title: mm_aorta_ppe_lenvatinib_4

city: Munich

first: Lars

last: Maegdefessel

address: Ismaninger Strasse 22

institute: Technical University of Munich

hyb_protocol: The MTA procedure was performed by the Center for Molecular Medicine (CMM) core facility at Karolinska Institutet, Stockholm, Sweden, according to the manufacturer’s protocol.

data_processing:
Transcriptome Analysis Console v4.0.1.36 (Affymetrix) in accordance with the manufacturer’s default settings and SST-RMA summarization method
annotation=MTA-1_0.r3.na36.mm10.a1.transcript.csv

source_name: abdominal aorta

growth_protocol: AAAs (PPE model) were induced in 10-week-old ApoE–/– male mice (Charles River Laboratories).

extract_protocol: Approximately 1mm long pieces of mouse aortic tissue were homogenized in Qiazol using Multi-Gen probes (Pro-Scientific, Stockholm, Sweden). RNA extraction was performed using the Qiagen miRNeasy Micro Kit (Qiagen, Sollentuna, Sweden) following the manufacturer’s protocol. Total RNA concentration was assessed using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA). Samples from n=6 PPE, n=7 PPE+Lenvatinib, and n=5 control aortas were included with RIN numbers between 5.7-9.8.

treatment_protocol: Lenvatinib (5 mg/kg in DMSO) was administered daily through oral gavage days 7-24. Mice were sacrificed on day 28.

value: abdominal aorta

tag: gender

value: male

value: ppe+lenvatinib


title: mm_aorta_ppe_lenvatinib_6

status: Public on Mar 07 2023

type: RNA

country: Germany

scan_protocol: The MTA procedure was performed by the Center for Molecular Medicine (CMM) core facility at Karolinska Institutet, Stockholm, Sweden, according to the manufacturer’s protocol.

label: biotin

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: treatment


title: mm_aorta_ppe_lenvatinib_7

label_protocol: The MTA procedure was performed by the Center for Molecular Medicine (CMM) core facility at Karolinska Institutet, Stockholm, Sweden, according to the manufacturer’s protocol.


title: mm_aorta_ppe_lenvatinib_5


title: mm_aorta_ppe_lenvatinib_2


title: mm_aorta_ppe_lenvatinib_3


title: DF1637_V4

type: SRA

city: Boston

first: Jean

last: Zhao

state: MA

address: 450 Brookline Ave

country: USA

institute: Dana Farber Cancer Institute

description:
PDX, vehicle control, biol rep 4
Column names: gene_id,gene_name,DF1510_V1,DF1510_V2,DF1510_V3,DF1510_V4,DF1510_AZD1,DF1510_AZD2,DF1510_AZD3,DF1510_AZD4,DF1613_V1,DF1613_V2,DF1613_V3,DF1613_V4,DF1613_AZD1,DF1613_AZD2,DF1613_AZD3,DF1613_AZD4,DF1637_V1,DF1637_V2,DF1637_V3,DF1637_V4,DF1637_AZD1,DF1637_AZD2,DF1637_AZD3,DF1637_AZD4,DF1732_V1,DF1732_V2,DF1732_V3,DF1732_V4,DF1732_AZD1,DF1732_AZD2,DF1732_AZD3,DF1732_AZD4,DF1807_V1,DF1807_V2,DF1807_V3,DF1807_V4,DF1807_AZD1,DF1807_AZD2,DF1807_AZD3,DF1807_AZD4

library_source: transcriptomic

data_processing:
For mouse samples, data processing used the ampliSeqRNA plugin v5.12.0.1 available inside the Ion Torrent suite 5.12 for Ion torrent sequencing platform with default settings for all steps
For human PDX samples, RNA-Seq was performed by Novogene. Original image data file was transformed to sequenced reads by CASAVA base recognition. Alignments were performed with HISAT2 to reference genome.
Assembly: Mouse 4.6K: WG00278_Reference, (WG00278_Designed2.bed); Mouse 3.8K , Dana_Farbers_081215_Reference.fasta (Dana_Farbers_081215_Designed.bed); Human: hg38
Supplementary files format and content: xls: Tab-separated values and matrix file

organism: Homo sapiens

source_name: Bulk tumor

extract_protocol:
Total RNA was extracted using RNeasy Plus Mini Kit (QIAGEN, # 74134).
RNA libraries for mouse samples were prepared using Ampliseq Library Prep Kit following manufacturer's protocols for targeted amplicon amplification
For mouse samples, other: Ion AmpliSeq Panels Mouse  3.8K (PP tumors_AZD6482-PD1) and 4.6K (all other mouse data sets) genes
For PDX samples, RNA-Seq

value: Bulk tumor

tag: cell line

value: PDX DFBC-1637

tag: cell type

value: Breast cancer

value: Breast cancer PDX treated with vehicle control in vivo


title: mm_aorta_ppe_3

value: ppe


title: mm_aorta_ppe_5


title: mm_aorta_ppe_4


title: mm_aorta_ppe_1


title: DF1637_V3

description:
PDX, vehicle control, biol rep 3
Column names: gene_id,gene_name,DF1510_V1,DF1510_V2,DF1510_V3,DF1510_V4,DF1510_AZD1,DF1510_AZD2,DF1510_AZD3,DF1510_AZD4,DF1613_V1,DF1613_V2,DF1613_V3,DF1613_V4,DF1613_AZD1,DF1613_AZD2,DF1613_AZD3,DF1613_AZD4,DF1637_V1,DF1637_V2,DF1637_V3,DF1637_V4,DF1637_AZD1,DF1637_AZD2,DF1637_AZD3,DF1637_AZD4,DF1732_V1,DF1732_V2,DF1732_V3,DF1732_V4,DF1732_AZD1,DF1732_AZD2,DF1732_AZD3,DF1732_AZD4,DF1807_V1,DF1807_V2,DF1807_V3,DF1807_V4,DF1807_AZD1,DF1807_AZD2,DF1807_AZD3,DF1807_AZD4


title: DF1637_V1

description:
PDX, vehicle control, biol rep 1
Column names: gene_id,gene_name,DF1510_V1,DF1510_V2,DF1510_V3,DF1510_V4,DF1510_AZD1,DF1510_AZD2,DF1510_AZD3,DF1510_AZD4,DF1613_V1,DF1613_V2,DF1613_V3,DF1613_V4,DF1613_AZD1,DF1613_AZD2,DF1613_AZD3,DF1613_AZD4,DF1637_V1,DF1637_V2,DF1637_V3,DF1637_V4,DF1637_AZD1,DF1637_AZD2,DF1637_AZD3,DF1637_AZD4,DF1732_V1,DF1732_V2,DF1732_V3,DF1732_V4,DF1732_AZD1,DF1732_AZD2,DF1732_AZD3,DF1732_AZD4,DF1807_V1,DF1807_V2,DF1807_V3,DF1807_V4,DF1807_AZD1,DF1807_AZD2,DF1807_AZD3,DF1807_AZD4


title: DF1637_AZD2

description:
PDX, AZD6482, biol rep 2
Column names: gene_id,gene_name,DF1510_V1,DF1510_V2,DF1510_V3,DF1510_V4,DF1510_AZD1,DF1510_AZD2,DF1510_AZD3,DF1510_AZD4,DF1613_V1,DF1613_V2,DF1613_V3,DF1613_V4,DF1613_AZD1,DF1613_AZD2,DF1613_AZD3,DF1613_AZD4,DF1637_V1,DF1637_V2,DF1637_V3,DF1637_V4,DF1637_AZD1,DF1637_AZD2,DF1637_AZD3,DF1637_AZD4,DF1732_V1,DF1732_V2,DF1732_V3,DF1732_V4,DF1732_AZD1,DF1732_AZD2,DF1732_AZD3,DF1732_AZD4,DF1807_V1,DF1807_V2,DF1807_V3,DF1807_V4,DF1807_AZD1,DF1807_AZD2,DF1807_AZD3,DF1807_AZD4

value: Breast cancer PDX treated with AZD6482 in vivo


title: DF1637_AZD1

description:
PDX, AZD6482, biol rep 1
Column names: gene_id,gene_name,DF1510_V1,DF1510_V2,DF1510_V3,DF1510_V4,DF1510_AZD1,DF1510_AZD2,DF1510_AZD3,DF1510_AZD4,DF1613_V1,DF1613_V2,DF1613_V3,DF1613_V4,DF1613_AZD1,DF1613_AZD2,DF1613_AZD3,DF1613_AZD4,DF1637_V1,DF1637_V2,DF1637_V3,DF1637_V4,DF1637_AZD1,DF1637_AZD2,DF1637_AZD3,DF1637_AZD4,DF1732_V1,DF1732_V2,DF1732_V3,DF1732_V4,DF1732_AZD1,DF1732_AZD2,DF1732_AZD3,DF1732_AZD4,DF1807_V1,DF1807_V2,DF1807_V3,DF1807_V4,DF1807_AZD1,DF1807_AZD2,DF1807_AZD3,DF1807_AZD4


title: mm_aorta_control_3


title: mm_aorta_ppe_2


title: mm_aorta_ppe_6


title: DF1613_AZD4

description:
PDX, AZD6482, biol rep 4
Column names: gene_id,gene_name,DF1510_V1,DF1510_V2,DF1510_V3,DF1510_V4,DF1510_AZD1,DF1510_AZD2,DF1510_AZD3,DF1510_AZD4,DF1613_V1,DF1613_V2,DF1613_V3,DF1613_V4,DF1613_AZD1,DF1613_AZD2,DF1613_AZD3,DF1613_AZD4,DF1637_V1,DF1637_V2,DF1637_V3,DF1637_V4,DF1637_AZD1,DF1637_AZD2,DF1637_AZD3,DF1637_AZD4,DF1732_V1,DF1732_V2,DF1732_V3,DF1732_V4,DF1732_AZD1,DF1732_AZD2,DF1732_AZD3,DF1732_AZD4,DF1807_V1,DF1807_V2,DF1807_V3,DF1807_V4,DF1807_AZD1,DF1807_AZD2,DF1807_AZD3,DF1807_AZD4

value: PDX DFBC-1613


title: mm_aorta_control_5


title: mm_aorta_control_2


title: DF1613_AZD2


title: DF1613_AZD3

description:
PDX, AZD6482, biol rep 3
Column names: gene_id,gene_name,DF1510_V1,DF1510_V2,DF1510_V3,DF1510_V4,DF1510_AZD1,DF1510_AZD2,DF1510_AZD3,DF1510_AZD4,DF1613_V1,DF1613_V2,DF1613_V3,DF1613_V4,DF1613_AZD1,DF1613_AZD2,DF1613_AZD3,DF1613_AZD4,DF1637_V1,DF1637_V2,DF1637_V3,DF1637_V4,DF1637_AZD1,DF1637_AZD2,DF1637_AZD3,DF1637_AZD4,DF1732_V1,DF1732_V2,DF1732_V3,DF1732_V4,DF1732_AZD1,DF1732_AZD2,DF1732_AZD3,DF1732_AZD4,DF1807_V1,DF1807_V2,DF1807_V3,DF1807_V4,DF1807_AZD1,DF1807_AZD2,DF1807_AZD3,DF1807_AZD4


title: mm_aorta_control_4


title: DF1613_V4


title: DF1613_AZD1


title: mm_aorta_control_1


title: mm_aorta_ppe_lenvatinib_1


title: DF1613_V3


title: DF1637_V2

description:
PDX, vehicle control, biol rep 2
Column names: gene_id,gene_name,DF1510_V1,DF1510_V2,DF1510_V3,DF1510_V4,DF1510_AZD1,DF1510_AZD2,DF1510_AZD3,DF1510_AZD4,DF1613_V1,DF1613_V2,DF1613_V3,DF1613_V4,DF1613_AZD1,DF1613_AZD2,DF1613_AZD3,DF1613_AZD4,DF1637_V1,DF1637_V2,DF1637_V3,DF1637_V4,DF1637_AZD1,DF1637_AZD2,DF1637_AZD3,DF1637_AZD4,DF1732_V1,DF1732_V2,DF1732_V3,DF1732_V4,DF1732_AZD1,DF1732_AZD2,DF1732_AZD3,DF1732_AZD4,DF1807_V1,DF1807_V2,DF1807_V3,DF1807_V4,DF1807_AZD1,DF1807_AZD2,DF1807_AZD3,DF1807_AZD4


title: DF1613_V2


title: DF1510_AZD2

value: PDX DFBC-1510


title: DF1613_V1


title: DF1510_AZD4


title: DF1510_AZD3


title: DF1510_V4


title: DF1510_V2


title: DF1510_V1


title: DF1510_V3


title: THP1-Mɸ 2

city: Arlington

first: Subhrangsu

middle: S

last: Mandal

state: TX

address: 700 Planetarium Place

department: Chemistry and Biochemistry

institute: The University of Texas at Arlington

data_processing: Reads with phred quality scores less than 20 and less than 35 bp after trimming were removed from further analysis using trimgalore (v0.4.1). Quality-filtered reads were then aligned to the reference genome using the HISAT (v 2.0.1)  PMID: 27560171) aligner using default settings and marked duplicates using Sambamba (v0.6.6) (PMID: 25697820). Aligned reads were quantified using ‘featurecount’ (v1.4.6) (PMID: 30783653) per gene ID against GENCODE (PMID: 30357393). Differential gene expression analysis was done using the R package edgeR (v3.10.5) (PMID:19910308). Cutoff values of absolute fold change greater than 2.0 and FDR <= 0.05 were then used to select for differentially expressed genes between sample group comparisons.

