title: EHT_UNC0224_500nM_rep2

city: Boston

first: Mohamad Ali

last: Najia

address: 1 Blackfan Circle

department: Hematology/Oncology

institute: Boston Children's Hospital

description: Replicate 2

data_processing:
ATAC-seq data processing and alignment was completed using the PEPATAC pipeline (http://code.databio.org/PEPATAC/). The hg38 genome build used for alignment was obtained using Refgenie (https://github.com/databio/refgenie). We utilized the consensus, non-overlapping peak-set generated from the PEPATAC pipeline to construct an ATAC-Seq counts matrix across all samples. Reads were counted in ATAC-Seq peaks using “bedtools multicov” from the aligned, deduplicated BAM files for each sample. Differentially accessible chromatin was determined with DESeq2 (Love et al., 2014). Statistically significant peaks varying between two conditions were identified at an independent hypothesis weighting (IHW) value of 0.05 (Ignatiadis et al., 2016). Differentially accessible peaks were then used as input to GREAT analysis to determine enrichment of biological pathways or processes.
Assembly: hg38
Supplementary files format and content: R data file containing a dataframe of the raw or CPM normalized ATAC-Seq counts matrix for all samples

source_name: 1157.2 iPS cell line

growth_protocol: Human 1157.2 iPSCs were differentiated into CD34+ HE cells using a previous described protocol (Ditadi et al., 2015). Briefly, iPSC colonies cultured on mouse embryonic fibroblast (MEF) feeder cells (Gibico, A34181) were scraped and transferred to ultra-low attachment plates and cultured with aggregation media contains BMP4 (10ng/ml, day 0-2), bFGF (5ng/ml, day 1-2), CHIR99021 (3μM, day 2), and SB431542 (6μM, day2) to allow EB formation. After 4 days, EBs were cultured with StemPro-34 media (Gibco, 10639011) supplemented with VEGF (15ng/ml, day3-8), bFGF (5ng/ml, day3-8), SCF (50ng/ml, day 6-8), EPO (day6-8), IL-6 (day 6-8), IL-11 (day 6-8), and IGF-1 (day 6-8). On day 8, EBs were dissociated using EB Dissociation Kit (Miltenyi, 130096348), and HE cells were isolated by magnetic-activated cell sorting (MSCS) using the human CD34 Microbead Kit (Miltenyi, 130046702).

extract_protocol:
DAPI-CD45+ cells were isolated by FACS and at least 50,000 cells/sample were used for ATAC-Seq
Nuclei isolation, tagmentation and library construction was performed as described in the Omni-ATAC-Seq protocol (Corces et al. 2017). The concentration of the final ATAC-Seq libraries was quantified using a High Sensitivity DNA Bioanalyzer Assay (Agilent) in the size range of 100-1000 bp. The libraries were then equimolar pooled and shallow sequenced on a MiniSeq to determine the quality of the libraries. The ATAC-Seq libraries were then deep sequenced on a NextSeq 550 with a 150-cycle High Output Kit v2 with the following read configuration: 76-8-8-75.

value: 1157.2 iPS cell line

value: iPSC-derived hematopoietic progenitor cells


title: B2508_D60_10.7Gy_Female

status: Public on Sep 30 2024

type: SRA

city: Bethesda

first: Uma

middle: T

last: Shankavaram

state: MD

address: 9000 Rockville Pike

department: NCI

country: USA

institute: NIH

description:
B2508_D60_S0
B2508_D60_10.7Gy

library_source: transcriptomic

data_processing:
The FASTQ sequences were trimmed using CutAdapt v. 2.10 [https://doi.org/10.14806/ej.17.1.200] with the following settings: “--nextseq-trim=2 --trim-n -n 5 -O 5 -q 10,10 -m 15 -j 0” and aligned using STAR v. 2.7.6a [https://doi.org/10.1093/bioinformatics/bts635] with parameters set as recommended by ENCODE3 consortium (https://www.encodeproject.org/pipelines/ENCPL444CYA/). Macaca mulatta (Rhesus monkey) genome assembly Mmul_10 (release date: Feb. 2019) with RefSeq annotation (accession number GCF_003339765.1) was used as a reference. Counting was performed with the help of Subread package v. 2.0.1 [10.1093/bioinformatics/btt656]. The count matrix was processed in R (1) for further analysis.
Assembly: Macaca mulatta (Rhesus monkey) genome assembly Mmul_10 (release date: Feb. 2019).
Supplementary files format and content: *.txt: Tab-delimited text files include raw counts and normalized counts for each Sample.

molecule: total RNA

organism: Macaca mulatta

source_name: Whole blood

extract_protocol: Blood samples were procured from each of the animals (n = 28) two days before irradiation as control, every three days post-irradiation for the initial 30 days, on days 40, 50, and 60, and approximately every 30 days until the euthanization of all surviving animals at day 270 post-irradiation.

tag: tissue

value: Whole blood

tag: Sex

value: Female

tag: treatment

value: 10.7Gy thoracic radiation

tag: time point

value: 60 days

tag: animal id


title: Human induced Treg cells, transduced with empty vector (EV), donor 2

city: La Jolla

first: Gabriel

last: Ascui

state: California

address: 9420 Athena Circle

institute: La Jolla Institute for Immunology

data_processing:
FASTQ was merged and filtered using fastp (v0.23.3)
Reads were aligned with the STAR aligner (2.7.10b)
Samtools (v1.17) was used to index and sort BAM friles from STAR
QC report was performed with bamCoverage (v3.5.1), and Qualimap (v.2.2.2-dev)
Raw and transcripts per million reads (TPM) counts were taken from STAR’s BAM aligned output.
Assembly: hg19
Supplementary files format and content: LACC1_counts.txt.gz raw counts for 18 samples in TAB delimited TXT
Supplementary files format and content: LACC1_tpm.txt.gz transcripts per million reads (TPM) counts for 18 samples in TAB delimited TXT
Supplementary files format and content: LACC1_metadata.txt.gz metadata for 18 samples in TAB delimited TXT

molecule: polyA RNA

organism: Homo sapiens

source_name: PBMC

growth_protocol: Naïve CD4+ T cells were enriched from human PBMCs. 1 x 105 cells were seeded into each well of a 96-well plate pre-coated with 5 ug/mL purified anti-human CD3 antibody (Clone UCHT1, BioLegend) in 200 ul human T cell culture medium containing 2.5 ug/mL purified anti-human CD28 antibody (Clone CD28.2, BioLegend) and cytokine polarization cocktails. 24h after activation, the supernatant was replaced with medium containing shRNA-expressing lentivirus for transduction. After transduction, the virus medium was replaced by T cell culture medium containing anti-human CD28 antibody and cytokine polarization cocktails for another 48h. The cells were expanding in fresh T cell polarization medium for 4 days, and were split as needed every 2 days. Th0 cell polarization medium contained 5 ng/mL IL-2 (BioLegend). Treg cell polarization medium contained 5 ng/mL IL-2 (BioLegend), and doses of human TGFb from 0 to 5 ng/mL (R&D Systems).

extract_protocol:
Total RNA was purified using the miRNeasy Micro Kit (QIAGEN).
cDNA was reversely transcribed from total RNA with oligo-dT primer, random hexamers with SuperScript™ II Reverse Transcriptase (Invitrogen) and then amplified with IS PCR primers and Kapa HiFi Hotstart Ready Mix (Roche). Then the cDNA library was fragmented and tagged with sequencing adapters using Nextera XT DNA Library Preparation Kit (Illumina), and finally ~500 bp amplicons were got. Quality of library was assessed using the High Sensitivity RNA ScreenTape Kit (Agilent Life Sciences). DNA was quantified using Quant-iT PicoGreen dsDNA Assay Kits (Invitrogen) and purified using AMPure XP beads (Beckman Coulter). Libraries were subjected to 2 × 50-bp paired-end sequencing on an Illumina NovaSeq6000 (Illumina), generating at least 8 million uniquely mapped reads for each sample.

value: PBMC

tag: cell type

value: CD4 T cells

tag: genotype

value: EV

value: Transduced with empty vector (EV)


title: ST-00008601-T

city: Portland

first: Rosalie

last: Sears

state: OR

address: 2730 SW Moody Ave, CL4RS

department: Molecular and Medical Genetics

institute: Oregon Health & Science University

description: Primary pancreas tumor

data_processing:
Paired-end fastq sequences were trimmed using trim-galore (ver 0.6.3) and default parameters.
Pseudoalignment was performed with kallisto (ver 0.44.0) using genome assembly GRCh38.p5 and gencode (ver 24) annotation using default parameters.
Bioconda package bioconductor-tximport (ver 1.12.1) was used to create gene level counts and abundances (TPMs).
Quality checks were assessed with FastQC (ver 0.11.8) and MultiQC (ver 1.7).
Assembly: GRCh38.p5
Supplementary files format and content: Gene level count estimates are provided as a matrix in tab delimited text format.  Feature annotations are provided in the first few columns.
Supplementary files format and content: Gene level TPM estimates are provided as a matrix in tab delimited text format.  Feature annotations are provided in the first few columns.
Supplementary files format and content: Per sample h5 file output from the kallisto pipeline is provided.
Supplementary files format and content: Gene level TMM normalized (edgeR method) estimates are provided as a matrix in tab delimited text format. Feature annotations are provided in the first few columns as well as a column with expression level filtering status. The TMM gene level estimates provided are not log scaled and are generated from the h5 files using general recommendations for importing from the kallisto method as given here: https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html#kallisto & https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html#edgeR

source_name: Pancreas

extract_protocol:
Starting with sectioned FFPE PDAC specimen blocks, Clinical pathologists marked regions of high tumor content (>20% ratio of tumor to normal nuclei) on H&E stained slides for RNA extraction. Solid tumor total nucleic acid was extracted from these tumor regions on adjacent FFPE tissue sections using Chemagic 360 sample-specific extraction kits (Perkin Elmer) and digested by proteinase K. RNA was purified from the total nucleic acid by DNase-I digestion.
100ng of RNA for each tumor sample was heat fragmented in the presence of magnesium to an average size of 200 bp. Library preps were hybridized to the xGENExome Research Panel v1.0 (Integrated DNA Technologies) and target recovery was performed using Streptavidin-coated beads, followed by amplification with the KAPA HiFi Library Amplification Kit.

tag: tumor type

value: Primary

value: Pancreas

value: scraped tumor


title: B2508_D30_10.7Gy_Female

description:
B2508_D30_S0
B2508_D30_10.7Gy

value: 30 days


title: EHT_UNC0224_500nM_rep1

state: MA

description: Replicate 1

library_source: genomic

molecule: genomic DNA

tag: cell line


title: Human induced Treg cells, transduced with empty vector (EV), donor 1


title: serum_manual_healthy_1

type: RNA

city: Cambridge

first: Josephine

middle: Yen

last: Fang

address: 40 Landsdowne Street

department: DMPK

institute: Takeda Pharmaceuticals

hyb_protocol: NanoString protocol

scan_protocol: The miRNA expressions were profiled using NanoString nCounter® with the Human v3 miRNA CodeSet kit (CSO-MMIR15-12) with nCounter® miRNA Sample Prep (Mu-MIRTAG-12). The codeset consists of 827 unique miRNAs barcodes, including six positive controls, eight negative controls, six ligation controls, five spike-in controls (ath-miR-159a, cel-miR-248, miR-254, and osa-miR-414 and 442). Additionally, five reference controls (housekeeping mRNAs: RPL10, ACTB, B2M, GAPDH, and RPL19) were included. Input material comprised 5 µL of concentrated RNA, and the experiment was run according to the manufacturer’s protocol. All hybridizations were carried out for 19 hours, and data counts were obtained by scanning on the MAX model for 555 fields of view (FOV) per sample.

data_processing:
The normalization of data (RCC file) was performed using nSolver Analysis Software v4.0 (NanoString Technologies, https://nanostring.com/products/analysis-solutions/ncounter-analysis-solutions/). Background correction was performed by subtracting the geometric mean of negative control counts by sample within NanoString nSolver™. Positive control and CodeSet normalization utilized the geometric mean of positive controls and the top 100 highly expressed miRNAs probe set according to nSolver™ guidelines.
The processed data in "FinalProcessFabryDiffIsoMethod" is obtained as following:
Fold change expression differences were calculated using nSolver Ratio data based on normalized count data. The data was further filtered for miRNA measured above detection levels in at least 15% of samples. Subsequent data analysis was performed using Rosalind (https://nanostring.rosalind.bio/login). Rosalind conducts differential expression analysis using the R package limma to obtain fold change values and p-values. The comparison of disease and healthy controls was performed within samples in either one of the isolation methods (manual or automated isolation). In this step, we could receive output datasheets:  "FabryManualNormalizedExpression,"  "FabryAutoNuomalizedExpression, "VolcanoManualFvH," "VolcanoAutoFvH, " "heatmapFabryHealthyManualOnly," and HeatmapFvHAutoOnly" from Rosaline processed result. According to the method section from Rosaline's website, Heatmaps of differentially expressed miRNAs from Rosalind were scaled and generated using Ward's hierarchical agglomerative clustering method with the fpc R package. Then I used p<0.05 as threshold to select miRNAs from "VolcanoManualFvH" and "VolcanoAutoFvH" to generate sheets "HighDeFvHManual" and" HighDeFvHAutomated". " Sequentially, the highly differential candidates from "HighDeFvHManual" and" HighDeFvHAutomated" were sorted into ERT treated and non-treated samples for comparison. The results were recorded in "HighDEFvHERTimpact" and "HighlyDEFvHAutoERTimpact" datasheet.
To predict and validate the miRNA-target interactions of the highly differential miRNAs(listed in heatmap) between Fabry and healthy control groups, we used MiRWalk (http://mirwalk.umm.uni-heidelberg.de). We employed the following default parameters: species human, miRNAID, GeneSymbol, Statistic power: 0.95, Position: 3UTR. The databases used for prediction were TargetScan, miRDB, and miRTarBase, and only interactions listed in all three (plus miRWalk's own database) were included. The results are recorded in "miRWalk_miRNA_TargetsManual" and "miRWalk_miRNA_TargetsAuto."
Gene set enrichment analysis (GSEA) was performed to identify significantly enriched functions of the predicted target genes. System analysis, annotation, and visualization of gene function were conducted using the Reactome, the Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene ontology enrichment analysis. The results are recorded in datasheet: ReactomeManual, ReactomeAuto, KEGGMaual, KEGGAutomated, GO_BPManual, GO_BPAutomated, GO_CCManual, GO_CCAutomated, GO_MFManual, GO_MFAutomated. The last two datasheets are the pathyways achieving and FDR(False Discovery Rate)-corrected p<0.05 from Reactome, KEGG, and GO_BP, GO_CC, and GO_MF.

