title: Donor1_06_DC_plus_CMV_0h_plus_Afu_4h30min

first: Bastian

last: Seelbinder

address: Adolf-Reichwein-Straße 23

tag: cell type

value: dendritic cells

tag: strainorline

value: DC; A. fumigatus ATCC 46645; Human herpesvirus 5 strain TB40/E clone TB40-BAC4

value: CellGro GMP serum-free DC medium

tag: kit


title: Dabrafenib_Dose1_Rep1

status: Public on Oct 01 2020

type: SRA

city: Chicago

first: Sonia

last: Brockway

state: IL

address: 303 E Superior St, SQBRC 7-500

department: Biochemistry and Molecular Genetics

country: USA

institute: Northwestern University

library_source: genomic

data_processing:
Library strategy: QMAP-Seq
Individual samples were demultiplexed based on i5 and i7 index sequences by running bcl2fastq Conversion Software (Illumina).
Data was processed using QMAP-Seq bioinformatic analysis pipeline (https://github.com/mendillolab/QMAP-Seq). Briefly, sgRNA and cell line barcode sequences were extracted from Read 1 sequences as follows: [ACACCG][sgRNA:20][Interval:102][CellLineBarcode:8]. The number of reads for each cell line-sgRNA pair was counted, allowing up to one nucleotide mismatch per barcode. Cell number was interpolated from sequencing reads using sample-specific standard curves. The number of cells for a compound-treated sample was normalized to the median number of cells for the DMSO-treated samples.
Data was filtered using the following exclusion criteria. First, samples with low read counts were excluded. Second, cell line-sgRNA pairs with high variation (standard deviation of log2(cell number) > 0.7) were excluded. Third, compounds with an AUC > 550 for any cell line-sgRNA pair were excluded. Fourth, noncytotoxic cell line-compound pairs (relative cell number of sgNT with highest dose ≥ 90%) were excluded. Fifth, cell line-compound pairs without a dose-dependent reduction in cell viability (difference in relative cell number of sgNT between lowest and highest dose < 25%) were excluded.
Genome_build: N/A (sgRNA library sequencing)
Supplementary_files_format_and_content: Plain text document (.txt) files with read counts for each cell line-sgRNA pair. Individual files for each sample.
Supplementary_files_format_and_content: Comma-separated values (.csv) file with relative cell numbers (i.e., cell number (%DMSO)) for each cell line-sgRNA-compound-dose-replicate combination. Matrix table with data for all samples.

molecule: genomic DNA

organism: Homo sapiens

source_name: Pool of 5 breast cancer cell lines

growth_protocol: Cell line pools were cultured in RPMI-1640, 10% Tet System Approved FBS, 1% Penicillin/Streptomycin, 100 ng/mL doxycycline for 7 days prior to compound treatment.

extract_protocol:
Cell line pools were lysed with lysis buffer (10% 10x Taq DNA Polymerase Buffer, 0.45% IGEPAL CA-630, 0.45% TWEEN 20, 10% Proteinase K, 79.1% Nuclease-Free Water) containing cell spike-in standards. Cells were incubated at 60°C for 1 hour. Proteinase K from lysis buffer was inactivated at 95°C for 15 minutes.
Barcoded region was PCR amplified with a unique set of indexed primers for each sample. PCR products were pooled and purified twice. Sequencing library was diluted, combined with PhiX, denatured, and sequenced on a NovaSeq 6000 (Illumina).

treatment_protocol: Cell line pools were treated with compound or DMSO over a four-point concentration range (10-fold dilutions) in duplicate using either a standard dose range (10 nM to 10 μM) or a low dose range (1 nM to 1 μM). Dose1=lowest dose. Dose4=highest dose. Cells were treated for 72 hours.

tag: cell lines

tag: sgrnas

value: sgNT, sgHSF1, sgHSF2, sgERN1, sgXBP1, sgATF3, sgATF4, sgATF6, sgNFE2L2, sgKEAP1, sgATG7, sgSLC35F2

tag: compound treatment


title: DMSOPlate1WellF3_Dose1_Rep1


title: NCH1681_DMSO_rep1

city: Heidelberg

first: Jongwhi

last: Park

address: INF 460

country: Germany

institute: Heidelberg university hospital

library_source: transcriptomic

data_processing:
fastq files were aligned to human reference genome hg19 using the STAR aligner
BAM files resulting from the alignments were summarized to genes using the featureCounts algorithm
Expression data was normalized and differentially expressed genes were analyzed using DESeq2 package
Genome_build: human reference genome hg19
Supplementary_files_format_and_content: excel file include log2(FC) and P-adj values for each sample

molecule: total RNA

source_name: glioma cells

growth_protocol: All cells were cultured in 5 % CO2 humidified incubator at 37 °C

extract_protocol:
Total RNA was isolated using the RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s protocol
RNA-seq libraries were created with TruSeq Stranded mRNA Library Prep Kit (Illumina)

treatment_protocol: Cells were treated with 500 nM DAC for 7 days prior to total RNA isolation

tag: cell line

value: glioma cells

tag: treatment

value: DMSO


title: NCH1681_DMSO_rep2


title: NCH612_DMSO_rep2


title: High PCB 21

type: RNA

city: Costa Mesa

first: Alvine

middle: C

last: Mehinto

address: 3535 Harbor Blvd, Suite 110

institute: Southern California Coastal Water Research Project

description: Gene expression, high PCB

hyb_protocol: Microarray hybridizations were conducted on an Agilent custom-designed 8 x 15K microarray.

scan_protocol: Raw microarray data were collected using an Agilent DNA microarray scanner and processed using Agilent Feature Extraction (FE) software v11.5.1.

data_processing: After evaluation of quality control, raw data were imported into GeneSpring v13 where they were quantile normalized and log2 transformed. Hepatic transcriptome analyses were conducted using a one-way analysis of variance (ANOVA) with a threshold of significance set at p < 0.05.  No FDR (false discovery rate) correction was applied in order to include as many genes as possible for pathway analyses. Hierarchical clustering analyses were conducted using the genes significantly different (p < 0.05; fold change > ±1.2) among treatments.

organism: Pleuronichthys verticalis

source_name: Liver, high PCB treatment group, Intraperitoneally injected with a mixture of PCBs (PCB49, 52, 66, 87, 99, 101, 105, 118, 138, 149, 153, 170, 180) at a dose of 10 µg/g body mass

label_protocol: Conversion of RNA to labelled cRNA was performed using Agilent’s Low Input Quick Amp Labeling kit and Agilent’s Gene Expression Hybridization kit according to the manufacturer’s instructions

extract_protocol: Total RNA was isolated using Trizol Plus RNA Purification kit (Life Technologies) according to the manufacturer’s instructions. RNA was quantified on a NanoDrop ND-8000 spectrophotometer (NanoDrop Technologies) and RNA integrity was determined using a TapeStation (Agilent). The average RNA integrity number equivalent (RINe) was 8.9 with individual RINe ranging between 7.1 and 9.2.

treatment_protocol: Hornyhead turbot (n = 7 – 9) were exposed to 0.5 µg/g body weight (bw) PBDEs, 5 µg/g bw PBDEs, 1 µg/g bw PCBs or 10 µg/g bw PCBs via a single intraperitoneal (IP) injection. The IP injections were performed at a volume of 2 ml oil/kg body. IP control fish received an injection of peanut oil only, while seawater (SW) control fish were not injected. After 96 hours, fish were sacrificed with a lethal dose of tricaine methanesulfonate (MS 222), and body weight and standard length were recorded. Fish livers were excised, a small piece was flash frozen in liquid nitrogen and stored at -80ᵒC for gene expression analyses

tag: Sex

value: Male

tag: tissue

value: Liver


title: DC-plus-WT-MOI05-6h

city: Jena

department: Systems Biology and Bioinformatics

institute: Hans-Knoell-Institute Jena

data_processing:
Quality and adapter trimming were performed using Trimmomatic version 0.36, including windows size trimming (size 15, Q25), 3’ ad 5’ quality clipping (Q3) and sequences with less than 30 bp were removed.
Read mapping was performed using HiSat2 with default parameters and -k 2.
Gene abunstance estimation (counting) was performed using featureCounts with default parameters.
Genome_build: GRCH38 89; Af293 s03-m05-r05
Supplementary_files_format_and_content: Gene abundance matrix was created by featureCounts based on the combined annotation of both organisms.

organism:
Homo sapiens
Aspergillus fumigatus

source_name: dendritic cells

extract_protocol:
Total RNA has been extracted and purified using the RiboPure RNA purification kit. Fragments were sequenced using Sequencing by synthesis (Illumina NextSeq 500).
RNA libraries were prepared for single-end sequencing using standard Illumina protocols.

value: DC; A. fumigatus ATCC 46645

tag: number of fungal cells

tag: sampling time point (hours)

tag: temperature

value: 37 degreeC

tag: atmosphere

value: 5percent  CO3

tag: compound

value: A. fumigatus ATCC 46645

tag: media

tag: parameter

value: rin/rna integrity number:8.2

value: concentration (ng/microliter):98.6

value: volume (microliter):71


title: DC-plus-WT-MOI1-6h

tag: cell type

value: rin/rna integrity number:7.8

value: concentration (ng/microliter):119.25

value: volume (microliter):70


title: Erlotinib_Dose1_Rep1


title: High PCB 25

description: Gene expression, high PCB


title: NCH612_DMSO_rep1


title: DMSOPlate1WellC3_Dose1_Rep1


title: DC-plus-WT-MOI05-4h

value: dendritic cells

tag: strainorline

value: rin/rna integrity number:8.5

value: concentration (ng/microliter):101.65

value: volume (microliter):67


title: SU-AO3_DAC_rep2

value: glioma cells

value: DAC


title: NCH612_DAC_rep2


title: DC-plus-WT-MOI1-4h

value: CellGro GMP serum-free DC medium

value: concentration (ng/microliter):99.62

value: volume (microliter):66


title: NCH612_DAC_rep1


title: Low PCB 52

description: Gene expression, low PCB

source_name: Liver, low PCB treatment group, Intraperitoneally injected with a mixture of PCBs (PCB49, 52, 66, 87, 99, 101, 105, 118, 138, 149, 153, 170, 180) at a dose of 1 µg/g body mass

value: Female

value: Liver


title: High PCB 17

description: Gene expression, high PCB

value: Male


title: Donor1_05_DC_plus_CMV_0h_plus_Afu_0h

data_processing:
Quality and adapter trimming were performed using Trimmomatic version 0.36, including windows size trimming (size 10, Q25), 3’ ad 5’ quality clipping (Q5) and sequences with less than 30 bp were removed.
Read mapping was performed using HiSat2 with default parameters.
Gene abunstance estimation (counting) was performed using featureCounts with default parameters.
Genome_build: GRCH38 89; Af293 s03-m05-r09; Human herpesvirus 5 strain TB40E clone TB40-BAC4
Supplementary_files_format_and_content: Gene abundance matrix was created by featureCounts based on the combined annotation of all 3 organisms.

organism:
Homo sapiens
Human betaherpesvirus 5
Aspergillus fumigatus

growth_protocol: CellGro GMP serum-free DC medium for up to 9h

extract_protocol:
Total RNA has been extracted and purified using the RiboPure RNA purification kit. Fragments were sequenced using Sequencing by synthesis (Illumina NextSeq 500).
RNA libraries were prepared for strand-specific sequencing using standard Illumina protocols.