growth_protocol: THP1 cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS), 1% L-Glutamine and 1% antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using RNeasy RNA extraction kit (Qiagen). 2 ug of total RNA was used for the construction of sequencing libraries.
The input for library construction was 500 ng of total RNA which was delivered in a 10 µL volume. Then total RNA samples (500 ng) were hybridized with Ribo-Zero Gold to substantially deplete cytoplasmic and mitochondrial rRNA from the samples. Stranded RNA sequencing libraries were prepared as described using the Illumina TruSeq Stranded Total RNA Library Prep Gold kit.
The average insert size of libraries constructed with the TruSeq Stranded Total RNA Library Prep Kit was 200 bp. Purified libraries were qualified on an Agilent Technologies 4200 TapeStation using a D1000 ScreenTape assay (cat# 5067-5582). The molarity of adapter-modified molecules was defined by quantitative PCR using the Kapa Biosystems Kapa Library Quant Kit (Cat#KK4824, KAPA). Individual libraries were normalized to 1.30 nM in preparation for Illumina sequence analysis. Sequencing libraries (1.3 nM) were chemically denatured and applied to an Illumina NovaSeq flow cell using the NovaSeq XP chemistry workflow (Cat# 20021664, Illumina, USA). Following transfer of the flow cell to an Illumina NovaSeq instrument, a 2 x 151 cycle paired end sequence run was performed using a NovaSeq S4 reagent Kit (Cat# 200122866, Illumina, USA).

treatment_protocol:
Monocyte to macrophage differentiation was induced by treatment of 25 nM of phorbol 12-myristate-13-acetate (PMA) in complete RPMI-1640 for 48 hours followed by 24 hours of recovery with complete RPMI-1640
Inflammation was induced with 1µg/mL of lipopolysaccharide (LPS) for 4 hours

value: Monocyte

tag: genotype

value: WT

tag: time

value: 4 hours


title: THP1-Mɸ + LPS 1

value: LPS


title: THP1-Mɸ 3


title: THP1-Mɸ + LPS 3


title: THP1-Mɸ + LPS 2


title: DUSP6KO_EDTA_PD0325901-1h_2 [2021_L62]

city: Cheongju

first: Yong-Ou

last: Kim

state: Chungchung buk do

address: Osongsangmyeong 2ro

country: South Korea

institute: Korea National Institute of Health

data_processing:
fastq files were aligned to human reference genome hg38 using the Subread aligner in the RSubread package.
BAM files resulting from the alignments were summarized to genes using the featureCounts algorithm
Expression data was normalized using the VOOM function in the Limma package in R
Differentially expressed genes (³1.5-fold and £5% false discovery rate) were identified by linear modeling and Bayesian statistics using the Limma package
Assembly: human hg38

source_name: human induced pluripotent stem cells

growth_protocol: 1x10^6 cells/well were plated in 35 mm tissue culture dishes and placed in a 5% CO2 37 °C incubator.

extract_protocol:
RNA was isolated using the Maxwell RSC RNA FFPE kit with the automated Maxwell RSC Instrument (Promega) according to the manufacturer’s instructions.
Libraries were prepared using the TruSeq Stranded mRNA Prep Kit, according to the manufacturer’s instructions.

treatment_protocol: Cells were cultured in the indicated condition and differentiated with 5% FBS for 1, 2 weeks.

value: human pluripotent stem cells

value: 0.1 uM PD0325901 treated for 1 h


title: DUSP6KO-A_EDTA_5%FBS_1W_2 [2021_L137]

value: differentiated with 5% FBS for 1 W


title: DUSP6KO_EDTA_PD0325901-1h_5%FBS_1W_1 [2021_L63]

value: 0.1 uM PD0325901 treated for 1 h and differentiated with 5% FBS for 1 W


title: DUSP6KO_EDTA_PD0325901-1h_5%FBS_1W_2 [2021_L64]


title: DUSP6KO_EDTA_PD0325901-1h_5%FBS_2W_2 [2021_L66]

value: 0.1 uM PD0325901 treated for 1 h and differentiated with 5% FBS for 2 W


title: DUSP6KO_EDTA_PD0325901-1h_5%FBS_2W_1 [2021_L65]


title: DUSP6KO_EDTA_PD0325901-1h_1 [2021_L61]


title: DUSP6KO-A_EDTA_5%FBS_1W_1 [2021_L136]


title: DUSP6KO-A_EDTA_1 [2021_L134]

value: untreated


title: DUSP6KO_EDTA_5%FBS_2W_2 [2021_L145]

value: differentiated with 5% FBS for 2 W


title: DF1510_AZD1

value: Bulk tumor

value: Breast cancer


title: DUSP6KO_EDTA_5%FBS_2W_1 [2021_L144]


title: THP1-Mɸ 1


title: CD3+ TCRγδ- CD4- CCR7+ EVI2B- and CD3+/low TCRγδ- CD4- CCR7- EVI2B+ T cells from Donor 2, ADT-derived cDNA

city: Ghent

first: Laurenz

last: De Cock

address: Corneel Heymanslaan 10

department: Department of Diagnostic Sciences

country: Belgium

institute: Ghent University

description:
Antibody-derived oligonucleotide library
Antibody-derived oligonulceotide (ADT)
BVK03_ADT

library_source: other

data_processing:
 The Cell Ranger pipeline (10x Genomics, version 3.1.0) was used to perform sample demultiplexing and to generate FASTQ files for read 1, read 2 and the i7 sample index for the gene expression and cell surface protein libraries. Read 2 of the gene expression libraries was mapped to the reference genome (GRCh38.99) using STAR.
Subsequent barcode processing, unique molecular identifiers filtering and gene counting was performed using the Cell Ranger suite version 3.1.0 and Seurat v.4.0.5
CITE-seq antibody reads were quantified using the feature-barcoding functionality within the Seurat package
Further processing, e.g. clustering, differential gene expression analysis and data integration was performed with Seurat v.4.0.5.
Assembly: GRCh38.99
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: CITE-Seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

molecule: protein

source_name: Cord Blood

extract_protocol: The populations of interest were sorted from two CD4/CD14/CD19/CD235- depleted CB from different donors. From the first donor, CD3+/low TCRγδ- CD4- CD8α+ as CD3lowPD-1+ (sort 1) or CCR7- EVI2B+ (sort 2) were sorted separately. Both fractions were labeled with different TotalSeq anti-human Hashtag antibodies (Biolegend) before being pooled in equal portions and processed together. From the second donor, CD3+ TCRγδ- CD4- PD-1- and CD3+/low TCRγδ- CD4- PD-1+ (sort 3), CD3+ TCRγδ- CD4- CCR7+ EVI2B- and CD3+/low TCRγδ- CD4- CCR7- EVI2B+ (sort 4) were sorted. Considering the smaller percentage of unconventional T cells, the conventional cells were sorted separately and later added in equal portions. Sort 4 was combined with CITE-seq labeling. Cells were incubated for 30 min on ice with 50 µL of staining mix in PBS containing 0.04% BSA, Fc receptor block (PN 422301, TruStain FcX, BioLegend) and a  human cell surface protein antibody panel containing 277 oligo-conjugated antibodies (TotalSeq-A, BioLegend) including 6 TotalSeq-A isotype controls. TotalSeq antibodies were diluted in concentrations as recommended by the manufacturer. Sorted single-cell suspensions were resuspended  at an estimated final concentration of 1200 cells/µl and loaded on a Chromium GemCode Single Cell Instrument (10x Genomics) to generate single-cell gel beads-in-emulsion (GEM) at the VIB Single Cell Core.The scRNA-Seq libraries were prepared using the GemCode Single Cell 3’ Gel Bead and Library kit, version NextGEM 3.1 (10x Genomics) according to the manufacturer’s instructions with the addition of amplification primers (3nM, 5’CCTTGGCACCCGAGAATT*C*C and 5’GTGACTGGAGTTCAGACGTGTGC*T*C during cDNA amplification to enrich the TotalSeq-A cell surface and hashtag protein oligos. Library construction was performed according to the manufacturer’s instructions. Sequencing libraries were loaded on an Illumina NovaSeq flow cell at VIB Nucleomics core with sequencing settings according to the recommendations of 10x Genomics, pooled in a 80:25 ratio for the combined 3’ gene expression and cell surface protein libraries, respectively.

value: Cord Blood

value: T cells

tag: library type

value: ADT

tag: antibodies/tags

value: 277 oligo-conjugated antibodies (TotalSeq-A, BioLegend) including 6 TotalSeq-A isotype controls (See supplementary file CITE-Seq_Cell_Surface_Protein_Antibody_Panel.xlsx)


title: DUSP6KO_EDTA_1 [2021_L140]


title: DUSP6KO_EDTA_5%FBS_1W_1 [2021_L142]


title: postpartum 1

city: Birmingham

first: Robert

last: Welner

state: AL

address: WTI 510D Zip 3300

department: Department of Medicine

institute: University of Alabama at Birmingham

description: inDrop on viable islet cells postpartum

library_source: transcriptomic single cell

data_processing:
Basecalls performed using Partek Flow software, version 8.0
For scRNA-seq: Bowtie v.1.1.1 was used with parameter -e 80 and reads were aligned to the Ensembl release 85 Mus musculus GRCm38 reference as described earlier (Wolock et al., 2019a). Each library was initially filtered to include only abundant barcodes (> 500 total counts for all in vivo libraries; > 800 counts for cultured sample 1; > 1,000 counts for cultured samples 2 and 3), based on visual inspection of the histograms of total transcript counts per cell barcode. Next, we excluded putatively stressed or dying cells with > 30% (in vivo samples) or > 20% (cultured samples) of their transcripts coming from mitochondrial genes. Normalization of data was carried out as described earlier (Wolock et al., 2019a). For the in vivo samples, we also used Scrublet (Wolock et al., 2019b) to identify two clusters of cell doublets that co-expressed marker genes of distinct cell types
Assembly: mm10
Supplementary files format and content: tab-delimited text files for each Sample are provided

molecule: polyA RNA

source_name: Isolated and dissoiated islets

extract_protocol:
tissue isolation - islets were prepared as described in iScience paper
Libraries were prepared according to inDrop's instructions

value: Islets

tag: organ

value: pancreas

tag: murine strain

tag: treatement

value: Post-partum


title: pregnant 2

description: inDrop on viable islet cells from pregnant mouse

value: Pregnant


title: DUSP6KO-A_EDTA_5%FBS_2W_2 [2021_L139]

value: human pluripotent stem cells


title: DUSP6KO-A_EDTA_5%FBS_2W_1 [2021_L138]


title: CD3+ TCRγδ- CD4- CCR7+ EVI2B- and CD3+/low TCRγδ- CD4- CCR7- EVI2B+ T cells from Donor 2, HTO-derived cDNA

description:
Cell Hashing library
Hashtag-derived oligonucleotide (HTO)
BVK03_HTO

value: HTO

value: TotalSeq-A0253 anti-human Hashtag 3 Antibody and TotalSeq-A0254 anti-human Hashtag 4 Antibody (BioLegend)


title: postpartum 2

description: inDrop on viable islet cells postpartum


title: DUSP6KO_EDTA_2 [2021_L141]


title: pregnant 1


title: non-preg or control

description: inDrop on viable islet cells

value: Non-pregnant


title: Vehicle X4762

city: Little Rock

first: Stephanie

middle: D

last: Byrum

state: Arkansas

address: 501 Jack Stephens Dr, Jackson T. Stephens Bldg 4th floor

institute: University of Arkansas for Medical Sciences

description: Vehicle

data_processing:
nf-core-rnaseq-3.4 was used for the following steps of data processing: fastq quality control, adapter trimming, alignment to the reference genome (GRCm39, GCA_000001635.9) using STAR, quantification using salmon.
The resulting gene counts were transformed to Log2 counts per million (CPM). Lowly expressed genes were filtered out and libraries were normalized by trimmed mean of M-values. The Limma R package was used to calculate differential expression among genes. Log2 fold change values were calculated for Ethanol compared to Control, and genes with an adjusted (adj.) p ≤ 0.05 were considered statistically significant.
Assembly: GRCm39, GCA_000001635.9
Supplementary files format and content: comma-delimited text file including gene count data calculated using salmon.

