title: ccr7ko_tumor_gex

description:
Gene expression CITEseq library
single_cell_metadata.csv.gz

data_processing:
Library strategy: CITEseq
For CITEseq GEX libraries: Read 1 is technical: Cell barcode is bp 1-16; UMI is bp 17-26. Read 2 is biological.
For CITEseq ADT libraries: Read 1 is technical: Cell barcode is bp 1-16; UMI is bp 17-26. Read 2 is biological: bp 1-7 identify a CITEseq antibody (as indicated in ADT_TAGS.CSV).
After library demultiplexing, gene expression libraries were aligned to the mm10 or GRCh38 reference transcriptomes and count matrices were generated using the default Cell Ranger 2.1 workflow, using the “raw” matrix output. CITEseq library reads were directly queried for antibody barcodes (listed in ADT_TAGS.CSV) and cell barcodes in the appropriate read positions, including antibody sequences within a Hamming distance of 1 from the reference sequence.
single_cell_metadata.csv.gz represents the results of QC filtering and transcriptome-based clustering on CITEseq data.
For RNAseq: Fastqs were aligned to the mm10 reference genome, reads were dereplicated for PCR duplicates, and gene counts were generated using STAR v2.5 using –quantMode GeneCounts.
Genome_build: mm10
Supplementary_files_format_and_content: gene counts

source_name: lung conventional dendritic cells (CD45+ Siglec F- Ly6G- MHCII+ CD11c+) of CCR7-/- mice bearing cells expressing the KrasG12D activating mutation and Tp53 deletion (KP cells)

extract_protocol:
Prior to sorting, cells were stained with a mix of fluorescent antibodies and antibodies which had been conjugated to oligonucleotide barcodes using the Thunder-Link PLUS Oligo Conjugation kits (Expedeon) according to manufacturer’s instructions. The sorted cells were encapsulated using the 10X Chromium platform, and libraries were prepared as previously described (Stoeckius, M. et al. Nat. Methods, doi:10.1038/nmeth.4380, 2017), with minor modifications. Briefly, cDNA amplification was performed in the presence of 2pM of an antibody-oligo specific primer to increase yield of antibody derived tags (ADTs). The amplified cDNA was then separated by SPRI size selection into cDNA fractions containing mRNA derived cDNA (>300bp) and ADT-derived cDNAs (<180bp), which were further purified by additional rounds of SPRI selection. Independent sequencing libraries were generated from the mRNA and ADT cDNA fractions, which were quantified, pooled and sequenced together on an Illumina Nextseq to a depth of 80 million reads per gene expression library and 20 million reads per ADT library.
Single cell suspensions were obtained from lung and LN by digestion with collagenase IV 0.25mg/ml (Sigma) at 37C for 30min (lung) or 25min (LN) followed by passing through a 70um cell strainer and RBC lysis (RBC lysis buffer, BioLegend) for 2min at room temperature. For flow cytometry or FACS cells were stained in FACS buffer (PBS supplemented with 2% BSA and 5mM EDTA) with mAbs specific to CD45 (clone 30-F11, BioLegend), Siglec F (clone E50-2440, BD Pharmingen), CD11c (clone N418, Invitrogen), CD24 (clone M1/69, Invitrogen), CD103 (clone 2E7, BioLegend), I-A/I-E (clone M5/114.15.2, eBioscience), CD11b (clone M1/70, eBioscience)

treatment_protocol: 8-week-old mice were injected intravenously with 5x10e5 KP cells. Lungs were analyzed on day 28.

value: DCs


title: Wild-type non-treated rep1

status: Public on Mar 26 2020

type: SRA

city: Gent

first: Patrick

last: Willems

address: Technologiepark 927

department: PSB

country: Belgium

institute: Ghent University

library_source: transcriptomic

data_processing:
Reads were aligned to the Arabidopsis genome by STAR (v2.5.2b) (Dobin et al., 2013) using the Araport11 annotation (Cheng et al. 2017).
The number of reads per gene was quantified with the featureCounts function as implemented in the Subread package v1.6.2 (Liao et al., 2014).
Genome_build: Araport11
Supplementary_files_format_and_content: Tab-delimited text files include gene counts by featureCounts function

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Plant rosette

growth_protocol: Four-week-old Arabidopsis thaliana Columbia-0 gl1 (Col-0 gl1) wild-type plants and three mutant lines, phot1, phot2 and phot1/phot2, all in the Col-0 gl1 background, were used in this study. Plants were grown in Jiffy pots in standard laboratory conditions (8 h photoperiod, PPFD: 80 mol m ̄² s ̄¹, 50% relative air humidity and temperature day/night: 22/18 °C).

extract_protocol:
Whole rosettes were harvested from non-treated plants and 30 min after UV-C treatment. The RNA was isolated from three biological replicates, each consisting of at least four rosettes. Total RNA isolation was performed using a GeneMATRIX Universal RNA Purification Kit (EURX, Gdańsk, Poland) with the additional step of on-column DNase I digestion.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Precise amount of UV-C radiation (100 mJ cm ̄²) was applied using 500 Crosslinker (Hoefer Pharmacia Biotech, San Francisco, CA, USA), equipped with lamps emitting light in the wavelength ranging from 250 to 258 nm (type G8T5, 8W; Sankyo Denki, Hiratsuka, Japan).

tag: tissue

value: whole rosette

tag: genotype

value: Wild-type

tag: background ecotype

value: Col-0 gl1

tag: treatment

value: Non-treated control

tag: age

value: Four weeks


title: ccr7ko_tumor_adt

city: NEW YORK

first: Miriam

last: Merad

state: New York

address: 1470 Madison Ave, Room 5-301

department: Oncological Sciences

country: USA

institute: ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI

description:
ADT CITEseq library
adt_tags.csv

molecule: polyA RNA

organism: Mus musculus

tag: strain

value: lung

tag: cell type


title: A1-2 cells, D1hr_rep3, Bulk RNAseq

city: Research Triangle Park

first: Jackson

middle: Andrew

last: Hoffman

state: North Carolina

address: 111 TW Alexander Dr, Building 101 Room C432

department: DIR

institute: NIEHS

data_processing:
For bulk RNAseq, adapter sequences were trimmed from RNA-seq reads using Cutadapt (Martin, 2011) and low quality reads were removed from analysis using Sickle (Joshi NA et al., 2011). Alignment was performed using STAR (Dobin et al., 2013) to generate coverage tracks and using Salmon (Patro et al., 2017) and to obtain gene counts for differential expression analysis using limma-voom (Law et al., 2014) with cutoffs of Fold Change > 1.5, p-value<0.01, and False Discovery Rate < 0.05
For single-cell RNAseq, read 1 was technical and read 2 was biological. Barcode and UMI sequence positions are not fixed, so Bio-Rad ddSEQ reads were parsed for cell barcode and UMI information. Reads were filtered out according to the following constraints: no 6nt barcode segment is more than a Hamming distance of 1 from a valid barcode block; all linker segments are within 1nt length of the expected value; the UMI has a length of 8nt; and only 1 mismatch is allowed within the ACG-GAC segments flanking the UMI. Reads with cell barcode information passing these filters were then aligned to the hg19 reference genome using STAR v2.5.2b (Dobin et al., 2013) and annotated with the Gencode comprehensive v28lift37. Uniquely-mapped reads were subsequently assigned to genes using featureCounts v1.5.3 (Liao et al., 2013). PCR duplicates were removed using umi_tools (Smith et al., 2017) in per-gene mode. The knee-calling algorithm from umi_tools was used to identify an appropriate total transcript count cut-off for cells in each sample, yielding a total of 4001 cells. Cells with mitochondrial gene percentage greater than 5% were removed. Biological replicates of 4hr and 8hr treatments were combined and cell counts were balanced between all time points by randomly sub-setting each time point to 400 cells. Cyclone from the scran package (Lun et al., 2016; Scialdone et al., 2015) was used to determine cell-cycle scores for all cells, and Seurat v3 (Stuart et al., 2019) was then use to normalize and scale the data such that the impacts of transcript counts, mitochondrial percent, and cell-cycle scores were regressed-out.
Genome_build: hg19
Supplementary_files_format_and_content: raw Counts and normalized Counts
bigwigs were generated from STAR coverage files using bedGraphToBigWig.

organism: Homo sapiens

source_name: A1-2 breast cancer cells

growth_protocol: Cells were cultured in modified Eagle medium (MEM) containing 10% fetal bovine serum, 1X Penicillin/Streptomycin (Sigma P0781), 1% HEPES (Sigma H0887), 1X Glutamax (Gibco 35050), and 250 ug/ml G418 (Gibco 10131).

extract_protocol:
For bulk RNAseq, Qiagen RNeasy kits with on-column DNase treatment were used to isolate total RNA. For single-cell RNAseq, cells were dissociated using 0.25% Trypsin-EDTA (Gibco 25200) into single cell suspension and the BioRad ddSeq Single-Cell Isolator was used to create single cell emulsions
Bulk RNAseq libraries were generated using Ribo-Zero Gold and the Illumina TruSeq RNA Stranded kit. Single-cell RNAseq libraries were generated using the Illumina SureCell WTA 3’ Library Prep kit

treatment_protocol: For Dexamethasone treatments, cells were initially cultured for 24 hours in reduced-serum, hormone-stripped media (Phenol-red free MEM (Gibco 51200) with 5% Charcoal/Dextran treated FBS (Atlanta S11650), 1X Penicillin/Streptomycin (Sigma P0781), 1% HEPES (Sigma H0887), 1X Glutamax (Gibco 35050), and 250 ug/ml G418 (Gibco 10131)). Subsequently, Dexamethasone (Sigma D4902) was added to the media at 100 nM for all treatments timepoints and 9.5 x 10e-4% ethanol was used as vehicle control. For both RNAseq experiments, control cells were treated with ethanol for 18 hours.

value: A1-2 breast cancer cells

value: 1hr Dex


title: Wild-type UV-treated rep2

value: UV-C radiation (100 mJ cm-2)


title: SM-AYS2O

type: genomic

city: LA

first: Sungyong

last: You

state: CA

address: Beverly Blvd 8400

department: Surgery

institute: Cedars-Sinai Medical Center

hyb_protocol: Approximately 80ng of gDNA was used in the Affymetrix OncoScan FFPE Assay kit (Affymetrix) according to manufacturer’s instructions.

scan_protocol: The arrays were washed and stained using GeneChip Fluidics Station 450 (Affymetrix, Inc.) and scanned in GeneChip Scanner 3000 7G (Affymetrix, Inc.). The fluorescence of clusters was measured to generate a DAT file. Cluster intensity values were automatically calculated using a built-in algorithm from DAT files using GeneChip Command Console software (Affymetrix, Inc.), and a CEL file was generated.

data_processing:
data was processed with Affymetrix Chromosome Analysis Suite 3.1 (ChAS 3.1) to generate probe level and gene level log2-ratio using normalized data.
Primary data description: Output (probe level) of OncoScan profiles using ChAS: Log2Ratio, WeightedLog2Ratio, AllelicDifference, NormalDiploid, BAF (B allele frequency)

label: biotin

molecule: genomic DNA

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Primary tumor tissues

extract_protocol: DNA was extracted from 1mm FFPE cores with AnaPrep 12 Automated Nucleic Acid Preparation Instrument (Biochain) and quantitated with Qubit (Life technology).

treatment_protocol: No treatment

tag: disease stage

tag: tissue/sample type

value: prostate needle biopsy (PNBx)


title: BC159-T#3 [Bulk RNAs]

city: Seoul

first: Woosung

last: Chung

state: State...

address: Samsung Medical Center

country: South Korea

institute: Samsung Genome Institute

description:
Bulk RNA sequencing
GEO_processed_BC159T_time_series_log2TPM_matrix.txt

data_processing:
The sequenced reads were mapped to the human genome reference (hg19) by STAR aligner with default parameters.
Transcripts Per Million (TPM) values were estimated using RSEM v1.2.17 with default parameters.
TPM values < 1 were substituted with zero and log2-transformed after adding a value of one.
Genome_build: hg19
Supplementary_files_format_and_content: A processed file is tab-delimited and contains the normalized gene expression for 3 bulk tumors.

extract_protocol:
Bulk RNAs of BC159-T#1 and BC159-T#2 were extracted from FFPE tissues using Allprep DNA/RNA FFPE kit (Qiagen, USA) and bulk RNA of BC159-T#3 was extracted from frozen tissue using Allprep DNA/RNA mini kit (Qiagen, USA). All of RNAs were quantified and qualified by the Qubit® 2.0 Fluorometer (Life Technologies, USA) and 2100 Bioanalyzer (Agilent Technologies, USA).
Sequencing libraries were constructed with the TruSeq RNA sample preparation v2 kit (Illumina, USA). All of constructed libraries were quantified and qualified by the Qubit® 2.0 Fluorometer (Life Technologies) and 2100 Bioanalyzer (Agilent Technologies). The constructed libraries were sequenced using the HiSeq 2500 system (Illumina, USA) on the 100-bp paired-end mode.