value: DC; A. fumigatus ATCC 46645; Human herpesvirus 5 strain TB40/E clone TB40-BAC4

tag: number of fungal organisms (moi)

tag: samplingtimepoint (hours)

tag: rin/rna integrity number

tag: concentration (ng/ul)

tag: volume (ul)

tag: kit

value: RiboPure RNA purification kit

value: adapter ligation; strand specific


title: SU-AO3_DAC_rep1

tag: cell line

tag: treatment


title: Anastrozole_Dose1_Rep1

tag: cell lines

tag: sgrnas

value: sgNT, sgHSF1, sgHSF2, sgERN1, sgXBP1, sgATF3, sgATF4, sgATF6, sgNFE2L2, sgKEAP1, sgATG7, sgSLC35F2

tag: compound treatment


title: DC-plus-WT-MOI05-2h

value: DC; A. fumigatus ATCC 46645

tag: number of fungal cells

tag: sampling time point (hours)

tag: temperature

value: 37 degreeC

tag: atmosphere

value: 5percent  CO3

value: A. fumigatus ATCC 46645

value: rin/rna integrity number:8.2

value: concentration (ng/microliter):73.42

value: volume (microliter):63


title: Low PCB 39

description: Gene expression, low PCB

tag: Sex

tag: tissue


title: Low PCB 29

description: Gene expression, low PCB


title: SU-AO3_DMSO_rep2

tag: cell type

value: glioma cells

value: DMSO


title: DC-plus-WT-MOI1-2h

value: dendritic cells

tag: strainorline

tag: compound

tag: media

value: CellGro GMP serum-free DC medium

tag: parameter

value: rin/rna integrity number:8.1

value: concentration (ng/microliter):106.23

value: volume (microliter):62


title: SU-AO3_DMSO_rep1


title: Alisertib_Dose1_Rep1


title: Low PCB 33

description: Gene expression, low PCB

value: Male

value: Liver


title: Donor4_03_DC_plus_Afu_4h30min

tag: number of fungal organisms (moi)

tag: samplingtimepoint (hours)

tag: rin/rna integrity number

tag: concentration (ng/ul)

tag: volume (ul)

tag: kit

value: RiboPure RNA purification kit

value: adapter ligation; strand specific


title: Donor4_02_DC_plus_Afu_0h

value: DC; A. fumigatus ATCC 46645


title: TS603_DAC_rep1

tag: cell line

tag: treatment

value: DAC


title: Exemestane_Dose1_Rep1

tag: cell lines

tag: sgrnas

value: sgNT, sgHSF1, sgHSF2, sgERN1, sgXBP1, sgATF3, sgATF4, sgATF6, sgNFE2L2, sgKEAP1, sgATG7, sgSLC35F2

tag: compound treatment


title: Donor3_03_DC_plus_Afu_4h30min

tag: temperature

tag: atmosphere

value: A. fumigatus ATCC 46645


title: Low PCB 2

description: Gene expression, low PCB

tag: Sex

value: Female

tag: tissue


title: TS603_DMSO_rep2

tag: cell type


title: Donor3_02_DC_plus_Afu_0h

tag: strainorline

tag: compound

tag: media


title: Nelarabine_Dose1_Rep1


title: Abiraterone_Dose1_Rep1


title: Regorafenib_Dose1_Rep1


title: Donor2_03_DC_plus_Afu_4h30min

tag: number of fungal organisms (moi)

tag: samplingtimepoint (hours)

tag: rin/rna integrity number


title: High PBDE 44

description: Gene expression, high PBDE

source_name: Liver, High PBDE treatment group, Intraperitoneally injected with a mixture of PBDEs (BDE47, 99, 100) at a dose of 5 µg/g body mass


title: TS603_DMSO_rep1


title: Blebbistatin_Dose1_Rep1


title: High PBDE 4

description: Gene expression, high PBDE


title: Mitoxantrone_Dose1_Rep1


title: High PBDE 26

description: Gene expression, high PBDE


title: cel6SDHB1NORMTR

city: Budapest

first: István

last: Likó

address: Üllői út 26.

country: Hungary

institute: Semmelweis University

data_processing:
FASTQ Generation | Version: 1.0.0  on Illumina BaseSpaceFS version: 2.0.1018 system
Sequenced reads were trimmed for adaptor and low-quality sequence with trim_galore version 0.4.1 and cutadapt version 1.14
The trimmed sequence sets were aligned to the WBcel235 genome with TopHat v2.1.0 (bowtie2-align-s version 2.3.4.3), using default parameters
Performed union-exon based count with R Rsubread package version 1.34.7 , and count processing and rpkm calculation with R edgeR package version 3.26.8
Genome_build: C. elegans WBcel235 genome Ensembl release 94
Supplementary_files_format_and_content: tab-delimited text files include union-exon based RPKM values and annotation information for each Sample

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: whole worm mRNA extract

growth_protocol: C. elegans strains were maintained under standard conditions, on NGM plates seeded with OP50 bacteria at 20°C degrees.

extract_protocol:
The total nucleic acid extraction of wild-type and mutant animals was conducted by TRI Reagent® (Molecular Research Center, Inc, Cincinnati, Ohio USA) as recommended by the manufacturer. The crude extract was further purified with RNeasy Mini Kit (Qiagen, Hilden, Germany) using the manufacturer’s protocol. To remove DNA contamination which might interfere with downstream applications, Column DNase treatment with Qiagen RNase free DNase kit was applied. To purify pure mature polyA-tailed mRNA, we performed a magnetic bead based separation on the purified total RNA with NEB NEXT Poly(A) mRNA magnetic Isolation Module (New England Biolabs, Ipswich, MA, USA).  100 ng of mature polyA-tailed mRNA per sample was used to construct RNA-SEQ libraries.
NEB NEXT ULTRA II Directional RNA Library Preparation Kit (Illumina,San Diego, CA, USA)

value: whole worm

tag: condition

value: wild type L4 transgenic control

tag: age

value: L4 larvae

tag: genotype


title: Donor2_02_DC_plus_Afu_0h

value: dendritic cells

tag: concentration (ng/ul)

tag: volume (ul)

tag: kit


title: High PBDE 18

description: Gene expression, high PBDE

value: Immature


title: High PBDE 23

description: Gene expression, high PBDE


title: Cimetidine_Dose1_Rep1

tag: cell lines

tag: sgrnas

tag: compound treatment


title: cel3N2L4

tag: tissue

value: wild type L4 larvae

value: wild type


title: TS603_DAC_rep2

tag: cell line

tag: cell type

value: glioma cells

tag: treatment


title: NVPAUY922_Dose1_Rep1


title: Donor1_03_DC_plus_Afu_4h30min

tag: strainorline

tag: temperature

tag: atmosphere

tag: compound

tag: media

value: CellGro GMP serum-free DC medium


title: cel2N2L3

tag: condition

value: wild type L3 larvae

tag: age

value: L3 larvae


title: Donor4_07_DC_plus_Afu_0h_plus_CMV_2h

value: DC; A. fumigatus ATCC 46645; Human herpesvirus 5 strain TB40/E clone TB40-BAC4

tag: number of fungal organisms (moi)

tag: samplingtimepoint (hours)

tag: rin/rna integrity number

tag: concentration (ng/ul)

value: RiboPure RNA purification kit

value: adapter ligation; strand specific


title: RITA_Dose1_Rep1

tag: cell lines

tag: sgrnas

value: sgNT, sgHSF1, sgHSF2, sgERN1, sgXBP1, sgATF3, sgATF4, sgATF6, sgNFE2L2, sgKEAP1, sgATG7, sgSLC35F2


title: Low PBDE 51

description: Gene expression, low PBDE

source_name: Liver, Low PBDE treatment group, Intraperitoneally injected with a mixture of PBDEs (BDE47, 99, 100) at a dose of 0.5 µg/g body mass

tag: Sex

value: Male

tag: tissue

value: Liver


title: Low PBDE 5

description: Gene expression, low PBDE


title: Donor1_02_DC_plus_Afu_0h

tag: cell type

value: DC; A. fumigatus ATCC 46645

value: A. fumigatus ATCC 46645

tag: volume (ul)

tag: kit


title: cel1N2L2

value: whole worm

value: wild type L2 larvae

value: L2 larvae

tag: genotype


title: Cediranib_Dose1_Rep1

tag: compound treatment


title: cel5SDHB1PMTR

value: sdhb-1 R244H point mutant

value: L4 larvae


title: High PBDE 11

description: Gene expression, high PBDE


title: CSN5_RNA_Seq

city: Wuxi

first: Fengjiao

last: Ma

state: CHINA

address: No.69 Xuejia, Xuelang Street, Binhu District

country: China

institute: Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences

data_processing:
Prior to assembly, Cutadapt and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases.
Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). including the Q20, Q30 and GC-content of the clean data.
De novo assembly of the transcriptome was performed with Trinity 2.4.0.
Gene expression levels were measured by calculating TPM. The differentially expressed Unigenes were selected with log2 (fold change)>1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05).
Genome_build: FASTA file with assembled transcripts is available on the series record.
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample.

organism: Coilia nasus

source_name: gastric mucosa

extract_protocol:
The stomach of each individual was extracted, rinsed with pre-cooled deionized water,and total RNA of each sample fish was extracted from the stomachs of both feeding and control C. nasus using TRIzol reagent (Invitrogen, CA, USA) in accordance with the manufacturer’s instructions.
Twelve cDNA libraries were constructed using the mRNASeq Sample Preparation Kit (Illumina, San Diego, USA). And then transcriptome sequencing was carried out on an Illumina Hiseq 4000 platform (LC Sceiences, USA) that generated 300 bp (±50 bp) paired-end (PE) raw reads.

value: stomach

value: no food intake


title: CSN6_RNA_Seq


title: cel4SDHB1DELTR

value: sdhb-1 deletional mutant


title: Low PBDE 48

description: Gene expression, low PBDE

value: Female


title: CSN4_RNA_Seq


title: Thalidomide_Dose1_Rep1


title: CSN3_RNA_Seq


title: CSN2_RNA_Seq


title: Low PBDE 38

description: Gene expression, low PBDE


title: Dexamethasone_Dose1_Rep1


title: CSN1_RNA_Seq


title: Temozolomide_Dose1_Rep1


title: Bendamustine_Dose1_Rep1


title: PHA793887_Dose1_Rep1


title: Tacrolimus_Dose1_Rep1


title: CSI6_RNA_Seq

value: food intake


title: Low PBDE 13

description: Gene expression, low PBDE


title: Low PBDE 19

description: Gene expression, low PBDE


title: Low PBDE 12

description: Gene expression, low PBDE


title: Oil Control 8

description: Gene expression, vehicle control

source_name: Liver, Vehicle Control, Intraperitoneally injected with peanut oil at a volume of 2 mL/kg body mass


title: CSI5_RNA_Seq


title: Oil Control 49

description: Gene expression, vehicle control


title: Fracture [O-83]

city: Valencia

first: Miguel Angel

last: Garcia Perez

state: Comunidad Valenciana

address: Av. Menéndez Pelayo, 4 accesorio

department: Research Unit

country: Spain

institute: INCLIVA Health Research Institute

description: Gene expression data from primary osteoblast at confluence.

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Gene 2.0 ST Array. Arrays were washed and stained according to the EukGene_ws_2v5 in the Fluidics Station (Affymetrix)

scan_protocol: GeneChip scanner 3000

data_processing: Transcriptome Analysis Console (TAC) software (version 4.0.1) (Applied Biosystems) using default analysis settings and global scaling as normalization method.

label: biotin

source_name: Primary OB obtained from the femoral head of patients undergoing hip replacement due to osteoporotic fracture

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: The femoral head of patients was obtained during surgery and placed in a sterile bottle at 4ºC until processed once surgery was completed. Bone cylinders 1 cm in diameter were obtained from the central part of the femoral head with a trephine, avoiding the fracture zone. Once the cortical area was removed, cylinders were washed thoroughly with PBS supplemented with 1% Fungizone to remove bone marrow remains. The cylinders were then cut into discs about 2-3 mm thick and 3-4 bone fragments were seeded into T-25 plastic flasks containing Dulbecco's Modified Eagle's Medium, 20% FBS, 1% antibiotics and 1% Fungizone. Under these conditions OBs precursor cells can migrate from bone fragments and proliferate. After confluence, cells were trypsinized to obtain RNA.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: subject status

value: patients undergoing hip replacement

value: femoral head

tag: primary osteoblast (ob)

value: Fracture OB


title: Fracture [O-69]


title: Im-GCT-4072__A4__p13p16__G34W-repair__H3K27ac

city: Montreal

first: Nada

last: Jabado

state: Québec

address: 1001 Décarie Boulevard

department: Department of Pediatrics

country: Canada

institute: McGill University

description: Corresponding input is: Im-GCT-4072__A4__p13p16__G34W-repair__Input

data_processing:
The ChIP-seq pipeline from C3G’s GenPipes toolset6 (v3.1.0) was used to trim, merge and align ChIP-seq data. Clean reads were aligned to the human genome (hg19) using bwa-mem. Duplicates were marked using picardtools and samtools.  We used the “bamCoverage” functionality of deeptools (v3.1.3) to produce duplicate-depleted RPKM-normalized BigWig tracks
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

