title: T_at_E14.5_M_embryo

city: Fujimi, Chiyoda-ku

first: Taisuke

last: Hani

state: Tokyo

department: Pathology

institute: Nippon Dental University, School of Life Dentistry at Tokyo

description: Gene expression data from 4 embryos

hyb_protocol: The cDNA was hybridized to a 60K Agilent 60-mer oligomicrroarray accoding to the manufacturer's instruction.

scan_protocol: A hybridized microarray slides were scanned by an Agilent scanner.

data_processing: Relative hybridization intensities and background hybridization values were calculated using Agilent Feature Extraction Software (9.5.1.1).

source_name: Tongue from E14.5 mouse embryos

label_protocol: Low Input Quick Amp Labeling Kit (Agilent) was employed according to the manufactuer's instruction.

growth_protocol: Timed-pregnant ICR mice were kept under a 12 h light/12 h dark cycle with free access to standard laboratory feed and water.

extract_protocol: The total RNA was isolated from cerebellums of each individual animal using TRIzol Reagent (Thermo Fisher Scientific) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

treatment_protocol: Pregnant mice were euthanized by cervical dislocation after inhalation anesthesia. Embryos were collected into fresh  Hanks’ balanced salt solution (HBSS) at 4℃ and maxillofacial tissues were dissected from the head under a stereomicroscope.

value: ICR

tag: developmental stage

value: Tongue

tag: region

value: Medial


title: Mammary epithelium luminal progenitors, MMTVcre/Brca2/Trp53 knockdown, bio rep 3

status: Public on Dec 06 2023

type: SRA

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

library_source: transcriptomic

data_processing:
Sequencing was undertaken on an Illumina NextSeq 500 to produce 81bp pair-end reads.
Read alignment was performed with the align function of the Rsubread package version 2.6.1.
Genewise read counts were obtained with the featureCounts function of the Rsubread package and Rsubread's inbuilt mm10 annotation.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files with columns for Entrez Gene ID, gene length (number of bases in union of all exons), and the number of reads. The supplementary file GenewiseCounts.txt.gz gives read counts for all samples in one file.

molecule: total RNA

organism: Mus musculus

source_name: Mammary epithelium

extract_protocol:
miRNeasy micro kit (Qiagen Cat#217084) following manufacturer's protocol.
Illumina TruSeq RNA v2 protocol (Illumina #RS-122-2001, RS-122-2002).

tag: strain

value: MMTVcre Brca2(fl/fl) Trp53(fl/+)

tag: tissue

value: Mammary epithelium

tag: cell type

value: Luminal progenitors (LP)

tag: genotype


title: blood_CR_24 [GC31994]

type: RNA

city: Castanet-Tolosan

first: Laurence

last: Liaubet

address: 24 chemin de Borde Rouge

department: Animal genetics

country: France

institute: INRAE

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE microarray (8X60K, Design 028005) enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min), Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters (protocol GE1_1010_Sep10 and Grid: 037880_D_F_2012). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 39072 rows each corresponding to a unique ProbeName (provided as data Matrix) and 35 columns (individuals).

organism: Sus scrofa

source_name: whole blood

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNeasy purification (QIAGEN). Dye incorporation and cRNA yield were checked with the Biospec nano spectrophotometer (Shimadzu).

growth_protocol: The animals were raised at the French Experimental Unit PTEA, INRAE, Petit-Bourg in Guadeloupe. Blood were collected in an experiment involving 36 pigs from 3 breeds slaughtered before (n=18) or after a 5-days exposure to 32°C (n=18). 35 samples were available for the following steps.

extract_protocol: Total RNA was extracted according to the manufacturer's recommendations (PAXgene Blood RNA Kit, Qiagen) and the extracted total RNA was eluted in 40 µl of buffer BR5 and stored at -80°C. Quantification was performed using a Nanodrop to determine the concentration of each purification and the 260/230, 260/280 ratios. Quality was checked by electrophoresis on 0,8% agarose gel. RNA Integrity Numbers (RINs) were determined using a 2100 Bioanalyzer Instrument (Agilent). Then, RNAs were diluted at 135 and 400ng/µL in RNAse-free water for transcriptomic experiments on GeT-TRiX platform.

treatment_protocol: Whole blood RNA were collected on PAXgene Blood RNA Tubes (PreAnalytiX) and were conserved at -80°C until extraction.

tag: breed

value: Creole

tag: temperature

value: 24 degreeC

tag: gender

value: castrated


title: Mammary epithelium mature luminal cells, MMTVcre/Brca2/Trp53 knockdown, bio rep 3

value: Mature luminal (ML)


title: Mammary epithelium luminal progenitors, wildtype, bio rep 3

value: WT


title: blood_CR_30 [GC32015]

value: 30 degreeC


title: LLS_at_E11.5_M_embryo

country: Japan

description: Gene expression data from 4 embryos

source_name: Lateral Lingual Swelling from E11.5 mouse embryos

value: Lateral lingual Swellings


title: LMA_at_E11.5_L_embryo

description: Gene expression data from 4 embryos

source_name: Lateral region Mandibular arch from E11.5 mouse embryos

value: Mandibular arches

value: Lateral


title: MMA_at_E9.5_M_embryo

description: Gene expression data from 12 embryos

source_name: Medial region Mandibular arch from E9.5 mouse embryos


title: blood_F1_30 [GC32010]


title: Mammary epithelium mature luminal cells, wildtype, bio rep 2


title: Mammary epithelium basal cells, MMTVcre/Brca2/Trp53 knockdown, bio rep 3

value: Basal


title: Mammary epithelium basal cells, wildtype, bio rep 2


title: Mammary epithelium luminal progenitors, wildtype, bio rep 2


title: Mammary epithelium mature luminal cells, MMTVcre/Brca2/Trp53 knockdown, bio rep 2


title: Mammary epithelium luminal progenitors, MMTVcre/Brca2/Trp53 knockdown, bio rep 2


title: Mammary epithelium basal cells, MMTVcre/Brca2/Trp53 knockdown, bio rep 2


title: WT_IL-13_rep3

city: Richmond

first: Eun-Ah

last: Sung

state: VA

address: 401 College Street

country: USA

institute: Virginia Common Wealth University

data_processing:
The quality of RNA-seq reads was assessed with FastQC v0.11.9
The reads were aligned using STAR aligner v2.7.6a to mouse reference genome GRCm39
Raw gene counts of mapped reads were aggregated using featurCounts
The differential gene expression analysis was performed
with Bioconductor package DESeq2 v1.30.0 using the normalized and filtered counts per gene from the RNAseq analysis
Differentially expressed genes with adjusted p value < 0.05 were subject to further downstream bioinformatics analysis

source_name: bone marrow-derived macrophages

growth_protocol: 1x106 BMDMs/well were plated in 6-well tissue culture-treated dishes and placed in a 5% CO2 37 °C incubator for 24 hours

extract_protocol:
RNA was isolated using the Trizol and RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.
libraries were prepared using the TruSeq Stranded Total RNA LT Kit with Ribo-Zero Gold, according to the manufacturer’s instructions.

treatment_protocol: BMDMs were either left unstimulated, or stimulated with DKK1 (30 ng/ml), IL-13 (2 ng/ml) or DKK1 and IL-13  for 24 hrs.

value: bone marrow-derived macrophages

tag: background strain

value: wild-type

tag: treatment

value: IL-13 stimulation for 24 hr


title: WT_unstim_rep2

value: untreated


title: Mammary epithelium luminal progenitors, wildtype, bio rep 1

value: MMTVcre Brca2(fl/fl) Trp53(fl/+)


title: Mammary epithelium mature luminal cells, MMTVcre/Brca2/Trp53 knockdown, bio rep 1

value: Mammary epithelium


title: Mammary epithelium luminal progenitors, MMTVcre/Brca2/Trp53 knockdown, bio rep 1

value: Luminal progenitors (LP)


title: Mammary epithelium mature luminal cells, wildtype, bio rep 3


title: Mammary epithelium mature luminal cells, wildtype, bio rep 1


title: Mammary epithelium basal cells, MMTVcre/Brca2/Trp53 knockdown, bio rep 1


title: Mammary epithelium basal cells, wildtype, bio rep 1


title: RNASeq, 42 days post-SCI-IP, biological sample 3

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

data_processing:
Illumina BaseSpace FastQ v1.0.0 used for basecalling
Raw sequences were checked for quality values using fastQC v0.10.1.  Quality trimming was not deemed necessary.
The sequences were directly aligned to the Mus musculus reference genome assembly (mm10) using Star version 2.6.
Read counts for gene regions were obtained with HTSeq v.0.10.0 using Ensembl annotations (GRCm38.93).
The annotation file was parsed to exclude mitochondria and ribosomal protein genes in an effort to reduce non-relevant variation in subsequent steps of the analysis. The resulting annotation file tested 21,965 gene locations.
Assembly: GRCm38.p6

molecule: polyA RNA

source_name: OL translatome

extract_protocol:
Frozen tissue samples were homogenized with pre-chilled Dounce homogenizer (40 strokes using type A pestle, 40 strokes using type B pestle) in cold homogenization buffer on ice [RNAse-free water, 50 mM Tris (Sigma), pH 7.5, 100 mM KCl (Sigma), 12 mM MgCl2 (Sigma), 1% Nonidet P-40 (Sigma), 200 U/mL RNAsin (Promega, catalog #N2115), 1 mM DTT (Sigma-Aldrich), proteinase inhibitors (Roche), 1 mg/mL heparin (Sigma-Aldrich), 0.1 mg/mL cyclohexamide (Sigma-Aldrich)] to a wt/vol ratio of ~2-5%. Total RNA samples were also pooled respective to the OL samples for consistency. Homogenates were centrifuged at 10,000 x g for 10 minutes at 4°C to remove excess tissue. 10% of the cleared lysate was taken as input (IN, total spinal cord RNA) and stored at -80°C for subsequent analysis. The remaining lysate was incubated with monoclonal mouse anti-hemagglutinin (HA) antibody (HA.11 Clone 1612) for 4-6 h at 4°C in a microtube rotator and end-over-end gentle mixing. Protein A/G magnetic beads (Pierce) were prewashed in homogenization buffer and added to the lysates and further incubated at 4°C overnight with end-over-end mixing. The following day, samples were placed in a magnetic microtube stand on ice to isolate the magnetic beads, and the supernatant was stored in -80°C. Magnetic beads with the bound immunoprecipitated mRNA (IP) were washed 3 times using ice-cold high salt buffer solution (50 mM Tris, pH 7.5, 300 mM KCl, 12 mM MgCl2, 1% Nonidet P-40, 1 mM DTT, 100 g/mL cycloheximide) for at least 5 mins at 4°C and end-to-end mixing. Input and immunoprecipitated mRNA were purified using RNeasy Mini, RNA isolation kit (Qiagen, catalog # 74104) and Arcturus PicoPure RNA Isolation Kit (Applied Biosystems, catalog # LSKIT0204) according to the manufacturers’ protocol, respectively. Concentration and quality of isolated RNA was first determined using a NanoDrop 1,000 spectrophotometer (Thermo Scientific). Then, the concentration was measured by Qubit Fluorometer (Thermo Scientific), and RNA integrity was assessed by capillary electrophoresis (Bioanalyzer, Agilent Technologies).
Libraries were prepared using the Universal Plus mRNA-Seq (NuGEN Cat# 0508).

treatment_protocol: Spinal cord injury at the T9 level, using the IH impactor (50 kdyn) in  10-12 week old female mice

value: Mature oligodendrocyte (OL)


title: RNASeq, 42 days post-SCI-IN, biological sample 3

source_name: total spinal cord transcriptome

value: spinal cord


title: blood_CR_24 [GC32018]

value: Creole

value: 24 degreeC

value: castrated


title: RNASeq, 42 days post-SCI-IP, biological sample 2


title: RNASeq, 42 days post-SCI-IN, biological sample 2


title: RNASeq, 42 days post-SCI-IP, biological sample 1


title: RNASeq, 42 days post-SCI-IN, biological sample 1


title: RNASeq, 10 days post-SCI-IN, biological sample 3


title: RNASeq, 10 days post-SCI-IP, biological sample 3


title: RNASeq, 10 days post-SCI-IP, biological sample 2


title: RNASeq, 10 days post-SCI-IN, biological sample 2


title: RNASeq, 2 days post-SCI-IN, biological sample 3


title: RNASeq, 2 days post-SCI-IP, biological sample 3


title: RNASeq, 10 days post-SCI-IN, biological sample 1


title: RNASeq, 2 days post-SCI-IN, biological sample 2


title: RNASeq, control-IP, biological sample 3


title: RNASeq, control-IP, biological sample 2


title: RNASeq, control-IN, biological sample 1


title: Pooled Input

city: Tampa

first: Elsa

middle: Renee

last: Flores

state: FL

address: 12902 USF Magnolia Drive

department: Department of Molecular Oncology

institute: Moffit Cancer Center

library_source: genomic

data_processing:
The data quality was assessed using FastQC
ChIP-Seq reads were mapped to the mouse genome build UCSC mm10 using bowtie2 and duplicate reads were removed.
ChIP-Seq tracks were prepared using bedtools, normalized to reads per million reads mapped (rpm).
Binding sites (peaks) were determined using MACS2, with and FDR<0.05
Genome_build: mm10
Supplementary_files_format_and_content: ChIP-Seq tracks represented signal normalized to reads per million mapped in TDF format

molecule: genomic DNA

source_name: mouse primary keratinocytes

growth_protocol: WT, TAp63-/-, and ΔNp63-/- primary keratinocytes were grown to near confluence on J2- 3T3m feeder cells in F media. Feeder cells were removed with 0.02% EDTA 24 hours prior to collecting keratinocytes for chromatin extraction.