value: Bladder

tag: tnm stage

value: Neoadjuvant chemotherapy

tag: molecular subtpye

value: Basal squamous


title: SM-AYS2Z


title: SM-AYS1S


title: beadneg_dc1_1

description: bulk RNAseq

data_processing:
For CITEseq GEX libraries: Read 1 is technical: Cell barcode is bp 1-16; UMI is bp 17-26. Read 2 is biological.
For CITEseq ADT libraries: Read 1 is technical: Cell barcode is bp 1-16; UMI is bp 17-26. Read 2 is biological: bp 1-7 identify a CITEseq antibody (as indicated in ADT_TAGS.CSV).
After library demultiplexing, gene expression libraries were aligned to the mm10 or GRCh38 reference transcriptomes and count matrices were generated using the default Cell Ranger 2.1 workflow, using the “raw” matrix output. CITEseq library reads were directly queried for antibody barcodes (listed in ADT_TAGS.CSV) and cell barcodes in the appropriate read positions, including antibody sequences within a Hamming distance of 1 from the reference sequence.
single_cell_metadata.csv.gz represents the results of QC filtering and transcriptome-based clustering on CITEseq data.
For RNAseq: Fastqs were aligned to the mm10 reference genome, reads were dereplicated for PCR duplicates, and gene counts were generated using STAR v2.5 using –quantMode GeneCounts.
Genome_build: mm10
Supplementary_files_format_and_content: gene counts

source_name: lung conventional type-1 dendritic cells (CD45+ Siglec F- Ly6G- MHCIIhi CD11c+ CD24hi CD11b- CD103+) negative for beads in mice treated with fluorescent beads intranasally

extract_protocol:
10e4 DC were sorted as described above into 700 mL Trizol. RNA was isolated using RNeasy Micro Kits (Qiagen). 0.5-1 ng of RNA was synthesized into cDNA using the Smart-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Bio). Sequencing libraries were prepared using the Low Input Library Prep Kit (Takara Bio).
Single cell suspensions were obtained from lung and LN by digestion with collagenase IV 0.25mg/ml (Sigma) at 37C for 30min (lung) or 25min (LN) followed by passing through a 70um cell strainer and RBC lysis (RBC lysis buffer, BioLegend) for 2min at room temperature. For flow cytometry or FACS cells were stained in FACS buffer (PBS supplemented with 2% BSA and 5mM EDTA) with mAbs specific to CD45 (clone 30-F11, BioLegend), Siglec F (clone E50-2440, BD Pharmingen), CD11c (clone N418, Invitrogen), CD24 (clone M1/69, Invitrogen), CD103 (clone 2E7, BioLegend), I-A/I-E (clone M5/114.15.2, eBioscience), CD11b (clone M1/70, eBioscience)

treatment_protocol: 50ml Polybead Dyed Blue 1.0 Micron Microspheres (Polysciences Inc) were coated while rotating for 20h at 4°C with ovalbumin (Worthington Ovalbumin, Low EndoTM, purified; 50mg/ml in PBS), washed twice with PBS, and intranasally applied into mouse lungs. Lungs were analyzed 5h after beads application.


title: ccr7ko_naive_gex

source_name: lung conventional dendritic cells (CD45+ Siglec F- Ly6G- MHCII+ CD11c+) from CCR7-/- mice


title: BC159-T#2 [Bulk RNAs]

value: BCG


title: SM-AYS3P


title: HCT116 sh UHRF1

city: Grand Rapids

first: Scott

last: Rothbart

state: MI

address: 333 Bostwick Ave NE

department: Center for Epigenetics

institute: Van Andel Research Institute

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to the Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using iScan using standard recommended Illumina scanner setting

data_processing: openSesame from SeSAMe R package

label: Cy3, Cy5

label_protocol: Standard Illumina Protocol

growth_protocol: 37ºC, 5% CO2, McCoy's 5A media with 10% FBS and 1% penicillin-streptomycin

extract_protocol: 3x extraction: phenol, phenol/chlorofom/isoamyl alcohol (25:24:1), chloroform/isoamyl alcohol (24:1); precipitation; RNase treatment; precipitation

tag: cell line

tag: shRNA


title: BC159-T#1 [Bulk RNAs]

value: Luminal papillary


title: wt_tumor_adt

description:
ADT CITEseq library
adt_tags.csv

source_name: lung conventional dendritic cells (CD45+ Siglec F- Ly6G- MHCII+ CD11c+) of mice bearing cells expressing the KrasG12D activating mutation and Tp53 deletion (KP cells)


title: A1-2 cells, D1hr_rep1, Bulk RNAseq


title: SM-AYS3R


title: BC159-T#3

description: Single-cell RNA sequencing

data_processing:
After the sequenced reads were processed using CellRanger toolkit (version 2.1.0, 10x Genomics), the human and mouse genomes were mapped to the GRCh38 human genome reference and mm10 mouse genome reference, respectively, using STAR aligner and the unique molecular identifier (UMI) counts was quantified.
The raw gene expression matrces were generated using the Seurat R package (version 2.1) and the cells were filtered according to the following criteria: cells with 1) > 1000 UMI counts, 2) > 500 genes, and < 10,000 genes, 3) < 10% for mitochondrial genome, 4) averaged housekeeping genes expression > 3 and 5) at least 1% of mouse (human) reads. For tumor cells, strict criteria was applied (>2,000 genes).
After filteration, the raw gene expression matrix was transformed to TPM-like values by normalizing for differences in coverages and sequencing depth, and the TPM-like values were log2-transfromed after adding a value of one.
With two cutoffs of 0.02 of the CNV score and 0.2 of the CNV correlation, we assigned cells to tumor cells if the two measured values were above the two cutoffs and to non-tumor cells if the two measured values were below the two cutoffs. Undetermined cells were discarded.
Outliers of nGene were excluded from non-tumor cell clusters.
Genome_build: GRCh38; mm10
Supplementary_files_format_and_content: Processed files are tab-deliminated and contain the normalized gene expression for QC filtered cells. The cell information file is excel format including the information of cell type and QC stat.

source_name: BC159-T#3_Primary bladder cancer

extract_protocol:
After resection from a patient and PDX mouse models, bladder tumor tissues were dissociated with mechanical and enzymatical method. In detail, the tumor tissues were chopped and minced, then treated dissociation enzyme mix (Collagenase, DNase I, Dispase, and DMEM). The digested samples were filtered through a 70-µm strainer with phosphate-buffered saline (PBS).  After resuspension in 1× PBS, all single-cell suspensions were loaded into a 10x Chromium Controller (10x Genomics, USA), aiming for 7,000 cells.
Barcoded sequencing libraries were generated using Chromium Single Cell 3’ v2 kits (10x Genomics, USA) and sequenced on a Hiseq 2500 platform (Illumina, USA) targeting 100,000 reads per cell.


title: HCT116 sh Luciferase

value: luciferase


title: SM-AYS3S


title: BC159-T#3-PDX-tipifarnib

description:
Single-cell RNA sequencing
GEO_processed_BC159-T#3_PDX_human_matrix_final.txt
GEO_processed_BC159-T#3_PDX_mouse_matrix_final.txt

organism:
Homo sapiens
Mus musculus

source_name: BC159-T#3_PDX_tipifarnib treatment

value: Tipifarnib


title: wt_tumor_gex

value: DCs


title: A1-2 cells, EtOH_rep3, Bulk RNAseq

value: 18hr EtOH


title: SM-AYS3T


title: ccr7ko_naive_adt

description:
ADT CITEseq library
adt_tags.csv


title: wt_naive_adt

description:
ADT CITEseq library
adt_tags.csv

source_name: lung conventional dendritic cells (CD45+ Siglec F- Ly6G- MHCII+ CD11c+)


title: A1-2 cells, EtOH_rep2, Bulk RNAseq


title: 200930770229_R04C01: genomic DNA from Sample Tum196

status: Public on Mar 25 2020

city: Lund

first: Göran

middle: B

last: Jönsson

address: Scheelevägen 2

department: Clinical Sciences

country: Sweden

institute: Lund University

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol.

scan_protocol: Standard Illumina Protocol.

data_processing: Raw idat files were processed using R package ChAMP and ssNoob was used as background correction method from minfi . Background corrected data was then normalized for type I/II probe using BMIQ and filtered for polymorphic and off-target probes. Samples with a large number of failed probes (probe detection-p > 0.01; Sample cut-off: >4% of total probes) were removed and probes that failed in more than 10% of the remaining samples were also removed. Next, methylation β values of probes failed in 10% or less samples, were imputed using the impute.knn function in R and default settings. After preprocessing, the methylation dataset contained 788,174 probes and 196 samples.

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol.

extract_protocol: genomic DNA and RNA was extracted simultaneously using Qiagen AllPrep Kit according to standard instructions.

value: Melanoma tumor sample

tag: slide

tag: array

tag: sample plate

tag: sample well

tag: sample group

value: Tumour

tag: clinical class

value: SSM

tag: Stage

value: Regional Lymph Node


title: A1-2 cells, EtOH_rep1, Bulk RNAseq

value: A1-2 breast cancer cells

tag: treatment


title: BC159-T#3-PDX-vehicle

source_name: BC159-T#3_PDX_vehicle treatment

tag: tissue

value: Vehicle


title: wt_naive_gex

tag: strain

value: lung


title: 200930770095_R07C01: genomic DNA from Sample Tum195

value: Unknownprimary


title: A1-2 cells, D1hr_rep2, Bulk RNAseq

tag: cell type

value: 1hr Dex


title: 200930770085_R07C01: genomic DNA from Sample Tum193

value: Local Recurrence


title: 200930770085_R06C01: genomic DNA from Sample Tum192

value: Distant Metastasis


title: 200930770085_R03C01: genomic DNA from Sample Tum189


title: 200930770085_R05C01: genomic DNA from Sample Tum191

value: ALM

value: Primary


title: 200930770085_R04C01: genomic DNA from Sample Tum190


title: 200930770085_R02C01: genomic DNA from Sample Tum188

value: NM

value: Regional Other


title: gfppos_dc1_2

description: bulk RNAseq

source_name: lung conventional type-1 dendritic cells (CD45+ Siglec F- Ly6G- MHCIIhi CD11c+ CD24hi CD11b- CD103+) positive for GFP in mice bearing GFP-expressing tumors

treatment_protocol: 8-week-old mice were injected intravenously with 5x10e5 KP-GFP cells. Lungs were analyzed on day 28.