source_name: serum, healthy control, Discovery Life Sciences

extract_protocol: Serum samples were thawed on ice and 200 µL of each sample was transferred into new tubes. miRNAs were isolated using miRNeasy Serum/Plasma Kit (cat. no. 217184, Qiagen, MD). Some samples were alternatively extracted using KingFisher™ Flex Magnetic Particle Processor 96DW with MagMAX mirVana™ Total RNA Isolation Kit (cat. no. 5400630 and A2728, both from ThermoFisher Scientific, MA), following the manufacturer’s protocol. For comparison purposes, eight samples were proceeded using both manual and machine-based methods. The miRNA concentrations were quantified using Qubit™ microRNA assay Kits (ThermoFisher Scientific, MA) with Qubit™ Flex Fluorometers.

treatment_protocol: Serum samples were derived from healthy and Fabry Disease patients.

tag: patientid

tag: age

value: Male

tag: isolation

value: manual

tag: race

value: Unknown

value: serum


title: ST-00010904-T

description: Primary pancreas tumor


title: EHT_UNC0224_1uM_rep2

description: Replicate 2

value: 1157.2 iPS cell line

value: iPSC-derived hematopoietic progenitor cells

value: UNC0224 1uM


title: Human Th0 cells, transduced with shLACC1 (KD), donor 4

value: KD

value: Transduced with shLACC1 (KD)


title: EHT_UNC0224_1uM_rep1

description: Replicate 1


title: B2508_D9_10.7Gy_Female

description:
B2508_D9_S73
B2508_D9_10.7Gy

value: Whole blood

value: Female

value: 10.7Gy thoracic radiation

value: 9 days


title: Human Th0 cells, transduced with shLACC1 (KD), donor 5

value: PBMC

value: CD4 T cells


title: B2508_D6_10.7Gy_Female

description:
B2508_D6_S124
B2508_D6_10.7Gy

value: 6 days


title: Human Th0 cells, transduced with shLACC1 (KD), donor 3


title: serum_manual_healthy_3

value: Caucasian


title: Human Th0 cells, transduced with shLACC1 (KD), donor 2


title: ST-00008056-T

description: Primary pancreas tumor

value: Primary

value: Pancreas

value: scraped tumor


title: EHT_DMSO_rep2

description: Replicate 2

value: DMSO


title: EHT_DMSO_rep1

description: Replicate 1

value: 1157.2 iPS cell line


title: ST-00008043-T

description: Primary pancreas tumor


title: Human Th0 cells, transduced with shLACC1 (KD), donor 1


title: ST-00006291-M

description: Metastisis to the Retroperitoneum

source_name: Retroperitoneum

value: Met

value: Retroperitoneum


title: B2508_D40_10.7Gy_Female

description:
B2508_D40_S0
B2508_D40_10.7Gy

value: 40 days


title: B2508_D3_10.7Gy_Female

description:
B2508_D3_S107
B2508_D3_10.7Gy

value: 3 days


title: keratinocyte_3 treated with IL-4/IL-13 and trehalose

city: Ube

first: Yoichi

last: Mizukami

state: Yamaguchi

department: Science Research Center

country: Japan

institute: Yamaguchi university

data_processing:
FASTQ files produced by Illimina NEXTSeq were imported to CLC Genomics Workbench software (ver.22.0.1).
The 3' end of the sequenced read was trimmed by one nucleotide. Reads with more than 2 ambiguous nucleotides and reads with low quality scores were removed using CLC Genomics Workbench software (ver.22.0.1).
Trimmed sequence reads were mapped to GRCh37 release-75 using CLC genomics workbench with default setting.
Reads Per Kilobase of exon per Million mapped reads (RPKM) and Transcripts Per Million (TPM) were calculated using CLC Genomics Workbench software (ver.22.0.1).
Assembly: GRCh37
Supplementary files format and content: tab-delimited text files include RPKM and TPM values for each sample.

source_name: Human primary keratinocyte

extract_protocol:
Total RNA was isolated from the keratinocytes using the RNeasy Mini Kit (Qiagen). Polyadenylated mRNA was purified using oligo dT beads included in the NEBNext Poly (A) mRNA Magnet Isolation Module (New England Biolabs, NEB). Purified mRNA was used for the construction of sequencing libraries using NEBNext Ultra II RNA library Prep kit (NEB) and NEBNext Multiplex Oligos for Illumina (NEB).
Extracted mRNA was incubated with NEBNext Random Primers in NEBNext First Strand Synthesis Reaction Buffer at 94°C for 15 min, and reverse transcription was performed with NEBNext Strand Synthesis Enzyme Mix. After reverse transcription, index sequences included in NEBNext Multiplex Oligos for Illumina were inserted to cDNA fragments with PCR amplification. Following purification with AMPureXP beads (Beckman Coulter), the quality and the concentration of the libraries was evaluated using a Tapestation 4200 D1000 (Agilent). The confirmed libraries were mixed to equal molecular amounts against the clustering and sequencing on an Illumina NextSeq DNA sequencer with 75 bp paired-end cycle sequencing kit (Illumina).

value: Human primary keratinocyte

value: treated with IL-4/IL-13 and trehalose for 17 hours


title: ST-00006291-T

description: Primary pancreas tumor


title: Human Th0 cells, transduced with empty vector (EV), donor 5

value: EV

value: Transduced with empty vector (EV)


title: B2508_D21_10.7Gy_Female

description:
B2508_D21_S0
B2508_D21_10.7Gy

value: Whole blood

value: Female

value: 10.7Gy thoracic radiation

value: 21 days


title: ST-00009790-M

description: Metastisis to the Peritoneum

source_name: Peritoneum

value: Peritoneum


title: keratinocyte_1 treated with IL-4/IL-13 and trehalose


title: ST-00008108-T

description: Primary pancreas tumor

value: Primary

value: Pancreas


title: keratinocyte_2 treated with IL-4/IL-13 and trehalose


title: B2508_D15_10.7Gy_Female

description:
B2508_D15_S88
B2508_D15_10.7Gy

value: 15 days


title: Human Th0 cells, transduced with empty vector (EV), donor 4

value: PBMC

value: CD4 T cells


title: Human Th0 cells, transduced with empty vector (EV), donor 3


title: keratinocyte_3 treated with IL-4/IL-13

value: treated with IL-4/IL-13 for 17 hours


title: ST-00009788-M

description: Metastisis to the Liver

source_name: Liver

value: Met

value: Liver

value: scraped tumor


title: ST-00007613-T

description: Primary pancreas tumor


title: keratinocyte_2 treated with IL-4/IL-13

value: Human primary keratinocyte


title: B2507_D60_10.7Gy_Female

description:
B2507_D60_S0
B2507_D60_10.7Gy

value: 60 days


title: B2507_D90_10.7Gy_Female

description:
B2507_D90_S0
B2507_D90_10.7Gy

value: 90 days


title: ST-00007313-T

description: Primary pancreas tumor


title: keratinocyte_3 treated with trehalose

value: treated with trehalose for 17 hours


title: Huh7.SMYD5KO.Torin1.riboseq.rep3

city: Shanghai

first: Chenxi

last: He

address: 131 Dong'an Rd, Mingdao Bldg, Rm 512

country: China

institute: Fudan University

data_processing:
Paired-end reads were trimmed trim_galore (v0.4.4).
RNA-seq clean reads were analyzed using a combination of HISAT2 v2.2.1 and StringTie v2.1.7. Raw mRNA counts were normalized using DESeq2.
Ribo-seq reads were filtered by mapping to human rRNA sequences and aligned using STAR v2.7.10b. Ribosome Protected Footprint (RPF) reads were normalized relative to the cumulative counts of mitochondrial RPFs.
Translation efficiency (TE) was determined by the R package Xtail.
Assembly: hg38
Supplementary files format and content: tab-delimited file includes normalized counts for each sample.
Library strategy: Ribo-seq

molecule: cytoplasmic RNA

growth_protocol: DMEM with 10% FBS, 1x penicllin/streptomyci. Cultured at 37℃ at 5% CO2.

extract_protocol:
RNA Clean & Concentrator-5 kit (RCC-5 R1016, zymo)
VAHTS Universal RNA-seq Library Prep Kit (NR605, Vazyme) and Small RNA Library Prep Kit (NR811, Vazyme)
RNA-Seq and ribo-seq

value: hepatocellular carcinoma cell line

value: SMYD5 knockout

value: 50 nM Torin1 for 12 hr

tag: fraction

value: ribosome protected footprint


title: ST-00007585-T

description: Primary pancreas tumor

value: Primary


title: Huh7.SMYD5KO.Torin1.riboseq.rep2


title: Human Th0 cells, transduced with empty vector (EV), donor 1

value: EV

value: Transduced with empty vector (EV)


title: ST-00007307-T

description: Primary pancreas tumor

value: Pancreas


title: B2507_D30_10.7Gy_Female

description:
B2507_D30_S0
B2507_D30_10.7Gy

value: Whole blood

value: Female

value: 10.7Gy thoracic radiation

value: 30 days


title: B2507_D120_10.7Gy_Female

description:
B2507_D120_S0
B2507_D120_10.7Gy

value: 120 days


title: Huh7.SMYD5KO.Torin1.riboseq.rep1


title: keratinocyte_2 treated with trehalose

value: Human primary keratinocyte


title: ST-00007307-M

description: Metastisis to the Jejunum

source_name: Jejunum

value: Met

value: Jejunum

value: scraped tumor


title: B2508_Ctl_0Gy_Female

description:
B2508_Ctl_S33
B2508_Ctl_0Gy

value: control

value: -2 days


title: Human Th0 cells, transduced with empty vector (EV), donor 2

value: PBMC

value: CD4 T cells


title: B2507_D9_10.7Gy_Female

description:
B2507_D9_S72
B2507_D9_10.7Gy

value: 9 days


title: keratinocyte_1 treated with trehalose

value: treated with trehalose for 17 hours


title: B2507_D21_10.7Gy_Female

description:
B2507_D21_S199
B2507_D21_10.7Gy

value: 21 days


title: Huh7.NC.Torin1.riboseq.rep3

value: hepatocellular carcinoma cell line

value: Negative Control

value: 50 nM Torin1 for 12 hr

value: ribosome protected footprint


title: ST-00007594-M

description: Metastisis to the Liver

value: Liver


title: untreated keratinocyte_3

value: untreated


title: ST-00007590-M

description: Metastisis to the Liver


title: untreated keratinocyte_2

value: Human primary keratinocyte


title: ST-00007303-T

description: Primary pancreas tumor

value: Primary

value: Pancreas


title: B2506_D60_10.7Gy_Female

description:
B2506_D60_S0
B2506_D60_10.7Gy

value: Whole blood

value: Female

value: 10.7Gy thoracic radiation

value: 60 days


title: untreated keratinocyte_1


title: Huh7.SMYD5KO.Torin1.input.rep3

data_processing:
Paired-end reads were trimmed trim_galore (v0.4.4).
RNA-seq clean reads were analyzed using a combination of HISAT2 v2.2.1 and StringTie v2.1.7. Raw mRNA counts were normalized using DESeq2.
Ribo-seq reads were filtered by mapping to human rRNA sequences and aligned using STAR v2.7.10b. Ribosome Protected Footprint (RPF) reads were normalized relative to the cumulative counts of mitochondrial RPFs.
Translation efficiency (TE) was determined by the R package Xtail.
Assembly: hg38
Supplementary files format and content: tab-delimited file includes normalized counts for each sample.

