title: NX_Lung

data_processing:
Data was mapped using Cell Ranger (10X Genomics) to mm10 and analyzed using the Seurat R toolkit for single cell genomics (Satija et al., 2015).
Genome_build: mm10
Supplementary_files_format_and_content: cell bar codes; gene name; UMI

source_name: Sorted lung myeloid cells

extract_protocol:
Sorted lung myeloid cells were suspended in PBS containing 0.04% molecular biology grade non-acetylated BSA at a concentration of 1,000cells/ µL. The purity of the sorted cells was verified and the sorted cell number was verified by manual counting. Using the 10x GemCode technology single cells were captured with barcoded beads in a droplet emulsion for the RT reaction. After obtaining 10x barcoded cDNA, libraries were prepared following the standard protocol of 10X Single Cell 3’ v1. The libraries were sequenced with Hi-Seq 4000 (Illumina).
scRNA-Seq generated using 10x genomics Single Cell 3’ Reagent Kits V1

tag: age

tag: Sex

value: male

value: Lung

value: myeloid cells


title: 8272

status: Public on Jan 20 2020

type: SRA

city: Salt Lake City

first: Diane

middle: M

last: Ward

state: UT

address: 15 N Medical Dr Suite 1100

department: Pathology Department - School of Medicine

country: USA

institute: University of Utah

description: wildtype replicate 1

library_source: transcriptomic

data_processing:
Fastq reads were aligned to genome index containing known splice junctions using Novocraft Novoalign (v2.8). Splice junctions were generated using USeq MakeTranscriptome (v8.8) and UCSC EnsGene annotation.
Spliced alignments were converted back to genomic coordinates using USeq SamTranscriptomeParser (v8.8).
Differential expression was performed using USeq DefinedRegionDifferentialSeq and DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file containing the raw counts, regularized log2 counts, FPKM counts, and DESeq2 log2 ratio and -10log10 transformed adjusted P-value from DESeq2.

molecule: total RNA

organism: Mus musculus

source_name: Liver

growth_protocol: Mice were maintained on a standard rodent chow (Harland, Teklad).

extract_protocol:
Liver tissues were homogenized in Trizol and flash frozen in liquid nitrogen.  mRNA was extracted using a Zymo Research kit with DNAseI treatment. QC was done on an Agilent tapestation RNA assay.
TruSEq Stranded total RNA sample prep kit with ribo-zero gold treatment

tag: genotype

value: WT


title: IM_LPS02h_nasalA171227

city: La Jolla

first: Eniko

last: Sajti

state: CA

address: 9500 Gilman Drive

department: Pediatrics

institute: UCSD

data_processing:
Preprocessing: FASTQ files from sequencing experiments were mapped to the mouse mm10 genome. STAR with default parameters was used to map RNA-seq experiments (Dobin et al., 2013). HOMER was used to convert aligned reads into “tag directories” for further analysis (Heinz et al., 2010).
Each experiment was quantified using the “analyzeRepeats” script of HOMER. To generate a table of TPM values, the parameters -condenseGenes -count exons  -tpm were used which extract only one transcript (most aboundace) for a gene. And the smaller genes (<250bp) were removed from downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited text file: Table of TPM values for RNA-Seq

