title: OVCAR3, shRNA#78-GPX3, replicate 1

city: Pittsburgh

first: Nadine

last: Hempel

state: PA

address: 5051 Centre Ave

department: UPMC Hillman Cancer Center

institute: University of Pittsburgh

data_processing:
Raw data (raw reads) in fastq format were processed through in-house perl scripts (Novogene). In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content were calculated. All the downstream analyses were based on the clean data.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built 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. Then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: hg38
Supplementary files format and content: tab delimited text file contains raw counts for each sample
Supplementary files format and content: tab delimited text file contains fpkm data for each sample

growth_protocol: Human ovarian cancer NIH:OVCAR3 (OVCAR3) cells were purchased from the American Type Culture Collection (ATCC HTB-161) and maintained in RPMI 1640 medium (Gibco, 11875) supplemented with 10% FBS and 0.01 mg/ml bovine insulin (MilliporeSigma, I0516).

extract_protocol:
Total RNA was extracted using tDirect-zol RNA Miniprep kit (Zymo Research).
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 second strand cDNA synthesis using dTTP, end repair, A-tailing, adapter ligation, size selection, amplification, and purification for non-directional library preparation. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

value: ovarian cancer

value: GPX3 knock-down


title: OVCAR3, shRNA#78-GPX3, replicate 2

status: Public on Feb 14 2024

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: cell type

tag: genotype


title: OVCAR3, shRNA#78-GPX3, replicate 3


title: Caco-2 cells, ΔespF post-infection-rep2

city: Guangzhou

first: Yuting

last: Fang

state: Guangdong, China

address: No. 1023-1063 Shatai South Road, Baiyun District

country: China

institute: School of Public Health, Southern Medical University

data_processing:
StringTie (v2.1.1) was used for gene and transcript quantification.
Differential gene expression analysis and GSEA of the EHEC and ΔespF groups were performed with DESeq2 and ClusterProfiler (v4.2.2), respectively.
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes FPKM values for all samples.

extract_protocol:
Total RNA was extracted using AG RNAex Pro Reagent (Accurate Biotechnology) according to the manufacturer’s instructions.RNA quality evaluation, library construction and sequencing were performed by APE ×Bio Technology LLC. 2 μg of total RNA was used for the constuction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Tn5 DNA library Prep Kit for Illumina (APE ×Bio Technology LLC) following the manufacturer’s protocol

value: Colon adenocarcinoma cell

tag: infection

value: ΔespF


title: Trpm3 M/M lens 3

city: St. Louis

first: Philip

last: Ruzycki

state: MO

department: Ophthalmology and Visual Sciences

institute: Washington University in St. Louis

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq2 software. RNA-seq reads were then aligned and quantitated to the Ensembl release 101 primary assembly with an Illumina DRAGEN Bio-IT on-premise server running version 3.9.3-8 software. All gene counts were then imported into the R/Bioconductor package EdgeR for read depth normalization and pairwise comparison of each line to the appropriate Control group. Only genes with counts-per-million (CPM) >5 within at least 3 samples were included in the analysis. Samples were validated for consistency across biological replicates by plotMDS function of the R package Limma. Differential expression analysis was then performed to analyze for differences between conditions and the results were filtered for only those genes with Benjamini-Hochberg false-discovery rate adjusted p-values less than or equal to 0.05 and fold-change >2.
Assembly: mm10
Supplementary files format and content: fastq

molecule: polyA RNA

organism: Mus musculus

source_name: Lens

extract_protocol:
Lens total RNA was prepared using the RNeasy Kit (Qiagen, Valencia, CA, USA)
Samples were subjected to poly-A selection (oligo-dT), chemical fragmentation, random hexamer priming, cDNA synthesis, and adapter-ligation using the TruSeq RNA Library Prep Kit (Illumina, San Diego, CA, USA)

tag: tissue

value: Lens

value: Trpm3 M/M


title: Trpm3 M/M lens 2


title: Trpm3 M/M lens 1


title: Caco-2 cells, Uninfected-rep2

value: uninfected


title: Trpm3 I/M lens 2

value: Trpm3 I/M


title: OVCAR3, shRNA-scramble Control, replicate 3

value: WT


title: Trpm3 I/M lens 3


title: OVCAR3, shRNA#76-GPX3, replicate 3


title: OVCAR3, shRNA-scramble Control, replicate 2


title: Trpm3 I/M lens 1


title: Trpm3 KO lens 2

value: Trpm3 KO


title: Trpm3 KO lens 3


title: OVCAR3, shRNA#76-GPX3, replicate 1


title: Screening_first_8

city: Beijing

first: jiang

middle: xiao

last: yu

address: 15 Datun Road Chaoyang District

institute: institute of zoology, CAS

library_source: genomic

data_processing:
MAGeCK (version 0.5.9.2) was used to calculate the CRISPR-based screening sequencing data. The data (reproducible data separated by spaces) was first trimmed and counted by the “count” subcommand. Then, using the “test” subcommand, we ran a statistical test on a supplied count table. Finally, we used the positive rate to rank the calculated findings and considered genes with P values less than 0.05 to be significant.
Assembly: hg19
Supplementary files format and content: Txt file of screened gene ranking

molecule: genomic DNA

source_name: Mesenchymal stem cell

extract_protocol:
For our CRISPR screen, we first constructed a RAG library containing single guide RNAs (sgRNAs) targeting ribosome-related genes and based on the lentiCRISPRv2 plasmid (Addgene # 52961) as previously described. Then, we obtained a lentivirus library and infected senescent hMPCs at a low multiplicity of infection (MOI) (0.3) to ensure that one cell receives no more than one sgRNA. At the same time, we set up a control in which hMPCs were transduced with non-targeting control (NTC) at the same MOI. After two days, the cells transduced with sgRNA were put under puromycin selection (1 μg/ml) (InvivoGen) for six days, after which the cells switched to fresh medium without puromycin and passaged until the control cells underwent growth arrest. We harvested cells at different time points and extracted the genomic DNA using TIANamp Genomic DNA Kit (TIANGEN), according to the manufacturer’s protocol.
Finally, the sgRNA library was constructed as previously described (PMID: 33408182).

value: Mesenchymal stem cell


title: Screening_second

description: For our CRISPR screen, we first constructed a RAG library containing single guide RNAs (sgRNAs) targeting ribosome-related genes and based on the lentiCRISPRv2 plasmid (Addgene # 52961) as previously described. Then, we obtained a lentivirus library and infected senescent hMPCs at a low multiplicity of infection (MOI) (0.3) to ensure that one cell receives no more than one sgRNA. At the same time, we set up a control in which hMPCs were transduced with non-targeting control (NTC) at the same MOI. After two days, the cells transduced with sgRNA were put under puromycin selection (1 μg/ml) (InvivoGen) for six days, after which the cells switched to fresh medium without puromycin and passaged until the control cells underwent growth arrest. We harvested cells at different time points and extracted the genomic DNA using TIANamp Genomic DNA Kit (TIANGEN), according to the manufacturer’s protocol.


title: WT lens 3


title: Trpm3 KO lens 1


title: Screening_first_10


title: Screening_first_5


title: Cav1-null

city: Columbia

first: SUSANTA

last: BEHURA

address: 920 East Campus Dr

institute: University of Missouri

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
The base call (BCL) files were processed by the Cell Ranger pipeline (v. 3.0.1) to generate the FASTQ files. The processed data were  analyzed by R package Seurat to identify expression clusters, and to annotate cell types.
Assembly: GRCm39
Supplementary files format and content: Tab seprated value files and matrix file

source_name: Placenta

extract_protocol:
Single nuclei from WT and Cav1-null placenta were isolated using Pure Prep Nuclei Isolation kit (Product No. NUC-201, Sigma, St. Louis, MO, USA) as per manufacturer’s instructions.
The nuclei were used to prepare sequencing libraries using 10X Genomics Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1 at the University of Missouri Genomics Technology Core according to manufacturer’s specifications.

value: Placenta


title: OVCAR3, shRNA#76-GPX3, replicate 2


title: WT lens 2


title: Subject6_ControlKnockdown_Poly(I:C)

city: Ann Arbor

first: Poulami

last: Dey

address: 1301 Catherine St

institute: Michigan Medicine

description: ddsHTSeq_count.txt column:  R1189_9

data_processing:
STAR alignment
HTSeq for gene quantification
Assembly: hg19
Supplementary files format and content: gene by sample count matrix

source_name: Skin epithelium

extract_protocol:
RNA was isolated using Qiagen RNeasy Plus kit
RNA sequencing was performed by the U-M Advanced Genomics Core on the Novaseq 6000 platform

value: Skin epithelium

value: Primary human epidermal keratinocytes

tag: individual

value: ControlKnockdown

tag: treatment


title: OVCAR3, shRNA-scramble Control, replicate 1


title: WT lens 1


title: Subject2_HERC6Knockdown_Poly(I:C)

description: ddsHTSeq_count.txt column:  R1188_9


title: Subject6_HERC6Knockdown_Poly(I:C)

description: ddsHTSeq_count.txt column:  R1189_12


title: Subject4_HERC6Knockdown_Poly(I:C)

description: ddsHTSeq_count.txt column:  R1185_18


title: Screening_first_2


title: ATAC-seq_Cg1_KO_4d_immunization_rep2

city: Chicago

first: Vipul

last: Shukla

state: Illinois

address: 303 E. Superior Street

department: Department of Cell and Developmental Biology

institute: Northwestern University

description:
R_4240_KO_S4
cg1_immunized_4days_counts_RPKM_MEDIPS_EDGER.csv

data_processing:
Paired-end reads (50 bp) were mapped to the mouse genome mm10 GRCm38 (Dec. 2011) from UCSC using Bowtie 1.0.0 (D) ("--p 12 -m 1 --best --strata -X 2000 -S --fr --chunkmbs 1024").
Duplicated reads were marked and removed with picard-tools-2.21.4 MarkDuplicates (E).
Subsequent These fragments were used to call peaks using HOMER (v4.9.1) (F)  findPeaks function for each replicate (-center -style dnase "). The intersected peaks from the same condition were obtained with HOMER mergePeaks and filtered with grep.
The union of peaks from control and ko conditions were obtained with mergePeaks and were further used to identify differentially accessible regions (DARs) using MEDIPS (G); DARs were defined by an adjusted p value (FDR) lower than 0.05 and a log 2 fold enrichment higher equal than 1.
Assembly: mm10

source_name: Hematopoietic

growth_protocol: Naïve B cells were co cultured with 40 LB and IL4 for 4 days.

extract_protocol:
B cells were enriched by depleting 40LB cells after 4 days of co culture; Early GC B cells were FACS sorted using appropriate cell surface markers
Corces et.al 2017 ATAC seq protocol

treatment_protocol: Immunizations with SRBC single dose (10^9 cells)

value: Hematopoietic

value: B cells

value: early GC B cells

value: Cd19 Arid1a KO

value: SRBC immunization


title: Subject4_ControlKnockdown_Poly(I:C)

description: ddsHTSeq_count.txt column:  R1185_12


title: Subject3_HERC6Knockdown_Poly(I:C)

description: ddsHTSeq_count.txt column:  R1189_6


title: Subject1_HERC6Knockdown_Poly(I:C)

description: ddsHTSeq_count.txt column:  R1185_9


title: Subject1_ControlKnockdown_Poly(I:C)

description: ddsHTSeq_count.txt column:  R1185_3


title: ATAC-seq_Cg1_KO_40LB stim_rep2

description:
ATAC_4529_KO_S22
cg1_40lb_counts_RPKM_MEDIPS_EDGER.csv

value: ex vivo activated B cells

value: Cg1 Arid1a KO

value: 40LB + IL4


title: WT

description: 10X Genomics


title: C6

data_processing:
The raw sequence data were processed for quality control using the fastp tool.
Read alignment to the reference mouse genome (GRCm39) was performed using the STAR aligner.
Differential gene expression analysis was performed by edgeR.
Assembly: GRCm39
Supplementary files format and content: tab seprated text file with gene ID, gene symbol, sample ID and read counts as values.