source_name: Brain

extract_protocol:
Tissue was homogenized using a B2X24B Bullet Blender and 0.5 mm glass beads as described by the manufacturer (Next Advance, Troy, NY).  RNA was isolated using the RNeasy Lipid Tissue Mini Kit with on-column DNase digestion using the RNase-free DNase Set (Qiagen, Valencia, CA, Cat #74804 and #79254).
RNA-seq libraries were prepared using Illumina TruSeq mRNA Library Prep Kit with TruSeq Unique Dual Indexed adapters (Illumina, San Diego, CA) and were quantified with Qubit 1X dsDNA High-Sensitivity NGS Gel Kit (Thermo Fisher Scientific). KAPA Library Quantification (Roche, Basel, Switzerland) was used for further library characterization and Agilent Fragment Analyzer with the High-sensitivity NGS Gel Kit (Agilent) was used for determining fragment size

value: Brain

value: Vehicle


title: Vehicle X4770

description: Vehicle


title: Vehicle X4768

description: Vehicle


title: CD3+ TCRγδ- CD4- PD-1- and CD3+/low TCRγδ- CD4- PD-1+ T cells from Donor 2, HTO-derived cDNA

description:
Cell Hashing library
Hashtag-derived oligonucleotide (HTO)
BVK02_HTO

value: TotalSeq-A0251 anti-human Hashtag 1 Antibody and TotalSeq-A0252 anti-human Hashtag 2 Antibody (BioLegend)


title: CD3+ TCRγδ- CD4- PD-1- and CD3+/low TCRγδ- CD4- PD-1+ T cells from Donor 2, mRNA-derived cDNA

description:
3' mRNA library
polyA RNA
BVK02_mRNA

value: mRNA


title: Ethanol X4760

description: Ethanol

value: Ethanol


title: DUSP6KO-A_EDTA_2 [2021_L135]

value: untreated


title: Vehicle X4761

description: Vehicle


title: CD3+ TCRγδ- CD4- CCR7+ EVI2B- and CD3+/low TCRγδ- CD4- CCR7- EVI2B+ T cells from Donor 2, mRNA-derived cDNA

description:
3' mRNA library
polyA RNA
BVK03_mRNA

value: Cord Blood

value: T cells


title: Ethanol X4766

description: Ethanol


title: CD3+/low TCRγδ- CD4- CD8α+ PD-1+ (CD3lowPD-1+) and CCR7- EVI2B+  T cells from Donor 1, HTO-derived cDNA

description:
Cell Hashing library
Hashtag-derived oligonucleotide (HTO)
BVK01_HTO


title: Ethanol X4758

description: Ethanol


title: Vehicle X4697

description: Vehicle


title: CD3+/low TCRγδ- CD4- CD8α+ PD-1+ (CD3lowPD-1+) and CCR7- EVI2B+  T cells from Donor 1, mRNA-derived cDNA

description:
3' mRNA library
polyA RNA
BVK01_mRNA


title: CF-2099 (ATAC-seq)

city: Los Angeles

first: Simon

last: Knott

state: California

address: 8723 Alden Dr

department: Biomedical Sciences

institute: Cedars-Sinai Medical Center

description:
single nuclei ATAC-seq
peakMatrix_update.rds

library_source: genomic

data_processing:
aligment to reference genome "refdata-cellranger-atac-GRCh38-1.2.0" with 10x genomics CellRanger ATAC v1.2.0
doublet removal in ArchR (v.1.0.0) and batch correction with Harmony (v.1.0)
dimensional reduction using iterative-semantic indexing and UMAP
cluster annotation by correlating gene activity scores with clusters identified in RNA-seq data
Assembly: GRCh38
Supplementary files format and content: R object (.rds)

molecule: genomic DNA

source_name: reduction mammoplasy

extract_protocol:
dounce homogenizers were used to mechanically extract nuclei from cryopreserved mammary tissue. Single nuclei were sorted into reaction buffers (10x genomics) and immediately processed into ATAC-seq libraries
single nuclei ATAC-seq libraries were generated using 10x Genomics Chromium Single Cell ATAC Reagent Kits (v1.1)

tag: gender identity

value: cis-female

value: mammary tissue

tag: hormone therapy

value: no hormone therapy

tag: hormone treatment time (months)

tag: menstrual status

value: pre menopausal

tag: age


title: Ethanol X4694

description: Ethanol


title: DUSP6KO_EDTA_5%FBS_1W_2 [2021_L143]

value: differentiated with 5% FBS for 1 W


title: Ethanol X4692

description: Ethanol


title: Vehicle X4686

description: Vehicle


title: Ethanol X4765

description: Ethanol


title: CF-1380 (ATAC-seq)


title: C-3

city: Ningbo

first: Chen

last: Jiameng

address: No.169 Qixing South Road, Meishan Street, Beilun District, Ningbo City, Zhejiang Province, China

country: China

institute: Ningbo University

description: crab

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0   pmol Cy3/μg cRNA) was fragmented at 60°C for 30   minutes in a reaction volume of 22.5μl containing 1x   Agilent fragmentation buffer and 2x Agilent blocking   agent following the manufacturers' instructions. On   completion of the fragmentation reaction, 22.5μl of   2x Agilent hybridization buffer was added to the   fragmentation mixture and hybridized to Agilent   Portunus trituberculatus Gene Expression（8*60K）for 17 hours at 65°C   in a rotating Agilent hybridization oven. After   hybridization, microarrays were washed 1 minute at   room temperature with GE Wash Buffer 1 (Agilent)   and 1 minute with 37°C GE Wash buffer 2 (Agilent),   then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on   the Agilent DNA Microarray Scanner (G2505C) using   one color scan setting for 4x180k array slides (Scan   Area 61x21.6 mm, Scan resolution 3um, Dye channel   is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature   Extraction Software 10.7.1.1 (Agilent) using default   parameters to obtain background subtracted and   spatially detrended Processed Signal intensities as   the raw data. Raw data were normalized in quantile   algorithm with Genespring 13.0(Agilent). Probe that   at least 1 out of 2 samples flagged as Detected were   maintained.

organism: Portunus trituberculatus

source_name: Portunus trituberculatus larvae

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2   μg RNA using the One-Color Low RNA Input Linear   Amplification PLUS kit (Agilent) according to the   manufacturer's instructions, followed by RNAeasy   column purification (QIAGEN, Valencia, CA). Dye   incorporation and cRNA yield were checked with the   NanoDrop ND-1000 Spectrophotometer.

growth_protocol: In short, rotifers (Branchionus plicatilis) 30-40 ind /mL   and microalga (Platymonas subcordiformis) (5-10) ×104/mL   were fed every two hours during Z1-2) while Artemia nauplii   2-3 ind /mL was provided to Z3-C.

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit   (Applied Biosystem p/n AM1556 ) following the   manufacturer's instructions.

treatment_protocol: Samples were collected when 70%-80% of the population has   molted to the desired stage. The samples were immediately   rinsed with sterilized seawater, snap-frozen in liquid nitrogen,   and then stored at -80 ℃. Three biological replicates of six stages were used for the following analysis.

tag: stages


title: Vehicle X4685

description: Vehicle

tag: tissue


title: M-3

description: megalopa


title: C-2

description: crab


title: Ethanol X4681

description: Ethanol

tag: treatment


title: Ethanol X4683

description: Ethanol


title: CF-1380

description: single nuclei RNA-seq

data_processing:
aligment to reference genome "refdata-gex-GRCh38-2020-A" with 10x genomics CellRanger v4.0.0 with modification to retain intronic reads
removal of low quality nuclei and doublets by thresholding number of UMIs (<30.000) and fraction of mitochondrial genes (<2.5%)
doublet removal via DoubletFinder (v2.0.2) and manual exclusion of double positive subclusters
integration of all samples into one dataset via Seurat (v.3.2.0) "FindIntegrationAnchors" and "IntegrateData"
standard Seurat preprocessing pipeline to normalize raw counts, clustering and dimensional reduction (UMAP)
Assembly: GRCh38
Supplementary files format and content: Seurat Object (.rds) containing raw counts and normalized counts of all samples with metadata and dimensional reduction

source_name: reduction mammoplasty

extract_protocol:
dounce homogenizers were used to mechanically extract nuclei from cryopreserved mammary tissue. Single nuclei were sorted into reaction buffers (10x genomics) and immediately processed into RNA-seq libraries
single nuclei RNA-seq libraries were generated using 10x Genomics Chromium Single Cell 3' (v3) reagent kits


title: Vehicle X4679

description: Vehicle


title: Vehicle X4677

description: Vehicle


title: Vehicle X4695

description: Vehicle


title: TM-3937 (ATAC-seq)

description: single nuclei ATAC-seq

data_processing:
aligment to reference genome "refdata-cellranger-atac-GRCh38-1.2.0" with 10x genomics CellRanger ATAC v1.2.0
doublet removal in ArchR (v.1.0.0) and batch correction with Harmony (v.1.0)
dimensional reduction using iterative-semantic indexing and UMAP
cluster annotation by correlating gene activity scores with clusters identified in RNA-seq data
Genome_build: GRCh38
Supplementary_files_format_and_content: R object (.rds)

source_name: subcutaneous mastectomy (gender affirmation surgery)

value: trans-male

value: Testosterone

value: menstruation seized


title: Ethanol X4674

description: Ethanol


title: Ethanol X4673

description: Ethanol


title: TM-2768 (ATAC-seq)

description: single nuclei ATAC-seq


title: C-1

description: crab


title: M-2

description: megalopa


title: Vehicle X4571

description: Vehicle


title: Vehicle X4570

description: Vehicle


title: TM-7567 (ATAC-seq)

description: single nuclei ATAC-seq


title: Z4-2

description: zoea


title: CF-2099

description: single nuclei RNA-seq


title: Ethanol X4569

description: Ethanol


title: M-1

description: megalopa


title: Z4-3

description: zoea


title: Ethanol X4568

description: Ethanol


title: TM-6477 (ATAC-seq)

description: single nuclei ATAC-seq


title: TM-8249 (ATAC-seq)

description: single nuclei ATAC-seq


title: TM-6544 (ATAC-seq)

description: single nuclei ATAC-seq


title: TM-1956 (ATAC-seq)

description: single nuclei ATAC-seq


title: TM-9469 (ATAC-seq)

description: single nuclei ATAC-seq


title: CF-4014 (ATAC-seq)

description: single nuclei ATAC-seq


title: CF-428-112 (ATAC-seq)

description: single nuclei ATAC-seq


title: NPs-brain cells, scRNAseq

city: Suzhou

first: Qianyu

last: Yang

address: Suzhou

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Supplementary files format and content: GRCm38.96
Supplementary files format and content: Tab-separated values files and matrix files

source_name: brain

extract_protocol:
Mouse/rat intestine tissue and brain tissue were obtained from BALB/c mice (age 5 weeks) and ICR mice (age 6 months)). Place a sterile RNase free culture dish containing an appropriate amount of calcium free and magnesium free 1 × PBS on ice, the tissue was transferred into the culture dish and cut it into 0.5 mm 2 pieces, the tissues were washed with 1 × PBS, and remove as many non purpose tissues as possible such as blood stains and fatty layers.  Tissue s were dissociated into single cells in dissociation solution 0.35% collagenase IV5,2 mg/ml papain, 120 Units/ml DNase I ) in 37 water bath with shaking for 20 min at 100 rpm.  Digestion was terminated with 1 × PBS containing 10% fetal bovine serum FBS V/V then pipetting 5 10 times with a Pasteur pipette. The resulting cell suspension was filtered by passing through 70 30um stacked cell strainer and centrifuged at 300g for 5 min at 4 C. The cell pellet was resuspended in 100ul 1× PBS (0.04% BSA) and added w ith 1 ml 1 × red blood cell lysis buffer MACS 130 094 183, 10 × and incubated at room temperature or on ice for 2 10 min to lyse remaining red blood cells. After incubation, the suspension was centrifuged at 300g for 5 min at room temperature. The suspension was resuspended in 100 μ l Dead Cell Removal MicroBeads(MACS 130 090 101) and remove dead cells using Miltenyi ® Dead Cell Removal Kit (MACS 130 090 101). Then the suspension was resuspended in 1 × PBS(0.04% BSA) and centrifuged at 300 g for 3 min at 4 C repeat twice ））. The cell pellet was resuspended in 50μ l of 1 × PBS (0.04% BSA). The overall cell viability was confirmed by trypan blue exclusion , which needed to be above 85%, single cell suspensions were counted using a haemocytometer/ Countess II Automated Cell Counter and concentration adjusted to 700 1200 cells/ μl.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, intestinal cells and brian cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: brain

value: WT

value: 2 months NPs treatment


title: WT_CDDO-Me5

city: Seattle

first: Yoko

last: Yagishita

state: WA

address: 1100 Fairview Ave N

department: Public Health Sciences

institute: Fred Hutchinson Cancer Center

data_processing:
The quality control of the raw fastq files were performed using fastp
The reads were then mapped to the reference using STAR version 2.7.7
Quality checks on the binary alignment map were donw using tool RSeQC version 3.0.0
Differential expression analysis was performed between groups using edgeR version 3.36.0
Assembly: mm10
Supplementary files format and content: tab-delimited raw counts text file for each sample

source_name: Liver

extract_protocol: RNA was prepared using Trizol (Thermo Fisher Scientific) and RNeasy Mini Kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.

