title: npTh17

value: non-pathogenic Th17


title: Enalapril, Con7, Optimization plate 4, Well F10 [S4881Nr4_F10]

status: Public on Oct 10 2023

type: SRA

city: Göttingen

first: Christopher

last: Bruhn

address: Marie-Curie-Str. 7

country: Germany

institute: Evotec International GmbH

library_source: transcriptomic

data_processing:
Transcriptomic profiling was performed in batches of 382 samples. Each batch contained 22 negative-control (i.e. DMSO-treated) samples, and 15 blocks of compound-treated samples. Every block included 8 compound concentrations, each in triplicate.
Reads were mapped to the human genome (genome-build GRCh38.p13 – accession GCA_000001405.28) using STAR (version 2.7.9a).
Multi-mapped reads, reads with mapping to inter-genic regions (with respect to Ensembl gene annotation information version 104) and reads with ambiguous mapping location (i.e. location associated with more than one gene) were discarded, and UMI-based deduplication was performed.
Sequencing files were demultiplexed and barcodes were stripped.
Assembly: GRCh38.p13 – accession GCA_000001405.28
Supplementary files format and content: processed_data_counts.txt: RNA unique moecular identifier (UMI) counts per gene. The column EnsemblID provides the unique gene identifier. One column is included per sample with column names matching the column "description" in the table "SAMPLES".

molecule: polyA RNA

organism: Homo sapiens

source_name: hiPSC-CM

growth_protocol: human iPSC-derived cardiomyocytes (hiPSC-CMs) were seeded in 384-well plates (Corning® Cat. No.: 3764) pre-coated with a 0.1 µg/mL fibronectin solution (Sigma Cat. No. F1141) in phosphate buffered saline (PBS) containing Mg2+ and Ca2+. Fibronectin pre-coated plates were incubated at 37°C for 3 h (5% CO2, 95% humidity), after which the coating was carefully removed using an automated liquid handling robot (Bravo Agilent). Subsequently, hiPSC-CMs were seeded at 10,000 cells/well and cultured for 10 days in CD-4 media. Media was initially refreshed 24 h post-seeding and then, every 48 h thereafter while the cells were in culture.

extract_protocol:
High-throughput transcriptomics was performed using Evotec’s (semi)-automated ScreenSeqTM platform. Cell lysis was performed in a 384-well plate format followed by well-specific labeling of samples.
Plate RNASeq of polyA RNA (ScreenSeqTM); Purified mRNAs were labeled with a unique molecular identifier (UMI). After pooled cDNA synthesis, adapters containing Illumina’s unique dual indexes were attached for final library preparation and sequenced on a NovaSeq 6000 system.

treatment_protocol: All compounds were dissolved in 100% dimethylsulfoxide (DMSO) (stock solutions). The stock solutions were further diluted in CD-4 media and cells were dosed in triplicate at an eight-point dose response range using a half-log dilution series to achieve a final DMSO concentration of 0.5% (v/v). Vehicle controls were dosed with 0.5% (v/v) DMSO, while positive controls were dosed with sunitinib, a functional and structural cardiotoxicant.

tag: cell line

value: hiPSC-CM

tag: genotype

value: WT

tag: treatment

value: Enalapril, Con7

tag: time


title: CD4, D7, sheep4

city: Madrid

first: Isabel

last: García-García

state: Madrid

address: Calle José Antonio Novais, 12

department: Genética, Fisiología y Microbiología

country: Spain

institute: Universidad Complutense de Madrid (UCM)

data_processing:
Quality of raw reads was checked using FastQC v0.11.9
Adapter sequences were trimmed and low-quality reads were removed using fastp v0.20.1, retaining reads with a Phred score higher than 15 and with more than 36 bases
Reads were aligned to the Ovis aries reference genome using subread-align and gene counts were obtained using featureCounts, both included in the Subread v2.0.3 package
Genes with low counts (below 15 reads per group) were removed, counts were normalized and differentially expressed genes (DEGs) were identified using edgeR v3.32.1 . An FDR correction was applied and genes with a q-value<0.05 were considered as DEGs
B cell marker+, CD4+, CD8+ and CD14+ cell samples were individually analyzed, comparing days 3, 7 and 15 post-infection to day 0 (prior to infection).
Relevant DEGs were selected based on the gene ontology (GO) terms associated to each gene. GO terms were obtained using biomaRt v2.46.3
An over-representation analysis (ORA) was performed to identify pathways enriched in DEGs, using clusterProfiler v3.18.1. The Ovis aries specific version of the KEGG (Kyoto Encyclopedia of Genes and Genomes) database was used. An FDR correction was applied and those pathways with a q-value<0.05 were considered significantly enriched in DEGs.
Assembly: Oar_rambouillet_v1.0
Supplementary files format and content: tab-delimited text file includes filtered counts for each sample (Bcells)
Supplementary files format and content: tab-delimited text file includes filtered counts for each sample (CD4)
Supplementary files format and content: tab-delimited text file includes filtered counts for each sample (CD8)
Supplementary files format and content: tab-delimited text file includes filtered counts for each sample (CD14)

organism: Ovis aries

source_name: blood

extract_protocol:
RNeasy Mini Kit (Qiagen)
SMARTer Ultra Low RNA Kit

value: BTV serotype 8 infection

tag: tissue

value: blood

tag: cell type

value: Day 7


title: CD4, D3, sheep2

value: Day 3


title: Pool_2, PBMC, snATACseq

city: Atlanta

first: Greg

last: Gibson

state: GA

address: North Ave NW

country: USA

institute: Georgia Institute of Technology

description:
2 male, 1 female
10x Genomics

library_source: genomic

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using Cell Ranger software cellranger-arc-2.0.0 for all samples (cellranger-arc-2.0.1 for Sample_0) (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: genomic DNA

source_name: PBMC

extract_protocol:
Frozen PBMC
snRNA-seq
snATAC-seq

value: PBMC

tag: number of_donors


title: Sample_2, PBMC, snATACseq

description:
male
10x Genomics


title: CD4, D0, sheep3

value: Day 0


title: Enalapril, Con7, Optimization plate 4, Well D10 [S4881Nr4_D10]


title: Sample_1, PBMC, snATACseq

description:
male
10x Genomics


title: CD4, D0, sheep4


title: CD4, D7, sheep2


title: Enalapril, Con8, Optimization plate 4, Well F9 [S4881Nr4_F9]

value: Enalapril, Con8


title: CD4, D0, sheep1


title: CD4, D3, sheep1


title: Imatinib, Con1, Optimization plate 4, Well F8 [S4881Nr4_F8]

value: Imatinib, Con1


title: CD4, D3, sheep3


title: CD4, D0, sheep2


title: Enalapril, Con8, Optimization plate 4, Well D9 [S4881Nr4_D9]


title: Pool_3, PBMC, snRNAseq

description:
2 male, 1 female
10x Genomics

library_source: transcriptomic single cell

molecule: total RNA


title: B-cells, D15, sheep4

value: B-cell

value: Day 15


title: Imatinib, Con1, Optimization plate 4, Well E8 [S4881Nr4_E8]


title: Pool_2, PBMC, snRNAseq

description:
2 male, 1 female
10x Genomics


title: iPSC4_WIC37_Total

city: Amsterdam

first: Marloes

last: Verkerke

address: De Boelelaan 1108

country: Netherlands

institute: Amsterdam UMC

description: fastqs have been demultiplexed

data_processing:
Raw reads were aligned to the human genome (Homo Sapiens GRCh38 Refseq) using the Burrows-Wheeler Aligner (BWA)
Duplicate reads and reads that mapped equally well to multiple locations were discarded.
Read counts were normalized by using the median of ratios method from the DESeq2 pipeline version 1.35.0
Assembly: Homo Sapiens GRCh38

source_name: iPSC 4

growth_protocol: induced pluripotent stem cells were differentiated into cerebral organoids according to Ormel et al. (2018)

extract_protocol:
miRNeasy mini kit (Qiagen)
CEL-Seq2 protocol (Hashimshony et al. 2012)

treatment_protocol: FACS of ITGA6 positive and negative cells from the total organoid after 5, 11, 19, and 37 weeks in culture

value: iPSC 4

value: induced pluripotent stem cells

value: female, 60 years old

value: cerebral organoid differentiation

value: 37 weeks in culture

tag: fraction

value: Total Organoid


title: B-cells, D15, sheep3


title: Enalapril, Con7, Optimization plate 4, Well E10 [S4881Nr4_E10]

value: hiPSC-CM

value: WT

value: Enalapril, Con7


title: Sample_1, PBMC, snRNAseq

description:
male
10x Genomics


title: B-cells, D15, sheep2

value: BTV serotype 8 infection

value: blood


title: iPSC4_WIC37_ITGA6plus

description: fastqs have been demultiplexed

value: ITGA6 positive cells


title: Back skin of atopic dermatitis model mouse (with treated by Fangji dihuang Formulation) 4

city: Hong Kong

first: chunhao

last: cao

address: Hong Kong

department: School of Chinese Medicine

country: Hong Kong

institute: Hong Kong Baptist University

data_processing:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure
A cDNA library constructed by technology from the pooled RNA from skin samples of mus musculus was sequenced run with Illumina Novaseq TM 6000 sequence platform
We aligned reads of all samples to the mus musculus reference genome using HISAT package
The mapped reads of each sample were assembled using StringTie  with default parameters
Genes differential expression analysis was performed by DESeq2 software between two different group
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited Excel files include FPKM values for each Sample

organism: Mus musculus

source_name: Skin

growth_protocol: C57BL/6 male mice aged 6-8 weeks.  All mice were kept in a temperature-controlled (20-22°C) and humidity-controlled (55%) SPF environment, with free access to food and water.

extract_protocol:
The RNA of the total sample was isolated and purified by TRIzol (thermofisher, 15596018) according to the operation scheme provided by the manufacturer
We performed paired-end sequencing on it using the Illumina NovaseqTM 6000 platform following standard procedures

treatment_protocol: On day 0, each mouse was shaved on the back within a 2*2 cm area.  On day 1, the back skin of all mice were sensitized with 200 μL of a 1% DNCB solution.  Starting from day 4, the back skin of all mice were repeatedly stimulated with 100 μL of a 0.5% DNCB solution for the duration of the experiment (days 4, 7, 9, 11, 13, 15, 17, 19 and 21).  After the 7th day, the FJDHF group received FJDHF by oral feeding daily until the end of the experiment (day 28). Model group (Model)  were given equal amounts of water.

value: Skin

value: FJDHF


title: Back skin of atopic dermatitis model mouse (with treated by Fangji dihuang Formulation) 3


title: Imatinib, Con1, Optimization plate 4, Well D8 [S4881Nr4_D8]

value: Imatinib, Con1


title: Back skin of atopic dermatitis model mouse (with treated by Fangji dihuang Formulation) 5


title: Back skin of atopic dermatitis model mouse (with treated by Fangji dihuang Formulation) 2


title: Imatinib, Con2, Optimization plate 4, Well F7 [S4881Nr4_F7]

value: Imatinib, Con2


title: Enalapril, Con8, Optimization plate 4, Well E9 [S4881Nr4_E9]

value: Enalapril, Con8


title: B-cells, D15, sheep1

value: B-cell

value: Day 15


title: Sample_2, PBMC, snRNAseq

description:
male
10x Genomics

value: PBMC


title: B-cells, D7, sheep4

value: Day 7


title: Back skin of atopic dermatitis model mouse 4

value: No


title: Back skin of atopic dermatitis model mouse (with treated by Fangji dihuang Formulation) 1


title: Imatinib, Con2, Optimization plate 4, Well E7 [S4881Nr4_E7]


title: 293T+LNP23-3

city: Abu Dhabi

first: Piergiorgio

last: Percipalle

state: Abu Dhabi

address: Saadiyat Campus, Abu Dhabi

department: Biology Department, Science Division

country: United Arab Emirates

institute: New York University Abu Dhabi

data_processing: Raw FASTQ sequenced reads where first assessed for quality using FastQC v0.11.5 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). The reads where then passed through Trimmomatic v0.36 for quality trimming and adapter sequence removal, with the parameters (ILLUMINACLIP: trimmomatic_adapter.fa:2:30:10 TRAILING:3 LEADING:3 SLIDINGWINDOW:4:15 MINLEN:36) 1. The surviving trimmed read pairs were then processed with Fastp in order to remove poly-G tails and Novaseq/Nextseq specific artefacts 2. Following the quality trimming, the reads were assessed again using FastQC. Post QC and QT, the reads were aligned to the human reference genome GRCh38.81 using HISAT2 3 with the default parameters and additionally by providing the –dta flag. The resulting SAM alignments were then converted to BAM, whilst retaining only the unmapped read pairs using SAMtools 4 v1.9 “samtools view -f 12 -F 256 -b INPUT.sam > OUTPUT.bam”. The resulting unmapped BAM reads were then sorted and converted to fastq reads using samtools sort ”samtools sort -@ 14 -o OUTPUT.sorted.bam INPUT.bam” and samtools fastq “samtools fastq -1 read1.fastq -2 read2.fastq -@ 14 INPUT.sorted.bam”. These unmapped reads where then aligned to the SARS-COV-2 reference genome available through NCBI with the accession NC_045512.2 using HISAT2 with the same parameters that were used in the initial mapping to the human reference. The resulting SAM alignments were then converted to BAM format and coordinate sorted using samtools view and samtools sort respectively. Read groups were then added to the sorted SARS-COV-2 mapped BAM files using Picard AddOrReplaceReadGroups (http://broadinstitute.github.io/picard/). A consensus genome was then generated for each SARS-COV-2 sample using samtools mpileup and ivar 5 version 1.3 with the minimum depth set at 20 “samtools mpileup -A -d 0 -Q 0 INPUT.sorted.bam | ivar consensus -m 20 -p OUTPUT.sars-cov-2-consensus.fasta”. Finally, Qualimap 6 v2.2.2 was used to generate alignment specific QC metrics per sample, both for alignments vs the human reference, as well as the SARS-COV-2 reference. The BAM alignment files were processed using HTseq-count, using the reference annotation file to produce raw counts for each sample.