title: 200930770085_R01C01: genomic DNA from Sample Tum187


title: 200970070004_R05C01: genomic DNA from Sample Tum183


title: 200970070004_R08C01: genomic DNA from Sample Tum186


title: 200970070004_R03C01: genomic DNA from Sample Tum181

value: Other


title: 200970070004_R06C01: genomic DNA from Sample Tum184


title: 200970070004_R01C01: genomic DNA from Sample Tum178


title: 200970070004_R07C01: genomic DNA from Sample Tum185


title: 200970070004_R02C01: genomic DNA from Sample Tum180


title: 200970070003_R08C01: genomic DNA from Sample Tum177


title: 200970070003_R02C01: genomic DNA from Sample Tum172


title: 200970070003_R06C01: genomic DNA from Sample Tum175


title: 200970070003_R05C01: genomic DNA from Sample Tum174


title: 200970070003_R07C01: genomic DNA from Sample Tum176


title: 200930770085_R08C01: genomic DNA from Sample Tum194


title: 200970070003_R03C01: genomic DNA from Sample Tum173


title: 200923040005_R07C01: genomic DNA from Sample Tum170


title: 200970070003_R01C01: genomic DNA from Sample Tum171


title: 200970080006_R07C01: genomic DNA from Sample Tum168


title: 200970080006_R06C01: genomic DNA from Sample Tum167


title: 200970080006_R04C01: genomic DNA from Sample Tum166


title: 200970080006_R03C01: genomic DNA from Sample Tum165


title: 200970080006_R02C01: genomic DNA from Sample Tum164


title: 200970060029_R08C01: genomic DNA from Sample Tum162


title: 200970080006_R01C01: genomic DNA from Sample Tum163


title: 200970060029_R06C01: genomic DNA from Sample Tum161


title: 200970060029_R04C01: genomic DNA from Sample Tum159


title: 200970070004_R04C01: genomic DNA from Sample Tum182


title: 200970060029_R05C01: genomic DNA from Sample Tum160


title: 200970060029_R03C01: genomic DNA from Sample Tum158


title: 200970060029_R02C01: genomic DNA from Sample Tum157


title: 200923040005_R02C01: genomic DNA from Sample Tum179


title: 200930770034_R08C01: genomic DNA from Sample Tum155


title: 200930770034_R07C01: genomic DNA from Sample Tum154


title: 200930770034_R04C01: genomic DNA from Sample Tum152


title: 200970080006_R08C01: genomic DNA from Sample Tum169


title: 200923040005_R06C01: genomic DNA from Sample Tum145


title: 200930770034_R03C01: genomic DNA from Sample Tum151


title: 200970070007_R06C01: genomic DNA from Sample Tum146


title: 200930770034_R01C01: genomic DNA from Sample Tum149


title: 200930770034_R02C01: genomic DNA from Sample Tum150


title: 200970070007_R07C01: genomic DNA from Sample Tum147


title: 200970070007_R08C01: genomic DNA from Sample Tum148


title: 200970070007_R04C01: genomic DNA from Sample Tum143


title: 200970070007_R05C01: genomic DNA from Sample Tum144


title: 200970070007_R02C01: genomic DNA from Sample Tum141


title: 200970070007_R03C01: genomic DNA from Sample Tum142


title: 200970080053_R08C01: genomic DNA from Sample Tum139


title: 200970070007_R01C01: genomic DNA from Sample Tum140


title: 200970080053_R06C01: genomic DNA from Sample Tum137


title: 200970080053_R07C01: genomic DNA from Sample Tum138


title: 200970080053_R04C01: genomic DNA from Sample Tum135


title: 200970080053_R03C01: genomic DNA from Sample Tum134


title: 200970080053_R01C01: genomic DNA from Sample Tum132


title: 200930770093_R08C01: genomic DNA from Sample Tum131


title: 200970060029_R01C01: genomic DNA from Sample Tum156


title: 200970080053_R02C01: genomic DNA from Sample Tum133


title: 200930770034_R06C01: genomic DNA from Sample Tum153


title: 200930770093_R04C01: genomic DNA from Sample Tum128


title: 200930770093_R03C01: genomic DNA from Sample Tum127


title: 200930770093_R02C01: genomic DNA from Sample Tum126


title: 200970080044_R06C01: genomic DNA from Sample Tum121


title: 200970080044_R02C01: genomic DNA from Sample Tum117


title: 200970080044_R04C01: genomic DNA from Sample Tum119


title: 200923040005_R01C01: genomic DNA from Sample Tum123


title: 200970080004_R08C01: genomic DNA from Sample Tum115


title: 200970080004_R06C01: genomic DNA from Sample Tum114


title: 200970080053_R05C01: genomic DNA from Sample Tum136


title: 200970080004_R05C01: genomic DNA from Sample Tum112


title: 200970080004_R04C01: genomic DNA from Sample Tum111


title: 200970080004_R03C01: genomic DNA from Sample Tum110


title: 200821630021_R07C01: genomic DNA from Sample Tum109


title: 200970080004_R01C01: genomic DNA from Sample Tum108


title: 200821640015_R08C01: genomic DNA from Sample Tum107


title: 200821630021_R05C01: genomic DNA from Sample Tum103


title: 200923040005_R05C01: genomic DNA from Sample Tum106


title: 200821630021_R06C01: genomic DNA from Sample Tum104


title: 200970080044_R08C01: genomic DNA from Sample Tum124


title: 200821640015_R04C01: genomic DNA from Sample Tum100


title: 200821630021_R08C01: genomic DNA from Sample Tum113


title: 200821640015_R06C01: genomic DNA from Sample Tum102


title: 200930770093_R07C01: genomic DNA from Sample Tum130


title: 200970080044_R01C01: genomic DNA from Sample Tum116


title: 200930770093_R01C01: genomic DNA from Sample Tum125


title: 200821640015_R03C01: genomic DNA from Sample Tum98


title: 200970080044_R07C01: genomic DNA from Sample Tum122


title: 200821640015_R01C01: genomic DNA from Sample Tum96


title: 200970070017_R08C01: genomic DNA from Sample Tum95


title: 200930770093_R06C01: genomic DNA from Sample Tum129


title: 200821630021_R04C01: genomic DNA from Sample Tum99


title: 200970080044_R05C01: genomic DNA from Sample Tum120


title: 200970080044_R03C01: genomic DNA from Sample Tum118


title: 200970070017_R07C01: genomic DNA from Sample Tum94


title: 200821640015_R05C01: genomic DNA from Sample Tum101


title: 200821640015_R02C01: genomic DNA from Sample Tum97


title: 200821640015_R07C01: genomic DNA from Sample Tum105


title: 200923040005_R04C01: genomic DNA from Sample Tum88


title: 200970070017_R02C01: genomic DNA from Sample Tum90


title: 200970070017_R03C01: genomic DNA from Sample Tum91


title: 200970070017_R01C01: genomic DNA from Sample Tum89


title: 200970070017_R04C01: genomic DNA from Sample Tum92


title: 200970070016_R08C01: genomic DNA from Sample Tum87


title: 200970070016_R06C01: genomic DNA from Sample Tum85


title: 200970070016_R07C01: genomic DNA from Sample Tum86


title: 200970070016_R04C01: genomic DNA from Sample Tum83


title: 200970060023_R07C01: genomic DNA from Sample Tum78


title: 200970070016_R03C01: genomic DNA from Sample Tum82

value: Mucosal


title: 200970070016_R05C01: genomic DNA from Sample Tum84

value: Melanoma tumor sample


title: 200970070016_R01C01: genomic DNA from Sample Tum80

value: Tumour


title: 200923040005_R03C01: genomic DNA from Sample Tum81

value: LMM


title: 200970060023_R08C01: genomic DNA from Sample Tum79


title: 200970060023_R04C01: genomic DNA from Sample Tum74


title: 200821630021_R03C01: genomic DNA from Sample Tum77


title: 200970060021_R02C01: genomic DNA from Sample Tum73


title: 200970070017_R05C01: genomic DNA from Sample Tum93


title: 200970060008_R08C01: genomic DNA from Sample Tum71


title: 200970060021_R01C01: genomic DNA from Sample Tum72


title: 200970060008_R05C01: genomic DNA from Sample Tum68


title: 200970060008_R06C01: genomic DNA from Sample Tum69


title: 200970060023_R05C01: genomic DNA from Sample Tum75

value: SSM


title: 200970060008_R04C01: genomic DNA from Sample Tum67


title: Control replicate 2

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

country: France

institute: Institut Pasteur

data_processing:
Reads were cleaned of adapter sequences and low-quality   sequences using cutadapt version 1.11. Only sequences at least 25 nt length were considered for further analysis.
Bowtie version 0.12.7  with default parameters, was used for alignment on the reference genome (CP000253.1, NCBI)
Genes were counted using featureCounts version 1.4.6-p3 from Subreads package (parameters: -t gene -g ID -s 1).
Count data were analyzed using R  version 3.4.1  and the Bioconductor package DESeq2 version 1.16. The normalization and  dispersion estimation were performed with DESeq2 using the default parameters and statistical tests  for differential expression were performed applying the independent filtering algorithm. A  generalized linear model was set in order to test for the differential expression between the  intracellular persisters and control conditions. Raw P values were adjusted for multiple testing according to the Benjamini and Hochberg (BH) procedure and genes with an adjusted p value lower than 0.05 were considered differentially expressed.
Genome_build: CP000253.1 from NCBI
Supplementary_files_format_and_content: Matrix from DESseq2

organism: Staphylococcus aureus

source_name: cultured cells

growth_protocol: For differential expression analysis, bacterial reference samples  (hereafter named “control samples” in RNA-seq experiments) were collected from an overnight  culture (MHB-CA supplemented with 125 ng/mL tetracycline) by centrifugation at 5000g for 5 min,  resuspended in RPMI 1640 and incubated for 30 min at 37°C. This bacterial suspension was then  mixed with a cell lysate obtained from non-infected macrophages incubated in RPMI 1640 with 10 %  FBS for 24 h. The relative amount of bacteria and cells was adjusted to that obtained in 24 h-infected  cells. Intracellular bacteria were collected from macrophages as described for flow cytometry.  Bacteria were sorted on the basis of their propidium iodide profile and GFP expression level using the gating methods described above, in a FACSAria III cytometer operated by the BD FACSDiva 8.0.1 software (BD Biosciences).

extract_protocol:
S. aureus recovered from infected macrophages or from control samples were  Centrifuged at 5000g for 5 min and lysed using the following procedure: pellets were resuspended in  Tris-EDTA buffer containing freshly prepared 13 mg/mL lysozyme (Sigma) and 130 μg/mL lysostaphin (Sigma) for 30 min at room temperature. Resulting suspensions were processed for total RNA extraction with RNA extraction InviTrap Spin Universal RNA Mini Kit (Stratec) following the  manufacturer’s instructions. Traces of contaminating genomic DNA were removed from samples by  treatment with TURBO DNase (Ambion) for 30 min at 37°C according to the manufacturer’s  instructions. RNA purity was checked using a NanoDropM spectrophotometer (Thermo Fisher  Scientific).
Total RNA from three independent replicates were checked on the Bioanalyser system (Agilent) for its quality and integrity. Ribosomal RNA depletion was performed using the Bacteria RiboZero kit (Illumina). From rRNA-depleted RNA, directional libraries were prepared using the TruSeq Stranded mRNA Sample preparation kit following the manufacturer’s instructions (Illumina). Libraries were checked for quality on Bioanalyser DNA chips Bioanalyser (Agilent). Quantification was performed with the fluorescent-based quantitation Qubit dsDNA HS Assay Kit  (Thermo Fisher Scientific). Sequencing was performed as an SRM run (SR: Single Read, PE: Paired-end Reads, M: multiplexed samples) for 65 bp sequences on HiSeq 2500 Illumina sequencer (65 cycles). The multiplexing level was 6 samples per lane.


title: Control replicate 1


title: Intracellular persister replicate 2

source_name: mouse J774A.1 macrophages


title: Intracellular persister replicate 3


title: Control replicate 3


title: 200970060008_R03C01: genomic DNA from Sample Tum66


title: 200970060023_R03C01: genomic DNA from Sample Tum65


title: Intracellular persister replicate 1


title: 200970060023_R02C01: genomic DNA from Sample Tum64

value: Regional Lymph Node


title: 200970060023_R06C01: genomic DNA from Sample Tum76


title: 200970060021_R07C01: genomic DNA from Sample Tum62


title: 200970060021_R08C01: genomic DNA from Sample Tum63


title: 200970060008_R07C01: genomic DNA from Sample Tum70


title: 200970060021_R03C01: genomic DNA from Sample Tum58


title: 200970060021_R04C01: genomic DNA from Sample Tum59


title: 200970060008_R02C01: genomic DNA from Sample Tum57


title: 200970060021_R05C01: genomic DNA from Sample Tum60


title: ONS_998: ONS_Patient 2

city: Oxford

first: Georgios

last: Baskozos

address: Level 6, West Wing, John Radcliffe Hospital

department: NDCN

country: United Kingdom

institute: Oxford University

data_processing:
Sequencing, base calling, demultiplexing and QC using Illumina HiSeq4000 analysis software version HD 3.4.0.38
Demux of files and FastQ preparation by BcltoFastq 2.17.1.14
Reads were mapped to GRCh38 human genome (Homo_sapiens.GRCh38.dna.primary_assembly.fa, Homo_sapiens.GRCh38.88.chr.gtf) using STAR aligner
BAM files were merged across sequencing lanes and sorted using SAMtools
Features were counted using HTSeq with the intersection not empty strategy
Differential expression analysis was carried out using DESeq2
Genome_build: GRCh38
Supplementary_files_format_and_content: CSV files *res*.csv include DESeq2 results for ENSEMBL genes. CSV files toc.csv include read-pairs counts calculated using HTSeq.