source_name: Tumor-derived cell-line

extract_protocol:
ChIP-seq was performed as previously described5. Briefly, cells were fixed with 1% formaldehyde (Sigma). Fixed cell preparations were washed, pelleted and stored at −80 °C. Sonication of lysed nuclei (lysed in a buffer containing 1% SDS) was performed on a BioRuptor UCD-300 for 60 cycles, 10s on 20s off. Samples were checked for sonication efficiency using the criteria of 150–500 bp by gel electrophoresis. After sonication, the chromatin was diluted to reduce SDS level to 0.1% and before ChIP reaction 2% of sonicated Drosophila S2 cell chromatin was spiked-in the samples.  ChIP reaction for histone modifications was performed on a Diagenode SX-8G IP-Star Compact using Diagenode automated Ideal ChIP-seq Kit. Twenty-five microliter Protein A beads (Invitrogen) were washed and then incubated with antibodies (anti-H3K27me3 (1:40, CST 9733), (anti-H3K27ac (1:80, Diagenode C15410196)), (anti-H3K36me3 (1:100, Active Motif 61021)), (anti-H3.3 (1:66, Millipore 09–838)), (anti-H3.3G34W (1:100, RevMAb 31-1145-00)), (anti-H3K36me2 (1:50, CST 2901)), (anti-H3K9me3 (1:66, Abcam 8898)), and 2 million cells of sonicated cell lysate combined with protease inhibitors for 10 h, followed by 20 min wash cycle with provided wash buffers.   Reverse cross linking took place on a heat block at 65°C for 4 h. ChIP samples were then treated with 2 µl RNase Cocktail at 65°C for 30 min followed by 2 µl Proteinase K at 65°C for 30 min. Samples were then purified with QIAGEN MiniElute PCR purification kit as per manufacturers’ protocol. In parallel, input samples (chromatin from about 50,000 cells) were reverse crosslinked and DNA was isolated following the same protocol.
Library preparation was carried out using Kapa HTP Illumina library preparation reagents, following manufacturer’s instructions. Briefly, 25 µl of ChIP sample was incubated with 45 µl end repair mix at 20°C for 30 min followed by Ampure XP bead purification. A tailing: bead bound sample was incubated with 50 µl buffer enzyme mix at 30°C for 30 min, followed by PEG/NaCl purification. Adaptor ligation: bead-bound sample was incubated with 45 µl buffer enzyme mix and 5 µl of TruSeq DNA adapters (Illumina), for 20°C 15 min, followed by PEG/NaCl purification (twice). Library enrichment: 12 cycles of PCR amplification. Size selection was performed after PCR using a 0.6 × /0.8x ratio of Ampure XP beads (double size selection) set to collect 250–450 bp fragments. 50-bp single end sequencing was performed on the Illumina HiSeq 2500/4000 platforms, whereas paired-end sequencing was peformed on the Illumina NovaSeq 6000 S4 platform.

value: G34W repair to WT

tag: cell line

tag: chip antibody

value: H3K27ac (Rabbit polyclonal/Diagenode C15410196)


title: CSI4_RNA_Seq

tag: condition


title: Oil Control 47

description: Gene expression, vehicle control

value: Male

value: Liver


title: Fracture [O-75]


title: Im-GCT-4072__U3__T14__G34W-unedited__H3K27ac

description: Corresponding input is: Im-GCT-4072__E3__p14__G34W-repair__Input

value: G34W unedited


title: Im-GCT-4072__A4__p13p16__G34W-repair__Input


title: CSI3_RNA_Seq


title: Fracture [O-65]


title: Oil Control 45

description: Gene expression, vehicle control


title: Oil Control 20

description: Gene expression, vehicle control

value: Immature


title: Im-GCT-4072__E3__p14__G34W-repair__Input


description: Corresponding input is: Im-GCT-4072__D6__p18p24__G34W-repair__Input


title: Osteoarthritis [C-79]

source_name: Primary OB obtained from the femoral head of patients undergoing hip replacement due to severe osteoarthritis.

value: Osteoarthritis OB


title: CSI1_RNA_Seq


title: Fracture [O-64]


title: Fracture [O-66]


description: Corresponding input is: Im-GCT-4072__U3__T14__G34W-unedited__Input


title: F2 CONTROL nr 39

city: Palavas

first: Mélanie

last: Blanc

address: Route de Maguelone

department: UMR MARBEC

country: France

institute: INRAE

data_processing:
Illumina Real Time Analysis (RTA) software used for basecalling.
bcl2fastq for demultiplexing to remove Illumina control PhiX sequences
cutadapt 2.1 for trimming of adaptor sequences
STAR 2.7 for alignment of the reads to DanRer11 whole genome with default parameters
Counts of reads per gene were obtained with HTSeq v0.11.2 (gtf annotation file GRCz11.97)
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Use of DESeq2 v1.24.0 for differential gene expression analysis
Genome_build: DanRer11
Supplementary_files_format_and_content: txt file including raw counts obtained from htseq (unnormalized).

organism: Danio rerio

source_name: adult whole brain

extract_protocol:
Fish were euthanized, brains were dissected and flash frozen in liquid nitrogen, and RNA was extracted using Rneasy Universal Mini kit protocol (Qiagen). Illumina TruSeq mRNA Sample Prep Kit  was used with X ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: line

value: TU

tag: developmental stage

value: adult

value: whole brain

tag: generation

tag: treatment

value: CONTROL


title: Im-GCT-4072__2B2__T19__G34W-unedited__Input.

description: Corresponding input is: Im-GCT-4072__2B2__T19__G34W-unedited__Input


description: Corresponding input is: Im-GCT-4072__parental__p21__G34W-parental__Input


title: F2 CONTROL nr 31


title: F2 CONTROL nr 27


title: apo-treated WT rep 3

city: New York

first: Christopher

middle: E

last: Mason

address: 1305 York Ave

department: Physiology and Biophysics

institute: Weill Cornell Medical College

data_processing:
Reads were aligned with default parameters to the mouse reference genome (mm10) using STAR. Gene expression estimates were obtained with Homer and EdgeR using composite gene models (union of the exons of all transcript isoforms per gene) from analyzeRepeats.pl rna mm10 -strand both -count exons -condenseGenes.
Differentially expressed genes (DEG) were determined with Homer and EdgeR
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw abundance values for each sample as obtained from featureCounts

organism: Mus musculus

source_name: bone marrow

extract_protocol:
Phlebotomy was performed via retro-orbital puncture with an average total of 0.4 mL of blood removed over two days; mice were sacrificed 24 hours after the second phlebotomy.  Total RNA was extracted from freshly sorted bone marrow Pro-E as above and stored at -80C until processing
The library preparation was performed using polyA+ enriched RNA according to the manufacturer's instructions (Illumina) and then sequenced on a Solexa sequencing cell.

treatment_protocol: Mice were injected IP with 10 mg (400 mg/kg/day) of human apo-transferrin (Kamada, Israel) or equal volume (200 ul) PBS for 20 days, sacrificed 3 days following the last injection. Bone marrow cells were sorted as per Chen PNAS 2009 and pro-erythroblasts collected for RNA extraction.

tag: strain

value: sorted bone marrow pro-erythroblasts

tag: age

value: 5 month old


title: Im-GCT-4072__A4__p13p16__G34W-repair__SUZ12


title: Seawater Control 7

description: Gene expression, vehicle control

source_name: Liver, Seawater Control

tag: Sex

tag: tissue


title: Seawater Control 6

description: Gene expression, uninjected control

value: Female


title: F2 CONTROL nr 25


title: CSI2_RNA_Seq

value: stomach

value: food intake


title: Oil Control 15

description: Gene expression, vehicle control


title: Osteoarthritis [C-57]

value: patients undergoing hip replacement

value: femoral head


title: Osteoarthritis [C-73]


title: PBS-injected th1/th1 rep 3

value: wild type


title: PBS-injected WT rep 3


title: Osteoarthritis [C-68]


title: F2 CONTROL nr 21


title: Im-GCT-4072__E3__p14__G34W-repair__SUZ12

value: G34W repair to WT


title: Seawater Control 35

description: Gene expression, uninjected control

value: Male

value: Liver


title: Seawater Control 46

description: Gene expression, uninjected control


title: Seawater Control 24

description: Gene expression, uninjected control


title: Im-GCT-4072__D6__p28p24__G34W-repair__SUZ12


title: small_RNA_oblong_2

city: Copenhagen

first: Nicolai

last: Krogh

address: Blegdamsvej 3B

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

description:
Whole cell RNA from tissue
Ion GeneStudio S5
There is no processed data for the small_RNA*fastq samples. Reads were used directly from the fastq file to search for genomic genes.

data_processing:
Library strategy: RiboMeth-seq
Barcode separation using python script
Adaptor trimming using Cutadapt v. 2.0
Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1
Counting read ends and calculating RiboMeth-seq scores using python scripts
The output FASTA files from small RNA-seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially, SNORDs were identified by running the merged FASTA file through snoScan (Schattner et al. 2005) against zebrafish early- and late-rRNA reference sequences (Locati et al. 2017).
Genome_build: early and late zebrafish rRNA (locati et al). The reference sequences are available in the FASTA file on the series record.
Supplementary_files_format_and_content: MS Excel file contains 5' and 3' read count and calculated RiboMeth-seq score at all positions in the rRNA sequence.

source_name: oblong

extract_protocol:
Tissues were homogenized and whole cell RNA was extracted using Qiazol (Qiagen) according to the manufacturer.
For small RNA library construction, one  ug of whole-cell RNA was subjected to rRNA depletion using the RiboMinusT Eukaryote System v2 (Invitrogen), and small RNA libraries were constructed using Ion Total RNA-Seq Kit v2 (ThermoFisher Scientific) with minor modifications. In short, the rRNA-depleted RNA samples were enriched for small RNA (<200 nt) using the magnetic bead clean-up module supplied with the kit or MonarchR RNA Cleanup Kit (New England Biolabs), adapters diluted 1:2 were ligated to the RNA for 2 h and the RNA subsequently reverse transcribed using Superscript IV (ThermoFisher Scientific). The cDNA was purified using the magnetic bead clean-up module, without size-selection. Amplification of cDNA and purification was performed according to the manufacturer. Manual template preparation of libraries was carried out on the Ion OneTouchTM 2 System (ThermoFisher Scientific) and sequenced on Ion 540TM chips the Ion GeneStudio S5 System.

value: oblong

tag: rna fraction

value: whole cell RNA depleted for rRNA and size selected for RNA < 200 nt


title: Osteoarthritis [C-56]

value: Osteoarthritis OB


title: F2 CONTROL nr 11 run 2

description:
F2_S11_2
second run to increase the number of reads

value: TU

value: adult


title: Seawater Control 50

description: Gene expression, uninjected control


title: apo-treated th1/th1 rep 3


title: Im-GCT-4072__U3__T14__G34W-unedited__SUZ12

value: G34W unedited


title: small_RNA_oblong_1


title: Seawater Control 22

description: Gene expression, uninjected control


title: apo-treated WT rep 2

value: sorted bone marrow pro-erythroblasts


title: small_RNA_32_cell

source_name: 32-cell stage

value: 32-cell stage


title: Im-GCT-4072__2B2__T19__G34W-unedited__SUZ12


title: F2 TREATED nr 38 run 2

description:
F2_M38_2
second run to increase the number of reads

value: whole brain

value: TREATED


title: PBS-injected th1/th1 rep 2

value: 5 month old


title: Im-GCT-4072__parental__p21__G34W-parental__SUZ12


title: Osteoarthritis [C-51]

value: patients undergoing hip replacement


title: PBS-injected WT rep 2


title: small_RNA_15E


title: apo-treated th1/th1 rep 2


title: F2 TREATED nr 30


title: Im-GCT-6176__parental__p16__G34W-parental

data_processing:
Trimmomatic14 (v0.32) was used to remove adaptor sequences as well as the first four nucleotides of each read. Reads were truncated when the average quality (phred33) of a 4-nucleotide sliding window fell below 30. Short reads (<30bp) were discarded. Multiple quality control metrics were obtained using FASTQC (v0.11.2), samtools15 (v0.1.19), BEDtools16 (v2.17.0) and custom scripts.  The remaining read sets were aligned to the reference genome build hg19 (GRCh37) using the default parameters of STAR17 (v2.3.0e). Primary alignments of reads mapping to 9 or fewer locations in the genome were retained, and the rest was discarded. We quantified gene expression by counting the number of reads (primary alignments; MAPQ>3) over genes described in Ensembl’s ensGene “exon” reference (GRCh37; n=60234 genes) using featureCounts18 (v1.4.4). Bigwig tracks from BAM files were generated and normalized to library depth using BEDtools16 (v2.17.0) and UCSC tools and visualized using Integrative Genomic Viewer (IGV)13.
Genome_build: hg19
Supplementary_files_format_and_content: tab separated values containing raw or RPKM-normalized raw read counts

extract_protocol:
Total RNA was extracted from cell pellets using the Aurum Total RNA Mini Kit (Bio-Rad) according to manufacturer’s instructions.
Library preparation was performed with ribosomal RNA (rRNA) depletion according to instructions from the manufacturer (Epicentre) to achieve greater coverage of mRNA and other long non-coding transcripts. Paired-end sequencing was performed on the Illumina HiSeq 4000 and Illumina NovaSeq 6000 S4 platforms.