extract_protocol:
Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. An automated system (Apollo 342, Wafergen Biosystems/Takara) was used.  After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 500 (75 nt reads, single end).

tag: age

value: primary keratinocytes

tag: chip antibody


title: RNASeq, control-IN, biological sample 2


title: TAp63-/- ChIP-Seq mouse keratinocytes

value: p63 (Santa Cruz, sc-8344, lot # F2008)


title: ΔNp63-/- ChIP-Seq mouse keratinocytes


title: Wild-type ChIP-Seq mouse keratinocytes

value: Wild-type


title: RNASeq, control-IP, biological sample 1


title: TMD8-#9

city: Madison

first: Lixin

last: Rui

state: WI - Wisconsin

address: 1111 Highland Ave R.4060

department: Medicine

institute: University of Wisconsin-Madison

data_processing:
BAM file were generated by STAR-2.5.2b;picard to remove duplicated reads
RNAseq fpkm were generated by HISAT, StringTie and Ballgown by following Pertea et al.(2016).
Assembly: hg19
Supplementary files format and content: RNA-seq (txt file: gene fpkm)

organism: Homo sapiens

growth_protocol: DLBCL cells were grown in RPMI1640 media plus 20%FBS,1%  penicillin, 1% streptomycin.

extract_protocol:
Total mRNA was extracted by Rneasy plus mini kit (Qiagen) following the manufacturer’s instructions.
cDNA library was construbuted by using Illumina Truseq RNA Library Prep Kit (RS-122-2002).

treatment_protocol: Cells were treated with Ibrutinib (10-20nM) for a year. Resistant clones were generated by serial dilution at 1:3 ratio. Resistant phenotype were confirmed by treat cells with ibrutinib compared to parental cell lines

tag: cell line

value: DLBCL

value: Ibrutinib resistant clone

value: Ibrutinib (10nM)


title: TMD8-#10


title: RNASeq, 2 days post-SCI-IP, biological sample 2


title: TMD8-#8


title: TMD8-#11


title: RNASeq, 2 days post-SCI-IN , biological sample 1


title: RNASeq, 2 days post-SCI-IP, biological sample 1


title: RNASeq, control-IN, biological sample 3


title: TMD8-parental 3

value: Parental


title: TMD8-#2


title: TMD8-parental 2


title: OCI-LY10-#12

value: Ibrutinib (20nM)


title: TMD8-#3


title: TMD8-#1


title: TMD8-parental 1


title: RNASeq, 10 days post-SCI-IP, biological sample 1


title: OCI-LY10-#9


title: TMD8-#7


title: OCI-LY10-#8


title: OCI-LY10-#11


title: OCI-LY10-#10


title: OCI-LY10-#6


title: OCI-LY10-#5


title: OCI-LY10-#1


title: OCI-LY10-#3


title: OCI-LY10-parental 3


title: TMD8-#6


title: 6632_4_6601_1_FB_pool_13_tumors_CTACGGGCTT_S4

city: Amsterdam

first: Maarten

last: Slagter

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

description:
Multiplexed library of multiple experimental conditions
Feature barcoding

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Cellranger-GRCh38-3.0.0
Supplementary files format and content: 10x Genomics CellRanger output

extract_protocol:
Tumor cells from tumors intratumorally injected with IFNg, TNFa or the combination were harvested from  NSG-b2m-/- mice, manually minced and enzymatically digested in RPMI medium (Gibco) supplemented with 5 Wünsch units/ml TH Liberase/ml (Roche) 25 μg/ml DNase I (Roche) for 20 min at 37 °C under continuous shaking. Subsequently, cell digests were filtered through a 70-μm strainer (Falcon) and single-cell suspensions were stained with IR-Dye (Invitrogen) and TotalSeq Hastag antibodies (TotalSeq-A or B, Biolegend). Cells from each sample were combined at equal numbers, and CFP+ (i.e. bystander) tumor cells were sorted from this cell pool on a FACSaria Fusion (BD biosciences). Sorted single cell suspensions were diluted to a final concentration of 1,000 cells/μl in 1xPBS containing 0.04% weight/volume BSA.
The Chromium Controller platform of 10X Genomics was used for single cell partitioning and barcoding. Per single cell suspension, each cell’s transcriptome was barcoded during reverse transcription, pooled cDNA was amplified and Single Cell 3’ Gene Expression libraries and Cell Hashing libraries via Feature barcode technology were prepared, according to the manufacturer’s protocol (CG000183, CG000206 and CG000317, 10X Genomics). All libraries were quantified on a 2100 Bioanalyzer Instrument following the Agilent Technologies Protocol (Agilent DNA 7500 kit, G2938-90024). Sequence library pools were composed and quantified by qPCR, according to the KAPA Library Quantification Kit Illumina® Platforms protocol (KR0405, KAPA Biosystems)
HiSeq 2500 Illumina sequencing was used for paired-end sequencing of the Single Cell 3’ Gene Expression library and Cell Hashing libraries, respectively, at a sequencing depth of between 20,000-60,000 reads /cell and approximately 3,500 genes/cell. HiSeq 2500 paired-end sequencing was performed using 100 cycles for Read 1, 8 cycles for Read i7, and 100 cycles for Read 2, using HiSeq PE Cluster Kit V4 (PE-401-4001, Illumina) and multiple HiSeq SBS Kit V4 50 cycle kits (FC-401-4002, Illumina)

treatment_protocol: intratumoral injection of IFNg, TNFa and combination in OVACR5 in vivo tumors in NSG-B2m-/- mice

value: Ovarian carcinoma

value: IFNy-sensing reporter, CFP+

value: 10 ng/ml TNFa - 6h

tag: time

value: 6h continuous


title: OCI-LY10-parental 2

description:
Raw data missing for this sample.
FPKM-LY10.txt


title: 6632_2_6601_1_GE_pool_13_tumors_GCTACAAAGC_S2

description:
Multiplexed library of multiple experimental conditions
Experimental conditions (separated by ';'): 10 ng/ml TNFa - 6h; 10 ng/ml TNFa - 6h; 10 ng/ml TNFa - 6h; 100 ng/ml IFNy 10 ng/ml TNFa - 6h; 100 ng/ml IFNy 10 ng/ml TNFa - 6h; Unexposed in vivo - 6h; Unexposed in vivo - 6h; 100 ng/ml IFNy - 24h; 100 ng/ml IFNy - 24h; Unexposed in vivo - 24h; Unexposed in vivo - 24h; 100 ng/ml IFNy - 48h; Unexposed in vivo – 48h

value: Unstimulated in vitro - 6h


title: OCI-LY10-parental 1


title: TMD8-#4


title: 6632_3_6600_1_FB_pool_of_5_tumors_CFP_ATTCGTTGGG_S3

data_processing:
Barcode processing, gene counting and aggregation was performed using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Cellranger-GRCh38-3.0.0
Supplementary files format and content: 10x Genomics CellRanger output

growth_protocol: Tumor cells were harvested from  NSG-b2m-/- mice, manually minced and enzymatically digested in RPMI medium (Gibco) supplemented with 5 Wünsch units/ml TH Liberase/ml (Roche) 25 μg/ml DNase I (Roche) for 20 min at 37 °C under continuous shaking. Subsequently, cells were  ex-vivo treated with recombinant cytokines.

extract_protocol:
Cells were harvested and  filtered through a 70-μm strainer (Falcon) and single-cell suspensions were stained with IR-Dye (Invitrogen) and TotalSeq Hastag antibodies (TotalSeq-A or B, Biolegend). Cells from each sample were combined at equal numbers, and CFP+ (i.e. bystander) tumor cells were sorted from this cell pool on a FACSaria Fusion (BD biosciences). Sorted single cell suspensions were diluted to a final concentration of 1,000 cells/μl in 1xPBS containing 0.04% weight/volume BSA.
The Chromium Controller platform of 10X Genomics was used for single cell partitioning and barcoding. Per single cell suspension, each cell’s transcriptome was barcoded during reverse transcription, pooled cDNA was amplified and Single Cell 3’ Gene Expression libraries and Cell Hashing libraries via Feature barcode technology were prepared, according to the manufacturer’s protocol (CG000183, CG000206 and CG000317, 10X Genomics). All libraries were quantified on a 2100 Bioanalyzer Instrument following the Agilent Technologies Protocol (Agilent DNA 7500 kit, G2938-90024). Sequence library pools were composed and quantified by qPCR, according to the KAPA Library Quantification Kit Illumina® Platforms protocol (KR0405, KAPA Biosystems)
HiSeq 2500 Illumina sequencing was used for paired-end sequencing of the Single Cell 3’ Gene Expression library and Cell Hashing libraries, respectively, at a sequencing depth of between 20,000-60,000 reads /cell and approximately 3,500 genes/cell. HiSeq 2500 paired-end sequencing was performed using 100 cycles for Read 1, 8 cycles for Read i7, and 100 cycles for Read 2, using HiSeq PE Cluster Kit V4 (PE-401-4001, Illumina) and multiple HiSeq SBS Kit V4 50 cycle kits (FC-401-4002, Illumina)


title: 6632_1_6600_1_GE_pool_of_5_tumors_CFP_TCGGCTCTAC_S1

description:
Multiplexed library of multiple experimental conditions
Experimental conditions (separated by ';'): Unstimulated in vitro - 6h; 10 ng/ml TNFa - 6h; 100 ng/ml IFNy 10 ng/ml TNFa - 6h; Unstimulated in vitro - 6h; 10 ng/ml TNFa - 6h; 100 ng/ml IFNy 10 ng/ml TNFa - 6h; Unstimulated in vitro - 6h; 10 ng/ml TNFa - 6h; 100 ng/ml IFNy 10 ng/ml TNFa - 6h; Unstimulated in vitro - 6h; 10 ng/ml TNFa - 6h; 100 ng/ml IFNy 10 ng/ml TNFa - 6h; Unstimulated in vitro - 6h; 10 ng/ml TNFa - 6h; 100 ng/ml IFNy 10 ng/ml TNFa - 6h


title: THP-1 cells, R1 2

city: HOUSTON

first: Chunxiao

last: Liu

state: Texas

address: 6565 MD Anderson Blvd., Zayed building. Z11.4000A

institute: MD Anderson Cancer center

data_processing:
Original data file from Illumina is transformed into sequenced reads (raw data, FASTQ formate files) by CASAVA base recognition.
Raw data is filtered by removal of reads with adaptor contamination,reads when uncertain nucleotides constitute more than 10 percent of either read (N > 10%),reads when low quality nucleotides (Base Quality less than 20) constitute more than 50 percent of the read. The Qscore (Quality value) of over 50% bases of these read is <= 5.
Sequencing is mapped to Homo_sapiens_hg19 by STAR software. The alignment by STAR performs precise and effective in positioning junction reads for RNA sequencing data analysis.
FPKM (short for the expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) is the most common method of estimating gene expression levels, which takes the effects into consideration of both sequencing depth and gene length on counting of fragments (Mortazavi et al. 2008).
For the samples with biological replicates, differential expression analysis of two conditions/groups was performed using the Limma R package.
Assembly: Homo_sapiens_hg19
Supplementary files format and content: A txt file of gene expression level (FPKM value) of all samples.

extract_protocol:
Flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: monocyte

value: 1 µg/ml RNase1


title: THP-1 cells, R1 1


title: THP-1 cells, M2 2

value: 20 ng/ml human IL-4


title: THP-1 cells, M2 1


title: THP-1 cells, M1 2

value: 10 ng/ml human IFN-γ plus 200 ng/ml LPS


title: 6547_4_6493_1_FB_pool_10_tumors_CFP_and_GFP_cells_AGATGAGAAT_S4

description:
Multiplexed library of multiple experimental conditions
Experimental conditions (separated by ';'): Exposed to T-cells in vivo - 16h; Exposed to T-cells in vivo - 16h; Exposed to T-cells in vivo - 16h; Unexposed in vivo - 16h; Unexposed in vivo - 16h; Exposed to T-cells in vivo - 44h; Exposed to T-cells in vivo - 44h; Exposed to T-cells in vivo - 44h; Unexposed in vivo - 44h; Unexposed in vivo - 44h

growth_protocol: Tumor cells were harvested from  NSG-b2m-/- mice, manually minced and enzymatically digested in RPMI medium (Gibco) supplemented with 5 Wünsch units/ml TH Liberase/ml (Roche) 25 μg/ml DNase I (Roche) for 20 min at 37 °C under continuous shaking. Cells were harvested and filtered through a 70-μm strainer (Falcon) and single-cell suspensions were stained with IR-Dye (Invitrogen) and TotalSeq Hastag antibodies (TotalSeq-A or B, Biolegend). Cells from each sample were combined at equal numbers, and CFP+ (i.e. bystander) tumor cells were sorted from this cell pool on a FACSaria Fusion (BD biosciences).