growth_protocol: The HEK 293T cells were grown in full Dulbecco’s Modified Eagle Medium (DMEM) containing 10% fetal bovine serum, 100 U/ml penicillin and 100 mg/ml streptomycin (Millipore-Sigma) in the humidified incubator at 37°C with 5% CO2. These cells have been engineered to overexpress the ACE2 receptor for SARS-CoV-2 entry.

extract_protocol:
HEK 293T cells either infected with the SARS-CoV-2 virus or uninfected, treated with LNPs containing mRNA sequences of either the anti-NSP9 nanobody or tdTomato were used for total mRNA isolation by TRI Reagent (Millipore-Sigma) according to the manufacturer’s protocol.
Three biological replicates for each condition were used for transcriptional profiling. The RNA-Seq library was prepared by using the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB) and sequenced with the NextSeq 500/550 sequencing platform (performed at the NYUAD Sequencing Center).

treatment_protocol: Half of the 293T cells was treated with lipid nanoparticles (LNPs) containing mRNA sequence of the Nsp9 nanobody (2NSP23) and the other half treated with tdTomato as a control. Next cells were infected with different variants of SARS-CoV-2 virus. The uninfected samples were also either treated with the nanobody-containing LNPs or tdTomato.


title: iPSC4_WIC19_Total

description: fastqs have been demultiplexed

value: iPSC 4

value: induced pluripotent stem cells

value: female, 60 years old

value: cerebral organoid differentiation

value: 19 weeks in culture

value: Total Organoid


title: iPSC4_WIC19_ITGA6plus

description: fastqs have been demultiplexed

value: ITGA6 positive cells


title: Back skin of atopic dermatitis model mouse 3

value: Skin


title: Imatinib, Con2, Optimization plate 4, Well D7 [S4881Nr4_D7]

value: hiPSC-CM

value: WT


title: B-cells, D7, sheep2

value: BTV serotype 8 infection

value: blood


title: B-cells, D7, sheep3

value: B-cell


title: Imatinib, Con3, Optimization plate 4, Well F6 [S4881Nr4_F6]

value: Imatinib, Con3


title: Back skin of atopic dermatitis model mouse 2


title: Back skin of atopic dermatitis model mouse 1


title: Imatinib, Con3, Optimization plate 4, Well E6 [S4881Nr4_E6]


title: iPSC4_WIC19_ITGA6min

description: fastqs have been demultiplexed

value: ITGA6 negative cells


title: B-cells, D3, sheep4

value: Day 3


title: B-cells, D7, sheep1

value: Day 7


title: Imatinib, Con4, Optimization plate 4, Well F5 [S4881Nr4_F5]

value: Imatinib, Con4


title: mycn5

city: New York

first: Mohamed

last: Omar

state: New York

address: 413 East 69th Street

department: Department of Pathology and Laboratory Medicine

institute: Weill Cornell Medicine

data_processing:
Expression matrices were generated from raw Illumina sequencing output using CellRanger. Bcl files were demultiplexed by bcl2fastq, then reads were aligned using STAR. All data collected from mouse models were aligned to GRCm38 reference transcriptome. To identify cells with trans-gene expression, we indexed and aligned to human ERG and GFP from the T-ERG model, human MYC from the Hi-MYC model, and human MYCN from the PRN model.
Assembly: mm10
Supplementary files format and content: anndata (annotated data matrix) object saved in h5ad-file format. The file contains the preprocessed, normalized and annotated count data of all mouse models

source_name: Prostate

extract_protocol:
Mouse prostate tissues were digested in Advanced DMEM/F12/Collagenase II (1.5mg/ml)/Hyaluronidase VIII (1000 u/ml) (Thermo Fisher Scientific) plus 10  μM Y-27632 (Tocris) for 1 hour at 37°C with 1500 rpm mixing, continuously agitated. Subsequently, after centrifuging at 150 g for 5 min at 4°C, digested cells were suspended in 1 ml TrypLE with 10 µM Y-27632 and digested for 15 min at 37°C and neutralized in aDMEM/F12/FBS (0.05%). Dissociated cells were subsequently passed through 70 μm and 40 μm cell strainers (BD Biosciences, San Jose, CA) to obtain a single cells suspension. Samples were resuspended in 1x PBS and sorted by Flow Cytometry (Becton-Dickinson Aria II and/or Becton-Dickinson Influx) for 4′,6-diamidino-2-phenylindole (DAPI) to enrich for living cells.
Barcoded cDNA libraries were created from single-cell suspensions using the Chromium Single Cell 3’ Library and Gel Bead Kit, and Chip Kit from 10x Genomics, according to manufacturer recommendations. 8,000-16,000 cells were targeted for 3’ RNA library preparation, multiplexed in an Illumina NovaSeq 6000, and sequenced at an average depth of 25,000 reads per cell.

value: Prostate

value: Pb-Cre4 +/-;Pten f/f; LSL-MYCN +/+; Rb1 f/f


title: iPSC4_WIC11_ITGA6min

description: fastqs have been demultiplexed

value: iPSC 4

value: induced pluripotent stem cells

value: female, 60 years old

value: cerebral organoid differentiation

value: 11 weeks in culture


title: mycnwt

value: C57BL6/129x1/SvJ) - littermates


title: iPSC4_WIC37_ITGA6min

description: fastqs have been demultiplexed

value: 37 weeks in culture


title: Imatinib, Con3, Optimization plate 4, Well D6 [S4881Nr4_D6]

value: hiPSC-CM

value: WT


title: B-cells, D3 sheep3

value: BTV serotype 8 infection

value: blood

value: B-cell


title: iPSC4_WIC11_Total

description: fastqs have been demultiplexed

value: Total Organoid


title: mycn4


title: iPSC4_WIC5_Total

description: fastqs have been demultiplexed

value: 5 weeks in culture


title: B-cells, D3, sheep1

value: Day 3


title: B-cells, D0, sheep4

value: Day 0


title: Imatinib, Con4, Optimization plate 4, Well E5 [S4881Nr4_E5]

value: Imatinib, Con4


title: mycn3

value: Prostate

value: Pb-Cre4 +/-;Pten f/f; LSL-MYCN +/+; Rb1 f/f


title: iPSC4_WIC5_ITGA6plus

description: fastqs have been demultiplexed

value: iPSC 4

value: induced pluripotent stem cells

value: female, 60 years old

value: ITGA6 positive cells


title: mycn2


title: iPSC4_WIC5_ITGA6min

description: fastqs have been demultiplexed

value: cerebral organoid differentiation

value: ITGA6 negative cells


title: mycn1


title: B-cells, D0, sheep2


title: Imatinib, Con5, Optimization plate 4, Well E4 [S4881Nr4_E4]

value: hiPSC-CM

value: WT

value: Imatinib, Con5


title: iPSC2_WIC37_Total

description: fastqs have been demultiplexed

value: male, 61 years old

value: 37 weeks in culture


title: iPSC4_WIC11_ITGA6plus

description: fastqs have been demultiplexed

value: 11 weeks in culture


title: B-cells, D0, sheep1

value: BTV serotype 8 infection

value: blood

value: B-cell


title: Imatinib, Con5, Optimization plate 4, Well D4 [S4881Nr4_D4]


title: Imatinib, Con6, Optimization plate 4, Well F3 [S4881Nr4_F3]

value: Imatinib, Con6


title: iPSC2_WIC37_ITGA6plus

description: fastqs have been demultiplexed


title: 129b6_pten

value: Prostate

value: B6129SF2/J - littermates


title: Imatinib, Con4, Optimization plate 4, Well D5 [S4881Nr4_D5]

value: Imatinib, Con4


title: Imatinib, Con6, Optimization plate 4, Well E3 [S4881Nr4_E3]


title: NP1

value: Nkx3.1creERT2;Ptenf/f ; EYFPf/+


title: iPSC2_WIC19_Total

description: fastqs have been demultiplexed

value: induced pluripotent stem cells

value: 19 weeks in culture

value: Total Organoid


title: NP2


title: iPSC2_WIC37_ITGA6min

description: fastqs have been demultiplexed

value: cerebral organoid differentiation

value: ITGA6 negative cells


title: Imatinib, Con5, Optimization plate 4, Well F4 [S4881Nr4_F4]

value: hiPSC-CM

value: WT

value: Imatinib, Con5


title: Hi-MYC2


title: Imatinib, Con7, Optimization plate 4, Well F2 [S4881Nr4_F2]

value: Imatinib, Con7


title: B-cells, D0, sheep3

value: BTV serotype 8 infection

value: Day 0


title: iPSC2_WIC19_ITGA6plus

description: fastqs have been demultiplexed

value: male, 61 years old

value: ITGA6 positive cells


title: Hi-MYC1

value: Prostate


title: iPSC2_WIC19_ITGA6min

description: fastqs have been demultiplexed


title: miR4734-t0_3

type: RNA

city: Rehovot

first: Ester

last: Feldmesser

state: Rehovot

address: POB 25

department: Life Science Core Facilities

country: Israel

institute: Weizmann Institute

description: Gene expression data

scan_protocol: According to Affymetrix standard protocols, using Affymetrix GeneChip 3000 7G plus scanner

data_processing: RMA was carried out using Partek Genomic Suite 6.5 (Inc. St. Charles, MO; www.partek.com)

label: biotin

label_protocol: 100 ng total RNA was taken for microarray analysis. Arrays were processed with Gene Chip WT PLUS reagent kit (REF 902281), according to Affymetrix standard protocols

growth_protocol: Cells were grown in Eagle's Minimum Essential Medium with Earle's salts and non-essential amino acids (01-040-1A, Biological Industries, Israel) supplemented with 2.6 mM L-Glutamine, Ampicillin and Streptomycin and 15% FBS. For routine culturing, cell were split 1:3 or 1:4 every 3-4 days.

extract_protocol: RNA was extracted with Qiazol (Qiagen, Germany)

treatment_protocol: HFF cells were transfected either with miR-CTRL or miR-4734.