extract_protocol:
Total RNA was extracted from whole placenta using an AllPrep DNA/RNA Mini Kit (Qiagen, Cat No./ID: 80204) following the manufacturer’s instruction.
Novogene workflow of RNA-seq library construction

tag: strain


title: C9


title: C5


title: ATAC-seq_Cg1_KO_40LB stim_rep1

description:
ATAC_4527_KO_S21
cg1_40lb_counts_RPKM_MEDIPS_EDGER.csv


title: Subject5_HERC6Knockdown_Poly(I:C)

description: ddsHTSeq_count.txt column:  R1188_18


title: ATAC-seq_Cg1_Cre_4d_immunization_rep2

description:
R_4239_cre-_S2
cg1_immunized_4days_counts_RPKM_MEDIPS_EDGER.csv

value: Arid1a fl/fl


title: Subject6_HERC6Knockdown_CGAMP

description: ddsHTSeq_count.txt column:  R1189_11

value: CGAMP


title: Subject5_ControlKnockdown_Poly(I:C)

description: ddsHTSeq_count.txt column:  R1188_12


title: ATAC-seq_Cg1_ctrl_40LB stim_rep2

description:
ATAC_2575_ctrl_S19
cg1_40lb_counts_RPKM_MEDIPS_EDGER.csv

value: Cg1 cre


title: Subject2_ControlKnockdown_Poly(I:C)

description: ddsHTSeq_count.txt column:  R1188_3


title: Subject3_HERC6Knockdown_CGAMP

description: ddsHTSeq_count.txt column:  R1189_5


title: Subject3_HERC6Knockdown_NT

description: ddsHTSeq_count.txt column:  R1189_4

value: NT


title: Cg1_KO_40LB stim_rep2

description:
RNA_4529_KO_S16
cg1_40lb_gene_name_counts_s2_rf.txt
cg1_40lb_All_regions_DESEQ_KO_vs_Cre.csv

data_processing:
Paired-end (50bp) reads were mapped to the mouse genome mm10/GRCm38 using STAR(A)(2.7.10a) (--genomeLoad LoadAndRemove --outFilterMismatchNmax 4 --outFilterMultimapNmax 100 --winAnchorMultimapNmax 100).
Counts were obtained with featureCounts (subread v2.0.1 (B)) (-g gene_name -s 2 -S rf).
Differentially expressed genes were calculated with DESeq2(C)71, filtering out genes that did not have any count in any condition; cut off to define DEGs was an adjusted pvalue 0.05 and a log2 fold change >= +/−1
Assembly: mm10
Supplementary files format and content: tab delimited file with the raw counts
Supplementary files format and content: tab delimited file with normalized counts and DESeq2 analysis

extract_protocol:
B cells were enriched by depleting 40LB cells after 4 days of co culture; Early GC B cells were FACS sorted using appropriate cell surface markers
NEBNext Ultra II Directional RNA library prep protocol


title: ATAC-seq_Cg1_Cre_4d_immunization_rep1

description:
R_4218_cre-_S1
cg1_immunized_4days_counts_RPKM_MEDIPS_EDGER.csv


title: ATAC-seq_Cg1_KO_4d_immunization_rep1

description:
R_4216_KO_S3
cg1_immunized_4days_counts_RPKM_MEDIPS_EDGER.csv


title: Cg1_KO_40LB stim_rep1

description:
RNA_4527_KO_S15
cg1_40lb_gene_name_counts_s2_rf.txt
cg1_40lb_All_regions_DESEQ_KO_vs_Cre.csv


title: ATAC-seq_Cg1_KO_40LB stim_rep3

description:
ATAC_4530_KO_S23
cg1_40lb_counts_RPKM_MEDIPS_EDGER.csv


title: Subject3_ControlKnockdown_Poly(I:C)

description: ddsHTSeq_count.txt column:  R1189_3


title: Subject6_HERC6Knockdown_NT

description: ddsHTSeq_count.txt column:  R1189_10


title: Cg1_cre_4d_immunized_rep1

description:
A_4218_cre-_S1
cg1_immunized_4d_gene_name_counts_s2_rf.txt
cg1_immunized_4d_All_regions_DESEQ_KO_vs_Cre.csv


title: Cg1_KO_4d_immunized_rep2

description:
A_4239_cre-_S2
cg1_immunized_4d_gene_name_counts_s2_rf.txt
cg1_immunized_4d_All_regions_DESEQ_KO_vs_Cre.csv


title: Cg1_ctrl_40LB stim_rep1

description:
RNA_2572_ctrl_S12
cg1_40lb_gene_name_counts_s2_rf.txt
cg1_40lb_All_regions_DESEQ_KO_vs_Cre.csv


title: Subject3_ControlKnockdown_NoTreatment

description: ddsHTSeq_count.txt column:  R1189_1

value: NoTreatment


title: ATAC-seq_Cg1_ctrl_40LB stim_rep1

description:
ATAC_2572_ctrl_S18
cg1_40lb_counts_RPKM_MEDIPS_EDGER.csv


title: ATAC-seq_Cg1_ctrl_40LB stim_rep3

description:
ATAC_2576_ctrl_S20
cg1_40lb_counts_RPKM_MEDIPS_EDGER.csv


title: Cg1_KO_40LB stim_rep3

description:
RNA_4530_KO_S17
cg1_40lb_gene_name_counts_s2_rf.txt
cg1_40lb_All_regions_DESEQ_KO_vs_Cre.csv


title: Subject6_ControlKnockdown_CGAMP

description: ddsHTSeq_count.txt column:  R1189_8


title: Subject3_ControlKnockdown_CGAMP

description: ddsHTSeq_count.txt column:  R1189_2


title: Subject2_HERC6Knockdown_NT

description: ddsHTSeq_count.txt column:  R1188_7


title: Subject6_ControlKnockdown_NoTreatment

description: ddsHTSeq_count.txt column:  R1189_7


title: Arid1a_KO_rep3

description:
S_4186_KO_S23
Cd19_Arid1a_invivo_counts_s2_rf.txt
Cd19_Arid1a_invivo_All_regions_DESEQ_KO_vs_Cre.csv

value: naive B cells


title: Cg1_ctrl_40LB stim_rep2

description:
RNA_2575_ctrl_S13
cg1_40lb_gene_name_counts_s2_rf.txt
cg1_40lb_All_regions_DESEQ_KO_vs_Cre.csv


title: Cg1_cre_4d_immunized_rep2

description:
A_4240_KO_S4
cg1_immunized_4d_gene_name_counts_s2_rf.txt
cg1_immunized_4d_All_regions_DESEQ_KO_vs_Cre.csv


title: Subject5_ControlKnockdown_CGAMP

description: ddsHTSeq_count.txt column:  R1188_11

value: Skin epithelium


title: Arid1a_KO_rep2

description:
S_4181_KO_S21
Cd19_Arid1a_invivo_counts_s2_rf.txt
Cd19_Arid1a_invivo_All_regions_DESEQ_KO_vs_Cre.csv


title: Subject5_HERC6Knockdown_CGAMP

description: ddsHTSeq_count.txt column:  R1188_17

value: Primary human epidermal keratinocytes


title: Subject5_ControlKnockdown_NoTreatment

description: ddsHTSeq_count.txt column:  R1188_10

value: ControlKnockdown


title: Arid1a_Cre_rep3

description:
S_4185_Cre-_S22
Cd19_Arid1a_invivo_counts_s2_rf.txt
Cd19_Arid1a_invivo_All_regions_DESEQ_KO_vs_Cre.csv

value: Hematopoietic


title: Subject2_HERC6Knockdown_CGAMP

description: ddsHTSeq_count.txt column:  R1188_8


title: Subject5_HERC6Knockdown_NT

description: ddsHTSeq_count.txt column:  R1188_16


title: Cg1_KO_4d_immunized_rep1

description:
A_4216_KO_S3
cg1_immunized_4d_gene_name_counts_s2_rf.txt
cg1_immunized_4d_All_regions_DESEQ_KO_vs_Cre.csv

value: B cells


title: Subject2_ControlKnockdown_CGAMP

description: ddsHTSeq_count.txt column:  R1188_2


title: Cg1_ctrl_40LB stim_rep3

description:
RNA_2576_ctrl_S14
cg1_40lb_gene_name_counts_s2_rf.txt
cg1_40lb_All_regions_DESEQ_KO_vs_Cre.csv


title: Subject2_ControlKnockdown_NoTreatment

description: ddsHTSeq_count.txt column:  R1188_1


title: Subject4_HERC6Knockdown_CGAMP

description: ddsHTSeq_count.txt column:  R1185_17


title: Subject1_HERC6Knockdown_NT

description: ddsHTSeq_count.txt column:  R1185_7


title: Arid1a_Cre_rep2

description:
S_4180_Cre-_S20
Cd19_Arid1a_invivo_counts_s2_rf.txt
Cd19_Arid1a_invivo_All_regions_DESEQ_KO_vs_Cre.csv


title: Subject1_ControlKnockdown_NoTreatment

description: ddsHTSeq_count.txt column:  R1185_1


title: Arid1a_KO_rep1

description:
S_4179_KO_S19
Cd19_Arid1a_invivo_counts_s2_rf.txt
Cd19_Arid1a_invivo_All_regions_DESEQ_KO_vs_Cre.csv


title: ASC, bio rep2

first: Fanying

last: Jiang

address: No. 7, Jinsui Road

institute: Zhongshan Ophthalmic Center, Sun Yat-Sen University

data_processing:
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq format were firstly processed through fastp software.
Reference genome and gene model annotation files were downloaded from genome website directly. 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.
Supplementary files format and content: xls file includes raw counts for each sample

source_name: lens capsule

growth_protocol: Adult C57BL/6 mice aged six to eight weeks were utilized to create the injury-induced ASC model

extract_protocol:
Total RNA was extracted with the Trizol reagent.
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained. In order to ensure the quality of the library, the library needs to be tested. After the construction of the library, the library was initially quantified by Qubit2.0 Fluorometer, then diluted to 1.5ng/ul, and the insert size of the library is detected by Agilent 2100 bioanalyzer. After insert size meets the expectation, qRT-PCR is used to accurately quantify the effective concentration of the library (the effective concentration of the library is higher than that of 2nM) to ensure the quality of the library

treatment_protocol: A small incision was made at the center of the anterior capsule by vertically inserting a 26-gauge hypodermic needle through the cornea. The depth of insertion reached a quarter of the blade's length

value: lens capsule

tag: age

value: six to eight weeks

value: WT

value: injury-induced ASC


title: Subject4_HERC6Knockdown_NT

description: ddsHTSeq_count.txt column:  R1185_16


title: ASC, bio rep1


title: CDX2-KO, replicate 2, snATACseq

city: San Francisco

first: Emily

last: Bulger

state: CA

address: 1650 Owens St.