molecule: polyA RNA

extract_protocol:
Total RNA was isolated from in vitro culture cells and purified using a Direct-zol RNA MicroPrep Kit (Zymo Research) according to the manufacturer’s instructions (Zymo Research). FACS purified cells were pelleted and put into 150 μl lysis/Oligo d(T) Magnetic Beads binding buffer (100mM Tris-HCl pH7.5, 500mM LiCl, 10mM EDTA pH8.0, 1% LiDS, 5mM DTT) and stored at –80°C until processing. mRNAs were enriched by incubation with Oligo d(T) Magnetic Beads (NEB, S1419S).
Sequencing libraries were prepared according to the Smart-seq2 method45 with some modifications. 500-5000 FACS isolated cells in Trizol (Thermo Fisher) were used as starting material. RNA was extracted with the Direct-zol MicroPrep kit (Zymo Research) with on-column DNAseI treatment. 10 µL purified RNA was mixed with 5.5 µL of SMARTScribe 5X First-Strand Buffer (Clontech), 1 µL polyT-RT primer (2.5 µM, 5’-AAGCAGTGGTATCAACGCAGAGTAC(T30)VN, 0.5 µL SUPERase-IN (Ambion), 4 µL dNTP mix (10 mM, Invitrogen), 0.5 µL DTT (20 mM, Clontech) and 2 µL Betaine solution (5 M, Sigma), incubated 50C 3 min. 3.9 µL of first strand mix, containing 0.2 µL 1% Tween-20, 0.32 µL MgCl2 (500 mM), 0.88 µL Betaine solution (5 M, Sigma), 0.5 µL (5 M, Sigma) SUPERase-IN (Ambion) and 2 µL SMARTScribe Reverse Transcriptase (100 U/µL Clontech) was added and incubated one cycle 25C 3 min., 42C 60 min. 1.62 µL template switch (TS) reaction mix containing 0.8 µL biotin-TS oligo (10 µM, Biotin-5’-AAGCAGTGGTATCAACGCAGAGTACATrGrG+G-3’), 0.5 µL SMARTScribe Reverse Transcriptase (100 U/µL Clontech) and 0.32 µL SMARTScribe 5X First-Strand Buffer (Clontech) was added, then incubated at 50C 2 min., 42C 80 min., 70C 10 min. 14.8 µL second strand synthesis, pre-amplification mix containing 1 µL pre-amp oligo (10 µM, 5’AAGCAGTGGTATCAACGCAGAGT-3’), 8.8 µL KAPA HiFi Fidelity Buffer (5X, KAPA Biosystems), 3.5 µL dNTP mix (10 mM, Invitrogen) and 1.5 µL KAPA HiFi HotStart DNA Polymerase (1U/µL, KAPA Biosystems), was added,  then amplified by PCR: 95C 3 min., 8 cycles 98C 20 seconds, 67C 15 sec and 72C 6 min, final extension 72C 5 min.  The synthesized dsDNA was purified using Sera-Mag Speedbeads (Thermo Fisher Scientific) with final 8.4% PEG8000, 1.1M NaCl, then eluted with 13 µL UltraPure water (Invitrogen). The product was quantified by Qubit dsDNA High Sensitivity Assay Kit (Invitrogen) and libraries were prepared using the Nextera DNA Sample Preparation kit (Illumina). Tagmentation mix containing 11 µL 2X Tagment DNA Buffer and 1 µL Tagment DNA Enzyme was added to 10 µL purified DNA, then incubated at 55C 15 min. 6 µL Nextera Resuspension Buffer (Illumina) was added and incubated at room temperature for 5 min. Tagmented DNA was purified using Sera-Mag Speedbeads (Thermo Fisher Scientific) with final 7.8% PEG8000, 0.98M NaCl, then eluted with 25 µL UltraPure water (Invitrogen). Final enrichment amplification was performed with Nextera primers,  adding 1 µL  Ad1 (100 µM, universal no barcode), 1 µL unique Ad2.n (100 µM, N7xx) barcoding primers and 27 µL NEBNext High-Fidelity 2X PCR Master Mix (New England BioLabs), then amplified by PCR: 72C 5 min., 98C 30 sec., 8-13 cycles 98C 10 seconds, 63C 30 sec., and 72C 1 min. Libraries were purified using 1.5 volumes of SpeedBeads in 2.5M NaCl, 20% PEG8000, further size selected using 10% PAGE/TBE gels, eluted and quantified with Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific), pooled and sequenced on a NextSeq 500 (Illumina) for 76 cycles at a depth of 25 to 30 million single end reads per sample.