extract_protocol:
Cells were harvested and diluted to a final concentration of 1,000 cells/μl in 1xPBS containing 0.04% weight/volume BSA.
The Chromium Controller platform of 10X Genomics was used for single cell partitioning and barcoding. Per single cell suspension, each cell’s transcriptome was barcoded during reverse transcription, pooled cDNA was amplified and Single Cell 3’ Gene Expression libraries and Cell Hashing libraries via Feature barcode technology were prepared, according to the manufacturer’s protocol (CG000183, CG000206 and CG000317, 10X Genomics). All libraries were quantified on a 2100 Bioanalyzer Instrument following the Agilent Technologies Protocol (Agilent DNA 7500 kit, G2938-90024). Sequence library pools were composed and quantified by qPCR, according to the KAPA Library Quantification Kit Illumina® Platforms protocol (KR0405, KAPA Biosystems)
HiSeq 2500 Illumina sequencing was used for paired-end sequencing of the Single Cell 3’ Gene Expression library and Cell Hashing libraries, respectively, at a sequencing depth of between 20,000-60,000 reads /cell and approximately 3,500 genes/cell. HiSeq 2500 paired-end sequencing was performed using 100 cycles for Read 1, 8 cycles for Read i7, and 100 cycles for Read 2, using HiSeq PE Cluster Kit V4 (PE-401-4001, Illumina) and multiple HiSeq SBS Kit V4 50 cycle kits (FC-401-4002, Illumina)


title: OCI-LY10-#7


title: 6547_2_6493_1_GE_pool_10_tumors_CFP_and_GFP_cells_GTAGCCCTGT_S2


title: 6575_2_6493_1_GE_pool_10_tumors_CFP_and_GFP_cells_GTAGCCCTGT_S2


title: 6575_4_6493_1_FB_pool_10_tumors_CFP_and_GFP_cells_AGATGAGAAT_S4


title: Non-Responder, A16_557T

source_name: tumor

value: tumor

tag: disease state

value: HCC

tag: group

value: Nonresponder


title: THP-1 cells, untreated 1

value: non


title: 5310_5_Pool_of_GAS_cells_in_vivo_and_in_vitro_5_ATTACTCG_S13

description:
Library consisting of multiple experimental conditions
Experimental conditions (separated by ';'): Exposed to T-cells in vivo - SC digest; Unexposed in vivo - SC digest; Unstimulated in vitro - 24h; 100 ng/ml IFNy - 24h; 10 ng/ml TNFa - 24h; 100 ng/ml IFNy 10 ng/ml TNFa - 24h; 100 ng/ml IFNy 10 ng/ml TNFa - 24h - SC digest
Mixture of experimental conditions (separated by ‘;’): Exposed to T-cells in vivo - SC digest;Unexposed in vivo - SC digest;Unstimulated in vitro - 24h;100 ng/ml IFNy - 24h;10 ng/ml TNFa - 24h;100 ng/ml IFNy 10 ng/ml TNFa - 24h;100 ng/ml IFNy 10 ng/ml TNFa - 24h – SC digest

growth_protocol: in vitro cells were cultured at 37°C/ 5% CO2 in IMDM (Gibco) supplemented with 10% FCS (Sigma), 100 U/ml penicillin (Roche), 100 μg/ml streptomycin (Roche), and GlutaMax (Gibco, 1x). In vivo tumors were injected in NSG-b2m-/- mice

extract_protocol:
Harvested tumors from NSG-B2m-/- mice were manually minced and enzymatically digested in RPMI medium (Gibco) supplemented with 5 Wünsch units/ml TH Liberase/ml (Roche) 25 μg/ml DNase I (Roche) for 20 min at 37 °C under continuous shaking. Subsequently, cell digests were filtered through a 70-μm strainer (Falcon) and single-cell suspensions were stained with IR-Dye (Invitrogen) and TotalSeq Hastag antibodies (TotalSeq-A or B, Biolegend). Cells from each sample were combined at equal numbers, and CFP+ (i.e. bystander) tumor cells were sorted from this cell pool on a FACSaria Fusion (BD biosciences). Sorted single cell suspensions were diluted to a final concentration of 1,000 cells/μl in 1xPBS containing 0.04% weight/volume BSA.
The Chromium Controller platform of 10X Genomics was used for single cell partitioning and barcoding. Per single cell suspension, each cell’s transcriptome was barcoded during reverse transcription, pooled cDNA was amplified and Single Cell 3’ Gene Expression libraries and Cell Hashing libraries via Feature barcode technology were prepared, according to the manufacturer’s protocol (CG000183, CG000206 and CG000317, 10X Genomics). All libraries were quantified on a 2100 Bioanalyzer Instrument following the Agilent Technologies Protocol (Agilent DNA 7500 kit, G2938-90024). Sequence library pools were composed and quantified by qPCR, according to the KAPA Library Quantification Kit Illumina® Platforms protocol (KR0405, KAPA Biosystems)
HiSeq 2500 Illumina sequencing was used for paired-end sequencing of the Single Cell 3’ Gene Expression library and Cell Hashing libraries, respectively, at a sequencing depth of between 20,000-60,000 reads /cell and approximately 3,500 genes/cell. HiSeq 2500 paired-end sequencing was performed using 100 cycles for Read 1, 8 cycles for Read i7, and 100 cycles for Read 2, using HiSeq PE Cluster Kit V4 (PE-401-4001, Illumina) and multiple HiSeq SBS Kit V4 50 cycle kits (FC-401-4002, Illumina)

treatment_protocol: In vitro cells were treated with  various (combinations of) cytokines. In vivo tumors were treated with PBS (control) or T cells


title: Non-Responder, A12_949T


title: THP-1 cells, untreated 2


title: 5310_2_Pool_of_GAS_cells_in_vivo_and_in_vitro_2_CTCCTAGT_S10


title: 5310_1_Pool_of_GAS_cells_in_vivo_and_in_vitro_1_AGGTATTG_S9


title: Non-Responder, A11_385T


title: 5310_3_Pool_of_GAS_cells_in_vivo_and_in_vitro_3_TCAAGGCC_S11


title: 5029_2h_1_200_sn

description: 1/200 SN - 2h

data_processing:
Merge re-sequenced FastQ files (cat) (https://github.com/nf-core/rnaseq)
Read QC (FastQC)
UMI extraction (UMI-tools)
Adapter and quality trimming (Trim Galore!)
Removal of genome contaminants (BBSplit)
Removal of ribosomal RNA (SortMeRNA)
STAR -> Salmon
Sort and index alignments (SAMtools)
UMI-based deduplication (UMI-tools)
Duplicate read marking (picard MarkDuplicates)
Transcript assembly and quantification (StringTie)
Create bigWig coverage files (BEDTools, bedGraphToBigWig)
Extensive quality control: (RSeQC, Qualimap, dupRadar, Preseq, DESeq2)
Pseudo-alignment and quantification (Salmon)
Assembly: Cellranger-GRCh38-3.0.0
Supplementary files format and content: Salmon counts

growth_protocol: Cells were cultured at 37°C/ 5% CO2 in IMDM (Gibco) supplemented with 10% FCS (Sigma), 100 U/ml penicillin (Roche), 100 μg/ml streptomycin (Roche), and GlutaMax (Gibco, 1x).

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (74106, Qiagen), including an on-column DNase digestion (79254, Qiagen)
Total RNA samples having RIN values>8 were subjected to TruSeq stranded mRNA library preparation, according to the manufacturer's instructions (Document # 1000000040498, Illumina)
Stranded mRNA libraries were analyzed on a 2100 Bioanalyzer instrument, following the manufacturer’s protocol “Agilent DNA 7500 kit” (G2938-90024, Agilent Technologies), diluted to 10nM and pooled equimolar into multiplex sequencing pools for sequencing on HiSeq 2500 instrument (Illumina).

treatment_protocol: Cells were treated with  various (combinations of) cytokines (TNFa, IFNy, tumor-cell T-cell co-culture supernatant) for 4 different durations (2, 6, 12, 24 hours of continuous stimulation)

tag: duration

value: 2h continuous


title: 5029_2h_1_2_sn

description: 1/2 SN - 2h


title: Non-Responder, A19_16T


title: Responder, A19_1T

value: Responder


title: 5029_2h_10_ng_ml_tnfa

description: 10 ng/ml TNFa - 2h

value: 10 ng/ml TNFa - 2h


title: 5029_2h_0.1_ng_ml_tnfa

description: 0.1 ng/ml TNFa - 2h

value: 0.1 ng/ml TNFa - 2h


title: 5029_2h_1_ng_ml_tnfa

description: 1 ng/ml TNFa - 2h

value: Ovarian carcinoma

value: 1 ng/ml TNFa - 2h


title: Responder, A19_121T


title: Responder, A19_171T


title: Responder, A19_174T


title: 5029_24h_100_ng_ml_ifng_10_ng_ml_tnfa

description: 100 ng/ml IFNy 10 ng/ml TNFa - 24h

value: IFNy-sensing reporter, CFP+

value: 100 ng/ml IFNy 10 ng/ml TNFa - 24h

value: 24h continuous


title: THP-1 cells, M1 1

value: monocyte


title: Responder, A18_440T


title: 5029_24h_1_2_sn

description: 1/2 SN - 24h


title: 5029_24h_1_20000_sn

description: 1/20000 SN - 24h


title: 5029_24h_1_200_sn

description: 1/200 SN - 24h


title: Non-Responder, A17_152T


title: 5029_2h_100_ng_ml_ifng

description: 100 ng/ml IFNy - 2h

value: 100 ng/ml IFNy - 2h


title: 5029_24h_10_ng_ml_tnfa

description: 10 ng/ml TNFa - 24h

value: 10 ng/ml TNFa - 24h


title: polysomal RNA from cell bodies of mouse PCNs expressing exogenous TDP43-A315T, rep 1

city: Povo (TN)

first: Fabio

last: Lauria

address: Via alla Cascata 56

country: Italy

institute: Institute of Biophysics (Italian National Research Council)

data_processing:
One hundred bp single-end reads were processed by removing the 3ʼ Illumina Universal Adapter (AGATCGGAAGAG), trimming the first 8 nucleotides and discarding reads shorter than 40 nucleotides (Cutadapt v2.5). Processed reads were aligned to the mouse genome (GRCm38.p6) with STAR (v2.5.3a), using the Gencode M17 gene annotation, based on ENSEMBL release 92. A maximum of 10 multiple alignments for each read was allowed. Reads mapping at the same positions, but the one with the highest mapping quality score, were removed with Picard Tools MarkDuplicates (v2.18.9, REMOVE_DUPLICATES=true). Counts of mapped reads per gene were retrieved by HTSeq (v0.11.0, --stranded=no). All programs were used with default settings unless otherwise specified.
Assembly: GRCm38.p6
Supplementary files format and content: Matrix table with raw gene counts for each sample

source_name: mouse primary cortical neurons

growth_protocol: Primary cortical neurons were isolated from wild type C56BL/6J mice. The pregnant female was euthanized by CO2 at 14.5 days of gestation. The cortex was isolated from the embryos and purified from meninges, cut into small pieces and incubated for 5 minutes in DMEM/F12, 0.0125 M glucose, 1% P/S, 1 mM EDTA and then digested in trypsin by incubation in DMEM/F12, 0.0125 M glucose, 1% P/S, 0.25% trypsin, for 10 minutes at 37°C. After trypsin neutralisation in DMEM/F12, 0.0125 M glucose, 1% P/S, 20% FBS, samples were mechanically dissociated into single cells in DMEM/F12, 0.0125 M glucose, 1% P/S, 10% FBS, 4 KU/mL DNAseI, using fire-polished glass pipettes. The cells suspension was then filtered with a 70 μm cell strainer nylon filter, counted and centrifuged for 5 minutes at 950 rpm in ALC PK120R centrifuge at RT to be resuspended in complete Neurobasal medium (Neurobasal, 2% B27 supplement, 18 mM HEPES, 1% P/S, 0.5 mM L-Glutamine). Microfluidic chambers (SD450 Xona microfluidics) were used to separate cell bodies and axons. Glass coverslips were cleaned with 1 M HCI for 4 hours, extensively washed in milliQ water and dried in the oven. Next, the coverslips and the microfluidic chambers were sterilised in 70% ethanol and dried under a laminar flux hood at RT. The coverslips were coated overnight with 500 μg/mL poly-D-lysine and then assembled with the microfluidic device. The microfluidic chambers were equilibrated with PBS, followed by equilibration in the neurobasal medium. Cortical neurons resuspended in neurobasal medium at the concentration of 25,000 cells/μL were plated in a final amount of 25,0000 cells/chamber following the SD450 Xona microfluidics protocol. BDNF at a final concentration of 10 ng/mL was added every two days in the axonal compartment starting from DIV2.

extract_protocol:
For studying both the transcriptional and the translational levels of the axons and cells, total cytosolic RNA (pool of all the fractions) and polysomal RNA (collection of fractions corresponding to the polysomal peaks) were purified from the polysomal profiles. Both total and polysomal RNA extractions were performed with Direct-zol™ RNA purification Kit (Zymo Research). For free/granule transcriptome and translatome analysis at subcellular resolution, after sucrose gradient fractionation, sucrose fractions not associated to polysomes containing RNPs, ribosomal subunits and 80S were pooled in the “free/granule fraction”. Sucrose fractions containing polysomes were pooled into the “polysome fraction”. Trizol was used to extract the RNA. After purification, the RNA was resuspended in DNAse-RNAse nuclease free-water and quantified at the Agilent 2100 Bionalyzer by using the Agilent RNA 6000 Pico kit.
The libraries were obtained using Ovation® Single Cell RNA-Seq System (Nugen) or Ovation® SoLo® RNA-Seq library preparation kit (Tecan) according to the manufacturer's protocol. The qualitative and quantitative control of the libraries was performed with High Sensitivity DNA Chip (Agilent Technologies) before sequencing. RNA sequencing was performed with Illumina HiSeq 2500.