source_name: HSN1 998 SENSORY NEURONS  SERINE TREATED

growth_protocol: Induced pluripotent stem cell generation  NHDF1 (from 44-year-old female) was reprogrammed with Yamanaka retroviruses SOX2, KLF4, OCT3/4, c-MYC and NANOG (Takahashi et al., 2006), and has previously been described (Hartfield et al., 2014). AD2-01 (from 51-year-old male) (Buskin et al., in preparation) and AD3-01 (from 37-year-old female) (Baud et al, 2017) were reprogrammed using the CytoTune™-iPS Reprogramming Kit (ThermoFisher). The fibroblasts to generate AD2-01 and AD3-01 were obtained from a commercial source (Lonza, CC-2511, LOT 264781).   CytoTune-iPS reprogramming was performed as directed by the manufacturer’s instructions (ThermoFisher). The CytoTune reprogramming kit contains four Sendai virus-based reprogramming vectors each capable of expressing one of the four Yamanaka factors (KLF4, OCT3/4, SOX2 and c-MYC). Briefly, after fibroblast transduction with the four Sendai virus-based reprogramming vectors, cells are cultured for 5-6 days, with medium changes every other day (DMEM, high glucose (Sigma), 10% FBS (ThermoFisher), 1% Pen/Strep (100x, ThermoFisher), 200mM L-glutamine (Sigma), 1% non-essential amino acids (ThermoFisher)). The transduced fibroblasts are then passaged using 0.05% Trpsin-EDTA onto pre-prepared feeder layer plates containing mitotically inactivated mouse embryonic fibroblasts (MEF). 3-4 weeks after transduction, colonies should have grown to an appropriate size to allow for manual picking. Using an inverted microscope, a single colony displaying iPSC morphology is cut into 5-6 pieces using a 25 gauge needle, transferred into iPS media (KO-DMEM (ThermoFisher), 25% Knock Serum Replacement (ThermoFisher), 1% nonessential amino acids (100x, ThermoFisher), 200mM L- glutamine (Sigma), 1% Pen/Strep (100x, ThermoFisher), 8 ng/ml human FGF2 (Miltenyi Biotec)) and plated onto pre-prepared MEF plates. Colonies are allowed to attach for 48 hours, and thereafter medium changes are performed daily. iPSCs were adapted to feeder-free conditions onto Matrigel (Scientific Laboratory Supplies)-coated plates in mTeSR1 medium (ScienCell). Bulk passaging was by 0.5 mM ethylenediaminetetraacetic acid (EDTA) to make large-scale, quality-controlled stocks that were cryopreserved in liquid nitrogen. The number of feeder-free passages was kept to a minimum. When selecting iPSCs from frozen stocks for differentiation, vials with the same passage number were selected for each cell line throughout all experiments performed in this study.  The iPSC lines AD2-01 and AD3-01 were obtained through the IMI/EU sponsored StemBANCC consortium via the Human Biomaterials Resource Centre, University of Birmingham, UK (http://www.birmingham.ac.uk/facilities/hbrc).  All iPSC lines were subject to strict quality control checks before the initiation of differentiation. Quality control checks of these lines included: tests for Sendai virus clearance, fluorescence-activated cell sorting (FACS) for pluripotency markers, genomic integrity checks and embryoid body tri-lineage differentiation experiments. Cells are also confirmed as negative for Mycoplasma before cryopreservation.  Sensory neuron differentiation  For neuronal differentiation, iPSCs were passaged onto Matrigel®-coated six-well plates using TrypLE express (ThermoFisher Scientific) and maintained in mTeSR1 supplemented with 10 μM ROCK inhibitor (ScienCell). Twenty-four hours after plating, the medium was exchanged to mouse embryonic fibroblast (MEF) conditioned medium (ScienCell) supplemented with 10 ng/ml human recombinant FGF2. Cells were allowed to expand on MEF-conditioned medium until ∼50% confluent, at which time differentiation was started according to Chambers et al. (2012). Briefly, medium was exchanged to knockout serum replacement (KSR) medium containing; knockout-DMEM, 15% knockout-serum replacement, 1% GlutaMAX™, 1% non-essential amino acids, 100 μM β-mercaptoethanol, 1% antibiotic/antimycotic (ThermoFisher Scientific), supplemented with the SMAD inhibitors SB431542 (Sigma, 10 μM) and LDN-193189 (Stratech, 100 nM). The medium was gradually transitioned from KSR medium to N2 medium (Neurobasal® medium, 2% B27 supplement, 1% N2 supplement, 1% GlutaMAX™, 1% antibiotic/antimycotic) (ThermoFisher Scientific) over an 11-day period. On Day 2, the small molecules CHIR99021 (Apollo Scientific, 3 μM), SU5402 (R&D Systems, 10 μM) and DAPT (Sigma, 10 μM) were also added. SMAD inhibitors were removed from the media from Day 6 onwards. On Day 11, the now immature neurons were replated onto Matrigel®-coated coverslips (25 000 cells per 13 mm coverslip) in 100% N2 medium containing human recombinant NGF, GDNF, BDNF, NT3 (all at 25 ng/ml, PeproTech) and 10 μM ROCK inhibitor. CHIR99021 (3 μM) was included in the medium until Day 14, and laminin (1 μg/ml, ThermoFisher Scientific) was supplemented into the medium from Day 20 onwards. Medium changes were performed twice weekly after replating. Cytosine β-D-arabinofuranoside (AraC, 2 μM, Sigma) was included in the medium for 24 h following replating to remove the few non-neuronal dividing cells remaining in the culture. This differentiation resulted in a completely pure neuronal culture with extensive arborized neurites by 3 weeks after the end of the small inhibitor stage.  Ethics statement   Human iPSC lines used in this study were derived from human skin biopsy fibroblasts, following signed informed consent. Three control cells lines were used in this study – AD2-01, AD4-01 and NHDF1. NHDF1 were reprogrammed with approval from research ethics committee: National Health Service, Health Research Authority, NRES Committee South Central, Berkshire, UK (REC 10/H0505/71).

extract_protocol:
RNA was extracted from 'young' neurons (N) at 2 months, and 'old' neurons (ON) at 6 months according to the hybrid method of combined phenol extraction (TriPure, Roche) and column purification (High Pure RNA tissue Kit, Roche) (Bartus et al., 2016). The concentration of RNA in the samples was measured using a nanodrop and proved sufficient for sequencing. According to the hybrid method, DRG tissue was first homogenized in TriPure and then mixed with chloroform, following the phenol extraction method. After centrifuging the aqueous liquid, which stays on the top of the tube and contains the nucleic acids, was removed. This solution was then subjected to the column purification method. Following this protocol, the clear aqueous liquid was placed in Roche High Pure RNA tissue Kit columns and washed several times in order to purify the RNA. RNA was then extracted with the mRNeasy kit and all samples were subjected to on-column DNAse digestion in order to prevent genomic contamination i.e. presence of DNA in the RNA samples.
RNA libraries were prepared for sequencing using standard Illumina protocols. Second strand cDNA  synthesis incorporated dUTP. The cDNA was end-repaired, A-tailed and adapter-ligated. Prior to amplification,  samples underwent uridine digestion. The prepared libraries were size selected, multiplexed and QC’ed before paired  end sequencing over eight lanes of a flow cell.

treatment_protocol: Serine treatment: L-serine was included in all medium changes at a concentration of 10mM.

tag: disease state

value: Hereditary sensory neuropathy type 1 (HSN1)

value: Differentiated sensory neurons late plus serine treatment

tag: genome build


title: ONS_999: ONS_Patient 3

source_name: HSN1 999 SENSORY NEURONS  SERINE TREATED


title: ON_999: ON_Patient 3

source_name: HSN1 999 SENSORY NEURONS

value: Differentiated sensory neurons late


title: N2_999: N2_Patient 3

value: Differentiated sensory neurons


title: ON_997: ON_Patient 1

source_name: HSN1 997 SENSORY NEURONS


title: ONS_997: ONS_Patient 1

source_name: HSN1 997 SENSORY NEURONS SERINE TREATED


title: ON_998: ON_Patient 2

source_name: HSN1 998 SENSORY NEURONS


title: N2_998: N2_Patient 2


title: 200970070041_R08C01: genomic DNA from Sample Tum55


title: N2_997: N2_Patient 1


title: 200970070041_R07C01: genomic DNA from Sample Tum54


title: N1_998: N1_Patient 2


title: N1_999: N1_Patient 3


title: 200970070041_R06C01: genomic DNA from Sample Tum53


title: N1_997: N1_Patient 1


title: iPSC_999: iPSC_Patient 3

source_name: HSN1 999 IPSC

value: IPSC


title: 200970070041_R03C01: genomic DNA from Sample Tum51


title: 200970070041_R05C01: genomic DNA from Sample Tum52


title: iPSC_998: iPSC_Patient 2

source_name: HSN1 998 IPSC


title: 200970060021_R06C01: genomic DNA from Sample Tum61


title: 200970070041_R02C01: genomic DNA from Sample Tum50

value: Local Recurrence


title: iPSC_997: iPSC_Patient 1

source_name: HSN1 997 IPSC


title: 200970070041_R01C01: genomic DNA from Sample Tum49


title: ONS_NHDF: ONS_Control 4

source_name: SENSORY NEURONS

value: healthy control

value: Differentiated sensory neurons plus serine treatment


title: ONS_AH017: ONS_Control 3


title: 200970070040_R08C01: genomic DNA from Sample Tum48

value: Primary


title: 200970070040_R07C01: genomic DNA from Sample Tum47

value: NM


title: ONS_AD3: ONS_Control 2


title: 200970060008_R01C01: genomic DNA from Sample Tum56

value: ALM


title: ONS_AD2: ONS_Control 1


title: 200970070040_R06C01: genomic DNA from Sample Tum46


title: 200970070040_R05C01: genomic DNA from Sample Tum45


title: 200821630021_R02C01: genomic DNA from Sample Tum44


title: ON_NHDF: ON_Control 4


title: 200970070054_R08C01: genomic DNA from Sample Tum40


title: ON_AH017: ON_Control 3


title: N2_NHDF: N2_Control 4


title: 200970070040_R02C01: genomic DNA from Sample Tum41


title: ON_AD3: ON_Control 2


title: ON_AD2: ON_Control 1


title: 200970070054_R06C01: genomic DNA from Sample Tum38


title: N2_AH017: N2_Control 3


title: 200970070054_R07C01: genomic DNA from Sample Tum39


title: N2_AD3: N2_Control 2


title: N2_AD2: N2_Control 1


title: N1_NHDF: N1_Control 4


title: N1_AH017: N1_Control 3


title: N1_AD3: N1_Control 2


title: 200970070054_R05C01: genomic DNA from Sample Tum37


title: 200970070054_R04C01: genomic DNA from Sample Tum36


title: 200970070054_R03C01: genomic DNA from Sample Tum35

value: Distant Metastasis


title: 200970070054_R02C01: genomic DNA from Sample Tum34

value: Melanoma tumor sample

value: Unknownprimary


title: N1_AD2: N1_Control 1


title: 200970070054_R01C01: genomic DNA from Sample Tum33

value: Tumour


title: 200970070040_R03C01: genomic DNA from Sample Tum42


title: iPSC_NHDF: iPSC_Control 4

source_name: NHDF IPSC


title: 200970070042_R08C01: genomic DNA from Sample Tum32


title: iPSC_AH017: iPSC_Control 3

source_name: AH017 IPSC


title: 200970070042_R07C01: genomic DNA from Sample Tum31


title: iPSC_AD3: iPSC_Control 2

source_name: AD3 IPSC


title: iPSC_AD2: iPSC_Control 1

source_name: AD2 IPSC


title: 200970070042_R06C01: genomic DNA from Sample Tum30


title: 200970070042_R01C01: genomic DNA from Sample Tum25


title: 200970070042_R02C01: genomic DNA from Sample Tum26

value: SSM


title: 200821630021_R01C01: genomic DNA from Sample Tum27

value: Regional Lymph Node


title: wt_1_mRNA-seq

city: Daejeon

first: Yoonjung

last: Choi

address: 291 Daehak-ro, Yuseong-gu

institute: KAIST

data_processing:
Prepared libraries were sequenced on a HiSeq2500 with single-end method (50-bp reads).
ChIP-seq reads were aligned to the S.pombe genome (ASM294v2) using NovoAlign (Novocraft technologies, Malaysia).
Significantly enriched peaks were identified using Homer and mapped reads were quantified using DeepTools and bwtool.
For mRNA-seq analysis, raw reads were aligned to S. pombe genome (ASM294v2) using STAR aligner.
The number of mapped reads was further analyzed using HOMER and DESeq
Genome_build: S. pombe EF2 genome assembly; ASM294v2
Supplementary_files_format_and_content: RNA-seq : tab-delimited text files include RPKM values for each Sample, ChIP-seq : bigwig files

organism: Schizosaccharomyces pombe

source_name: wild-type

growth_protocol: S. pombe: exponentially growing yeast in YES medium.

extract_protocol:
S. pombe (RNA isolation): DNase-treated mRNA was purified using NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB), and subjected to library preparation using NEXTflex™ Rapid Directional mRNA-Seq Kit (BIOO) following the manufacturer’s instructions.
ChIP-seq libraries for genome-wide sequencing were prepared using 10 ng of input DNA or 1 to 10 ng of eluted ChIP DNA using NEXTflex ChIP-Seq kit, Bioo Scientific (cat.5143).  mRNA-seq libraries were made using NEXTflexTM Rapid RNA-Seq kit (cat. 5138) from isolated mRNA.

tag: genotype

value: wild-type


title: Chp1_1_ChIP-seq

library_source: genomic

extract_protocol:
S. pombe (ChIP) :Cells grown in YES medium were harvested at OD595 of ~1.0, followed by fixation with 1% formaldehyde for 15 min. Cell pellets were re-suspended in the lysis buffer (50 mM HEPES, pH 7.6, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.2% SDS and proteinase inhibitors), and were disrupted in a bead beater (Biospec). The cell lysate was sonicated six times (20s on, 180s off) using an ultrasonicator with a microtip at 35% of maximum amplitude. The lysates were immunoprecipitated with antibodies and protein A/G beads over-night. The immunoprecipitated DNA was eluted using SigmaPrep™ spin column and then subjected to protease treatment and cross-linking reversal. Subsequently, the DNA was purified using Qiaquick PCR purification kit (Qiagen).
ChIP-seq libraries for genome-wide sequencing were prepared using 10 ng of input DNA or 1 to 10 ng of eluted ChIP DNA using NEXTflex ChIP-Seq kit, Bioo Scientific (cat.5143).  mRNA-seq libraries were made using NEXTflexTM Rapid RNA-Seq kit (cat. 5138) from isolated mRNA.