value: Liver

value: wild-type

value: CDDO-Me


title: P8

city: Esch-sur-Alzette

first: Kamil

last: Grzyb

email: kamilgen@gmail.com, kamil.grzyb@uni.lu

address: 2, avenue de l'Université

country: Luxembourg

institute: University of Luxembourg - LCSB

description: mouse single cells isolated from untreated glioblastoma PDOX model

data_processing:
Bcl2fastq ver 2.0 was used for the base calling
Paired end sequencing reads were trimmed for adaptor sequence. Based on the original Dropseq implementation (Macosko et al; 2015), the reads were demultiplexed for the cell barcode and UMI. The genes mapped to GRCm38.87 using STAR genome aligner - with default parameters
Assembly: Genome_build: GRCm38.87 (mm10)
Supplementary files format and content: Supplementary_files_format_and_content: tab-delimited text files include raw counts

source_name: Tumor microenvironment

extract_protocol:
Glioblastoma tumor derived in nude mouse brains  and normal brain were enzymatically dissociated into single cells. Human glioblastoma tumor cells were separated from mouse-derived TME using either FACS of MACS mouse cell depletion kit. Mouse TME cells and normal brain single cell were processed for single cell RNA-seq using Dropseq - 3' bead based enrichment technique.
mRNA libraries were prepared according to the standard Illumina NextSeq 500 protocol

treatment_protocol: P3TMZ PDOX was treated with temozolomide

tag: strain

value: Nude

value: Brain

tag: model

value: glioblastoma tumor model


title: Nude-Brain

description: single cells isolated from normal nude brain

source_name: Normal brain

value: normal


title: T347


title: P3TMZ

description: mouse single cells isolated from temozolomide-treated glioblastoma PDOX model


title: P3


title: WT_Vehicle5

tag: genotype

value: Vehicle


title: T101


title: T16


title: T233


title: T192


title: T470


title: P13


title: CF-0404 (ATAC-seq)

description: single nuclei ATAC-seq

value: cis-female

value: mammary tissue

value: no hormone therapy

value: post menopausal


title: WT_Vehicle3


title: Z2-3

description: zoea


title: mixed sample of mammary gland - WT, K14-cKO, MMTV-cKO

city: beijing

first: lei

last: zhang

address: xueyuan road 38th

department: heath science center

institute: peking university

description: GEXSCOPER

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the CeleScope v1.6.1 (https://github.com/singleron-RD/CeleScope)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Mammary gland

extract_protocol:
The fresh mammary gland tissues were washed with Hanks Balanced Salt Solution (HBSS) for 3 times and minced into 1-2 mm pieces. Then the tissue pieces were digested with 2ml GEXSCOPE® Tissue Dissociation Solution (Singleron) at 37℃ for 15min in 15ml centrifuge tube with sustained agitation. After digestion, using 40-micron sterile strainers to filter the samples and centrifuging the samples at 1,000 rpm for 5 minutes. Then the supernatant was discarded, and the sediment was resuspended in 1ml PBS (HyClone). To remove the red blood cells, 2 mL GEXSCOPE® red blood cell lysis buﬀer (Singleron) was added at 25°C for 10 minutes. The solution was then centrifuged at 500 × g for 5 min and suspended in PBS. Cells were incubated with 7-AAD (1:1000, Invitrogen) on ice for 30 minutes, and sorted by flow cytometry to filter dead cells.
Single-cell suspensions with 1×105 cells/mL in concentration in PBS (HyClone) were prepared. Single-cell suspensions were then loaded onto microfluidic devices and scRNA-seq libraries were constructed according to Singleron CLindex® protocol by GEXSCOPE® Single-Cell RNA Library Kit (Singleron Biotechnologies). mixture libraries were diluted to 4nM and pooled for sequencing. Pools were sequenced on Illumina HiSeq X with 150 bp paired end reads.

tag: cell type

value: mammary epithelium

value: Mammary gland

value: 12-16 weeks old


title: Z3-3

description: zoea


title: UNTX-brain cells, scRNAseq

description: 10x Genomics

value: brain

value: WT

value: untreated


title: WT_Vehicle2

value: Liver

value: wild-type


title: Z4-1

description: zoea


title: Z3-1

description: zoea


title: Z1-2

description: zoea


title: WT_Vehicle4


title: Z2-2

description: zoea


title: CF-318-813 (ATAC-seq)

description: single nuclei ATAC-seq

value: pre menopausal


title: Z2-1

description: zoea


title: WT_CDDO-Me4

value: CDDO-Me


title: Z1-1

description: zoea


title: WT_CDDO-Me3


title: N0_CDDO-Me5

value: Nrf2 kockout


title: C57BL/6J MMPdKO P21 Cortical biol rep 6

city: Rehovot

first: Jerome

last: Janssen

address: Herzl 229

country: Israel

institute: Hebrew University of Jerusalem

data_processing:
fastq files were generated by the usage bcl2fastq-v2.20.0.422 (basecalling)
Reads were trimmed using cutadapt
Reads were aligned to the Mus musculus genome build GRCm38 using STAR (2.7.3a)
Deduplication (UMI is in read 2) was carried out by flagging all reads that were mapped to the same gene and had the same UMI (read 2 has the UMI)
Reads were counted using Ensembl annotations (1000 bases of the 3’ UTR), using HTSeq-Counts (version 0.11.2), and corrected for UMI saturation
Normalization and differential expression analysis were performed using DESeq2 (1.26.0)
Assembly: GRCm38
Supplementary files format and content: Excel file includes the raw counts, genereted by HTSeq-count
Supplementary files format and content: Excel file includes the normalized counts (DESeq Normalization)

source_name: Cortical

growth_protocol: WT and MMP9-/- mice were purchased from Jackson laboratories (Rehovot, Israel), while MMP2-/- mice were kindly provided from Martignetti Lab (Mount Sinai School of Medicine, NY, USA). Single KO mice mutated for MMP2 or MMP9 genes were crossed to generate the double heterozygote KO mice (MMP2+/-MMP9+/-), which were further crossed to receive the full homozygous dKO genotype (MMP2-/-MMP9-/-). Mice were maintained at the Hebrew University Specific Pathogen Free animal facility according to animal care regulations. All procedures were approved by the Hebrew University Animal Care Committee (license number 21-16657-3).

extract_protocol:
Total RNA was extracted and purified using TRI reagent (Sigma, USA) according to the manufacturer’s protocol.
A bulk adaptation of the MARS-Seq protocol (Jaitin et al., Science, 2014; Keren-Shaul et al., Nature Protocols, 2019)
Briefly, 30 ng of input RNA from each sample was barcoded during reverse transcription and pooled. Following Agencourct Ampure XP beads cleanup (Beckman Coulter, Indianapolis, IN), the pooled samples underwent second strand synthesis and were linearly amplified by T7 in vitro transcription. The resulting RNA was fragmented and converted into a sequencing-ready library by tagging the samples with Illumina sequences during ligation, RT, and PCR. Libraries were quantified by Qubit and TapeStation as well as by qPCR for ActB housekeeping gene.

value: Cortical

tag: Sex

value: female

value: MMPdKO


title: CF-2797 (ATAC-seq)

description: single nuclei ATAC-seq

value: cis-female

value: mammary tissue


title: CF-7780 (ATAC-seq)

description: single nuclei ATAC-seq

value: no hormone therapy

value: post menopausal


title: UNTX-intestinal cells, scRNAseq

description: 10x Genomics

source_name: intestine

value: intestine


title: NPs-intestinal cells, scRNAseq

description: 10x Genomics

value: 1 week NPs treatment


title: N0_Vehicle4

value: Vehicle


title: WT_CDDO-Me1


title: Z1-3

description: zoea


title: N0_Vehicle5


title: Z3-2

description: zoea


title: C57BL/6J MMPdKO P21 Cortical biol rep 5


title: C57BL/6J MMPdKO P21 Cortical biol rep 4


title: CF-3920 (ATAC-seq)

description: single nuclei ATAC-seq


title: N0_CDDO-Me4


title: N0_CDDO-Me3


title: TM-3937

description: single nuclei RNA-seq

data_processing:
aligment to reference genome "refdata-gex-GRCh38-2020-A" with 10x genomics CellRanger v4.0.0 with modification to retain intronic reads
removal of low quality nuclei and doublets by thresholding number of UMIs (<30.000) and fraction of mitochondrial genes (<2.5%)
doublet removal via DoubletFinder (v2.0.2) and manual exclusion of double positive subclusters
integration of all samples into one dataset via Seurat (v.3.2.0) "FindIntegrationAnchors" and "IntegrateData"
standard Seurat preprocessing pipeline to normalize raw counts, clustering and dimensional reduction (UMAP)
Genome_build: GRCh38
Supplementary_files_format_and_content: Seurat Object (.rds) containing raw counts and normalized counts of all samples with metadata and dimensional reduction

value: trans-male

value: Testosterone

value: menstruation seized


title: WT_Vehicle1

value: Liver

value: wild-type


title: WT_CDDO-Me2

value: CDDO-Me


title: N0_Vehicle3

value: Nrf2 kockout


title: TM-2768

description: single nuclei RNA-seq


title: C57BL/6J MMPdKO P21 Cortical biol rep 3

value: Cortical


title: N0_CDDO-Me2


title: N0_Vehicle2


title: N0_CDDO-Me1


title: C57BL/6J MMPdKO P21 Cortical biol rep 2

value: female


title: C57BL/6J MMPdKO P21 Cortical biol rep 1

value: MMPdKO


title: TM-9817

description: single nuclei RNA-seq


title: N0_Vehicle1


title: TM-6477

description: single nuclei RNA-seq


title: C57BL/6J MMP9-/- P21 Cortical biol rep 6


title: TM-8249

description: single nuclei RNA-seq


title: C151S_CDDO-Me4


title: C57BL/6J MMP9-/- P21 Cortical biol rep 5


title: C151S_CDDO-Me5


title: C151S_CDDO-M3


title: TM-6544

description: single nuclei RNA-seq


title: C57BL/6J MMP9-/- P21 Cortical biol rep 7


title: DUSP6KO-A_EDTA_PD0325901-1h_5%FBS_1W_1 [2021_L15]

value: human pluripotent stem cells

value: 0.1 uM PD0325901 treated for 1 h and differentiated with 5% FBS for 1 W


title: DUSP6KO-A_EDTA_PD0325901-1h_5%FBS_1W_2 [2021_L16]


title: DUSP6KO-A_EDTA_PD0325901-1h_5%FBS_2W_2 [2021_L18]

value: 0.1 uM PD0325901 treated for 1 h and differentiated with 5% FBS for 2 W


title: TM-1956

description: single nuclei RNA-seq

value: mammary tissue


title: DUSP6KO-A_EDTA_PD0325901-1h_5%FBS_2W_1 [2021_L17]


title: C151S_CDDO-Me1


title: C151S_Vehicle4


title: DUSP6KO-A_EDTA_PD0325901-1h_2 [2021_L14]

value: 0.1 uM PD0325901 treated for 1 h


title: CF-4014

description: single nuclei RNA-seq

value: cis-female

value: no hormone therapy

value: pre menopausal


title: C151S_CDDO-Me2


title: TM-9469

description: single nuclei RNA-seq

value: trans-male

value: Testosterone


title: TM-7567

description: single nuclei RNA-seq

value: menstruation seized


title: C151S_Vehicle3

value: Liver

value: Vehicle


title: C57BL/6J MMP9-/- P21 Cortical biol rep 3


title: C151S_Vehicle5


title: C57BL/6J MMP9-/- P21 Cortical biol rep 2


title: C57BL/6J MMP9-/- P21 Cortical biol rep 4


title: DUSP6KO-A_EDTA_PD0325901-1h_1 [2021_L13]


title: C57BL/6J MMP9-/- P21 Cortical biol rep 1


title: hFSiPS1_EDTA_PD0325901-1h_5%FBS_2W_2 [2020_L80]


title: CF-0404

description: single nuclei RNA-seq

value: post menopausal


title: CF-318-813

description: single nuclei RNA-seq


title: C151S_Vehicle1


title: hFSiPS1_EDTA_PD0325901-1h_5%FBS_2W_1 [2020_L79]


title: CF-2797

description: single nuclei RNA-seq


title: C57BL/6J MMP2-/- P21 Cortical  biol rep 5

value: Cortical


title: hFSiPS1_EDTA_PD0325901-1h_5%FBS_1W_2 [2020_L78]


title: E15.5, replicate 2, scRNAseq

city: Bronx

first: Pengfei

last: Lu

state: NY

address: 1301 Morris Park Ave

department: Genetics

institute: Albert Einstein College of Medicine

description: 10x Genomics

data_processing:
The standard CellRanger v3.1.0 software population was used for demultiplexing, barcoded processing, gene counting and aggregation (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Cardiac cells

extract_protocol: 10X Genomics

value: Cardiac cells

value: whole heart


title: E14.5, replicate 2, scRNAseq

description: 10x Genomics


title: E13.5, replicate 2, scRNAseq

description: 10x Genomics


title: hFSiPS1_EDTA_PD0325901-1h_5%FBS_1W_1 [2020_L77]

value: human pluripotent stem cells


title: C57BL/6J MMP2-/- P21 Cortical  biol rep 3

value: female


title: C57BL/6J MMP2-/- P21 Cortical  biol rep 4


title: CF-428-112

description: single nuclei RNA-seq


title: CF-7780

description: single nuclei RNA-seq


title: hFSiPS1_EDTA_PD0325901-1h_2 [2020_L76]


title: hFSiPS1_EDTA_PD0325901-1h_1 [2020_L75]


title: C151S_Vehicle2


title: lipopolysaccharide (LPS) sample 10

city: Fitzroy

first: Helen

last: Thomas

state: Victoria

address: 9 Princes Street

department: Immunology and Diabetes

country: Australia

institute: St Vincent's Institute

data_processing:
FastQC was used to check Illumina short reads quality and Trimmomatic was used to trim and remove low quality reads. FastQC was applied to trimmed reads to ensure the quality.
STAR index was built using Esembl mouse genome and STAR was used to allign read to the reference.
Samtools was used to sort STAR-aligned BAM files. HTSeq-count was used to quantify aligned reads into gene expression matices.
DESeq2 was applied to determine gene expression changes and differentially expressed genes were extracted to perform gene ontology and pathway enrichment analysis by gprofiler2.
Assembly: Mus_muscuslus.GRCm39
Supplementary files format and content: tab-delimited text files includes raw read counts for each sample

source_name: pancreatic islets

extract_protocol: Islets were then dispersed to single cells with trypsin and beta cells were sorted using FACS. RNA was isolated and subjected to RNA sequencing.