institute: Gladstone Institutes/UCSF

data_processing:
Datasets were processed using CellRanger-Arc 2.0.0.
Filtered Feature-Barcode Matrix outputs generated by the CellRanger-Arc counts pipeline were analyzed using the Seurat package (version 4.3.0)(Satija et al., 2015; Butler et al., 2018; Stuart et al., 2019) (snRNA-seq) or ArchR v1.0.2(Granja et al., 2021) (multiomic snRNA-seq + snATAC-seq) in R (v4.2.0).
Indexed Fragment files generated by the CellRanger-Arc counts pipeline served as input for the generation of sample-specific ArrowFiles (minTSS = 4 & minFrags = 1000) using the R package ArchR v1.0.2(Granja et al., 2021).
Assembly: hg38
Supplementary files format and content: counts matrix and tab delimited txt fragment file

source_name: hiPSC 2D gastruloid

growth_protocol: hiPSCs were grown to confluence in mTeSR+ as micropatterned colonies on GFR-matrigel before being treated with 50ng/mL BMP4 for 48hrs

extract_protocol:
For each sample within the batch, all wells of a 24-well plate that each contained 12 micropatterned colonies were pooled, yielding a cell suspension comprising approximately 288 colonies per sample.  Nuclei were isolated following the manufacturer's instructions (CG000365_DemonstratedProtocol_NucleiIsolation_ATAC_GEX_Sequencing_RevC.pdf).
Nuclei were isolated and ~10,000-19,000 nuclei/sample were transposed and loaded onto a 10x Chromium Chip J to generate gel bead-in emulsions (GEMs) following the 10x Chromium Next GEM Single Cell Multiome ATAC and Gene Expression Kit (10x Genomics, CG000338).
Multiomic scRNA-seq and scATAC-seq

value: hiPSC 2D gastruloid

value: 48hr BMP4


title: Control, biol rep4

value: sham operation


title: Control, biol rep3


title: ASC, bio rep4


title: Subject4_ControlKnockdown_CGAMP

description: ddsHTSeq_count.txt column:  R1185_11

value: CGAMP


title: Control, biol rep2


title: Arid1a_Cre_rep1

description:
S_4178_Cre-_S18
Cd19_Arid1a_invivo_counts_s2_rf.txt
Cd19_Arid1a_invivo_All_regions_DESEQ_KO_vs_Cre.csv

value: Arid1a fl/fl


title: Subject4_ControlKnockdown_NoTreatment

description: ddsHTSeq_count.txt column:  R1185_10


title: WT_SAN_M_5

city: Amsterdam

first: Vincent

middle: M.

last: Christoffels

state: N/A (NA)

address: Meibergdreef 15  K2-159

department: Medical Biology

country: Netherlands

institute: Amsterdam UMC

data_processing:
Reads were mapped to mm10 build of the mouse transcriptome using STAR (Dobin et al. 2013).
Differential expression analysis was performed using the DESeq2 package based on a model using the negative binomial distribution (Love, Huber, and Anders 2014).
Assembly: mm10
Supplementary files format and content: Excel file with differential expression analysis (DESeq2)

source_name: Whole dissected sinoatrial node

growth_protocol: Animal care and experiments conform to the Directive 2010/63/EU of the European Parliament. All animal work was approved by the Animal Experimental Committee of the Academic Medical Center, Amsterdam, and was carried out in compliance with the Dutch government guidelines.

extract_protocol:
Tissue was homogenized and RNA was extracted using ReliaPrep RNA Miniprep System (Promega) and used as input for library preparation according to protocol. Libraries were sequenced on an Illumina Hiseq4000.
KAPA mRNA Hyperprep

treatment_protocol: Whole left atria were dissected from 12+ week old mice

value: adult 12+ weeks

value: sinoatrial node


title: Subject1_ControlKnockdown_CGAMP

description: ddsHTSeq_count.txt column:  R1185_2


title: ASC, bio rep3


title: CDX2-KO, replicate 2, snRNAseq

description: 10x Chromium Next GEM Single Cell Multiome  Gene Expression

molecule: nuclear RNA


title: CDX2-Het, replicate 2, snATACseq

description: 10x Chromium Next GEM Single Cell Multiome   ATAC


title: Control, biol rep1


title: CDX2-Het, replicate 1, snATACseq


title: Subject1_HERC6Knockdown_CGAMP

description: ddsHTSeq_count.txt column:  R1185_8


title: CDX2-KO, replicate 1, snATACseq


title: WT_SAN_M_4


title: WT_SAN_F_3


title: WT_RA_M_5

source_name: Whole dissected right atrium

value: right atrium


title: uterosacral ligament, POP, rep2

city: Taiyuan

first: Minna

last: Su

state: Shanxi

address: No.99 Longcheng Street, Xiaodian district

department: department of gynecology and obstetrics

institute: Shanxi Bethune Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. 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.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: uterosacrol ligament

extract_protocol:
Uterosacral ligament were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
Single cell suspension was loaded onto a microfluidic chip and single cell RNA-seq libraries were constructed according to the manufacturer’s instructions (Singleron GEXSCOPE Single Cell RNAseq Library Kit, Singleron Biotechnologies).

value: uterosacral ligament

tag: condition

value: POP


title: CDX2-Het, replicate 1, snRNAseq


title: CDX2-Het, replicate 2, snRNAseq


title: WT_SAN_M_3


title: CDX2-KO, replicate 1, snRNAseq


title: WT_RA_M_4


title: WT_SAN_M_1


title: uterosacral ligament, control

value: control


title: WT_SAN_F_4


title: uterosacral ligament, POP, rep3


title: WT_SAN_F_1


title: WT_SAN_F_2


title: uterosacral ligament, POP, rep1


title: LLW, scRNAseq

city: Chongqing

first: Wei

last: Fan

address: Youyi Road, No1

department: Urology

institute: The First affiliated hospital of Chongqing Medical University

description: 10X Genomics

data_processing:
The demultiplexing,barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.0.0,
After filtering, Seurat v3.0 (Satija et al., 2015) functions were used for dimension reduction and clustering
Assembly: GRCh38
Supplementary files format and content: matrix files

source_name: blood

extract_protocol:
PBMCs were extracted by Ficoll gradient centrifugation. Whole blood cells were diluted at a 1:1 ratio with 1× PBS before being layered onto lymphocyte separation medium and subjected to centrifugation at 500g for 20 minutes at 4°C. The PBMC-containing white-cloud layer was carefully isolated using capillaries and subsequently washed twice with PBS after removal of erythrocytes. For each sample, the cell viability exceeded 80%.10x Genomics® Cell Preparation Guide describes best practices and general protocols for washing, counting and concentrating cells from both abundant and limited cell suspensions (greater than or less than 100000 total cells, respectively) in preparation for use in 10x Genomics Single Cell Protocols.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: blood

value: primary PBMCs

value: PBMCs

value: no


title: XRG, scRNAseq

description: 10X Genomics


title: TX, scRNAseq

description: 10X Genomics


title: WT_RA_M_1

value: WT


title: FB, scRNAseq

description: 10X Genomics


title: Wit-49cells, Overexpression of aquaporin1, rep2

city: Qingdao

first: Hong

last: Liu

address: 16 Jiangsu Road

institute: Qingdao 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 hg38 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 normalization were performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: kidney

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: kidney

value: Wit-49 cell

value: tumor cell

value: Overexpression of aquaporin1


title: WT_RA_F_5


title: Hom_SAN_M_6


title: DY, scRNAseq

description: 10X Genomics


title: WT_RA_F_4


title: Hom_SAN_M_1


title: WT_RA_F_3A


title: WT_RA_F_2


title: Wit-49cells, normal control, rep3


title: Wit-49cells, normal control, rep1


title: WT_RA_F_1


title: Wit-49cells, Overexpression of aquaporin1, rep3


title: Wit-49cells, Overexpression of aquaporin1, rep1


title: Hom_SAN_M_2


title: Hom_SAN_F_4


title: Hom_SAN_F_2


title: Hom_SAN_F_1


title: Hom_SAN_M_4


title: Hom_RA_M_5


title: Gctrl, control

city: Lausanne

first: Frédéric

last: Schütz

address: Batiment Amphipole

country: Switzerland

institute: Swiss Institute of Bioinformatics

description: Gctrl

data_processing:
Sequencing was performed on an Illumina NovaSeq 6000 for 100 cycles single read.
Sequencing data were demultiplexed using the bcl2fastq2 Conversion Software (version 2.20, Illumina)
Raw reads were aligned to the human (hg38) genome using STAR (2.7.10b)
Gene counts were generated using FeatureCounts and differential expression analysis was performed with the DESeq2 (v.1.36.0) package from Bioconductor (v3.15)
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

source_name: Fibroblast

growth_protocol: Cells were grown in standard conditions (DMEM, 10% FBS - no antibiotics)

extract_protocol:
RNA was extracted with RNeasy Mini Kit (QIAstock, QIAGEN AG). RNA quality was assessed on a Fragment Analyzer (Agilent Technologies)
RNA-seq libraries were prepared from 500 ng of total RNA with the Illumina TruSeq Stranded mRNA reagents (Illumina) using a unique dual indexing strategy, and following the official protocol automated on a Sciclone liquid handling robot (PerkinElmer). Libraries were quantified by a fluorometric method (QubIT, Life Technologies) and their quality assessed on a Fragment Analyzer (Agilent Technologies).

value: Fibroblast


title: Hom_RA_F_4


title: Hom_RA_M_3


title: TBXT-Het, replicate 2, snATACseq

library_source: genomic single cell

data_processing:
Datasets were processed using CellRanger-Arc 2.0.0.
Filtered Feature-Barcode Matrix outputs generated by the CellRanger-Arc counts pipeline were analyzed using the Seurat package (version 4.3.0)(Satija et al., 2015; Butler et al., 2018; Stuart et al., 2019) (snRNA-seq only) or ArchR v1.0.2(Granja et al., 2021) (multiomic snRNA-seq + snATAC-seq) in R (v4.2.0).
Indexed Fragment files generated by the CellRanger-Arc counts pipeline served as input for the generation of sample-specific ArrowFiles (minTSS = 4 & minFrags = 1000) using the R package ArchR v1.0.2(Granja et al., 2021).
Assembly: hg38
Supplementary files format and content: counts matrix and tab delimited txt fragment file

extract_protocol:
For each sample within the batch, all wells of a 24-well plate that each contained 12 micropatterned colonies were pooled, yielding a cell suspension comprising approximately 288 colonies per sample.  Nuclei were isolated following the manufacturer's instructions (CG000365_DemonstratedProtocol_NucleiIsolation_ATAC_GEX_Sequencing_RevC.pdf).
Nuclei were isolated and ~9,000-12,000 nuclei/sample (TBXT-KO-2 = 19000 nuclei) were transposed and loaded onto a 10x Chromium Chip J to generate gel bead-in emulsions (GEMs) following the 10x Chromium Next GEM Single Cell Multiome ATAC and Gene Expression Kit (10x Genomics, CG000338).
Multiomic scRNA-seq and scATAC-seq

value: hiPSC 2D gastruloid

value: TBXT-Het

value: 48hr BMP4


title: Hom_RA_F_3

value: adult 12+ weeks

value: right atrium


title: C444, control


title: C509SY, control


title: TBXT-KO, replicate 1, snATACseq

value: TBXT-KO


title: no34_notrim

city: Grenoble

first: Florent

last: Chuffart

state: La Tronche

address: Site Santé - Allée des Alpes

country: France

institute: IAB - INSERM (U1209) - CNRS (UMR5309)

data_processing:
The sequenced reads from the raw sequence (.fastq files) were aligned on the UCSC mm10 genome using the STAR software (2.7.1a) (Dobin et al. 2013) [PMID:23104886] to produce bam files.
The aligned reads (.bam files) were counted using HTSeq framework (0.11.2) (Anders et al. 2015) [PMID:25260700], with options: -t exon -f bam -r pos –stranded=reverse -m intersection-strict –nonunique none.
Assembly: Mus_musculus_mm10
Supplementary files format and content: raw counts

source_name: liver

extract_protocol:
TRIzol Reagent manufacturer protocol (Invitrogen, 15596026)
TruSeq Stranded mRNA manufacturer protocol (Illumina, 20020595)

value: liver

tag: Sex

value: male

tag: age at_the_treatment_onset

value: 16 weeks

value: C57BL/6JRj (Janvier Labs)

tag: treatment duration

tag: diet

value: regular chow diet (LASQC diet, Rod16, Altromin international)


title: Gproband, patient B7

description: Gproband

value: biallelic missense variant in AFF3 (compound heterozygote for the p.(Val1036Ile) and p.(Arg1186Gln) variants)


title: Hom_RA_F_7


title: no33_notrim


title: Wit-49cells, normal control, rep2

value: kidney

value: WT


title: Hom_RA_M_1


title: TBXT-Het, replicate 1, snATACseq


title: 6089VEJ, control

value: control


title: WT, replicate 1, snATACseq


title: TBXT-Het, replicate 2, snRNAseq


title: TBXT-KO, replicate 2, snATACseq


title: WT, replicate 2, snRNAseq


title: ih39_notrim


title: WT, replicate 2, snATACseq


title: ih38_notrim


title: Nproband, patient B1

description: Nproband

value: biallelic missense variant in AFF3 (homozygous for the p.(Lys528Arg) variants)


