples were pooled intoonebig left.fq file, and right files (read2 files) into one big right.fq file. Transcriptomeassembly was accomplished based on the left.fq and right.fq using Trinity with min_kmer_cov set to 2 by default and all other parameters set default.
Assembly: mm10
Supplementary files format and content: tab-deliminited text file includes raw counts for each Sample.
Supplementary files format and content: tab-deliminited text file includes RPKM values for each Sample.

organism: Pardosa pseudoannulata

source_name: Individual

extract_protocol:
RNA was harvested using  Rneasy mini plus kit (Qiagen).
RNA  libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Individual

value: Cadmium treatment, microinjection of dsRNA


title: dsFactin rep2

description: Library name: sample5


title: CE_saline_ingAT_AdipoCre_H3K4me3_1

value: Inguinal Adipose Tissue

value: Adipocytes

value: AdipoCre x NuTRAP x Ucp1DTRGfp on C57BL6 background

value: 10 week old at death, 1 week cold exposure at 8 degrees celsius at week 8, then saline injections and euthanasia


title: aging_study_Age_69_Surv_16_Rep4

description: Library name: aging_study_Age_69_Surv_16_Rep4

value: Oregon R; y+ w+


title: Te, fmi, 28dpme, Te135

description: 10x Genomics

value: uterus + placenta

value: Female

value: 29 days post male exposure


title: dsFactin rep1

description: Library name: sample4


title: aging_study_Age_69_Surv_16_Rep3

description: Library name: aging_study_Age_69_Surv_16_Rep3


title: iCM, MGT3

description: Library name: MGT TCA_012_08

value: mouse embryonic fibroblast

value: ICR

value: MGT transdused MEFs


title: CE_DT_ingAT_AdipoCre_H3K4me1_2

value: biol rep 2

value: 10 week old at death, 1 week cold exposure at 8 degrees celsius at week 8, then diphtheria toxin injections and euthanasia


title: CE_DT_ingAT_AdipoCre_H3K4me1_3

value: biol rep 3


title: aging_study_Age_69_Surv_16_Rep2

description: Library name: aging_study_Age_69_Surv_16_Rep2

value: Whole Fly

value: aging

value: Male


title: iCM, MGT2

description: Library name: MGT TCA_012_07


title: dsNC rep3

description: Library name: sample3

value: Individual

value: Cadmium treatment, microinjection of dsRNA


title: dsNC rep2

description: Library name: sample2


title: CE_saline_ingAT_AdipoCre_H3K4me1_1

value: Inguinal Adipose Tissue

value: Adipocytes

value: AdipoCre x NuTRAP x Ucp1DTRGfp on C57BL6 background

value: biol rep 1


title: aging_study_Age_68_Surv_19_Rep2

description: Library name: aging_study_Age_68_Surv_19_Rep2

value: Oregon R; y+ w+


title: aging_study_Age_69_Surv_16_Rep1

description: Library name: aging_study_Age_69_Surv_16_Rep1


title: CE_DT_ingAT_AdipoCre_H3K4me1_1


title: dsNC rep1

description: Library name: sample1


title: CE_DT_ingAT_AdipoCre_H3K27ac_3


title: iCM, MGT1

description: Library name: MGT TCA_012_06


title: MEF, Ctrl5

description: Library name: MEF TCA_012_05

value: MEF


title: MEF, Ctrl4

description: Library name: MEF TCA_012_04

value: mouse embryonic fibroblast


title: Cp, fmi, 30.5dpc, 200684

description: 10x Genomics

organism: Cavia porcellus

value: uterus + placenta

value: Female

value: 30.5 days post copulation


title: CE_DT_ingAT_AdipoCre_H3K27ac_2

value: biol rep 2

value: 10 week old at death, 1 week cold exposure at 8 degrees celsius at week 8, then diphtheria toxin injections and euthanasia