treatment_protocol: HEK293T cells were transient co-transfected using the calcium-phosphate precipitation method with the transfer vectors, the MDLg/pRRE plasmid, the RSV-Rev plasmid and the MDLg plasmid encoding the G glycoprotein of the vesicular stomatitis virus. Cell supernatants containing lentiviral particles were collected 72 h after transfection, filtered and subjected to ultracentrifugation. The pellets were resuspended, divided into aliquots and stored at -80°C. To calculate the titer of lentiviral particles, cortical neurons were seeded in a 24-well plate and infected at 5 DIV with a serial dilution (from 10-3 to 10-7) of lentiviral particles overexpressing TRFP-TDP-43-WT, TRFP-TDP-43- A315T and TRFP. Uninfected cortical neurons were used as control. The experiment was repeated in triplicate for each condition. Cortical neurons were fixed at 9 DIV and processed for immunofluorescence with tRFP and TuJ1 primary antibodies. ArrayScan microscope (Thermo Fisher ArrayScan XTI HCA Reader) was used to acquire 20 random fields per well. For every field the TRFP-positive infected cells (red) and the total number of cells, stained with a nuclear marker (DAPI), were counted. Then, TRFP-positive cells and DAPI-positive cells coming from all fields were summed. A ratio between the number of the total TRFP-positive cells and the total DAPI-positive cells present in each well was calculated. To calculate the titer a percentage ratio between tRFP-positive cells and total DAPI positive cells between 0.1% and 10% (dynamic range) was chosen, and this formula was used: (Infected cells/Total cells) *Dilution factor*Number of seeded cells. In our experiments a MOI (multiplicity of infections) of 4 was used to ensure the infection of almost total cells without inducing cellular toxicity. Cortical neurons were infected at 5 DIV and treated, fixed or lysed at different DIV based on the experimental needs.

tag: tretment

value: transfection with lentiviral particles overexpressing tRFP-TDP43- A315T

tag: replicate

tag: molecule

value: polysomal RNA


title: polysomal RNA from cell bodies of mouse PCNs expressing exogenous TDP43-A315T, rep 3


title: free RNA from cell bodies of mouse PCNs expressing exogenous TDP43-A315T, rep 3

value: free RNA


title: 5029_24h_0.1_ng_ml_tnfa

description: 0.1 ng/ml TNFa - 24h

tag: cell type

value: 0.1 ng/ml TNFa - 24h


title: polysomal RNA from cell bodies of mouse PCNs expressing exogenous TDP43-A315T, rep 2


title: 5029_24h_100_ng_ml_ifng

description: 100 ng/ml IFNy - 24h

tag: genotype

value: 100 ng/ml IFNy - 24h


title: free RNA from cell bodies of mouse PCNs expressing exogenous TDP43-A315T, rep 2


title: 5029_24h_1_ng_ml_tnfa

description: 1 ng/ml TNFa - 24h

value: 1 ng/ml TNFa - 24h


title: 5310_4_Pool_of_GAS_cells_in_vivo_and_in_vitro_4_GATGCCAA_S12


title: free RNA from cell bodies of mouse PCNs expressing exogenous TDP43-A315T, rep 1


title: polysomal RNA from axons of mouse PCNs expressing exogenous TDP43-A315T, rep 3


title: 5029_24h_0.01_ng_ml_ifng

description: 0.01 ng/ml IFNy - 24h

value: 0.01 ng/ml IFNy - 24h


title: polysomal RNA from axons of mouse PCNs expressing exogenous TDP43-A315T, rep 2


title: 5029_12h_100_ng_ml_ifng_10_ng_ml_tnfa

description: 100 ng/ml IFNy 10 ng/ml TNFa - 12h

value: 100 ng/ml IFNy 10 ng/ml TNFa - 12h

value: 12h continuous


title: polysomal RNA from axons of mouse PCNs expressing exogenous TDP43-A315T, rep 1


title: free RNA from axons of mouse PCNs expressing exogenous TDP43-A315T, rep 3


title: free RNA from axons of mouse PCNs expressing exogenous TDP43-A315T, rep 2


title: 5029_12h_1_20000_sn

description: 1/20000 SN - 12h

value: Ovarian carcinoma


title: 5029_12h_1_200_sn

description: 1/200 SN - 12h


title: 5029_12h_10_ng_ml_tnfa

description: 10 ng/ml TNFa - 12h

value: 10 ng/ml TNFa - 12h


title: 5029_12h_1_ng_ml_tnfa

description: 1 ng/ml TNFa - 12h

value: IFNy-sensing reporter, CFP+

value: 1 ng/ml TNFa - 12h


title: 5029_12h_1_ng_ml_ifng

description: 1 ng/ml IFNy - 12h

value: 1 ng/ml IFNy - 12h


title: free RNA from cell bodies of mouse PCNs expressing exogenous TDP43-WT, rep 1

value: transfection with lentiviral particles overexpressing tRFP-TDP43- WT


title: free RNA from axons of mouse PCNs expressing exogenous TDP43-A315T, rep 1


title: polysomal RNA from cell bodies of mouse PCNs expressing exogenous TDP43-WT, rep 2


title: 5029_12h_0.01_ng_ml_ifng

description: 0.01 ng/ml IFNy - 12h

value: 0.01 ng/ml IFNy - 12h


title: free RNA from axons of mouse PCNs expressing exogenous TDP43-WT, rep 1


title: 5029_12h_0.1_ng_ml_tnfa

description: 0.1 ng/ml TNFa - 12h

value: 0.1 ng/ml TNFa - 12h


title: 5029_12h_100_ng_ml_ifng

description: 100 ng/ml IFNy - 12h

value: 100 ng/ml IFNy - 12h


title: 5029_12h_1_2_sn

description: 1/2 SN - 12h


title: polysomal RNA from cell bodies of mouse PCNs expressing exogenous TDP43-WT, rep 1

value: polysomal RNA


title: polysomal RNA from axons of mouse PCNs expressing exogenous TDP43-WT, rep 1


title: polysomal RNA from cell bodies of mouse PCNs expressing tRFP, rep 2

value: transfection with lentiviral particles overexpressing tRFP


title: polysomal RNA from cell bodies of mouse PCNs expressing tRFP, rep 1


title: polysomal RNA from axons of mouse PCNs expressing exogenous TDP43-WT, rep 2


title: 5029_24h_1_ng_ml_ifng

description: 1 ng/ml IFNy - 24h

value: 1 ng/ml IFNy - 24h

value: 24h continuous


title: 5029_12h_unstim

description: Unstimulated in vitro - 12h

value: Unstimulated in vitro - 12h


title: 5029_24h_unstim

description: Unstimulated in vitro - 24h

value: Unstimulated in vitro - 24h


title: free RNA from cell bodies of mouse PCNs expressing tRFP, rep 2

value: free RNA


title: 5029_6h_1_20000_sn

description: 1/20000 SN - 6h

value: 6h continuous


title: 5029_6h_100_ng_ml_ifng_10_ng_ml_tnfa

description: 100 ng/ml IFNy 10 ng/ml TNFa - 6h

value: Ovarian carcinoma

value: 100 ng/ml IFNy 10 ng/ml TNFa - 6h


title: 5029_6h_1_200_sn

description: 1/200 SN - 6h

value: IFNy-sensing reporter, CFP+


title: free RNA from axons of mouse PCNs expressing exogenous TDP43-WT, rep 2


title: free RNA from cell bodies of mouse PCNs expressing tRFP, rep 1


title: free RNA from cell bodies of mouse PCNs expressing exogenous TDP43-WT, rep 2


title: 5029_2h_1_ng_ml_ifng

description: 1 ng/ml IFNy - 2h

value: 1 ng/ml IFNy - 2h

value: 2h continuous


title: 5029_2h_0.01_ng_ml_ifng

description: 0.01 ng/ml IFNy - 2h

value: 0.01 ng/ml IFNy - 2h


title: polysomal RNA from axons of mouse PCNs expressing tRFP, rep 1


title: 5029_6h_1_ng_ml_tnfa

description: 1 ng/ml TNFa - 6h

value: 1 ng/ml TNFa - 6h


title: 5029_6h_100_ng_ml_ifng

description: 100 ng/ml IFNy - 6h

value: 100 ng/ml IFNy - 6h


title: 5029_6h_1_2_sn

description: 1/2 SN - 6h


title: free RNA from axons of mouse PCNs expressing tRFP, rep 2


title: 5029_6h_0.1_ng_ml_tnfa

description: 0.1 ng/ml TNFa - 6h

value: 0.1 ng/ml TNFa - 6h


title: total RNA from cell bodies of mouse PCNs, rep 1

value: untreated

value: total RNA


title: polysomal RNA from cell bodies of mouse PCNs, rep 2

value: polysomal RNA


title: polysomal RNA from cell bodies of mouse PCNs, rep 1


title: total RNA from axons of mouse PCNs, rep 1


title: polysomal RNA form axons of mouse PCNs, rep 1


title: free RNA from axons of mouse PCNs expressing tRFP, rep 1

value: transfection with lentiviral particles overexpressing tRFP


title: 5029_6h_unstim

description: Unstimulated in vitro - 6h

value: Unstimulated in vitro - 6h


title: W/+ mice control group [PBS-1]

city: Shanghai

first: Jia

middle: bing

last: Li

address: 197, Ruijin Er Street

country: China

institute: Shanghaijiaotong university

description:
w-sar-3
PBS-1
Tumor tissues from p53R282W/+ mice with sarcomas.

data_processing:
The raw reads were initially processed using FastQC (v0.10.1) for quality control;
adapter sequences and poor-quality reads were removed using Cutadapt (v1.9.1).
Quality-filtered reads were then aligned to the Mus musculus genome (GRCm38) using HISAT2 (v2.0.1).
Assembly: mm10
Supplementary files format and content: all.fpkm.txt: Tab-delimited text file includes counts and FPKM values for each Sample.

source_name: sarcoma tumor

growth_protocol: 1uM dexamethasone (Sigma), and 0.5mM isobutylmethylxanthine (Sigma) in the presence of 10% FBS until day 2. Cells were then fed with DMEM supplemented with 10% FBS and 10ug/ml insulin for 2 days, after which they were fed every other day with DMEM containing 10% FBS.

extract_protocol:
Total RNA was isolated using TRIzol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

tag: tissue

value: sarcoma tumor

value: PBS


title: W/+ mice ATO group [ATO-2]

description:
w-sar-2
ATO-2
Tumor tissues from ATO-treated p53R282W/+ mice with sarcomas.

value: ATO


title: 5029_2h_100_ng_ml_ifng_10_ng_ml_tnfa

description: 100 ng/ml IFNy 10 ng/ml TNFa - 2h

value: Ovarian carcinoma

value: 100 ng/ml IFNy 10 ng/ml TNFa - 2h


title: 5029_6h_10_ng_ml_tnfa

description: 10 ng/ml TNFa - 6h

value: IFNy-sensing reporter, CFP+

value: 10 ng/ml TNFa - 6h

value: 6h continuous


title: 5029_2h_1_20000_sn

description: 1/20000 SN - 2h

value: 2h continuous


title: 5029_2h_unstim

description: Unstimulated in vitro - 2h

value: Unstimulated in vitro - 2h


title: 5029_6h_1_ng_ml_ifng

description: 1 ng/ml IFNy - 6h

value: 1 ng/ml IFNy - 6h


title: 5029_6h_0.01_ng_ml_ifng

description: 0.01 ng/ml IFNy - 6h

value: 0.01 ng/ml IFNy - 6h


title: W/+ mice ATO group [ATO-1]

description:
w-sar-1
ATO-1
Tumor tissues from ATO-treated p53R282W/+ mice with sarcomas.


title: 24h_100_ng_ml_IFNg_10_ng_ml_TNFa

description:
24h_100_ng_ml_IFNg_10_ng_ml_TNFa
100 ng/ml IFNy 10 ng/ml TNFa - 24h

data_processing:
Reads were aligned paired-end, strand and transcriptome aware, with hisat
Counts per gene were made using itreecount (https://github.com/NKI- GCF/itreecount) and annotated using ensembl gtf version 87
Assembly: GRCm38
Supplementary files format and content: itreecount count output

source_name: NRAS-mutated mouse melanoma (NMM)

value: 24h continuous

tag: stim group

value: 100 ng/ml IFNy 10 ng/ml TNFa

tag: tnf conc

tag: ifn conc

tag: lt conc

tag: tgf conc

tag: ifna conc

tag: il2 conc

tag: sample origin

tag: sample type

value: bulk

tag: condition name

value: 100 ng/ml IFNy 10 ng/ml TNFa - 24h

value: NRAS-mutated mouse melanoma (NMM)

value: Melanoma

value: NRAS mutated


title: polysomal RNA from axons of mouse PCNs expressing tRFP, rep 2

value: transfection with lentiviral particles overexpressing tRFP

value: polysomal RNA


title: 24h_100_ng_ml_IFNg

description:
24h_100_ng_ml_IFNg
100 ng/ml IFNy - 24h

tag: duration

value: 100 ng/ml IFNy

value: 100 ng/ml IFNy - 24h

tag: cell line

tag: treatment


title: MCD mice-2

city: Nankoku

first: Shuji

last: Sakamoto

state: Kochi

address: Oko-cho, Kohasu

department: Science Research Center

institute: Kochi University

hyb_protocol: The single-stranded cDNA was hybridized with a Mouse Gene 2.1 ST Array Strip (ThermoFisher Scientific).