tag: strain

tag: treatment

value: nasal LPS

tag: treatment time

tag: tissue

value: lung

tag: cell type

value: interstitial macrophages (IM)


title: JZ190116

city: Orange

first: Matthew

last: Simon

state: CT

address: West Campus, 100 West Campus Drive, Ste MIC312A

department: MBB

institute: Yale University

description:
s4U nascent
Reads filtered for number of T-to-C mutations (0-5+) and strandedness (min/pos)

data_processing:
Reads were filtered for unique sequences using FastUniq
Reads were trimmed using cutadapt (--minimum-length=20)
Reads were aligned to the GRCm38 genome using HISAT2 aligned with default parameters and --mp 4,2 .
Reads were processed using Picard tools, including FixMateInformation, SortSam and BuildBamIndex
Reads were filtered for those that aligned uniquely (flag: 83/163, 99/147), with MAPQ ≥ 2, and without insertions.
HTSeq-count was used to identify mapped reads in UCSC transcripts (union mode)
T-to-C mutations were identified using Rsamtools and a custom R script (available upon request). Only mutations at positions with a base quality score of greater than 45 that were at least three nt from the end of the read were counted. Reads were excluded where there were greater than five T-to-C mutations and these mutations did not account for at least one third of the observed mutations (NM tag).
SNP sites were filtered from our data in two ways: 1, bcftools was used to identify T-to-C SNP sites in control samples, and these sites were excluded from analysis; 2, sites exhibiting high T-to-C mutation rates in non-s4U treated controls were excluded from analysis.
To examine the distribution of reads with each minimum number of T-to-C mutations, bam files were filtered using Picard tools.
STAR aligner was used to make genome-coverage tracks (inputAlignmentsFromBam mode, outWigType bedGraph), and tracks were normalized using DESeq2 (estimateSizeFactors).
Tracks were converted to binary format using IGVtools (toTDF).
Genome_build: GRCm38
Supplementary_files_format_and_content: bedgraph

source_name: Mouse lung adenocarcinoma (K-rasLA2-G12D/+; p53LSL/LSL; Rosa26-CreERT2+, KPR) cells

growth_protocol: KPR cells, previously infected with with an sgRNA targeting the PVT1 p53RE or a nontargeting control, were grown in Dulbecco’s Modified Essential Media supplemented with 10% fetal bovine serum (Gibco), 0.1 mM nonessential amino acids, 2 mM L-glutamine, and Pen/Strep (50 U/ml). All cell cultures were maintained at 37℃ in a humidified incubator with 5% carbon dioxide.

extract_protocol:
RNA was harvested with Trizol reagent, followed by chloroform extraction and ethanol precipitation.   Genomic DNA was depleted using Turbo DNAse, followed by cleanup with RNAclean beads. RNA for transient-transciptome RNA-seq was enriched with MTS-biotin and all RNA was treated with oxidative-nucleophilic-aromatic-substitution chemistry as described in Schofield et al. Nature Methods 2018.
Libraries were generated following standard protocols using the SMARTer Stranded Total RNA-Seq Kit-Pico Input Mammalian, V2 (Takara Bio USA, cat. 634413).

treatment_protocol: Tamoxifen-treated cells had media spiked to a final concentration of 0.5 µM tamoxifen and untreated (no tamoxifen) cells had media spiked with vehicle control.  s4U-treated cells had their media spiked with s4U to a final concentration of 100 µM for total RNA-seq or 1 mM for transient-transcriptome RNA-seq. Untreated (no s4U) cells had their media left unsupplemented. Cells were incubated with s4U for 1h or 5m for total RNA-seq or transient-transcriptome RNA-seq, respectively.

tag: infected with

value: sgRNA targeting the Pvt1 p53RE (gΔRE)

value: +Tamoxifen

tag: s4u feed

value: Yes


title: AM_LPS20h_nasalB171227

value: alveolar macrophages (AM)


title: AM_LPS20h_nasalA171227


title: Genomic DNA from non-cancerous mucosa sample [MPC_N4]

type: genomic

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

country: Japan

institute: Chiba University

description: SAMPLE 4

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol.