value: Human foreskin fibroblasts (HFF) (AG14608)


title: Imatinib, Con7, Optimization plate 4, Well E2 [S4881Nr4_E2]


title: T-ERG2


title: miR4734-t48_3

description: Gene expression data

hyb_protocol: According to Affymetrix standard protocols


title: T-ERG1


title: iPSC2_WIC11_Total

description: fastqs have been demultiplexed

value: 11 weeks in culture


title: miRCTR-t0_3

description: Gene expression data


title: miRCTR-t48_3

description: Gene expression data


title: iPSC2_WIC11_ITGA6plus

description: fastqs have been demultiplexed


title: Imatinib, Con8, Optimization plate 4, Well F1 [S4881Nr4_F1]

value: Imatinib, Con8


title: miR4734-t0_2

description: Gene expression data


title: Imatinib, Con8, Optimization plate 4, Well E1 [S4881Nr4_E1]


title: B6

value: C57Bl/6Jn- pure background


title: iPSC2_WIC11_ITGA6min

description: fastqs have been demultiplexed

value: induced pluripotent stem cells


title: Imatinib, Con6, Optimization plate 4, Well D3 [S4881Nr4_D3]

value: Imatinib, Con6


title: Imatinib, Con7, Optimization plate 4, Well D2 [S4881Nr4_D2]


title: FVBN2

value: FVB/N- pure background


title: Imatinib, Con8, Optimization plate 4, Well D1 [S4881Nr4_D1]


title: miR4734-t48_2

description: Gene expression data


title: FVBN1


title: iPSC2_WIC5_ITGA6min

description: fastqs have been demultiplexed

value: cerebral organoid differentiation

value: 5 weeks in culture

value: ITGA6 negative cells


title: miRCTR-t48_2

description: Gene expression data


title: iPSC2_WIC5_ITGA6plus

description: fastqs have been demultiplexed


title: iPSC2_WIC5_Total

description: fastqs have been demultiplexed

value: Total Organoid


title: DMSO, Con0, Optimization plate 4, Well P8 [S4881Nr4_P8]

value: hiPSC-CM

value: WT

value: DMSO, Con0


title: DMSO, Con0, Optimization plate 4, Well P9 [S4881Nr4_P9]


title: miR4734-t48_1

description: Gene expression data


title: miR4734-t0_1

description: Gene expression data


title: VP1-10-3

city: Changsha

first: yujie

last: sun

address: Juzizhou street

country: China

institute: Hunan University

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated
Raw reads of fastq format were processed using fastp 1 and the low quality reads were removed to obtain the clean reads
The clean reads were mapped to the reference genome using HISAT2
FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count
Assembly: StringTie2
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: tumor tissue

extract_protocol:
RNA was harvested using  TRIzol reagent (Invitrogen, CA, USA)
the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions

value: tumor tissue

value: colon cancer cells

value: WT C57BL/6 mice

value: HCS1 1x108 i.v. injection post 1 day


title: miRCTR-t48_1

description: Gene expression data

value: Human foreskin fibroblasts (HFF) (AG14608)


title: miRCTR-t0_2

description: Gene expression data


title: VP1-10-2


title: iPSC1_WIC37_Total

description: fastqs have been demultiplexed

value: male, 62 years old

value: 37 weeks in culture


title: B6.129

value: Prostate

value: B6129SF2/J- pure background


title: DMSO, Con0, Optimization plate 4, Well P7 [S4881Nr4_P7]


title: DMSO, Con0, Optimization plate 4, Well P6 [S4881Nr4_P6]


title: iPSC1_WIC37_ITGA6plus

description: fastqs have been demultiplexed

value: induced pluripotent stem cells

value: ITGA6 positive cells


title: MCF-7 PR shMITF cells 3

city: WASHINGTON

first: Wenge

last: Zhu

state: DC

address: 800 22ND ST NW, Room 8480, Science & Engineering Hall

department: Biochemistry and Molecular Medicine

institute: George Washington University

data_processing:
GLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork
Read cout extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file include raw counts for each Sample

source_name: Breast

growth_protocol: All cells were maintained in DMEM supplemented with 10% FBS at 37 °C with 5% CO2.

extract_protocol:
Total RNA was harvested using Rneasy mini plus kit (Qiagen). 2ug of the total RNA was used for the construction of sequencing libraries
Total RNA was extracted and prepared for cDNA libraries within Illumina TruSeq Stranded mRNA sample preparation kit

value: Breast

value: MCF-7 PR shMITF

value: Breast cancer cells

value: PR MITF knockdown

value: shMITF


title: VP1-10-1


title: VP1-1-3

value: HCS1 1x107 i.v. injection post 1 day


title: iPSC1_WIC37_ITGA6min

description: fastqs have been demultiplexed

value: cerebral organoid differentiation

value: ITGA6 negative cells


title: DMSO, Con0, Optimization plate 4, Well P5 [S4881Nr4_P5]

value: hiPSC-CM

value: WT

value: DMSO, Con0


title: MCF-7 PR shMITF cells 2


title: iPSC1_WIC19_Total

description: fastqs have been demultiplexed

value: male, 62 years old

value: 19 weeks in culture

value: Total Organoid


title: DMSO, Con0, Optimization plate 4, Well P4 [S4881Nr4_P4]


title: iPSC1_WIC19_ITGA6plus

description: fastqs have been demultiplexed


title: MCF-7 PR shMITF cells 1


title: miRCTR-t0_1

description: Gene expression data

value: Human foreskin fibroblasts (HFF) (AG14608)


title: MCF-7 PR control cells 3

value: MCF-7 PR

value: PR

value: Palbociclib


title: VP1-1-2

value: tumor tissue

value: colon cancer cells

value: WT C57BL/6 mice


title: DMSO, Con0, Optimization plate 4, Well P3 [S4881Nr4_P3]


title: VP1-1-1


title: DMSO, Con0, Optimization plate 4, Well P23 [S4881Nr4_P23]


title: MCF-7 PR control cells 2

value: Breast

value: Breast cancer cells


title: iPSC1_WIC11_ITGA6plus

description: fastqs have been demultiplexed

value: induced pluripotent stem cells

value: cerebral organoid differentiation

value: 11 weeks in culture

value: ITGA6 positive cells


title: iPSC1_WIC19_ITGA6min

description: fastqs have been demultiplexed

value: ITGA6 negative cells


title: iPSC1_WIC11_ITGA6min

description: fastqs have been demultiplexed

value: male, 62 years old


title: DMSO, Con0, Optimization plate 4, Well P22 [S4881Nr4_P22]

value: hiPSC-CM

value: WT

value: DMSO, Con0


title: MCF-7 PR control cells 1

value: MCF-7 PR


title: VNP-2

value: VNP20009 1x107 i.v. injection post 1 day


title: VNP-3


title: VNP-1


title: DMSO, Con0, Optimization plate 4, Well P21 [S4881Nr4_P21]


title: DMSO, Con0, Optimization plate 4, Well P20 [S4881Nr4_P20]


title: MCF-7 PR3 cells 3

value: PR

value: Palbociclib


title: MCF-7 PR3 cells 2


title: P3

value: tumor tissue

value: colon cancer cells

value: PBS i.v. injection post 1 day


title: iPSC1_WIC5_ITGA6plus

description: fastqs have been demultiplexed

value: 5 weeks in culture


title: iPSC1_WIC5_Total

description: fastqs have been demultiplexed

value: induced pluripotent stem cells

value: Total Organoid


title: DMSO, Con0, Optimization plate 4, Well P2 [S4881Nr4_P2]


title: MCF-7 PR3 cells 1

value: Breast

value: Breast cancer cells


title: 3O_33T organoids tumor, Control

city: Seoul

first: Nayun

last: Kim

address: 33, Samyang-ro 144-gil, Dobong-gu, Seoul, Republic of Korea

country: South Korea

institute: Duksung women's university

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: tumor

growth_protocol: The animal experiments were approved by the Duksung Women's University Institu-tional Animal Care and Use Committee (2021-001-002) in accordance with the guidelines for the treatment and use of laboratory animals. The mice were acclimated to the animal laboratory room for a week. The following parameters were used: 28 °C, 50% humidity, a 12-h light/dark cycle, and food and water were provided ad libitum.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: Fisetin was intraperitoneally injected five days per week for three weeks.

value: tumor

value: organoid


title: MCF-7 WT cells 1

value: MCF-7 WT

value: No


title: P1

value: WT C57BL/6 mice


title: MCF-7 WT cells 3

value: WT


title: DMSO, Con0, Optimization plate 4, Well P16 [S4881Nr4_P16]

value: hiPSC-CM

value: DMSO, Con0


title: DMSO, Con0, Optimization plate 4, Well P19 [S4881Nr4_P19]


title: P2


title: Various treated and untreated cells

city: NEW YORK

first: LLOYD

middle: A.

last: GREENE

state: NEW YORK

address: 650 W. 168TH STREET

department: PATHOLOGY AND CELL BIOLOGY

institute: COLUMBIA UNIVERSITY

data_processing:
This protocol is as described by and quoted from: PLATE-Seq for genome-wide regulatory network analysis of high-throughput screens.
Bush EC, Ray F, Alvarez MJ, Realubit R, Li H, Karan C, Califano A, Sims PA. Nat Commun. 2017 Jul 24;8(1):105. doi: 10.1038/s41467-017-00136-z. PMID: 28740083.
PLATE-Seq data are comprised of sets of two paired-end reads. The first read contains an 8-base barcode sequence that identifies the well from which a given sample originates. The second read contains a sequence that typically maps strand-specifically to the 3’-end of an mRNA transcript. We first record the barcode sequence associated with each read. The barcode sequences are designed so that a single error can be corrected, and so we allow an edit distance of one from the actual barcode sequences. Next, we use the bwa-mem aligner to map the set of second reads to a pre-assembled human transcriptome (hg19, UCSC known genes). We then demultiplex the resulting alignments and count the number of uniquely mapped reads associated with each gene. We define a read as uniquely mapped if the maximum alignment score among alignments that map to the correct strand is associated with a single gene.
Assembly: H19
Supplementary files format and content: Processed files are formatted as tab-delimited text and contain the number of uniquely mapped reads for each gene in each sample.
Supplementary files format and content: Processed files are formatted as tab-delimited text and include LogFC, LogCPM,F, Pvalue and FDR for each gene in each pair of samples (control vs Dpep treated).

source_name: various cell lines

growth_protocol: T98G, MDA-MB-231, MCF7, A549, HCT116, and A375 cells were from, and authenticated by, the ATCC. Cells were cultured prior to experiments in DMEM supplemented with 10% fetal bovine serum. All cultures were maintained at 37 deg C in a humidified incubator in an atmosphere containing 5% CO2. All lines were tested and found negative for mycoplasma (ATCC Universal Mycoplasma Detection Kit).  A375RESISTANT cells were cultured from a tumor of A375 cells that were implanted into a mouse and that became resistant to Dpep treatment.  A375RESPONSIVE cells were cultured from a tumor of A375 cells that were implanted into a mouse and that responsive to Dpep treatment.

extract_protocol:
The cells were then dissolved in 20 µl/well of TCL lysis buffer (Qiagen) containing 1% freshly added 2-mercaptoethanol. The plates were then shaken for 5 minutes on a rotary shaker and centrifuged at 3000 rpm for 1 minute. The plates were then sealed, quick frozen on dry ice and stored at -80 ℃ until use. When all lines had been treated and harvested in this way, the samples were thawed and transferred to mRNA TurboCapture plates (Qiagen)
This protocol is as described by and quoted from: PLATE-Seq for genome-wide regulatory network analysis of high-throughput screens. Bush EC, Ray F, Alvarez MJ, Realubit R, Li H, Karan C, Califano A, Sims PA. Nat Commun. 2017 Jul 24;8(1):105. doi: 10.1038/s41467-017-00136-z. PMID: 28740083. "Cells are lysed for PLATE-Seq in Buffer TCL (Qiagen) supplemented with 2-mercaptoethanol in 96-well plates. We transfer 30 uL of cell lysate from each well to a 96-well plate with oligo(dT) grafted to the wells (mRNA TurboCapture Plate, Qiagen) and added 1 uL of 1:100 dilution of ERCC Ex-Fold Spike-Ins (ThermoFisher) to a subset of the sample wells. The plate is then centrifuged at 295xg for 1 minute to eliminate air bubbles followed by incubation for 90 minutes at room temperature with shaking at 200 rpm. Lystate is then removed from the oligo(dT) capture plate and wells are washed three times with Buffer TCW (Qiagen) using the 96 CO-RE Head of a Hamilton Microlab STAR automated liquid handling system. After drying the plate, mRNA is then eluted by adding 30 uL of Elution Buffer (nuclease-free water supplemented with 0.4 U/uL SUPERaseIN (ThermoFisher)), incubation at 65°C for five minutes, and incubation at room temperature for 5 minutes. mRNA samples are then transferred to a new PCR plate (Hard-Shell PCR plate, 96-well, Bio-Rad) using sterile-filter 96-well, 50 uL tips on the Hamilton STAR. To anneal primers for reverse transcription, 3 uL of 100 uM adapter-linked oligo(dT) primers are added to each well along with 10 uL of 5x ProtoScript RT Buffer (New England BioLabs) with the Hamilton STAR CO-RE Head and 1000 uL channel pipetting system. The plate is then heated to 94°C for two minutes and placed immediately on ice for 5 minutes. The remaining components of the reverse transcription master mix including 0.5 mM of each dNTP, 10 mM DTT, 35.8 U of Protoscript II Reverse Transcriptase (New England BioLabs), and water are then added to bring the final reaction volume to 50 uL per well. The plate is then centrifuged at 295xg for 1 minute and incubated at 42°C for 2 hours. At this point, the samples can optionally be frozen at -80°C. To remove excess primer, 1 uL of a four-fold dilution of Exonuclease I (New England BioLabs) is added to each sample. The Exonculease I reaction is incubated at 25°C for one hour. To hydrolyze the RNA, we add 20 uL of a 1:1 mixture of 1M sodium hydroxide and 0.5M EDTA to each well and incubate at 65°C for 15 minutes. The wells are then pooled together into a single tube to which 80 uL of 12 M hydrochloric acid are added to neutralize the sample. At this point, the pooled sample can optionally be frozen at -80°C. The pooled, neutralized sample is purified and concentrated using a Qiagen MinElute column using a vacuum apparatus according to the manufacturer?s instructions, and pooled cDNA is eluted in 15 uL of nuclease-free water. For second-strand synthesis, 1 uL of 10 mM dNTP mixture and 1 uL of 100 mM adapter-linked random hexamer primers are added to the pooled cDNA sample. The mixture is then heated to 70°C for two minutes and immediately placed on ice for five minutes. Next, 2 uL of NEB Buffer 2 (New England BioLabs) and 1 uL of Klenow Large Fragment DNA Polymerase (New England BioLabs) are added and the reaction is incubated at room temperature for 30 minutes. The reaction is then stopped by addition of EDTA to a final concentration of 50 μM the double-stranded cDNA is purified with two rounds of bead clean-up using AMPure XP beads (Beckman Counter) at a 1:1 bead-to-sample ratio. Finally, the double-stranded cDNA pool is amplified by PCR using Phusion DNA Polymerase (New England BioLabs) with 0.5 μM Illumina RP1 primer and Illumina RPIx primer (where x is a number indicating the Illumina index). The thermocycling protocol begins with 98 °C for 30 s followed by 10–12 cycles of 98 °C for 15 s, 62 °C for 15 s, and 72 °C for 60 s followed by a 7-min incubation at 72 °C.