title: aging_study_Age_68_Surv_19_Rep1

description: Library name: aging_study_Age_68_Surv_19_Rep1

value: Whole Fly


title: Cp, fmi, 30.5dpc, 200683

description: 10x Genomics


title: aging_study_Age_67_Surv_22_Rep4

description: Library name: aging_study_Age_67_Surv_22_Rep4

value: aging


title: MEF, Ctrl1

description: Library name: MEF TCA_012_01

value: ICR


title: MEF, Ctrl2

description: Library name: MEF TCA_012_02


title: aging_study_Age_67_Surv_22_Rep3

description: Library name: aging_study_Age_67_Surv_22_Rep3

value: Male


title: CE_saline_ingAT_AdipoCre_H3K27ac_1

value: 10 week old at death, 1 week cold exposure at 8 degrees celsius at week 8, then saline injections and euthanasia


title: MEF, Ctrl3

description: Library name: MEF TCA_012_03


title: E18.5,RNAseq,Aortic smooth muscle,Dmut2

city: Shanghai

first: Chunxiao

last: Wang

address: Siping road

institute: Tongji university

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

source_name: Aortic smooth muscle

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.4 μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using mRNA-Seq Library Prep Kit following manufacturer’s protocols.

value: Aortic smooth muscle

value: Pinch1,2 knockout


title: aging_study_Age_67_Surv_22_Rep1

description: Library name: aging_study_Age_67_Surv_22_Rep1


title: CE_DT_ingAT_AdipoCre_H3K27me3_3

value: Inguinal Adipose Tissue

value: Adipocytes

value: AdipoCre x NuTRAP x Ucp1DTRGfp on C57BL6 background

value: biol rep 3


title: CE_DT_ingAT_AdipoCre_H3K27me3_2


title: aging_study_Age_66_Surv_25_Rep2

description: Library name: aging_study_Age_66_Surv_25_Rep2

value: Oregon R; y+ w+


title: anti-P53_CUT-RUN_mTEChi_Rep2

city: Chicago

first: Noah

last: Gamble

state: IL

department: Pathology

institute: University of Chicago

description: Library name: anti-P53_CUT-RUN_mTEChi_Rep2

data_processing:
CUT&RUN reads were mapped to the mm10 mouse genome assembly using Bowtie 2 (v.2.2.9) with the settings --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700
PCR duplicates were removed using Picard’s (v.2.21.8) MarkDuplicates REMOVE_DUPLICATES = true VALIDATION_STRINGENCY = LENIENT. Reads with MAPQ scores below 30 were purged and excluded from downstream analysis using the Samtools (v.1.9) parameters view -b -q 30 -f 2 -F 1804
Peaks were called for each sample using MACS2 (v2.2.7.1) with settings --shift 0 --extsize 200 --nomodel --call-summits --keep-dup all -p 0.01. For each sample, a 301 bp fixed-width peak set was generated by extending the MACS2 summits by 150 bp in both directions
Assembly: mm10
Supplementary files format and content: Sequence depth-normalized Big Wig files, Bed files of sample-specific peaks
Library strategy: CUT&Run