title: Chp1_2_ChIP-seq


title: 200821640029_R07C01: genomic DNA from Sample Tum23


title: 200970070042_R04C01: genomic DNA from Sample Tum29


title: ago1∆ x aoc2∆N_H3K9me2_1_input

source_name: ago1∆ x aco2∆N

value: ago1{delta} x aco2{delta}N


title: 200821640029_R08C01: genomic DNA from Sample Tum24


title: 200821640029_R06C01: genomic DNA from Sample Tum22


title: 200821640029_R05C01: genomic DNA from Sample Tum21


title: aoc2∆N_H3K9me2_1_input


title: aoc2∆N_H3K9me2_2_input


title: H3K9me2_1_input


title: 200930770229_R07C01: genomic DNA from Sample Tum20


title: ago1∆ x aoc2∆N_H3K9me2_2_ChIP-seq


title: aco2DN_1_mRNA-seq


title: aco2DN_2_mRNA-seq


title: 200821640029_R04C01: genomic DNA from Sample Tum19


title: 200821640029_R03C01: genomic DNA from Sample Tum18


title: 200970070042_R03C01: genomic DNA from Sample Tum28


title: 200930770229_R06C01: genomic DNA from Sample Tum17


title: aoc2∆N_H3K9me2_1_ChIP-seq


title: aoc2∆N_H3K9me2_2_ChIP-seq


title: 200821640029_R02C01: genomic DNA from Sample Tum16


title: ago1∆ x aoc2∆N_H3K9me2_1_ChIP-seq


title: 200821640029_R01C01: genomic DNA from Sample Tum15


title: 200970070040_R04C01: genomic DNA from Sample Tum43


title: H3K9me2_1_ChIP-seq


title: ago1∆ x aoc2∆N_H3K9me2_2_input


title: 200970070006_R06C01: genomic DNA from Sample Tum14


title: 200970070006_R05C01: genomic DNA from Sample Tum13


title: 200930770229_R05C01: genomic DNA from Sample Tum12


title: 200970070006_R04C01: genomic DNA from Sample Tum11


title: 200970070006_R03C01: genomic DNA from Sample Tum10


title: 200970070006_R02C01: genomic DNA from Sample Tum9


title: 200970070006_R01C01: genomic DNA from Sample Tum8


title: 200930770095_R08C01: genomic DNA from Sample Tum7


title: 200930770095_R06C01: genomic DNA from Sample Tum6


title: 200930770095_R05C01: genomic DNA from Sample Tum5


title: 200930770095_R03C01: genomic DNA from Sample Tum3


title: 200930770095_R02C01: genomic DNA from Sample Tum2


title: 200930770095_R04C01: genomic DNA from Sample Tum4


title: 200930770095_R01C01: genomic DNA from Sample Tum1


title: H3K27ac_D7-WT-IC1

city: Nantes

first: Alice

last: Mollé

address: 30 bd Jean Monnet

institute: University of Nantes

data_processing:
RNA-seq: Reads were mapped to mm10 genome using STAR with default parameters. The number of fragments mapped to each gene was counted using featureCounts and mm10.gtf gene annotation.
ChIP-seq: Single-end reads were mapped to the mm10 genome by the BWA algorithm and reads mapping to non-canonical and mitochondrial chromosomes were also removed. For each sample, ChIP-seq peaks were detected using DFilter at a P-value threshold of 1x10-6. A set of consensus peaks was then obtained by taking the union of all peaks and counting reads these peaks using HOMER.
Genome_build: mm10
Supplementary_files_format_and_content: Peaks files are generated with Dfilter; TMM normalized counts after filtering for low abundance genes on which the differential analyzes were performed

source_name: wild type_infection-cured_AM

growth_protocol: Purified AMs (5x10^5 cells from ~15 pooled mice).

extract_protocol:
RNA-seq: RNA was extracted from FACS sorted cells ext using the QIAGEN RNEasy plus mini-kit.
ChIP-seq: Cells were lysed and chromatin was fragmented with Micrococcal nuclease (MNase) and incubuated with 2 mg of anti-H3K27ac (39133, Active Motif) for immunoprecipitation
RNA-seq: Poly-A selected mRNA was then converted to Illumina sequencing ready libraries using NEB kit following the user-guide. cDNA libraries were pooled and sequenced at the Institut Cochin, Paris with one run of Illumina NextSeq 500
ChIP-seq: Libraries were prepared as follows. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~300 bp (insert plus adaptor and PCR primer sequences) were purified by double-sided SPRI size selection . The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were send to a sequencing platform core facility and sequenced on  a Next-seq 500 (Illumina).

treatment_protocol: E.Coli were injected intra-tracheally in anesthetized mice to induce a non-lethal acute pneumonia.

tag: strain background

tag: genotype/variation

value: wild type

tag: state

value: infection-cured

tag: time (day)

value: alveolar macrophages (AM)

tag: chip antibody

value: anti-H3K27ac (39133, Active Motif)


title: H3K27ac_D7-WT-IC2


title: H3K27ac_input

source_name: wild type_AM


title: ZmPep5b_1

type: RNA

city: La Jolla

first: Alisa

last: Huffaker

address: 9500 Gilman Dr.

department: Cell & Developmental Biology

institute: U.C. San Diego

hyb_protocol: Hybridization to Agilent-016047 maize 44 K genome array, washing as per Agilent protocols

scan_protocol: Scanning as per Agilent protocols

data_processing: 3 samples were removed after outlier detection using arrayQualityMetrics. Limma backgroundCorrect(method=normexp, offset=5) was used for background correction, followed by within-group quantile normalization using qsmooth

organism: Zea mays

source_name: Leaf 5

label_protocol: cDNA synthesis, reverse transcription, and biotin labeling using the Agilent Quick Amp Gene Expression Labeling kit and protocol

growth_protocol: Zea mays plants were grown in BM2 soil (Berger Mixes) and supplemented with a 18-18-21 Tomato Plant Food fertilizer (Miracle-Gro) inside a greenhouse (12-h light, minimum of 300 µmol m-2s-1, and 12-h dark) at 24°C/28°C (night/day) temperature cycle

extract_protocol: Total RNA was isolated with TRIzol (Invitrogen) as per the manufacturer’s protocol

treatment_protocol: The youngest fully-expanded leaf of greenhouse-grown 21 day old plants (leaf 5 of stage V3 plants) was excised and placed in a glass vial containing either water or five micromolar solutions of ZmPeps for 12 hours (time 0 = 5 PM, harvest time 5 AM).   Leaves were harvested and frozen in liquid nitrogen.  Each biological sample is a combined pool of two leaves.

value: Leaf 5


title: H3K27ac_D0-WT-UN1

source_name: wild type_uninfected_AM

value: uninfected


title: ZmPep5all_3


title: ZmPep5all_4


title: ZmPep5b_2


title: ZmPep5a_3


title: ZmPep5b_4


title: ZmPep5a_2


title: D7-WT-R3_AM


title: H3K27ac_D0-WT-UN2


title: ZmPep5all_1


title: ZmPep4all_2


title: ZmPep5a_4


title: ZmPep5b_3


title: ZmPep5all_2


title: ZmPep4all_4


title: D7-WT-R2_AM


title: D7-WT-R1_AM


title: ZmPep4all_1


title: ZmPep4all_3


title: ZmPep4d_3


title: ZmPep4d_4

description: This sample removed from analysis after outlier detection using arrayQualityMetrics


title: D7-SIRPa-R2_AM

value: SIRP-alpha-/-


title: ZmPep5a_1


title: D7-SIRPa-R1_AM


title: D7-SIRPa-R3_AM


title: ZmPep4d_1


title: ZmPep4c_4


title: ZmPep4d_2


title: D0-WT-R3_AM


title: ZmPep4c_3


title: ZmPep4c_2


title: D0-WT-R2_AM


title: D0-SIRPa-R3_AM


title: ZmPep4b_4


title: D0-SIRPa-R2_AM


title: ZmPep4b_3


title: ZmPep4c_1


title: D0-SIRPa-R1_AM


title: ZmPep4b_2


title: BPF_D

city: Darlinghurst

first: Ruth

last: Pidsley

state: NSW

address: 384 Victoria Street

country: Australia

institute: Garvan Institute of Medical Research

description: Normal Prostate Fibroblast

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Raw intensity data (IDAT) files were imported into R using the minfi package (version 1.12.0) [PMID: 24478339]. The data was processed in minfi with background correction.  Poor quality probes with a detection p-value >0.01 in at least 10% samples were removed.  To reduce the risk of false discoveries we removed probes that mapped to multiple locations or overlapped SNPs as identified by Pidsley and colleagues [PMID: 27717381]. The resulting datasets comprised 808,100 CpG sites. β values were calculated from unmethylated (U) and methylated (M) signal [M/(U + M + 100)] and ranged from 0 to 1 (0 to 100% methylation).

source_name: BPF

growth_protocol: Prostate tissue was chopped into small pieces, approximately 2 mm3, and digested overnight at 37°C in RPMI containing 10% fetal calf serum (FCS), 25 mM HEPES, 100 U/mL penicillin, 100 mg/mL streptomycin, 0.5 mg/mL fungizone, 100 mg/mL gentamicin, 225 U/mL Collagenase Type I and 125 U/mL Hyaluronidase Type II (Sigma Aldrich) as previously described [PMID: 23558784]. Cell suspensions were seeded in RPMI containing 5% FCS, penicillin/streptomycin, 1 nM testosterone (Sigma Aldrich) and 10 ng/mL bFGF (Millipore), a medium that selects for fibroblasts compared to other prostatic cell types. Cells were grown at 37°C in a humidified incubator with 5% O2 and 5% CO2. The first passage of cells typically reached confluency within 2 weeks.

extract_protocol: DNA was extracted from CAF, NPF and BPF samples using the DNeasy kit (Qiagen) with on-column RNase A digestion. Eluates were precipitated with 0.1 volume sodium acetate and 2.5 volumes ethanol and then resuspended in nuclease-free water. DNA was quantified using a NanoDrop 2000.

treatment_protocol: Cells were cultured in standard media to approximately 80% confluency before being trypsinised, resuspended in media and then centifuged to create cell pellets. Cells were stored at -80°C until DNA extraction.

tag: gender

value: Male

value: Prostate

tag: gleason

tag: gleason grade group


title: BPF_C

description: Normal Prostate Fibroblast


title: BPF_E

description: Normal Prostate Fibroblast


title: NPF22

description: Normal Prostate Fibroblast

source_name: NPF


title: ZmPep4b_1


title: NPF23

description: Normal Prostate Fibroblast


title: BPF_A

description: Normal Prostate Fibroblast


title: NPF18

description: Normal Prostate Fibroblast


title: Ad-NGN3-GFP+Ad-REST GFP+ E

city: Rehovot

first: Ofer

last: Elhanani

address: Herzl St 234

department: Dept. of Biomolecular Sciences

country: Israel

institute: Weizmann Institute of Science

description:
NGN3_REST_GFP_p_E
3' end-RNA-seq
MARS-seq
mRNA
processed data file: RawUMIcounts.txt
processed data file: Report-Deseq2.xlsx

data_processing:
Bcl files were converted into fastq by bcl2fastq. Demultiplexing is done using the sample barcode found on R2, the UMI found on R2 is inserted in the read name (in R1 fastq). R1 Fastq data submitted. All further steps were done using UTAP (UTAP: User-friendly Transcriptome Analysis Pipeline, Kohen et al. BMC Bioinformatics 2019, 20(1):154)).
Adapters and low quality bases were removed from the raw reads using cutadapt version 1.8.3 (parameters -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a "A{100}" -a "T{100}" --times 2 --cut 3 -q 20 -m 30).
The remaining reads were mapped to the Mus musculus genome (mm10) using STAR.
Read counts per gene were calculated using HTSeq-count and a Refseq gtf file (downloaded from igenomes UCSC), which was modified to contain a window surrounding the 3' UTR . For further analysis genes were filtered out if their sum counts was less or equal to 5.
Normalization and differential expression analysis were performed using the DESeq2 R-package (Bioconductor, https://bioconductor.org/packages/release/bioc/html/DESeq2.html). Differentially expressed genes were defined as genes that had a significant adjusted p value (BH) of less than 0.05 and at least 2-fold change.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: RawUMIcounts.txt contains genes raw UMI counts.
Supplementary_files_format_and_content: Report-Deseq2.xlsx contains DESeq2 statistical data regarding 3921 differentially expressed genes in at least one of the contrasts between experimental groups: M3+LacZ (mcherry- vs. mCherry+); M3+REST (mCherry- vs. mCherry+); mCherry+ (M3+LacZ vs. M3+REST); M3+LacZ mCherry- vs. NGN3+LacZ GFP+; M3+REST mCherry- vs. NGN3+REST GFP+; GFP+ (NGN3+LacZ vs. NGN3+REST).