treatment_protocol: Cells were seeded onto 96-well culture plates in 0.2 ml of DMEM supplemented with 10% FBS. The plates were pre-coated with polylysine (0.1 µg/µL) and dried overnight. There were 6 replicates per condition for each cell line.  To assure uniformity of cultures, 1-2 lines were processed at one time After 24 hrs, the medium was replaced with DMEM supplemented with 2% FBS with or without 20 µM Dpep. Cell confluency was at least 70% at this time. After 48 hrs, culture medium was removed and the wells were washed 2x with PBS.

value: various cell lines


title: MCF-7 WT cells 2


title: PCNSL_Spleen_4282

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

data_processing:
Basecalls performed using RTA 2.7.3
Bad quality reads were filtered out using Trimmomatic (v 0.36) with the following paramters: HEADCROP:3 TRAILING:10 MINLEN:25
paired-end reads were aligned to the hg19 genome assembly using STAR (v2.5.2b), and read count per gene was subsequently estimated with the following parameters: --outFilterType BySJout --outFilterMultimapNmax 10 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999  --outFilterMismatchNoverLmax 0.05 i--alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMatchNmin 16  --quantMode GeneCounts
Assembly: hg19
Supplementary files format and content: tab-delimited txt file including read count per gene for each sample

source_name: PCNSL PDX 4282

growth_protocol: implantation of human stereotactic biopsy of CNS lymphoma lesion into NSG/NOG mice to generate xenografts.

extract_protocol:
high pure RNA Isolation Kit from Roche Life Science (11828665001)
For library preparation RNA was converted to cDNA and amplified (10 PCR cycles) with the  SMART Seq v4 ultra-low RNA kit from Takara following the manufacturer´s instructions. For library preparation 10ng or the respective maximum available amount of RNA were used as input for the NEB ChIP Seq protocol following the manufacturer´s recommendations but skipping the size selection and using the high fidelity 2x PCR master mix from NEB.
RNA-Seq, Two pools consisting of 7 libraries each were sequenced on HiSeq 4000 in 100 bp paired end mode, which produced an output of at least 48 Mio. Reads pairs per sample.

treatment_protocol: not applicable

value: hCD19 sorted cells from spleen

value: PCNSL B-lymphoma cells


title: DMSO, Con0, Optimization plate 4, Well P18 [S4881Nr4_P18]


title: 3Blue_33T organoids tumor, Fisetin 200mpk

value: Fisetin 200mpk


title: Acrylamide treatment - 4

city: Egkomi

first: Panagiotis

last: Papageorgis

state: Nicosia

address: 6 Diogenous street

department: Life Sciences

country: Cyprus

institute: European University Cyprus

data_processing:
lΙlumina conversion software bcl2fastq
Data processing was performed using the lΙlumina bcl2fastq software
Sequence reads were trimmed for adaptor sequence / low quality sequence using the lΙlumina bcl2fastq software
Trimmed sequence reads were mapped to GrCM38/mm10 usingthe lΙlumina bcl2fastq software
Read count and normalization was performed using the lΙlumina bcl2fastq software
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text files include RPKM values for each sample

source_name: Colon

extract_protocol:
Total RNA was extracted using standard Trizol protocol followed by cleanup using Rneasy mini kit (Qiagen). 100-1000ng per sample was used for the construction of libraries.
Library from total RNA was prepared using Illumina TrueSeq stranded mRNA library prep kit, according to manufacturer's protocol

treatment_protocol: Male Balb/c mice orally received acrylamide (0.1 mg/kg/day) or PBS daily for 4 weeks. RNA was extracted from colon tissue samples, followed by RNA sequencing.

value: Colon

tag: mouse strain

value: Balb/c

value: Acrylamide


title: 3B2_33T organoids tumor, Control


title: Acrylamide treatment - 3


title: SCNSL_Spleen_2972

source_name: SCNSL PDX 2972

value: SCNSL B-lymphoma cells


title: 3B_33T organoids tumor, Fisetin 200mpk


title: Acrylamide treatment - 2


title: DMSO, Con0, Optimization plate 4, Well P14 [S4881Nr4_P14]


title: PCNSL_CNS_4282

value: hCD19 sorted cells from CNS


title: DMSO, Con0, Optimization plate 4, Well P15 [S4881Nr4_P15]


title: SCNSL_CNS_2972


title: iPSC1_WIC5_ITGA6min

description: fastqs have been demultiplexed

value: induced pluripotent stem cells

value: male, 62 years old

value: cerebral organoid differentiation

value: 5 weeks in culture

value: ITGA6 negative cells


title: Acrylamide treatment - 1


title: 1R_33T organoids tumor, Control

value: tumor

value: organoid

value: WT


title: DMSO, Con0, Optimization plate 4, Well P13 [S4881Nr4_P13]

value: hiPSC-CM

value: DMSO, Con0


title: DMSO, Con0, Optimization plate 4, Well P17 [S4881Nr4_P17]


title: PBS treatment - 4

value: PBS


title: Acrylamide treatment - 5


title: 1B_33T organoids tumor, Fisetin 200mpk

value: Fisetin 200mpk


title: DMSO, Con0, Optimization plate 4, Well P12 [S4881Nr4_P12]


title: SMF012_MOLM13_Cas9_PosIAA_PosDOX_Rep2_RNAseq

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

data_processing:
Quality control filtering and adapter trimming of fastq files was performed with trim_galore.
Paired-end reads were mapped by STAR(v2.7.1a) using parameters "-c -p 4 --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJstitchMismatchNmax 5 -1 5 5 --alignSJDBoverhangMin 10 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 100000 --alignMatesGapMax 100000 --outSAMmapqUnique 60 --outSAMmultNmax 1 --outSAMstrandField intronMotif --outSAMattributes NH HI AS nM NM MD --outSAMunmapped Within --outSAMtype BAM SortedByCoordinate --outReadsUnmapped None --chimJunctionOverhangMin 12 --chimSegmentReadGapMax 3 --chimMultimapNmax 10 --chimMultimapScoreRange 10 --chimNonchimScoreDropMin 10 --chimOutJunctionFormat 1 --quantMode TranscriptomeSAM GeneCounts --twopassMode Basic --peOverlapNbasesMin 12 --peOverlapMMp 0.1 --outWigType wiggle --outWigStrand Stranded --outWigNorm RPM".
Read duplication was marked with MarkDuplicates from GATK (v4.1.2.0).
RSEM was used to quantify read counts per gene.
Assembly: hg19 (GRCh37.p13)
Supplementary files format and content: gene-based raw counts as well as FPKM and TPM normalized txt files

growth_protocol: All cell lines were maintained in RPMI 1640 medium (GIBCO, Life Technologies) supplemented with 10% heat-inactivated fetal bovine serum and 2 mM L-glutamine, at 37°C in 5% CO2.

extract_protocol:
Total RNA was extracted by Trizol (Thermo Fisher Scientific, 15596026) from replicate samples.
About 200 ng total RNA was treated using Kapa rRNA depletion reagents to remove ribosomal RNA, then converted into cDNA libraries using Kapa RNA HyperPrep Kit with RiboErase (HMR).
After the end repair procedure, dA-tailing and adapter ligation, each cDNA library was purified and enriched by 11 cycles of PCR amplification.

treatment_protocol: We devised a doxycycline-Tet-On inducible system to express HOXA9-AID cassette in MLL-r leukemia cell lines (SEM and MOLM13) to reveal transcriptome changes associated with HOXA9 expression. Overexpression of the HOXA9-AID fusion protein can be induced by doxycycline (1uM 24hrs), and the fusion protein can also be rapidly degraded by auxin treatment without affecting the mRNA level of HOXA9 (1uM 5-Ph-IAA, 6hrs).

value: acute myeloid leukemia


title: 1127, Batch 8, scRNA-seq

city: South San Francisco

first: Robin

last: Zhou

state: California

address: 170 Harbor Way

institute: Neurona Therapeutics

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregating were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Seurat V3 was used to QC, clustering and visualizing thed data
Assembly: GRCh38
Supplementary files format and content: A Seurat project with information of gene counting, cell clustering, PCA and UMAP visualization

source_name: interneurons

extract_protocol:
Suspension from each sample were prepared with cells post cryopreservation and thaw, and loaded onto chips according to 10X genomic's instructions
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics).

tag: sample id

value: interneurons

value: unsorted

value: End of Process


title: DMSO, Con0, Optimization plate 4, Well P10 [S4881Nr4_P10]


title: SMF011_MOLM13_Cas9_PosIAA_PosDOX_Rep1_RNAseq


title: 1156, Batch 9, scRNA-seq

description: 10x Genomics


title: SMF010_MOLM13_Cas9_NegIAA_PosDOX_Rep2_RNAseq


title: PBS treatment - 2

value: Colon

value: Balb/c


title: 1158, Batch 7, scRNA-seq

description: 10x Genomics


title: SMF009_MOLM13_Cas9_NegIAA_PosDOX_Rep1_RNAseq


title: PBS treatment - 1


title: DMSO, Con0, Optimization plate 4, Well P11 [S4881Nr4_P11]


title: DMSO, Con0, Optimization plate 4, Well B24 [S4881Nr4_B24]


title: 1469, Batch 5, scRNA-seq

description: 10x Genomics


title: S16_Opa1-flox_Cre+_Male

city: Iowa City

first: Renata

middle: O

last: Pereira

state: Iowa

address: 169 Newton Rd

department: Internal Medicine

institute: University of Iowa

data_processing:
psuedoalignment and quantification performed using Kallisto (v0.45.0)
Assembly: mm10
Supplementary files format and content: tab-delimited text files with transcripts per million

extract_protocol:
Total RNA was extracted from tissues with TRIzol reagent (Invitrogen) and purified with the RNeasy kit (Qiagen Inc).
Illumina TruSeq mRNA Stranded kit

value: brown adipose tissue

value: KO

tag: Sex

value: M


title: S15_Opa1-flox_Cre-_Male


title: DMSO, Con0, Optimization plate 4, Well A24 [S4881Nr4_A24]

city: Göttingen

first: Christopher

last: Bruhn

address: Marie-Curie-Str. 7

institute: Evotec International GmbH

data_processing:
Transcriptomic profiling was performed in batches of 382 samples. Each batch contained 22 negative-control (i.e. DMSO-treated) samples, and 15 blocks of compound-treated samples. Every block included 8 compound concentrations, each in triplicate.
Reads were mapped to the human genome (genome-build GRCh38.p13 – accession GCA_000001405.28) using STAR (version 2.7.9a).
Multi-mapped reads, reads with mapping to inter-genic regions (with respect to Ensembl gene annotation information version 104) and reads with ambiguous mapping location (i.e. location associated with more than one gene) were discarded, and UMI-based deduplication was performed.
Sequencing files were demultiplexed and barcodes were stripped.
Assembly: GRCh38.p13 – accession GCA_000001405.28
Supplementary files format and content: processed_data_counts.txt: RNA unique moecular identifier (UMI) counts per gene. The column EnsemblID provides the unique gene identifier. One column is included per sample with column names matching the column "description" in the table "SAMPLES".