value: SMYD5 knockout

value: cytoplamic RNA


title: ST-00006597-M

description: Metastisis to the Falciform Ligament

source_name: Falciform Ligament

value: Met

value: Falciform Ligament

value: scraped tumor


title: VBRNASQ012_S1

city: Boulogne

first: Valerie

last: Bardet

address: 9 avenue Charles de Gaulle

department: CHU A Paré

country: France

institute: AP-HP

data_processing:
Librairies were sequenced on an Illumina NextSeq 500 sequencing system to produce 75-bp paired-ended reads at the Versailles-Saint Quentin University Genome Sequencing facility
RNA-seq fastq data files were processed using the fastp toolkit followed by read quality assessment with the FastQC analysis tool.
Reads were mapped to the GRCh38 version of the human genome and transcriptome using the STAR RNA-seq alignment tool
Reads were used for subsequent analysis if they mapped to a single genomic location, and gene counts were compiled using FeatureCounts
Normalization and differential expression were carried out using the DESeq2 Bioconductor package
Assembly: Hs GRCh38 v44
Supplementary files format and content: tab-delimited text file includes raw count for each sample

extract_protocol:
RNA was harvested using the RNeasy kit (Qiagen®).
Libraries were prepared with the Illumina total RNA stranded with Ribozero plus prep kit following manufacturer's instructions.

value: acute myeloid leukemia

value: darglitazone


title: Huh7.NC.Torin1.riboseq.rep2

value: hepatocellular carcinoma cell line

value: Negative Control

value: 50 nM Torin1 for 12 hr

value: ribosome protected footprint


title: ST-00007300-T

description: Primary pancreas tumor

value: Primary


title: B2506_D90_10.7Gy_Female

description:
B2506_D90_S0
B2506_D90_10.7Gy

value: 90 days


title: VBRNASQ011_S12

value: pioglitazone


title: keratinocyte_1 treated with IL-4/IL-13

value: Human primary keratinocyte

value: treated with IL-4/IL-13 for 17 hours


title: B2506_D30_10.7Gy_Female

description:
B2506_D30_S0
B2506_D30_10.7Gy

value: Whole blood

value: Female

value: 10.7Gy thoracic radiation

value: 30 days


title: B2507_D6_10.7Gy_Female

description:
B2507_D6_S123
B2507_D6_10.7Gy

value: 6 days


title: B2506_D120_10.7Gy_Female

description:
B2506_D120_S0
B2506_D120_10.7Gy

value: 120 days


title: Huh7.SMYD5KO.Torin1.input.rep1

value: SMYD5 knockout

value: cytoplamic RNA


title: B2506_D129_10.7Gy_Female

description:
B2506_D129_S0
B2506_D129_10.7Gy

value: 129 days


title: ST-00007302-T

description: Primary pancreas tumor

value: Pancreas

value: scraped tumor


title: VBRNASQ010_S9

value: acute myeloid leukemia

value: DMSO


title: ST-00007595-M

description: Metastisis to the Liver

value: Met

value: Liver


title: Huh7.NC.Torin1.input.rep3

value: hepatocellular carcinoma cell line

value: Negative Control

value: 50 nM Torin1 for 12 hr


title: ST-00007298-T

description: Primary pancreas tumor

value: Primary


title: VBRNASQ09_S7

value: darglitazone


title: VBRNASQ08_S5

value: pioglitazone


title: B2506_D9_10.7Gy_Female

description:
B2506_D9_S71
B2506_D9_10.7Gy

value: Whole blood

value: Female

value: 10.7Gy thoracic radiation

value: 9 days


title: Huh7.NC.Torin1.input.rep2

value: cytoplamic RNA


title: ST-00007296-T

description: Primary pancreas tumor

value: Pancreas


title: B2506_D6_10.7Gy_Female

description:
B2506_D6_S122
B2506_D6_10.7Gy

value: 6 days


title: Huh7.NC.Torin1.input.rep1


title: B2506_D21_10.7Gy_Female

description:
B2506_D21_S198
B2506_D21_10.7Gy

value: 21 days


title: ST-00007288-M

description: Metastisis to the Peritoneum

value: Peritoneum

value: scraped tumor


title: Huh7.SMYD5KO.riboseq.rep3

value: SMYD5 knockout

value: ribosome protected footprint


title: VBRNASQ06_S2

value: acute myeloid leukemia


title: B2505_D60_10.7Gy_Female

description:
B2505_D60_S0
B2505_D60_10.7Gy

value: 60 days


title: ST-00007389-M

description: Metastisis to the Liver

value: Met

value: Liver


title: Huh7.SMYD5KO.riboseq.rep2

value: hepatocellular carcinoma cell line


title: Huh7.SMYD5KO.Torin1.input.rep2

value: 50 nM Torin1 for 12 hr


title: VBRNASQ04_S3

value: DMSO


title: Huh7.SMYD5KO.riboseq.rep1


title: B2505_D9_10.7Gy_Female

description:
B2505_D9_S70
B2505_D9_10.7Gy

value: Whole blood

value: Female

value: 10.7Gy thoracic radiation


title: ST-00007279-T

description: Primary pancreas tumor

value: Primary

value: Pancreas


title: Huh7.NC.riboseq.rep3

value: Negative Control


title: VBRNASQ03_S6

value: darglitazone


title: B2505_D30_10.7Gy_Female

description:
B2505_D30_S0
B2505_D30_10.7Gy

value: 30 days


title: VBRNASQ05_S4

value: pioglitazone


title: VBRNASQ02_S11


title: Huh7.NC.riboseq.rep1

value: ribosome protected footprint


title: Huh7.NC.riboseq.rep2


title: VBRNASQ01_S10

value: acute myeloid leukemia


title: ST-00021353-M

description: Metastisis to the Liver

value: scraped tumor


title: ST-00007382-M

description: Metastisis to the Peritoneum

value: Met

value: Peritoneum


title: B2505_D3_10.7Gy_Female

description:
B2505_D3_S106
B2505_D3_10.7Gy

value: 3 days


title: VBRNASQ07_S8


title: ST-00007284-T

description: Primary pancreas tumor


title: Huh7.SMYD5KO.input.rep3

value: hepatocellular carcinoma cell line

value: SMYD5 knockout

value: cytoplamic RNA


title: HEK293T_siSRSF1_10Gy_bio_rep5

city: Oxford

first: Majd

last: Abdulghani

state: oxfordshire

address: Old Road Campus Research Building

country: United Kingdom

institute: University of Oxford

description: Collected 48 hours after irradiation or mock irradiation

data_processing:
Paired reads were discarded in the following situations: when either one read contains adapter contamination; when either one read contains more than 10 percent uncertain nucleotides; when either one read contains more than 50 percent low quality nucleotides (base quality less than 5).
Salmon v1.10.0 was used in mapping-based mode to align and quantify reads.
The parameter --keepDuplicates was used during indexing with Salmon v1.10.0
The parameters -l ISR --seqBias --gcBias were used in the quantification step using Salmon v1.10.0
Assembly: chm13v2.0.fa + chm13v2.0_RefSeq_Liftoff_v5.1.gff3
Supplementary files format and content: Each processed file is a gzipped tar file of a directory, as is the standard output of the Salmon tool

growth_protocol: Cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% FBS and 1% Penicillin-Streptomycin.  During transfections, the media used contained the same supplements, except the antibiotics.

extract_protocol:
RNA extraction was carried out as per Qiagen RNAeasy Mini Kit instructions for animal cells using vacuum technology. Samples were eluted in 30 μl RNase-free water and stored at -80°C until subsequent steps were performed.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: The following conditions were used for the knockdown in 6-well plates, as recommended by the Lipofectamine RNAiMAX reverse transfection protocol: 500µl OptiMEM (ThermoFisher, #11058021) per well, 2.5ml antibiotic-free medium (see Cell Culture) per well, 20nM siRNA (siSRSF1 targeting oligo or siControl oligo pool) per well, 5µl Lipofectamine RNAiMAX reagent/well.  Reverse-transfection using the aforementioned conditions was carried out on 200,000 cells per well. After transfection, cells were left to grow for 16 hours, then their media was before being either irradiated at 10 Gy or not.  Cells were collected by scraping 48-hours post-irradiation or mock irradiation.

value: SRSF1 knockdown, 10 Gy radiation


title: Huh7.SMYD5KO.input.rep2


title: ST-00006625-T

description: Primary pancreas tumor


title: B2505_D15_10.7Gy_Female

description:
B2505_D15_S126
B2505_D15_10.7Gy

value: Whole blood

value: Female

value: 10.7Gy thoracic radiation

value: 15 days


title: HEK293T_siSRSF1_10Gy_bio_rep4


title: ST-00007267-T

description: Primary pancreas tumor

value: Primary

value: Pancreas


title: Huh7.SMYD5KO.input.rep1


title: B2505_Ctl_0Gy_Female

description:
B2505_Ctl_S32
B2505_Ctl_0Gy

value: control

value: -2 days


title: HEK293T_siSRSF1_10Gy_bio_rep3


title: B2504_D94_10.7Gy_Female

description:
B2504_D94_S0
B2504_D94_10.7Gy

value: 94 days


title: B2505_D40_10.7Gy_Female

description:
B2505_D40_S0
B2505_D40_10.7Gy

value: 40 days


title: ST-00007266-T

description: Primary pancreas tumor

value: scraped tumor


title: HEK293T_siSRSF1_10Gy_bio_rep2


title: ST-00007256-T

description: Primary pancreas tumor


title: Huh7.NC.input.rep2

value: Negative Control


title: Huh7.NC.input.rep1


title: B2505_D21_10.7Gy_Female

description:
B2505_D21_S197
B2505_D21_10.7Gy

value: 21 days


title: ST-00007255-T

description: Primary pancreas tumor


title: HEK293T_siControl_10Gy_bio_rep5

value: no knockdown, 10 Gy radiation


title: HEK293T_siControl_10Gy_bio_rep4


title: B2504_D60_10.7Gy_Female

description:
B2504_D60_S0
B2504_D60_10.7Gy

value: 60 days


title: ST-00007257-T

description: Primary pancreas tumor


title: PM_2,scRNAseq

city: Guangzhou

first: zhijie

last: Lin

address: Baiyun Jingxi road

institute: Southern Medical University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing,gene counting and aggregation were made using the Cell Ranger software v 4.0.0
The upstream quantitative part of the data analysis only used the Cell Ranger count function, and did not use the Cell Ranger aggr function to integrate the samples. The integration part was processed using the CCA method of the Seurat package.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes TPM values for each Sample

source_name: M1 hEPSC

extract_protocol:
The cell suspension was loaded into Chromium microfluidic chips with 3’(v2 or v3depends on project) chemistry and barcoded with a 10x Chromium Controller (10XGenomics). RNA from the barcoded cells was subsequently reverse-transcribed
Sequencing libraries constructed with reagents from a Chromium Single Cell 3’ v2(v2 or v3, depends on project) reagent kit (10X Genomics) according to the manufacturer’s instructions. Sequencing was performed with Illumina (HiSeq 2000 or NovaSeq ,depends on project) according to the manufacturer’s instructions (Illumina)

treatment_protocol: (1) Human expended pluripotent stem cells (hEPSC) derived-cartilaginous pellets were treated with hypertrophic induction medium containing either 1 μM phentolamine (PM) or DMSO. After 14 days of incubation, the PM-treated and vehicle-treated pellets were then processed for RNA sequencing analysis.

value: M1 hEPSC

value: chondrocytes

value: knock in

tag: differentiation

value: chondrocytic differentiation

value: PM


title: ST-00007380-M

description: Metastisis to the Gallbladder

source_name: Gallbladder

value: Met

value: Gallbladder


title: ST-00007270-T

description: Primary pancreas tumor

value: Primary

value: Pancreas


title: HEK293T_siControl_10Gy_bio_rep3


title: ST-00007239-T

description: Primary pancreas tumor


title: PM_1,scRNAseq

description: 10x Genomics


title: Huh7.NC.input.rep3

value: hepatocellular carcinoma cell line

value: cytoplamic RNA


title: B2504_D6_10.7Gy_Female

description:
B2504_D6_S0
B2504_D6_10.7Gy

value: Whole blood

value: Female

value: 10.7Gy thoracic radiation

value: 6 days


title: HEK293T_siControl_10Gy_bio_rep2

value: no knockdown, 10 Gy radiation


title: CTRL_2,scRNAseq

description: 10x Genomics

value: control


title: HEK293T_siSRSF1_10Gy_bio_rep1

value: SRSF1 knockdown, 10 Gy radiation


title: CTRL_1,scRNAseq

description: 10x Genomics

value: M1 hEPSC

value: chondrocytes


title: B2504_D40_10.7Gy_Female

description:
B2504_D40_S0
B2504_D40_10.7Gy

value: 40 days


title: B2504_D30_10.7Gy_Female

description:
B2504_D30_S0
B2504_D30_10.7Gy

value: 30 days


title: ST-00007234-T

description: Primary pancreas tumor

value: scraped tumor


title: C6

city: zhongshan

first: yongyan

last: pei

address: Long life water, wuguishan street, zhongshan city

department: School of Pharmaceutical and Chemical Engineering

institute: Guangdong Pharmaceutical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
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.
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene FPKM values for every gene and every sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: LUAD-adjacent tissue sample

extract_protocol:
Total RNA was extracted from lung adenocarcinoma tissue samples using the RNA Easy Fast Animal tissue/Cell Total RNA Extraction kit (TIANGEN, China)
The target RNA in the Sample was enriched with magnetic beads with Oligo (dT), and  transcriptome library was constructed using the TruSeq™ RNA Sample Prep Kit(Illumina, USA).