title: no35_notrim


title: TBXT-Het, replicate 1, snRNAseq


title: no31_notrim


title: TBXT-KO, replicate 2, snRNAseq


title: ih40_notrim


title: Control_24m_F_rep1

city: Los Angeles

first: Constanza

middle: J

last: Cortes

state: California

address: 3715 McClintock Ave

institute: University of Southern California

description:
PE150
AA1450

data_processing:
Raw data (raw reads) of fastq format were processed through Novogene in-house perl scripts.
Reference genome and gene model annotation file were downloaded from genome website directly. 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. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: mm10
Supplementary files format and content: tab-delimited text files including raw counts for each sample
Supplementary files format and content: tab-delimited text files including FPKM for each sample

source_name: hippocampus

extract_protocol:
Animals were anesthetized with 3.8% Avertin Solution. All animals received a transcardial perfusion with 60 mLs of cold 1x Phosphate Buffer Saline. The hippocampus was micro-dissected from sagitally sectioned hemibrain and flash-frozen in liquid nitrogen. Flash frozen tissue was homogenized and total RNA was extracted via TRIzol.
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. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

value: hippocampus

value: TFEB;HAS-cre

value: female


title: WT, replicate 1, snRNAseq

value: hiPSC 2D gastruloid

value: 48hr BMP4


title: TBXT-KO, replicate 1, snRNAseq


title: ih37_notrim


title: no32_notrim


title: cTFEB;HSACre_24m_F_rep2

description:
PE150
AA1432


title: SRA01/04 cells, shSmurf1, bio rep3

growth_protocol: The human LEC line SRA01/04 was cultured in Dulbecco's Modified Eagle's Medium supplemented with 10% fetal bovine serum, 100 IU/ml penicillin, and 100 μg/ml streptomycin .

treatment_protocol: LECs were treated with 20 ng/ml recombinant human TGF-β2 for 48 hours

value: lens epithelial cell

value: Smurf1 knockdown


title: SRA01/04 cells, shSmurf1, bio rep2


title: Control_24m_M_rep3

description:
PE150
AA1458

value: Control


title: Control_24m_F_rep4

description:
PE150
TH0209


title: Control_24m_F_rep3

description:
PE150
TH0180


title: WHJ, scRNAseq

description: 10X Genomics

value: blood

value: primary PBMCs

value: PBMCs

value: no


title: PA4-treated H9 cells, rep 1

city: Duarte

first: Wendong

last: Huang

address: 1500 E. Duarte Road

institute: Beckman Research Institute of the City of Hope

data_processing:
Sequence reads passing quality check were preprocessed for adaptor and polyA removal using trimmomatic v.0.39 and fastp v.0.23.2.
Trimmed sequence reads were mapped to human reference genome hg38 with an index build containing the transcript/gene annotations using STAR v.2.7.9a.
Strand-specific read counts of each gene annotated in RefGene were calculated by featureCounts function in the Subread package v.1.6.4.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file containing read counts for each sample.

growth_protocol: Cells were cultured with RPMI 1640 with 10% tetal bovin serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37 degree Celsius

extract_protocol:
The RNA was directly isolated by the Direct-zol RNA kit (Zymo Research) and eluted in RNase-free water. About 1 ug of total RNA was used for library constuction
Libraries were prepared with Kapa RNA mRNA HyperPrep kit (Kapa Biosystems) according to the manufacturer's protocol.

treatment_protocol: H9 cells were treated with either DMSO or 1 uM PA4 for 24 hours.

value: cutaneous T lymphocyte cell

value: PA4 compound


title: ih36_notrim

value: liver

value: male

value: 16 weeks

value: C57BL/6JRj (Janvier Labs)

value: regular chow diet (LASQC diet, Rod16, Altromin international)


title: PA4-treated H9 cells, rep 2


title: Control_24m_M_rep1

description:
PE150
AA1380

value: hippocampus


title: H9 cells, rep 2


title: cTFEB;HSACre_24m_F_rep4

description:
PE150
AA1449

value: female


title: cTFEB;HSACre_24m_F_rep3

description:
PE150
AA1447


title: H9 cells, rep 1


title: Control_24m_M_rep4

description:
PE150
AA1459

value: TFEB;HAS-cre


title: cTFEB;HSACre_24m_F_rep1

description:
PE150
AA1430


title: SRA01/04 cells, shSmurf1, bio rep4

value: lens epithelial cell


title: cTFEB;HSACre_24m_M_rep4

description:
PE150
AA1379


title: SRA01/04 cells, shControl, biol rep1

value: WT


title: P1+CP2+CP3+CP4, HTO-derived cDNA

city: Bethesda

first: Chaim

middle: A

last: Schramm

state: MD

address: 40 Convent Dr

department: Vaccine Research Center

institute: NIAID, NIH

description:
Hashtag-derived oligonucleotide (HTO)
finalSeurat.RDS
ptcra-d_barcodes.tsv.gz
ptcra-d_features.tsv.gz
ptcra-d_matrix.mtx.gz
HTO-barcode_assignments.tsv

library_source: other

data_processing:
10X single-cell transcriptome libraries were processed with Cellranger (v6.1.1) and Seurat (v4.0.4).
The TCR-⍺β and TCR-γδ libraries were demultiplexed and cell barcodes were assigned with Minnn (v10.1).  TCR libraries were annotated with MiXCR (v3.0.13) and then separated by subject. The numbers of αβ or γδ TCRs for the patients and controls were calculated by counting the numbers of cells expressing both TRA and TRB V-J genes and both TRG and TRD V-J genes.
Assembly: hg38
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: tab-delimited HTO assignments for each cell
Supplementary files format and content: tab-delimited TCR gene assignments and CDR3s
Supplementary files format and content: RDS-formatted R data files with complete Seurat objects

molecule: protein

source_name: PBMC

extract_protocol:
Cryopreserved peripheral blood mononuclear cells (PBMC) in R10 medium (RPMI 1640, 10% FBS, 2 mM L-glutamine, 100 U/ml penicillin, and 100 μg/ml streptomycin) were thawed and immediately centrifuged to obtain a cell pellet. The cells were then incubated for 15 min at 37°C under an atmosphere containing 5% CO2 in the presence of Benzonase (Millipore Sigma, cat. 70664) diluted 1:1000 in R10 medium.  The cells were then washed once in R10 and once in FACS buffer (2% FBS in PBS). For staining, cells were resuspended in 50 µl of a mixture of LIVE/DEAD Fixable Blue Dead Cell Stain (cat. L34962) diluted 1:200 in PBS and anti-CCR7 APC-Cy7 antibody (Biolegend, cat. 353212), and incubated for 10 min at 37°C under an atmosphere containing 5% CO2. Cells were then labeled with 1µL oligonucleotide-linked hashing antibody (Totalseq-C, Biolegend) and stained by incubation with 50 µL antibody cocktail diluted in Brilliant Stain Buffer (BD Biosciences, cat. 566349) for 20 min at room temperature. The antibody cocktail contained the following antibodies: anti-CD14 BV510 (Biolegend, cat. 301842), anti-CD19 BV510 (Biolegend, cat. 302242), anti-CD56 BV510 (Biolegend, cat. 362534), anti-CD8 BV785 (Biolegend, cat. 301046), anti-CD4 PECy7 (Biolegend, cat. 300512), anti-CD95 AlexaFluor 700 (Biolegend, cat. 305648), anti-PD-1 BV750 (Biolegend, cat. 329966), anti-CD69 FITC (Biolegend, cat. 310904), anti-CD40L BV421 (Biolegend, cat. 310824), anti-CD3 BUV805 (BD Biosciences, cat. 741999), anti-CD45RA PECF594 (BD Biosciences, cat. 562298), anti-CD25 BUV661 (BD Biosciences, cat. 741685), anti-CXCR3 BV711 (BD Biosciences, cat. 563156), anti-HLA-DR PECy5.5 (Invitrogen, cat. MHLDR18), anti-CXCR5 APC (Invitrogen, cat. 17-9185-42). The cells were washed twice with FACS buffer and resuspended in R10 for sorting. 12,000 T cells (CD3+CD14−CD19−CD56−Live/Dead−) were sorted from each sample with a BD FACSymphony S6 Cell Sorter instrument (BD Biosciences) running BD FACSDiva Software version 9.5.1 (BD Biosciences). Sorted cells were pooled four by four, and each pool was loaded in a different lane of the 10x Genomics Chromium Chip for sequencing.
For the sequencing of single-cell V(D)J repertoires for sorted T cells, the cell suspension was loaded on the 10x Genomics Chromium Instrument according to the manufacturer’s protocol for the Next GEM Single-Cell 5′ Kit v1.1 (10x Genomics PN-1000165) to generate gel bead-in-emulsions, and to perform GEM-RT and the amplification of total cDNA. Following purification with SPRIselect beads (Beckman Coulter), specific TCR targets were amplified from the cDNA with the PTCR1 primer (5′-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTC-3′) and constant region primers: TRB (5′-TGCTTCTGATGGCTCAAACACAGCGACCT-3′), TRA (5′-TCTCAGCTGGTACACGGCAGGGTCAGGGT-3′), TRG (5′-GAAGGAAGAAAAATAGTGGGCTTGGGGGAAAC-3′), or TRD (5′-CACCAGACAAGCGACATTTGTTCC-3′) with a barcode and the P7 sequence added to the constant region primers. The Illumina-ready libraries were sequenced by paired-end MiSeq with 2×300 base-pair reads to obtain VDJ sequences
scRNA-seq with FeatureSeq and scAIRR-seq

value: PBMC

value: CD3+ T cells

tag: library type

value: HTO

tag: tags

value: Anti CD298 + Anti beta2-microglobulin:P1/TotalSeq-C0255 ; CP2/TotalSeq-C0256 ; CP3/TotalSeq-C0257 ; CP4/TotalSeq-C0258


title: SRA01/04 cells, shSmurf1, bio rep1

value: Smurf1 knockdown


title: SRA01/04 cells, shControl, biol rep3


title: PA4-treated H9 cells, rep 3

value: cutaneous T lymphocyte cell


title: Control_24m_F_rep2

description:
PE150
TH0179

value: Control


title: H9 cells, rep 3


title: SRA01/04 cells, shControl, biol rep2


title: cTFEB;HSACre_24m_M_rep3

description:
PE150
AA1377


title: P2+CP5+CP6, HTO-derived cDNA

description:
Hashtag-derived oligonucleotide (HTO)
finalSeurat.RDS
ptcra-b_barcodes.tsv.gz
ptcra-b_features.tsv.gz
ptcra-b_matrix.mtx.gz
HTO-barcode_assignments.tsv

value: Anti CD298 + Anti beta2-microglobulin:P2/TotalSeq-C0255 ; P2/TotalSeq-C0256 ; CP5/TotalSeq-C0257 ; CP6/TotalSeq-C0258


title: P2+CP5+CP6, mRNA-derived cDNA

description:
poly A RNA via 10x Chromium
finalSeurat.RDS
ptcra-b_barcodes.tsv.gz
ptcra-b_features.tsv.gz
ptcra-b_matrix.mtx.gz

value: mRNA


title: cTFEB;HSACre_24m_M_rep2

description:
PE150
AA1375

value: male


title: SRA01/04 cells, shControl, biol rep4


title: P3+P4+CA3+CA4, mRNA-derived cDNA

description:
poly A RNA via 10x Chromium
finalSeurat.RDS
ptcra-a_barcodes.tsv.gz
ptcra-a_features.tsv.gz
ptcra-a_matrix.mtx.gz


title: cTFEB;HSACre_24m_M_rep1

description:
PE150
AA1374


title: P1+CP2+CP3+CP4, mRNA-derived cDNA

description:
poly A RNA via 10x Chromium
finalSeurat.RDS
ptcra-d_barcodes.tsv.gz
ptcra-d_features.tsv.gz
ptcra-d_matrix.mtx.gz