extract_protocol:
High-throughput transcriptomics was performed using Evotec’s (semi)-automated ScreenSeqTM platform. Cell lysis was performed in a 384-well plate format followed by well-specific labeling of samples.
Plate RNASeq of polyA RNA (ScreenSeqTM); Purified mRNAs were labeled with a unique molecular identifier (UMI). After pooled cDNA synthesis, adapters containing Illumina’s unique dual indexes were attached for final library preparation and sequenced on a NovaSeq 6000 system.


title: SMF008_MOLM13_Cas9_NegIAA_NegDOX_Rep2_RNAseq


title: S14_Opa1-flox_Cre+_Female

value: F


title: 1470, Batch 4, scRNA-seq

description: 10x Genomics


title: SMF007_MOLM13_Cas9_NegIAA_NegDOX_Rep1_RNAseq


title: SMF006_SEM_Cas9_PosIAA_PosDOX_Rep2_RNAseq

source_name: SEM

value: SEM

value: B cell precursor leukemia


title: S13_Opa1-flox_Cre-_Female

value: WT


title: 528, Batch 3, scRNA-seq

description: 10x Genomics

value: sorted


title: DMSO, Con0, Optimization plate 4, Well B23 [S4881Nr4_B23]

value: hiPSC-CM

value: DMSO, Con0


title: PBS treatment - 3

value: PBS


title: DMSO, Con0, Optimization plate 4, Well C24 [S4881Nr4_C24]


title: 527, Batch 3, scRNA-seq

description: 10x Genomics


title: DMSO, Con0, Optimization plate 4, Well A23 [S4881Nr4_A23]


title: SMF004_SEM_Cas9_NegIAA_PosDOX_Rep2_RNAseq


title: S11_Opa1-flox_Cre-_Male


title: 1126, Batch 6, scRNA-seq

description: 10x Genomics


title: SMF003_SEM_Cas9_NegIAA_PosDOX_Rep1_RNAseq


title: 460, Lot 1U, Batch 1, scRNA-seq

description: 10x Genomics


title: SMF002_SEM_Cas9_NegIAA_NegDOX_Rep2_RNAseq


title: DMSO, Con0, Optimization plate 4, Well B22 [S4881Nr4_B22]


title: S09_Opa1-flox_Cre-_Female


title: 280, Lot 2S, Batch 2, scRNA-seq

description: 10x Genomics


title: S08_Opa1-flox_Cre+_Male


title: DMSO, Con0, Optimization plate 4, Well C23 [S4881Nr4_C23]


title: DMSO, Con0, Optimization plate 4, Well A22 [S4881Nr4_A22]


title: DMSO, Con0, Optimization plate 4, Well C21 [S4881Nr4_C21]


title: SMF112_SEM_dCas9-KRAB-BSD_sgNT_control_Rep2_ATACseq

description:
SRM260372.featureCounts.tsv
SRM260372.reproduciblePeaks.bed

data_processing:
Sequenced reads were processed with Trim-Galore tool v0.4.4 (Krueger F. 2012, https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
Potential adapters were removed, and the 3’ ends of reads were quality trimmed with cutadapt (DOI:10.14806/ej.17.1.200) using the quality cutoff of Q20.
The first 15 bp of each read were clipped to avoid GC bias and reads containing more than 50% of soft-clipped bases were removed.
Reads were then mapped to the human reference genome (hg19) with bwa sampe v0.7.17-r1198 (PMID: 19451168).
Duplicated reads identified with the bamsormadup tool from biobambam2 (v2.0.87, DOI: 10.1186/1751-0473-9-13)
Properly paired and uniquely mapped reads were extracted in BAM format with samtools v1.2 (PMID: 19505943).
Then, using bedtools v2.24.0 (PMID: 20110278), nucleosome free fragments (defined as fragments <100 bp), were extracted, and MACS2 tool v2.1.1.20160309 (PMID: 18798982) was used to call peaks in narrow format with --extsize 200 ---nomodel -q 0.05 flags (high confidence peaks). Nucleosome free fragments were also used to generate bigWig files for visualization purposes.
Separately, ATAC-seq peaks were also called using more relaxed criteria, setting the -q flag to 0.5, which are here referred to as low-confidence peaks. Finally, the reproducible high-confidence peaks between the biological replicates from the same condition were identified as those that, for the same genomic region, either had high or low confidence peaks called in all other biological replicates. Reproducible peaks from each condition were then merged into one collection of reproducible peaks.
Assembly: hg19 (GRCh37.p13)
Supplementary files format and content: Reproducible peaks (BED file format). Feature counts (i.e. number of nucleosome free fragments) per reproducible peak, per sample (TSV format). Nucleosome free signal per sample (bigWig format).

growth_protocol: SEM cells were maintained in RPMI 1640 medium (GIBCO, Life Technologies) supplemented with 10% heat-inactivated fetal bovine serum and 2 mM L-glutamine, at 37°C in 5% CO2.

extract_protocol:
Briefly, 10,000 of SEM cells were treated with transposition mix consisting of 22 μL nuclease-free water; 25 μL 2 × TD Buffer; 2.5 μL TDE1 transposase; and 0.5 μL of 1% digitonin (added immediately before removing the supernatant from cell pellets), followed by incubation at 37°C on an Eppendorf ThmorMixer at 300 rpm for 30 minutes. DNA was purified with using the MinElute Reaction Cleanup Kit (Qiagen, 28204) and amplified for 5 cycles using the PCR mix composed of 10 μL transposed DNA, 2.2 μL nuclease-free water, 6.25 μL 10 μM barcoded Nextera primer-F, 6.25 μL 10 μM barcoded Nextera primer-R, 0.3 μL 100 × SYBR Green I (Invitrogen, S-7563), and 25 μL NEBNext® High-Fidelity 2 × PCR Master Mix (NEB, M0541). PCR products were subsequently re-amplified for another 6 PCR cycles, followed by purification using SPRIselect beads (Beckman Coulter, B23317).
Paired-end sequencing (2 × 100 bp) was performed using the Illumina HISeq 4000 platform. Paired-end reads were analyzed using cutadapt (version 1.18) for adaptor trimming and then mapped to the human hg19 genome by Bowtie2 (version 2.2.9)

treatment_protocol: SEM cells were maintained under regular antibiotics condition with penicillin and streptomycin.

value: dCas9-KRAB-BSD with non-specific guide RNA


title: 279, Lot 2U, Batch 2, scRNA-seq

description: 10x Genomics

value: interneurons


title: NPCs, scRNAseq

description: 10x Genomics

source_name: NPC

value: NPC

value: day 14

value: Day 14 of differentiation


title: DMSO, Con0, Optimization plate 4, Well B21 [S4881Nr4_B21]


title: S07_Opa1-flox_Cre-_Male


title: SMF001_SEM_Cas9_NegIAA_NegDOX_Rep1_RNAseq


title: S12_Opa1-flox_Cre+_Male


title: S06_Opa1-flox_Cre+_Female


title: SMF005_SEM_Cas9_PosIAA_PosDOX_Rep1_RNAseq


title: SMF111_SEM_dCas9-KRAB-BSD_sgNT_control_Rep1_ATACseq


title: ESCs, scRNAseq

description: 10x Genomics

source_name: ESC

value: ESC

value: day 0

value: Day 0 of differentiation


title: 461, Lot 1S, Batch 1, scRNA-seq

description: 10x Genomics

value: End of Process


title: DMSO, Con0, Optimization plate 4, Well C22 [S4881Nr4_C22]

source_name: hiPSC-CM


title: SMF110_SEM_dCas9-KRAB-BSD_sgFLT3_DE-1_Rep2_ATACseq

value: dCas9-KRAB-BSD with guide RNA targeting FLT3


title: S10_Opa1-flox_Cre+_Female

value: brown adipose tissue

value: KO

value: F


title: DMSO, Con0, Optimization plate 4, Well C20 [S4881Nr4_C20]

value: WT


title: DMSO, Con0, Optimization plate 4, Well A21 [S4881Nr4_A21]

value: hiPSC-CM


title: S05_Opa1-flox_Cre-_Female


title: SMF109_SEM_dCas9-KRAB-BSD_sgFLT3_DE-1_Rep1_ATACseq

value: SEM

value: B cell precursor leukemia


title: DMSO, CDKI-73, 4h, rep3

city: Bedford Park

first: Luke

last: Selth

state: SA

address: Flinders Drive

department: College of Medicine and Public Health

country: Australia

institute: Flinders University

data_processing:
Raw data were analyzed and quality checked using the FastQC program (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Reads were mapped against the human reference genome (hg38) using the STAR spliced alignment algorithm (version 2.6.1d with default parameters and --chimSegmentMin 20, --quantMode GeneCounts), returning an average unique alignment rate of 86.7%.
Differential expression analysis was evaluated from TMM normalized gene counts using R (version 3.2.3) and edgeR (version 3.3).
Graphical representations of differentially expressed genes were generated using Glimma.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file that includes normalised counts (counts per million) for all samples

source_name: LNCaP

growth_protocol: LNCaP cells were grown in baseline conditions (RPMI-1640 supplemented with 10% FBS).

extract_protocol:
Total RNA was extracted using a PureLink RNA Mini Kit (Life Technologies).
PolyA+ enriched RNA-seq libraries were generated using NEBNext stranded library prep kits.
PolyA+ enriched RNA-seq libraries from biological replicates of the untreated and treated groups were multiplexed and sequenced on the Illumina NextSeq 500 platform at the Australian Cancer Research Foundation (ACRF) Cancer Genomics Facility using a stranded, single end protocol with a read length of 75 bp.

treatment_protocol: Cells were treated with DMSO/CDKI-73 for 4h.

value: LNCaP

value: DMSO (vehicle control)


title: S04_Opa1-flox_Cre+_Male

value: M


title: DMSO, CDKI-73, 4h, rep2


title: PDX CNS 2938

data_processing:
Basecalls performed using RTA 2.7.3
Bad quality reads were filtered out using Trimmomatic (v 0.36) with the following paramters: HEADCROP:3 TRAILING:10 MINLEN:25
paired-end reads were aligned to the hg19 genome assembly using STAR (v2.5.2b), and read count per gene was subsequently estimated with the following parameters: --outFilterType BySJout --outFilterMultimapNmax 10 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999  --outFilterMismatchNoverLmax 0.05 i--alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMatchNmin 16  --quantMode GeneCounts
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited txt file including read count per gene for each sample

source_name: SCNSL PDX 2938

extract_protocol:
high pure RNA Isolation Kit from Roche Life Science (11828665001)
For library preparation RNA was converted to cDNA and amplified (10 PCR cycles) with the  SMART Seq v4 ultra-low RNA kit from Takara following the manufacturer´s instructions. For library preparation 10ng or the respective maximum available amount of RNA were used as input for the NEB ChIP Seq protocol following the manufacturer´s recommendations but skipping the size selection and using the high fidelity 2x PCR master mix from NEB.

value: hCD19 sorted cells from CNS

value: SCNSL B-lymphoma cells


title: S03_Opa1-flox_Cre-_Male


title: DMSO, CDKI-73, 4h, rep1


title: DMSO, Con0, Optimization plate 4, Well A20 [S4881Nr4_A20]

value: DMSO, Con0


title: PDX Spleen 2938

value: hCD19 sorted cells from spleen


title: S02_Opa1-flox_Cre+_Female


title: DMSO, Con0, Optimization plate 4, Well C19 [S4881Nr4_C19]


title: LNCaP, CDKI-73, 4h, rep3

value: 250nM CDKI-73


title: PDX Liver 2938

value: hCD19 sorted cells from liver


title: LNCaP, CDKI-73, 4h, rep2


title: DMSO, Con0, Optimization plate 4, Well B19 [S4881Nr4_B19]


title: S01_Opa1-flox_Cre-_Female


title: PDX CNS 4113

source_name: PCNSL PDX 4113

value: PCNSL B-lymphoma cells


title: LNCaP, CDKI-73, 4h, rep1


title: DMSO, Con0, Optimization plate 4, Well A19 [S4881Nr4_A19]


title: Splenic YFP+ Tregs, KO

city: xian

first: Cangang

last: Zhang

state: State...