value: pancreatic islets

value: male

value: beta cells

value: NOD

value: 48 hours with 50ng/ml LPS


title: CF-3920

description: single nuclei RNA-seq

value: cis-female

value: mammary tissue

value: no hormone therapy


title: C57BL/6J MMP2-/- P21 Cortical  biol rep 1


title: lipopolysaccharide (LPS) sample 8


title: lipopolysaccharide (LPS) sample 9


title: C57BL/6J WT P21 Cortical biol rep 6

value: WT


title: C57BL/6J MMP2-/- P21 Cortical  biol rep 2


title: C57BL/6J WT P21 Cortical biol rep 7


title: hFSiPS1_EDTA_5%FBS_2W_1 [2020_L61]

source_name: human induced pluripotent stem cells

value: differentiated with 5% FBS for 2 W


title: 24h-DR-1-10-22 | 005 | Desmin

type: protein

city: Charlottesville

first: Ana Karina

last: de Olliiveirra

state: VA

address: 1340 Jefferson Park Avenue

department: Department of Pathology

institute: UVA

description:
24H-LD-5-Sum
Protein Count
three fluorescent-labeled visualization antibodies to detect muscle fibers (desmin), leu-kocytes (CD45), and nuclear stain (Syto 83), along with a cocktail of 48 oligonucleo-tide-labeled antibodies to detect a variety of cellular markers (Supplementary Table S1). Eighteen regions of interest (ROI) from 416 to 652 μm diameter were selected based on desmin staining intensity to generate Low Desmin (LD) and High Desmin (HD) areas

hyb_protocol: Once the 18 ROIs were processed, indexing oligos were hybridized to NanoString optical barcodes for digital counting on the nCounter

scan_protocol: UV light illumination of the ROIs, the eluent was collected via microcapillary aspiration and transferred into individual wells of a microtiter plate.

data_processing: Raw data coount was subjeted to Quality Conrtol (QC) analysis, data normalization, background exclusion, and imputation data

label: Barcode probe

source_name: gastrocnemius muscle

extract_protocol: Muscle tissue sections (4 µm thick) were deparaffinized, subjected to antigen retrieval, and incubated overnight with three fluorescent-labeled visualization antibodies to detect muscle fibers (desmin), leukocytes (CD45), and nuclear stain (Syto 83), along with a cocktail of 48 oligonucleotide-labeled antibodies to detect a variety of cellular markers

treatment_protocol: Groups of mice (CD-1 strain, 18-20 grams) received an intramuscular injection, in the right gastrocnemius, of 30 µg venom. Control mice were injected with 50 µL PBS only. At the time intervals of 1 h, 6 h, 24 h following injection, groups of three mice were sacrificed by CO2 inhalation, and the tissue was excised and added to 10% formalin solution in water.

value: CD-1 strain

value: 30 ug D. Russelli venom

tag: roi name

value: Low Desmin (LD)

tag: segmentation (aoi)

value: Desmin

tag: merge

tag: group


title: 24h-DR-1-10-22 | 005 | Others

label_protocol: Eighteen regions of interest (ROI) from 416 to 652 μm diameter were selected based on desmin staining intensity to generate Low Desmin (LD) and High Desmin (HD) areas

growth_protocol: Groups of mice (CD-1 strain, 18-20 grams)

value: Others


title: lipopolysaccharide (LPS) sample 7


title: lipopolysaccharide (LPS) sample 6


title: 24h-DR-1-10-22 | 005 | CD45


title: C57BL/6J WT P21 Cortical biol rep 3

value: Cortical


title: hFSiPS1_EDTA_5%FBS_1W_2 [2020_L60]

data_processing:
fastq files were aligned to human reference genome hg38 using the Subread aligner in the RSubread package.
BAM files resulting from the alignments were summarized to genes using the featureCounts algorithm
Expression data was normalized using the VOOM function in the Limma package in R
Differentially expressed genes (³1.5-fold and £5% false discovery rate) were identified by linear modeling and Bayesian statistics using the Limma package
Assembly: human hg38

value: human pluripotent stem cells

value: differentiated with 5% FBS for 1 W


title: C57BL/6J WT P21 Cortical biol rep 4

value: female


title: Untreated (UT) sample 5

value: pancreatic islets

value: male

value: beta cells

value: Untreated


title: C57BL/6J WT P21 Cortical biol rep 2


title: hFSiPS1_EDTA_5%FBS_1W_1 [2020_L59]


title: 24h-DR-1-10-22 | 003 | Desmin

description:
24H-LD-3-Sum
Protein Count
three fluorescent-labeled visualization antibodies to detect muscle fibers (desmin), leu-kocytes (CD45), and nuclear stain (Syto 83), along with a cocktail of 48 oligonucleo-tide-labeled antibodies to detect a variety of cellular markers (Supplementary Table S1). Eighteen regions of interest (ROI) from 416 to 652 μm diameter were selected based on desmin staining intensity to generate Low Desmin (LD) and High Desmin (HD) areas


title: hFSiPS1_EDTA_5%FBS_2W_2 [2020_L62]


title: hFSiPS1_EDTA_2 [2020_L58]

value: untreated


title: 24h-DR-1-10-22 | 003 | CD45


title: 24h-DR-1-10-22 | 003 | Others


title: C57BL/6J WT P21 Cortical biol rep 1


title: hFSiPS1_ActivinA(2days)_5%FBS_2W_2 [2020_L44]


title: Untreated (UT) sample 3

value: NOD


title: C57BL/6J WT P21 Cortical biol rep 5

value: WT


title: hFSiPS1_EDTA_1 [2020_L57]


title: Untreated (UT) sample 2


title: 24h-DR-1-10-22 | 001 | Desmin

description:
24H-LD-1-Sum
Protein Count
three fluorescent-labeled visualization antibodies to detect muscle fibers (desmin), leu-kocytes (CD45), and nuclear stain (Syto 83), along with a cocktail of 48 oligonucleo-tide-labeled antibodies to detect a variety of cellular markers (Supplementary Table S1). Eighteen regions of interest (ROI) from 416 to 652 μm diameter were selected based on desmin staining intensity to generate Low Desmin (LD) and High Desmin (HD) areas


title: C57BL/6J MMPdKO P21 Calvaria biol rep 6

source_name: Calvaria

value: Calvaria

value: MMPdKO


title: hFSiPS1_ActivinA(2days)_5%FBS_1W_2 [2020_L42]


title: C57BL/6J MMPdKO P21 Calvaria biol rep 7


title: 24h-DR-1-10-22 | 001 | Others

value: CD-1 strain

value: 30 ug D. Russelli venom


title: 24h-DR-1-10-22 | 001 | CD45

value: Low Desmin (LD)


title: C57BL/6J MMPdKO P21 Calvaria biol rep 5


title: Untreated (UT) sample 1


title: Untreated (UT) sample 4


title: hFSiPS1_ActivinA(2days)_5%FBS_1W_1 [2020_L41]


title: hFSiPS1_ActivinA(2days)_5%FBS_2W_1 [2020_L43]

value: differentiated with 5% FBS for 2 W


title: C57BL/6J MMPdKO P21 Calvaria biol rep 4


title: 24h-DR-1-10-22 | 006 | Others

description:
24H-HD-6-Sum
Protein Count
three fluorescent-labeled visualization antibodies to detect muscle fibers (desmin), leu-kocytes (CD45), and nuclear stain (Syto 83), along with a cocktail of 48 oligonucleo-tide-labeled antibodies to detect a variety of cellular markers (Supplementary Table S1). Eighteen regions of interest (ROI) from 416 to 652 μm diameter were selected based on desmin staining intensity to generate Low Desmin (LD) and High Desmin (HD) areas

value: High Desmin (HD)

value: Others


title: 24h-DR-1-10-22 | 006 | Desmin

value: Desmin


title: REFED, scRNAseq

city: New York

first: Darwin

last: D'Souza

address: 1470 Madison Avenue

department: ImmunoBio

institute: Human Immune Monitoring Center

description:
10x Genomics
SCrnaseq_filtered_feature_bc_matrix.h5

data_processing:
RNAseq Files were processed using nf-core rnaseq pipeline v3.0
Single cell FASTQs alignment, UMI counting and identification of cells was performed with cellranger version 6.1.2; Individual count matrices were aggregated using cellranger aggr with no normalization applied
Assembly: GRCm39 for RNAseq; refdata-gex-mm10-2020-A for scRNAseq
Supplementary files format and content: RNA Seq matrix of gene-level raw counts across all samples; Single cell detected cell-associated barcodes and genes matrix in h5 format

source_name: blood

extract_protocol:
blood Ly6Chi monocytes were sorted from single cell suspension
RNA-seq libraries B43were constructed from total RNA using Clontech SMARTer v4 kit  following manufacturer's protocols; Single Cell librarries was constructed on the Chromium 10x instrument using Chromium single cell 3 ’reagent v3.0 kits, followed by sequencing on Illumina HiSeq 2500 instruments, which resulted in approximately 205-209 million reads per sample

value: blood

value: 24h fast + 4h re-feeding

value: 8-10 weeks old


title: hFSiPS1_ActivinA(2days)_2 [2020_L40]

value: human pluripotent stem cells


title: C57BL/6J MMPdKO P21 Calvaria biol rep 3

value: female


title: FED, scRNAseq

value: continuously fed


title: E15.5, scRNAseq

description: 10x Genomics

extract_protocol:
10X Genomics
10X Genomics

value: Cardiac cells

value: whole heart

value: ICR


title: C57BL/6J MMPdKO P21 Calvaria biol rep 2

value: Calvaria

value: MMPdKO


title: hFSiPS1_ActivinA(2days)_1 [2020_L39]

extract_protocol:
RNA was isolated using the Maxwell RSC RNA FFPE kit with the automated Maxwell RSC Instrument (Promega) according to the manufacturer’s instructions.
Libraries were prepared using the TruSeq Stranded mRNA Prep Kit, according to the manufacturer’s instructions.

value: untreated


title: DUSP6KO9_EDTA_5%FBS_2W_2 [2019_L24]


title: 24h-DR-1-10-22 | 004 | Desmin

description:
24H-HD-4-Sum
Protein Count
three fluorescent-labeled visualization antibodies to detect muscle fibers (desmin), leu-kocytes (CD45), and nuclear stain (Syto 83), along with a cocktail of 48 oligonucleo-tide-labeled antibodies to detect a variety of cellular markers (Supplementary Table S1). Eighteen regions of interest (ROI) from 416 to 652 μm diameter were selected based on desmin staining intensity to generate Low Desmin (LD) and High Desmin (HD) areas

value: CD-1 strain

value: 30 ug D. Russelli venom


title: C57BL/6J MMPdKO P21 Calvaria biol rep 1


title: 24h-DR-1-10-22 | 004 | Others

value: High Desmin (HD)


title: E13.5, scRNAseq

description: 10x Genomics


title: C57BL/6J MMP9-/- P21 Calvaria biol rep 7


title: DUSP6KO9_EDTA_5%FBS_2W_1 [2019_L23]

value: differentiated with 5% FBS for 2 W


title: DUSP6KO9_EDTA_5%FBS_1W_2 [2019_L22]

value: differentiated with 5% FBS for 1 W


title: E12.5, scRNAseq

description: 10x Genomics


title: DUSP6KO9_EDTA_5%FBS_1W_1 [2019_L21]


title: 24h-DR-1-10-22 | 006 | CD45


title: C57BL/6J MMP9-/- P21 Calvaria biol rep 6


title: E14.5, scRNAseq

description: 10x Genomics


title: 24h-DR-1-10-22 | 004 | CD45


title: 24h-DR-1-10-22 | 002 | Desmin

description:
24H-HD-2-Sum
Protein Count
three fluorescent-labeled visualization antibodies to detect muscle fibers (desmin), leu-kocytes (CD45), and nuclear stain (Syto 83), along with a cocktail of 48 oligonucleo-tide-labeled antibodies to detect a variety of cellular markers (Supplementary Table S1). Eighteen regions of interest (ROI) from 416 to 652 μm diameter were selected based on desmin staining intensity to generate Low Desmin (LD) and High Desmin (HD) areas

value: Desmin


title: 24h-DR-1-10-22 | 002 | Others

value: Others


title: C57BL/6J MMP9-/- P21 Calvaria biol rep 5


title: DUSP6KO9_EDTA_2 [2019_L20]


title: 24h-DR-1-10-22 | 002 | CD45


title: C57BL/6J MMP9-/- P21 Calvaria biol rep 3


title: DUSP6KO9_Mech_5%FBS_2W_2 [2019_L18]


title: DUSP6KO9_EDTA_1 [2019_L19]


title: 6h-DR-1-10-22 | 006 | Desmin

description:
6H-LD-6-Sum
Protein Count
three fluorescent-labeled visualization antibodies to detect muscle fibers (desmin), leu-kocytes (CD45), and nuclear stain (Syto 83), along with a cocktail of 48 oligonucleo-tide-labeled antibodies to detect a variety of cellular markers (Supplementary Table S1). Eighteen regions of interest (ROI) from 416 to 652 μm diameter were selected based on desmin staining intensity to generate Low Desmin (LD) and High Desmin (HD) areas

value: Low Desmin (LD)


title: DUSP6KO9_Mech_5%FBS_2W_1 [2019_L17]

value: human pluripotent stem cells


title: 6h-DR-1-10-22 | 006 | Others


title: 10_FL-1

city: VILLEJUIF

first: christophe

last: desterke

address: 14-16 avenue Paul Vaillant Couturier

department: UFR medecine institute Andre Lwoff

country: France

institute: university Paris Sud11

description: single sample array

hyb_protocol: samples hybridized on GeneChip™ Mouse Gene 2.0 ST Array (Affymetrix™).

scan_protocol: samples scanned on Affymetrix Station

data_processing: RMA normalisation

source_name: Fetal liver

label_protocol: cDNAs were obtained using Ovation® Pico WTA System V2 (NuGEN Technologies)

growth_protocol: ES cell medium containing high glucose Dulbecco's modified Eagle's medium supplemented with 15% FBS, β-mercaptoethanol, sodium pyruvate, Penicillin/Streptomycin and LIF.