source_name: Thymus

extract_protocol:
500,000 cells were washed three times in wash buffer (20 mM HEPES, pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 1× EDTA-free protease inhibitor cocktail, Roche), then bound to Concanavalin-A beads (Bangs Laboratories) according to the manufacturer’s instructions. Cells were incubated with 1:100 dilution of anti-BAF155 antibody (G. Crabtree) for 2 h or overnight at 4 °C in permeabilization buffer (1× permeabilization buffer, eBioscience, 0.5 mM spermidine, 1× EDTA-free protease inhibitor cocktail, 2 mM EDTA). The sample was then incubated with 700 ng ml−1 protein A-MNase (S. Henikoff) in permeabilization buffer at 4 °C for 1 h. Digestion was performed in 0.5× permeabilization buffer supplemented with 2 mM CaCl2 at 4 °C for 1 h. The reaction was stopped by adding 2× Stop buffer (final concentration 100 mM NaCl, 10 mM EDTA, 2 mM EGTA, 20 μg ml−1 glycogen, 25 μg ml−1 RNase A, Thermo Fisher Scientific) and the sample was incubated at 37 °C for 20 min. Protein in the sample was then digested in 0.1% SDS and 250 μg ml−1 proteinase K (New England Biolabs) for 2 h at 56 °C, shaking gently. CUT&RUN fragments were purified using phenol chloroform extraction.
CUT&RUN libraries were generated using the NEBNext Ultra II DNA Library Prep Kit for Illumina coupled with NEBNext Multiplex Oligos for Illumina (New England Biolabs) with modifications optimized for small fragments as detailed in https://doi.org/10.17504/protocols.io.wvgfe3w. Paired-end, dual-index sequencing was performed on the Illumina NextSeq 500 system.

value: Thymus

value: mTEChi


title: E18.5,RNAseq,Aortic smooth muscle,WT2

value: WT


title: CE_saline_ingAT_AdipoCre_H3K27me3_1

value: biol rep 1


title: aging_study_Age_65_Surv_29_Rep4

description: Library name: aging_study_Age_65_Surv_29_Rep4


title: E18.5,RNAseq,Aortic smooth muscle,WT1


title: CE_DT_ingAT_AdipoCre_H3K27me3_1

value: 10 week old at death, 1 week cold exposure at 8 degrees celsius at week 8, then diphtheria toxin injections and euthanasia


title: aging_study_Age_65_Surv_29_Rep3

description: Library name: aging_study_Age_65_Surv_29_Rep3

value: Whole Fly


title: anti-P53_CUT-RUN_mTEClo_Rep2

description: Library name: anti-P53_CUT-RUN_mTEClo_Rep2

value: mTEClo


title: RM-1 tumors treated with vehicle

city: Jinan

first: Fei

middle: fei

last: Sun

state: Shandong

address: WENHUAXI road

institute: Department of Pathology, Qilu Hospital, Shandong University

description:
Library name: vehicle
10X Genomics

data_processing:
The demultiplexing,barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: RM-1 tumors

extract_protocol:
Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.
Library was performed according to the manufacter's instructions (single cell 3' v2 protocol,10x Genomics). RNA libraries were prepared for sequencing using standard Illumina protocols

value: RM-1 tumors

value: prostate caner cell

value: vehicle


title: TN_ingAT_AdipoCre_H3K9me3_1

value: AdipoCre x NuTRAP on C57BL6 background

value: 9 week old at death, born and kept at 30 degrees during whole life


title: E14.5,RNAseq,Aortic smooth muscle,Dmut3

value: Aortic smooth muscle

value: Pinch1,2 knockout


title: aging_study_Age_65_Surv_29_Rep1

description: Library name: aging_study_Age_65_Surv_29_Rep1

value: aging

value: Male


title: RM-1 tumors treated with enzalutamide

description:
Library name: enzalutamide
10X Genomics

value: enzalutamide


title: anti-P53_CUT-RUN_mTEChi_Rep1

description: Library name: anti-P53_CUT-RUN_mTEChi_Rep1

value: Thymus


title: anti-P53_CUT-RUN_mTEClo_Rep1

description: Library name: anti-P53_CUT-RUN_mTEClo_Rep1


title: E18.5,RNAseq,Aortic smooth muscle,Dmut1


title: E14.5,RNAseq,Aortic smooth muscle,Dmut2


title: TN_ingAT_AdipoCre_H3K4me3_1

value: Inguinal Adipose Tissue

value: Adipocytes


title: aging_study_Age_64_Surv_32_Rep2

description: Library name: aging_study_Age_64_Surv_32_Rep2

value: Oregon R; y+ w+


title: C57BL6_Multiome_ATAC

data_processing:
Following sequencing, BCL files were converted to FASTQ using cellranger-arc (v2.0.2) mkfastq. FASTQ files were aligned to the mm10 or hg38 genome assembly using cellranger-arc count. ATAC fragment files were used as inputs to the ArchR (v1.0.2) analysis pipeline in R (v4.3.2). Transcript count matrices were used as inputs to the Seurat gene expression analysis pipeline.
Assembly: mm10 or hg38
Supplementary files format and content: BAM
Supplementary files format and content: Zip file of multiome processed results
Library strategy: scMultiome