value: LUAD-adjacent tissue sample


title: ST-00007381-M

description: Metastisis to the Peritoneum

value: Met

value: Peritoneum


title: B2504_D90_10.7Gy_Female

description:
B2504_D90_S0
B2504_D90_10.7Gy

value: 90 days


title: HEK293T_siSRSF1_0Gy_bio_rep5

value: SRSF1 knockdown, no radiation


title: HEK293T_siControl_10Gy_bio_rep1


title: ST-00006371-T

description: Primary pancreas tumor

value: Primary

value: Pancreas


title: B2504_D21_10.7Gy_Female

description:
B2504_D21_S0
B2504_D21_10.7Gy

value: Whole blood

value: Female

value: 10.7Gy thoracic radiation

value: 21 days


title: B2504_D3_10.7Gy_Female

description:
B2504_D3_S0
B2504_D3_10.7Gy

value: 3 days


title: B2504_D9_10.7Gy_Female

description:
B2504_D9_S0
B2504_D9_10.7Gy

value: 9 days


title: C4


title: ST-00007175-T

description: Primary pancreas tumor


title: C5


title: B2504_D15_10.7Gy_Female

description:
B2504_D15_S0
B2504_D15_10.7Gy

value: 15 days


title: ST-00007223-M

description: Metastisis to the Liver

value: Liver


title: HEK293T_siSRSF1_0Gy_bio_rep4


title: HEK293T_siSRSF1_0Gy_bio_rep3


title: B2504_Ctl_0Gy_Female

description:
B2504_Ctl_S0
B2504_Ctl_0Gy

value: control

value: -2 days


title: ST-00007216-T

description: Primary pancreas tumor

value: scraped tumor


title: T6

source_name: LUAD surgical tissue sample

value: LUAD surgical tissue sample


title: HEK293T_siSRSF1_0Gy_bio_rep2


title: HEK293T_siSRSF1_0Gy_bio_rep1


title: ST-00007213-T

description: Primary pancreas tumor


title: T4


title: HEK293T_siControl_0Gy_bio_rep5

value: no knockdown, no radiation


title: B2503_D6_10.7Gy_Female

description:
B2503_D6_S0
B2503_D6_10.7Gy

value: 6 days


title: ST-00007208-T

description: Primary pancreas tumor


title: HEK293T_siControl_0Gy_bio_rep4


title: B2503_D40_10.7Gy_Female

description:
B2503_D40_S0
B2503_D40_10.7Gy

value: 40 days


title: ST-00007369-M

description: Metastisis to the Liver

value: Met


title: HEK293T_siControl_0Gy_bio_rep3


title: iMAC with GM-CSF infected M.tb (H37Rv) at MOIs of 5,RNAseq [GM_5_1]

city: Cheongju-si

first: Dayeon

last: Gil

state: Chungcheongbuk-do

address: 202 Osongsaengmyung 2-ro, Heungdeok-gu

department: Division of intractable disease research

country: South Korea

institute: Korea national institute of health

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to GRCh38 whole genome by using STAR version 2.7.11b
TPM were calculated by using RSEM.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: iMAC with GM-CSF

extract_protocol: A library was independently prepared with 1ug of total RNA for each sample by Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina, Inc., San Diego, CA, USA). The libraries were quantified using KAPA Library Quantificatoin kits for Illumina Sequecing platforms according to the qPCR Quantification Protocol Guide (KAPA BIOSYSTEMS) and qualified using the TapeStation D1000 ScreenTape  (Agilent Technologies, Böblingen, Germany).

value: iMAC with GM-CSF

value: infected M.tb (H37Rv) at MOIs of 5


title: B2503_D30_10.7Gy_Female

description:
B2503_D30_S0
B2503_D30_10.7Gy

value: Whole blood

value: Female

value: 30 days


title: iMAC with GM-CSF infected M.tb (H37Rv) at MOIs of 10,RNAseq [GM_10_2]

value: infected M.tb (H37Rv) at MOIs of 10


title: B2503_D3_10.7Gy_Female

description:
B2503_D3_S0
B2503_D3_10.7Gy

value: 10.7Gy thoracic radiation

value: 3 days


title: HEK293T_siControl_0Gy_bio_rep2


title: ST-00007206-T

description: Primary pancreas tumor

value: Primary

value: Pancreas


title: ST-00007203-T

description: Primary pancreas tumor


title: HEK293T_siControl_0Gy_bio_rep1


title: T5


title: B2503_D9_10.7Gy_Female

description:
B2503_D9_S0
B2503_D9_10.7Gy

value: 9 days


title: ST-00007195-T

description: Primary pancreas tumor

value: scraped tumor


title: iMAC with GM-CSF infected ,RNAseq [GM_0_2]


title: ST-00007193-T

description: Primary pancreas tumor


title: B2503_D15_10.7Gy_Female

description:
B2503_D15_S0
B2503_D15_10.7Gy

value: 15 days


title: 345_KD+CP+MET

city: Salzburg

first: Rodolphe

last: Poupardin

address: Strubergasse 22

country: Austria

data_processing:
Reads in fastq format were generated using the Illumina bcl2fastq command line tool (v2.19.1.403) including trimming of the sequencing adapters
Since the samples are human xenografts in mouse, an additional stringent prealignment was performed where all reads in fastq format were aligned to the murine reference genome version GRCm38/mm10 (1) using STAR aligner (2) version 2.6.1a in 2-pass mode to computationally remove reads that originate from the mouse portion in the tissue sample.
Reads that remained unmapped in the prealignment step were recovered and were aligned to the human reference genome version GRCh38 (3) with Gencode 29 annotations (4) using STAR aligner (2) version 2.6.1a in 2-pass mode Raw reads per gene were counted by STAR (2). Differential gene expression was calculated using DESeq2 (5) version 1.22.2. TPM were generated by RSEM (6) .
Assembly: GRCm38(mm10) / GRCh38 (hg38) (human xenograft in mouse)
Supplementary files format and content: Tab seperated text files (.TSV) include TPM values for each Sample (Only human)

source_name: tumor

growth_protocol: SKNBE(2) xenografts were established by injecting 200 µl of a 1:1 mixture of NB cells (2*10^7 cells per mouse) in serum-free medium and Matrigel (Corning) in the right flank of 5 to 6 week old female CD-1 nude mice (Charles River).

extract_protocol:
RNA was extracted from SKNBE(2) xenograft tissue using the AllPrep DNA/RNA/Protein Mini Kit (Qiagen) according to the manufacturer´s instruction
Sequencing libraries were be prepared at the Core Facility Genomics, Medical University of Vienna using the NEBNext Poly(A) mRNA Magnetic Isolation Module and the NEBNext UltraTM II Directional RNA Library Prep Kit for Illumina according to manufacturer's protocols (New England Biolabs). Libraries were QC-checked on a Bioanalyzer 2100 (Agilent) using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay (Invitrogen). Pooled libraries were sequenced on 2 flowcells of a NextSeq500 instrument (Illumina) in 1x75bp single-end sequencing mode.

treatment_protocol: Mice were randomized based on tumor size and allocated to treatment groups to different therapy groups (n=6-10): Control diet (CTRL), CTRL + Cyclophosphamid Monohydrat (CP), CTRL+CP+Metformin (MET), Ketogenic diet (KD)+CP, and KD+CP+MET groups.

value: tumor

value: neuroblast

value: MYCN-amplified

value: KD+CP+MET


title: iMAC with GM-CSF,RNAseq [GM_0_1]

value: iMAC with GM-CSF


title: iMAC with GM-CSF infected M.tb (H37Rv) at MOIs of 5,RNAseq [GM_5_2]

value: infected M.tb (H37Rv) at MOIs of 5


title: 344_KD+CP+MET


title: ST-00007402-M

description: Metastisis to the Mesocolon

source_name: Mesocolon

value: Met

value: Mesocolon


title: iMAC infected M.tb (H37Rv) at MOIs of 5,RNAseq [0_5_2]

source_name: iMAC

value: iMAC


title: 343_KD+CP+MET


title: B2503_Ctl_0Gy_Female

description:
B2503_Ctl_S0
B2503_Ctl_0Gy

source_name: Whole blood

value: Whole blood

value: Female

value: control

value: -2 days


title: B2502_D90_10.7Gy_Female

description:
B2502_D90_S0
B2502_D90_10.7Gy

value: 10.7Gy thoracic radiation

value: 90 days


title: B2505_D6_10.7Gy_Female

description:
B2505_D6_S121
B2505_D6_10.7Gy

value: 6 days


title: ST-00007185-T

description: Primary pancreas tumor

source_name: Pancreas

value: Primary

value: Pancreas

value: scraped tumor


title: iMAC infected M.tb (H37Rv) at MOIs of 5,RNAseq [0_5_1]


title: 339_KD+CP+MET

value: tumor

value: neuroblast

value: MYCN-amplified


title: iMAC with GM-CSF infected M.tb (H37Rv) at MOIs of 10,RNAseq [GM_10_1]

value: iMAC with GM-CSF

value: infected M.tb (H37Rv) at MOIs of 10


title: B2502_D60_10.7Gy_Female

description:
B2502_D60_S0
B2502_D60_10.7Gy

value: 60 days


title: ST-00007183-T

description: Primary pancreas tumor


title: iMAC infected M.tb (H37Rv) at MOIs of 10,RNAseq [0_10_2]

value: iMAC


title: B2503_D21_10.7Gy_Female

description:
B2503_D21_S0
B2503_D21_10.7Gy

value: Whole blood

value: 21 days


title: B2502_D30_10.7Gy_Female

description:
B2502_D30_S0
B2502_D30_10.7Gy

value: Female

value: 30 days


title: iMAC infected M.tb (H37Rv) at MOIs of 10,RNAseq [0_10_1]


title: ST-00007377-M

description: Metastisis to the Peritoneum

value: Met

value: Peritoneum


title: 337_KD+CP+MET

value: KD+CP+MET


title: B2502_D270_10.7Gy_Female

description:
B2502_D270_S0
B2502_D270_10.7Gy

value: 10.7Gy thoracic radiation

value: 270 days


title: ST-00007180-T

description: Primary pancreas tumor

value: Primary

value: Pancreas

value: scraped tumor


title: iMAC,RNAseq [0_0_2]


title: B2502_D240_10.7Gy_Female

description:
B2502_D240_S0
B2502_D240_10.7Gy

value: 240 days


title: iMAC,RNAseq [0_0_1]


title: ST-00007179-T

description: Primary pancreas tumor


title: 335_KD+CP

value: tumor

value: neuroblast

value: MYCN-amplified

value: KD+CP


title: B2502_D210_10.7Gy_Female

description:
B2502_D210_S0
B2502_D210_10.7Gy

value: Whole blood

value: 210 days


title: SI_DMSO_rep2

city: Guadalajara

first: Adriana

middle: Del Carmen

last: Aguilar Lemarroy

state: Jalisco

address: Sierra Mojada 800, Independencia Oriente, 44340 Guadalajara, Jal.

department: División de Inmunología

country: Mexico

institute: Centro de Investigación Biomédica de Occidente

data_processing:
The execution of the bioinformatics pipeline analysis was carried out as follow: R (ver. 4.3.1), RStudio (ver. 2023.09.1 +494) and Galaxy (https://www.usegalaxy.orgaccessed on 02 February 2024) open-source platforms were used to analyze the Illumina raw data
The Quality Check was conducted through the FastQC tool (v0.74+galaxy0).
Afterward, all the reads were processed by the Rsubread package (v2.14.2); at that point, the reads were trimmed and aligned to the Human Genome Reference (GRCh38.p14 v44).
The obtained output was the BAM files, of which the number of reads was counted by the FeatureCounts tool (v2.0.3).
at the final step, the Differential Expression Analysis was settled by the DESeq2 package for R (v1.42. 0). The differential gene expression measurements were normalized by DESeq2's median of ratios (median of ratio of gene counts relative to geometric mean per gene) method.
Assembly: All reads were mapped and aligned to the Human Reference Genome GRCh38.p14v44 using the Rsubread package (Ver. 2.14.2) with the align function.
Supplementary files format and content: Tab-delimited text file includes normalized counts for each sample.

source_name: Uterus; Cervix

growth_protocol: All cell lines were thawed at 37°C and immediately centrifuged at 1,000 rpm for 10 minutes to remove DMSO. Cells were resuspended in Dulbecco's Modified Eagle Medium (DMEM) supplemented with GlutaMAX™ (584 mg/L), sodium pyruvate (110 mg/L), D-glucose (1 g/L) (Cat. No. 10567-014 Gibco, Thermo Fisher Scientific, Waltham, MA, USA), penicillin (100 U/mL), streptomycin (100 μg/mL), and 10% fetal bovine serum. Cell cultures were incubated at 37°C in a humidity atmosphere with 5% CO2.

extract_protocol:
Cell lines were seeded in 100 mm tissue culture dishes (Corning, NY, USA, Cat. 430167) at a density of 2.5x106 for HeLa and 3x106 for SiHa cells, both cell lines were incubated under previous conditions overnight. Subsequently, cells were treated with a 1:5,000 dilution of AEO or DMSO alone (vehicle control). After 4 hours of incubation, the cells were harvested for RNA extraction using the column-based extraction and purification system Zymo Quick-RNA MiniPrep (Zymo Research Corp., Irvine, CA, USA) following manufacturer's instructions. The obtained RNA was quantified by absorbance at 260/280 nm and stored at -80°C until further use
First, total RNA is fragmented into 150 pb segmentes. Second, Reverse transcription is achive to obtain cDNA. Third, ligation of adapters at the ends.