extract_protocol: Total RNAs were extracted using PureLink® RNA Mini Kit (Thermo Fisher Scientific) and treated with DNase using On-column PureLink® DNase Treatment (Thermo Fisher Scientific)

treatment_protocol: nothing - basal condition

value: LSK cells

tag: tissue source

value: Fetal liver


title: C57BL/6J MMP9-/- P21 Calvaria biol rep 1

value: female


title: 6h-DR-1-10-22 | 006 | CD45


title: DUSP6KO9_Mech_5%FBS_1W_2 [2019_L16]


title: C57BL/6J MMP9-/- P21 Calvaria biol rep 2


title: C57BL/6J MMP2-/- P21 Calvaria  biol rep 7


title: 11_FL-2

description: single sample array


title: 6h-DR-1-10-22 | 003 | Desmin

description:
6H-LD-3-Sum
Protein Count
three fluorescent-labeled visualization antibodies to detect muscle fibers (desmin), leu-kocytes (CD45), and nuclear stain (Syto 83), along with a cocktail of 48 oligonucleo-tide-labeled antibodies to detect a variety of cellular markers (Supplementary Table S1). Eighteen regions of interest (ROI) from 416 to 652 μm diameter were selected based on desmin staining intensity to generate Low Desmin (LD) and High Desmin (HD) areas


title: DUSP6KO9_Mech_5%FBS_1W_1 [2019_L15]


title: C57BL/6J MMP2-/- P21 Calvaria  biol rep 6


title: C57BL/6J MMP9-/- P21 Calvaria biol rep 4


title: 09_BM-3

description: single sample array

source_name: Bone marrow

value: Bone marrow


title: 07_BM-1

description: single sample array


title: 12_FL-3

description: single sample array


title: 6h-DR-1-10-22 | 003 | CD45


title: DUSP6KO9_Mech_2 [2019_L14]


title: DUSP6KO9_Mech_1 [2019_L13]


title: 06_HSCL#C3

description: single sample array

source_name: HSCL#C

value: embryonic derived


title: 08_BM-2

description: single sample array


title: C57BL/6J MMP2-/- P21 Calvaria  biol rep 5

value: Calvaria


title: 6h-DR-1-10-22 | 002 | Desmin

description:
6H-LD-2-Sum
Protein Count
three fluorescent-labeled visualization antibodies to detect muscle fibers (desmin), leu-kocytes (CD45), and nuclear stain (Syto 83), along with a cocktail of 48 oligonucleo-tide-labeled antibodies to detect a variety of cellular markers (Supplementary Table S1). Eighteen regions of interest (ROI) from 416 to 652 μm diameter were selected based on desmin staining intensity to generate Low Desmin (LD) and High Desmin (HD) areas


title: C57BL/6J MMP2-/- P21 Calvaria  biol rep 3


title: 6h-DR-1-10-22 | 002 | Others


title: hFSiPS1_EDTA_5%FBS_2W_2 [2019_L36]


title: hFSiPS1_EDTA_5%FBS_2W_1 [2019_L35]


title: C57BL/6J MMP2-/- P21 Calvaria  biol rep 2


title: 6h-DR-1-10-22 | 002 | CD45


title: 6h-DR-1-10-22 | 003 | Others


title: 05_HSCL#C2

description: single sample array


title: 04_HSCL#C1

description: single sample array


title: 6h-DR-1-10-22 | 005 | Desmin

description:
6H-HD-5-Sum
Protein Count
three fluorescent-labeled visualization antibodies to detect muscle fibers (desmin), leu-kocytes (CD45), and nuclear stain (Syto 83), along with a cocktail of 48 oligonucleo-tide-labeled antibodies to detect a variety of cellular markers (Supplementary Table S1). Eighteen regions of interest (ROI) from 416 to 652 μm diameter were selected based on desmin staining intensity to generate Low Desmin (LD) and High Desmin (HD) areas


title: hFSiPS1_EDTA_5%FBS_1W_2 [2019_L34]


title: CD3+/low PD-1+ T cells Donor 3

data_processing:
Generation of FASTQ files an adapter trimming were performed in illumina's BaseSpace environment using bcl2fastq.
Sequence reads were mapped to hg38-noalt with STAR v2.6.0.c and quantified on Ensembl v93
Assembly: hg38-noalt
Supplementary files format and content: tab-delimited format, raw count data

source_name: Cord Blood

extract_protocol:
Prior to extraction the PNT and CB cell populations were sorted in IMDM supplemented with 10% FCS, 2 mM L-glutamine, 100 IU/mL penicillin and 100 IU/mL streptomycin. Afterwards RNA extraction was performed using the miRNeasy Mini Kit from Qiagen.
The RNA libraries for poly(A) RNA-Seq were constructed with the QuantSeq 3' mRNA FWD kit from Lexogen according to the manufacturer's protocols.

value: Cord Blood

value: T cells

value: WT

value: Untreated


title: hFSiPS1_EDTA_5%FBS_1W_1 [2019_L33]


title: 02_HSCL#A2

description: single sample array

source_name: HSCL#A


title: C57BL/6J MMP2-/- P21 Calvaria  biol rep 4


title: 6h-DR-1-10-22 | 005 | Others

value: CD-1 strain

value: 30 ug D. Russelli venom

value: High Desmin (HD)


title: C57BL/6J WT P21 Calvaria biol rep 7


title: hFSiPS1_EDTA_2 [2019_L32]

value: untreated


title: CD3+ PD-1- T cells Donor 3


title: 03_HSCL#A3

description: single sample array


title: 6h-DR-1-10-22 | 005 | CD45


title: hFSiPS1_EDTA_1 [2019_L31]


title: CD3+/low PD-1+ T cells Donor 2


title: C57BL/6J WT P21 Calvaria biol rep 5


title: 01_HSCL#A1

description: single sample array


title: 6h-DR-1-10-22 | 004 | Desmin

description:
6H-HD-4-Sum
Protein Count
three fluorescent-labeled visualization antibodies to detect muscle fibers (desmin), leu-kocytes (CD45), and nuclear stain (Syto 83), along with a cocktail of 48 oligonucleo-tide-labeled antibodies to detect a variety of cellular markers (Supplementary Table S1). Eighteen regions of interest (ROI) from 416 to 652 μm diameter were selected based on desmin staining intensity to generate Low Desmin (LD) and High Desmin (HD) areas

value: Desmin


title: hFSiPS1_Mech_5%FBS_2W_2 [2019_L30]

value: differentiated with 5% FBS for 2 W


title: 6h-DR-1-10-22 | 004 | Others

value: Others


title: C57BL/6J MMP2-/- P21 Calvaria  biol rep 1


title: TCRγδ+ T cells Donor 2


title: hFSiPS1_Mech_5%FBS_2W_1 [2019_L29]

value: human pluripotent stem cells


title: 6h-DR-1-10-22 | 004 | CD45


title: CD3+/low PD-1+ T cells Donor 1


title: C57BL/6J WT P21 Calvaria biol rep 4


title: C57BL/6J WT P21 Calvaria biol rep 2


title: CD3+ PD-1- T cells Donor 1


title: hFSiPS1_Mech_5%FBS_1W_2 [2019_L28]

value: differentiated with 5% FBS for 1 W


title: C57BL/6J WT P21 Calvaria biol rep 3

value: female


title: C57BL/6J WT P21 Calvaria biol rep 6


title: 6h-DR-1-10-22 | 001 | Others

description:
6H-HD-1-Sum
Protein Count
three fluorescent-labeled visualization antibodies to detect muscle fibers (desmin), leu-kocytes (CD45), and nuclear stain (Syto 83), along with a cocktail of 48 oligonucleo-tide-labeled antibodies to detect a variety of cellular markers (Supplementary Table S1). Eighteen regions of interest (ROI) from 416 to 652 μm diameter were selected based on desmin staining intensity to generate Low Desmin (LD) and High Desmin (HD) areas


title: C57BL/6J WT P21 Calvaria biol rep 1


title: 6h-DR-1-10-22 | 001 | Desmin


title: hFSiPS1_Mech_5%FBS_1W_1 [2019_L27]


title: C57BL/6J MMPdKO P21 GP biol rep 7

source_name: Growth plate

value: Growth plate

value: MMPdKO


title: TCRγδ+ T cells Donor 1


title: CD3+ PD-1- T cells Donor 2


title: hFSiPS1_Mech_2 [2019_L26]


title: hFSiPS1_Mech_1 [2019_L25]


title: C57BL/6J MMPdKO P21 GP biol rep 6


title: SNUhES31_EDTA_2 [2019_L12]

source_name: human embryonic stem cells


title: 1 h-DR-1-=10-22 | 006 | Desmin

description:
1H-LD-6-Sum
Protein Count
three fluorescent-labeled visualization antibodies to detect muscle fibers (desmin), leu-kocytes (CD45), and nuclear stain (Syto 83), along with a cocktail of 48 oligonucleo-tide-labeled antibodies to detect a variety of cellular markers (Supplementary Table S1). Eighteen regions of interest (ROI) from 416 to 652 μm diameter were selected based on desmin staining intensity to generate Low Desmin (LD) and High Desmin (HD) areas

value: Low Desmin (LD)


title: C57BL/6J MMPdKO P21 GP biol rep 5


title: TCRγδ+ T cells Donor C

source_name: Thymus

value: Thymus


title: TCRγδlow CD4- CD8+ PD-1+ CD10+ T cells Donor C

value: T cells


title: 1 h-DR-1-=10-22 | 006 | Others


title: 6h-DR-1-10-22 | 001 | CD45


title: SNUhES31_EDTA_1 [2019_L11]


title: TCRγδlow CD4- CD8+ PD-1+ CD10+ T cells Donor B

value: WT


title: SNUhES31_Mech_2 [2019_L10]


title: C57BL/6J MMPdKO P21 GP biol rep 4


title: C57BL/6J MMPdKO P21 GP biol rep 3


title: SNUhES31_Mech_1 [2019_L9]


title: 1 h-DR-1-=10-22 | 004 | Desmin

description:
1H-LD-4-Sum
Protein Count
three fluorescent-labeled visualization antibodies to detect muscle fibers (desmin), leu-kocytes (CD45), and nuclear stain (Syto 83), along with a cocktail of 48 oligonucleo-tide-labeled antibodies to detect a variety of cellular markers (Supplementary Table S1). Eighteen regions of interest (ROI) from 416 to 652 μm diameter were selected based on desmin staining intensity to generate Low Desmin (LD) and High Desmin (HD) areas

value: ROI Label+D2:D73


title: C57BL/6J MMPdKO P21 GP biol rep 2


title: TCRγδlow CD4- CD8+ PD-1- CD10- T cells Donor C

value: Untreated


title: TCRγδ+ T cells Donor B


title: 1 h-DR-1-=10-22 | 004 | Others

value: CD-1 strain

value: 30 ug D. Russelli venom


title: TCRγδlow CD4- CD8+ PD-1+ CD10+ T cells Donor A


title: rnaseq of wt rep3

city: Edmonton

first: Guanxiang

last: Liang

state: Alberta

address: 410 Agriculture/Forestry Centre

country: Canada

institute: University of Alberta

description: rnaseq of wt rep3

data_processing:
Quality control was perfomed by Fastp
High-quality reads were mapped to mm10 using STAR with default options
Read count extraction and normalization were performed using Htseq-count and edgeR
Assembly: mm10

source_name: testis

extract_protocol:
Total RNA was isolated from 6 pairs of PND21 mouse testes (3 pairs of wild type and 3 pairs of Mov10-/-) using TRIzol reagents (Thermo Fisher Scientific). A total of 1 μg of RNA from each sample was used to generate RNA-seq libraries using TruSeq
Stranded mRNA Library Preparation Kit Set A (Cat. No. RS-122-2101, Illumina) according to the manufacturer’s instruction. The quality of libraries was evaluated using the Agilent 4200 TapeStation (Agilent Technologies).