title: apo-treated WT rep 1


title: RCH2_input_1

city: Berkeley

first: Alexey

last: Kazakov

state: CA

address: 1 Cyclotron Road

department: Environmental Genomics and Systems Biology Division

institute: Lawrence Berkeley National Laboratory

description:
adaptor-ligated sheared genomic DNA
RCH2_input_1_S49_L002

data_processing:
library strategy: DAP-seq
Read trimming using Trimmomatic
Alignment using Bowtie
Peak calling using SPP
Closest features were called using dap-seq-utils(https://github.com/novichkov-lab/dap-seq-utils)
Genome_build: GCF_000327065.1, GCF_001623525.1, GCF_000007565.2, GCF_001307275.1
Supplementary_files_format_and_content: wig

organism: Stutzerimonas stutzeri

source_name: purified genomic DNA from liquid cultures

growth_protocol: Pseudomonas strains were cultured in either LB or minimal media.

extract_protocol:
Genomic DNA was extracted with Promega wizard genomic kit according to the manufacturers protocols for gram negative bacteria. 6XHIS-tagged DNA-binding response regulator proteins were heterologously expressed in E. coli, purified with metal affinity resin, and mixed with 60 uL DNA binding buffer before elution. DNA binding buffer contained  0.4 ng/uL sheared adapter-ligated Pseudomonas genomic DNA, 10 mM imidazole, 0.1% Tween20 with or without 50 mM acetyl phosphate in TBS buffer pH 7.4. To enrich for specific protein-DNA interactions, resin bound protein-DNA was washed in a low concentration of imidazole before elution in a high concentration of imidazole. DNA was then amplified with index primers and sequenced with Illumina NovaSeq 6000.
DNA libraries were prepared for sequencing using a protocol from Chiniquy et al., BMC Genomics, 2020.

value: untreated


title: PBS-injected th1/th1 rep 1

value: wild type


title: F2 TREATED nr 28

value: Female


title: F2 TREATED nr 38

value: Male


title: RCH2_input_2

description:
adaptor-ligated sheared genomic DNA
RCH2_input_2_S61_L002


title: Psest_4267_3

description:
adaptor-ligated sheared genomic DNA bound by phosphorylated Psest_4267
Psest_4267_3_S92_L002

value: 50 mM acetyl phosphate

tag: protein


title: F2 TREATED nr 28 run 2

description:
F2_M28_2
second run to increase the number of reads


title: Psest_4267_4

description:
adaptor-ligated sheared genomic DNA bound by phosphorylated Psest_4267
Psest_4267_4_S93_L002


title: Im-GCT-6176__parental__p15__G34W-parental

tag: genotype


title: PBS-injected WT rep 1


title: F2 TREATED nr 24


title: F2 CONTROL nr 11

value: CONTROL


title: Im-GCT-6176__U12__p16__G34W-unedited


title: Psest_4267_2

description:
adaptor-ligated sheared genomic DNA bound by Psest_4267
Psest_4267_2_S91_L002


title: Im-GCT-6176__2C2__p20__G34W-repair

value: G34W repair to WT


title: F2 TREATED nr 10


title: apo-treated th1/th1 rep 1


title: Im-GCT-6176__2C2__p14__G34W-repair


title: Psest_4267_1

description:
adaptor-ligated sheared genomic DNA bound by Psest_4267
Psest_4267_1_S90_L002


title: F2 TREATED nr 6


title: Psest_4132_4

description:
adaptor-ligated sheared genomic DNA bound by phosphorylated Psest_4132
Psest_4132_4_S81_L002


title: Im-GCT-6176__1G9__p14__G34W-KO


title: Im-GCT-6176__U12__p17__G34W-unedited


title: CDT04ANXX.3.1

first: Alec

last: Kimmelman

address: 550 1st Avenue

department: Department of Radiation Oncology, Perlmutter Cancer Center

institute: NYU School of Medicine

data_processing:
Counts were determined using the PoolQ Version 2 software from the Broad Institute.
Genome_build: GRCm38
Supplementary_files_format_and_content: B6_scores-FP_GPP414_Aguirre_2018_07_25_P1_SP20180806.txt: tab-delimited file containing raw counts for the 2D culture and B6 mouse condtiions
Supplementary_files_format_and_content: B6_scores-FP_GPP414_Aguirre_2018_07_25_P2_SP20180806.txt: tab-delimited file containing raw counts for the 2D culture and B6 mouse condtiions
Supplementary_files_format_and_content: Nude_scores-FP_GPP526_20181130_Aguirre_sgRNA_DB1.txt: tab-delimited file containing raw counts for the Nude mouse condtiions
Supplementary_files_format_and_content: scores-FP_GPP817_Biancur_sgRNA_20190813_reseq.txt: tab-delimited file containing raw counts for the 3D mouse condtiions
Supplementary_files_format_and_content: FP_GPP414_Aguirre_CP1195_2018-07-31_sgRNA_Plate2.csv: csv file matching the barcode sequence to column headers for B6_scores-FP_GPP414_Aguirre_2018_07_25_P2_SP20180806.txt
Supplementary_files_format_and_content: FP_GPP526_Aguirre_CP1195_2018-12-11_sgRNA_DB1.csv: csv file matching the barcode sequence to column header for Nude_scores-FP_GPP526_20181130_Aguirre_sgRNA_DB1.txt
Supplementary_files_format_and_content: FP20190828-GPP817_Biancur_sgRNA.csv: csv file matching the barcode sequence to column header for scores-FP_GPP817_Biancur_sgRNA_20190813_reseq.txt
Supplementary_files_format_and_content: FP_GPP414_Aguirre_CP1195_2018-07-31_sgRNA_Plate1.csv: csv file matching the barcode sequence to column headers for B6_scores-FP_GPP414_Aguirre_2018_07_25_P1_SP20180806.txt

source_name: Pancreatic Cancer

growth_protocol: A custom library of lentiviral vectors encoding ~18,000 sgRNAs targeting ~3,000 mouse metabolic genes and performed CRISPR-Cas9 screens using a C/57BL6 (B6) mouse pancreatic cancer cell line derived from a KrasG12D-driven autochthonous PDA model. After transduction and selection, parallel screens were performed by in vitro passage or tumor implantation subcutaneously into the flanks of syngeneic hosts. Genomic DNA was then harvaested in vitro after 7 passages (21 days in culture) and in vivo 21 days after implantation.

extract_protocol:
RNA harvested using trizol extraction and Invitrogen purelink mRNA kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: growth condition

value: mixed sample (non-demultiplexed)

value: WT

value: KrasG12D-driven autochthonous PDA model


title: CCVVNANXX.3.1


title: F0 CONTROL nr 33 run 2

description:
F0_S33_2
second run to increase the number of reads

value: TU

value: adult


title: Im-GCT-6176__1G9__p13__G34W-KO


title: Psest_4132_3

description:
adaptor-ligated sheared genomic DNA bound by phosphorylated Psest_4132
Psest_4132_3_S80_L002


title: F0 CONTROL nr 33


title: Im-GCT-6176__1F4__p21__G34W-repair


title: F0 CONTROL nr 31 run 2

description:
F0_S31_2
second run to increase the number of reads


title: Im-GCT-6176__1F4__p15__G34W-repair


title: Psest_4132_1

description:
adaptor-ligated sheared genomic DNA bound by Psest_4132
Psest_4132_1_S78_L002


title: F0 CONTROL nr 31


title: RNA-seq_AR6_Gfap-Cre_Wlsfl+_RP2

city: Baltimore

first: Amir

last: Rattner

state: MD - Maryland

address: 725 North Wolfe St.

institute: Johns Hopkins University

data_processing:
RNA-Seq: Read alignment to the mm10 reference mouse genome sequence was performed with the RSEM-1.3.0 program (Li and Dewey, 2011) using the Bowtie2-2.2.9 aligner (Langmead and Salzberg, 2012).  Differential gene expression analysis was performed with EBseq 1.24.0 (Leng et al., 2013).
snRNA-Seq: Reads were aligned to a mm10 pre-mRNA index using Cellranger version 3.1.0.  Libraries were merged using Cellranger and data was analyzed using both the Monocle 3 (Qiu et al., 2017).

source_name: Adult control hippocampus

extract_protocol: RNA from both hippocampi from a single male mouse was extract with TRIzol (Invitrogen 15596026) followed by purification with the RNeasy Mini kit (QIAGEN 74104).  Libraries were constructed with the NEBNExt Ultra II directional library prep kit (NEB E7760L)

value: hippocampus

value: Gfap-Cre;Wlsfl/+


title: CCKNPANXX.4


title: Healthy_PBMC_4

city: Ann Arbor

first: Marina

last: Pasca Di Magliano

state: MI

address: 1500 E Medical Center Dr.

institute: University of Michigan

data_processing:
Samples were run using paired end 50 cycle reads on HiSeq 4000 or the NovaSeq 6000 (Illumina) to a depth of 100,000 reads.
The raw data were processed and aligned by the University of Michigan DNA Sequencing Core. Cellranger count version 3.0.0 with default settings was used, with an initial expected cell count of 10,000. In all casesthe hg19 reference supplied with the cellranger software was used for alignment.
Genome_build: Genome Reference Consortium Human Build 37 (GRCh37)
Supplementary_files_format_and_content: Zipped .tar containing .mtx.gz, and .tsv.gz files for reading into R using the Seurat Pipeline

source_name: PBMC

extract_protocol:
Tissues  were  mechanically  minced  and  enzymatically  digested  with  collagenase  P (1mg/mL DMEM) and subsequently filtered through a 40µm mesh to obtain single cells. Dead cells were removed using MACS®Dead Cell Removal Kit (Miltenyi Biotec Inc.).
Single-cell cDNA libraries were  prepared  and sequenced using  the  10x Genomics  Platform

value: Healthy Control


title: Healthy_PBMC_3


title: RNA-seq_AR4_Gfap-Cre_Wlsfl+_RP1


title: Psest_3845_3

description:
adaptor-ligated sheared genomic DNA bound by phosphorylated Psest_3845
Psest_3845_3_S68_L002


title: F0 CONTROL nr 25

value: whole brain


title: F0 CONTROL nr 15


title: Psest_3845_2

description:
adaptor-ligated sheared genomic DNA bound by Psest_3845
Psest_3845_2_S67_L002


title: F0 CONTROL nr 9


title: RNA-seq_AR5_Gfap-Cre_Wlsfl-_RP2

source_name: Adult mutant hippocampus

value: Gfap-Cre;Wlsfl/-


title: RNA-seq_AR3_Gfap-Cre_Wlsfl-_RP1


title: Healthy_PBMC_1


title: F0 CONTROL nr 3


title: PDAC_PBMC_14

value: Treatment Naïve PDA


title: Healthy_PBMC_2


title: CCKNPANXX.5.1


title: Psest_3845_1

description:
adaptor-ligated sheared genomic DNA bound by Psest_3845
Psest_3845_1_S66_L002

value: untreated


title: Psest_4132_2

description:
adaptor-ligated sheared genomic DNA bound by Psest_4132
Psest_4132_2_S79_L002


title: F0 TREATED nr 38

value: TREATED


title: F0 TREATED nr 36 run 2

description:
F0_M36_2
second run to increase the number of reads

value: Male


title: Psest_3845_4

description:
adaptor-ligated sheared genomic DNA bound by phosphorylated Psest_3845
Psest_3845_4_S69_L002

value: 50 mM acetyl phosphate


title: PDAC_PBMC_12


title: PDAC_PBMC_11


title: delta_pspA_3

city: Wenzhou

first: Ya-Ni

last: Mou

state: China

address: Chashan University Town, Ouhai District, Wenzhou City, Zhejiang Province

institute: Wenzhou Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Beauveria bassiana

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. Total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ARSEF 2860

value: hyphal

tag: characteristics

value: genotype:pspA mutant


title: WT-1

value: genotype:wild type


title: MDTH high performer #1 [7_mdth_44_AGTCAA]

city: Ithica

first: Praveen

last: Sethupathy

state: NY

address: Cornell University College of Veterinary Medicine, Box 17

institute: Cornell University

data_processing:
RNA-seq samples were aligned using STAR, quantified using Salmon, and normalized counts were determined using DESeq2
Genome_build: m38.p4
Supplementary_files_format_and_content: Normalized counts files are comma separated value matrices containing the DESeq2 normalized counts for each of the samples.