treatment_protocol: All cells were incubated at 37°C in 5% CO2 and grown to 80-90% confluence before addition of a dilution of 1:5,000 [v/v] of döTERRA Arborvitae essential oil, or dimethyl sulfoxide for 4 hrs. in supplemented Dulbecco's Modified Eagle Medium

value: Uterus; Cervix

value: SiHa

value: Epithelial cell

tag: disease state

value: Squamous Cell Carcinoma

value: Dimethyl sulfoxyde


title: B2502_D180_10.7Gy_Female

description:
B2502_D180_S0
B2502_D180_10.7Gy

value: Female

value: 10.7Gy thoracic radiation

value: 180 days


title: 334_KD+CP


title: ST-00007178-T

description: Primary pancreas tumor

value: Primary

value: Pancreas


title: SI_DMSO_rep1


title: ST-00007174-T

description: Primary pancreas tumor

value: scraped tumor


title: B2502_D150_10.7Gy_Female

description:
B2502_D150_S0
B2502_D150_10.7Gy

value: 150 days


title: 338_KD+CP+MET

value: tumor

value: neuroblast

value: KD+CP+MET


title: SI_ARBO_rep2

value: Arborvitae essential oil


title: 329_KD+CP

value: MYCN-amplified

value: KD+CP


title: ST-00007168-T

description: Primary pancreas tumor


title: B2502_D120_10.7Gy_Female

description:
B2502_D120_S0
B2502_D120_10.7Gy

value: Whole blood

value: 120 days


title: ST-00005536-T

description: Primary pancreas tumor


title: Huh7.NC.Torin1.riboseq.rep1

value: hepatocellular carcinoma cell line

value: Negative Control

value: 50 nM Torin1 for 12 hr

value: ribosome protected footprint


title: 328_KD+CP


title: 327_KD+CP


title: SI_ARBO_rep1

value: Uterus; Cervix

value: SiHa

value: Epithelial cell

value: Squamous Cell Carcinoma


title: B2502_D9_10.7Gy_Female

description:
B2502_D9_S69
B2502_D9_10.7Gy

value: Female

value: 10.7Gy thoracic radiation

value: 9 days


title: ST-00007146-T

description: Primary pancreas tumor

value: Primary

value: Pancreas

value: scraped tumor


title: 336_KD+CP

value: tumor

value: neuroblast

value: MYCN-amplified

value: KD+CP


title: HE_DMSO_rep2

value: HeLa

value: Adenocarcinoma

value: Dimethyl sulfoxyde


title: 326_CTRL+CP+MET

value: CTRL+CP+MET


title: B2502_D6_10.7Gy_Female

description:
B2502_D6_S49
B2502_D6_10.7Gy

value: Whole blood

value: 6 days


title: HE_DMSO_rep1

value: Uterus; Cervix

value: Epithelial cell


title: ST-00007165-T

description: Primary pancreas tumor


title: B2502_D40_10.7Gy_Female

description:
B2502_D40_S227
B2502_D40_10.7Gy

value: Female

value: 10.7Gy thoracic radiation

value: 40 days


title: ST-00005813-T

description: Primary pancreas tumor

value: Primary

value: Pancreas


title: HE_ARBO_rep2

value: Arborvitae essential oil


title: 324_CTRL+CP+MET

value: tumor

value: neuroblast


title: ST-00006650-M

description: Metastisis to the Lung

source_name: Lung

value: Met

value: Lung

value: scraped tumor


title: 322_CTRL+CP+MET

value: MYCN-amplified


title: ST-00007120-T

description: Primary pancreas tumor


title: Bulk RNAseq from PC9 EGFR-low lung cancer cell line - SAHA treated- Replicate Sample 3

city: Helsinki

first: Heidi

middle: M

last: Haikala

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

description:
PC9_EGFR-low_SAHA_3
Cuff_Gene_Counts_PC9_saha.csv

data_processing:
Sequenced reads were aligned to the UCSC hg19 reference genome assembly and gene counts were quantified using STAR (v2.5.1b). Differential gene expression testing was performed by DESeq2 (v1.10.1) and normalized read counts (FPKM) were calculated using cufflinks (v2.2.1). RNAseq analysis was performed using the VIPER snakemake pipeline
Assembly: hg19
Supplementary files format and content: csv file includes raw counts for each sample

source_name: Lung cancer

growth_protocol: PC-9 cells were cultured in RPMI + 10% FBS + 1% P/S.

extract_protocol:
RNA was harvested using RNA easy kit (Qiagen). 500ng-1ug RNA was submitted for run.
This RNA library preparation method takes total purified RNA as input and enriches for polyadenylated (polyA+) transcripts using oligo-dT coated beads. PolyA+ RNA was subsequently fragmented using heat and Mg+ and reverse transcribed into cDNA using random priming. Illiumina adapters were ligated to dsDNA and PCR amplified. Roche Kapa mRNA Hyper Prep was used as the library prep kit.

treatment_protocol: Cells were seeded into 6-well plates and harvested after 24 hours. For DMSO or 1uM SAHA (Vorinostat) treated cells, cells were seeded and drug treatments were started after 24 hours. Treatment time was 72 hours after which RNA was collected for analysis.

value: Lung cancer

value: Cancer cell

value: EGFR delE746-A770

value: 1uM SAHA (Vorinostat)


title: 319_CTRL+CP+MET

value: CTRL+CP+MET


title: B2502_D15_10.7Gy_Female

description:
B2502_D15_S125
B2502_D15_10.7Gy

value: Whole blood

value: Female

value: 15 days


title: B2502_D21_10.7Gy_Female

description:
B2502_D21_S0
B2502_D21_10.7Gy

value: 10.7Gy thoracic radiation

value: 21 days


title: ST-00007099-T

description: Primary pancreas tumor

value: Primary

value: Pancreas


title: B2502_Ctl_0Gy_Female

description:
B2502_Ctl_S31
B2502_Ctl_0Gy

value: control

value: -2 days


title: Bulk RNAseq from PC9 EGFR-low lung cancer cell line - SAHA treated- Replicate Sample 2

description:
PC9_EGFR-low_SAHA_2
Cuff_Gene_Counts_PC9_saha.csv

value: EGFR delE746-A769


title: ST-00007085-T

description: Primary pancreas tumor

value: scraped tumor


title: 315_CTRL+CP

value: tumor

value: neuroblast

value: MYCN-amplified


title: Bulk RNAseq from PC9 EGFR-low lung cancer cell line - SAHA treated- Replicate Sample 1

description:
PC9_EGFR-low_SAHA_1
Cuff_Gene_Counts_PC9_saha.csv

value: Lung cancer

value: Cancer cell

value: EGFR delE746-A768


title: ST-00007071-T

description: Primary pancreas tumor


title: 318_CTRL+CP+MET

value: CTRL+CP+MET


title: 325_CTRL+CP+MET


title: B2501_D60_10.7Gy_Female

description:
B2501_D60_S0
B2501_D60_10.7Gy

value: Whole blood

value: Female

value: 60 days


title: B2501_D77_10.7Gy_Female

description:
B2501_D77_S0
B2501_D77_10.7Gy

value: 10.7Gy thoracic radiation

value: 77 days


title: 314_CTRL+CP

value: CTRL+CP


title: Bulk RNAseq from PC9 EGFR-low lung cancer cell line - DMSO treated- Replicate Sample 2

description:
PC9_EGFR-low_DMSO_2
Cuff_Gene_Counts_PC9_saha.csv

value: EGFR delE746-A766

value: DMSO


title: 312_CTRL+CP


title: ST-00007067-T

description: Primary pancreas tumor

value: Primary

value: Pancreas


title: B2501_D30_10.7Gy_Female

description:
B2501_D30_S0
B2501_D30_10.7Gy

value: 30 days


title: Bulk RNAseq from PC9 EGFR-low lung cancer cell line - DMSO treated- Replicate Sample 1

description:
PC9_EGFR-low_DMSO_1
Cuff_Gene_Counts_PC9_saha.csv

value: EGFR delE746-A765


title: B2502_D3_10.7Gy_Female

description:
B2502_D3_S42
B2502_D3_10.7Gy

value: 3 days


title: ST-00007061-T

description: Primary pancreas tumor

value: scraped tumor


title: HE_ARBO_rep1

value: Uterus; Cervix

value: HeLa

value: Epithelial cell

value: Adenocarcinoma

value: Arborvitae essential oil


title: B2501_D9_10.7Gy_Female

description:
B2501_D9_S68
B2501_D9_10.7Gy

value: Whole blood

value: Female

value: 9 days


title: 310_CTRL+CP

value: tumor

value: neuroblast

value: MYCN-amplified

value: CTRL+CP


title: Bulk RNAseq from PC9 EGFR-high lung cancer cell line - SAHA treated- Replicate Sample 3

description:
PC9_EGFR-high_SAHA_3
Cuff_Gene_Counts_PC9_saha.csv

value: Lung cancer

value: Cancer cell

value: EGFR delE746-A764

value: 1uM SAHA (Vorinostat)


title: 308_CTRL+CP


title: EtOH_24h_3

city: Madrid

first: Alicia

last: Sanchez

address: Joaquín Rodrigo, 2 Majadahonda

country: Spain

institute: Instituto de Investigación Sanitaria Puerta de Hierro-Segovia de Arana

data_processing:
FastQC v0.12.1 and Cutadapt v4.4 were used for quality control of the raw reads and removal of the adapter sequences, respectively. Trimmomatic v0.39 was employed to further select trimmed reads larger than 20 nucleotides and with a mapping quality greater than 30. Reads were aligned with HISAT2 v2.2.1 to the rat genome assembly mRatBN7.2. Mapped reads were annotated using the Ensembl gene annotation v111 for the rat genome and were quantified using HTSeq v2.0.3. Gene counts were analysed using principal components with custom R scripts (R version 4.3.1). DESeq2 v1.40.2 was used for differential expression analysis
Assembly: mRatBN7.2
Supplementary files format and content: Raw counts of sequencing read in TSV format

organism: Rattus norvegicus

source_name: Hippocampal neuron

growth_protocol: Primary hippocampal neurons were obtained from Wistar rats at embryonic day 18. Briefly, embryos were removed from the womb under sterile conditions and decapitated to dissect the brains. Hippocampi were isolated at 4 ºC in Hank’s balanced salt solution (HBSS) without calcium and magnesium, supplemented with 10 mM HEPES buffered saline and 100 U/ml of penicillin-streptomycin. The hippocampi were mechanically disaggregated using fire-polished pipettes and plated for 2-4 hours in neuronal plating medium composed of minimum essential medium (MEM) enriched with 0.6% D-glucose and 10% horse serum. Neuronal plating medium was replaced by neurobasal medium supplemented with 1X B-27 and 2 mM L-glutamine. Neurons were grown for 7 days prior to experiments. Cells were maintained at 37 ºC in a humidified incubator with 5% CO2. All culture media were purchased from Thermo Fisher Scientific (Waltham, MA, USA).

extract_protocol:
RNA was extracted using the Maxwell® 16 LEV simply RNA Cells kit and the robotic platform Maxwell® 16 (both from Promega Biotech Ibérica), following the manufacturer’s instructions.
Poly(A)+ mRNA fraction was isolated from total RNA and cDNA libraries were obtained following Illumina’s recommendations. Briefly, poly(A)+ RNA was isolated on poly-T oligo-attached magnetic beads and chemically fragmented prior to reverse transcription and cDNA generation. The cDNA went through an end repair process, addition of a single “A” base to the 3’ end and ligation to the adapters. Finally, the products were purified and enriched with PCR to create the indexed final double stranded DNA library. The quality and quantity of the libraries were analysed in tapeStation 4200, using the High Sensitivity assay (Agilent Technologies)

treatment_protocol: DMF and MMF (both from Sigma-Aldrich, Saint Louis, MO, USA) were prepared as stock solutions in dimethyl sulfoxide (DMSO); CBD (Cayman chemical, Ann Arbor, MI, USA) was prepared in ethanol (EtOH). All the compounds were titrated in their respective vehicle and diluted into the culture media for cell treatments. The final concentration of vehicle (DMSO or EtOH) was consistent for all treated cells (0.2%). For RNA-seq experiments, neurons were treated with 30 µM DMF, 30 µM MMF or 6 µM CBD and their respective vehicles for 4 and 24 hours. Each experiment was repeated 3 times.