scan_protocol: The array was scanned by the GeneAtlas system (Affymetrix, MA, USA) to measure the intensities of the microarray spots.

data_processing: The intensities of the spots were analyzed by the Transcriptome Analysis Console (TAC) software (ThermoFisher Scientific).

label: biotin

source_name: Wild-type mice fed with MCD

label_protocol: Single-stranded cDNA was generated from the amplified cRNA derived from the total RNA and labeled biotin with the GeneChip WT PLUS Reagent Kit (ThermoFisher Scientific, MA, USA).

growth_protocol: Mice were maintained at 19-25 ºC with 55 % ± 25 % humidity under a 14-hour light/10-hour dark cycle in specific-pathogen-free are.

extract_protocol: Total RNA was prepared from the liver of mice fed with ND or MCD by miRNeasy mini kit (QIAGEN, Hilden, Germany).

treatment_protocol: Wild type male C57BL/6J mice at 6 weeks of age were randomly assigned into two groups (normal diet or MCD groups). Mice were fed with normal diet (ND) or MCD for 20 weeks.

tag: strain

tag: Sex

value: male

value: Liver


title: W/+ mice control group [PBS-2]

description:
w-sar-4
PBS-2
Tumor tissues from p53R282W/+ mice with sarcomas.

value: sarcoma tumor

tag: genotype

value: PBS


title: 24h_1_ng_ml_IFNg

description:
24h_1_ng_ml_IFNg
1 ng/ml IFNy - 24h

value: 1 ng/ml IFNy

value: 1 ng/ml IFNy - 24h

tag: cell type


title: 24h_10_ng_ml_TNFa

description:
24h_10_ng_ml_TNFa
10 ng/ml TNFa - 24h

value: 24h continuous

tag: stim group

value: 10 ng/ml TNFa

value: 10 ng/ml TNFa - 24h


title: 24h_0_1_ng_ml_TNFa

description:
24h_0_1_ng_ml_TNFa
0.1 ng/ml TNFa - 24h

value: 0.1 ng/ml TNFa

tag: tnf conc

value: bulk

value: 0.1 ng/ml TNFa - 24h


title: GDF8 Ab-treated mouse, ACLT-injured cartilage, 2

city: Lexington

first: Alexander

middle: Romano

last: Keeble

state: KY

address: 900 S Limestone st

institute: University of Kentucky

data_processing:
Sequenced reads were trimmed from the 3' end based on quality score with a minumum Phred score of 20 and a minumum read length of 50 bp
Trimmed reads were alligned to the GRCm3/mm10 reference genome using STAR 2.7.3a aligner with default parameters.
Aligned reads were quantified to the mm39 reference assembly with requrement of junction reads to match introns and strict paired-end compatibility.  Quantified reads went through a noise reduction filter with maximum feature exclusion set less than or equal to 10.
Filtered counts were normalized per million and tested for statistical significance using DESeq2. Raw p-values were adjusted for multiple testing using the Benjamini-Hochberg false discovery rate (FDR) step-up method.
All steps were performed using the Partek® Flow® Software.
Assembly: mm39
Supplementary files format and content: tab-delimited text files include raw counts for each sample

source_name: Cartilage

extract_protocol:
Murine cartilage RNA was isolated using TRI Reagent and the Zymo Direct-zol RNA Miniprep Kit and prepared for RNA-sequencing
Conducted at NovoGene

tag: tissue

value: Cartilage

value: GDF8 Ab-treated mouse, ACLT-injured


title: GDF8 Ab-treated mouse, ACLT-injured cartilage, 1


title: GDF8 Ab-treated mouse, non-injured (control) cartilage, 2

value: GDF8 Ab-treated mouse, non-injured (control) quadricep


title: Placebo Ab-treated mouse, ACLT-injured cartilage, 1

value: Placebo Ab-treated mouse, ACLT-injured


title: 24h_1_ng_ml_TNFa

description:
24h_1_ng_ml_TNFa
1 ng/ml TNFa - 24h

value: 1 ng/ml TNFa

tag: ifn conc

tag: lt conc

value: 1 ng/ml TNFa - 24h

value: NRAS-mutated mouse melanoma (NMM)

value: Melanoma

value: NRAS mutated


title: MCD mice-1

value: male

value: Liver


title: 24h_2ng_ml_Lymphotoxin_a1_B2

description:
24h_2ng_ml_Lymphotoxin_a1_B2
2 ng/ml lymphotoxin A1 B2 - 24h

value: 24h continuous

value: 2 ng/ml lymphotoxin A1 B2

tag: tgf conc

tag: ifna conc

value: 2 ng/ml lymphotoxin A1 B2 - 24h


title: 24h_5000_U_ml_IFNa1

description:
24h_5000_U_ml_IFNa1
5000 U/ml IFNA1 - 24h

value: 5000 U/ml IFNA1

tag: il2 conc

tag: sample origin


title: Placebo Ab-treated mouse, non-injured (control) cartilage, 1

value: Placebo Ab-treated mouse, non-injured (control) quadricep


title: GDF8 Ab-treated mouse, non-injured (control) cartilage, 1


title: ND mice-1

source_name: Wild-type mice fed with normal diet


title: 12h_100_ng_ml_IFNg

description:
12h_100_ng_ml_IFNg
100 ng/ml IFNy - 12h

value: 12h continuous

value: 100 ng/ml IFNy

tag: sample type

value: bulk

tag: condition name

value: 100 ng/ml IFNy - 12h


title: ND mice-2


title: 12h_100_ng_ml_IFNg_10_ng_ml_TNFa

description:
12h_100_ng_ml_IFNg_10_ng_ml_TNFa
100 ng/ml IFNy 10 ng/ml TNFa - 12h

tag: duration

value: 100 ng/ml IFNy 10 ng/ml TNFa

value: 100 ng/ml IFNy 10 ng/ml TNFa - 12h

tag: cell line


title: 24h_unstim

description:
24h_unstim
Unstimulated in vitro - 24h

value: Unstimulated in vitro

value: Unstimulated in vitro - 24h

tag: treatment


title: Placebo Ab-treated mouse, non-injured (control) cartilage, 2

value: Cartilage


title: GDF8 Ab-treated mouse, ACLT-injured quadricep, 5

data_processing:
Sequenced reads were trimmed from the 3' end based on quality score with a minumum Phred score of 20 and a minumum read length of 50 bp
Trimmed reads were alligned to the GRCm3/mm10 reference genome using STAR 2.7.3a aligner with default parameters.
Aligned reads were quantified to the mm10 reference assembly with requrement of junction reads to match introns and strict paired-end compatibility.  Quantified reads went through a noise reduction filter with maximum feature exclusion set less than or equal to 10.
Filtered counts were normalized per million and tested for statistical significance using DESeq2. Raw p-values were adjusted for multiple testing using the Benjamini-Hochberg false discovery rate (FDR) step-up method.
All steps were performed using the Partek® Flow® Software.
Assembly: mm39
Supplementary files format and content: tab-delimited text files include raw counts for each sample

source_name: Skeletal muscle

extract_protocol:
Murine quadricep RNA was isolated using TRI Reagent and the Zymo Direct-zol RNA Miniprep Kit and prepared for RNA-sequencing
Conducted at NovoGene

value: Skeletal muscle


title: 24h_10_ng_ml_TGFB

description:
24h_10_ng_ml_TGFB
10 ng/ml TGFb - 24h

value: 10 ng/ml TGFb

value: 10 ng/ml TGFb - 24h

value: NRAS-mutated mouse melanoma (NMM)

value: Melanoma

value: NRAS mutated


title: 12h_0_01_ng_ml_IFNg

description:
12h_0_01_ng_ml_IFNg
0.01 ng/ml IFNy - 12h

value: 0.01 ng/ml IFNy

value: 0.01 ng/ml IFNy - 12h


title: GDF8 Ab-treated mouse, ACLT-injured quadricep, 4


title: GDF8 Ab-treated mouse, ACLT-injured quadricep, 3


title: 24h_0_01_ng_ml_IFNg

description:
24h_0_01_ng_ml_IFNg
0.01 ng/ml IFNy - 24h

value: 24h continuous

value: 0.01 ng/ml IFNy - 24h


title: 12h_1_ng_ml_IFNg

description:
12h_1_ng_ml_IFNg
1 ng/ml IFNy - 12h

value: 12h continuous

value: 1 ng/ml IFNy

value: bulk

value: 1 ng/ml IFNy - 12h


title: GDF8 Ab-treated mouse, ACLT-injured quadricep, 2


title: GDF8 Ab-treated mouse, ACLT-injured quadricep, 1


title: 12h_10_ng_ml_TNFa

description:
12h_10_ng_ml_TNFa
10 ng/ml TNFa - 12h

value: 10 ng/ml TNFa

value: 10 ng/ml TNFa - 12h


title: Placebo Ab-treated mouse, ACLT-injured cartilage, 2

value: Cartilage

value: Placebo Ab-treated mouse, ACLT-injured


title: 24h_6000_U_ml_IL-2

description:
24h_6000_U_ml_IL-2
6000 U/ml IL-2 - 24h


title: Placebo Ab-treated mouse, ACLT-injured quadricep, 5

value: Skeletal muscle


title: 12h_0_1_ng_ml_TNFa

description:
12h_0_1_ng_ml_TNFa
0.1 ng/ml TNFa - 12h

value: 0.1 ng/ml TNFa

value: 0.1 ng/ml TNFa - 12h


title: 12h_2ng_ml_Lymphotoxin_a1_B2

description:
12h_2ng_ml_Lymphotoxin_a1_B2
2 ng/ml lymphotoxin A1 B2 - 12h

value: 2 ng/ml lymphotoxin A1 B2

value: 2 ng/ml lymphotoxin A1 B2 - 12h

value: NRAS-mutated mouse melanoma (NMM)

value: Melanoma


title: Placebo Ab-treated mouse, ACLT-injured quadricep, 3


title: Placebo Ab-treated mouse, ACLT-injured quadricep, 4


title: 12h_1_ng_ml_TNFa

description:
12h_1_ng_ml_TNFa
1 ng/ml TNFa - 12h

value: 1 ng/ml TNFa

value: 1 ng/ml TNFa - 12h

value: NRAS mutated


title: Placebo Ab-treated mouse, ACLT-injured quadricep, 2


title: Placebo Ab-treated mouse, ACLT-injured quadricep, 1


title: 12h_10_ng_ml_TGFB

description:
12h_10_ng_ml_TGFB
10 ng/ml TGFb - 12h

value: 12h continuous

value: 10 ng/ml TGFb

value: 10 ng/ml TGFb - 12h


title: GDF8 Ab-treated mouse, non-injured (control) quadricep, 1


title: 12h_6000_U_ml_IL-2

description:
12h_6000_U_ml_IL-2
6000 U/ml IL-2 - 12h

value: bulk


title: 12h_unstim

description:
12h_unstim
Unstimulated in vitro - 12h

value: Unstimulated in vitro

value: Unstimulated in vitro - 12h


title: GDF8 Ab-treated mouse, non-injured (control) quadricep, 5


title: GDF8 Ab-treated mouse, non-injured (control) quadricep, 3


title: GDF8 Ab-treated mouse, non-injured (control) quadricep, 4


title: 6h_100_ng_ml_IFNg

description:
6h_100_ng_ml_IFNg
100 ng/ml IFNy - 6h

value: 6h continuous

value: 100 ng/ml IFNy

value: 100 ng/ml IFNy - 6h


title: 6h_0_01_ng_ml_IFNg

description:
6h_0_01_ng_ml_IFNg
0.01 ng/ml IFNy - 6h

value: 0.01 ng/ml IFNy

value: 0.01 ng/ml IFNy - 6h


title: 6h_10_ng_ml_TNFa

description:
6h_10_ng_ml_TNFa
10 ng/ml TNFa - 6h

value: 10 ng/ml TNFa

value: 10 ng/ml TNFa - 6h


title: GDF8 Ab-treated mouse, non-injured (control) quadricep, 2

value: Skeletal muscle


title: Placebo Ab-treated mouse, non-injured (control) quadricep, 4


title: 12h_5000_U_ml_IFNa1

description:
12h_5000_U_ml_IFNa1
5000 U/ml IFNA1 - 12h

value: 5000 U/ml IFNA1

value: NRAS-mutated mouse melanoma (NMM)

value: Melanoma


title: Placebo Ab-treated mouse, non-injured (control) quadricep, 3


title: 6h_100_ng_ml_IFNg_10_ng_ml_TNFa

description:
6h_100_ng_ml_IFNg_10_ng_ml_TNFa
100 ng/ml IFNy 10 ng/ml TNFa - 6h

value: 100 ng/ml IFNy 10 ng/ml TNFa

value: 100 ng/ml IFNy 10 ng/ml TNFa - 6h

value: NRAS mutated


title: 6h_1_ng_ml_IFNg

description:
6h_1_ng_ml_IFNg
1 ng/ml IFNy - 6h

value: 1 ng/ml IFNy

value: bulk

value: 1 ng/ml IFNy - 6h


title: 6h_0_1_ng_ml_TNFa

description:
6h_0_1_ng_ml_TNFa
0.1 ng/ml TNFa - 6h

value: 6h continuous

value: 0.1 ng/ml TNFa

value: 0.1 ng/ml TNFa - 6h


title: Placebo Ab-treated mouse, non-injured (control) quadricep, 5


title: Placebo Ab-treated mouse, non-injured (control) quadricep, 2


title: 6h_1_ng_ml_TNFa

description:
6h_1_ng_ml_TNFa
1 ng/ml TNFa - 6h

value: 1 ng/ml TNFa

value: 1 ng/ml TNFa - 6h


title: Placebo Ab-treated mouse, non-injured (control) quadricep, 1


title: 1629

city: Milwaukee

first: Michael

last: Pisano

state: Wisconsin

address: 8701 W Watertown Plank Rd MFRC 6033

institute: Medical College of Wisconsin

data_processing:
Somatic variants were called using Mutect2 program from the GATK (Genome Analysis Tool Kit) software package (version 4.0.5.2). The Mutect2 program was run in Tumor only mode.
The Ensembl Variant Effect Predictor (VEP) software was used for variant annotation.
Assembly: mm10
Supplementary files format and content: VCF File with Summary of indels and SNPs in IL6Myc tumor
Library strategy: WES