extract_protocol:
Mouse: Thymic epithelial cells were isolated using a previously published protocol (Kim & Serwold, Methods in Molecular Biology, 2019) with minor modifications. Briefly, thymi from 4-5 week-old mice were harvested and connective tissue was removed. Stromal tissue was perforated using scissors and incubated with rotation in DMEM-F12 (Sigma D6421) at room temperature for for 10min to liberate thymocytes. Remaining stromal tissue was enzymatically digested (0.5mg/mL Collagenase D (Sigma 11088858001), 0.2mg/mL DNaseI (Sigma 10104159001), 0.5mg/mL Papain (Worthington Biochemical LS003126)). Cells were stained with anti-EpCAM antibodies conjugated to APC-Cy7 and EpCAM+ cells were enriched via positive selection using magnetic anti-Cy7 beads (Miltenyi 130-091-652). Enriched fraction was stained with fluorescently conjugated antibodies for FACS or analysis.  Human: Excised thymic tissue from one patient (3-month-old male) was obtained during the course of corrective cardiac surgery at the Advocate Children’s Hospital, Chicago, IL, USA. Patient was de-identified upon receipt with written informed consent for release of genomic sequence data in accordance with IRB approved protocols by the Advocate Children’s Hospital, University of Chicago, and the National Institute of Health. Connective tissue was removed, and stromal tissue was minced using scissors. Tissue was incubated with rotation in DMEM-F12 (Sigma) at 4C for 20min to liberate thymocytes. Further thymocyte liberation was achieved via enzymatic digestion using 0.5mg/mL Collagenase D (Millipore 11088858001) and 0.2mg/mL DNase I (Sigma 10104159001) at 37C for 20min. Remaining fragments were incubated with rotation in 0.5mg/mL Papain (Worthington), 0.25mg/mL Collagenase D and 0.1mg/mL DNase I at 37C for 20min. Digestion was quenched by addition of FACS buffer. Cells were stained with anti-EpCAM antibodies conjugated to APC-Cy7 (BioLegend 324245 clone 9C4 1:100) and EpCAM+ cells were enriched via positive selection with magnetic anti-Cy7 beads (Miltenyi). Enriched fraction was stained with DAPI (Invitrogen), CD45 (BioLegend 368508 clone 2D1 1:100), LY51/CD249 (Fisher Scientific BDB564533 clone 2D3/APA 1:100) and HLA-DRA (BioLegend 307622 clone L243 1:100) and sorted on a Symphony S6 (BD Biosciences).
For all multiome experiments, we used the ATAC+GEX single-cell kit and protocol (10X Genomics 1000236 with protocol CG000338 RevE) with minor modifications to sample preparation. Briefly, 40,000 mTECs were FACS-sorted into 1X PBS supplemented with 2% BSA and centrifuged at 300rcf for 5 min. Cells were gently washed in 50uL Lysis Buffer (10mM Tris, 10mM NaCl, 3mM MgCl2 in nuclease-free water) and centrifuged at 300rcf for 5 min. Cells were resuspended in  50uL permeabilization buffer (10mM Tris, 10mM NaCl, 3mM MgCl2, 0.1% Tween20, 0.01% digitonin, and RNase inhibitor (Millipore) in nuclease-free water) and incubated for 5 minutes on ice. Nuclei were gently washed with wash buffer (10mM Tris, 10mM NaCl, 3mM MgCl2, 0.1% Tween20, and RNase inhibitor in nuclease-free water) and centrifuged at 500rcf for 5 min. Finally, nuclei wee resuspended in 5uL chilled diluted nuclei buffer (10X Genomics) and added to transposition mix. Paired-end, dual-index sequencing was performed on the Illumina NextSeq 500 or NovaSeq 6000 platform.