address: Yanta district, xi 'an city, shaanxi province

institute: xian jiaotong university

data_processing:
The 10x Genomics Cell Ranger (5.0.1 version) pipeline was used to demultiplex raw files into FASTQ files, extract barcodes and UMI, filter, and map reads to the corresponding reference genome, and generate a matrix containing UMI counts.
A 10x Genomics Cell Ranger pipeline was used to identify clonotypes by alignment and annotation with the default settings.
Genome_build: mm10
Supplementary_files_format_and_content: Cell Ranger output files (features.tsv.gz, barcodes.tsv.gz, matrix.mtx.gz)

source_name: spleen

extract_protocol:
Spleen tissues were processed with the flat end of a syringe in a 100 mm culture dish containing 5 ml cold FACS buffer (2% FBS in PBS), then passed through a 70 μm cell strainer into a 15 ml tube. Cells were centrifuged to remove the supernatant. Cell pellets were treated with 1ml ACK (Ammonium-Chloride-Potassium) Lysing Buffer to remove the red blood cells. After washing with 10 ml cold FACS buffer, the remaining cells were stained with 7AAD (Part 76332; Lot B226294 Biolegend) for 30 min at 4 °C, then washed and resuspended in cold FACS buffer for flow cytometric sorting using FACS Aria II Cell Sorter (BD Biosciences). Sorted YFP+7AAD- cells with a viability higher than 90% were used for 10X genomics scRNA-seq. Finally, libraries were sequenced on a NovaSeq 6000 system with NovaSeq 6000 S4 Reagent Kit (300 cycles).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: YFP+7AAD- cells were sorted from the spleens of  from 7-day-old WT and KO (Zfp335fl/flFoxp3-Cre) mice

value: spleen

value: Tregs

tag: strain

value: KO (Zfp335fl/flFoxp3-Cre)


title: Splenic YFP+ Tregs, WT

value: WT


title: DMSO, Con0, Optimization plate 4, Well B20 [S4881Nr4_B20]

value: hiPSC-CM


title: Cohort LT-ART, Subject 728, month 5

status: Public on Oct 09 2023

city: Chapel Hill

first: Mark

last: Woodcock

state: NC

address: 170 Manning Drive

institute: University of North Carolina at Chapel Hill

description:
p728_month5
TCR beta-chain 5’ RACE

data_processing:
Quality assessment with FastQC (v0.11.7)
Local alignment, clonotype estimation and assembly, and inference of CDR1,2,3 regions, V,D,J,C alleles and relative clone frequencies were assessed with MiXCR (v2.1.9-6)
Assembly: Local alignment against human IMGT TCR allelic data
Supplementary files format and content: MiXCR T-cell beta chain clonotype estimation, tab-separated text file

source_name: CD4 cells isolated via magnetic beads from peripheral blood mononuclear cells

growth_protocol: Peripheral blood cells were washed with PBS and CD4+ T cells isolated with Miltenyi Biotec CD4+ magnetic bead sorting, prior to 4 hours of stimulation with CD3/28 beads.

extract_protocol: Libraries were prepared for TCR sequencing using the SMARTer Human TCR a/b Profiling Kit v2 (Takara Bio USA, Inc., Cat# 634479). Typically, 30ng total RNA was used as input for cDNA synthesis using Takara’s oligo dT primers (TCR SMART UMI Oligo). β-chain repertoire of the TCR variable region was targeted for library construction. Library quantity, purity and size selection were assessed using Qubit fluorometer (Qubit DNA Assay kit, Invitrogen Q32854) and an Agilent Bioanalyzer (D5000 ScreenTape, Agilent 5067-5592) with acceptable library size distribution between 600 to 1150bp. Sample TCR libraries were pooled with 10% PhiX control v3 (Illumina, Cat# FC-110-3001). Sequencing was performed on an Illumina NextSeq2000 sequencer with 2x150 base paired end read chemistry through the UNC High-Throughput  Sequencing Facility.

treatment_protocol: Stimulated CD4+ T cells were then washed with PBS, lysed and total RNA extracted using the RNeasy Plus Micro kit (Qiagen 74034). RNA was quantified using a Qubit fluorometer (Qubit RNA Assay kit, Invitrogen Q32855), and quality was assessed with the Agilent TapeStation using High Sensitivity RNA ScreenTape (Agilent 5067-5579) to measure the integrity of the extracted RNA. All samples had a RIN score >8. Extracted RNA was stored at -80°C.

value: CD4+ T cells


title: Cohort LT-ART, Subject 867, month 17

description:
p867_month17
TCR beta-chain 5’ RACE

value: CD4 cells isolated via magnetic beads from peripheral blood mononuclear cells


title: Cohort LT-ART, Subject 867, month 5

description:
p867_month5
TCR beta-chain 5’ RACE


title: Cohort LT-ART, Subject 674, month 19

description:
p674_month19
TCR beta-chain 5’ RACE


title: Cohort LT-ART, Subject 867, month 0

description:
p867_month0
TCR beta-chain 5’ RACE


title: Cohort LT-ART, Subject 728, month 0

description:
p728_month0
TCR beta-chain 5’ RACE


title: Cohort LT-ART, Subject 674, month 4

description:
p674_month4
TCR beta-chain 5’ RACE


title: Cohort LT-ART, Subject 728, month 18

description:
p728_month18
TCR beta-chain 5’ RACE


title: Cohort LT-ART, Subject 674, month 0

description:
p674_month0
TCR beta-chain 5’ RACE


title: Cohort A5248, Subject 611183, day 504

description:
p611183_day504
TCR beta-chain 5’ RACE


title: Cohort A5248, Subject 611183, day 21

description:
p611183_day21
TCR beta-chain 5’ RACE


title: Cohort A5248, Subject 363044, day 84

description:
p363044_day84
TCR beta-chain 5’ RACE


title: Cohort A5248, Subject 611183, day 84

description:
p611183_day84
TCR beta-chain 5’ RACE


title: Cohort A5248, Subject 363044, day 504

description:
p363044_day504
TCR beta-chain 5’ RACE


title: Cohort A5248, Subject 363044, day 21

description:
p363044_day21
TCR beta-chain 5’ RACE


title: Cohort A5248, Subject 363044, day 10

description:
p363044_day10
TCR beta-chain 5’ RACE


title: PDX Spleen 4113


title: Cohort A5248, Subject 363043, day 504

description:
p363043_day504
TCR beta-chain 5’ RACE


title: Cohort A5248, Subject 363044, day 0

description:
p363044_day0
TCR beta-chain 5’ RACE


title: Cohort A5248, Subject 363043, day 21

description:
p363043_day21
TCR beta-chain 5’ RACE


title: Cohort A5248, Subject 363043, day 10

description:
p363043_day10
TCR beta-chain 5’ RACE


title: Cohort A5248, Subject 363043, day 0

description:
p363043_day0
TCR beta-chain 5’ RACE


title: Cohort A5248, Subject 363043, day 84

description:
p363043_day84
TCR beta-chain 5’ RACE


title: Cohort A5248, Subject 291374, day 504

description:
p291374_day504
TCR beta-chain 5’ RACE


title: Cohort A5248, Subject 291374, day 84

description:
p291374_day84
TCR beta-chain 5’ RACE


title: Cohort A5248, Subject 291374, day 7

description:
p291374_day7
TCR beta-chain 5’ RACE


title: Cohort A5248, Subject 291374, day 21

description:
p291374_day21
TCR beta-chain 5’ RACE


title: Cohort A5248, Subject 611183, day 7

description:
p611183_day7
TCR beta-chain 5’ RACE


title: Cohort A5248, Subject 291374, day 0

description:
p291374_day0
TCR beta-chain 5’ RACE


title: Cohort A5248, Subject 611183, day 0

description:
p611183_day0
TCR beta-chain 5’ RACE


title: Patient 26 cgMVI26

city: Rotterdam

first: Iacopo

last: Cristoferi

state: Zuid-Holland

address: Doctor Molewaterplein, 40

institute: Erasmus MC

hyb_protocol: Erasmus MC Samples: The tubes were incubated for 24 hours at 65°C with probes of the B-HOT panel and successively preserved at 4°C following manufacturer instructions. Massachusetts General Hospital Samples: following manufacturer instructions.

scan_protocol: Erasmus MC Samples: 100ng total RNA of each of the ErasmusMC-cases were used for analyses using the B-HOT panel within the nCounter® FLEX Analysis System (NanoString Technologies, Inc., Seattle, Washington, United States) following manufacturer instructions to generate gene expression profiles scanning 490 fields of view. Massachusetts General Hospital Samples: Gene expression of the FFPE tissue–derived RNA isolates was quantified using the nCounter MAX System (NanoString Technologies, Seattle, WA) scanning 490 fields of view.

data_processing: Gene expression data of all the included cases were imported within the R environment for further analysis. Quality control and normalization were performed according to Bhattacharya et al. (DOI: 10.1093/bib/bbaa163) and succesively log-transofrmed.

source_name: Kidney allograft for-cause biopsy

extract_protocol: ErasmusMC Samples: the ErasmusMC samples used in the RNA isolation procedure were prepared from snap-frozen for-cause biopsy material of which tissue sections were cut using a cryotome. A 4 µm section was stained by H&E to assess cortical tissue. After removing all non-cortical tissue, six consecutive 10 µm sections were obtained from each tissue specimen and stored at -80°C. Between blocks, microtome blades were replaced and the equipment was sterilized using RNase AWAY™ Decontamination Reagent (Thermo Fisher Scientific Inc., Waltham, Massachusetts, United States). Approximately 30 mg of each sample were used. The tissue fragments were placed into 700 µL QIAzol Lysis Reagent (QIAGEN, Venlo, the Netherlands; Cat. No. 79306) for disruption and homogenization using TissueLyser LT/II (QIAGEN). Homogenates were incubated at 15°C to 25°C for 5 min and 140 µL of chloroform were added to each sample for phase separation. Successively, the mixtures were incubated again at 15°C to 25°C for 3 min and successively centrifuged at 4°C and 12000 x g for 15 min. RNA was then extracted and purified using the miRNeasy Kit (QIAGEN; Cat. No. 217004) following the manufacturer’s instructions. Using the 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, California, United States) and the NanoDrop Spectrophotometers (Thermo Fisher Scientific, Inc., Waltham, Massachusetts, United States) the RNA samples were quantified (in ng/µL) and quality was assessed. Extracted RNA was stored at -80°C for later use. Massachusetts General Hospital Samples: The microtome area was cleaned with 95% ethanol and RNase AWAY (Thermo Fisher Scientific, Waltham, MA) before cutting. Five to six consecutive 20-μm curls cut from each FFPE block were immediately transferred to sterile microcentrifuge tubes and stored at room temperature. Microtome blades were then replaced, and equipment sterilized with RNase AWAY between blocks. Deparaffinization and RNA extraction were performed with the Quick-RNA FFPE Miniprep (Zymo Research, Irvine, CA). RNA concentration and purity were measured with a Nano-Drop 2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA).

value: Kidney allograft biopsy

tag: diagnosis

value: cg+MVI DSA-/C4d-

tag: recipient sex

value: female

tag: batch

value: A


title: Patient 32 cgMVI32

value: male

value: B


title: Patient 33 cgMVI33


title: Patient 35 cgMVI35


title: Patient 28 cgMVI28


title: Patient 24 cgMVI24


title: Patient 30 cgMVI30


title: Patient 29 cgMVI29


title: Patient 34 cgMVI34


title: Patient 22 cgMVI22


title: Patient 23 cgMVI23


title: Patient 21 cgMVI21

value: CA-AMR DSA+/C4d+


title: Patient 17 cgMVI17


title: Patient 18 cgMVI18


title: Patient 19 cgMVI19


title: Patient 20 cgMVI20


title: Patient 14 cgMVI14


title: Patient 13 cgMVI13


title: Patient 12 cgMVI12


title: Patient 11 cgMVI11


title: Patient 10 cgMVI10


title: Patient 09 cgMVI09


title: Patient 27 cgMVI27


title: Patient 31 cgMVI31


title: Patient 25 cgMVI25


title: Patient 08 cgMVI08


title: Patient 07 cgMVI07


title: Patient 06 cgMVI06


title: K. aerogenes 35°C, CT18, rep2

city: Lexington

first: Kinga

middle: B.