value: Hippocampal neuron

value: Wild-type


title: Bulk RNAseq from PC9 EGFR-high lung cancer cell line - SAHA treated- Replicate Sample 2

description:
PC9_EGFR-high_SAHA_2
Cuff_Gene_Counts_PC9_saha.csv

value: EGFR delE746-A763


title: CBD_24h_3


title: MMF_24h_3


title: B2501_D3_10.7Gy_Female

description:
B2501_D3_S41
B2501_D3_10.7Gy

value: 10.7Gy thoracic radiation

value: 3 days


title: B2501_D6_10.7Gy_Female

description:
B2501_D6_S120
B2501_D6_10.7Gy

value: 6 days


title: DMF_24h_3


title: Bulk RNAseq from PC9 EGFR-high lung cancer cell line - DMSO treated- Replicate Sample 3

description:
PC9_EGFR-high_DMSO_3
Cuff_Gene_Counts_PC9_saha.csv

value: EGFR delE746-A761

value: DMSO


title: B2501_D21_10.7Gy_Female

description:
B2501_D21_S210
B2501_D21_10.7Gy

value: Whole blood

value: Female

value: 21 days


title: 305_CTRL

value: tumor

value: neuroblast

value: MYCN-amplified

value: CTRL


title: 306_CTRL


title: Bulk RNAseq from PC9 EGFR-low lung cancer cell line - DMSO treated- Replicate Sample 3

description:
PC9_EGFR-low_DMSO_3
Cuff_Gene_Counts_PC9_saha.csv

value: Lung cancer

value: Cancer cell

value: EGFR delE746-A767


title: Bulk RNAseq from PC9 EGFR-high lung cancer cell line - DMSO treated- Replicate Sample 2

description:
PC9_EGFR-high_DMSO_2
Cuff_Gene_Counts_PC9_saha.csv

value: EGFR delE746-A760


title: DMSO_24h_3

value: Hippocampal neuron

value: Wild-type


title: Bulk RNAseq from PC9 EGFR-high lung cancer cell line - DMSO treated- Replicate Sample 1

description:
PC9_EGFR-high_DMSO_1
Cuff_Gene_Counts_PC9_saha.csv

value: EGFR delE746-A759


title: 303_CTRL


title: B2501_D15_10.7Gy_Female

description:
B2501_D15_S87
B2501_D15_10.7Gy

value: 10.7Gy thoracic radiation

value: 15 days


title: B2501_Ctl_0Gy_Female

description:
B2501_Ctl_S30
B2501_Ctl_0Gy

value: control

value: -2 days


title: 304_CTRL


title: EtOH_4h_3


title: Bulk RNAseq from PC9 EGFR-low lung cancer cell line- Replicate Sample 3

description:
PC9_EGFR_low_3
Cuff_Gene_Counts_PC9.csv

value: EGFR delE746-A758

value: No treatment


title: 302_CTRL

value: tumor


title: B2008_D30_10.7Gy_Male

description:
B2008_D30_S0
B2008_D30_10.7Gy

value: Whole blood

value: Male

value: 30 days


title: CBD_4h_3


title: 307_CTRL+CP

value: neuroblast

value: MYCN-amplified

value: CTRL+CP


title: Bulk RNAseq from PC9 EGFR-low lung cancer cell line- Replicate Sample 2

description:
PC9_EGFR_low_2
Cuff_Gene_Counts_PC9.csv

value: Lung cancer

value: Cancer cell

value: EGFR delE746-A757


title: MMF_4h_3

value: Hippocampal neuron

value: Wild-type


title: Bulk RNAseq from PC9 EGFR-high lung cancer cell line - SAHA treated- Replicate Sample 1

description:
PC9_EGFR-high_SAHA_1
Cuff_Gene_Counts_PC9_saha.csv

value: EGFR delE746-A762

value: 1uM SAHA (Vorinostat)


title: B2501_D40_10.7Gy_Female

description:
B2501_D40_S226
B2501_D40_10.7Gy

value: Female

value: 10.7Gy thoracic radiation

value: 40 days


title: B2008_D9_10.7Gy_Male

description:
B2008_D9_S67
B2008_D9_10.7Gy

value: 9 days


title: 301_CTRL

value: tumor

value: CTRL


title: Bulk RNAseq from PC9 EGFR-low lung cancer cell line- Replicate Sample 1

description:
PC9_EGFR_low_1
Cuff_Gene_Counts_PC9.csv

value: EGFR delE746-A756

value: No treatment


title: DMSO_4h_3


title: DMF_4h_3


title: Bulk RNAseq from PC9 EGFR-high lung cancer cell line- Replicate Sample 3

description:
PC9_EGFR_high_3
Cuff_Gene_Counts_PC9.csv

value: EGFR delE746-A755


title: B2008_D6_10.7Gy_Male

description:
B2008_D6_S119
B2008_D6_10.7Gy

value: Whole blood

value: Male

value: 6 days


title: RB-p53 DKO Replicate 4 EZ

city: London

first: Fred

last: Dick

state: Ontario

address: 1151 Richmond St

department: Pathology and Laboratory Medicine

country: Canada

institute: Western University

data_processing:
Genome indexes were generated for Homo_sapiens.GRCh38.99 with genomic sequence length around annotated junctions (used in constructing splice junctions database) set to 100 using STAR aligner  (v2.7.3a)
Sequence reads were mapped to the indexed genome Homo_sapiens.GRCh38.99 and counted using STAR aligner (v2.7.3a)
Assembly: Homo_sapiens.GRCh38.99.gtf
Supplementary files format and content: tab-delimited text file, read counts for each sample

source_name: Prostate

growth_protocol: LNCaP cells were maintained in RMPI-1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested from cells (4 replicates each, 16 samples total) using NEB Monarch Total RNA Miniprep Kit. 1 ug of total RNA was used for each sample for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using VAHTS Total RNA-seq (H/M/R) Library Prep Kit (including rRNA reduction) following manufacturer's protocols.

treatment_protocol:
RB-p53 double knockout (DKO) LNCaP cells were first generated using CRISPR-Cas9
LNCaP WT and DKO cells were treated with 50 uM enzalutamide or an equal volume of DMSO for 6 days

value: Prostate

value: LNCaP

value: Prostate Adenocarcinoma

value: RB-p53 Double Knockout

value: Enzalutamide (50 uM)


title: B2008_D21_10.7Gy_Male

description:
B2008_D21_S196
B2008_D21_10.7Gy

data_processing:
The FASTQ sequences were trimmed using CutAdapt v. 2.10 [https://doi.org/10.14806/ej.17.1.200] with the following settings: “--nextseq-trim=2 --trim-n -n 5 -O 5 -q 10,10 -m 15 -j 0” and aligned using STAR v. 2.7.6a [https://doi.org/10.1093/bioinformatics/bts635] with parameters set as recommended by ENCODE3 consortium (https://www.encodeproject.org/pipelines/ENCPL444CYA/). Macaca mulatta (Rhesus monkey) genome assembly Mmul_10 (release date: Feb. 2019) with RefSeq annotation (accession number GCF_003339765.1) was used as a reference. Counting was performed with the help of Subread package v. 2.0.1 [10.1093/bioinformatics/btt656]. The count matrix was processed in R (1) for further analysis.
Assembly: Macaca mulatta (Rhesus monkey) genome assembly Mmul_10 (release date: Feb. 2019).
Supplementary files format and content: *.txt: Tab-delimited text files include raw counts and normalized counts for each Sample.

value: 21 days


title: Bulk RNAseq from PC9 EGFR-high lung cancer cell line- Replicate Sample 2

description:
PC9_EGFR_high_2
Cuff_Gene_Counts_PC9.csv

value: Lung cancer

value: Cancer cell

value: EGFR delE746-A754


title: CBD_24h_2

value: Hippocampal neuron

value: Wild-type


title: B2007_D30_10.7Gy_Male

description:
B2007_D30_S0
B2007_D30_10.7Gy

value: 10.7Gy thoracic radiation

value: 30 days


title: RB-p53 DKO Replicate 3 EZ


title: RB-p53 DKO Replicate 2 EZ


title: Bulk RNAseq from PC9 lung cancer cell line- Replicate Sample 3

description:
PC9_Parental_3
Cuff_Gene_Counts_PC9.csv

value: EGFR delE746-A752

value: No treatment


title: Bulk RNAseq from PC9 EGFR-high lung cancer cell line- Replicate Sample 1

description:
PC9_EGFR_high_1
Cuff_Gene_Counts_PC9.csv

value: EGFR delE746-A753


title: RB-p53 DKO Replicate 1 EZ


title: MMF_24h_2


title: B2007_D6_10.7Gy_Male

description:
B2007_D6_S118
B2007_D6_10.7Gy

value: Whole blood

value: Male

value: 6 days


title: Bulk RNAseq from PC9 lung cancer cell line- Replicate Sample 2

description:
PC9_Parental_2
Cuff_Gene_Counts_PC9.csv

value: EGFR delE746-A751


title: B2007_D9_10.7Gy_Male

description:
B2007_D9_S66
B2007_D9_10.7Gy

value: 9 days


title: DMF_24h_2


title: LNCaP WT Replicate 4 EZ

value: Prostate

value: LNCaP

value: Prostate Adenocarcinoma

value: WT

value: Enzalutamide (50 uM)


title: LNCaP WT Replicate 3 EZ


title: Bulk RNAseq from PC9 lung cancer cell line- Replicate Sample 1

description:
PC9_Parental_1
Cuff_Gene_Counts_PC9.csv

value: Lung cancer

value: Cancer cell

value: EGFR delE746-A750


title: B2007_D40_10.7Gy_Male

description:
B2007_D40_S202
B2007_D40_10.7Gy

value: 10.7Gy thoracic radiation

value: 40 days


title: LNCaP WT Replicate 2 EZ


title: DMSO_24h_2

value: Hippocampal neuron

value: Wild-type


title: CBD_4h_2


title: B2007_D3_10.7Gy_Male

description:
B2007_D3_S40
B2007_D3_10.7Gy

value: Whole blood

value: 3 days


title: LNCaP WT Replicate 1 EZ


title: EtOH_4h_2


title: B2007_D21_10.7Gy_Male

description:
B2007_D21_S195
B2007_D21_10.7Gy

value: Male

value: 21 days


title: tm_GB smRNA

city: West Haven

first: Francesc

last: Lopez

state: CT

department: Department of Genetics

institute: Yale University

library_source: other

data_processing:
The reads were trimmed with standard Trimmomatic to remove Illumina primers and linkers and aligned to Hg19.
Using PartekTM FlowTM v11.0.23, the aligned miRNAs with <3 average counts were pruned, and differential expression analysis was performed with DEseq2.
Common miRNA with |log2([Treatment]/[Control])|>0.5 were evaluated for seed sequences in IL15 using miRDB, DIANA-MicroT 2023, and TargetScan.
Assembly: hg19
Supplementary files format and content: csv file containing counts for each mature small RNA

molecule: other

source_name: Endothelial colony forming cell

growth_protocol: Primary cultured human endothelial colony forming cells in EGM-2-MV on 0.1% gelatin coated tissue culture plastics at 37C 5% CO2.

extract_protocol:
Monolayers were washed with Hank's Buffered Saline Solution (Gibco). Lysates and miRNA were purified with Qiagen miRNeasy kit per protocol.
miRNA Seq Libraries were prepared using the Qiagen miRNA Library Prep Kit (Cat# 331505):  RNA was normalized to a starting input between 1ng-500ng. Adapters are ligated sequentially to the 3’ and 5’ ends of miRNAs prior to cDNA synthesis with UMI assignment, cDNA cleanup, amplification, and final library cleanup. The library was run on the Agilent Tapestation, and size selection was performed if there is excess adapter dimer. The library was then quantified by qRT-PCR using a commercially available kit (KAPA Biosystems).  According to Illumina protocol, the libraries underwent 100-bp paired-end sequencing using an Illumina NovaSeq6000.

treatment_protocol: Cytokine treatment as described above in EGM-2-MV.

value: Endothelial colony forming cell

value: 50ng/mL IFN-gamma/100pg/mL IL-1-beta


title: RB-p53 DKO Replicate 3 DMSO

value: Prostate

value: LNCaP

value: RB-p53 Double Knockout

value: DMSO


title: B2007_D15_10.7Gy_Male

city: Bethesda

first: Uma

last: Shankavaram

description:
B2007_D15_S86
B2007_D15_10.7Gy

extract_protocol: Blood samples were procured from each of the animals (n = 28) two days before irradiation as control, every three days post-irradiation for the initial 30 days, on days 40, 50, and 60, and approximately every 30 days until the euthanization of all surviving animals at day 270 post-irradiation.