source_name: Primary pancreatic exocrine cells

growth_protocol: After isolation, exocrine cell clusters were infected with adenoviruses overnight in 6-well plates in Waymouth’s MB752/1 culture medium supplemented with 2.5% FBS, 2 mM glutamine 1%, 1% penicillin-streptomycin solution, 25 ng/ml murine EGF and 0.3 mg/ml trypsin inhibitor (Sigma, #T9128). After 24 hours, cell clusters were washed and plated on collagen coated plates. On day 5 after isolation, cells were dissociated and FACS sorted.

extract_protocol:
Cells were sorted into RLT lysis buffer and RNA was purified using RNeasy micro kit (QIAGEN #74004).
30 ng of purified RNA was used for library preparation with the bulk MARS-seq protocol (Jaitin et al. 2014 Science.343:776-9). MARS-seq libraries were sequenced using Illumina NextSeq 500 High Output v2 Kit (75 cycles).

treatment_protocol: Infections with Ad-M3-mCherry, Ad-NGN3-GFP, Ad-LacZ and Ad-REST were carried overnight at a titer of 10*10^6 IFU/ml.

value: Primary pancreatic exocrine cells

tag: virus

tag: sorted population

value: GFP+


title: NPF19

description: Normal Prostate Fibroblast


title: Ad-NGN3-GFP+Ad-REST GFP+ C

description:
NGN3_REST_GFP_p_C
3' end-RNA-seq
MARS-seq
mRNA
processed data file: RawUMIcounts.txt
processed data file: Report-Deseq2.xlsx


title: BPF_B

description: Normal Prostate Fibroblast


title: NPF16

description: Normal Prostate Fibroblast


title: NPF21

description: Normal Prostate Fibroblast


title: Ad-NGN3-GFP+Ad-REST GFP+ B

description:
NGN3_REST_GFP_p_B
3' end-RNA-seq
MARS-seq
mRNA
processed data file: RawUMIcounts.txt
processed data file: Report-Deseq2.xlsx


title: NPF15

description: Normal Prostate Fibroblast


title: NPF12

description: Normal Prostate Fibroblast


title: NPF14

description: Normal Prostate Fibroblast


title: NPF20

description: Normal Prostate Fibroblast


title: NPF8

description: Normal Prostate Fibroblast


title: ZmPep4a_2


title: Ad-NGN3-GFP+Ad-LacZ GFP+ F

description:
NGN3_LacZ_GFP_p_F
3' end-RNA-seq
MARS-seq
mRNA
processed data file: RawUMIcounts.txt
processed data file: Report-Deseq2.xlsx


title: Ad-NGN3-GFP+Ad-LacZ GFP+ E

description:
NGN3_LacZ_GFP_p_E
3' end-RNA-seq
MARS-seq
mRNA
processed data file: RawUMIcounts.txt
processed data file: Report-Deseq2.xlsx


title: ZmPep4a_1


title: NPF13

description: Normal Prostate Fibroblast


title: NPF2

description: Normal Prostate Fibroblast


title: NPF4

description: Normal Prostate Fibroblast


title: CAF22

description: Cancer Associated Fibroblast

source_name: CAF


title: Ad-NGN3-GFP+Ad-LacZ GFP+ C

description:
NGN3_LacZ_GFP_p_C
3' end-RNA-seq
MARS-seq
mRNA
processed data file: RawUMIcounts.txt
processed data file: Report-Deseq2.xlsx


title: NPF1

description: Normal Prostate Fibroblast


title: ZmPep4a_3


title: NPF10

description: Normal Prostate Fibroblast


title: NPF9

description: Normal Prostate Fibroblast


title: CAF23

description: Cancer Associated Fibroblast


title: Ad-NGN3-GFP+Ad-LacZ GFP+ B

description:
NGN3_LacZ_GFP_p_B
3' end-RNA-seq
MARS-seq
mRNA
processed data file: RawUMIcounts.txt
processed data file: Report-Deseq2.xlsx


title: ZmPep4a_4


title: Ad-M3-mCherry+Ad-REST mCherry+ F

description:
M3_REST_Cherry_p_F
3' end-RNA-seq
MARS-seq
mRNA
processed data file: RawUMIcounts.txt
processed data file: Report-Deseq2.xlsx

value: mCherry+


title: K562 cells_shNSD2#1_rep2

city: seoul

first: JinWoo

last: Park

state: Soul-t'ukpyolsi

address: Department of life science, college of nature science

institute: Chung-Ang Univ

description: replicate 2

hyb_protocol: Following fragmentation, 0.75 ug of cRNA were hybridized to the Illumina Expression Beadchip according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Illumina Bead Array Reader Confocal Scanner

data_processing:
Data were analyzed via a  company called Macrogen, which provided a single set of non-normalized data which were used to draw conclusions for the study. Thus no normalization was performed.
Array data export processing and analysis was performed using Illumina GenomeStudio v2011.1 (Gene Expression Module v1.9.0)
Statistical significance of the expression data was determined using LPE test and fold change in which the null hypothesis was that no difference exists among 2 groups. False discovery rate (FDR) was controlled by adjusting p value using Benjamini-Hochberg algorithm.

source_name: NSD2 shRNA #1

label_protocol: Biotinylated cRNA were prepared from 0.55 ug total RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin,TX)

extract_protocol: Total RNA was extracted using Trizol (Invitrogen Life Technologies, Carlsbad, USA), purified using RNeasy columns (Qiagen, Valencia, USA) according to the manufacturers’ protocol. After processing with DNase digestion, clean-up procedures, RNA samples were quantified, aliquot and stored at -80°C until use. For quality control, RNA purity and integrity were evaluated by denaturing gel electrophoresis, OD 260/280 ratio, and analyzed on Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA).

tag: cell line

tag: knockdown

value: NSD2 shRNA #1


title: K562 cells_shNSD2#1_rep1

description: replicate 1


title: Ad-M3-mCherry+Ad-REST mCherry+ E

description:
M3_REST_Cherry_p_E
3' end-RNA-seq
MARS-seq
mRNA
processed data file: RawUMIcounts.txt
processed data file: Report-Deseq2.xlsx

tag: strain


title: K562 cells_shNSD2#2_rep2

description: replicate 2

source_name: NSD2 shRNA #2

value: NSD2 shRNA #2


title: NPF7

description: Normal Prostate Fibroblast

tag: tissue


title: K562 cells_shNSD2#2_rep1

description: replicate 1


title: ZmPep3_1


title: Ad-M3-mCherry+Ad-REST mCherry+ B

description:
M3_REST_Cherry_p_B
3' end-RNA-seq
MARS-seq
mRNA
processed data file: RawUMIcounts.txt
processed data file: Report-Deseq2.xlsx

tag: cell type


title: ZmPep3_4


title: ZmPep3_3


title: K562 cells_shNC_rep1

description: replicate 1

source_name: non-target shRNA

value: non-target shRNA


title: r2w9bdKO1

city: Cheonan

first: Jeong Kyo

last: Yoon

address: 25 Bonjeong-ro, Dongnam-gu

institute: Soonchunhyang University

data_processing:
PolyA/t strech and Illumina adpaters were trimmed using "cutadapt"
Reads were mapped to the mouse refernce genome using "STAR"
Gene annotations were supplied by Ensembl v82
Expression levels fro each gene were quantified using "htseq-count"
Differentially expressed genes were identified using "DEseq2"
Genome_build: Mus Musculus GRCm38

source_name: embryonic facial processes

extract_protocol:
Total RNA extraction by Trizol
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Mixed

value: facial process explants

tag: age

value: embryonic day 10.5

value: Rspo2;Wnt9b double homozygous mutant


title: CAF18

description: Cancer Associated Fibroblast


title: K562 cells_shNC_rep2

description: replicate 2


title: ZmPep2_3


title: r2w9bdKO3


title: Ad-M3-mCherry+Ad-REST mCherry+ A

description:
M3_REST_Cherry_p_A
3' end-RNA-seq
MARS-seq
mRNA
processed data file: RawUMIcounts.txt
processed data file: Report-Deseq2.xlsx


title: CAF12

description: Cancer Associated Fibroblast


title: ZmPep2_4


title: CAF16

description: Cancer Associated Fibroblast


title: Ad-M3-mCherry+Ad-REST mCherry- F

description:
M3_REST_Cherry_m_F
3' end-RNA-seq
MARS-seq
mRNA
processed data file: RawUMIcounts.txt
processed data file: Report-Deseq2.xlsx

value: mCherry-


title: CAF15

description: Cancer Associated Fibroblast


title: w9bKO1

value: Wnt9b gene homozygous mutant


title: w9bKO2


title: Ad-M3-mCherry+Ad-REST mCherry- E

description:
M3_REST_Cherry_m_E
3' end-RNA-seq
MARS-seq
mRNA
processed data file: RawUMIcounts.txt
processed data file: Report-Deseq2.xlsx


title: r2KO1

value: Rspo2 gene homozygous mutant


title: r2w9bdKO2


title: Ad-M3-mCherry+Ad-REST mCherry- B

description:
M3_REST_Cherry_m_B
3' end-RNA-seq
MARS-seq
mRNA
processed data file: RawUMIcounts.txt
processed data file: Report-Deseq2.xlsx


title: r2KO2


title: wt2

value: wild type


title: ZmPep2_2

value: Leaf 5


title: CAF21

description: Cancer Associated Fibroblast

value: Male


title: ZmPep1_4


title: Klk6_f_64272

city: Ann Arbor

first: William

middle: R

last: Swindell

address: 1500 E. Medical Center Drive

department: Dermatology

institute: University of Michigan

description: RNA extracted from skin

data_processing:
Quality-filtered reads were mapped to the UCSC GRCm38/mm10 genome using Tophat2. Default settings were applied with disabling of multi-mapping (-g 1) and the coverage-based search for junctions (--no-coverage-search). This generated an aligment bam file for each sample that was subsequently sorted and indexed using samtools. The number of reads aligned to each genomic feature was tabulated using the HTSeq library and “htseq-count” algorithm. A read was required to completely overlap the reference gene’s sequence to be tabulated as a mapped read (-m intersection-strict). FPKM and associated confidence intervals were calculated using Cufflinks (version 2.2.1) with default settings.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Processed data includes FPKM values and mapped read counts for all mouse genes (GRCm38/mm10) and each sample (.txt files).

source_name: Skin

growth_protocol: We developed “Tet-off” transgenic mice that overexpressed C-terminal Myc/His-tagged murine Klk6 in keratinocytes in the absence of doxycycline (Klk6+ transgenic mice). In these mice, transgene overexpression is under control of the bovine Keratin 5 (K5) promoter, which drives expression in epidermal keratinocytes and some other stratified squamous epithelia. To generate these mice, F2 Tetos-Klk6 offspring that were genetically positive for Tetos-Klk6 were next mated to the keratinocyte-directed tetracycline transactivator (Tetoff) driver line K5-tTA (2). When crossing Tetos-Klk6 mice with the K5-tTA driver line in the absence of doxycycline, 10 litters yielded no transgenic offspring, indicating that embryonic overexpression of Klk6 in keratinocytes likely led to embryonic lethality. Mice were then mated in the presence of doxycycline, resulting in successful generation of Tetos-Klk6 mice carrying the K5-tTA driver (Klk6+ mice). Klk6+ transgenic and K5-tTA driver lines were maintained by backcrossing to C57BL/6 mice, and only transgenic mice from the F4 generation and onward were used for analyses. Littermates inheriting a single, non-expressing transgene (Tetos-Klk6 or K5-tTA) or wild-type littermates served as controls.

extract_protocol:
Mouse tissue was collected from transgenic and control mice following euthanasia. To generate RNA, skin samples were then snap-frozen in liquid nitrogen, pulverized, and dissolved in Buffer RLT (Qiagen) for RNA extraction. RNA was isolated using the RNeasy Mini kit (Qiagen).
Murine samples were submitted to a core facility for sequencing (University of Michigan, Ann Arbor, MI). Sample preparation was performed using the Illumina TruSeq mRNA Sample Prep v2 kit (catalog no. RS-122-2001 and RS-122-2002). Preparation of mRNA via polyA purification was carried out using 0.1–3.0 μg of total RNA per sample. mRNA was converted to cDNA using reverse transcriptase and random primers, and cDNA libraries were enriched and purified using Kapa’s library quantification kit (catalog no. KK4835; Kapa Biosystems, Wilmington, MA, USA). cDNA quantification and quality assessment was performed using the Agilent TapeStation. The Illumina clonal amplification system (cBot) was used to cluster samples with adaptor barcodes prior to Illumina HiSeq 2000 sequencing (50-cycle single end).

treatment_protocol: Klk6+ mice were maintained until reintroduction of doxycycline chow at 10-11 weeks, just prior to cessation of per os intake and becoming moribund. Animals were then euthanized and tissues collected and examined at 14-16 weeks of age.