source_name: MDTH high performer

extract_protocol: Libraries were prepared according to the Illumina TruSeq stranded mRNA LT sample preparation kit.

tag: mouse group

value: high performing mouse

value: mouse MDTH


title: PFC low performer #3 [1_PFC65_TGACCA]

source_name: PFC low performer

value: low performing mouse

value: prefrontal cortex (PFC)


title: WT-3


title: F0 TREATED nr 24

value: TU

value: adult


title: PFC low performer #2 [1_PFC136_CGATGT]


title: delta_pspA_2


title: WT-2


title: F0 TREATED nr 36

value: whole brain


title: PDAC_PBMC_10B

description: Samples 10A and 10B are from the same patient, processed at two different core facilities


title: F0 TREATED nr 16 run 2

description:
F0_M16_2
second run to increase the number of reads


title: PFC low performer #1 [1_PFC130_ACAGTG]


title: PDAC_PBMC_9


title: delta_pspA_1


title: MDTH high performer #3 [9_mdth_165_ATGTCA]


title: MDTH low performer #3 [1_MDTH6_CAGATC]

source_name: MDTH low performer


title: MDTH low performer #2 [1_MDTH163_GCCAAT]


title: F0 TREATED nr 16


title: F0 TREATED nr 10


title: IMX-101_40mg-L_RepD

city: Vicksburg

first: Kurt

middle: A

last: Gust

state: MS

address: 3909 Halls Ferry Rd.

department: Environmental Laboratory

institute: US Army ERDC

description:
5 tadpoles per replicate
IMX-101_processed_GS1.txt
All Sequence Runs for GEO.txt

data_processing:
Analysis of RNA-seq data:  Multiplexed reads were stored as bcl files by the sequencer using a unique barcode as an indicator for each sample. Multiplexed reads were demultiplexed to fastq files matching their respective samples using bcl2fastq v1.8.4 from Illumina.  Next, the bioinformatics team at the US Army Engineer Research and Development Center in Vicksburg, MS, USA utilized the Rana pipiens transcriptome library described in section 2.8 to annotate RNAseq reads and map all to this reference transcriptome.  The transcriptome was indexed and reads were quantified at the transcript level using Salmon software (Patro et al 2017). To facilitate the analysis in Salmon, a Docker image was created and can be downloaded from: https://hub.docker.com/r/datasciburgoon/mrna_seq_workflow/.  The majority of the sequence-read results (62 out of 72 samples) consisted of two technical replicate read-sets for each biological sample.  In the event that two technical replicates were available, the mean of the technical replicates was calculated for each true replicate which was then used for subsequent transcript expression analyses.
Differential transcript expression analysis:  For each exposure experiment (TNT, IMX-101, NQ and MeNQ), the quantified RNA-seq data were normalized to the 75th percentile within each replicate followed by median scaling among all treatment replicates using GeneSpring Software version GX14.5 (Agilent Technologies, Santa Clara, CA, USA).  GeneSpring was also used to conduct statistical analyses to identify differentially expressed transcripts (DET) among treatments.  One-way ANOVA with Benjamini-Hochberg multiple-test corrected p = 0.05 was used to identify transcripts having significant differential expression for each exposure experiment.  Post-hoc tests within each exposure experiment was conducted using a moderated t-test (p = 0.05) and log2 fold change cutoff of ≥ 1.5 to discern statistically significant differences in transcript expression for each chemical exposure concentration relative to the control.
Pathway and annotation enrichment:  Annotation of the 19,128 uniquely annotated transcript sequences represented in the Rana pipiens transcriptomic library primarily matched to homologous genes in the African clawed frogs of the genus Xenopus (X. laevis and X. tropicalis).  The database for annotation, visualization and integrated discovery (DAVID, version 6.8, Huang et al 2009) was used to conduct statistical enrichment analysis where significant annotation clusters as well as significantly enriched pathways and protein domains were derived based on gene-transcripts that had significant differential expression within each exposure.  Given that the Xenpus genomes provided the best homolog match for nearly all transcript annotations within the R. pipiens transcriptome, Xenopus sp served as the “background” transcriptome for the enrichment analyses.  Annotation clusters included gene ontology, canonical pathway and protein motif annotations provided an integrated suite of classifications within each significant cluster.  Pathway enrichment tests were derived for the full suite of Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways.  The significantly enriched annotation clusters and KEGG pathways were used to posit categorical matches to summary exposure-responses as well as matches to the toxicological phenotypes identified in each exposure.
Genome_build: Transcriptome Library Annotation for R. pipiens.  A transcriptome library for R. pipiens was leveraged from a study by Christenson et al (2014, https://doi.org/10.7150/jgen.9760) where the assembled transcriptome sequences we re-annotated prior to RNAseq-based transcript quantification.  All sequences in the transcriptome library were searched against the NCBI Genbank protein database using blastx where E ≤ 10-5 was considered a significant match.  A total of 28,007 unique annotations met the significance criterion and were used as the foundational transcriptome sequence reference and annotation set for RNAseq-based expression analyses
Supplementary_files_format_and_content: Quantification of sequence reads against the annotated transcriptome for R. pipiens.  The "All Sequence Reads…" file includes all sequence reads.  All other files provide values for the mean of the 2 technical replicate sequence runs for each biological sample.
Supplementary_files_format_and_content: tab delimited text files

organism: Lithobates pipiens

source_name: whole body tissue

growth_protocol: The R. pipiens eggs were obtained from a commercial supplier (Nasco, Fort Atkinson, WI, USA) and hatched in the laboratory.  R. pipiens tadpoles were fed ad libitum once a day a commercially available frog brittle for tadpoles (Nasco), and their diet was supplemented with washed organic lettuce.  R. pipiens were 7 to 10 d old at the initiation of each experiment where the cohort of experimental animals all hatched within 24-h of one another.  Dilution and control water for all treatments was Vicksburg, MS municipal tap water dechlorinated using activated carbon filtration.

extract_protocol:
Total RNA was extracted from whole tadpoles for all transcript expression experiments.  The same 5 individuals sampled per replicate for microbiome characterization were utilized in the RNAseq analysis for a total of 4 true replicates.  Each tadpole sample was individually flash frozen in liquid nitrogen and stored in a -80°C freezer.  RNA was extracted by homogenizing each individual tadpole in lysis buffer with a disposable pestle before RNA isolation with RNeasy mini kits (Qiagen, Valencia, CA). Total RNA concentrations were measured using a NanoDrop One Spectrophotometer (NanoDrop technologies, Wilmington, DE, USA). The integrity of total RNA for each tadpole was assessed on an Agilent 2100 Bioanalyzer (Palo Alto, CA).  Criteria for acceptable RNA integrity included a RNA integrity number > 7.0 from the Agilent 2100 Bioanalyzer and a 260/280 spectrophotometric reading > 2.0, a requirement enforced on each subsampled tadpole within the exposure replicate.  Tadpoles not meeting this requirement were not included in the pooled exposure replicate.
RNAseq-based global transcriptomic expression assays were conducted for each of the munitions exposures.  The TNT exposure included control, 1.5, 2.3, and 3.4 mg/L exposures; IMX-101 included control, 10, 20, and 40 mg/L; NQ included control, 30, 150, 750 and 3750 mg/L exposures; and finally, MeNQ included control, 34, 170,  851, and 4225 mg/L exposures (nominal concentrations).  All RNA samples were shipped on dry ice to the US Army, Center for Environmental Health Research (USACEHR) for sequencing.  Once received, the total RNA samples were diluted, quantified using the Nanodrop 8000 spectrophotometer (Thermo Scientific, Waltham, MA), and 100ng total RNA was used to prepare libraries for sequencing using the TruSeq Stranded mRNA LT Sample Preparation Kit (Illumina, San Diego, CA, USA) following the manufacturer’s instructions.  Briefly, poly-A mRNA molecules were purified, fragmented, and copied into first strand cDNA.  Then the second strand cDNA was synthesized, the 3’ ends were adenylated, single-index adapters were ligated onto the cDNA, and the products were enriched with PCR and purified to create the final cDNA library.  The quality of the libraries were determined using the D1000 ScreenTape on the Agilent TapeStation 4200 (Agilent Technologies, Santa Clara, CA, USA).  Libraries were then size selected using SPRIselect beads (Beckman Coulter Life Sciences, Indianapolis, IN) and quantified by the dsDNA HS Kit on the Qubit 3.0 Fluorometer (Invitrogen, Carlsbad, CA, USA).  Next, the libraries were normalized, pooled (8 libraries per lane), and quantified using the dsDNA HS Kit on the Qubit 3.0 Fluorometer, followed by sequencing 1x150 cycles single-read on an Illumina HiSeq 4000 platform (Illumina) using the Illumina HiSeq 3000/4000 SBS kit following the manufacturer’s instructions.

treatment_protocol: The energetic compounds IMX-101 and TNT were obtained from the Holston Army Ammunition Plant (Kingsport, TN, USA).  NQ was obtained from Sigma-Aldrich (St. Louis, MO, USA; product number N17351) and MeNQ was obtained from TCI America (Portland, OR, USA; product number M0749). Due to low solubility in water, TNT was spiked into water using a “shell coating” technique (Allred and Giesy 1985) in which the TNT was dissolved into an acetone carrier, added to a glass flask (acute studies) or carboy (chronic study) in a thin layer around the sides of the container, and allowed to evaporate completely.  Tap water (City of Vicksburg, MS, municipal source) dechlorinated using carbon filtration was then added to the container and allowed to stir using a magnetic stir plate for 24-h before use.  IMX-101, NQ, and MeNQ were dissolved directly into water with no carrier solvent using magnetic stirring for 24-48 h before use.  Due to the acidic nature of NTO within the IMX-101 mixture, solutions were pH adjusted to a pH of 7.5 using NaOH.  Dechlorinated tap water was used for making dilution series and as control for all toxicity tests.  All other variables were assessed using the non-parametric Kruskal-Wallis ANOVA on ranks with a Student-Newman-Keuls post hoc test as assumptions of parametric ANOVA were not met.  All animal testing was conducted using methods and protocols approved by the US Army, Engineer Research and Development Center’s Institutional Animal Care and Use Committee (IACUC Protocol #EL-6009-2017-1).  The munitions exposure protocol is provided in the "Overall Design" section above.

tag: Stage

value: larvae (tadpole stage)

tag: experiment

value: IMX-101 Exposure Experiment


title: IMX-101_40mg-L_RepC


title: PDAC_PBMC_8

value: Treatment Naïve PDA


title: F0 TREATED nr 2

value: TREATED


title: MDTH low performer #1 [1_MDTH130_CTTGTA]


title: PDAC_PBMC_6


title: IMX-101_40mg-L_RepB


title: PDAC_PBMC_5


title: IMX-101_40mg-L_RepA


title: PDAC_PBMC_10A


title: HPF high performer #2 [44EF-HPF_CTTGTA]

source_name: HPF high performer

value: mouse HPF


title: PDAC_PBMC_3


title: IMX-101_20mg-L_RepD


title: SC-25 [miRNA]

city: Houston

first: David

middle: Earl

last: Cogdell

state: Tx

address: 1515 Holcombe

department: Pathology

institute: UT MD Anderson Cancer Center

data_processing:
Applied Biosystem's Sequence Detection System (SDS 2.2) software was used  to compute Ct values using the default threshold and baseline parameters
Ct Values are from SDS 2.2. Delta Ct values were generated by subtracting experimental genes from endogenous control gene (RNU48-001006). Fold change values were created by subtracting the Target sample delta Ct from the control Sample delta Ct (Sample1 was used as control) then evaluated in the expression 2^-(delta-deltaCt).