value: mTEC


title: TN_ingAT_AdipoCre_H3K4me1_1

value: biol rep 1


title: E14.5,RNAseq,Aortic smooth muscle,Dmut1


title: aging_study_Age_64_Surv_32_Rep1

description: Library name: aging_study_Age_64_Surv_32_Rep1

value: Whole Fly


title: C57BL6_Multiome_GEX

molecule: nuclear RNA


title: TN_ingAT_AdipoCre_H3K27ac_1


title: E14.5,RNAseq,Aortic smooth muscle,WT3

value: WT


title: aging_study_Age_63_Surv_36_Rep4

description: Library name: aging_study_Age_63_Surv_36_Rep4


title: MEC1_mouse_control_01

city: Kyoto

first: Yoshinori

last: Yoshida

address: 53, Kawahara-cho, Shogoin, Sakyo-ku

institute: Kyoto University

data_processing:
Illumina bcl2fastq (v2.17.14) were performed for converting fastq files and separation by samples with default setting
Too short (<20base) reads were removed and adapter sequence were trimmed by cutadapt (v1.15) with parameters -m 20 --nextseq-trim=20.
For removing human rRNA tRNA mapped reads, bowtie2 (v2.2.5), with parameters --very-sensitive --score-min L,0,-0.6.
The reads were mapped by STAR  (v2.5.3a)
HTSeq (v0.9.1) were perfomed for counting reads with the GENCODE (version 27) annotation gtf file.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file including DESeq2 nomalized count values for each sample.

source_name: embryonic epicardial cell line (MEC1)

growth_protocol: hiPSC-EPI was differentiated from hiPSC line 409B2 by modulating WNT and BMP4 signaling and maintained with TGFb inhibitor. Mouse embryonic epicardial cell was emerged from heart explant ex vivo and maintained with TGFb inhibitor. MEC1 was maintained without TGFb inhibitor.

extract_protocol:
RNeasy Micro Kit
Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus

treatment_protocol: Cells were treated with Rapamycin (200 nM), Tacrolimus (200 nM) or Torin1 (200 nM) for 7 days before extraction.

value: embryonic epicardial cell line (MEC1)

value: control


title: CERT_ingAT_Ucp1ERCre_H3K9me3_1

data_processing:
*library strategy: Cut&Tag
TrimGalore v0.6.6 used for trimming low quality bases + adapter sequences
Bowtie2 v2.4.4 used for read mapping
samtools v1.13 used for sorting bam files
bedtools v2.30 used for converting sorted bam files into bedgraph files
SEACR v1.3 used for calling peaks
Assembly: mm10
Supplementary files format and content: tab delimited called peak regions for each sample