tag: genotype

tag: Sex

value: Female


title: wt1

tag: genotype/variation


title: CAF19

description: Cancer Associated Fibroblast

value: Prostate


title: CAF20

description: Cancer Associated Fibroblast


title: ZmPep1_3


title: Klk6_m_64270

description: RNA extracted from skin


title: CAF10

description: Cancer Associated Fibroblast


title: Klk6_f_64271

description: RNA extracted from skin


title: Ad-M3-mCherry+Ad-LacZ mCherry+ F

description:
M3_LacZ_Cherry_p_F
3' end-RNA-seq
MARS-seq
mRNA
processed data file: RawUMIcounts.txt
processed data file: Report-Deseq2.xlsx

value: Primary pancreatic exocrine cells


title: CAF13

description: Cancer Associated Fibroblast


title: Ad-M3-mCherry+Ad-REST mCherry- A

description:
M3_REST_Cherry_m_A
3' end-RNA-seq
MARS-seq
mRNA
processed data file: RawUMIcounts.txt
processed data file: Report-Deseq2.xlsx


title: ZmPep1_2


title: Ad-M3-mCherry+Ad-LacZ mCherry+ E

description:
M3_LacZ_Cherry_p_E
3' end-RNA-seq
MARS-seq
mRNA
processed data file: RawUMIcounts.txt
processed data file: Report-Deseq2.xlsx

value: mCherry+


title: ZmPep3_2


title: Klk6_m_64269

description: RNA extracted from skin


title: WT_f_64266

description: RNA extracted from skin

value: WT


title: ZmPep1_1


title: Ad-M3-mCherry+Ad-LacZ mCherry+ B

description:
M3_LacZ_Cherry_p_B
3' end-RNA-seq
MARS-seq
mRNA
processed data file: RawUMIcounts.txt
processed data file: Report-Deseq2.xlsx


title: CAF14

description: Cancer Associated Fibroblast


title: CAF9

description: Cancer Associated Fibroblast


title: w9bKO3


title: WT_m_64265

description: RNA extracted from skin


title: WT_m_64264

description: RNA extracted from skin


title: Water_4

description: This sample removed from analysis after outlier detection using arrayQualityMetrics


title: WT_f_64267

description: RNA extracted from skin


title: WT_m_64263

description: RNA extracted from skin


title: CAF7

description: Cancer Associated Fibroblast


title: Ad-M3-mCherry+Ad-LacZ mCherry- F

description:
M3_LacZ_Cherry_m_F
3' end-RNA-seq
MARS-seq
mRNA
processed data file: RawUMIcounts.txt
processed data file: Report-Deseq2.xlsx


title: Ad-M3-mCherry+Ad-LacZ mCherry- E

description:
M3_LacZ_Cherry_m_E
3' end-RNA-seq
MARS-seq
mRNA
processed data file: RawUMIcounts.txt
processed data file: Report-Deseq2.xlsx


title: Ad-M3-mCherry+Ad-LacZ mCherry+ A

description:
M3_LacZ_Cherry_p_A
3' end-RNA-seq
MARS-seq
mRNA
processed data file: RawUMIcounts.txt
processed data file: Report-Deseq2.xlsx


title: Brain organoid RNAseq [25644_CMV_14048_BO_D30]

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

data_processing:
Sequences were aligned to hg19 using Tophat2 with default settings
Gene expression level of Refseq coding genes were quantified using HTseq-count
Genome_build: hg19
Supplementary_files_format_and_content: text format with RPKM values

source_name: hiPSC-derived brain organoids infected with TB40/E

growth_protocol: hiPSC-derived brain organoids were differentiated for  45 days.

extract_protocol:
Total RNA was isolated from TB40/E-infected organoids or control organoids 15 days post infection using Trizol (Invitrogen).
Kapa mRNA stranded protocol

treatment_protocol: hiPSC-derived brain organoids  were infected for 15 days with 5x10^5 pfu/ml TB40/E or UV-irradiated TB40/E as a control.

value: iPSC derived brain organoids

tag: treatment

value: CMV infection

tag: time point

value: 15 days post infection


title: Nfki1_18

city: Cambridge

first: Alastair

last: Crisp

address: Francis Crick Avenue

institute: MRC Laboratory of Molecular Biology

data_processing:
Reads trimmed and quality filtered using trim_galore (v 0.4.3)
Reads aligned to C. elegans genome using TopHat (v2.1.0)
Genes identified as oscillating in Hendriks et al 2014 were filtered out so they did not effect normalisation
Expression quantified using Cufflinks (v2.2.1)
Genome_build: C. elegans PRJNA13758.WS255
Supplementary_files_format_and_content: Tab separated cuffdiff output

organism: Caenorhabditis elegans

source_name: C. elegans (whole animal)

growth_protocol: 10 gravid adults were left to lay eggs for 2h on an OP50 lawn seeded 24h previously, before being picked away. Progeny were left to grow until late L4 stage. 8-10 plates were used per replicate.

extract_protocol:
Worm pellets were washed twice in M9 and frozen in LN2, and 1ml Qiazol Lysis Regaent (Qiagen) and 300-400μl 0.7mm Zirconia beads (BioSpec) were added. Samples were disrupted with a TissueLyser (Qiagen), using 1min at maximum power followed by 1min on ice (repeated 4 times). RNA was extracted using the RNeasy Plus Universal Mini Kit (Qiagen), following the manufacturer’s instructions with the exception that 1-Bromo-3-chloropropane (Sigma, B673) was used instead of chloroform.
Libraries were prepared using the TruSeq Stranded mRNA kit (Illumina) with polyA capture for mRNA according to the manufacturer's instructions.

tag: strain strain background

tag: developmental stage


title: Nfki1_17


title: Nfki1_16


title: Water_2


title: Water_3


title: Ad-M3-mCherry+Ad-LacZ mCherry- B

description:
M3_LacZ_Cherry_m_B
3' end-RNA-seq
MARS-seq
mRNA
processed data file: RawUMIcounts.txt
processed data file: Report-Deseq2.xlsx


title: Nfki1_14


title: Brain organoid RNAseq [25643_14048_BO_D30]

source_name: hiPSC-derived brain organoids infected with UV-irradiated TB40/E

value: mock infection


title: Nfki1_13


title: Nfki1_12


title: CAF1

description: Cancer Associated Fibroblast

tag: gender

tag: gleason


title: Nfki1_10


title: TIG-3 cells_10 nM ARV82_4d_DXR1

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

description: DXR-induced senescent TIG-3 cells with 10 nM ARV82 for 4 days

data_processing:
Sequencing was performed on an Illumina HiSeq 2500/3000 platform in a 75-base single-end mode.
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to the human reference genome sequences (hg19) using TopHat v2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cufflinks version 2.2.1.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM values

source_name: TIG-3 cells_10 nM ARV82_4d_DXR1

extract_protocol:
Total RNA was extracted using the miRNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol.
Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

value: TIG-3 cells


title: Ad-PDX1+ Ad-DN-REST D

data_processing:
Bcl files were converted into fastq by bcl2fastq. Demultiplexing is done using the sample barcode found on R2, the UMI found on R2 is inserted in the read name (in R1 fastq).  R1 Fastq data submitted.  Raw UMI counts are submitted in sheet 2 - "Raw UMI counts".
Adapters and low quality bases were removed from the raw reads using cutadapt version 1.8.3 (parameters -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a "A{100}" -a "T{100}" --times 2 --cut 3 -q 20  -m 30 )
The remaining reads were mapped to the Mus musculus genome (mm10) using STAR.
Read counts per gene were calculated using HTSeq-count and a Refseq gtf file (downloaded from igenomes UCSC), which was modified to contain a window surrounding the 3' UTR. Analysis was done on UMI counts.
For further analysis genes were filtered out if thier sum counts was less or equal to  5. Normalization and differential expression analysis was performed using the DESeq2 R-package (Bioconductor, https://bioconductor.org/packages/release/bioc/html/DESeq2.html). Differentially expressed genes were defined as genes that had a significant adjusted p value of less than 0.05 and at least 2-fold change.
Genome_build: mm10
Supplementary_files_format_and_content: Report-Deseq2.xlsx contains DESeq2 statistical data regarding  2485 differentially expressed genes and the cluster number (described in article).

growth_protocol: After isolation, exocrine cell clusters were infected with adenoviruses overnight in 6-well plates in Waymouth’s MB752/1 culture medium  supplemented with 2.5% FBS, 2 mM glutamine 1% ,  1% penicillin-streptomycin solution, 25 ng/ml murine EGF and 0.3 mg/ml trypsin inhibitor (Sigma, #T9128). After 24 hours, cell clusters were washed and plated on collagen coated plates. RNA was extracted on day 5 after isolation and infection.

extract_protocol:
Cells were lysed in Tri-reagent and total RNA was extracted using the Direct-zol RNA miniprep kit (Zymo research, #R2052)
Purified messanger RNA was eluted at 70C with 6ul of 10mM Tris-Cl pH 7.5 and stored at -80C.For library preparation RNA was used for the bulk MARS-seq  protocol (Jaitin et al. 2014 Science.343:776-9). MARS-seq libraries were sequenced using Illumina NextSeq 500 High Output v2 Kit (75 cycles).

treatment_protocol: Infections with adenoviruses was carried overnight at the following titers:  Ad-mCherry: 40*10^6 IFU/ml, Ad-PDX1: 10*10^6 IFU/ml, Ad-DN-REST: 30*10^6 IFU/ml

tag: virus

value: Ad-PDX1+ Ad-DN-REST


title: Ad-PDX1+ Ad-DN-REST C


title: CAF8

description: Cancer Associated Fibroblast

tag: gleason grade group


title: TIG-3 cells_vehicle_4d_DXR1

description: DXR-induced senescent TIG-3 cells with vehicle for 4 days

source_name: TIG-3 cells_vehicle_4d_DXR1


title: Nfki1_9


title: Water_1


title: MOLM-13 shNT 12d #3

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

data_processing:
FASTQ sequence files were aligned to the human genome hg19 using STAR with corresponding reference transcriptome. The software AltAnalyze version 2.1.3 was used to derive gene expression (RPKM) and splicing profiles (MultiPath-PSI percent-spliced-in estimates) using Ensembl version 72. See http://www.altanalyze.org algorithm details.
Genome_build: hg19
Supplementary_files_format_and_content: RPKM

source_name: Leukemia cell line

growth_protocol: MOLM-13 cells were maintained in RPMI 1640 supplemented with 10% FBS; MV4;11 were maintained in IMDM supplemented with 10% FBS

extract_protocol:
After treatment, total RNA was isolated using the QIAGEN RNEasy Mini kit according to manufacturer's protocols.
Library construction was performed using the TruSeq RNA Library Prep Kit (Illumina) according to the manufacturer's protocols. Purified and adapter-ligated cDNA was captured on a flowcell, and sequenced on an Illumina HiSeq 2500. 12-day culture experiments were sequenced separately on a NovaSeq 6000

treatment_protocol: Cells were transduced with lentiviral shRNA against MBNL1 or non-targeting control, and selected with puromycin prior to harvest at the indicated timepoints

value: Acute myeloid leukemia

tag: translocation


title: Nfki1_7


title: Nfki1_8


title: Ad-PDX1+ Ad-DN-REST B


title: Nfki1_5


title: MOLM-13 shNT 12d #2


title: CAF2

description: Cancer Associated Fibroblast


title: Nfki1_6


title: Ad-PDX1+ Ad-DN-REST A


title: Nfki1_4


title: Ad-DN-REST D

value: Ad-DN-REST


title: MOLM-13 shNT 12d #1


title: Nfki1_11


title: Nfki1_2


title: Nfki1_3


title: MOLM-13 shMBNL1-64 12d #3


title: CAF4

description: Cancer Associated Fibroblast


title: Ad-DN-REST C


title: Ilc17_6_2


title: MOLM-13 shMBNL1-64 12d #1


title: Ilc17_4_2


title: Ad-DN-REST B


title: Ilc17_15


title: Ilc17_14


title: Ad-DN-REST A


title: MV4;11 shMBNL1-65 #3


title: Ilc17_12


title: Ad-PDX1 D


title: Ilc17_13


title: Ad-PDX1 C


title: Ilc17_11


title: Ilc17_9


title: Ilc17_10


title: MV4;11 shMBNL1-65 #2


title: Ilc17_8


title: Nfki1_1


title: MOLM-13 shMBNL1-64 12d #2


title: Ilc17_5_2


title: MV4;11 shMBNL1-65 #1


title: Ad-PDX1 A


title: Ad-PDX1 B


title: Ilc17_7


title: MV4;11 shMBNL1-64 #3


title: Ilc17_6


title: MV4;11 shMBNL1-64 #2


title: Ilc17_5


title: Ad-mCherry D

value: Ad-mCherry


title: Ilc17_4


title: ZmPep2_1

source_name: Leaf 5


title: MV4;11 shMBNL1-64 #1


title: Ilc17_3


title: Ilc17_2


title: MV4;11 shNT #3


title: Nfki1_15


title: Ad-mCherry C


title: Malt-1_18


title: Ad-mCherry B


title: MV4;11 shNT #2


title: Malt-1_17


title: Malt-1_16


title: Malt-1_15


title: Ad-mCherry A


title: Malt-1_14


title: MV4;11 shNT #1


title: Islets-MIP-GFP- GFP+ D

data_processing:
Bcl files were converted into fastq by bcl2fastq v2.17.1.14. Demultiplexing is done using the sample barcode found on R2, the UMI found on R2 is inserted in the read name (in R1 fastq).  R1 Fastq data submitted.  Raw counts are submitted in sheet 2.
Adapters and low quality bases were removed from the raw reads using cutadapt version 1.8.3 (parameters -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a "A{100}" -a "T{100}" --times 2 --cut 3 -q 20  -m 30 )
The remaining reads were mapped to the Mus musculus genome (mm10) using STAR.
Read counts per gene were calculated using HTSeq-count and a Refseq gtf file (downloaded from igenomes UCSC), which was modified to contain a window surrounding the 3' UTR. Analysis was done on read counts (not UMI counts).
For further analysis genes were filtered out if thier sum counts was less or equal to  5. Normalization and differential expression analysis was performed using the DESeq2 R-package (Bioconductor, https://bioconductor.org/packages/release/bioc/html/DESeq2.html). Differentially expressed genes were defined as genes that had a significant adjusted p value of less than 0.05 and at least 2-fold change.
Genome_build: mm10
Supplementary_files_format_and_content: Report-Deseq2.xlsx contains DESeq2 statistical data regarding  3077 differentially expressed genes and the cluster number (described in article).