title: Control_6m_F_rep4

description:
PE150
TH0547


title: Control_6m_F_rep2

description:
PE150
TH0480


title: Control_6m_F_rep3

description:
PE150
TH0546


title: Control_6m_M_rep4

description:
PE150
TH0554


title: CA1+CA2+CA5+CP1, mRNA-derived cDNA

description:
poly A RNA via 10x Chromium
finalSeurat.RDS
ptcra-c_barcodes.tsv.gz
ptcra-c_features.tsv.gz
ptcra-c_matrix.mtx.gz


title: cTFEB;HSACre_6m_F_rep4

description:
PE150
TH0410


title: Control_6m_M_rep3

description:
PE150
TH0553


title: HEK293T cell model, Wt2C

first: Giovanna

last: Ambrosini

address: Station 19

institute: EPFL

data_processing:
Sequencing was performed on an Illumina NovaSeq 6000 for 100 cycles single read.
Sequencing data were demultiplexed using the bcl2fastq2 Conversion Software (version 2.20, Illumina)
Raw reads were aligned to the human (hg38) genome using STAR (2.7.10b)
Gene counts were generated using FeatureCounts and differential expression analysis was performed with the DESeq2 (v.1.36.0) package from Bioconductor (v3.15)
Assembly: hg38
Supplementary files format and content: raw_counts.txt
Supplementary files format and content: norm_counts.txt

tag: line


title: CA1+CA2+CA5+CP1, HTO-derived cDNA

description:
Hashtag-derived oligonucleotide (HTO)
finalSeurat.RDS
ptcra-c_barcodes.tsv.gz
ptcra-c_features.tsv.gz
ptcra-c_matrix.mtx.gz
HTO-barcode_assignments.tsv

value: Anti CD298 + Anti beta2-microglobulin:CA1/TotalSeq-C0251 ; CA2/TotalSeq-C0252 ; CA5/TotalSeq-C0253 ; CP1/TotalSeq-C0254


title: Control_6m_F_rep1

description:
PE150
TH0412


title: cTFEB;HSACre_6m_F_rep3

description:
PE150
TH0396


title: HEK293T cell model, Wt4C

tag: cell line


title: HEK293T cell model, Wt4B


title: cTFEB;HSACre_6m_F_rep1

description:
PE150
TH0393


title: HEK293T cell model, Wt1A


title: Control_6m_M_rep2

description:
PE150
TH0512


title: HEK293T cell model, Wt2B


title: cTFEB;HSACre_6m_M_rep2

description:
PE150
TH0481


title: HEK293T cell model, Wt2A


title: HEK293T cell model, 86C

value: DN/LoF


title: cTFEB;HSACre_6m_M_rep1

description:
PE150
TH0392

value: hippocampus


title: HEK293T cell model, 86B


title: HEK293T cell model, Wt4A


title: HEK293T cell model, Wt1C


title: HEK293T cell model, 86A


title: cTFEB;HSACre_6m_M_rep3

description:
PE150
TH0484


title: P3+P4+CA3+CA4, HTO-derived cDNA

description:
Hashtag-derived oligonucleotide (HTO)
finalSeurat.RDS
ptcra-a_barcodes.tsv.gz
ptcra-a_features.tsv.gz
ptcra-a_matrix.mtx.gz
HTO-barcode_assignments.tsv

tag: cell type

value: Anti CD298 + Anti beta2-microglobulin:P3/TotalSeq-C0251 ; CA3/TotalSeq-C0252 ; P4/TotalSeq-C0253 ; CA4/TotalSeq-C0254


title: Control_6m_M_rep1

description:
PE150
TH0511

tag: genotype


title: cTFEB;HSACre_6m_M_rep4

description:
PE150
TH0510

value: TFEB;HAS-cre


title: P5 parietal leaflet Sox9 epicardial KO 4

city: Charleston

first: Jeremy

last: Barth

state: SC

address: 173 Ashley Ave, BSB 627

institute: MUSC

data_processing:
Fastq files were imported into the Partek Flow system
Alignment was done with an implementation of STAR version 2.7.8a using mouse genome mm10
Quantification was done using Partek E/M annotation model for RefSeq transcripts 95 with the following settings: 1) strict paired-end compatibility, 2) require junctions to match introns, and 3) minimum reads of 10
Gene counts were analyzed by DESeq2 to determine normalized counts and statistical measures between samples types
Assembly: mm10
Supplementary files format and content: tab-delimited text file of DESeq2 output including gene symbols, FDR step up, Log2(Ratio), and Fold change

source_name: Parietal mitral valve leaflet

extract_protocol:
Microdissections were performed to isolate individual mitral valve leaflets from P5 mouse hearts. Single leaflets were used as individual samples. Total RNA was purified from each sample using the RNeasy Micro Kit (Qiagen) per manufacturer’s instructions. Quality of each total RNA isolation was assessed by Bioanalyzer 2100 (Agilent) and samples with low-quality (RIN<8)  were excluded.
RNA samples were submitted to a commercial provider (GeneWiz) for processing by a protocol for low input total RNA

value: Parietal mitral valve leaflet

tag: postnatal age

value: Wt1-Cre; Sox9 fl/fl

tag: strain background


title: HEK293T cell model, Wt1B


title: cTFEB;HSACre_6m_F_rep2

description:
PE150
TH0395

tag: tissue

value: female


title: HEK293T cell model, 90A

value: DN/DN


title: Gastric organoid, Pyr, scRNAseq

city: Jejusi

first: Hyesung

last: Kim

address: Aran 13 gil, 15

department: Convergence Biomedical Science

country: South Korea

institute: Jeju National University College of medicine

data_processing:
The sequencing data was analyzed and processed using PIPseeker (Fluent BioSciences) and PartekFlow (Partek).
Assembly: GRCm39
Supplementary files format and content: Tab separated values files and matrix file

source_name: Stomach corpus

extract_protocol:
To prepare cells from organoids for scRNA-seq, we followed the protocol outlined in the PIPseq Milli 3’ Single Cell Capture and Lysis User Guide (Fluent BioSciences).
The resulting emulsions carrying captured mRNA were visually inspected by Fluent Biosciences upon sample receipt to ensure their quality before proceeding with downstream processing. Samples that passed inspection were processed according to the specifications of the PIPseq™ T2 Single Cell Sequencing Kit, including mRNA isolation, cDNA generation, cDNA amplification, sequencing-ready library preparation, library pooling, and sequencing

value: Stomach corpus

value: Organoid

tag: treatment

value: Dysplasia induction

tag: agent

value: Pyr


title: Gastric organoid, DMSO, scRNAseq

value: DMSO


title: P5 parietal leaflet Sox9 epicardial KO 3


title: HEK293T cell model, 51C


title: HEK293T cell model, 51A


title: P5 parietal leaflet Sox9 epicardial KO 2


title: HEK293T cell model, 90B


title: HEK293T cell model, 54B


title: P5 parietal leaflet Sox9 epicardial KO 1


title: HEK293T cell model, 1A

value: No. 1

value: LoF/+


title: Atherosclerotic plaque, WT, Animal4, scRNAseq

first: Daniel

middle: R

last: Goldstein

state: MI

address: 2800 Plymouth Road

department: Department of Internal Medicine

institute: University of Michigan

description:
10x Genomics
cell_metadata.tsv.gz
cell_normalized_counts_20766x37266.txt.gz

data_processing:
Raw reads were processed by the Cell Ranger pipeline and aligned to the mm10 reference genome (version: mm10-2020-A). Gene count matrices were generated and used for downstream bioinformatics analysis in the R 4.0.5 environment.
As a preprocessing step, ambient RNA contamination was removed by SoupX which used empty droplets contained in the raw Cell Ranger output to calculate the profile of “soup” contamination. The corrected count matrices were then processed by the Seurat v4.1.0 package.
Low quality cells were filtered out with the following criteria: the number of detected genes per cell should be greater than 200, the number of unique molecule identifiers (UMIs) should be less than 50,000, the percentage of expressed mitochondrial genes smaller than 10%, and the percentage of hemoglobin genes smaller than 3%. Raw counts were normalized with the “LogNormalize” method. Top 2,000 highly variable genes were scaled and used for principal component analysis (PCA). Samples were then integrated by the Harmony package using the PCA result. The first 20 dimensions of the “harmony” reduction slot were used for constructing UMAP reduction and the shared nearest neighbor graph. The FindCluster function was used to identify clusters within the graph with a resolution of 0.4. Marker genes for each cluster were identified by the FindAllMarkers function using the default Wilcoxon Rank Sum test.
Clusters were annotated using the SingleR package with the mouse ImmGen dataset as the reference, and then confirmed manually by searching top cluster-specific marker genes within Cellmarker 2.0. To improve the resolution and accuracy of cell type assignment, a step-wise hierarchical annotation approach was adopted. For example, myeloid cells were subsetted out, re-integrated by Harmony and clustered again to distinguish macrophages/monocytes from neutrophils and dendritic cells. This strategy was applied to all major cell populations (stromal cells, lymphocytes, myeloid cells).
Assembly: mm10 reference genome (version: mm10-2020-A)
Supplementary files format and content: cell_metadata.tsv contains sample source, genotype and cell type annotation for each cell.
Supplementary files format and content: cell_normalized_counts 20766x37266.txt contains tab-delimited expression data normalized by the “LogNormalize” method in Seurat.

source_name: Aorta

extract_protocol:
Single cell suspensions from aortic root, ascending aorta and aortic arch, where most of the aortic plaques are, were prepared by mincing isolated tissues followed by enzymatic digestion with collagenase I (450 U/ml, Cat# LS004196, Worthington), collagenase XI (125 U/ml, Cat# C7657, Sigma-Aldrich), DNase I (60 U/ml, Cat# DN25, Sigma-Aldrich) and hyaluronidase (60 U/ml, Cat# H3506, Sigma-Aldrich) for 1 h at 37°C with agitation (64). Suspensions were then filtered, and dead cells were removed with a Dead Cell Removal Kit (Cat# 480157, Biolegend) to improve cell viability of the samples. Cells were then washed, resuspended in RPMI 1640 + 10% fetal bovine serum and processed further by the Advanced Genomics Core at the University of Michigan.
Single cells were partitioned into droplet emulsion using the Chromium Controller (10X Genomics, CA), where cells were lysed and cDNAs were reverse transcribed and barcoded. Amplified cDNAs were used to construct 5’ gene expression (GEX) library.All cDNA libraries were sequenced on an Illumina NovaSeq-6000 platform with 150bp paired end reads.