value: 15 days


title: RB-p53 DKO Replicate 4 DMSO

value: Prostate Adenocarcinoma


title: MMF_4h_2


title: tm_G smRNA

value: 50ng/mL IFN-gamma


title: EtOH_24h_2


title: DMSO_4h_2


title: B2007_Ctl_0Gy_Male

description:
B2007_Ctl_S29
B2007_Ctl_0Gy

value: control

value: -2 days


title: B2006_D60_10.7Gy_Male

description:
B2006_D60_S0
B2006_D60_10.7Gy

value: 10.7Gy thoracic radiation

value: 60 days


title: tm_Ctrl smRNA

value: Untreated


title: tm_B smRNA

value: 100pg/mL IL-1-beta


title: CBD_24h_1

value: Hippocampal neuron

value: Wild-type


title: jm_TNF smRNA

value: Endothelial colony forming cell

value: 10ng/mL TNF


title: RB-p53 DKO Replicate 2 DMSO

value: Prostate


title: RB-p53 DKO Replicate 1 DMSO

value: LNCaP


title: tm_TNF smRNA


title: B2006_D30_10.7Gy_Male

description:
B2006_D30_S0
B2006_D30_10.7Gy

value: Whole blood

value: Male

value: 30 days


title: LNCaP WT Replicate 4 DMSO

value: Prostate Adenocarcinoma

value: WT

value: DMSO


title: B2006_D9_10.7Gy_Male

description:
B2006_D9_S65
B2006_D9_10.7Gy

value: 9 days


title: EtOH_24h_1


title: MMF_24h_1


title: jm_G smRNA

value: 50ng/mL IFN-gamma


title: jm_GB smRNA

value: 50ng/mL IFN-gamma/100pg/mL IL-1-beta


title: LNCaP WT Replicate 3 DMSO


title: B2006_D6_10.7Gy_Male

description:
B2006_D6_S117
B2006_D6_10.7Gy

value: 10.7Gy thoracic radiation

value: 6 days


title: DMF_4h_2

value: Hippocampal neuron


title: B2006_D21_10.7Gy_Male

description:
B2006_D21_S0
B2006_D21_10.7Gy

value: 21 days


title: DMF_24h_1

value: Wild-type


title: jm_Ctrl smRNA

value: Endothelial colony forming cell

value: Untreated


title: jm_B smRNA

value: 100pg/mL IL-1-beta


title: LNCaP WT Replicate 1 DMSO

value: Prostate

value: LNCaP


title: DMSO_24h_1


title: B2005_D6_10.7Gy_Male

description:
B2005_D6_S0
B2005_D6_10.7Gy

value: Whole blood

value: Male


title: jj_TNF smRNA

value: 10ng/mL TNF


title: EZ TF Replicate 2

data_processing:
Reads were trimmed with at most 10% errors in single-end mode, for flanking annealing sequences using cutadapt (v1.16)
sgRNA sequence reads were matched and counted to the TKOv3 Guide Sequences reference file using MAGECK software (v0.5.7)
Supplementary files format and content: tab-delimited text file, read counts

extract_protocol:
gDNA from cells collected at initial (T0) and final (TF) timepoints (12 samples total) was harvested using Qiagen DNA Blood Maxi Kit
Next Generation Sequencing of sgRNA sequences: sgRNA sequences were PCR amplified and library was constructed following the TKOv3 CRISPR Screen Protocol. 200ng of DNA from each sample was used for sequencing

treatment_protocol:
LNCaP cells were infected with the TKOv3 lentiviral library at an MOI of 0.3. After puromycin selection, cells were split into 6 pools (3 control replicates and 3 treatment replicates). Just prior to first treatment period, cells were collected from each replicate to serve at T0 timepoint samples.
Cells were passaged every 9 days (for a total of 63 days), cells were allowed to seed and adhere to the plate for 3 days and then treated with 50 uM enzalutamide or equal volume DMSO for 6 days

value: Prostate Adenocarcinoma

value: TKOV3 Lentiviral Library

value: Enzalutamide (50 uM)

tag: molecule type

value: sgRNA PCR Amplicons from gDNA


title: B2005_D40_10.7Gy_Male

description:
B2005_D40_S0
B2005_D40_10.7Gy

tag: tissue

value: 10.7Gy thoracic radiation

value: 40 days


title: CBD_4h_1

value: Hippocampal neuron


title: jj_GB smRNA

value: 50ng/mL IFN-gamma/100pg/mL IL-1-beta


title: EZ TF Replicate 1


title: MMF_4h_1

value: Wild-type


title: EtOH_4h_1


title: B2005_D30_10.7Gy_Male

description:
B2005_D30_S0
B2005_D30_10.7Gy

tag: Sex

value: 30 days


title: DMSO TF Replicate 3

tag: treatment

value: DMSO


title: B2005_D3_10.7Gy_Male

description:
B2005_D3_S0
B2005_D3_10.7Gy

tag: time point

value: 3 days


title: DMF_4h_1


title: jj_G smRNA

value: Endothelial colony forming cell

value: 50ng/mL IFN-gamma


title: DMSO_4h_1


title: jj_B smRNA

value: 100pg/mL IL-1-beta


title: B2005_D21_10.7Gy_Male

description:
B2005_D21_S0
B2005_D21_10.7Gy

value: Whole blood

value: Male

value: 21 days

tag: animal id


title: DMSO TF Replicate 2

value: Prostate

value: LNCaP

tag: cell type

value: Prostate Adenocarcinoma

value: TKOV3 Lentiviral Library


title: B2005_D15_10.7Gy_Male

description:
B2005_D15_S0
B2005_D15_10.7Gy

value: 10.7Gy thoracic radiation

value: 15 days


title: B2005_D9_10.7Gy_Male

description:
B2005_D9_S0
B2005_D9_10.7Gy

value: 9 days


title: DMSO TF Replicate 1

tag: genotype

value: sgRNA PCR Amplicons from gDNA


title: EZ TF Replicate 3

value: Enzalutamide (50 uM)


title: tm_TNF

data_processing:
Reads were trimmed with fastp software v0.21.0 using default parameters.
Trimmed reads were mapped to the human reference genome (hg38) with HISAT2 v2.1.0indicating that reads correspond to the reverse complement of the transcripts. Alignments with a quality score below 20 were excluded from further analysis.
Gene counts were produced with StringTie v1.3.3b and the Python script “prepDE.py” provided in the package. StringTie was limited to reads matching the reference annotation GENCODE v27. After obtaining the matrix of read counts, differential expression analysis was conducted, and normalized counts were produced using DESeq2
Assembly: hg38
Supplementary files format and content: CSV file with the read counts per sample and gene

extract_protocol:
The monolayers were washed with Hank’s Buffered Saline Solution (Gibco) and lysed, and RNA was purified with Qiagen RNeasy kit per manufacturer protocol.   Using the Kapa RNA HyperPrep Kit with RiboErase (KR1351), rRNA was depleted starting from 25-1000ng of total RNA by hybridization of rRNA to complementary DNA oligonucleotides, followed by treatment with RNase H and DNase to remove rRNA duplexed to DNA.
Samples were then fragmented using heat and magnesium.  First strand synthesis was performed using random priming.  Indexed libraries that meet appropriate cut-offs for both quantity and quality were quantified by qRT-PCR, and insert size distribution was determined with the LabChip GX or Agilent Bioanalyzers. Samples with a yield of ≥0.5 ng/μl were used for sequencing. According to Illumina protocol, the libraries underwent 100-bp paired-end sequencing using an Illumina NovaSeq6000, generating an average of 250 million paired-end reads per library.

value: 10ng/mL TNF


title: LNCaP WT Replicate 2 DMSO

value: WT

value: DMSO


title: Kidney OSOM, TCP, Day90

city: Fuchu-shi

first: Shunsuke

last: Ozawa

state: Tokyo

address: 3-5-8 Saiwai-cho

institute: Tokyo University of Agriculture and Technology

data_processing:
An index of the reference genome (Rattus norvegicus_Rnor_6.0) was built using HISAT2 v2.0.5, and clean paired-end reads were mapped to the reference genome using HISAT2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads mapped to each gene. Then, the FPKM value of each gene were calculated based on the length of the gene and the count of reads mapped to that gene.
Assembly: rn6
Supplementary files format and content: fpkm

source_name: Kidney OSOM

growth_protocol: Five-week-old male F344/NSlc rats were purchased from Japan SLC, Inc. (Hamamatsu, Japan), and acclimated to a pelleted basal diet (CRF-1; Oriental Yeast Co., Ltd. Tokyo, Japan) and tap water ad libitum. The animals were housed in polycarbonate cages supplied with paper bedding in a room under controlled environmental conditions (temperature: 23 ± 2°C, relative humidity: 55 ± 15%) with a 12-h light/dark cycle.

extract_protocol:
Total RNA was purified with an AllPrep DNA/RNA Mini Kit (Qiagen) following the manufacturer's protocol.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads, and then the mRNA was fragmented into small pieces. The first-strand cDNA was synthesized using random hexamer primers, followed by synthesis of the second-strand cDNA using dTTP for the non-directional library. These cDNA fragments underwent an end repair process, adding a single “A” base and then ligating the adapters. These products were purified and enriched by PCR to create the final cDNA library.

treatment_protocol: Animals were treated with OTA, MCPD, or TCP for 13 weeks. In the OTA group, animals were administered OTA dissolved in corn oil at 210 µg/kg body weight by oral gavage (5 days/week). In the MCPD group, animals were exposed ad libitum to 400 ppm MCPD in tap water as drinking water with light-shielded bottles. In the TCP group, animals were administered TCP dissolved in corn oil at 125 mg/kg body weight by oral gavage (5 days/week). Untreated control animals were maintained on a basal diet and tap water without any treatment during the experimental period.

tag: strain

value: F344 rat

value: Kidney OSOM

value: day 90

value: TCP treatment


title: B2005_Ctl_0Gy_Male

institute: NIH

description:
B2005_Ctl_S0
B2005_Ctl_0Gy

value: Whole blood

value: Male

value: control

value: -2 days


title: Kidney OSOM, MCPD, Day90

value: MCPD treatment


title: tm_GB

value: Endothelial colony forming cell

value: 50ng/mL IFN-gamma/100pg/mL IL-1-beta


title: EZ T0 Replicate 2

value: Prostate

tag: cell line

value: LNCaP

value: Prostate Adenocarcinoma

value: TKOV3 Lentiviral Library


title: B2004_D71_10.7Gy_Male

description:
B2004_D71_S0
B2004_D71_10.7Gy

value: 10.7Gy thoracic radiation

value: 71 days


title: EZ T0 Replicate 3

value: Enzalutamide (50 uM)

value: sgRNA PCR Amplicons from gDNA


title: tm_G

value: 50ng/mL IFN-gamma


title: Kidney OSOM, OTA, Day90

value: F344 rat

value: Kidney OSOM

value: day 90

value: OTA treatment


title: B2004_D60_10.7Gy_Male

description:
B2004_D60_S0
B2004_D60_10.7Gy

value: Whole blood

value: Male

value: 60 days


title: jj_Ctrl smRNA

value: Endothelial colony forming cell

value: Untreated


title: Kidney OSOM, Control, Day90

value: control treatment


title: EZ T0 Replicate 1

value: Prostate

value: LNCaP

value: Prostate Adenocarcinoma


title: tm_Ctrl


title: B2004_D30_10.7Gy_Male

description:
B2004_D30_S0
B2004_D30_10.7Gy

value: 10.7Gy thoracic radiation

value: 30 days


title: tm_B

value: 100pg/mL IL-1-beta


title: B2004_D9_10.7Gy_Male

description:
B2004_D9_S64
B2004_D9_10.7Gy

value: 9 days


title: Primary tumor cells from co-culture with alveolar macrophages, biological replicate 3

city: The Bronx

first: Michael

last: Papanicolaou

state: New York

address: 1300 Morris Park Avenue

department: Cell Biology

institute: Albert Einstein College of Medicine

description:
RNAseq PT AM raw read counts.xlsx
RNAseq PT AM raw read counts.xlsx

data_processing:
Illumina HiSeq, 2x150bp configuration, single index, per lane
Assembly: mm10
The sequencing libraries were pooled and clustered on lane.  After clustering, the flowcell was loaded on the Illumina HiSeq instrument (4000 or equivalent) according to manufacturer’s instructions.  The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.
Supplementary files format and content: Extensible Markup Language file with raw counts for each sample

organism: Mus musculus

source_name: PT from co-culture with AM 3

growth_protocol: DMEM/F12, 5% horse serum, 500ng/ml Hydrocortisone (Lonza CC-403), 40 mg/ml Insulin (Gibco 12585-014), 20 ng/ml EGF (Pepro- tech AF-100-15-A), 100 units/ml penicillin and 100ug/ml streptomycin (Corning) in wells coated with 100% matrigel that has gellated

extract_protocol:
Total RNA was extracted from fresh frozen cell pellets using Qiagen RNeasy Plus Universal mini kit following manufacturer’s instructions (Qiagen, Hilden, Germany). Extracted RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA).
RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA). mRNAs were enriched with Oligo(dT) beads

treatment_protocol: Mammary early lesion cells or mammary primary tumor cells were isolated from the MMTV-HER2 mouse model and lung alveolar macrophages were isolated from congenic wildtype mice. Early lesion or primary tumor cells were co-culture with alveolar macrophages, and were FACS-sorted and bulk RNA-sequencing was performed. Mono-culture controls of each cell type were also sequenced. Cells were co-cultured for 7 days before being sorted and processed for RNA-seq.