last: Graniczkowska

state: KY

address: 675 Rose St

department: Biology

institute: University of Kentucky

data_processing:
Mapping to a reference was conducted using Hisat2 V2.1 software and --dta—phred33 parameters
Comparing transcriptomes was performed using Cuffcompare V2.1.1 software
Quantification was performed using FeatureCounts software (Liao Y, Smyth GK and Shi W, Bioinformatics, 30(7):923-30, 2014).
Differential expression analysis was performed using the DESeq2 (V2_1.6.3).  The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value <0.05 found by DESeq were assigned as differentially expressed.
Genome_build: Enterobacter aerogenes KCTC 2190, complete genome (https://www.ncbi.nlm.nih.gov/nuccore/CP002824)
Supplementary_files_format_and_content: Excel file including FPKM values for each sample

organism: Klebsiella aerogenes

source_name: K. aerogenes 35°C, CT18

growth_protocol: 2 uL of overnight culture of K.aerogenes was spotted on semisolid EMB agar. Then we implemented temperature entrainment using 12:12 cycle of  35°C and 36°C for 3 days. Samples were collected on day 3 at Zeitgeber time 6 (ZT6) and ZT18. Then bacteria were released into constant 35°C and samples were collected on day 4 at circadian time 6 (CT6) and CT18.

extract_protocol:
RNA was extracted using hot phenol method. RNA sample quality was assessed by High Sensitivity RNA Tapestation (Agilent Technologies Inc., California, USA) and quantified by Qubit 2.0 RNA HS assay (ThermoFisher, Massachusetts, USA). Ribosomal RNA depletion was performed with QIAseq® FastSelect rRNA (Qiagen, Hilden, Germany) per manufacturer’s instructions.
All library construction were prepared according to the the NEBNext® UltraTM II Non-Directional RNA Library Prep Kit for Illumina® (New England BioLabs Inc., Massachusetts, USA). Final libraries quantity was assessed by Qubit 2.0 (ThermoFisher, Massachusetts, USA) and quality was assessed by TapeStation with High Sensitivity D1000 ScreenTape (Agilent Technologies Inc., California, USA).
Equimolar pooling of libraries was performed based on QC values and sequenced on an Illumina® NovaSeq S4 (Illumina, California, USA) with a read length configuration of 150 PE for 13 M PE reads per sample (6.5M in each direction).

tag: timepoint

value: macrocolony biofilm


title: Patient 16 cgMVI16


title: K. aerogenes 35°C, CT18, rep3


title: Patient 15 cgMVI15


title: K. aerogenes 35°C, CT6, rep3

source_name: K. aerogenes 35°C, CT6


title: K. aerogenes 35°C, CT18, rep1


title: K. aerogenes 36°C, ZT18, rep3

source_name: K. aerogenes 36°C, ZT18


title: Patient 02 cgMVI02


title: Patient 04 cgMVI04


title: K. aerogenes 35°C, CT6, rep1


title: Patient 05 cgMVI05


title: K. aerogenes 35°C, ZT6, rep3

source_name: K. aerogenes 35°C, ZT6


title: Patient 01 cgMVI01


title: K. aerogenes 35°C, CT6, rep2


title: Patient 03 cgMVI03


title: K. aerogenes 36°C, ZT18, rep2


title: K. aerogenes 36°C, ZT18, rep1


title: RUN2_CDNA2_mRNA

city: Marseille

first: Romain

last: Fenouil

address: Parc Scientifique et Technologique de Luminy - Case 906

department: CIML

country: France

institute: CNRS

description: 3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

data_processing:
FASTQ raw files were aligned to the mouse genome reference (mm10) using 10x Genomics Cell Ranger 6.0.1, which performs filtering, barcode counting, and unique molecular identifier (UMI) counting.
After individual quality control, all count matrices were loaded and processed together using R package Seurat (6.1.0).
A second Quality control (QC) was performed to evaluate potential batch-related biases, perform HTO demultiplexing, and identify poor quality cells to be excluded before downstream analyses. Cells with less than 1000 counted UMIs or more than 5000 detected genes (potential doublets), and cells with more than 10% mitochondrial gene expression (apoptotic cells) or less than 5% ribosomal genes were excluded from analyses. Then,  19 datasets from two independent experiments were pooled and analyzed.
Assembly: mm10
Supplementary files format and content: Cellranger output: barcodes.tsv is a list of filtered barcodes associated with count matrix
Supplementary files format and content: Cellranger output: features.tsv is a list of filtered features associated with count matrix
Supplementary files format and content: Cellranger output: matrix.mtx is the (sparse) matrix containing feature counts across all selected barcodes

source_name: mRNA

growth_protocol: Subcutaneous MCA205 cell engraftment

extract_protocol:
Tumors from MCA-205 bearing mice treated with PBS or Pant were harvested at D20 or D28 in DMEM F12 medium. After dissociation and RBC lysis, cells suspension from the four experimental conditions were tagged using TotalSeq B0301 and pooled. CD45 positive Live Dead negative cells were sorted on ARIA SORP, collected in SVF-coated tube and pooled in equivalent ratio. Then, cells suspension was immediately processed according to the Chromium Next GEM Single Cell v3.1 GEM protocols.
HTO and DNA libraries were sequenced at the CIML genomic facility using a P2 flowcell in Illumina NextSeq 1000/2000. 2 independent experiments were performed and analyzed separately.

treatment_protocol: Intraperitoneal injections of pantethine (1g/kg-1)

value: tumor

value: mouse fibrosarcoma

tag: antibodies/tags

value: PBS and Pantethine


title: RUN1_CDNA2_HTO

description: Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads

library_source: other

molecule: other

source_name: HTO

tag: cell line

value: D21_PBS TotalSeq-B0301 anti-mouse CD45 and MHC-I Hashtag 1 Antibody / D21_Panth TotalSeq-B0302 anti-mouse CD45 and MHC-I Hashtag 2 Antibody / D29_PBS TotalSeq-B0303 anti-mouse CD45 and MHC-I Hashtag 3 Antibody / D29_Panth TotalSeq-B0304 anti-mouse CD45 and MHC-I Hashtag 4 Antibody


title: RUN2_CDNA2_HTO


title: RUN2_CDNA1_HTO


title: RUN1_CDNA2_mRNA


title: RUN1_CDNA1_HTO


title: RUN1_CDNA1_mRNA


title: RUN2_CDNA1_mRNA


title: CEG-stim

city: St. Louis

first: Emily

last: Landy

state: Missouri

address: 425 S. Euclid Ave

institute: Washington University in St. Louis

description:
s39
NLRC4_EXPRESSIONMATRIX_RPKM.xlsx

data_processing:
Reference sequence = Homo_sapiens_sequence_hg38
Gene track = Homo_sapiens_ensembl_v106.1_hg38
mRNA track = Homo_sapiens_ensembl_v106.1_hg38
CLC Genomics Workbench V22
Assembly: hg38
Supplementary files format and content: NLRC4_EXPRESSIONMATRIX_RPKM.xlsx is the raw counts for s33-s40
Supplementary files format and content: THP1_MATRIX.xlsx in the raw countsfor s01-s23 in TPMs

source_name: PBMC-derived Monocytes

growth_protocol: PBMC-derived monocytes were purified by CD14+ selection (Miltenyi) and cultured in recombinant human M-CSF (10ng/mL) for 7 days, changing the media every 2 days.

extract_protocol:
Cells were lysed in Trizol, RNA isolated, and RNA integrity analyzed with the Agilent 2200 Tapestation.
Messenger RNA purification and fragmentation, cDNA synthesis and target amplification were performed with Illumina TruSeq RNA Sample Preparation kit.

treatment_protocol:
Stably-transduced THP1 cells were stimulated with 10ng/mL PMA for up to 72 hours.
Cells were then de-adhered with accutase and cultured in Opti-MEM alone or with LPS  for 4 hours then in 1ug/mL DOTAP/flagellin for an additional 2 hours as in Canna et al. Nat Gen, 2014 [PMID:25217959].

value: PBMC-derived Monocytes

tag: genotype

value: CEG

tag: treatment time_(hrs)


title: NOMID-nostim

description:
s36
NLRC4_EXPRESSIONMATRIX_RPKM.xlsx

value: NOMID


title: NOMID-stim

description:
s40
NLRC4_EXPRESSIONMATRIX_RPKM.xlsx


title: Ctrl1-stim

description:
s37
NLRC4_EXPRESSIONMATRIX_RPKM.xlsx

value: Control


title: Ctrl2-stim

description:
s38
NLRC4_EXPRESSIONMATRIX_RPKM.xlsx


title: Ctrl1-nostim

description:
s33
NLRC4_EXPRESSIONMATRIX_RPKM.xlsx


title: Mut_72 - 3

description:
s23
THP1_MATRIX.xlsx


title: Mut_0 - 3

description:
s17
THP1_MATRIX.xlsx


title: Ctrl2-nostim

description:
s34
NLRC4_EXPRESSIONMATRIX_RPKM.xlsx


title: WT_6 - 3

description:
s18
THP1_MATRIX.xlsx

value: WT


title: K. aerogenes 35°C, ZT6, rep1

tag: treatment


title: K. aerogenes 35°C, ZT6, rep2

tag: tissue


title: WT_72 - 3

description:
s22
THP1_MATRIX.xlsx

tag: cell type


title: Mut_24 - 2

description:
s13
THP1_MATRIX.xlsx


title: Mut_24 - 3

description:
s21
THP1_MATRIX.xlsx


title: Mut_6 - 3

description:
s19
THP1_MATRIX.xlsx


title: WT_24 - 3

description:
s20
THP1_MATRIX.xlsx


title: WT_0 - 3

description:
s16
THP1_MATRIX.xlsx


title: Mut_0 - 2

description:
s10
THP1_MATRIX.xlsx


title: WT_0 - 2

description:
s09
THP1_MATRIX.xlsx


title: Mut_72 - 2

description:
s15
THP1_MATRIX.xlsx


title: WT_72 - 2

description:
s14
THP1_MATRIX.xlsx


title: WT_72 - 1

description:
s07
THP1_MATRIX.xlsx


title: Mut_72 - 1

description:
s08
THP1_MATRIX.xlsx


title: Mut_24 - 1

description:
s06
THP1_MATRIX.xlsx


title: WT_24 - 2

description:
s12
THP1_MATRIX.xlsx


title: WT_24 - 1

description:
s05
THP1_MATRIX.xlsx


title: WT_0 - 1

description:
s01
THP1_MATRIX.xlsx


title: Mut_6 - 2

description:
s11
THP1_MATRIX.xlsx


title: Mut_6 - 1

description:
s04
THP1_MATRIX.xlsx


title: CEG-nostim

description:
s35
NLRC4_EXPRESSIONMATRIX_RPKM.xlsx


title: Mut_0 - 1

description:
s02
THP1_MATRIX.xlsx


title: WT_6 - 1

description:
s03
THP1_MATRIX.xlsx


title: SV18359-1616

city: Boston

first: Joanne

last: Sordillo

state: MA

address: 181 Longwood Avenue

department: Channing Division of Network Medicine

institute: Mass General Brigham

data_processing:
The ExceRpt pipeline was used for quality control (QC) of the RNA-seq data
miRNAs with less than five mapped reads in at least 50% of subjects were removed prior to analysis
subjects with less than 100k mapped reads were dropped.
Assembly: hg38, miRBase v22
Supplementary files format and content: tab-delimited text file with raw counts of miRNA x Sample.