extract_protocol:
Nuclei were isolated from snap frozen adipose tissue depots in ice cold Nuclei Extraction Buffer (Miltenyi, #130-128-024) supplemented with 10 mM sodium butyrate and 1x cOmpleteTM EDTA-free Protease Inhibitor (Roche, #5056489001) using the gentleMACSTM Octo Dissociator (Miltenyi, #130-096-427) using C-tubes (Miltenyi, #130-093-237). All centrifugation steps were carried out in a to 4˚C cooled swinging bucket centrifuge with settings at 500 xg for 5 minutes. Nuclei were subsequently filtered through a 50µm cell strainer (Sysmex, #04-0042-2317) and washed two times in PBS-BSA (1% w/v) containing protease inhibitor and sodium butyrate. Nuclei were centrifuged and subsequently bound to pre-blocked Dynabeads MyOne Streptavidin C1 beads (ThermoFisher, #65002) for 30 minutes at 4˚C followed by 3 washes with PBS-BSA (1% w/v) on a magnetic stand. CUT&Tag was performed as previously described with minor adjustments36,37. All buffers were supplemented with 1 x cOmplete EDTA-free Protease inhibitor and 10mM sodium butyrate. Briefly, nuclei bound to beads were aliquoted into 96-well LoBind plates (Eppendorf, #0030129547) and incubated with primary antibodies – anti-H3K4me3 (abcam, #ab8580), anti-H3K27me3 (Cell Signaling Technology, #C36B11), anti-H3K27ac (abcam, #ab4729), anti-H3K4me1 (abcam, #ab8895), anti-H3K9me3 (abcam, #ab8898) – overnight at 4˚C. All antibodies were diluted 1:100. With the plate on a magnet the primary antibody solution was removed, the beads were resuspended in secondary antibody solution (guinea pig anti-rabbit IgG (antibodies-online gmbh, #ABIN101961); 1:200 dilution) and incubated at room temperature for 30 minutes while rocking. pA-Tn5 was bound to antibodies, transposition performed at 37 ˚C and stopped using TAPS-Wash solution. Nuclei were lysed and pA-Tn5 decrosslinked using SDS-release solution.
PCR was performed using Kapa HiFi plus dNTPs (Roche Diagnostics, #07958846001) with the following PCR settings: 72˚C 5 minutes, 98˚C 30 seconds, X cycles of 98˚C 10 seconds, 63˚C 30 seconds, 72˚C final extension for 1 minute, hold at 4˚C. After 5 cycles the PCR was put on hold at 4˚C and 10% of the reaction was transferred into a 384 well plate and mixed with KAPA SYBR 2x (qPCR) and primers and qPCR was run for 20 cycles to determine the number of PCR cycles to be added38. Libraries were cleaned using SPRI beads using a 1.3 ratio, eluted in nuclease free water and pooled equimolecularily after library quantification using the KAPA library quantification kit (Roche Diagnostics, #079602).

value: Beige Adipocytes

value: Ucp1ERCre x NuTRAP on C57BL6 background

value: 17 week old at death, 1 week cold exposure at 8 degrees celsius at week 8; tamoxifen application during cold exposure; Then recovery at 22 degrees celsius for 8 weeks


title: E14.5,RNAseq,Aortic smooth muscle,WT2

value: Aortic smooth muscle


title: MEC1_mouse_Torin1_01


title: aging_study_Age_63_Surv_36_Rep3

description: Library name: aging_study_Age_63_Surv_36_Rep3

value: aging


title: E14.5,RNAseq,Aortic smooth muscle,WT1


title: TN_ingAT_AdipoCre_H3K27me3_1

value: AdipoCre x NuTRAP on C57BL6 background

value: 9 week old at death, born and kept at 30 degrees during whole life


title: An05_control_02_mouse_epi

source_name: embryonic epicardial cell explant

value: embryonic epicardial cell explant


title: aging_study_Age_63_Surv_36_Rep2

description: Library name: aging_study_Age_63_Surv_36_Rep2

value: Male


title: STV_N2_K79me2-vs-H3_rep2

city: Houston

first: Qinghao

last: Zhang

email: qinghaoz@bcm.edu, qhzhang87@gmail.com

state: Texas

address: BCM N820, One Baylor Plaza

department: Huffington Center on Aging

institute: Baylor College of Medicine

description: Library name: STV_N2_K79me2-vs-H3_rep2

data_processing:
Illumina NextSeq 2000 system was used for base-calling.
Raw reads of ChIP-seq were filtered using Trim Galore (version 0.4.5).
Reads were aligned to the C. elegans reference genome by Bowtie2 (version 2.1.0).
Samtools (version 1.7) was used to converse sequence alignment/map (sam) format to binary alignment/map (bam).
MACS2 algorithm (version 2.1.0) was used to call peaks for H3K79me2 or histone H3 by arguments "-t -c --broad -g --broad-cutoff 0.1 -B --keep-dup auto --nomodel --extsize", where histone H3 ChIP-seq reads from the same sample were employed as controls to normalize the data and offset differences in nucleosome occupancy.
Assembly: Ce11
Supplementary files format and content: bigWig, broadpeak.