value: Aorta

value: wildtype

tag: animal


title: HEK293T cell model, 90C


title: Atherosclerotic plaque, Acod1-KO, Animal4, scRNAseq


title: P5 parietal leaflet control 5

value: Sox9 fl/fl


title: HEK293T cell model, 216A

value: LoF/LoF


title: P5 parietal leaflet control 4


title: HEK293T cell model, 54C


title: P5 parietal leaflet control 2


title: P5 parietal leaflet control 3


title: HEK293T cell model, 54A


title: P5 parietal leaflet control 1


title: HEK293T cell model, 1B


title: HEK293T cell model, 1C


title: Control_24m_M_rep2

description:
PE150
AA1406

value: hippocampus

tag: age

value: male


title: HEK293T cell model, 51B

value: DN/LoF


title: Atherosclerotic plaque, Acod1-KO, Animal2, scRNAseq


title: HEK293T cell model, 98B


title: Atherosclerotic plaque, Acod1-KO, Animal5, scRNAseq


title: HEK293T cell model, 98C


title: Atherosclerotic plaque, WT, Animal1, scRNAseq


title: HEK293T cell model, 216C


title: Atherosclerotic plaque, WT, Animal2, scRNAseq


title: Atherosclerotic plaque, WT, Animal3, scRNAseq


title: Atherosclerotic plaque, Acod1-KO, Animal3, scRNAseq


title: HEK293T cell model, 20A


title: HEK293T cell model, 216B


title: Atherosclerotic plaque, Acod1-KO, Animal1, scRNAseq


title: HEK293T cell model, 20C


title: HEK293T cell model, 98A


title: H3K18lac-ICM_rep2

city: Harbin

first: Hou

middle: wei

last: bo

state: Heilongjiang

address: Xiangfang District

institute: College of Life Science,Northeast Agricultural University

data_processing:
We aligned paired-end CUT&Tag reads of H3K18lac to the mm39 reference genome using Bowtie2 v2.5.0 software. Unmapped and non-uniquely mapped reads were removed. Next, we pooled the biological replicates for each stage and performed downstream analysis. For peak calling, we converted sequence alignments in BAM format into BEDPE records using the BEDTools function bamtobed. CUT&Tag peaks were called on merged replicates and normalized to input using MACS2 v2.2.7.1 software. Peak annotation was performed using the R package ChIPseeker with the default parameters. Peak comparisons and overlaps were evaluated using the BEDTools suite for autosomal chromosomes. For quantitative analysis, we normalized the read counts by computing the number of RPKMs using merged replicate BAM files with the bamCoverage tool in deepTools software.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&TAG

source_name: ICM

growth_protocol: DMEM, 15% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Embryos were incubated in 50 µL antibody buffer; 0.5 μg antibody was added and the mixture was incubated at 4℃ overnight. After washing twice with dig-wash buffer, 50 µL dig-wash buffer with 0.2 µg secondary antibody was added and the mixture was incubated at room temperature for 1 h. After washing twice with 100 µL dig-wash buffer, 1 µL pG-Tn5 and 49 µL dig-300 buffer were added, and the samples were incubated at room temperature for 1 h. Next, the samples were washed twice with 100 µL dig-wash buffer. We subsequently added 200 µL tagmentation buffer and incubated the samples at 37°C for 1 h. The reaction was stopped with 7 µL 0.5 M EDTA, 2 µL 10% SDS, and 1.7 µL 20 mg/mL proteinase K; for single-cell CUT&Tag assays, 5 µL stop buffer was used.
CUT&Tag was performed using the Hyperactive In-Situ ChIP Library Prep Kit for Illumina (Vazyme Biotech). Embryos were incubated in 50 µL antibody buffer; 0.5 μg antibody was added and the mixture was incubated at 4℃ overnight. After washing twice with dig-wash buffer, 50 µL dig-wash buffer with 0.2 µg secondary antibody was added and the mixture was incubated at room temperature for 1 h. After washing twice with 100 µL dig-wash buffer, 1 µL pG-Tn5 and 49 µL dig-300 buffer were added, and the samples were incubated at room temperature for 1 h. Next, the samples were washed twice with 100 µL dig-wash buffer. We subsequently added 200 µL tagmentation buffer and incubated the samples at 37°C for 1 h. The reaction was stopped with 7 µL 0.5 M EDTA, 2 µL 10% SDS, and 1.7 µL 20 mg/mL proteinase K; for single-cell CUT&Tag assays, 5 µL stop buffer was used. After extraction with phenol-chloroform and ethanol precipitation, PCR was performed to amplify the libraries under the following conditions: 72°C for 3 min, 98°C for 30 s, 17 cycles of 98°C for 10 s and 60°C for 5 s, and a final extension at 72°C for 1 min with a hold at 4°C. For single-cell CUT&Tag of human embryos, CUT&Tag was performed in well of a microplate. After tagmentation, single human embryos were transferred to 200µl tubes containing 5% Proteinase K. After embryos lysis, PCR buffer and adaptors were directly added to tubes, normal PCR cycle was performed. Post-PCR clean-up was performed by adding a 1.5× volume of DNA Clean Beads (Vazyme Biotech).

value: ICM

tag: chip antibody

value: H3K18lac(Cat# PTM-1406RM)


title: HEK293T cell model, 15B


title: H3K18lac-Morula_rep2

source_name: morula

value: morula


title: H3K18lac-TE_rep2

source_name: TE

value: TE


title: HEK293T cell model, 15A


title: HEK293T cell model, 20B


title: HEK293T cell model, 4B

value: No. 4


title: H3K18lac-4-cell_rep1


title: HEK293T cell model, 15C


title: H3K18lac-ICM_rep1


title: H3K18lac-Morula_rep3


title: H3K18lac-Morula_rep1


title: HEK293T cell model, 4C


title: HEK293T cell model, 4A


title: H3K18lac-8-cell_rep2


title: PBMCs,21U

city: Nairobi

first: Kelvin

middle: Muteru

last: Kimenyi

department: Biochemistry

country: Kenya

institute: University of Nairobi

data_processing:
Raw files processed via the nf-core RNAseq pipeline (v 21.10.6), with alignment to GRCh38 (release 95) via STAR (v.2.7.10a), followed by quantification with RSEM (v 1.3.1). All other parameters were kept as default. The pipeline handled the merging raw files for samples that had been sequenced mutliple times.
Hemoglobin related genes and genes with 5 counts per million or higher in less than 13 samples were dropped
TMM Normalization was done using edgeR package.
Differential expression analysis among the asymptomatic, uninfected and febrile sample groups was performed using edgeR package while adjusting for paired samples and sequencing batch
Assembly: GRCh38 release 95
Supplementary files format and content: tab-delimited text file containing expected counts, TPM, FPKM per gene detected

extract_protocol:
RNA was extracted from PBMCs using ISOLATE II Mini Kit (Bioline) and enriched for mRNA using the NEBNextTM Poly(A) mRNA magnetic isolation module
Libraries for RNA-seq were prepared using the NEBNextTM Ultra II FS DNA library preparation kit (New England Biolabs) following manufacturers protocol

tag: group

value: Uninfected

tag: paired samples

value: PBMC

tag: sequencing pool


title: H3K18lac-8-cell_rep1


title: PBMCs,16U


title: H3K18lac-4-cell_rep2


title: H3K18lac-Zygote_rep2

source_name: zygote

value: zygote


title: PBMCs,13A

value: Asymptomatic


title: PBMCs,S_1U


title: PBMCs,S_6U


title: H3K18lac-2-cell_rep3


title: H3K18lac-2-cell_rep2


title: PBMCs,20F

value: Febrile


title: H3K18lac-TE_rep1


title: PBMCs,S_8A


title: H3K18lac-2-cell_rep1


title: PBMCs,17F


title: H3K18lac-Zygote_rep1


title: PBMCs,18U


title: RNASeq-L2C-H3K18R_rep1

data_processing:
For RNA-seq analysis of embryos, FastQC was performed for Illumina reads. We used Trim Galore software to discard low-quality reads, trim adaptor sequences, and eliminate poor-quality bases. Next, we downloaded the mouse reference genome (genome assembly: mm39) from the UCSC database and used HISAT2 software for read alignment. The gene-level quantification approach was used to aggregate raw counts of mapped reads using the featureCounts tool. Gene expression was quantified by calculating the normalized fragments per kilobase of transcript per million mapped reads (FPKM) value. Next, we used the R package DESeq2 for differential gene expression analysis.
Assembly: mm39

source_name: late 2-cell

extract_protocol:
5 embryos were used per group, and three replicates were performed for each group. Embryos were washed three times in 0.5% BSA-PBS solution. cDNA was amplified using the Phusion Hot Start II High-Fidelity PCR Master Mix (Thermo Fisher).
Library preparation was performed using the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs) according to the manufacturer’s instructions.

value: late 2-cell

value: treat with H3K18R


title: RNASeq-L2C-G+N_rep2

value: treat with GNE140 & NMN


title: PBMCs,S_5U


title: PBMCs,17A


title: RNASeq-L2C-WT_rep1

value: WT


title: RNASeq-L2C-G+N-L_rep1

value: treat with GNE140 & NMN, lacking NaLac


title: PBMCs,S_9F


title: RNASeq-L2C-WT_rep2


title: RNASeq-L2C-G+N-L_rep2


title: PBMCs,4U


title: PBMCs,6F


title: PBMCs,S_7F


title: PBMCs,8U


title: PBMCs,S_4U


title: RNASeq-L2C-G+N-L+A_rep2

value: treat with GNE140 & NMN, CoA, lacking NaLac


title: PBMCs,20A


title: PBMCs,4F


title: RNASeq-L2C-H3K18R_rep2


title: RNASeq-E2C-G+N-L_rep1

source_name: early 2-cell

value: early 2-cell


title: RNASeq-E2C-G+N_rep2

value: treat with GNE140


title: RNASeq-E2C-G+N_rep1


title: PBMCs,18F


title: PBMCs,21F


title: RNASeq-L2C-G+N-L+A_rep1


title: Brain, young vehicle-treated mouse, rep4

city: Fort Collins

first: Alyssa

middle: N

last: Cavalier

state: CO

address: 1582 Campus Delivery, Moby Reception

department: Health and Exercise Science

institute: Colorado State University

data_processing:
Adapters trimmed & file QC by Fastp
Reads aligned and genes counted with STAR
Differential expression analyzed with DESeq2
Assembly: mm10
Supplementary files format and content: normalized-apiMS-reads.csv

source_name: postmortem whole brain

growth_protocol: Young and old C57BL/6 mice given 0.5mg/mL in 0,2% carboxymethylcellulose drinking water or 0.2% carboxymethylcellulose vehicle water

extract_protocol:
RNA was isolated using Zymo Direct-zol RNA kit
polyA RNA libraries for RNA-seq were prepared using using sera-mag magnetic oligo dT beads (ThermoFisher) and Illumina TruSeq kits.

value: 0.2% carboxymethylcellulose vehicle drinking water

tag: Sex

value: Male

tag: strain

value: 6 months

value: postmortem whole brain


title: PBMCs,13F


title: Brain, young vehicle-treated mouse, rep3


title: Brain, young vehicle-treated mouse, rep2


title: RNASeq-L2C-G+N_rep1


title: PBMCs,16F


title: Brain, young apigenin-treated mouse, rep4

value: 0.5mg/mL apigenin


title: PBMCs,11F

value: PBMC


title: PBMCs,S_3U

value: Uninfected


title: PBMCs,11U


title: Brain, young apigenin-treated mouse, rep3


title: PBMCs,7A

value: Asymptomatic


title: Brain, young apigenin-treated mouse, rep2


title: PBMCs,22F

value: Febrile


title: Brain, young apigenin-treated mouse, rep1


title: Brain, old vehicle-treated mouse, rep5

value: 27 months


title: PBMCs,10F


title: RNASeq-E2C-G+N-L_rep2


title: PBMCs,10A


title: Brain, old vehicle-treated mouse, rep4


title: PBMCs,22A


title: Brain, old vehicle-treated mouse, rep3


title: Brain, old vehicle-treated mouse, rep2


title: PBMCs,1F


title: PBMCs,1U


title: PBMCs,S_2U


title: Brain, old apigenin-treated mouse, rep5


title: Brain, young vehicle-treated mouse, rep1


title: Brain, old vehicle-treated mouse, rep1


title: PBMCs,3U


title: Brain, old apigenin-treated mouse, rep4


title: PBMCs,19F


title: PBMCs,19A


title: Brain, old apigenin-treated mouse, rep3


title: Brain, old apigenin-treated mouse, rep1


title: Brain, old apigenin-treated mouse, rep2


title: PBMCs,15F


title: PBMCs,14F


title: PBMCs,14A


title: PBMCs,12F


title: PBMCs,15A


title: Fibroblast in vitro IL-17A + TNFa, control

city: San Diego

first: Kellen

last: Cavagnero

address: 9500 Gilman Dr

institute: Univeristy of California, San Diego

data_processing:
Cell Ranger (10X Genomics) with default parameters was used to perform sample demultiplexing, barcode processing, alignment to the mm10 reference genome, and gene counting
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: skin

extract_protocol:
Single-cell suspensions generated from mouse skin or cultured fibroblasts
10X Genomics 3’ V3.1