value: mammary

value: primary cells

value: primary epithelial tumor cells

value: co-cultured with alveolar macrophages


title: Primary tumor cells from co-culture with alveolar macrophages, biological replicate 2

source_name: PT from co-culture with AM 2


title: jm_TNF

value: 10ng/mL TNF


title: Primary tumor cells from co-culture with alveolar macrophages, biological replicate 1

source_name: PT from co-culture with AM 1


title: jm_GB

value: 50ng/mL IFN-gamma/100pg/mL IL-1-beta


title: DMSO T0 Replicate 1

value: TKOV3 Lentiviral Library

value: DMSO

value: sgRNA PCR Amplicons from gDNA


title: H30-KTB85-NP-H

city: Indianapolis

first: Harikrishna

last: Nakshatri

state: IN

address: 980 W. Walnut St. R3C218C

department: General Surgery

institute: Indiana University School of Medicine

data_processing:
Adapters and low quality bases were trimmed using Trimmomatic (version 0.32) with following specific parameters ILLUMINACLIP:<adapters.fa>:2:20:5 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:17. Custom perl scripts  were used to truncate poly-G tails and then reduce fastq files to a non-redundant set of reads to decrease mapping computational load.
Reads were mapped against GRCh38 using TopHat2 version 2.1.0 with parameters “--b2-very-sensitive --read-edit-dist 2 --max-multihits 100 --library-type fr-secondstrand”
Read counts for each gene were created using custom perl scripts and Gencode v23 as the annotation
Differential expression analysis was performed using the DESeq2 package (version 1.10.1) in R/Bioconductor (R version 3.2.1).
Assembly: GRCh38
Supplementary files format and content: tab-delimited file includes raw gene count values for each sample

source_name: Hispanic

extract_protocol:
RNA was harvested using the RNAEasy kit (Qiagen)
Poly-A RNA libraries were constructed using mRNA Stranded TruSeq protocol (Illumina, San Diego, CA). Small RNA library construction was performed using the TruSeq Small RNA kit (Illumina). Purified libraries were visualized and quantified using a TapeStation HSD1000 (Agilent, Santa Clara, CA).

value: breast

value: Primary Mature luminal cells (CD49F-/EpCAM+) grown from breast tissues


title: B2004_D6_10.7Gy_Male

address: 9000 Rockville Pike

description:
B2004_D6_S116
B2004_D6_10.7Gy

value: Whole blood

value: Male

value: 6 days


title: Primary tumor cells from mono-culture, biological replicate 3

source_name: PT monoculture CTR 3

value: mono-culture


title: B2004_D40_10.7Gy_Male

description:
B2004_D40_S225
B2004_D40_10.7Gy

value: 10.7Gy thoracic radiation

value: 40 days


title: jm_G

value: Endothelial colony forming cell

value: 50ng/mL IFN-gamma


title: Primary tumor cells from mono-culture, biological replicate 1

source_name: PT monoculture CTR 1

value: mammary

value: primary cells

value: primary epithelial tumor cells


title: B2004_D3_10.7Gy_Male

description:
B2004_D3_S39
B2004_D3_10.7Gy

value: 3 days


title: jm_B

value: 100pg/mL IL-1-beta


title: jm_Ctrl

value: Untreated


title: B2004_D21_10.7Gy_Male

description:
B2004_D21_S194
B2004_D21_10.7Gy

value: 21 days


title: H28-KTB84-NP-H

value: breast


title: DMSO T0 Replicate 3

value: Prostate

value: LNCaP

value: Prostate Adenocarcinoma

value: TKOV3 Lentiviral Library

value: DMSO

value: sgRNA PCR Amplicons from gDNA


title: B2004_D15_10.7Gy_Male

description:
B2004_D15_S85
B2004_D15_10.7Gy

value: Whole blood

value: Male

value: 10.7Gy thoracic radiation

value: 15 days


title: Alveolar macrophage from co-culture with eprimary tumor cells,  biological replicate 3

source_name: AM from co-culture with PT 3

value: lung

value: primary cells

value: primary alveolar macrophage

value: wildtype FVB

value: co-cultured with primary tumor cells


title: DMSO T0 Replicate 2


title: Alveolar macrophage from co-culture with eprimary tumor cells,  biological replicate 2

source_name: AM from co-culture with PT 2


title: jj_TNF

value: Endothelial colony forming cell

value: 10ng/mL TNF


title: jj_GB

value: 50ng/mL IFN-gamma/100pg/mL IL-1-beta


title: H26-KTB82-NP-H

value: breast

value: Primary Mature luminal cells (CD49F-/EpCAM+) grown from breast tissues


title: H25-KTB82-PP-H

value: Primary Luminal progenitor cells (CD49F+/EpCAM+) grown from breast tissues


title: B2003_D9_10.7Gy_Male

description:
B2003_D9_S0
B2003_D9_10.7Gy

source_name: Whole blood

value: 9 days


title: Alveolar macrophage from co-culture with eprimary tumor cells,  biological replicate 1

source_name: AM from co-culture with PT 1


title: H24-KTB79-NP-H


title: Alveolar macrophage from mono-culture control from primary tumor experiment, biological replicate 3

source_name: AM mono-culture CTR 3

value: mono-culture


title: B2003_D60_10.7Gy_Male

description:
B2003_D60_S0
B2003_D60_10.7Gy

value: Whole blood

value: 60 days


title: jj_G

value: 50ng/mL IFN-gamma


title: H29-KTB85-PP-H


title: Primary tumor cells from mono-culture, biological replicate 2

source_name: PT monoculture CTR 2

value: mammary

value: primary epithelial tumor cells


title: H23-KTB79-PP-H


title: Alveolar macrophage from mono-culture control from primary tumor experiment, biological replicate 2

source_name: AM mono-culture CTR 2

value: lung

value: primary cells


title: H27-KTB84-PP-H


title: jj_B

value: 100pg/mL IL-1-beta


title: B2003_D40_10.7Gy_Male

description:
B2003_D40_S0
B2003_D40_10.7Gy

value: Male

value: 10.7Gy thoracic radiation

value: 40 days


title: Alveolar macrophage from mono-culture control from primary tumor experiment, biological replicate 1

source_name: AM mono-culture CTR 1

value: primary alveolar macrophage

value: wildtype FVB


title: Early lesion cells from co-culture with alveolar macrophages, biological replicate 3

description:
RNAseq EL AM_Raw read counts.xlsx
RNAseq EL AM_Raw read counts.xlsx

source_name: EL from co-culture with AM 3

value: primary epithelium

value: co-cultured with alveolar macrophages


title: TC71_siEF1_2

city: Iowa City

first: Emma

last: Croushore

state: Iowa

address: 25 S Grand Ave

department: Pediatric Hematology/Oncology

institute: University of Iowa

data_processing:
Samples were barcoded, pooled, and sequenced on an Illumina NovaSeq 6000 to obtain a minimum of 30 million, paired-end, 100 bp reads per sample.
FastQC was used to assess the quality of the sequencing reads. Since each paired-end sample was split over two flow cells, each of the 12 samples output 4 fastq files. For each sample, forward reads from lanes 1 and 2 were merged into one fastq file, and reverse reads from lanes 1 and 2 were combined into one fastq file.
Reads were then mapped against the human reference genome (hg38) using the STAR aligner and summarized at the exon level using featureCounts. Alignment quality was assessed using MultiQC.
Raw counts were transformed using the cpm function in EdgeR for sample clustering and principal components analysis (PCA). No outlier samples were identified or removed from the analysis.
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for each gene and sample

growth_protocol: The cell lines were cultured in DMEM with 10% FBS.

extract_protocol:
RNA was isolated from cell lines using RNeasy Plus Mini Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina TruSeq Stranded mRNA protocols.

treatment_protocol: Two parential Ewing sarcoma cell lines (EW8, TC71) were treated with siControl or siEWS-FLI1 for 48 hours.

value: Ewing sarcoma cell line

value: EWS-FLI1 KD

value: siEWS-FLI1 48h


title: B2003_D30_10.7Gy_Male

description:
B2003_D30_S0
B2003_D30_10.7Gy

value: Whole blood

value: 30 days


title: H20-KTB37-NP-C

source_name: European ancestry

value: breast

value: Primary Mature luminal cells (CD49F-/EpCAM+) grown from breast tissues


title: H22-KTB76-NP-H


title: TC71_siEF1_1


title: B2004_Ctl_0Gy_Male

description:
B2004_Ctl_S28
B2004_Ctl_0Gy

value: control

value: -2 days


title: TC71_siEF1_3


title: TC71_siControl_3

value: WT

value: siControl 48h


title: H18-KTB36-NP-C


title: B2003_D21_10.7Gy_Male

description:
B2003_D21_S0
B2003_D21_10.7Gy

value: Male

value: 10.7Gy thoracic radiation

value: 21 days


title: jj_Ctrl

source_name: Endothelial colony forming cell

value: Endothelial colony forming cell

value: Untreated


title: Early lesion cells from co-culture with alveolar macrophages, biological replicate 1

source_name: EL from co-culture with AM 1

value: mammary

value: primary cells

value: primary epithelium

value: co-cultured with alveolar macrophages


title: B2003_D3_10.7Gy_Male

description:
B2003_D3_S0
B2003_D3_10.7Gy

value: Whole blood

value: 3 days


title: B2003_D6_10.7Gy_Male

description:
B2003_D6_S0
B2003_D6_10.7Gy

value: 6 days


title: H17-KTB36-PP-C

value: breast

value: Primary Luminal progenitor cells (CD49F+/EpCAM+) grown from breast tissues


title: Early lesion cells from co-culture with alveolar macrophages, biological replicate 2

source_name: EL from co-culture with AM 2


title: B2003_Ctl_0Gy_Male

description:
B2003_Ctl_S0
B2003_Ctl_0Gy

value: control

value: -2 days


title: H19-KTB37-PP-C


title: B2003_D15_10.7Gy_Male

description:
B2003_D15_S0
B2003_D15_10.7Gy

value: 15 days


title: Early lesion cells from mono-culture, biological replicate 2

source_name: EL mono-culture control 2

value: mono-culture


title: TC71_siControl_2

value: Ewing sarcoma cell line

value: WT

value: siControl 48h


title: Early lesion cells from mono-culture, biological replicate 3

source_name: EL mono-culture control 3


title: H16-KTB35-NP-C

value: Primary Mature luminal cells (CD49F-/EpCAM+) grown from breast tissues


title: B2002_D60_10.7Gy_Male

description:
B2002_D60_S0
B2002_D60_10.7Gy

value: Male

value: 10.7Gy thoracic radiation

value: 60 days


title: H21-KTB76-PP-H

source_name: Hispanic


title: TC71_siControl_1


title: Early lesion cells from mono-culture, biological replicate 1

source_name: EL mono-culture control 1

value: mammary

value: primary cells

value: primary epithelium


title: H15-KTB35-PP-C


title: B2002_D30_10.7Gy_Male

description:
B2002_D30_S0
B2002_D30_10.7Gy

value: Whole blood

value: 30 days


title: EW8_siEF1_3

value: EWS-FLI1 KD

value: siEWS-FLI1 48h


title: H14-KTB34-NP-C

value: breast


title: EW8_siEF1_2


title: B2002_D9_10.7Gy_Male

description:
B2002_D9_S63
B2002_D9_10.7Gy

value: 9 days


title: Alveolar macrophage from co-culture with early lesion cells,  biological replicate 1

source_name: AM from co-culture with EL 1

value: lung

value: primary alveolar macrophage

value: wildtype FVB

value: co-cultured with early lesion cells


title: H13-KTB34-PP-C

value: Primary Luminal progenitor cells (CD49F+/EpCAM+) grown from breast tissues


title: Alveolar macrophage from mono-culture from early lesion experiment, biological replicate 2

source_name: AM mono-culture control 2

value: mono-culture


title: Alveolar macrophage from mono-culture from early lesion experiment, biological replicate 1

source_name: AM mono-culture control 1


title: B2002_D40_10.7Gy_Male

description:
B2002_D40_S0
B2002_D40_10.7Gy

source_name: Whole blood

value: Male

value: 10.7Gy thoracic radiation

value: 40 days


title: EW8_siEF1_1

value: Ewing sarcoma cell line


title: H12-KTB33-NP-C

value: Primary Mature luminal cells (CD49F-/EpCAM+) grown from breast tissues


title: EW8_siControl_2

value: WT

value: siControl 48h


title: EW8_siControl_1


title: B2002_D3_10.7Gy_Male

description:
B2002_D3_S105
B2002_D3_10.7Gy

value: Whole blood

value: 3 days


title: Chondrocyte-dKO-2

city: Rochester

first: Alexandra

last: Krivonos

state: MN

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

data_processing:
The samples were sequencing using a 2 x 150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the Control software.
Raw sequence data (.bcl files) generated by the sequencer were converted into fastq files and de-multiplexed using Illumina’s bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality. The trimmed reads were mapped to the reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
Assembly: mm10
Supplementary files format and content: tab-delimited text file contains raw counts for each sample

source_name: Chondrocytes

extract_protocol:
Primary epiphyseal chondrocytes were harvested from five-day-old female WT, Phlpp1-/-, Phlpp2-/-, and Phlpp1/2-/- mice. Chondrocytes were digested for one hour in 0.5mg/mL collagenase II in DMEM culture medium, then digested overnight in 3mg/mL collagenase II in DMEM culture media. Cells were then cryopreserved until a sufficient n was reached for each genotype. At that point, cells were thawed, plated in DMEM+10% FBS+1% antibiotic/antimycotic overnight. The next day, chondrocytes washed in ice-cold PBS three times, then resuspended in Trizol for RNA extraction. Total RNA was extracted using phenol-chloroform.
RNA Sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina per the manufacturer’s instructions (NEB, Ipswich, MA).

value: Chondrocytes

value: Female

value: Phlpp1/2 KO

value: 5 days old


title: B2002_D21_10.7Gy_Male

description:
B2002_D21_S0
B2002_D21_10.7Gy

value: 21 days


title: Chondrocyte-dKO-3


title: H11-KTB33-PP-C

value: breast