source_name: Islets of Langerhans

growth_protocol: After isolation, exocrine cell clusters were infected with adenoviruses overnight in 6-well plates in Waymouth’s MB752/1 culture medium  supplemented with 2.5% FBS, 2 mM glutamine 1% ,  1% penicillin-streptomycin solution, 25 ng/ml murine EGF and 0.3 mg/ml trypsin inhibitor (Sigma, #T9128). After 24 hours, cell clusters were washed and plated on collagen coated plates. On day 6 after isolation, cells were dissociated and FACS sorted.  MIP-GFP Islets were cultured overnight in RPMI medium supplemented with 10% FBS, 2 mM glutamine 1% ,  1% penicillin-streptomycin solution. 24 hours after isolation, islets were dissosiated and FACS sorted.

extract_protocol:
Cells were sorted into lysis buffer an messanger RNA was captured with 15ul of Dynabeads oligo(dT) (Life technologies), and washed according to manufacture guidelines.
Purified messanger RNA was eluted at 70C with 6ul of 10mM Tris-Cl pH 7.5 and stored at -80C.For library preparation RNA was used for the bulk MARS-seq  protocol (Jaitin et al. 2014 Science.343:776-9). MARS-seq libraries were sequenced using Illumina NextSeq 500 High Output v2 Kit (75 cycles).

treatment_protocol: Infection with Ad-mCherry or Ad-M3-mCherry was carried overnight at a titer of 10*10^6 IFU/ml

value: MIP-GFP

value: Islets of Langerhans

tag: sorted cell population

value: GFP+


title: MOLM-13 shMBNL1-65 #4


title: Malt-1_13


title: MOLM-13 shMBNL1-65 #3


title: Islets-MIP-GFP- GFP+ C

tag: strain


title: Malt-1_11


title: Islets-MIP-GFP- GFP+ B

tag: tissue


title: r2KO3

value: Mixed

value: facial process explants

value: embryonic day 10.5

value: Rspo2 gene homozygous mutant


title: MOLM-13 shMBNL1-65 #2

tag: cell type


title: Islets-MIP-GFP- GFP+ A


title: Malt-1_9


title: Ilc17_1


title: Malt-1_8


title: MOLM-13 shMBNL1-65 #1


title: Ad-M3-mCherry- Cherry+/GFP+ D

value: Primary pancreatic exocrine cells

value: mCherry+/GFP+


title: MOLM13-shNT #6


title: Ad-M3-mCherry- Cherry+/GFP+ C


title: Malt-1_5


title: Malt-1_7


title: Malt-1_6


title: Malt-1_3


title: Malt-1_2


title: Malt-1_1


title: Malt-1_12


title: MOLM13-shNT #5


title: Ad-M3-mCherry- Cherry+/GFP+ A


title: MOLM13-shNT #4


title: Malt-1_10


title: WT_18


title: Klk6_m_64268

description: RNA extracted from skin

value: Male


title: WT_16


title: ADAR3-OE-rep3

city: Guangzhou

first: Rui

last: Zhang

address: No. 135, Xingang Xi Road

country: China

institute: Sun Yat-sen University

data_processing:
Reads were trimmed by cutadapt v1.14, then mapped to hg19 genome using TopHat v2.1.1 with parameters  -N 6 -i 10 --read-edit-dist 6.
RPKM was calculated using cuffnorm v2.2.1.
Genome_build: hg19
Supplementary_files_format_and_content: Text files include RPKM values for each sample

source_name: HEK293 cell

growth_protocol: HEK293 cells were grown in DMEM containing 10% FBS and cultured in 37℃ with 5% CO2.

extract_protocol:
Total RNA was extracted with TRIzol and Direct-zol RNA Kit
RNA-seq libraries were constructed using VAHTS mRNA-seq v2 Library Prep Kit for Illumina (Vazyme)

treatment_protocol: HEK293 cells were transiently transfected with ADAR plasmids by Lipofectamine 3000

tag: cell line

tag: passages

value: ADAR3 overexpression


title: ADAR3-OE-rep2


title: Ad-M3-mCherry- Cherry+/GFP- D

value: mCherry+/GFP-


title: WT_17


title: WT_15


title: WT_14


title: ADAR3-OE-rep1


title: WT_13


title: Malt-1_4


title: WT_12


title: Ad-M3-mCherry- Cherry+/GFP+ B


title: WT_11


title: ADAR2-OE-rep3

value: ADAR2 overexpression


title: WT_9


title: ADAR2-OE-rep2


title: WT_10


title: WT_8


title: Ad-M3-mCherry- Cherry-/GFP- C

value: mCherry-/GFP-


title: ADAR2-OE-rep1


title: Ad-M3-mCherry- Cherry-/GFP- D


title: Ad-M3-mCherry- Cherry+/GFP- A


title: WT_5


title: WT_6


title: WT_4


title: Ad-M3-mCherry- Cherry+/GFP- C


title: WT_2


title: ADAR1-OE-rep3

value: ADAR1 overexpression


title: ADAR1-OE-rep2


title: WT_3


title: ADAR1-OE-rep1


title: Ad-M3-mCherry- Cherry-/GFP- A


title: Ad-M3-mCherry- Cherry-/GFP- B


title: Ad-M3-mCherry- Cherry+/GFP- B


title: Ad-mCherry- mCherry+ C

value: mCherry+


title: pCDH-vector-OE-rep3

value: pCDH-vector


title: MTCH2_KD_C646_R2

city: Toronto

first: Dilshad

middle: Hussain

last: Khan

state: Ontario

address: 101 College Street

country: Canada

institute: Princess Margaret Cancer Centre

data_processing:
Chip-seqdata has been aligned to the human genome using bowtie2.
Dipplicated reads and multiple loaci aligned reads have been discarded
Peaks were called using MACS2 peak caller.
Differentiallly binding peaks have been analyzed using edgeR package.
Genome coverage tracks have been created using the bamCoverage tool in the deeptools package.
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files are binary files that include the genome coverage tracks.  Bed files are 3 column text files that include the coordinates of the called peaks.

growth_protocol: TEX cells were cultured in IMDM supplemented with 20% FCS, 100  units/mL streptomycin, 100 µg/mL penicillin,SCF (20 ng/mL), IL-3 (2 ng/mL), and L-glutamine (2 mM).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with H3K27ac antibody.
Samples were prepared as outlined by Takara Bio USA Inc’s ThruPLEX DNA-seq Kit user guide. Briefly, samples were normalized to 10ng of DNA input and topped up to 10ul with nuclease-free water. Samples were then mixed with 3ul of template preparation master mix and incubated at 22°C for 25 minutes, then 55°C for 20 minutes in a Veriti 96-well thermocycler (Thermo Fisher). Following template preparation, samples were mixed with 2ul of library synthesis master mix and incubated at 22°C for 40 minutes on the same cycler. Samples were prepared for library amplification as outlined in the user guide and indexed individually. From here, PCR cycles were optimized by adding 0.75ul of 10x SYBR green I nucleic acid gel stain (Thermo Fisher) to each sample. Once mixed, 10ul from each sample was removed and run on a CFX96 Touch Real-Time PCR cycler (Bio-Rad). Samples were normalized to 1/3 of their amplification curve and amplified on a Veriti 96-well thermocycler. Samples were topped up to 50ul with nuclease-free water prior to bead cleanup with AMPure XP beads (Beckman Coulter). Final library sizing and QC was evaluated on Agilent’s high sensitivity DNA kit run on the 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: shRNA knockdown was performed with lentiviral infections. 2 mL of virus was added to 5 mL of media containing 5.0 x 106 cells and protamine sulfate (5 µg/mL) followed by overnight incubation (37C, 5% CO2). The following day, cells were centrifuged and washed, and re-suspended in 25 mL fresh medium with appropriate puromycin concentration (2.0 ug/ml) and subjected to selection for 3 days. After the selection period, knockdown cells were treated with or without with C646 (5 µM) for 3 days.

value: TEX

value: Acute Myeloid leukemia cell line

value: MTCH2 knockdown

value: C646 (5 µM) for 3 days

tag: chip antibody


title: Ad-mCherry- mCherry+ B

value: MIP-GFP

value: Ad-mCherry


title: WT_7

tag: genotype/variation


title: MTCH2_KD_C646_R3

tag: treatment


title: pCDH-vector-OE-rep2


title: MTCH2_KD_C646-Input


title: Ad-mCherry- mCherry+ A


title: pCDH-vector-OE-rep1


title: MTCH2_KD_C646_R1


title: MTCH2_KD-ChIP-R3


title: MTCH2_KD-Input


title: Ctrl-ChIP-R3

value: control


title: Ctrl-ChIP-R1


title: Ctrl-ChIP-R2


title: MTCH2_KD-ChIP-R1


title: WT_1


title: CDU279 10

city: Woluwé

first: Jérôme

last: Ambroise

address: Avenue Hippocrate 54

department: Institut de Recherche Expérimentale et Clinique

institute: Université catholique de Louvain

data_processing:
All sequencing data were analyzed using the Automated Reproducible MOdular workflow for preprocessing and differential analysis of RNA-seq data (ARMOR) pipeline
Reads were mapped using Salmon [reference Patroet al 2017] to the transcriptome index which was built using all Ensembl cDNA sequences obtained in the Mus_musculus.GRCm38.cdna.all.fa file
Estimated transcript abundances from Salmon were imported into R using the tximeta package and analyzed for differential gene expression with edgeR

source_name: Fibroblasts

growth_protocol: Human cardiac fibroblasts medium (Cell Applications) + 10% Growth factor (Cell Applications)

extract_protocol:
Each sample was homogenized in TriPure Isolation Reagent (Roche, 11667165001) in lysing matrix tubes (Lysing Matrix D, MP Bio, 116913100). After guanidinium thiocyanate-phenol-chloroform extraction, RNA was further extracted on column (RNEasy, QuiaGEN, 74104) and treated with DNAse (DNAse-set, QuiaGEN, 79254) to reduce gDNA contamination. In total, RNA from each sample was quantified by Qubit RNA BR assay kit (Thermo Fisher Scientific, Q10211) on a Qubit 4 Fluorometer (Thermo Fisher Scientific). RNA integrity was evaluated on the Agilent 2100 Bioanalyzer using the RNA 6000 nano kit (Agilent, 5067-1511). All samples had RNA integrity number values ≥ 7.8. Libraries were prepared starting from 150 ng of total RNA using the KAPA RNA HyperPrep Kit with RiboErase (HMR) (KAPA Biosystems, KK8560) following the manufacturer’s recommendations (KR1351 – v1.16).
Libraries were prepared starting from 150 ng of total RNA using the KAPA RNA HyperPrep Kit with RiboErase (HMR) (KAPA Biosystems, KK8560) following the manufacturer’s recommendations. Libraries were equimolarly pooled and sequenced on a single lane on an Illumina NovaSeq 6000 platform.

treatment_protocol: transfection with a control siRNA or a siRNA targeting AMPKa1

value: cultured cardiac fibroblasts

value: transfected with a siRNA targeting AMPKa1 30nM


title: CDU279 2

value: transfected with a control siRNA 30nM


title: CDU279 7


title: CDU279 9


title: CDU279 4


title: CDU279 8


title: CDU279 5