label: TaqMan

source_name: cystectomy

label_protocol: Human Pool A v2.1

extract_protocol: MasterPure Complete from Epicenter Biotechnologies

tag: subject age

value: 58 years

tag: subject gender

value: male

value: bladder

tag: tissue type

value: small cell carcinoma


title: HPF low performer #2 [168BD-HPF_GCCAAT]

source_name: HPF low performer


title: PDAC_PBMC_4


title: SC-24 [miRNA]

value: 72 years


title: IMX-101_20mg-L_RepB


title: SC-23 [miRNA]

value: 90 years

value: female


title: IMX-101_20mg-L_RepC


title: PDAC_PBMC_7


title: HPF high performer #1 [165FF-HPF_GCCAAT]

value: high performing mouse


title: SC-22 [miRNA]

value: 62 years


title: IMX-101_20mg-L_RepA


title: PDAC_PBMC_1


title: SC-21 [miRNA]

value: 34 years


title: SC-20 [miRNA]

value: 67 years


title: HPF low performer #1 [163BA-HPF_CTTGTA]

value: low performing mouse


title: IMX-101_10mg-L_RepD

value: larvae (tadpole stage)


title: HPF high performer #3 [88EF-HPF_ACAGTG]


title: AdjNorm_TISSUE_3

source_name: Adjancent Normal Pancreas Tissue

value: Treatment Naïve


title: AdjNorm_TISSUE_2


title: PFC high performer #3 [14_pfc_165_ATTCCT]

source_name: PFC high performer

value: prefrontal cortex (PFC)


title: SC-19 [miRNA]

value: 71 years


title: AdjNorm_TISSUE_1


title: HPF low performer #3 [179BD-HPF_GTGAAA]

value: mouse HPF


title: IMX-101_10mg-L_RepC

value: IMX-101 Exposure Experiment


title: PDAC_PBMC_2

value: Treatment Naïve PDA


title: PFC high performer #1 [12_pfc_44_GTGAAA]


title: IMX-101_10mg-L_RepB


title: IMX-101_10mg-L_RepA


title: PDAC_TISSUE_15

source_name: PANCREAS TUMOR


title: SC-18 [miRNA]

value: 57 years

value: male

value: bladder


title: SC-17 [miRNA]

value: 72 years

value: small cell carcinoma


title: PDAC_TISSUE_14


title: primary chondrocytes Week 1 rep3 [Bisulfite-Seq]

city: NEW YORK

first: Piali

last: Mukherjee

state: New York

department: Medicine

institute: Weill Cornell Medicine

data_processing:
Illumina’s CASAVA 2.17 software pipeline was used to perform image capture, base calling and demultiplexing of raw reads to produce FASTQ files.
FASTQ files passing Illumina's purity filter were adapter trimmed (using Flexbar) and trimmed reads were aligned to the mm10 build of the mouse genome.
RNA-Seq quality filtered and trimmed reads were aligned using STAR aligner with default parameters. Read counts for RefSeq (NCBI) transcripts were then quantified from the alignments using the featureCounts software package.
ERRBS quality filtered and trimmed reads were post-processed to produce methylation calls at base pair resolution using an in-house pipeline that features the Bismark aligner and methylation caller. CpG methylation calls for CpGs covered at least 10x were used for downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: raw gene counts (text file)
Supplementary_files_format_and_content: CpG methylation and coverage (text file)

source_name: articular cartilage 5-to-6 days-old C57BL6/J

growth_protocol: After isolation, murine primary chondrocytes were expanded in monolayer cultures in complete medium (DMEM /F12 medium supplemented with 10% FBS and Pen/Strep).

extract_protocol:
DNA was isolated using the Gentra Puregene DNA isolation kit (Qiagen)
Enhanced Reduced Representation Bisulfite Sequencing (ERRBS) library preparation is a modification of the reduced representation bisulfite sequencing approach, which generates single-base resolution DNA methylation bisulfite sequencing libraries that enrich for CpG-dense regions by methylation-insensitive restriction digestion. Briefly, DNA digested with the restriction enzyme MspI (New England Biolabs) was phenol extracted, ethanol precipitated, end-repaired, A-tailed and ligated to methylated TruSeq adapters (Illumina Inc. San Diego, CA). Two size fragment lengths of 150–250 bp and 250–400 bp were then gel isolated and subjected to overnight bisulfite conversion using EZ DNA methylation kit (Zymo Research, Irvine CA), purified and PCR amplified using TruSeq primers (Illumina Inc. San Diego, CA).

treatment_protocol: Murine primary chondrocytes were cultured in 3D/pellet cultures (in complete medium supplemented with Ascorbic acid and 1X ITS) for 1 week or 3 weeks.

value: cartilage:femoral head & tibial plateaus

value: 1 week


title: primary chondrocytes Week 3 rep3 [Bisulfite-Seq]

value: 3 weeks


title: PDAC_TISSUE_12


title: PDAC_TISSUE_11B

description: Sample 11A and 11B are the same patient, processed at two separate core facilities


title: SC-15 [miRNA]

value: 65 years


title: primary chondrocytes Week 3 rep2 [Bisulfite-Seq]


title: IMX-101_Control_RepC


title: SC-16 [miRNA]


title: IMX-101_Control_RepB


title: PDAC_TISSUE_11A

description: Sample 11A and 11B are from the same patient, processed at two separate core facilities


title: SC-14 [miRNA]


title: primary chondrocytes Week 3 rep1 [Bisulfite-Seq]


title: SC-13 [miRNA]

value: 67 years


title: PDAC_TISSUE_10


title: SC-12 [miRNA]

value: 76 years

value: female


title: primary chondrocytes Week 1 rep1 [Bisulfite-Seq]


title: IMX-101_Control_RepA

value: larvae (tadpole stage)


title: PDAC_TISSUE_9

value: Treatment Naïve


title: IMX-101_Control_RepD


title: primary chondrocytes Week 3 rep3 [RNA-Seq]

extract_protocol:
Total RNA was isolated using TRIzol followed by RNeasy mini RNA isolation kit protocol including DNase treatment step (Qiagen).
RNA-Seq library preparations were done using established Illumina methods for mRNA-Seq (Part #RS-122-2001). Briefly, poly A+ RNA was purified from 100 ng of total RNA with oligo-dT beads and fragmented with divalent cations at elevated temperature. First strand cDNA synthesis was performed with random hexamer priming and SuperScript II Reverse transcriptase (Invitrogen, part # 18064-014). Second strand cDNA synthesis was performed using RNAseH and DNA PolI. Following dscDNA synthesis, the double stranded products are end repaired, followed by addition of a single ‘A’ base and then ligation of the Illumina TruSeq adaptors. The resulting product was amplified with 15 cycles of PCR. Each library was made with a unique Index sequence and libraries are pooled for sequencing.


title: PDAC_TISSUE_8


title: MeNQ_4225mg-L_RepB

description:
5 tadpoles per replicate
MeNQ_processed_GS1.txt
All Sequence Runs for GEO.txt

value: MeNQ Exposure Experiment


title: SC-9 [miRNA]


title: MeNQ_4225mg-L_RepC


title: primary chondrocytes Week 1 rep3 [RNA-Seq]


title: primary chondrocytes Week 3 rep2 [RNA-Seq]


title: MeNQ_4225mg-L_RepA


title: SC-10 [miRNA]

value: 41 years


title: PDAC_TISSUE_6


title: primary chondrocytes Week 1 rep2 [Bisulfite-Seq]


title: MeNQ_851mg-L_RepD


title: SC-8 [miRNA]

value: 60 years


title: SC-7 [miRNA]

value: 79 years


title: PDAC_TISSUE_7


title: MeNQ_851mg-L_RepC


title: MeNQ_4225mg-L_RepD


title: primary chondrocytes Week 1 rep2 [RNA-Seq]


title: PDAC_TISSUE_4


title: MeNQ_851mg-L_RepB


title: SC-4 [miRNA]

value: male


title: SC-11 [miRNA]

value: bladder


title: PDAC_TISSUE_3


title: primary chondrocytes Week 1 rep1 [RNA-Seq]


title: SC-3 [miRNA]


title: MeNQ_851mg-L_RepA


title: SC-2 [miRNA]

value: 72 years


title: 115-P-sc

city: Melbourne

first: Katie

middle: Louise

last: Owen

state: VIC

address: 305 Grattan Street

department: Research

country: Australia

institute: Peter MacCallum Cancer Centre

description:
BASiCS_normalised_counts_all_samples.txt
BASiCS_normalised_counts_4_mice_of_interest.txt

data_processing:
Sequencing was performed at the Garvan Institute (Sydney, NSW, Australia) on the Illumina Hiseq2500 (125 bp paired-end reads) on a high-throughput mode with ~3 million reads per cell.)
Sequence adapters were trimmed and aligned to a modified version of the GRCm38/mm10 mouse genome (which also included ERCC and eCFP sequences) using the STAR aligner (Dobin, Davis, Schlesinger,  Drenkow et al., 2013)
All subsequent analysis was performed using the BASiCS package according to methods previously described (Vallejos, Richardson, Marioni, 2016; Eling, Richard, Richardson, Marioni & Vallejos, 2018).
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Summarized gene transcript counts and TPMs were generated using RSEM (Li & Dewey, 2011).

source_name: Single RM1 cell from bone metastases

growth_protocol: RM1536 cells were labelled with the lipophilic dye, PKH26 (Sigma), and introduced into C57BL/6 mice by intracardiac injection (D0).

extract_protocol:
Single dormant (PKH26+) and proliferating (PKH26-) RM1536 from murine bone metastases were FACS-isolated following bioluminescence-imaging confirmation of tumor cells in bone at ~16 days post-intracardiac injection of PKH26-labelled RM1536 (eCFP+/luc2+) prostate cancer cells. Single tumor cells from bone marrow suspensions were sorted directly into a 384 well plate (containg 2 ml of RNA lysis bufer per well), sealed and snap-frozen on dry ice. Plates were stored at -80C until extraction.
Single cell cDNA was generated using the SMARTer Ultra Low RNA Kit (Clontech) with modifications. Briefly, 1:2.5x106 dilution of ERCC spike-in controls (Ambion) were incorporated during first strand cDNA synthesis. Subsequent steps were performed according to manufacturer's instructions at half-reaction volumes. cDNA quality assessment using the Bioanalyzer HS DNA chip (Agilent technologies) according to manufacturer's instructions and via Qubit 4 (ThermoFisher).
Libraries (1 ng cDNA input) were subsequently generated in four batches (2 x 14 samples of PKH+ cells; 2 x 16 samples of PKH- cells sourced from 8 independent animals at different time points of metastasis (average d16) across independent experiments) and unique adapters incorporated using the Nextera XT Kit (Illumina) according to manufacturer’s protocol. Libraries were validated by Bioanalyzer 2100 (Agilent) and quantitated by Qubit 4 and pooled (2 x pools of equal numbers of PKH ± in each group) for sequencing across 2 lanes on the Illumina Hiseq2500.

tag: cancer type

value: Prostate

tag: label

tag: mouse id #

tag: endpoint post-injection

value: Day 17

tag: cell type

value: P' denotes PROLIFERATING single cell (sc)


title: PDAC_TISSUE_2

tag: treatment


title: 114-P-sc

tag: strain


title: MeNQ_170mg-L_RepC


title: PDAC_TISSUE_5


title: PDAC_TISSUE_1


title: 113-P-sc


title: MeNQ_170mg-L_RepB


title: primary chondrocytes Week 3 rep1 [RNA-Seq]

tag: tissue

value: cartilage:femoral head & tibial plateaus

value: 3 weeks


title: ATAA7

first: Yanming

last: Li

state: TX

address: One Baylor Plaza

department: Michael E. DeBakey Department of Surgery

institute: Baylor College of Medicine

data_processing:
Illumina CASAVA was used for base-calling.
Sequenced reads were aligned by using Cell Ranger 3.0, with GRCh38 as a reference.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw UMI counts for every gene and every single cell

source_name: ATAA_human ascending aortic tissue

extract_protocol:
Aortic tissue was separated into thin layers and cut into small pieces, and digested in enzyme cocktails. Live singlet cells were collected by flow cytometry sorting and submitted to 10X Chromiun System.
Libraries were constructed following the instructions of Chromium Single Cell 3' Reagent Kits user guide.

tag: disease state

value: Ascending thoracic aortic aneurysm (ATAA)

tag: gender

value: human ascending aortic tissue


title: ATAA6

value: female


title: 110-D-sc

value: D' denotes DORMANT single cell (sc)


title: 111-D-sc


title: MeNQ_34mg-L_RepD

value: larvae (tadpole stage)


title: ATAA5


title: 106-D-sc

description: BASiCS_normalised_counts_all_samples.txt

value: Day 15


title: MeNQ_34mg-L_RepC

value: MeNQ Exposure Experiment


title: ATAA4


title: 105-D-sc


title: 104-D-sc


title: ATAA3


title: MeNQ_34mg-L_RepB


title: MeNQ_170mg-L_RepD


title: ATAA8


title: FGFR3WT

city: Erlangen

first: Debomita

last: Chakraborty

address: Ulmenweg 18

institute: Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen

description: Dermal fibroblasts from wild type Bl6 mice.

hyb_protocol: RNA were hybridized to the murine genome U74A V2 Gene Chip.

scan_protocol: After hybridization, array membranes were scanned and CEL files were generated using a GeneChip System confocal scanner (Hewlett-Packard, Santa Clara, CA, USA).