value: testis


title: 1 h-DR-1-=10-22 | 006 | CD45


title: TCRγδlow CD4- CD8+ PD-1- CD10- T cells Donor A


title: rnaseq of wt rep2

description: rnaseq of wt rep2


title: TCRγδ+ T cells Donor A


title: rnaseq of wt rep1

description: rnaseq of wt rep1


title: C57BL/6J MMP9-/- P21 GP biol rep 6


title: TCRγδlow CD4- CD8+ PD-1- CD10- T cells Donor B


title: C57BL/6J MMP9-/- P21 GP biol rep 5


title: 1 h-DR-1-=10-22 | 002 | Desmin

description:
1H-LD-2-Sum
Protein Count
three fluorescent-labeled visualization antibodies to detect muscle fibers (desmin), leu-kocytes (CD45), and nuclear stain (Syto 83), along with a cocktail of 48 oligonucleo-tide-labeled antibodies to detect a variety of cellular markers (Supplementary Table S1). Eighteen regions of interest (ROI) from 416 to 652 μm diameter were selected based on desmin staining intensity to generate Low Desmin (LD) and High Desmin (HD) areas

value: Desmin


title: 1 h-DR-1-=10-22 | 002 | Others


title: 1 h-DR-1-=10-22 | 002 | CD45


title: rnaseq of mov10 ko rep3

description: rnaseq of mov10 ko rep3


title: hepatocytes of SARS-CoV-2 infected bv-LoC rep3

city: Kyoto

first: Kazuo

last: Takayama

state: Kyoto

address: Shogoin Kawaharacho 53, Sakyo-ku

department: Center for iPS Cell Research and Application

country: Japan

institute: Kyoto University

data_processing:
Sequencing was performed on an Illumina NextSeq500 platform in a 76-base single-end mode.
Illumina RTA version 2.11.3 and  bcl2fastq version 2.20 were used for basecalling and fastq generation, respectively.
Adapter sequences and low-quality bases were trimmed from the raw reads by Cutadapt v3.4. The trimmed reads were mapped to the human reference genome sequences (hg38) using STAR v2.7.9a with the GENCODE (release 36, GRCh38.p13) gtf file.
The raw counts for protein-coding genes were calculated using htseq-count v0.13.5 with the GENCODE gtf file.Gene expression levels were determined as transcripts per million (TPM).
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with TPM for every gene and every sample

source_name: hepatocytes

growth_protocol: To generate ibd- or bv-LoCs, cholangiocytes or endothelial cells were seeded into a bottom channel of the device. Before seeding cholangiocytes or endothelial cells, a bottom channel of the PDMS device was pre-coated with fibronectin (1 μg/mL, Sigma). Cholangiocytes (HuCCT1 cells, JCRB0425, JCRB Cell Bank) or endothelial cells (HUVECs, Lonza) were suspended at 5×106 cells/mL in RPMI-1640 medium containing 1×GlutaMAX (Thermo Fisher Scientific) and 10% FBS or EGM2 (Lonza), respectively. Ten μL suspension medium was injected into the fibronectin-coated bottom channel. Then, the device was turned upside down and incubated for 1 hr. After the incubation, the device was turned over, and medium was added into the bottom channel.   After 4 days, human hepatocytes (HUCPI, Lonza) were seeded into the top channel. Before seeding hepatocytes, the PDMS devices were pre-coated with Collagen I solution (30 μg/mL, Corning). The vials of human hepatocytes were rapidly thawed in a shaking water bath at 37°C. The contents of each vial were emptied into pre-warmed Cryopreserved Hepatocyte Recovery Medium (Thermo Fisher Scientific), and the suspension was centrifuged at 1,200 rpm for 5 min at room temperature. Hepatocytes were suspended at 5×106 cells/mL in Hepatocyte Culture Medium (HCM, Lonza) containing 10% FBS. Ten μL suspension medium was injected into a Collagen I-coated PDMS device. After 1 hr, medium was added into the top and bottom channels.

extract_protocol:
Total RNA was isolated from hepatocytes of uninfected or infected ibd- or bv-LoCs using ISOGENE (NIPPON GENE).
Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

treatment_protocol: SARS-CoV-2 (0.1 MOI) containing HCM was injected into the top channel of ibd- and bv-LoCs. After 1 dpi (days post infection), the culture medium was replaced with fresh medium.

tag: cell line

value: HUVEC

value: hepatocytes of bv-LoC

value: SARS-CoV-2 infection


title: hepatocytes of SARS-CoV-2 infected bv-LoC rep2


title: rnaseq of mov10 ko rep4

description: rnaseq of mov10 ko rep4


title: C57BL/6J MMPdKO P21 GP biol rep 1


title: rnaseq of mov10 ko rep2

description: rnaseq of mov10 ko rep2


title: 1 h-DR-1-=10-22 | 005 | Others

description:
1H-HD-5-Sum
Protein Count
three fluorescent-labeled visualization antibodies to detect muscle fibers (desmin), leu-kocytes (CD45), and nuclear stain (Syto 83), along with a cocktail of 48 oligonucleo-tide-labeled antibodies to detect a variety of cellular markers (Supplementary Table S1). Eighteen regions of interest (ROI) from 416 to 652 μm diameter were selected based on desmin staining intensity to generate Low Desmin (LD) and High Desmin (HD) areas

value: High Desmin (HD)

value: Others


title: hepatocytes of SARS-CoV-2 infected bv-LoC rep1


title: C57BL/6J MMP9-/- P21 GP biol rep 7

value: Growth plate

value: female


title: C57BL/6J MMP9-/- P21 GP biol rep 3


title: 1 h-DR-1-=10-22 | 005 | Desmin


title: hepatocytes of uninfected bv-LoC rep3

value: control


title: clipseq of mov10 in mice rep3

description: clipseq of mov10 in mice rep3


title: clipseq of mov10 in mice rep5

description: clipseq of mov10 in mice rep5


title: C57BL/6J MMP9-/- P21 GP biol rep 2


title: C57BL/6J MMP9-/- P21 GP biol rep 1


title: hepatocytes of uninfected bv-LoC rep2


title: 1 h-DR-1-=10-22 | 004 | CD45

value: Low Desmin (LD)


title: C57BL/6J MMP9-/- P21 GP biol rep 4


title: clipseq of mov10 in mice rep2

description: clipseq of mov10 in mice rep2


title: hepatocytes of uninfected bv-LoC rep1


title: 1 h-DR-1-=10-22 | 003 | Others

description:
1H-HD-3-Sum
Protein Count
three fluorescent-labeled visualization antibodies to detect muscle fibers (desmin), leu-kocytes (CD45), and nuclear stain (Syto 83), along with a cocktail of 48 oligonucleo-tide-labeled antibodies to detect a variety of cellular markers (Supplementary Table S1). Eighteen regions of interest (ROI) from 416 to 652 μm diameter were selected based on desmin staining intensity to generate Low Desmin (LD) and High Desmin (HD) areas


title: 1 h-DR-1-=10-22 | 003 | CD45


title: hepatocytes of SARS-CoV-2 infected ibd-LoC rep3

value: hepatocytes of ibd-LoC


title: 1 h-DR-1-=10-22 | 005 | CD45


title: C57BL/6J MMP2-/- P21 GP biol rep 6


title: Naïve male DRG cells - rep 1

city: Chicago

first: Rachel

middle: E

last: Miller

address: 1735 W Harrison St

institute: Rush University Medical Center

data_processing:
Sequencing reads were assembled and aligned against the mm10-2020-A mouse reference using Cell Ranger v6.0.0 (10x Genomics).
Assembly: mm10-2020-A mouse reference
Supplementary files format and content: filtered_feature_bc_matrix.h5 (counts matrix from cell ranger)
Supplementary files format and content: cloupe.cloupe (cloupe file from cell ranger)
Supplementary files format and content: metrics_summary.csv (metrics from cell ranger)

source_name: DRG cells

extract_protocol:
9,400 naïve cells were loaded into the Chromium Controller (10X Genomics, PN-120223) on a Chromium Next GEM Chip G (10X Genomics, PN-1000120), and processed to generate single cell gel beads in the emulsion (GEM) according to the manufacturer’s protocol.
The cDNA and library were generated using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10X Genomics, PN-1000286) and Dual Index Kit TT Set A (10X Genomics, PN-1000215) according to the manufacturer’s manual.
The multiplexed libraries were pooled and sequenced on Illumina HiSeq 4000 sequencer with 2 × 50 paired-end kits using the following read length: 28 bp Read1 for cell barcode and UMI, and 90 bp Read2 for transcript.

value: Lumbar Dorsal Root Ganglia (DRG)

value: L3-L5 DRG cells

value: male

value: 18 weeks

value: untreated

tag: cell count

value: 9,400 cells


title: 1 h-DR-1-=10-22 | 001 | Desmin

description:
1H-HD-1-Sum
Protein Count
three fluorescent-labeled visualization antibodies to detect muscle fibers (desmin), leu-kocytes (CD45), and nuclear stain (Syto 83), along with a cocktail of 48 oligonucleo-tide-labeled antibodies to detect a variety of cellular markers (Supplementary Table S1). Eighteen regions of interest (ROI) from 416 to 652 μm diameter were selected based on desmin staining intensity to generate Low Desmin (LD) and High Desmin (HD) areas

value: CD-1 strain

value: 30 ug D. Russelli venom

value: Desmin


title: C57BL/6J MMP2-/- P21 GP biol rep 5


title: hepatocytes of SARS-CoV-2 infected ibd-LoC rep2

value: SARS-CoV-2 infection


title: 1 h-DR-1-=10-22 | 001 | Others

value: High Desmin (HD)


title: hepatocytes of SARS-CoV-2 infected ibd-LoC rep1


title: C57BL/6J MMP2-/- P21 GP biol rep 3


title: 1 h-DR-1-=10-22 | 003 | Desmin


title: hepatocytes of uninfected ibd-LoC rep3


title: 1 h-DR-1-=10-22 | 001 | CD45


title: C57BL/6J MMP2-/- P21 GP biol rep 2


title: C57BL/6J MMP2-/- P21 GP biol rep 1


title: SHR3

city: Hefei

first: manman

last: Wang

address: 103 Meishan Road

institute: Anhui University of Chinese Medicine

data_processing:
Reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/ , version:cutadapt-1.9).
We aligned reads of all samples to the rat reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/ , version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/ , version:stringtie-1.3.4d) with default parameter.
The gene expression levels were quantified by FPKM (Fragments Per Kilobase of transcript per Million mapped reads).
Assembly: rn6
Supplementary files format and content: Tab-delimited text files include gene_count values for each Sample.

organism: Rattus norvegicus

source_name: hippocampal tissue

extract_protocol:
Total RNA was extracted using a Trizol reagent and analyzed for quantity and purity.
High-quality RNA samples were used to construct a sequencing library.

treatment_protocol: The rats were anesthetized by injection of sodium pentobarbital. The hippocampal tissue was quickly removed on ice and washed with phosphate-buffered saline.

value: hippocampal tissue

value: SHR

value: 32 weeks


title: SHR4


title: hepatocytes of uninfected ibd-LoC rep2

value: control


title: SHR1


title: clipseq of mov10 in mice rep1

description: clipseq of mov10 in mice rep1

value: testis


title: hepatocytes of uninfected ibd-LoC rep1

value: hepatocytes of ibd-LoC


title: REFED 3, RNA-Seq

value: blood

value: WT

value: 24h fast + 4h re-feeding


title: WKY4

value: Wistar-Kyoto


title: C57BL/6J MMP2-/- P21 GP biol rep 4

value: Growth plate

value: female


title: C57BL/6J WT P21 GP biol rep 7


title: C57BL/6J WT P21 GP biol rep 6


title: Control=-1-10-22 | 006 | Others

description:
Control-6-HD - Sum
Protein Count
three fluorescent-labeled visualization antibodies to detect muscle fibers (desmin), leu-kocytes (CD45), and nuclear stain (Syto 83), along with a cocktail of 48 oligonucleo-tide-labeled antibodies to detect a variety of cellular markers (Supplementary Table S1). Eighteen regions of interest (ROI) from 416 to 652 μm diameter were selected based on desmin staining intensity to generate Low Desmin (LD) and High Desmin (HD) areas

value: CD-1 strain

value: 50 ul PBS

value: Others

value: Control


title: WKY3


title: Control=-1-10-22 | 003 | Desmin

description:
Control-3-HD - Sum
Protein Count
three fluorescent-labeled visualization antibodies to detect muscle fibers (desmin), leu-kocytes (CD45), and nuclear stain (Syto 83), along with a cocktail of 48 oligonucleo-tide-labeled antibodies to detect a variety of cellular markers (Supplementary Table S1). Eighteen regions of interest (ROI) from 416 to 652 μm diameter were selected based on desmin staining intensity to generate Low Desmin (LD) and High Desmin (HD) areas

value: High Desmin (HD)

value: Desmin


title: REFED 2, RNA-Seq


title: C57BL/6J WT P21 GP biol rep 4


title: WKY2

value: hippocampal tissue


title: Control=-1-10-22 | 003 | Others


title: C57BL/6J WT P21 GP biol rep 3


title: WKY1

value: 32 weeks


title: SHR2

value: SHR


title: FED 3, RNA-Seq

value: continuously fed


title: Control=-1-10-22 | 006 | Desmin


title: Control=-1-10-22 | 001 | Desmin

description:
Control-1-HD - Sum
Protein Count
three fluorescent-labeled visualization antibodies to detect muscle fibers (desmin), leu-kocytes (CD45), and nuclear stain (Syto 83), along with a cocktail of 48 oligonucleo-tide-labeled antibodies to detect a variety of cellular markers (Supplementary Table S1). Eighteen regions of interest (ROI) from 416 to 652 μm diameter were selected based on desmin staining intensity to generate Low Desmin (LD) and High Desmin (HD) areas


title: C57BL/6J WT P21 GP biol rep 2


title: LBF_D220_scRNAseq

first: Chian-Yu

last: Peng

state: IL

address: Department of Neurology, 10-233 Ward Building, 303 E Chicago Ave.

institute: Northwestern University, Feinberg School of Medicine

data_processing:
Fastq files were processed with CellRanger v7 to generate the matrix files
Matrix files were imported into Seurat v4 for subsequent analyses
Assembly: hg38
Supplementary files format and content: matrix, barcodes, and features files in mtx or tsv formats

extract_protocol:
3 independently differentiated astrocyte progenitor cell lines at 160DIV were dissociated with accutase and resuspended in phosphate buffer saline before combining the cells and load into the Chromium chip G
libraries for scRNA-seq were prepared using 10x Genomics Chromium Next GEM Single Cells 3' Reagent Kit v3.1platform following manufacturer's protocols.