organism: Caenorhabditis elegans

source_name: whole hermaphrodite_day-1 adult

growth_protocol: Worms were grown on standard nematode growth medium (NGM) agar plates seeded with a pre-cultured common laboratory bacterial strain E. coli OP50 (straptomycin-resistant) at 20 °C

extract_protocol:
Age-synchronized worms at day-1 adulthood were used for sample preparation. Samples were fixed in 1% formaldehyde/PBS solution for 10 min. Crosslinking was quenched by adding glycine solution to a final concentration of 125 mM. Chromatin was fragmented by sonication at 4 °C. The ChIP-seq formulated antibodies were anti-histone H3 (CST #4620), H3K79me2 (CST #5427).
Sequencing libraries were constructed by NEBNext® Ultra™ II DNA Library Prep with Sample Purification Beads kit (NEB) according to manufacturer’s instructions. Liberaries were pooled together and sequenced on the Illumina NextSeq 2000 system.

treatment_protocol: Worm eggs were isolated using a bleach-based protocol and split between NGM plates seeded with OP50 bacteria (fed condition, Fed) and empty NGM plates (starvation condition, STV). Larvae hatched on empty NGM plates were arrested at the L1 stage and starved for six days. After starvation treatment, L1 larvae were collected using M9 buffer and transferred to NGM plates seeded with OP50 bacteria to resume growth. Age-synchronized worms at day-1 adulthood were collected for ChIP-seq.

value: whole hermaphrodite_day-1 adult

value: wild type


title: An04_Torin1_02_mouse_epi


title: TN_ingAT_AdipoCre_H3K9me3_4

source_name: Inguinal Adipose Tissue

value: Inguinal Adipose Tissue

value: Adipocytes

value: biol rep 4


title: aging_study_Age_63_Surv_36_Rep1

description: Library name: aging_study_Age_63_Surv_36_Rep1

value: Whole Fly

value: Oregon R; y+ w+


title: CERT_ingAT_Ucp1ERCre_H3K4me3_1

value: biol rep 1


title: aging_study_Age_62_Surv_40_Rep2

description: Library name: aging_study_Age_62_Surv_40_Rep2


title: TN_ingAT_AdipoCre_H3K9me3_2

value: biol rep 2


title: Fed_N2_K79me2-vs-H3_rep2

description: Library name: Fed_N2_K79me2-vs-H3_rep2


title: An03_control_01_mouse_epi

value: control


title: STV_N2_K79me2-vs-H3_rep1

description: Library name: STV_N2_K79me2-vs-H3_rep1


title: An02_Torin1_01_mouse_epi


title: TN_ingAT_AdipoCre_H3K4me3_4


title: E18.5,RNAseq,Aortic smooth muscle,Dmut3

value: Pinch1,2 knockout


title: aging_study_Age_61_Surv_43_Rep4

description: Library name: aging_study_Age_61_Surv_43_Rep4


title: CE_DT_ingAT_AdipoCre_H3K27ac_1

value: AdipoCre x NuTRAP x Ucp1DTRGfp on C57BL6 background

value: 10 week old at death, 1 week cold exposure at 8 degrees celsius at week 8, then diphtheria toxin injections and euthanasia


title: aging_study_Age_62_Surv_40_Rep1

description: Library name: aging_study_Age_62_Surv_40_Rep1

value: aging


title: Fed_N2_K79me2-vs-H3_rep1

description: Library name: Fed_N2_K79me2-vs-H3_rep1


title: Old D60, HTO

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description: 10x Genomics

data_processing:
Alignment of reads from the single cell RNA-seq library and unique molecular identifiers (UMIs) counting were performed with 10X Genomics Cell Ranger tool (v3.0.2).
Reads of oligonucleotides tags (HTOs) used for Cell Hashing were counted with CITE-seq-Count (v1.4.2)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: CITE-seq