source_name: Kidney

extract_protocol:
DNA was extracted using the DNeasy mini kit (Qiagen, 69504)
Agilent SureSelct Mouse Exon (50Mb))

value: Kidney

value: WT Kidney

value: Balb/c


title: 6h_2ng_ml_Lymphotoxin_a1_B2

description:
6h_2ng_ml_Lymphotoxin_a1_B2
2 ng/ml lymphotoxin A1 B2 - 6h

value: 2 ng/ml lymphotoxin A1 B2

value: 2 ng/ml lymphotoxin A1 B2 - 6h


title: 6h_10_ng_ml_TGFB

description:
6h_10_ng_ml_TGFB
10 ng/ml TGFb - 6h

value: 10 ng/ml TGFb

value: 10 ng/ml TGFb - 6h

value: NRAS-mutated mouse melanoma (NMM)

value: Melanoma


title: 6h_5000_U_ml_IFNa1

description:
6h_5000_U_ml_IFNa1
5000 U/ml IFNA1 - 6h

value: 5000 U/ml IFNA1

value: 5000 U/ml IFNA1 - 6h

value: NRAS mutated


title: 1627

source_name: mesenteric lymph node

value: mesenteric lymph node

value: Malignant Plasma Cell


title: 6h_6000_U_ml_IL-2

description:
6h_6000_U_ml_IL-2
6000 U/ml IL-2 - 6h

value: 6h continuous

value: bulk


title: 6h_unstim

description:
6h_unstim
Unstimulated in vitro - 6h

value: Unstimulated in vitro

value: Unstimulated in vitro - 6h


title: 1625


title: 1626


title: 2h_100_ng_ml_IFNg_10_ng_ml_TNFa

description:
2h_100_ng_ml_IFNg_10_ng_ml_TNFa
100 ng/ml IFNy 10 ng/ml TNFa - 2h

value: 2h continuous

value: 100 ng/ml IFNy 10 ng/ml TNFa

value: 100 ng/ml IFNy 10 ng/ml TNFa - 2h


title: 1624

value: Kidney

value: WT Kidney

value: Balb/c


title: 1623


title: 1622


title: 2h_10_ng_ml_TGFB

description:
2h_10_ng_ml_TGFB
10 ng/ml TGFb - 2h

value: 10 ng/ml TGFb

value: 10 ng/ml TGFb - 2h

value: NRAS-mutated mouse melanoma (NMM)


title: 2h_10_ng_ml_TNFa

description:
2h_10_ng_ml_TNFa
10 ng/ml TNFa - 2h

value: 10 ng/ml TNFa

value: 10 ng/ml TNFa - 2h

value: Melanoma


title: 2h_0_01_ng_ml_IFNg

description:
2h_0_01_ng_ml_IFNg
0.01 ng/ml IFNy - 2h

value: 0.01 ng/ml IFNy

value: 0.01 ng/ml IFNy - 2h

value: NRAS mutated


title: 2h_2ng_ml_Lymphotoxin_a1_B2

description:
2h_2ng_ml_Lymphotoxin_a1_B2
2 ng/ml lymphotoxin A1 B2 - 2h

value: 2 ng/ml lymphotoxin A1 B2

value: bulk

value: 2 ng/ml lymphotoxin A1 B2 - 2h


title: 2h_1_ng_ml_TNFa

description:
2h_1_ng_ml_TNFa
1 ng/ml TNFa - 2h

value: 2h continuous

value: 1 ng/ml TNFa

value: 1 ng/ml TNFa - 2h


title: 1628

value: mesenteric lymph node

value: Malignant Plasma Cell


title: 2h_5000_U_ml_IFNa1

description:
2h_5000_U_ml_IFNa1
5000 U/ml IFNA1 - 2h

value: 5000 U/ml IFNA1

value: 5000 U/ml IFNA1 - 2h


title: 1619


title: 1616


title: 1618


title: 2h_6000_U_ml_IL-2

description:
2h_6000_U_ml_IL-2
6000 U/ml IL-2 - 2h

value: NRAS-mutated mouse melanoma (NMM)


title: 1614


title: 1613


title: 1617


title: 1621

value: Kidney

value: WT Kidney

value: Balb/c


title: 2h_unstim

description:
2h_unstim
Unstimulated in vitro - 2h

value: Unstimulated in vitro

value: Unstimulated in vitro - 2h

value: Melanoma


title: 1620


title: 1615


title: 2h_100_ng_ml_IFNg

description:
2h_100_ng_ml_IFNg
100 ng/ml IFNy - 2h

value: 100 ng/ml IFNy

value: 100 ng/ml IFNy - 2h

value: NRAS mutated


title: 1612


title: 2h_1_ng_ml_IFNg

description:
2h_1_ng_ml_IFNg
1 ng/ml IFNy - 2h

value: 2h continuous

value: 1 ng/ml IFNy

value: bulk

value: 1 ng/ml IFNy - 2h


title: 2h_0_1_ng_ml_TNFa

description:
2h_0_1_ng_ml_TNFa
0.1 ng/ml TNFa - 2h

value: 0.1 ng/ml TNFa

value: 0.1 ng/ml TNFa - 2h


title: 1611

value: mesenteric lymph node

value: Malignant Plasma Cell


title: 1609


title: 1607


title: SUIT2-NEG-2-chip-MED12_CRISPRa

city: Cold Spring Harbor

first: Diogo

last: Maia e Silva

state: NY

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

data_processing:
For RNA-seq, sequencing reads were mapped onto reference human genome hg38 using STAR v2.7.9a with default settings. HTSeq-counts was used to generate raw gene counts, and DESeq2 was then used to perform differential expression analysis.
For ChIP-Seq, reads were mapped to hg38 with bowtie2 2.4.2 with very-sensitive setting. Bam files are then sorted with Samtools 1.11 with default settings, and used to call peaks with MACS2. Bedtools 2.30.0 was used to intersect and merge peaks
Deeptools v3.5.0 was used to generate BigWig files that were then visualized in the UCSC genome browser with the hg38 genome. HOMER v4.11 was used to assign the closest annotated ORFs to each peak and for motif discovery.
For CRISPR amplicon sequencing, raw reads were aligned to each sgRNA library to generate count files with MAGeCK.
For scRNA-seq experiments, data was genetically demultiplexed using cellsnp-lite 1.2.3 and Vireo 0.5.8, aligned to the human genome and assigned to cells using Cell Ranger 7.1.0, and downstream analyzed using Seurat 4.3.0.1.
Assembly: hg38
Supplementary files format and content: Htseq-count matrix for RNA-Seq. H5 Seurat files for scRNA-seq. Bigwig files for ChIP-Seq. Mageck count files for CRISPR libraries.

growth_protocol: Human cancer cell lines were cultured according to vendor recommendations in RPMI or DMEM 10% FBS supplemented with pen-strep.

extract_protocol:
For RNA-seq experiments, total RNA was isolated using TRIzol (Thermo Fisher, 15596026) according to the manufacturer’s instructions. For scRNA-seq experiments, cells were single cell captured and barcoded using the 10X Chromium chemistry. For ChIP-seq experiments, lysates were clarified from crosslinked, sonicated nuclei and protein-DNA complexes were immunoprecipitated with specific antibodies. For CRISPR libraries, genomic DNA was isolated using phenol-chloroform extraction and directly used for library preparation.
RNA-seq and ChIP-seq ibraries were constructed using  Illumina TruSeq RNA library prep kit v2 (Illumina, RS-122-2001) or  Illumina TruSeq ChIP library prep kit (Illumina, IP-202-1012) based on the manufacturer’s instructions. scRNA-seq libraries were biult using 10X Genomics NextGEM Single-Cell 3' Library Kit. CRISPR libraries were prepared using sgRNA flanking primers described in the article and 1 step PCR amplification.

value: human pancreatic cancer cell line

value: sgNT-2 (CRISPRa)

tag: chip antibody

value: MED12, CST, D9K5J


title: 1606

tag: genotype


title: 1605

tag: cell type


title: SUIT2-DELTAN-5-chip-p63_CRISPRa

value: sgTP63-2 (CRISPRa)

value: p63-alpha, CST, D2K8X


title: SUIT2-DELTAN-5-chip-MED12_CRISPRa


title: SUIT2-DELTAN-5-input_CRISPRa


title: 1604


title: SUIT2-DELTAN-3-chip-p63_CRISPRa

value: sgTP63-1 (CRISPRa)


title: 1602


title: 1601


title: SUIT2-DELTAN-3-chip-MED12_CRISPRa


title: 1590


title: SUIT2-NEG-2-input_CRISPRa


title: 1589


title: 1592


title: klm1-ko-tp63-2-input-chip-med12


title: 1588


title: klm1-ko-tp63-2-input-chip-p63_h3k27ac


title: SUIT2-NEG-1-chip-MED12_CRISPRa

value: sgNT-1 (CRISPRa)


title: SUIT2-NEG-1-input_CRISPRa


title: NHLF ITPKC-overexpressing 3

city: Rochester

first: Jack

middle: Henry

last: Wellmerling

state: Minnesota

address: 200 1st St SW

institute: Mayo Clinic

description: ITPKC 3

data_processing:
BasecallLite_1.5.0.323
Filtering with SOAPnuke v1.5.2, parameters: -l 15 -q 0.2 -n 0.05
Alignment with HISAT2 v2.0.4, parameters: --sensitive --no-discordant --no-mixed -I 1 -X 1000 -p 8 --rna-strandness RF
Assembly: hg38
Supplementary files format and content: tab-delimited file showing FPKM for each sample, as well as log fold-change and q-value comparing transfected samples to controls

source_name: Lung

growth_protocol: DMEM with 10% fetal bovine serum and 1% antimicrobial/antifungal cocktail

extract_protocol:
Total RNA isolated using Qiagen RNA Micro kit
DNBSEQ stranded mRNA library

treatment_protocol: Transient transfection for 48 hours with rhITPKC or vehicle using lipofectamine 3000

value: Lung

value: Primary

value: Fibroblast

value: rhITPKC


title: 1587


title: klm1-ko-tp63-1-input-chip-p63_h3k27ac


title: klm1-ko-tp63-2-chip-p63


title: klm1-ko-tp63-2-chip-med12

value: H3K27Ac, Abcam, Ab4729


title: NHLF ITPKC-overexpressing 2

description: ITPKC 2


title: 1571


title: NHLF Control 2

description: Control 2

value: Vehicle


title: klm1-ko-tp63-1-input-chip-med12


title: 1603


title: 1569


title: NHLF Control 1

description: Control 1


title: Mice skin tissue-Vehicle9

city: Beijing

first: Peiqiu

last: Zhu

address: Xishiku Street 8

department: Dermatology

institute: Peking University First Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts and fpkm for every gene and every sample

source_name: skin tissue

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Except Blank group, the Vehicle and TDM group were accepted twice application of solvents and drugs (0, 24h) with 60ul once a time.