value: ESC derived astrocyte progenitor cells

tag: agent

value: LIF, BMP4 and FGF1

tag: time point

value: Day 220


title: LBF_D160_scRNAseq

value: Day 160


title: FED 2, RNA-Seq

value: blood

value: WT


title: C57BL/6J WT P21 GP biol rep 5

value: Growth plate

value: female


title: Control=-1-10-22 | 006 | CD45

value: CD-1 strain

value: 50 ul PBS


title: C57BL/6J WT P21 GP biol rep 1


title: Control=-1-10-22 | 001 | Others

value: Others

value: Control


title: FED 1, RNA-Seq


title: 24h delay,  prefix: RIT735A6, replicate 1, scRNAseq

status: Public on Mar 06 2023

city: London

first: Tiago

last: Rito

address: 1 Midland Rd

country: United Kingdom

institute: The Francis Crick Institute

description: 10x Genomics Chromium Single-Cell 3′ mRNA V3.1

data_processing:
Reads were aligned to the Homo sapiens GRCh38-3.0.0 reference genome using CellRanger (v4.0.0, 10X Genomics) and the analyses were performed using Scanpy67 (v1.7.0). Cells were filtered for a minimum of 200 genes, mitochondrial UMIs between 1-20%, total counts between 10,000-50,000 and doublet cells were filtered using Scrublet68 with a threshold of 0.2. Counts were normalized to a target sum of 10000 excluding highly expressed genes. “Highly variable genes” were called using Scanpy’s function with default parameters. Data of different conditions were integrated using harmonypy69. PCA and UMAP were run with default parameters, with neighbourhood graph computed for 15 neighbours and 30 principal components. A 2D embedding using force-directed graph drawing was computed by taking the UMAP coordinates as initial position.
Assembly: Homo sapiens GRCh38-3.0.0

extract_protocol:
Coverslips with micropatterned posterior neuruloids and the two protocol variations of 24h and 48h delay in the TGFß family NODAL and BMP inhibitors (SB431542 and LDN193189) were dissociated by first washing with PBS-/- and then incubating with accutase for 10min at 37°C following mechanical dissociation. Accutase suspension was then diluted in 4x volume with resuspension buffer (DMEM/F12 with 1% BSA). The cell suspension was then spined for 4min at 0.6xg, resuspended in 250µL of resuspension buffer and filtered through a 40µm Flowmi cell strainer (cat. no. 136800040) and twice through a pre-wet 20µm pluriSelect strainer (43-10020-60). The yield was 1110, 950 and 1170 cells/uL respectively with a viability >95%.
The samples were separately loaded for capture with the Chromium System using the Single Cell 3′ v3.1 reagents (10X Genomics). cDNA amplification involved 12 PCR cycles. Libraries for the samples were multiplexed so that the number of reads matched one lane per sample and sequenced on an Illumina HiSeq4000 using 100 bp paired-end runs.

value: differentiated hESCs

tag: age


title: Control=-1-10-22 | 001 | CD45

value: High Desmin (HD)


title: Input Crosslinked RMC2C-SMARCB1 24h

city: Strasbourg

first: Guillaume

last: Davidson

address: 1 Rue Laurent Fries

institute: IGBMC

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequence reads were mapped to reference genome hg19 using Bowtie 1.0.0 with the following parameters -m 1 --strata --best -y -S -l 40 -p 2.
Peaks were called using MACS 2.1.1 with "--broad" parameter for H3K27ac, BRG1 and SMARCB1.
Assembly: hg19
Supplementary files format and content: Wig files were generated using with an in-house script (Variable step, span=25, reads were elongated to 200b).

source_name: IP-DNA from ChIP experiments performed on RMC2C cells stably expressing either SMARCB1 transgene or mCherry control.

growth_protocol: Fresh RMC2C bearing either SMARCB1 or mCHERRY were cultured for maximum 10 passages at a dilution of 1:2 in MEM + 10% FCS + AANE + PS + G418 (50uM).

extract_protocol:
Crosslinked ChIP was performed according standard protocols (see Strub et al, 2011). Native ChIP was performed according to standard protocols (see Wagschal et al., 2007).
ChIP samples were purified using Agencourt AMPure XP beads (Beckman Coulter) and quantified with the Qubit (Invitrogen). ChIP-seq libraries were prepared from 0.7 to 10 ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v2 (C05010014, Diagenode s.a., Seraing, Belgium), according to manufacturer's instructions. In the first step, the DNA was repaired and yielded molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5 prime ends were ligated to the 5 prime end of the genomic DNA, leaving a nick at the 3 prime end. The adaptors cannot ligate to each other and do not have single-strand tails, avoiding non-specific background. In the final step, the 3 prime ends of the genomic DNA were extended to complete library synthesis and Illumina compatible indexes were added through a PCR amplification (7 + 3cycles). Amplified libraries were purified and size-selected using Agencourt AMPure XP beads (Beckman Coulter) to remove unincorporated primers and other reagents.

treatment_protocol: Cells were treated with 2uM doxycyline for 24hrs.

tag: tissue

value: Adult Kidney

tag: antibody

tag: chip-seq condition

value: Crosslinked

tag: inducible transgene


title: control, prefix: RIT735A5, replicate 1, scRNAseq


title: IP H3K27ac RMC2C-mCherry 24h

value: H3K27ac (Active motif 39133)

value: mCherry


title: RMC Naive Tumor

description:
RMC
rmc_naive_raw_counts.tsv

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Alignment to reference genome hg19 (or combined hg19-mm10 for the PDX) and gene quantification for each cell was done using CellRanger.
Data are imported into R and analyzed using Seurat v3.
Genome_build: hg19
Supplementary_files_format_and_content: Tabulated text files containing raw UMI counts for each cell.

source_name: Captured single cell RNA

extract_protocol: Single Cell 3ʹ Gene Expression libraries comprise standard Illumina paired-end constructs which begin with P5 and end with P7. 16 bp 10x Barcodes are encoded at the start of TruSeq Read 1, while 8 bp sample index sequences are incorporated as the i7 index read. TruSeq Read 1 and Read 2 are standard Illumina sequencing primer sites used in paired-end sequencing. TruSeq Read 1 is used to sequence 16 bp 10x Barcodes and 12 bp UMI.

tag: patient treatment

value: Untreated.

tag: isolation column

value: Tumor dissociation kit (Miltenyi, 130-095-929); Tumor Cell isolation Kit (Miltenyi, 130-108-339); CD45 elimination column (Miltenyi, 130-045-801)

tag: pdx specificitiescharacteristics

tag: patient

value: Patient 3 (nephrectomy)

tag: sample type

value: Primary Tumour

value: Kidney


title: Tagmented BRG1 RMC2C-SMARCB1

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequence reads were mapped to reference genome hg19 using Bowtie 1.0.0 with the following parameters -m 1 --strata --best -y -S -l 40 -p 2.
Peaks were called using MACS 2.1.1 with "--broad" parameter for H3K27ac, BRG1 and SMARCB1.
Assembly: hg19
Supplementary files format and content: Wig files were generated using with an in-house script (Variable step, span=25, reads were elongated to 200b).
Library strategy: Cut&Tag

source_name: Tagmented-DNA from Cut and Tag experiments performed on RMC2C cells stably expressing either SMARCB1 transgene or mCherry control.

extract_protocol:
Native Cut&Tag were performed using the Active motif Cut&Tag kit (ref. 53160) following the manufacturer provided protocol.
Cut&Tag libraries were prepared using the Illumina Nextera adaptors provided by the Active Motif Cut&Tag kit following the manufacturer guidelines.

value: SMARCA4 (Abcam 110641)

value: Native


title: Tagmented SMARCB1 RMC2C-mCherry

source_name: Tagmented-DNAfrom Cut and Tag experiments performed on RMC2C cells stably expressing either SMARCB1 transgene or mCherry control.

value: SMARCB1 (CST 91735)


title: Tagmented BRG1 RMC2C-mCherry


title: 48h delay, prefix: RIT735A7, replicate 1, scRNAseq

tag: cell type


title: Input Crosslinked RMC2C-mCherry 24h


title: Tagmented SMARCB1 RMC2C-SMARCB1


title: IP H3K27ac RMC2C-SMARCB1 24h


title: REFED 1, RNA-Seq

source_name: blood

tag: strain

value: blood

tag: genotype

value: WT

tag: treatment

value: 24h fast + 4h re-feeding


title: Control=-1-10-22 | 003 | CD45

source_name: gastrocnemius muscle

value: CD-1 strain

value: 50 ul PBS

tag: roi name

tag: segmentation (aoi)

tag: merge

tag: group

value: Control


title: RMC Treated Tumor

description:
LRHX2
rmc_treated_raw_counts.tsv

value: High-dose methotrexate; vinblastine, doxorubicin, cisplatin (MVAC)

value: Tumor dissociation kit (Miltenyi, 130-095-929); Dead cell removal kit (Miltenyi, 130-090-101), CD45 elimination column (Miltenyi, 130-045-801)

value: Patient 1 (nephrectomy)

tag: tissue


title: RMC2C_48hr_1

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Reads were preprocessed in order to remove adapter and low-quality sequences (Phred quality score below 20) using cutadapt version 1.10.
Reads were mapped to rRNA sequences using bowtie version 2.2.8, and reads mapping to rRNA sequences were removed for further analysis. Reads were mapped to spike sequences using bowtie2 version 2.2.8, and reads mapping to spike sequences were removed for further analysis.
Sequence reads were mapped to reference genome hg19 using Tophat v2.0.10 51 and the bowtie2 v2.1.0 aligner. Only uniquely aligned reads were retained for further analyses.
Gene expression quantification was performed from uniquely aligned reads using htseq-count version v0.6.1 with annotations from Ensembl version 75.
Data normalization and quantification of gene expression was performed using the DESeq2 Bioconductor package. Significantly deregulated genes were selected using a log2 fold change >1 and <1 and adjusted p-value cutoff of 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: Excel file containing log2(fold-changes) and p-values computed by DESeq2 for SMARCB1 versus NEG comparisons at both timepoints in RMC219 and RMC-2C cells.

source_name: Cell line derived from human renal medullary carcinoma (RMC2C); see (Msaouel et al., 2020)

growth_protocol: Fresh RMC219 were cultured for maximum 10 passages at a dilution of 1:1,5 in DMEM/F12 + 10% FCS + Glutamine 2mM + AANE + PS. Fresh RMC2C were cultured for maximum 10 passages at a dilution of 1:2 in MEM + 10% FCS + AANE + PS.

extract_protocol:
RNA-seq libraries were generated using TruSeq Stranded Total RNA Library Prep Kit from Illumina.
RNA isolation was performed according to standard procedure (Macherey Nagel Nucleospin RNA Plus).

treatment_protocol: Genetically modified cells were cultured in adequate media supplemented with G418 (50uM) for selection. Reexpression experiments were done using 2uM doxycycline for the indicated amount of time.

tag: cell line

value: doxycycline

tag: time after treatment

value: 48 hours


title: RMC2C_48hr_3


title: RMC NAT

description:
LRHX3
rmc_treated_raw_counts.tsv

value: Tumor dissociation kit (Miltenyi, 130-095-929); Dead cell removal kit (Miltenyi, 130-090-101); CD45 elimination column (Miltenyi, 130-045-801)


title: RMC2C_12hr_1

value: 12 hours


title: RMC2C_NEG_3

value: DMSO

value: Kidney

value: 0 hours


title: RMC2C_12hr_2


title: RMC2C_12hr_3


title: RMC2C_NEG_2


title: RMC2C_48hr_2


title: RMC2C_NEG_1


title: RMC219_48hr_3

source_name: Cell line derived from human renal medullary carcinoma (RMC219); see (Dong et al., 2017)

extract_protocol:
RNA-Seq libraries were generated from 600 ng of total RNA using TruSeq Stranded mRNA Library Prep Kit and TruSeq RNA Single Indexes kits A and B (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.
RNA isolation was performed according to standard procedure (Macherey Nagel Nucleospin RNA Plus).


title: RMC219_48hr_2


title: RMC219_48hr_1


title: RMC219_12hr_3


title: RMC219_NEG_3


title: RMC219_NEG_2


title: RMC219_NEG_1


title: IP BRG1 RMC2C-SMARCB1

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequence reads were mapped to reference genome hg19 using Bowtie 1.0.0 with the following parameters -m 1 --strata --best -y -S -l 40 -p 2.
Peaks were called using MACS 2.1.1 with "--broad" parameter for H3K27ac and BRG1.  Peaks were called using MACS 1.4 for MYC and MAX.
Genome_build: hg19
Supplementary_files_format_and_content: Wig files were generated using with an in-house script (Variable step, span=25, reads were elongated to 200b).

source_name: Kidney

treatment_protocol: Cells were treated with 2uM doxycyline for 48hrs.

tag: antibody

value: SMARCA4 (Abcam 110641)

tag: chip-seq condition

value: Native

tag: inducible transgene


title: IP BRG1 RMC2C-mCherry

value: mCherry


title: RMC219_12hr_1


title: IP MYC RMC2C-SMARCB1

value: MYC (SCT sc-40)

value: Crosslinked


title: IP H3K27ac RMC2C-SMARCB1

value: H3K27ac (activemotif 39133)


title: Input Native RMC2C-mCherry

value: IgG (Abcam 171870)


title: Input Native RMC2C-SMARCB1


title: Input Crosslinked RMC2C-SMARCB1


title: IP H3K27ac RMC2C-mCherry


title: IP MYC RMC2C-mCherry


title: RMC PDX

description:
PDXRMC
rmc_pdx_raw_counts.tsv

organism:
Homo sapiens
Mus musculus

tag: patient treatment

value: Untreated.

tag: isolation column

value: Tumor dissociation kit (Miltenyi, 130-095-929)

tag: pdx specificitiescharacteristics

value: :3 PDX tumors from the same patient were pooled after 4 passages and sequenced together

value: Patient 2 (PDX)

value: Sub-cutaneous Mouse patient-derived xenograft


title: RMC219_12hr_2

value: doxycycline