value: skin

value: fibroblasts

value: wild type

value: vehicle

tag: in vitro or in vivo

value: in vitro


title: PBMCs,2F


title: PBMCs,8F


title: Skin, Topical imiquimod, control

value: all

value: in vivo


title: Skin, Intradermal S. aureus infection, infected

value: staph aureus


title: PBMCs,2A


title: Skin, Topical imiquimod, imq

value: imiquimod


title: Neut, FB CM, siScramble, IL-17A+TNFa

description:
IL-17A/TNF stimulated FB CM
KC54.csv

data_processing:
Alignment to reference genome using STAR
Raw counts table generated using FeatureCounts
Assembly: mm10 for mouse; hg38 for human
Supplementary files format and content: CSV files with raw counts values for each sample

source_name: bone marrow

extract_protocol:
ThermoFisher PureLink RNA Kit
Illumina stranded mRNA or Illumina total RNA prep (ribodepletion)

value: bone marrow

tag: cell line

value: neutrophil

value: Wild type

value: FB CM, siScramble, IL-17A+TNFa

tag: protocol

value: Illumina total RNA prep (ribodepletion)


title: Neut, FB CM, siNFKBIZ, IL-17A+TNFa

description:
IL-17A/TNF stimulated w NFKBIZ KD FB CM
KC54.csv

tag: cell type

tag: genotype

value: FB CM, siNFKBIZ, IL-17A+TNFa


title: PBMCs,6A

value: Asymptomatic

value: PBMC


title: PBMCs,7F

value: Febrile


title: PBMCs,23F


title: PBMCs,23A


title: Neut, FB CM, siScramble, Vehicle

description:
Unstimulated FB CM
KC54.csv

value: FB CM, siScramble, Vehicle


title: Neut, siScramble, IL-17A+TNFa

description:
Control media + IL-17A/TNFa
KC54.csv

value: siScramble, IL-17A+TNFa


title: Neut, siScramble, Vehicle

description:
Control media
KC54.csv

value: siScramble, Vehicle


title: Fibroblast in vitro IL-17A + TNFa, stimulated

value: skin

value: fibroblasts

value: wild type

value: in vitro


title: 3T3-L1, TNFa + siNFKBIZ

description:
tnf_sinfkbiz
KC43.csv

value: Fibroblast

value: TNFa + siNFKBIZ

value: Illumina stranded mRNA


title: 3T3-L1, IL-17A+TNFa + siNFKBIZ

description:
tnf_il17_sinfkbiz
KC43.csv

value: Wild type

value: IL-17A+TNFa + siNFKBIZ


title: 3T3-L1, TNFa + siScramble

description:
tnf
KC43.csv

value: TNFa + siScramble


title: 3T3-L1, Vehicle + siScramble

description:
null
KC43.csv

value: Vehicle + siScramble


title: 3T3-L1, IL-17A+TNFa + siScramble

description:
tnf_il17
KC43.csv

value: IL-17A+TNFa + siScramble


title: 3T3-L1, Adipogenesis

description:
diff
KC34.csv

value: Adipogenesis


title: MDFB, IL-17A+TNFa

description:
17_TNF
KC61.csv


title: 3T3-L1, TNFa

description:
tnfa
KC34.csv

value: TNFa


title: 3T3-L1, IL-17A+TNFa

description:
il17a_tnfa
KC34.csv


title: 3T3-L1, IL-17A

description:
il17a
KC34.csv


title: MDFB, Vehicle

description:
KC61
KC61.csv

value: Vehicle


title: 3T3-L1, Vehicle

description:
null
KC34.csv


title: Skin, Intradermal S. aureus infection, control

value: all

value: vehicle

value: in vivo


title: Mouse Skin, SNX-5422+CEES-1 (17R)

city: Vestavia Hills

first: Ritesh

last: Srivastava

state: Alabama

address: 1670 University Blvd.

department: Dermatology

institute: University of Alabama at Birmingham

data_processing:
Illumina bcl2fastq version 2.18.0.12 was used to convert basecalls to FASTQ files
Trim Galore (version 0.6.7) trimmed adapter primers from raw sequences using parameters --paired --trim-n --trim1 --nextseq20
Trimmed sequences were aligned with STAR (version 2.7.10a_alpha_220601) using parameters --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All
Transcript abundances were calculated from the alignment files with HTSeq-count (version 2.0.2) using parameters -r pos -t exon -i gene_id -a 10 -s no -f bam
Assembly: Gencode GRCm39 Release M26
Supplementary files format and content: Tab-delimited Excel file containing Ensembl ID#s and raw counts for each gene in each sample

source_name: Mouse whole Skin

extract_protocol: For RNAseq analysis total RNA was extracted from murine skin using Aurum total RNA extraction kit as per manufacturer protocol (BioRad, Hercules, CA). Ribosomal RNA was removed from each RNA samples using Ribo-Zero Gold rRNA Removal kit (Illumina, San Diego, CA).

treatment_protocol: The anesthetized animals were topically treated with either ethanol-diluted PAO (100 µg/mouse, equivalent to 25 µg/cm2) or ethanol-dilute CEES (2 mg/mouse, equivalent to 500 µg/cm2). 30 µL volume of diluted PAO or CEES were applied at 2X2 cm2 area on the dorsal skin. Control mice were identically treated with vehicle (ethanol) alone. For defining therapeutic efficacy of HSP90 inhibitor, a 20mg/kg dose of SNX-5422 was administered topically to PAO or CEES challenged animals. SNX-5422 was administered at 15 minutes post PAO or CEES exposure on the area of injury.

value: Mouse whole Skin

value: SKH-1 (hairless)

value: Male

tag: time-point


title: Mouse Skin, CEES-3 (15R)

tag: tissue

value: CEES


title: Mouse Skin, SNX-5422+CEES-1 (18R)

tag: treatment


title: Mouse Skin, CEES-1 (13R)


title: Mouse Skin, SNX-5422+CEES-1 (16R)


title: Mouse Skin, CEES-2 (14R)


title: Mouse Skin, SNX-5422+PAO-3, (9R)


title: Mouse Skin, SNX-5422+PAO-2, (8R)


title: 3T3-L1, IL-17A + siScramble

description:
il17
KC43.csv

value: Fibroblast

value: IL-17A + siScramble

value: in vitro


title: Mouse Skin, SNX-5422+PAO-1, (7R)


title: 3T3-L1, IL-17A + siNFKBIZ

description:
il17_sinfkbiz
KC43.csv

value: Wild type

value: IL-17A + siNFKBIZ

value: Illumina stranded mRNA


title: Mouse Skin, PAO-3, (6R)

value: PAO


title: Mouse Skin, PAO-2, (5R)


title: Mouse Skin, PAO-1, (4R)


title: electroporation GFP positive

city: Suita

first: Tomoaki

last: Hara

state: Osaka

address: Yamadaoka 2-2

department: Graduate School of Medicine

country: Japan

institute: Osaka university

data_processing:
Sequencing was performed on NovaSeq6000 platform in a 151-base single-end mode.
Illumina RTA 1.18.64 software was used for base calling.
Generated reads were mapped to the human (GRCh38) reference genome using Hisat2.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff v2.2.1 with parameter -max-bundle-frags 50000000.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

extract_protocol:
RNA was extracted according to protocol using ISOGEN LS (NIPPON Gene).
The reverse transcription to cDNA was performed using GenNext RamDA-seq Single Cell Kit and the library was prepared using Nextera XT DNA Library Preparation Kit.


title: lipofection GFP positive


title: electroporation GFP negative


title: CBC1, CD34pos HSCs, scRNAseq

city: Barcelona

first: Alfonso

last: Saera-Vila

address: Dr. Trueta 179

country: Spain

institute: Sequientia Biotech

description: 10x Chromium

data_processing:
Barcode processing and gene counting was performed using UMItools (V1.0.1)
Reads were mapped with STAR V2.7.9a
Assembly: GRCh38
Supplementary files format and content: Matrix files

source_name: Cord blood (CB)

extract_protocol:
This process was performed following 10x genomics recommended guidelines
Single Cell 3′ GEM, Library and Gel Bead Kit V3 (10× Genomics, Cat#PN-1000075)

value: Cord blood (CB)

value: Human Hematopoietic Stem Cell Populations from cord blood

tag: cell type (sorted)

value: 18LinnegCD34posCD133pos FACS sorted


title: CBC3, CD34neg HSCs, scRNAseq

description: 10x Chromium

value: 18LinnegCD34negCD133pos FACS sorted


title: ventromedial hypothalamus, high workload, ZT21, rep2

city: La Jolla

first: Laura

last: van Rosmalen

address: 10010 N Torrey Pines Rd

department: RBIO-P

institute: Salk Institute for Biological Studies

description:
VMH_H_ZT21_X28
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

data_processing:
Sequencing quality was assessed using FastQC, version 0.11.9
Cutadapt v4.1 was used to trim adapter sequences
Sequence reads were aligned to the Mus musculus (house mouse) genome GRCm38 (mm10) and counted per gene using STAR aligner v2.7.10a
Gene counts were filtered for low counts and normalized per tissue using DESeq2 v1.34.0
TES_L_ZT21_X27 was removed from the analysis because it was an extreme outlier
Assembly: mm10
Supplementary files format and content: csv file includes raw counts for each sample
Supplementary files format and content: csv file includes normalized counts for each sample

source_name: ventromedial hypothalamus

extract_protocol:
Total RNA was extracted from neural and peripheral tissues using TRIzol reagent according to the manufacturer’s instructions. 300ng of total RNA was used for the construction of sequencing libraries
Libraries were prepared using Illumina’s TruSeq Stranded mRNA (PolyA+) kit according to the manufacturer’s instructions

value: ventromedial hypothalamus

value: CBA/CaJ

value: male

value: high workload

tag: zeitgeber time


title: Mouse Skin, Control-2, (2R)

value: Mouse whole Skin

value: SKH-1 (hairless)

value: Male

value: vehilce (ethanol)


title: ventromedial hypothalamus, high workload, ZT21, rep1

description:
VMH_H_ZT21_X18
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: R24_EGF, 24 hr. RNA-Seq, rep 2

first: Shankar

last: Subramaniam

address: 3223 Voigt Dr

department: Bioengineering

institute: University of California San Diego

data_processing:
Quality testing was performed using FastQC and summarized for downstream analysis using multiQC. Trimming for Illumina Universal adaptors was performed using TrimGalore v0.6.6.  RNA read mapping and alignment was performed to human reference genome GrCh38.p13 using RSubread. The mapped reads were summarized to gene level using featureCounts and annotation corresponding to the reference genome.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

extract_protocol:
RNA extraction was done using a RNeasy Mini Kit (Qiagen, catalog no. 74104), including on-column DNase digestion using RNase-free DNase (Qiagen, catalog no. 79253).
RNA sequencing libraries were prepared with Kapa RNA mRNA HyperPrep kit (Kapa Biosystems, catalog no. KR1352) according to the manufacturer's protocol. The libraries were validated with the Bioanalyzer DNA High Sensitivity Kit (Agilent, catalog no. 5067-4626) and quantified with Qubit.