value: dorsal skin

tag: strain

value: Vehicle of TDM10842


title: SUIT2-DELTAN-3-input_CRISPRa


title: klm1-ko-tp63-1-chip-p63


title: Mice skin tissue-Vehicle8


title: 1568

value: mesenteric lymph node


title: Mice skin tissue-Vehicle7


title: klm1-ko-tp63-2-chip-h3k27ac


title: 1565

value: Malignant Plasma Cell


title: Mice skin tissue-Vehicle4


title: Mice skin tissue-Vehicle5


title: Mice skin tissue-Vehicle2


title: NHLF ITPKC-overexpressing 1

description: ITPKC 1


title: 1564


title: klm1-ko-tp63-1-chip-h3k27ac

value: human pancreatic cancer cell line


title: klm1-ko-rosa26-input-chip-p63_h3k27ac


title: Mice skin tissue-Vehicle3


title: Mice skin tissue-Vehicle1


title: klm1-ko-rosa26-input-chip-med12


title: 1563


title: Mice skin tissue-TDM9


title: Mice skin tissue-TDM7


title: 1561


title: Mice skin tissue-TDM8


title: Mice skin tissue-TDM5


title: klm1-ko-rosa26-chip-med12


title: Mice skin tissue-TDM6


title: klm1-ko-rosa26-chip-p63


title: 1559


title: 1562


title: Mice skin tissue-TDM3


title: klm1-ko-tp63-1-chip-med12


title: Mice skin tissue-TDM4


title: 1510


title: Mice skin tissue-TDM2


title: t3m4-parental-chip-p63


title: Mice skin tissue-Vehicle6


title: 1505


title: Mice skin tissue-TDM1


title: Mice skin tissue-Blank9


title: Mice skin tissue-Blank8


title: Mice skin tissue-Blank7


title: 1502


title: t3m4-parental-chip-med1

value: MED1, Bethyl, A300-793A


title: 1501


title: t3m4-parental-chip-med12

value: MED12, CST, D9K5J


title: Mice skin tissue-Blank4


title: 1293


title: Mice skin tissue-Blank6


title: Mice skin tissue-Blank3


title: klm1-ko-rosa26-chip-h3k27ac


title: t3m4-parental-input


title: 1292


title: Mice skin tissue-Blank1


title: klm1-parental-input


title: klm1-parental-chip-med12


title: KLM1-MedExonScan-p63-FACS-high

data_processing:
For RNA-seq, sequencing reads were mapped onto reference human genome hg38 using STAR v2.7.9a with default settings. HTSeq-counts was used to generate raw gene counts, and DESeq2 was then used to perform differential expression analysis.
For ChIP-Seq, reads were mapped to hg38 with bowtie2 2.4.2 with very-sensitive setting. Bam files are then sorted with Samtools 1.11 with default settings, and used to call peaks with MACS2. Bedtools 2.30.0 was used to intersect and merge peaks
Deeptools v3.5.0 was used to generate BigWig files that were then visualized in the UCSC genome browser with the hg38 genome. HOMER v4.11 was used to assign the closest annotated ORFs to each peak and for motif discovery.
For CRISPR amplicon sequencing, raw reads were aligned to each sgRNA library to generate count files with MAGeCK.
For scRNA-seq experiments, data was genetically demultiplexed using cellsnp-lite 1.2.3 and Vireo 0.5.8, aligned to the human genome and assigned to cells using Cell Ranger 7.1.0, and downstream analyzed using Seurat 4.3.0.1.
Assembly: hg38
Supplementary files format and content: Htseq-count matrix for RNA-Seq. H5 Seurat files for scRNA-seq. Bigwig files for ChIP-Seq. Mageck count files for CRISPR libraries.
Library strategy: CRISPR

value: MedExonScan

tag: time

tag: facs antibody


title: 1200

tag: tissue


title: eEBS01, EXP2

city: Padova

first: Mattia

last: Forcato

address: Via Ugo Bassi, 58/B

institute: University of Padova

description: amplicon generated by genomic DNA

data_processing:
The clipping of reads was performed using Trimmomatic (v 0.36) and paired-end reads were merged using software FLASH2 (v 2.2.00) to obtain a single, longer read that covers the full target region. The processed reads were mapped, using BMWA MEM (v 0.7.15), to the reference sequence (the wild type KRT14 exon1 sequence or off targets) with default alignment parameters. Only high quality, merged, on target reads were considered for further processing. Finally, the identification and quantification of sequences alleles using CRISPResso (v 1.0.13) occurred.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files with the results of the editing analysis

source_name: epidermis

growth_protocol: Keratinocytes were collected, plated on lethally irradiated 3T3-J2-Y cells and grown at 37°C, 5% CO2 in humidified atmosphere in KGM medium.

extract_protocol:
Cells were detached after trypsinization from in vitro cultivated human primary keratinocyte and genomic DNA was extracted. The region near the target site was amplified by specific PCR primers with sequence adaptor .
25 µl of purified amplicon was used for NGS analysis using Illumina sequencing platform.

treatment_protocol: 5 x 105 keratinocytes were resuspended in 100l primary cell nucleofection solution, mixed with the RNP complex solution and Cas9 electroporation enhancer. Cells were electroporated using a 4D-Nucleofector using the program DS-138.

value: epidermis

value: human primary keratinocytes

value: keratinocyte

value: wild-type allele and edited mutant allele (c.475/495del21 mutation in KRT14 exon1)

value: edited

tag: target


title: eEBS01, off-target MIPOL1

description: amplicon generated by genomic DNA


title: eEBS01, off-target BAIAP2L1

description: amplicon generated by genomic DNA


title: eEBS01, EXP3

description: amplicon generated by genomic DNA


title: eEBS01, EXP1

description: amplicon generated by genomic DNA


title: 1199


title: KLM1-MedExonScan-p63-FACS-low

value: p63-alpha, CST, D2K8X


title: Doub-KO-GMCSF rep2

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

country: Germany

institute: University clinics Freiburg

description:
CAST-seq performed at the CSF2 locus on sample treated with four RNP complexes (Cas9) targeting CD40L and CSF2
Double-KO-GMCSF_FINAL.xlsx

data_processing:
Mate paired reads were merged using BBmerge from BBmap (v38.76) software. BBmap  was also used for filtering and trimming as follow: merged reads containing the designer nuclease target site were filtered-in, whereas PCR mispriming products reads were filtered-out. Linker sequences, Illumina adapter sequences, targeted elongation sequence and bad quality reads were trimmed.
Selected reads were aligned to the human genome GRCh38 (hg38) using Bowtie2 (v2.3.4.2) and the very-sensitive preset parameters. Aligned reads with good mapping quality (MAPQ >15) were selected. The aligned BAM file was converted into bed file using bedtools (v2.27.1).
Translocated sites were identified using the CAST-Seq pipeline with default parameters, as described on https://github.com/AG-Boerries/CAST-Seq
Assembly: hg38
Supplementary files format and content: matrix table of translocation sites detected with CAST-Seq pipeline. It includes the genomic coordinates of translocated sites, read coverage, alignment score against gRNA, translocation event classification and nearest genes annotation.

source_name: PBMCs from healthy donors

growth_protocol: The T cells and the gene-edited CAR T cells T cells were cultivated in RPMI-1640 medium supplemented with 10% FCS, 1% P/S, 10 mM HEPES, 100 U/ml IL-2 , 25 U/ml IL-7 and 50 U/ml IL-15

extract_protocol:
Genomic DNA was isolated from cultured cells after 8 days using the DNeasy blood & tissue kit (Qiagen) according to the manufacturer’s instructions.
Library construction was essentially performed as described by Turchiano et. al (Cell Stem Cell, 2021). Briefly, gDNA was fragmented by enzymatic digestion using the NEBNext® Ultra™ II FS DNA Library Prep (NEB) to obtain average fragment lengths of 200-350 bp. The DNA was end repaired and a protruding 3’-A nucleotide was added according to the manufacturer’s instructions  in order to enable the ligation of a linker sequence with a protruding 3’-T. After linker ligation, fragments were purified using the QIAquick PCR Purification Kit (NEB). The region of interes (on-target site) was amplified in two rounds of PCR using Q5® Hot Start High-Fidelity DNA Polymerase (NEB). PCR conditions were: 20 cycles at 95°C for 15 s, 63°C (first reaction) or 68°C (second reaction) for 20 s, 72°C for 20 s. The first reaction was performed with primers complementary to the linker sequence and to a sequence in close proximity to the on-target site (bait primer). Two decoy primers were introduced to reduce full-length amplification of the fragments which contain the on-target sequence without a chromosomal aberration event. The second PCR utilized nested primers to reduce the amount of mis-amplified fragments and to introduce a binding platform for barcoding primers. DNA fragments from the second PCR with a size of 200-500bp were subsequently isolated using the QIAquick® Gel Extraction Kit (Qiagen) and barcoded.
Third PCR introduced the barcoded Illumina adapter for sequencing (NEBNext® Multiplex Oligos for Illumina; Index Primers Sets 1-4). Sequencing was outsourced to service NGS provider Genewiz (part of Azenta Life Sciences) on where it was performed on Illumina HiSeq or NovaSeq devices collecting 2x150 bp paired-end reads.

treatment_protocol: Electroporation of CAR T cells was carried out using the 4D-Nucleofector, kit P3 (Lonza) . The S.p. Cas9 was purchased from Integrated DNA Technologies. The gRNA was purchased from Biolegio. 48h before electroporation the cells were transduced with a lentivirus to generate the CAR T cells. 24h post-electroporation the IL-2 concentration was reduced in the media medium until reached 100 U/ml. 8 days po-electoporation the cells were checked for phynotiping and genotyping

value: PBMCs

tag: sample

value: CAST-seq derived amplicons from gDNA

value: Cas9-treated (two RNPs targeting CD40L; two RNPs targeting CSF2)


title: Mice skin tissue-Blank5

value: dorsal skin


title: T3M4-MedExonScan-D1.5


title: 1201


title: Mice skin tissue-Blank2


title: T3M4-MedExonScan-D14


title: eEBS01, off-target ZNF320

description: amplicon generated by genomic DNA


title: klm1-parental-chip-p63


title: SUIT2-MedExonScan-D1.5


title: GMCSF-KO rep2

description:
CAST-seq performed at the CSF2 locus on sample treated with two RNP complexes (Cas9) targeting CSF2
GMCSF-KO_FINAL.xlsx

value: Cas9-treated (two RNPs targeting CSF2)


title: Doub-KO-GMCSF rep1


title: spt16-197 FLO8-sfGFP grown at 37C in dextrose rep 1

city: Vancouver

first: LeAnn

last: Howe

state: BC

address: 2350 Health Sciences Mall

department: Biochemistry and Molecular Biology

country: Canada

institute: University Of British Columbia

description: Mata his3200 leu21 lys2-128 ura3-52 trp163 FLO8-sfGFP-HpH spt16-197

data_processing:
Sequence reads were mapped to a custom Saccer3 genome with the FLO8::sfGFP allele using BWA-MEM.
Mapped reads were filtered for MAPQ > 10 and sorted using Samtools view and sort.
Files were converted to bigwig using Deeptools bamcoverage with --centerReads and normalized based on relative number of reads mapping to the S. pombe genome.
Assembly: saccer3_FLO8_crypTSS_sfGFP.fa
Supplementary files format and content: wig files normalized to S. pombe spike-ins

organism: Saccharomyces cerevisiae

growth_protocol: SPT16 and spt16-197 cells were grown for one hour at the permissive (28ºC) or non-permissive temperature (37ºC) to a final OD of 0.75 in yeast extract, peptone, dextrose (2%) media.

extract_protocol:
Cells were disrupted by bead beating and chromatin was digested to ~80% mononucleosomes with an optimized quantity of MNase (50 units of MNase were used for samples grown at 28°C, and 25 units for samples grown at 37°C).  Fifteen percent crosslinked Schizosaccharomyces pombe cells were added to each sample as a spike-in.
Twenty ng of DNA was end-repaired, A-tailed, and ligated to adapters, before 13 rounds of PCR amplification with indexed primers. All DNA purification steps used Solid Phase Reversible Immobilization magnetic beads. Samples were pooled, gel-purified (200-600 bp fragments) and sequenced on an Illumina NextSeq.

treatment_protocol: Cells were cross-linked with 1% formaldehyde for 15 min, quenched with 300 mM glycine for 5 min, and frozen as 19 OD600 unit pellets.

value: Mata his3 200 leu2 1 lys2-128 ura3-52 trp1 63 FLO8-sfGFP-HpH spt16-197

value: 37C dextrose


title: GMCSF-KO rep1


title: spt16-197 FLO8-sfGFP grown at 37C in dextrose rep 2


title: spt16-197 FLO8-sfGFP grown at 28C in dextrose rep 2

value: 28C dextrose


title: UT-GMCSF rep2

description: Non-treated control for CAST-seq performed at the CSF2 locus. Used as control for samples treated with two and four RNP complexes (Cas9)

value: non-treated


title: SPT16 FLO8-sfGFP grown at 37C in dextrose rep 2

description: Mata his3200 leu21 lys2-128 ura3-52 trp163 FLO8-sfGFP-HpH

value: Mata his3 200 leu2 1 lys2-128 ura3-52 trp1 63 FLO8-sfGFP-HpH


title: spt16-197 FLO8-sfGFP grown at 28C in dextrose rep 1


title: SPT16 FLO8-sfGFP grown at 28C in dextrose rep 2


title: SPT16 FLO8-sfGFP grown at 37C in dextrose rep 1


title: SPT16 FLO8-sfGFP grown at 28C in dextrose rep1


title: 2B-OlapR

city: Sacramento

first: Clifford

middle: G.

last: Tepper

state: CA

address: 4645 2nd Avenue, Room 2300A

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

data_processing:
RNA-Seq data was analyzed using a Spliced Transcripts Alignment to a Reference (STAR)-Partek E/M quantify to annotation model pipeline. Raw sequence reads (FASTQ format) were mapped with the STAR aligner to the reference human genome index (GRCh38/hg38, GENCODE release 43) and quantified with the Partek E/M quantify to annotation model.
Processed data are gene-level read counts generated from the output of STAR alignment and subsequent quantification with the Partek E/M quantify to annotation model  for each sample.
Assembly: GRCh38/hg38, GENCODE release 43
Supplementary files format and content: Single file in tab-delimited text consisting of a data matrix for all four samples. The file contains the Ensembl Gene Symbol (column 1), gene name (column 2), and gene-level counts for each gene for each sample (columns 3-6).

extract_protocol:
Total cellular RNA was isolated from the prostate cancer cell lines using the TRIzol Reagent (ThermoFisher Scientific).
Indexed, stranded mRNA-seq libraries were prepared from total RNA (100 ng) using the KAPA Stranded mRNA-Seq (Roche) according to the manufacturer’s standard protocol.