data_processing:
The data was preprocessed using the GeneSpring software version 5.0.
The quality of the in vitro transcribed probes was evaluated by the 3`prime/5`prime ratio for the housekeeping genes spotted on the Affymetrix chips. The ratios of all housekeeping genes were lower than three and equal in all three samples.
Gene expression levels in the individual sample dataset were ascertained using the Affymetrix Microarray Suite 5.0 (Affymetrix) and the transcripts flagged as absent were filtered out and only genes flagged as marginal or present were further evaluated.
The expression levels in wildtype mouse fibroblasts were set to 100% and the normalized signals of array Fgfr3KO and Fgfr3Act fibroblast arrays were calculated as relative expression of the wildtype fibroblasts.

source_name: mouse fibroblast

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 15 μg ug total RNA.

growth_protocol: Fibroblast growth medium.

extract_protocol: The total RNA from homogenized fibroblasts RNA was extracted and purified with the RNeasy RNA extraction system (Macherey-Nagel, Düren, Germany). The RNA integrity and purity were determined with Nanodrop spectrophotometer (VWR, Ismaning, Germany) and further by electrophoresis in ethidium bromide containing 1% agarose gel. Further quality control of the total RNA was performed using RNA LabChips (Agilent Technologies, Palo Alto, CA, USA).

value: dermal fibroblasts

tag: genotype/variation

value: WT


title: dkfz_RCMB40_ht

type: genomic

city: La Jolla

first: Edwin

middle: Francisco

last: Juarez

address: 9500 Gilman Dr

institute: University of California San Diego

hyb_protocol: Illumina

scan_protocol: Illumina iScan System

data_processing: Raw signal intensities were obtained from IDAT-files using the minfi Bioconductor package. Signal intensities were normalized per sample by performing a background correction (shifting of mean negative control probe intensity to 0) and a dye-bias correction (scaling of mean normalization control probe intensity to 10,000). Standard beta-values were calculated.

label: biotin/DNP

source_name: human tumor

label_protocol: Illumina

extract_protocol: Extraction of high molecular weight DNA from frozen tumor samples was carried out using a Qiagen Blood & Cell Culture DNA Midi Kit (Qiagen, Hilden, Germany) after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany).

value: human medulloblastoma tumor

tag: tumor subgroup


title: FGFR3KO

description: Dermal fibroblasts from FGFR3G374Rneo+ mice (FGFR3KO), which do not express a functional FGFR3.


title: MeNQ_170mg-L_RepA

tag: Stage


title: FGFR3Act

description: Dermal fibroblasts from Fgfr3G374Rneo- mice with ligand-independent constitutive activation of Fgfr3 (FGFR3Act).


title: dkfz_RCMB38_XP

source_name: PDOX

value: PDOX


title: HCT116 sh-HAUS6 rep2

city: Fuzhou

first: Jun

last: Peng

state: Fujian

address: 1 Qiuyang Road, Minhou Shangjie

department: Academy of Integrative Medicine

institute: Fujian University of Traditional Chinese Medicine

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip PrimeView Human gene expression array with constant rotation at the speed of 60 rpm. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip  scanner 3000

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Colorectal cancer cells, transduced with lentivirus encoding sh-HAUS6

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Cat. AM1792, Ambion).

extract_protocol: Trizol (Thermo Fisher Scientific) extraction of total RNA was performed according to the manufacturer's instructions.

tag: cell line

tag: transduction

value: lentivirus encoding HAUS6 sh-RNA


title: MeNQ_34mg-L_RepA

tag: experiment


title: HCT116 sh-HAUS6 rep1


title: 103-D-sc

value: Prostate


title: 102-D-sc


title: HCT116 sh-HAUS6 rep3


title: MeNQ_Control_RepD


title: dkfz_RCMB38_ht


title: ATAA2


title: MeNQ_Control_RepC


title: Control9

source_name: control_human ascending aortic tissue

value: Non-aneurysmal diseased control


title: ATAA1


title: dkfz_RCMB40_XP1


title: 100-D-sc

value: Day 14


title: dkfz_RCMB32_ht


title: 98-D-sc


title: 101-D-sc


title: MeNQ_Control_RepB


title: MeNQ_Control_RepA


title: TNT_3-4mg-L_RepD

description:
5 tadpoles per replicate
TNT_processed_GS1.txt
All Sequence Runs for GEO.txt

value: TNT Exposure Experiment


title: Control4


title: dkfz_RCMB28_XP1


title: TNT_3-4mg-L_RepC


title: dkfz_RCMB24_XP2


title: dkfz_RCMB28_ht


title: 96-D-sc


title: 95-D-sc


title: TNT_3-4mg-L_RepB


title: 93-D-sc


title: dkfz_RCMB20_ht


title: TNT_2-3mg-L_RepD


title: 94-D-sc


title: dkfz_RCMB20_XP2


title: TNT_3-4mg-L_RepA


title: 89-P-sc

value: P' denotes PROLIFERATING single cell (sc)


title: dkfz_RCMB18_XP1


title: dkfz_RCMB32_XP1


title: TNT_2-3mg-L_RepC


title: TNT_2-3mg-L_RepB


title: dkfz_Med-2312FH_XP


title: Control6

value: male


title: 88-P-sc


title: TNT_2-3mg-L_RepA


title: 97-D-sc


title: dkfz_Med-2312FH_ht


title: 83-P-sc


title: dkfz_Med-211FH_P2


title: 86-P-sc


title: TNT_1-5mg-L_RepC


title: TNT_1-5mg-L_RepD


title: 82-D-sc


title: dkfz_Med-211FH_ht


title: dkfz_Med-1911FH_P2


title: 81-D-sc


title: TNT_1-5mg-L_RepB


title: TNT_1-5mg-L_RepA


title: 79-D-sc


title: dkfz_Med-1911FH_ht


title: TNT_Control_RepD


title: dkfz_Med-1712FH_P1


title: dkfz_Med-411FH_P3


title: TNT_Control_RepC


title: 76-P-sc

value: Day 16


title: TNT_Control_RepB


title: dkfz_Med-1712FH_ht


title: TNT_Control_RepA


title: 67-P-sc


title: 66-P-sc


title: dkfz_MB002_XP


title: dkfz_MB009_XP


title: 63-P-sc


title: NQ_3750mg-L_RepD

description:
5 tadpoles per replicate
NQ_processed_GS1.txt
All Sequence Runs for GEO.txt

value: NQ Exposure Experiment


title: dkfz_Icb984MB_XP11


title: 62-P-sc


title: dkfz_Icb1572MB_XP


title: dkfz_Icb1487MB_XP


title: NQ_3750mg-L_RepB


title: NQ_3750mg-L_RepC


title: 52-D-sc

value: D' denotes DORMANT single cell (sc)


title: NQ_3750mg-L_RepA

value: larvae (tadpole stage)


title: NQ_750mg-L_RepD


title: dkfz_Icb1299MB_XP4


title: 73-P-sc


title: dkfz_DMB006_XP3


title: NQ_750mg-L_RepC


title: 51-D-sc


title: 47-P-sc

value: Day 17


title: dkfz_BT084_XP1


title: NQ_750mg-L_RepA


title: dkfz_BT084_ht


title: 41-P-sc


title: NQ_150mg-L_RepD


title: 42-P-sc


title: 46-P-sc


title: NQ_150mg-L_RepB


title: NQ_150mg-L_RepA


title: 39-P-sc


title: NQ_150mg-L_RepC


title: NQ_30mg-L_RepD


title: 50-D-sc


title: 38-D-sc


title: 37-D-sc


title: 33-D-sc

value: Day 26


title: NQ_750mg-L_RepB


title: NQ_30mg-L_RepB


title: NQ_30mg-L_RepA


title: NQ_Control_RepD


title: 32-P-sc


title: 30-P-sc


title: 40-P-sc


title: 29-D-sc


title: NQ_Control_RepC


title: 27-D-sc


title: NQ_30mg-L_RepC


title: NQ_Control_RepA


title: 25-D-sc


title: 20-P-sc

value: Day 13


title: NQ_Control_RepB


title: SHR cardiac fibroblast+ACEI-rep2

city: Phoenix

first: Taben

middle: Mary

last: Hale

state: AZ

address: 425 N 5th St

department: Basic Medical Sciences

institute: University of Arizona

description:
M8
scRNASeq

data_processing:
cellranger (v3.0.2) count with default parameters
Genome_build: rn6 (Rnor_6.0)
Supplementary_files_format_and_content: Cellranger count produces feature matrices that can be directly imported into Seurat. Cellranger output is described here: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/overview#count

organism: Rattus norvegicus

source_name: left ventricle

growth_protocol: 3 days of cell culture.

extract_protocol:
Single cell suspension was then processed by the Chromium Controller (10x Genomics) using single Cell 3’ Reagent Kit v3 (Chromium Single Cell 3’ Library & Gel Bead Kit v3, catalog number: 1000075; Chromium Single Cell B Chip Kit, 48 runs, catalog number: 1000073; 10x Genomics). Two separate cell counts on a hemocytometer were used to load ~4000 cells/sample for 10X GEM creation. Any remaining cell suspension after GEM creation was stained with NucBlue Live Cell Stain (ref: R37605; Invitrogen | Thermo Fisher Scientific) and NucGreen Dead 488 (ref: R37109; Invitrogen | Thermo Fisher Scientific). After a 20-minute incubation, stained cells were again counted using a Countess™ II Automated Cell Counter (ref: A27977; Invitrogen | Thermo Fisher Scientific).
Single cell sample libraries were generated using 10X 3' V3 regents following 10X’s 3’ V3 instructions. After library generation, the single sample libraries were pooled equimolar and sequenced using HiSeq4000 (Illumina) and V4 chemistry (HiSeq PE Cluster Kit v4 cBot, catalog number: PE-401-4001; HiSeq SBS Kit V4 250 cycles, catalog number: FC-401-4003; Illumina) with 254 bp paired end reads.

treatment_protocol: Prior to cell isolation, ACEI rats were given an ACE inhibitor in drinking water for 2 weeks followed by a 2-week washout.

value: spontaneously hypertensive rat (SHR)

tag: Sex

tag: age

value: adult

value: heart

value: cardiac fibroblast

value: ACEI


title: SHR cardiac fibroblast-rep1

description:
M5
scRNASeq

value: control


title: SHR cardiac fibroblast-rep2

description:
M6
scRNASeq


title: genomic DNA patient T192 [T0251_X]

city: Luxembourg

first: Ann-Christin

last: Hau

address: 1, Rue Louis Rech

department: National Center of Pathology

country: Luxembourg

institute: Laboratoire National de sante

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation Beadchips using standard Illumina protocol. Processing of HumanMethylationEPIC BeadChip arrays was performed by the Helmholtz Zentrum Muenchen (Research Unit of Molecular Epidemiology/Institute of Epidemiology, German Research Center for Environmental Health, Neuherberg, Germany. Illumina HumanMethylation450 BeadChips were processed at the German Cancer Research Center (DFKZ) Genomics and Proteomics Core Facility.

scan_protocol: The arrays were scanned with the Illumina HiScan SQ scanner.

data_processing: The R package ʹRnBeadsʹ was used to generate individual 450k and EPIC RnBeadSets that were normalized using the ʹBMIQʹ method. Both platforms were combined using the ʹrnb.combine.arraysʹ function in order to extract only common sites present in both objects with corresponding DNA methylation level. The DNA methylation level for each locus was measured as a β-value score.

label: Cy5 and Cy3

source_name: xenograft

label_protocol: Standard Illumina Protocol

growth_protocol: patient specimen were: 1) flash frozen on dry ice after surgical removal or 2) mechanically cut, seeded on agar coated flasks (0.85%) and allowed to form spheroids for up to 2 weeks at 37°C under 5% CO2 and atmospheric oxygen in DMEM medium, 10% FBS, 2mM L-Glutamine, 0.4mM NEAA and 100U/ml Pen-Strep (all from Lonza).  Spheroids (generation 0) with a diameter of 300-1000 µm were then implanted in the brain of immunodeficient mice (NOD/Scid, Nude or NSG; 6 spheroids per mice). Cell lines were derived from xenotransplanted mice by papain-based enzymatic digestion of PDOX tissue and cultured in serum-free medium based on  Neurobasal® base medium (Life Technologies) supplemented with 1 x B27 (Life Technologies) 2 mM L-Glutamine, 30 U/ml Pen-Step, 1 U/ml Heparin (Sigma), 20 ng/ml bFGF (Miltenyi, 130-093-841) and 20 ng/ml EGF (Provitro, 1325950500).

extract_protocol: Genomic DNA was isolated from patient tissue, spheroid cultures or cell lines using the AllPrep DNA/RNA Mini Kit® (Qiagen) following manufacturer’s instructions for “Simultaneous purification of genomic DNA and total RNA from animal tissues”.