value: Breast cancer epithelial cells

tag: time

value: 24 hr


title: lipofection GFP negative


title: R24_HRG, 24 hr. RNA-Seq, rep 1


title: Mouse Skin, Control-1, (1R)


title: Mouse Skin, Control-3, (3R)


title: R24_EGF, 24 hr. RNA-Seq, rep 1


title: ventromedial hypothalamus, high workload, ZT17, rep2

description:
VMH_H_ZT17_X24
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: ventromedial hypothalamus, high workload, ZT09, rep1

description:
VMH_H_ZT09_X15
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: ventromedial hypothalamus, high workload, ZT17, rep1

description:
VMH_H_ZT17_X16
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: R24_HRG, 24 hr. RNA-Seq, rep 2


title: ventromedial hypothalamus, high workload, ZT13, rep1

description:
VMH_H_ZT13_X2
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: ventromedial hypothalamus, high workload, ZT13, rep2

description:
VMH_H_ZT13_X8
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: R12_HRG, 12 hr. RNA-Seq, rep 2

value: 12 hr


title: R24_Con, 24 hr. RNA-Seq, rep 2


title: R12_EGF, 12 hr. RNA-Seq, rep 1


title: R12_EGF, 12 hr. RNA-Seq, rep 2


title: ventromedial hypothalamus, high workload, ZT05, rep2

description:
VMH_H_ZT05_X3
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: ventromedial hypothalamus, high workload, ZT09, rep2

description:
VMH_H_ZT09_X9
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: ventromedial hypothalamus, high workload, ZT05, rep1

description:
VMH_H_ZT05_X13
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: R1_EGF, 1 hr. RNA-Seq, rep 1

value: 1 hr


title: R1_EGF, 1 hr. RNA-Seq, rep 2


title: R24_Con, 24 hr. RNA-Seq, rep 1


title: R12_HRG, 12 hr. RNA-Seq, rep 1


title: ventromedial hypothalamus, low workload, ZT17, rep1

description:
VMH_L_ZT17_X19
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

value: low workload


title: ventromedial hypothalamus, high workload, ZT01, rep2

description:
VMH_H_ZT01_X7
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: ventromedial hypothalamus, low workload, ZT21, rep2

description:
VMH_L_ZT21_X27
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: R1_HRG, 1 hr. RNA-Seq, rep 2


title: R12_Con, 12 hr. RNA-Seq, rep 1


title: ventromedial hypothalamus, low workload, ZT21, rep1

description:
VMH_L_ZT21_X21
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: R0_baseline, 0 hr. RNA-Seq, rep 1

value: 0 hr


title: ventromedial hypothalamus, low workload, ZT17, rep2

description:
VMH_L_ZT17_X25
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: ventromedial hypothalamus, low workload, ZT13, rep1

description:
VMH_L_ZT13_X11
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: R0_baseline, 0 hr. RNA-Seq, rep 2


title: ventromedial hypothalamus, low workload, ZT13, rep2

description:
VMH_L_ZT13_X5
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: R1_HRG, 1 hr. RNA-Seq, rep 1


title: R1_Con, 1 hr. RNA-Seq, rep 2


title: ventromedial hypothalamus, low workload, ZT09, rep1

description:
VMH_L_ZT09_X23
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: S24_HRG, 24 hr. RNA-Seq, rep 2


title: ventromedial hypothalamus, low workload, ZT05, rep2

description:
VMH_L_ZT05_X26
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: testis, high workload, ZT21, rep1

description:
TES_H_ZT21_X18
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

source_name: testis

value: testis


title: R1_Con, 1 hr. RNA-Seq, rep 1


title: ventromedial hypothalamus, high workload, ZT01, rep1

description:
VMH_H_ZT01_X1
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: R12_Con, 12 hr. RNA-Seq, rep 2


title: S24_EGF, 24 hr. RNA-Seq, rep 2


title: ventromedial hypothalamus, low workload, ZT01, rep1

description:
VMH_L_ZT01_X20
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: testis, high workload, ZT21, rep2

description:
TES_H_ZT21_X28
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: testis, high workload, ZT17, rep2

description:
TES_H_ZT17_X24
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: S24_HRG, 24 hr. RNA-Seq, rep 1


title: ventromedial hypothalamus, low workload, ZT05, rep1

description:
VMH_L_ZT05_X12
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: S24_Con, 24 hr. RNA-Seq, rep 2


title: testis, high workload, ZT17, rep1

description:
TES_H_ZT17_X16
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: S24_Con, 24 hr. RNA-Seq, rep 1


title: testis, high workload, ZT13, rep2

description:
TES_H_ZT13_X8
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: testis, high workload, ZT13, rep1

description:
TES_H_ZT13_X2
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: S12_EGF, 12 hr. RNA-Seq, rep 1


title: testis, high workload, ZT05, rep2

description:
TES_H_ZT05_X3
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: S24_EGF, 24 hr. RNA-Seq, rep 1


title: S12_Con, 12 hr. RNA-Seq, rep 1


title: testis, high workload, ZT01, rep2

description:
TES_H_ZT01_X7
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: testis, high workload, ZT09, rep2

description:
TES_H_ZT09_X9
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: S12_HRG, 12 hr. RNA-Seq, rep 2


title: testis, high workload, ZT09, rep1

description:
TES_H_ZT09_X15
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: testis, high workload, ZT01, rep1

description:
TES_H_ZT01_X1
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: S1_HRG, 1 hr. RNA-Seq, rep 2


title: testis, low workload, ZT21, rep1

description:
TES_L_ZT21_X21
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: S12_Con, 12 hr. RNA-Seq, rep 2


title: S1_EGF, 1 hr. RNA-Seq, rep 2


title: testis, low workload, ZT17, rep2

description:
TES_L_ZT17_X25
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: testis, high workload, ZT05, rep1

description:
TES_H_ZT05_X13
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: S1_EGF, 1 hr. RNA-Seq, rep 1


title: S12_EGF, 12 hr. RNA-Seq, rep 2


title: S1_Con, 1 hr. RNA-Seq, rep 2


title: testis, low workload, ZT17, rep1

description:
TES_L_ZT17_X19
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: testis, low workload, ZT21, rep2

description:
outlier
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: S12_HRG, 12 hr. RNA-Seq, rep 1


title: S0_Baseline, 0 hr. RNA-Seq, rep 2


title: testis, low workload, ZT13, rep1

description:
TES_L_ZT13_X11
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: S0_Baseline, 0 hr. RNA-Seq, rep 1


title: testis, low workload, ZT13, rep2

description:
TES_L_ZT13_X5
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: S1_Con, 1 hr. RNA-Seq, rep 1


title: R24_EGF, 24 hr, ATAC-Seq, rep 1

data_processing:
The sequenced fastq files (using Fastqc) indicated Nextera adaptor content and were subsequently processed and cleaned using TrimGalore (v.0.6.6). The cleaned sequences were then mapped to the most current version of NCBI reference human genome, at the time of analysis- hg38 (patch 13) using BBMap, available through the BBTools suite. The mapped reads were then sorted and indexed using SAM tools to allow for the use of Genrich peak caller. In addition to peak calling, Genrich was used on the sorted files, to remove mitochondrial reads and reads mapping to ENCODE black-listed regions.
Assembly: GRCh38.p13
Supplementary files format and content: Genrich peak caller narrow peak files

extract_protocol:
Briefly, 50,000 single cells were lysed using cell lysis buffer (0.1% NP-40, 0.1% Tween-20, and 0.01% Digitonin in resuspension buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, and 3 mM MgCl2 in water) for 3 min on ice.  After washing using resuspension buffer containing 0.1% Tween-20, cells were centrifuged at 500 g for 10 min at 4°C. The transposition reaction was performed using Tagment DNA enzyme and buffer (Illumina, catalog no. 20034197) at 37°C for 30 min in an Eppendorf ThermoMixer (1,000 rpm). DNA was purified using the MinElute Reaction Cleanup Kit (Qiagen, catalog no. 28204). Libraries were prepared by amplifying DNA for 5-9 cycles using DNA/RNA UD Indexes Set A (Illumina, catalog no. 20027213) and NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs, catalog no. M0541S). AMPure XP bead purification (Beckman Coulter, catalog no. A63880) was used for the PCR product cleanup.
Libraries were prepared by amplifying DNA for 5-9 cycles using DNA/RNA UD Indexes Set A (Illumina, catalog no. 20027213) and NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs, catalog no. M0541S). AMPure XP bead purification (Beckman Coulter, catalog no. A63880) was used for the PCR product cleanup. The libraries were validated with Agilent Bioanalyzer DNA High Sensitivity Kit and quantified with qPCR at the IGC


title: R24_EGF, 24 hr, ATAC-Seq, rep 2


title: testis, low workload, ZT05, rep2

description:
TES_L_ZT05_X26
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: S1_HRG, 1 hr. RNA-Seq, rep 1


title: R24_HRG, 24 hr, ATAC-Seq, rep 1


title: testis, low workload, ZT01, rep2

description:
TES_L_ZT01_X20
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: R24_Con, 24 hr, ATAC-Seq, rep 2


title: R24_Con, 24 hr, ATAC-Seq, rep 1


title: suprachiasmatic nucleus, high workload, ZT21, rep2

description:
SCN_H_ZT21_X28
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

source_name: suprachiasmatic nucleus

value: suprachiasmatic nucleus


title: testis, low workload, ZT01, rep1

description:
TES_L_ZT01_X10
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv

source_name: CBA/CaJ


title: suprachiasmatic nucleus, high workload, ZT21, rep1

description:
SCN_H_ZT21_X18
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: ventromedial hypothalamus, low workload, ZT09, rep2

description:
VMH_L_ZT09_X29
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: R12_EGF, 12 hr, ATAC-Seq, rep 1


title: suprachiasmatic nucleus, high workload, ZT17, rep2

description:
SCN_H_ZT17_X24
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: R12_HRG, 12 hr, ATAC-Seq, rep 2


title: suprachiasmatic nucleus, high workload, ZT17, rep1

description:
SCN_H_ZT17_X16
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: R12_HRG, 12 hr, ATAC-Seq, rep 1


title: suprachiasmatic nucleus, high workload, ZT13, rep2

description:
SCN_H_ZT13_X8
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: suprachiasmatic nucleus, high workload, ZT13, rep1

description:
SCN_H_ZT13_X2
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: R12_Con, 12 hr, ATAC-Seq, rep 2


title: testis, low workload, ZT09, rep2

description:
TES_L_ZT09_X29
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: suprachiasmatic nucleus, high workload, ZT09, rep2

description:
SCN_H_ZT09_X9
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: R12_Con, 12 hr, ATAC-Seq, rep 1


title: R1_EGF, 1 hr, ATAC-Seq, rep 2


title: suprachiasmatic nucleus, high workload, ZT09, rep1

description:
SCN_H_ZT09_X15
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: testis, low workload, ZT09, rep1

description:
TES_L_ZT09_X23
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: suprachiasmatic nucleus, high workload, ZT05, rep2

description:
SCN_H_ZT05_X3
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: R1_HRG, 1 hr, ATAC-Seq, rep 2


title: testis, low workload, ZT05, rep1

description:
TES_L_ZT05_X12
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: R24_HRG, 24 hr, ATAC-Seq, rep 2


title: R1_HRG, 1 hr, ATAC-Seq, rep 1


title: suprachiasmatic nucleus, high workload, ZT01, rep2

description:
SCN_H_ZT01_X7
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: R1_Con, 1 hr, ATAC-Seq, rep 2


title: suprachiasmatic nucleus, high workload, ZT05, rep1

description:
SCN_H_ZT05_X13
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: R1_Con, 1 hr, ATAC-Seq, rep 1


title: suprachiasmatic nucleus, low workload, ZT21, rep1

description:
SCN_L_ZT21_X27
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: R12_EGF, 12 hr, ATAC-Seq, rep 2


title: suprachiasmatic nucleus, high workload, ZT01, rep1

description:
SCN_H_ZT01_X1
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: suprachiasmatic nucleus, low workload, ZT17, rep2

description:
SCN_L_ZT17_X25
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: R0_baseline, 0 hr, ATAC-Seq, rep 1


title: suprachiasmatic nucleus, low workload, ZT17, rep1

description:
SCN_L_ZT17_X19
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: suprachiasmatic nucleus, low workload, ZT13, rep2

description:
SCN_L_ZT13_X5
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: R1_EGF, 1 hr, ATAC-Seq, rep 1


title: S24_HRG, 24 hr, ATAC-Seq, rep 2


title: suprachiasmatic nucleus, low workload, ZT09, rep2

description:
SCN_L_ZT09_X29
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: suprachiasmatic nucleus, low workload, ZT09, rep1

description:
SCN_L_ZT09_X23
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv


title: S24_HRG, 24 hr, ATAC-Seq, rep 1


title: S24_Con, 24 hr, ATAC-Seq, rep 2


title: suprachiasmatic nucleus, low workload, ZT05, rep2

description:
SCN_L_ZT05_X26
nocturnal_diurnal_mouse_tissue_expression_raw_counts.csv
nocturnal_diurnal_mouse_tissue_expression_normalized_counts.csv