tag: phenotype

value: Olaparib-reistant

value: prostatic adenocarcinoma

value: untreated


title: MiaPaCa2-MedExonScan-D1.5

value: human pancreatic cancer cell line

value: MedExonScan


title: PK1-MedExonScan-D1.5


title: PK1-MedExonScan-D8


title: C4-2B

value: Parental


title: Doub-KO-CD40L rep1

description:
CAST-seq performed at the CD40L locus on sample treated with four RNP complexes (Cas9) targeting CD40L and CSF2
Double-KO-CD40L_FINAL.xlsx


title: CD40L-KO rep2

description:
CAST-seq performed at the CD40L locus on sample treated with two RNP complexes (Cas9) targeting CD40L
CD40L-KO_FINAL.xlsx

value: Cas9-treated (two RNPs targeting CD40L)


title: MiaPaCa2-MedExonScan-D14


title: LNCaP

source_name: LNCaP

value: LNCaP


title: KARR-seq K562 Arsenite Nuclear G1 Rep 2

city: Farmington

first: Youzhi

last: Cheng

state: Connecticut

address: 400 Farmington Avenue

department: Genetics and Genome Sciences

institute: University of Connecticut Health Center

data_processing:
KARR-seq: For paired end FASTQ formatted files, SeqPrep (commit: 575507b) was first used to merge overlapping read pairs (2 x 150 bp) into single end reads. Unmerged read pairs were discarded. The resulting single end results were then aligned to mm10, hg19 or dm3 reference genome using STAR (v2.5.2a) as well as the species' corresponding RefSeq transcripts. The pre-merging step was skipped for single-end FASTQ files, and directly aligned using STAR. The following STAR parameters were used to recover gapped and chimeric reads (--runMode alignReads --outFilterMultimapNmax 100 --outSAMattributes all --alignIntronMin 1 --scoreGapNoncan -4 --scoreGapATAC -4 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --limitOutSJcollapsed 10000000 --limitIObufferSize 1500000000). Only chimeric reads (CIGAR N gap between mapped segments of the read) were kept, spliced sites filtered and interaction pairs tabulated. Pairix was used to index the interaction pairs file.
Assembly: mm10,hg19,dm3
Supplementary files format and content: Processed files are bgzipped text files that follows the 4DN-standard pairs file format (pairix)
Library strategy: KARR-seq

molecule: nuclear RNA

source_name: human bone marrow cells

growth_protocol: K562 cells (ATCC, CCL243) were cultured in RPMI 1640 (Gibco 11875) supplemented with 10% (v/v) fetal bovine serum (Gibco), and 1% penicillin/streptomycin at 37 ˚C with 5% CO2.

extract_protocol:
Resuspend cell pellets in 410 µL 25 mM K3BO3, with 50 µL 10% SDS, 30 µL proteinase K, 10 µL RNase inhibitor. The mixture was shaken at 55 ˚C for 2 h and was subjected to phenol-chloroform extraction and ethanol precipitation. Extracted RNA were used for enrichment, end repair, and proximity ligation.
Libraries were constructed by using the SMARTer Stranded Total RNA-seq kit v2 – pico input mammalian.

treatment_protocol: For lowXL samples, cells were crosslinked in 0.1% formaldehyde for 10 min and then quenched with 125 mM glycine for 5 min. No crosslinking was performed for the noXL samples. Cells were incubated 30 min in lysis buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2% IGEPAL CA-630, 5 mM EDTA) supplemented with 20 mM N3-kethoxal, proteinase inhibitor, and RNase inhibitor, and was collected by centrifuging. The cell pellet was then washed and shook in lysis buffer supplemented with 12.5 µM G1-DBCO-biotin dendrimer at 1,000 rpm at 37 ˚C for 1 h. After the reaction, cells were collected and washed once as above.

value: bone marrow cells

value: Cell treated with sodium arsenite, nuclei were used


title: KLM1-MedExonScan-D1.5


title: LN-OlapR

source_name: LN-OlapR

value: LN-OlapR


title: KLM1-MedExonScan-D14


title: KARR-seq K562 noXL G1 Rep 2

value: no formaldehyde


title: SUIT2-MedExonScan-D14


title: KARR-seq K562 Arsenite Nuclear G1 Rep 1


title: KARR-seq K562 noXL G1 Rep 1


title: UT-GMCSF rep1

value: PBMCs

value: CAST-seq derived amplicons from gDNA


title: Doub-KO-CD40L rep2

value: Cas9-treated (two RNPs targeting CD40L; two RNPs targeting CSF2)


title: UT-CD40L rep2

description: Non-treated control for CAST-seq performed at the CD40L locus. Used as control for samples treated with two and four RNP complexes (Cas9)

value: non-treated


title: CD40L-KO rep1


title: KARR-seq K562 lowXL G1 Rep 2

value: 0.1% formaldehyde


title: BxPC3-MedExonScan-D1.5


title: UT-CD40L rep1


title: Hep 3B OETP53-1

city: Hangzhou

first: Jiongjie

last: Yu

state: Zhejiang

address: Kaixuan Road

institute: Zhejiang University

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp (https://github.com/OpenGene/fastp) with default parameters. Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml) software. The mapped reads of each sample were assembled by StringTie (https://ccb.jhu.edu/software/stringtie/) in a reference-based approach.
To identify DEGs (differential expression genes) between two different samples/groups, the expression level of each gene was calculated according to the transcripts per million reads (TPM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances. Essentially, differential expression analysis was performed using the DESeq2/DEGseq/edgeR/Limma/NOIseq, DEGs with |log2 (foldchange)| ≥ 1 and P-adjust ≤ 0.05 (DESeq2/edgeR/Limma) / P-adjust ≤ 0.001 (DEGseq) / Prob > 0.8 (NOIseq) were considered to be significantly different expressed genes. In addition, functional-enrichment analysis including GO (Gene Ontology, http://www.geneontology.org) and KEGG (Kyoto Encycloedia of Genes and Genomes, http://www.genome.jp/kegg/) were performed to identify which DEGs were significantly enriched in GO terms and metabolic pathways at P-adjust ≤ 0.05  compared with the whole-transcriptome background. GO functional enrichment and KEGG pathway analysis were carried out by Goatools (https://github.com/tanghaibao/Goatools) and KOBAS (http://kobas.cbi.pku.edu.cn/home.do)
All the alternative splice events that occurred in our samples were identified by using recently releases program rMATS (http：//rnaseq-mats.sourceforge.net/index.html). Only the isoforms that were similar to the reference or comprised novel splice junctions were considered, and the splicing differences were detected as exon inclusion, exclusion, alternative 5′, 3′, and intron retention events.
Assembly: hg38
Supplementary files format and content: txt files

source_name: Hep 3B

extract_protocol:
RNA was extracted by Qiagen kit. 1 ug RNA was used for library construction.
RNA library for RNA sequencing was prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocol.

value: Hep 3B

value: hepatocellular carcinoma


title: Hep 3B OETP53-3


title: KARR-seq K562 lowXL G1 Rep 1


title: spatial-sample-D

city: Los Angeles

first: Feiyang

last: Ma

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

data_processing:
For single cell RNA-seq, libraries were then sequenced on the Illumina NovaSeq 6000 sequencer to generate 150 bp paired-end reads. Data processing including quality control, read alignment (hg38), and gene quantification was conducted using the 10X Cell Ranger software. The samples were then merged into a single expression matrix using the cellranger aggr pipeline. For spatial-seq, the reads were aligned to the human genome (hg38), and the expression matrix was extracted using the spaceranger pipeline.
Assembly: hg38
Supplementary files format and content: merged raw count expression matrix for scRNA-seq and spaceranger output for spatial-seq
Library strategy: Spatial Transcriptomics

source_name: Skin

extract_protocol:
Generation of single-cell suspensions for scRNA-seq was performed as follows: Skin biopsies were incubated overnight in 0.4% dispase (Life Technologies) in Hank’s Balanced Saline Solution (Gibco) at 4°C. Epidermis and dermis were separated. Epidermis was digested in 0.25% Trypsin-EDTA (Gibco) with 10U/mL DNase I (Thermo Scientific) for 1 hour at 37°C, quenched with FBS (Atlanta Biologicals), and strained through a 70μM mesh. Dermis was minced, digested in 0.2% Collagenase II (Life Technologies) and 0.2% Collagenase V (Sigma) in plain medium for 1.5 hours at 37°C and strained through a 70μM mesh. For spatial-seq, skin samples were frozen in OCT medium and stored at -80°C until sectioning. Optimization of tissue permeabilization was performed on 20 μm sections using Visium Spatial Tissue Optimization Reagents Kit (10X Genomics, Pleasanton, CA, USA), which established an optimal permeabilization time to be 9 minutes. Samples were mounted onto a Gene Expression slide (10X Genomics), fixed in ice-cold methanol, stained with hematoxylin and eosin, and scanned under a microscope (Keyence, Itasca, IL, USA). Tissue permeabilization was performed to release the poly-A mRNA for capture by the poly(dT) primers that are precoated on the slide and include an Illumina TruSeq Read, spatial barcode, and unique molecular identifier (UMI).
For single cell RNA-seq, for the samples collected from the University of Pittsburgh, epidermal and dermal cells were combined in 1:1 ratio. For three of the samples collected from the University of Michigan, the epidermal and dermal cells were prepared in different libraries that were constructed by the University of Michigan Advanced Genomics Core on the 10X Chromium system with chemistry v3.  For the remaining samples the epidermis and dermis were combined in 1:1 ratio.  Libraries were then sequenced on the Illumina NovaSeq 6000 sequencer to generate 150 bp paired-end reads. For spatial-seq, Visium Spatial Gene Expression Reagent Kit (10X Genomics) was used for reverse transcription to produce spatially barcoded full-length cDNA and for second strand synthesis followed by denaturation to allow a transfer of the cDNA from the slide into a tube for amplification and library construction. Visium Spatial Single Cell 3ʹ Gene Expression libraries consisting of Illumina paired-end sequences flanked with P5/P7 were constructed after enzymatic fragmentation, size selection, end repair, A-tailing, adaptor ligation, and PCR. Dual Index Kit TT Set A (10X Genomics) was used to add unique i7 and i5 sample indexes and generate TruSeq Read 1 for sequencing the spatial barcode and UMI and TruSeq Read 2 for sequencing the cDNA insert, respectively. Libraries were then sequenced on the Illumina NovaSeq 6000 sequencer to generate 150 bp paired end reads.

value: Skin

tag: experiment type

value: Visium spatial-seq

value: Epidermis and dermis cell

tag: disease

value: Scleroderma skin


title: Hep 3B NC2

value: NC


title: Hep 3B OETP53-2


title: Hep 3B NC3


title: spatial-sample-A


title: NS-AR019

library_source: transcriptomic single cell

data_processing:
For single cell RNA-seq, libraries were then sequenced on the Illumina NovaSeq 6000 sequencer to generate 150 bp paired-end reads. Data processing including quality control, read alignment (hg38), and gene quantification was conducted using the 10X Cell Ranger software. The samples were then merged into a single expression matrix using the cellranger aggr pipeline. For spatial-seq, the reads were aligned to the human genome (hg38), and the expression matrix was extracted using the spaceranger pipeline.
Assembly: hg38
Supplementary files format and content: merged raw count expression matrix for scRNA-seq and spaceranger output for spatial-seq

value: scRNA-seq

value: Healthy skin


title: AsPC1-MedExonScan-D1.5

value: human pancreatic cancer cell line

value: MedExonScan


title: spatial-sample-B


title: AsPC1-MedExonScan-D14


title: KLM1-Brunello-GW-p63-FACS-low

value: Brunello-GW

value: p63-alpha, CST, D2K8X


title: NS-AR017


title: NS-AR020


title: KLM1-Brunello-GW-p63-FACS-high


title: spatial-sample-C


title: NS-AR022


title: NS-AR018


title: NS-AR021


title: BxPC3-MedExonScan-D14


title: T3M4-CRISPRi-GW-KRT5-FACS-low

value: CRISPRi-GW

value: KRT5, CST, D4U8Q


title: Hep 3B NC1


title: SK-HEP-1 shTP53-4


title: NS-AR015


title: NS-AR014


title: KLM1-CRISPRi-GW-KRT5-FACS-high


title: NS-AR013


title: KLM1-CRISPRi-GW-KRT5-FACS-low


title: SCD-SC247


title: NS-AR010


title: NS-AR012


title: BxPC3-CRISPRi-GW-KRT5-FACS-high


title: SK-HEP-1 shTP53-2


title: SCD-SC240


title: SCD-SC237


title: SCD-SC229


title: BxPC3-CRISPRi-GW-KRT5-FACS-low


title: SCD-SC226


title: T3M4-CRISPRi-GW-p63-FACS-low


title: NS-AR016


title: SK-HEP-1 NC4


title: T3M4-CRISPRi-GW-KRT5-FACS-high


title: SK-HEP-1 shTP53-3


title: SK-HEP-1 shTP53-1


title: SCD-SC230


title: SCD-SC224


title: SK-HEP-1 NC3


title: SCD-SC212


title: T3M4-CRISPRi-GW-p63-FACS-high


title: SCD-SC202


title: SK-HEP-1 NC2


title: Edom_NSph_solvent

type: genomic

city: Miyazaki

first: Yoshikazu

last: Arai

department: Faculty of Agriculture

institute: University of Miyazaki

description:
Solvent (EtOH and HNO3) exposed Edom-iPSC-derived neurosphere (NSph)
Epi_NSph_EH

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

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

data_processing: GenomeStudio software V2011.1

label: Cy3 and Cy5

source_name: solvent exposed Edom-NSph

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from neurosphere samples using Qiagen DNeasy Blood & Tissue Kit according to standard instructions

tag: gender

value: female

tag: sample type

value: iPSC-derived neurosphere

tag: disease state

value: normal