tag: source subject status

value: glioma patient

tag: source patient id

tag: sample type

value: xenograft


title: 6-P-sc

tag: cancer type

value: Prostate

tag: label

tag: mouse id #

tag: endpoint post-injection

value: Day 18

tag: cell type

value: P' denotes PROLIFERATING single cell (sc)


title: 26-D-sc

tag: strain


title: SHR cardiac fibroblast-rep7

description:
M20
scRNASeq

value: male

tag: tissue

tag: treatment


title: 5-P-sc


title: 4-P-sc


title: genomic DNA patient T192 [T0251_B]

source_name: patient sample

value: patient sample


title: SHR cardiac fibroblast-rep6

description:
M19
scRNASeq


title: genomic DNA patient T16 [T16_X1]


title: 3-P-sc


title: SHR cardiac fibroblast+ACEI-rep7

description:
M18
scRNASeq


title: genomic DNA patient T0239 [T239_B1]


title: 2-P-sc


title: genomic DNA patient T0239 [T239_X1]


title: 9-P-sc


title: genomic DNA patient T185 [T185_X1]


title: genomic DNA patient T16 [T16_B1]


title: SHR cardiac fibroblast-rep5

description:
M16
scRNASeq


title: genomic DNA patient T185 [T185_B1]


title: RM1 tumor cells replicate b

data_processing:
Sequencing was performed by Novogene Bioinformatics (Hong Kong; 125-bp paired-end reads; 24 million pair reads per sample)
Clean reads meeting exclusion criteria (no adaptor contamination; undecided nucleotide call > 10%; low base quality > 50% of read) were aligned to GRCm38 using Tophat (v2.1.10; Kim, Pertea, Trapnell, Pimentel, Kelley & Salzberg, 2013)
Clean reads were counted using HTSeq-count (Anders, Pyl & Huber, 2015)
Differential gene expression was performed using edgeR and statistical significance determined by generalized linear model extraction (GLM; Robinson, McCarthy & Smyth, 2010)
Genome_build: GRCm38
Supplementary_files_format_and_content: The csv file includes raw counts for each sample

source_name: Tumor cells from culture

growth_protocol: Proliferating parental RM1 cells (unlabelled) and eCFP+/luc2+ RM1 cells (RM1536) from culture, and bone-derived RM1536 and lung-derived RM1536 from a single mouse (#369) at D16 post-intracardiac injection were FACS-isolated and expanded in vitro in DMEM (5% FBS) to T75 flask confluency of 85%.

extract_protocol:
~5x10e6 cells were pelleted and RNA extracted using the innuPREP RNA mini kit (Analytik Jena). RNA concentration was determined via Nanodrop 2000 (ThermoFisher), validated by Bioanalyzer 2100 (Agilent) and quality of RNA assessed by gel electrophoresis (1% agarose gel).
Purified RNA (RIN > 6.8) was prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA)

value: Tumor cells from culture

value: no label


title: SHR cardiac fibroblast-rep4

description:
M15
scRNASeq


title: SHR cardiac fibroblast+ACEI-rep5

description:
M14
scRNASeq


title: RM1 tumor cells expressing eCFP and luc2 replicate b

description:
536 denotes pooled clones 5,3 and 6 used to generate cell line following fluorescent and bioluminscent labeling
RM1536b


title: SHR cardiac fibroblast+ACEI-rep4

description:
M13
scRNASeq


title: RM1 tumor cells expressing eCFP and luc2 replicate a

description:
536 denotes pooled clones 5,3 and 6 used to generate cell line following fluorescent and bioluminscent labeling
RM1536a


title: SHR cardiac fibroblast+ACEI-rep3

description:
M12
scRNASeq


title: SHR cardiac fibroblast+ACEI-rep1

description:
M7
scRNASeq


title: RM1536 tumor cells from the femur of mouse #369

description:
536 denotes pooled clones 5,3 and 6 used to generate cell line following fluorescent and bioluminscent labeling
369Femur

source_name: Tumor cell from bone (ex vivo)

value: Tumor cell from bone (ex vivo)


title: genomic DNA from old exercise trained PBMCs 11

city: Boulder

first: Christopher

middle: R

last: Martens

state: CO

address: 354 UCB

department: Integrative Physiology

institute: University of Colorado Boulder

description:
O-Ex
OT11

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

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

data_processing: R (v3.2.2)/Bioconductor Package 'minfi' package (minfi_1.14.0) was used to pre-process data: RGset was processed using the function preprocessRaw.  Failed probes (p>0.05 in at least 1% of samples) were removed and data were normalized using SWAN normalization.  Methylation loci on sex chromosomes or containing random or known SNPs were removed.  Beta values were extracted using getBeta function.

label: Cy3 and Cy5

source_name: PBMCs old exercise trained

extract_protocol: DNA was extracted from PBMCs using the Qiagen Mini DNA isolation kit, following the manufacturer's instructions.

treatment_protocol: Sedentary was defined as not having performed regular exercise (<30 min/day, <2 days/week) during the previous 2 years; Exercise Trained was defined as performing ≥4 sessions/week of vigorous aerobic/endurance exercise for ≥45 minutes/session.

value: M

tag: training status

value: trained


title: genomic DNA from old exercise trained PBMCs 10

description:
O-Ex
OT10


title: Striatum tissue - Mn-exposed group [17T]

city: New York

first: Hector

last: Cordero

address: 650W 168th Street

institute: Columbia University

data_processing:
Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software.
Reads were aligned using STAR aligner v2.5.2b to map the reads to the reference rat genome (Rnor_6.0).
Normalized counts were generated using DESeq2 package for differential expression analysis (Love et al., 2014).
Genome_build: rn6 (Rnor_6.0)
Supplementary_files_format_and_content: raw_counts.csv: Comma-separated matrix table with raw gene counts for every gene and every sample.
Supplementary_files_format_and_content: *.counts.txt: Tab-delimited text files include raw counts.

source_name: Striatum

extract_protocol:
Total RNA extraction was performed using RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s instructions.
Library preparation was performed using the NEBNext Ultra RNA Library Preparation kit with PolyA selection workflow.

treatment_protocol: Sprague-Dawley male rats received an intraperitoneal injection of 0.9% NaCl (control group) or MnCl2 (treatment group) at 25mg/kg during 15 days. The striatum was collected after the treatment.

tag: ID

value: Sprague-Dawley

value: Male

value: Striatum

value: Manganese


title: splenic CD4+ T cells, KO_GFP_pos_replicate_3

city: Freiburg

first: Ekaterina

last: Lupar

address: Stuebeweg 51

department: Department of Cellular & Molecular Immunology

institute: Max Planck Institute of Immunobiology and Epigenetics

data_processing:
Raw data from the Illumina HiSeq 2500 sequencing machine was demultiplexed and converted into FASTQ files using Illumina bcl2fastq2 (version 1.8.4, http://support.illumina.com/downloads/bcl2fastq_conversion_software_184.html).
Screening for contamination with fastq_screen (version 0.5.1, (http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/).
Automatic detection and trimming of adaptors, quality control and mapping was performed with an rna-seq-qc pipeline (https://github.com/maxplanck-ie/rna-seq-qc).
Reads alignment against mouse genome was done with TopHat2 (version 2.0.13).
Reads were counted with featureCounts (version 1.5.0-p1).
Differential gene expression analysis was performed using the DESeq2 (version 1.6.1).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include non-normalized feature counts, differentially expressed genes

source_name: splenic CD4+ T cells, KO_GFP_pos

growth_protocol: FACS-Sorted splenic CD45RBhi CD25- naïve CD4+ T cells from Eomes-Het-GFP or Eomes-KO-GFP reporter mice were adoptively transferred into adult male Rag2-/- recipients. 3 weeks later recipient mice were killed and GFP+ and GFP- CD4+ cells were sorted from their spleens for RNAseq analysis.

extract_protocol:
Total RNA was extracted with TRI reagent (Sigma-Aldrich, Munich, Germany).
Depletion of the ribosomal RNA and library preparation was performed with the TruSeq® Stranded Total RNA Gold kit (former name TruSeq® Stranded Total RNA LT - (with Ribo-Zero TM GOLD), Illumina, San Diego, USA).

tag: donor genotype

value: Eomes flox/GFP; Lck-cre

tag: gfp expression

value: positive

tag: activation condition

value: 3 weeks in Rag2-/- recipient

value: splenic CD4+ T cells

tag: number of cells in sample


title: Striatum tissue - Mn-exposed group [14T]

tag: Sex


title: genomic DNA from old exercise trained PBMCs 8

description:
O-Ex
OT8

tag: age


title: splenic CD4+ T cells, KO_GFP_pos_replicate_2


title: Striatum tissue - Mn-exposed group [13T]


title: SHR cardiac fibroblast+ACEI-rep6

description:
M17
scRNASeq

value: spontaneously hypertensive rat (SHR)

value: adult

value: heart

value: cardiac fibroblast

value: ACEI


title: splenic CD4+ T cells, KO_GFP_pos_replicate_1


title: Striatum tissue - control group [4C]

value: NaCl (control)


title: 1-P-sc

value: Prostate

value: Day 17

value: P' denotes PROLIFERATING single cell (sc)


title: Striatum tissue - control group [2C]

value: Sprague-Dawley


title: genomic DNA from old exercise trained PBMCs 7

description:
O-Ex
OT7

value: M

value: trained


title: genomic DNA from old exercise trained PBMCs 5

description:
O-Ex
OT5

value: F


title: genomic DNA from old exercise trained PBMCs 6

description:
O-Ex
OT6


title: genomic DNA from old exercise trained PBMCs 9

description:
O-Ex
OT9


title: RM1536 tumor cells from the lung of mouse #369

description:
536 denotes pooled clones 5,3 and 6 used to generate cell line following fluorescent and bioluminscent labeling
369Lung

source_name: Tumor cell from lung (ex vivo)

value: Tumor cell from lung (ex vivo)


title: genomic DNA from old exercise trained PBMCs 4

description:
O-Ex
OT4


title: SHR cardiac fibroblast-rep3

description:
M10
scRNASeq

value: male

value: control


title: genomic DNA from old exercise trained PBMCs 3

description:
O-Ex
OT3


title: splenic CD4+ T cells, KO_GFP_neg_replicate_2

source_name: splenic CD4+ T cells, KO_GFP_neg

value: Eomes flox/GFP; Lck-cre

value: negative

value: 3 weeks in Rag2-/- recipient

value: splenic CD4+ T cells


title: Striatum tissue - control group [1C]

value: Male

value: Striatum


title: genomic DNA from old PBMCs 15

description:
O-SED
OS15

source_name: PBMCs old sedentary

value: sedentary


title: genomic DNA from old exercise trained PBMCs 1

description:
O-Ex
OT1


title: genomic DNA from old exercise trained PBMCs 2

description:
O-Ex
OT2


title: RM1 tumor cells replicate a

value: Tumor cells from culture

value: Prostate

value: no label


title: SHR_scRNAseq

city: Oxford

last: Paterson

address: Parks Road

department: Department of Physiology, Anatomy and Genetics

country: United Kingdom

institute: University of Oxford

description:
sc-RNA-seq
processed data file: Differential_Expression.csv

data_processing:
Cell Ranger (v3.0.2) for alignment and abundance measurements. Seurat (v3) for filtering, clustering and differential expression (via DESeq2).
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: Wistar_NeuronCluster_Expression.csv: Comma-separated text file of neuron cluster expression values in Wistar.
Supplementary_files_format_and_content: SHR_NeuronCluster_Expression.csv: Comma-separated text file of neuron cluster expression values in SHR.
Supplementary_files_format_and_content: Differential_Expression.csv: Comma-separated text file of differential expression between Wistar and SHR neuron clusters.

source_name: Stellate Ganglia

extract_protocol:
1mg/ml Collagenase IV for 25 minutes, 2mg/ml Trypsin for 30 minutes. Followed by mechanical disruption.
10x Genomics, Single cell 3' v3. Hiseq 4000.

value: SHR

value: 5-6 weeks

value: Stellate ganglia

tag: phenotype

value: Prehypertensive


title: splenic CD4+ T cells, KO_GFP_neg_replicate_1


title: genomic DNA from old PBMCs 12

description:
O-SED
OS12

value: F


title: splenic CD4+ T cells, Het_GFP_pos_replicate_3

source_name: splenic CD4+ T cells, Het_GFP_pos

value: Eomes flox/GFP; no cre

value: positive


title: splenic CD4+ T cells, Het_GFP_pos_replicate_2