source_name: serum

extract_protocol:
Total RNA was isolated from archival serum samples using the miRNeasy kit (Qiagen, Germantown, MD) according to the manufacturer's instructions
small RNA-seq libraries were prepared by using the Norgen Biotek Small RNA Library Prep Kit (Norgen Biotek, Therold, Canada), and sequenced on the Illumina NextSeq 500 platform.
NextSeq 500/550 High Output Kit v2 (51 Cycles using a 75-Cylce Kit)

value: serum

tag: age

value: F

tag: pctpred fev1_pre_bd

tag: inhaled steroids

tag: bdrbase


title: SV18359-1625

tag: Sex

value: M


title: SV18359-1622


title: SV18359-1624


title: SV18359-1608


title: SV18359-1621


title: SV18359-1619


title: SV18359-1618


title: SV18359-1626


title: SV18359-1606


title: SV18359-1615


title: SV18359-1604


title: SV18359-1605


title: SV18359-1602


title: SV18359-1612


title: SV18359-1613


title: SV18359-1611


title: SV18359-1609


title: SV18359-1620


title: SV18359-1610


title: SV18359-1617


title: SV18359-1598


title: SV18359-1607


title: SV18359-1597


title: SV18359-1623


title: SV18359-1591


title: SV18359-1589


title: SV18359-1592


title: SV18359-1588


title: SV18359-1587


title: SV18359-1600


title: SV18359-1599


title: SV18359-1601


title: SV18359-1614


title: SV18359-1603


title: SV18359-1585


title: SV18359-1596


title: SV18359-1584


title: SV18359-1593


title: SV18359-1595


title: SV18359-1594


title: SV18359-1579


title: SV18359-1575


title: SV18359-1590


title: SV18359-1574


title: SV18359-1572


title: SV18359-1573


title: SV18359-1571


title: SV18359-1586


title: SV18359-1570


title: SV18359-1583


title: SV18359-1581


title: SV18359-1580


title: SV18359-1566


title: SV18359-1578


title: SV18359-1565


title: SV18359-1564


title: SV18359-1582


title: SV18359-1560


title: SV18359-1561


title: SV18359-1569


title: SV18359-1562


title: SV18359-1555


title: SV18359-1554


title: SV18359-1568


title: SV18359-1567


title: SV18359-1563


title: SV18359-1558


title: SV18359-1577


title: SV18359-1557


title: SV18359-1556


title: SV18359-1552


title: SV18359-1547


title: SV18359-1551


title: SV18359-1546


title: SV18359-1543


title: SV18359-1550


title: SV18359-1539


title: SV18359-1537


title: SV18359-1535


title: SV18359-1540


title: SV18359-1534


title: SV18359-1549


title: SV18359-1548


title: SV18359-1545


title: SV18359-1544


title: SV18359-1542


title: SV18359-1532


title: SV18359-1538


title: SV18359-1530


title: SV18359-1533


title: SV18359-1531


title: SV18359-1529


title: SV18359-1528


title: SV18359-1524


title: SV18359-1553


title: SV18359-1523


title: SV18359-1541


title: SV18359-1525


title: SV18359-1536


title: SV18359-1526


title: SV18359-1518


title: SV18359-1520


title: SV18359-1521


title: SV18359-1522


title: SV18359-1513


title: SV18359-1519


title: SV18359-1515


title: SV18359-1517


title: SV18359-1516


title: SV18359-1512


title: SV18359-1514


title: SV18359-1510


title: SV18359-1527


title: SV18359-1511


title: SV18359-1509


title: SV18359-1507


title: SV18359-1508


title: SV18359-1506


title: SV18359-1504


title: SV18359-1503


title: SV18359-1502


title: SV18359-1496


title: SV18359-1505


title: SV18359-1501


title: SV18359-1498


title: SV18359-1500


title: SV18359-1495


title: SV18359-1499


title: SV18359-1494


title: SV18359-1493


title: SV18359-1490


title: SV18359-1488


title: SV18359-1491


title: SV18359-1489


title: SV18359-1484


title: SV18359-1485


title: SV18359-1486


title: SV18359-1482


title: SV18359-1492


title: SV18359-1483


title: SV18359-1480


title: SV18359-1479


title: SV18359-1481


title: SV18359-1487


title: SV18359-1477


title: SV18359-1475


title: SV18359-1474


title: SV18359-1473


title: SV18359-1469


title: SV18359-1465


title: SV18359-1471


title: SV18359-1478


title: SV18359-1470


title: SV18359-1468


title: SV18359-1466


title: SV18359-1464


title: SV18359-1463


title: SV18359-1462


title: SV18359-1459


title: SV18359-1461


title: SV18359-1456


title: SV18359-1458


title: SV18359-1455


title: SV18359-1460


title: SV18359-1467


title: SV18359-1454


title: SV18359-1452


title: SV18359-1451


title: SV18359-1453


title: SV18359-1476


title: SV18359-1472


title: SV18359-1450


title: SV18359-1448


title: SV18359-1447


title: SV18359-1445


title: SV18359-1446


title: SV18359-1441


title: SV18359-1442


title: SV18359-1439


title: SV18359-1436


title: SV18359-1426


title: SV18359-1457


title: SV18359-1432


title: SV18359-1430


title: SV18359-1434


title: SV18359-1435


title: SV18359-1431


title: SV18359-1427


title: SV18359-1437


title: SV18359-1421


title: SV18359-1433


title: SV18359-1422


title: SV18359-1420


title: SV18359-1423


title: SV18359-1425


title: SV18359-1419


title: SV18359-1417


title: SV18359-1416


title: SV18359-1440


title: SV18359-1449


title: SV18359-1444


title: SV18359-1415


title: SV18359-1443


title: SV18359-1414


title: SV18359-1429


title: SV18359-1424


title: SV18359-1428


title: SV18359-1413


title: SV18359-1410


title: SV18359-1412


title: SV18359-1406


title: SV18359-1408


title: SV18359-1405


title: SV18359-1411


title: SV18359-1404


title: SV18359-1407


title: SV18359-1401


title: SV18359-1402


title: SV18359-1409


title: SV18359-1418


title: SV18359-1403


title: SV18359-1396


title: SV18359-1399


title: SV18359-1393


title: SV18359-1394


title: SV18359-1398


title: SV18359-1390


title: SV18359-1397


title: SV18359-1392


title: SV18359-1391


title: SV18359-1389


title: SV18359-1387


title: SV18359-1400


title: SV18359-1388


title: SV18359-1385


title: SV18359-1386


title: SV18359-1395


title: SV18359-1382


title: SV18359-1383


title: SV18359-1381


title: SV18359-1374


title: SV18359-1376


title: SV18359-1378


title: SV18359-1379


title: SV18359-1370


title: SV18359-1369


title: SV18359-1377


title: SV18359-1375


title: SV18359-1373


title: SV18359-1371


title: SV18359-1364


title: SV18359-1365


title: SV18359-1363


title: SV18359-1384


title: SV18359-1368


title: SV18359-1362


title: SV18359-1366


title: SV18359-1360


title: SV18359-1380


title: SV18359-1357


title: SV18359-1359


title: SV18359-1372


title: SV18359-1358


title: SV18359-1356


title: SV18359-1353


title: SV18359-1367


title: SV18359-1347


title: SV18359-1361


title: SV18359-1354


title: SV18359-1352


title: SV18359-1342


title: SV18359-1355


title: SV18359-1351


title: SV18359-1348


title: SV18359-1349


title: SV18359-1337


title: SV18359-1336


title: SV18359-1350


title: SV18359-1343


title: SV18359-1340


title: SV18359-1344


title: SV18359-1339


title: SV18359-1346


title: SV18359-1333


title: SV18359-1341


title: SV18359-1332


title: SV18359-1334


title: SV18359-1338


title: SV18359-1331


title: SV18359-1335


title: SV18359-1330


title: SV18359-1329


title: SV18359-1326


title: SV18359-1327


title: SV18359-1328


title: SV18359-1345


title: SV18359-1324


title: SV18359-1325


title: SV18359-1323


title: SV18359-1322


title: SV18359-1321


title: SV18359-1320


title: SV18359-1319


title: SV18359-1318


title: SV18359-1316


title: SV18359-1315


title: SV18359-1314


title: SV18359-1311


title: SV18359-1313


title: SV18359-1312


title: SV18359-1304


title: SV18359-1307


title: SV18359-1305


title: SV18359-1302


title: SV18359-1303


title: SV18359-1306


title: SV18359-1309


title: SV18359-1300


title: SV18359-1301


title: SV18359-1299


title: SV18359-1296


title: SV18359-1297


title: SV18359-1295


title: SV18359-1293


title: SV18359-1292


title: SV18359-1291


title: SV18359-1290


title: SV18359-1317


title: SV18359-1289


title: SV18359-1310


title: SV18359-1288


title: SV18359-1438


title: SV18359-1287


title: SV18359-1308


title: SV18359-1284


title: SV18359-1285


title: SV18359-1283


title: SV18359-1281


title: SV18359-1280


title: SV18359-1282


title: SV18359-1279


title: SV18359-1278


title: SV18359-1298


title: SV18359-1277


title: SV18359-1276


title: SV18359-1274


title: SV18359-1275


title: SV18359-1273


title: SV18359-1272


title: SV18359-1294


title: SV18359-1271


title: SV18359-1270


title: SV18359-1267


title: SV18359-1269


title: SV18359-1266


title: SV18359-1265


title: SV18359-1264


title: SV18359-1286


title: SV18359-1263


title: SV18359-1261


title: SV18359-1262


title: SV18359-1259


title: SV18359-1260


title: SV18359-1258


title: SV18359-1256


title: SV18359-1257


title: SV18359-1254


title: SV18359-1255


title: SV18359-1251


title: SV18359-1253


title: SV18359-1249


title: SV18359-1250


title: SV18359-1248


title: SV18359-1246


title: SV18359-1244


title: SV18359-1243


title: SV18359-1268


title: SV18359-1242


title: SV18359-1247


title: SV18359-1245


title: SV18359-1241


title: SV18359-1238


title: SV18359-1236


title: SV18359-1237


title: SV18359-1235


title: SV18359-1240


title: SV18359-1239


title: SV18359-1231


title: SV18359-1234


title: SV18359-1252


title: SV18359-1232


title: SV18359-1230


title: SV18359-1228


title: SV18359-1227


title: SV18359-1223


title: SV18359-1226


title: SV18359-1224


title: SV18359-1225


title: SV18359-1222


title: SV18359-1220


title: SV18359-1219


title: SV18359-1221


title: SV18359-1215


title: SV18359-1216


title: SV18359-1214


title: SV18359-1217


title: SV18359-1212


title: SV18359-1213


title: SV18359-1233


title: SV18359-1211


title: SV18359-1209


title: SV18359-1210


title: SV18359-1208


title: SV18359-1229


title: SV18359-1206


title: SV18359-1203


title: SV18359-1202


title: SV18359-1205


title: SV18359-1207


title: SV18359-1204


title: SV18359-1200


title: SV18359-1198


title: SV18359-1199


title: SV18359-1197


title: SV18359-1218


title: SV18359-1196


title: SV18359-1195


title: SV18359-1194


title: SV18359-1193


title: SV18359-1192


title: SV18359-1191


title: SV18359-1189


title: SV18359-1190


title: SV18359-1188


title: SV18359-1186


title: SV18359-1184


title: SV18359-1182


title: SV18359-1185


title: SV18359-1181


title: SV18359-1178


title: SV18359-1187


title: SV18359-1183


title: SV18359-1180


title: SV18359-1177


title: SV18359-1175


title: SV18359-1176


title: SV18359-1201


title: SV18359-1174


title: SV18359-1173


title: SV18359-1179


title: SV18359-1169


title: SV18359-1171


title: SV18359-1168


title: SV18359-1170


title: SV18359-1165


title: SV18359-1166


title: SV18359-1167


title: SV18359-1164


title: SV18359-1159


title: SV18359-1162


title: SV18359-1172


title: SV18359-1161


title: SV18359-1157


title: SV18359-1160


title: SV18359-1158


title: SV18359-1155


title: SV18359-1151


title: SV18359-1154


title: SV18359-1156


title: SV18359-1153


title: SV18359-1152


title: SV18359-1146


title: SV18359-1149


title: SV18359-1145


title: SV18359-1143


title: SV18359-1147


title: SV18359-1148


title: SV18359-1139


title: SV18359-1137


title: SV18359-1135


title: SV18359-1134


title: SV18359-1133


title: SV18359-1142


title: SV18359-1141


title: SV18359-1140


title: SV18359-1138


title: SV18359-1136


title: SV18359-1150


title: SV18359-1144


title: SV18359-1131


title: SV18359-1130


title: SV18359-1129


title: SV18359-1122


title: SV18359-1123


title: SV18359-1118


title: SV18359-1117


title: SV18359-1116


title: SV18359-1127


title: SV18359-1128


title: SV18359-1113


title: SV18359-1124


title: SV18359-1126


title: SV18359-1111


title: SV18359-1109


title: SV18359-1115


title: SV18359-1114


title: SV18359-1106


title: SV18359-1105


title: SV18359-1132


title: SV18359-1112


title: SV18359-1103


title: SV18359-1108


title: SV18359-1102


title: SV18359-1120


title: SV18359-1121


title: SV18359-1100


title: SV18359-1101


title: SV18359-1098


title: SV18359-1119


title: SV18359-1097


title: SV18359-1095


title: SV18359-1096


title: SV18359-1110


title: SV18359-1089


title: SV18359-1088


title: SV18359-1094


title: SV18359-1086


title: SV18359-1090


title: SV18359-1091


title: SV18359-1084


title: SV18359-1092


title: SV18359-1104


title: SV18359-1099


title: SV18359-1080


title: SV18359-1107


title: SV18359-1083


title: SV18359-1085


title: SV18359-1082


title: SV18359-1081


title: SV18359-1079


title: SV18359-1077


title: SV18359-1075


title: SV18359-1076


title: SV18359-1071


title: SV18359-1078


title: SV18359-1072


title: SV18359-1074


title: SV18359-1087


title: SV18359-1068


title: SV18359-1070


title: SV18359-1069


title: SV18359-1067


title: SV18359-1066