source_name: Whole lung

extract_protocol:
Freshly collected DC and Si8 from RedMUC298trTg mice were flushed with ice-cold HBSSwo (Mg2+/Ca2+ free supplemented with 10mM HEPES, pH 7.2) to remove luminal content. The tissue was inverted and inflated by injection of HBSSwo. Epithelial isolation was performed by incubation of tissue with pre-digestion buffer (HBSSwo, 5 mM EDTA, 5% v/v FCS, 1 mM DTT) in a shaking incubator. The isolated epithelial cells were resuspended in digestion buffer (HBSS with Mg2+/Ca2+ supplemented with 2 mg/ml collagenase type I and 40 U/ml DNase I) and incubated at 37 °C for 30 min. Cells were washed and re-suspended in PBS and stained with a Viability Dye, washed and resuspended in FACS buffer (HBSSwo, 2% v/v FCS, 5mM EDTA). Alive GCs were sorted using a FACS Jazz (Becton Dickinson) according to the presence or absence of mCherry signal using a C57Bl6 mouse as negative control. Goblet cells were washed in HBSS-/- and resuspended in HBSS-/- supplemented with 0.04% w/v BSA.
After euthanasia, lung tissue was perfused with sterile saline through the heart and were inflated through the trachea with dissociation cocktail containing dispase (50 caseinolytic U/ml), collagenase (2 mg/ml), elastase (1 mg/ml), and DNase (30 μg/ml). Lung were immediately removed, minced to small pieces ~1mm3), and transferred for mild enzymatic digestion for 20–30 min at 37 °C in 4 mL of the dissociation cocktail. Enzymatic activity was inhibited by adding 5 mL of PBS supplemented with 10% fetal calf serum (FCS). Single cells suspension were passed through a 40 micron mesh, and then harvest by centrifugation at 300 g for 5 min (4°C). Reb blood cell lysis was performed using RBC lysis buffer (Thermo fisher) for 2 minutes at 4°C and stopped using PBS 10% FCS. After another centrifugation at 300g for 5 min (4°C) cells were counted and critically assessed for single cell separation and overall cell viability using the Countess 3 FL(Fisher Scientific). Samples were then stained for multiplexing using cell hashing, using the Cell Hashing Total-Seq-ATM protocol (Biolegend) following the protocol provided by the supplier, using 6 distinct Hash Tag Oligonucleotides-conjugated mAbs (3 PBS and 3 Bleo). Samples were then adjusted to the same concentration and mixed in PBS supplemented with 0.04% of bovine serum albumin at a final concentration of 100 cells/μl. Single-cell capture was performed using the 10X Genomics Chromium device (3′ V3). Single-cell libraries were sequenced on the Illumina NextSeq 500.

treatment_protocol: Seven-week (“young”) and 18-month (“old”)-old C57BL/6 male mice (Charles River) were divided randomly into two groups: (A) saline-only (PBS, n=3), or (B) bleomycin (Bleo, n=3). To induce fibrotic changes, 50-µl bleomycin (1 U/kg) or PBS was aerosolized in mouse lungs using a MicroSprayer Aerosolizer (Penn-Century, Inc.). Mice were sacrificed at designated time points (days 14, 28 and 60) after instillation.

value: All

value: Whole lung

tag: Stage

value: Old

tag: age

value: 18 months old

value: Bleomycin or PBS

tag: time


title: TN_ingAT_AdipoCre_H3K4me3_2

value: Inguinal Adipose Tissue

value: AdipoCre x NuTRAP on C57BL6 background

tag: histone

value: 9 week old at death, born and kept at 30 degrees during whole life


title: Old D60, scRNAseq

description: 10x Genomics