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

data_processing: BeadStudio software v3.2.

label: Not provided

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Standard Illumina Protocol.

extract_protocol: Genomic DNA was extracted and purified from clinical samples using QIAquick DNA mini kit according to standard instructions.

tag: disease state

value: normal

value: oropharyngeal non-cancerous mucosa

tag: gender


title: JZ190115

value: lung adenocarcinoma (K-rasLA2-G12D/+; p53LSL/LSL; Rosa26-CreERT2+, KPR) cells

value: control sgRNA (gCon)


title: Genomic DNA from non-cancerous mucosa sample [MPC_N5]

description: SAMPLE 5


title: JZ190119

description: Reads filtered for number of T-to-C mutations (0-5+) and strandedness (min/pos)

value: No


title: JZ190114

value: -Tamoxifen


title: Genomic DNA from non-cancerous mucosa sample [MPC_N3]

description: SAMPLE 3

value: male


title: IM_LPS06h_nasalA171227


title: PROG_071

type: RNA

city: Lund

first: Gottfrid

last: Sjodahl

address: Medicon Village

department: Department of Translational Medicine

country: Sweden

institute: Lund Univeristy

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials â€¢ Heat cocktails at 99Â° for 5 minutes, then 42Â° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). â€¢ Transfer 200Î¼l of hyb solution to each array, then tape holes and parafilm. â€¢ Hybridize 16 hours at 45Â° at 60rpmâ€¢ Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using Bioconductor R package Affy. Probe intensities were normalized in labeling batches using RMA.
The file Processed_data_supplement.txt is available on the series record and contains the full dataset of 200 CEL files. These CEL files were normalized using RMA by labeling batches. Batches were combined and RMA normalized. The data was filtered for probes with signal intensity less than the median of negative control probes for >80% of the values. Gene symbols and EntrezID were appended using Bioconductor (hugene10stprobeset.db Version 8.6.0). Probes not mapping to a gene symbol were removed. The probes were median merged by gene symbol and log-transformed. Batch correction was performed using ComBat, and the final data set was median centered.

label: biotin

source_name: FFPE tissue specimen

label_protocol: SensationPlus FFPE Amplification and WT labeling kit

extract_protocol: High Pure FFPET RNA isolation kit (Roche)

value: bladder cancer

tag: tissue preparation

value: FFPE

tag: labeling batch

tag: patient identifier

tag: tumor number

tag: primary, recurrence, or progression

value: prog

tag: tumor stage

tag: grade (who1999)

tag: molecular subtype

value: UroB


title: JZ190113


title: AM_LPS06h_nasalB171227

tag: strain

value: nasal LPS

value: lung


title: PROG_070

value: rec

value: UroA-Prog


title: Genomic DNA from OPSCC sample [MPC_T1]

description: SAMPLE 6

value: oropharyngeal squamous carcinoma (OPSCC)

value: oropharyngeal cancer


title: AM_LPS06h_nasalA171227

tag: treatment

value: alveolar macrophages (AM)


title: Genomic DNA from non-cancerous mucosa sample [MPC_N1]

description: SAMPLE 1

value: normal

value: oropharyngeal non-cancerous mucosa


title: PROG_069


title: PROG_068

value: primary


title: JZ190112

value: lung adenocarcinoma (K-rasLA2-G12D/+; p53LSL/LSL; Rosa26-CreERT2+, KPR) cells

value: sgRNA targeting the Pvt1 p53RE (gΔRE)

value: Yes


title: JZ190111

value: control sgRNA (gCon)

value: -Tamoxifen


title: AM_LPS02h_nasalB171227

tag: treatment time


title: AM ATAC-seq DBA2J rep2

library_source: genomic

data_processing:
For ATAC-Seq and RNA-Seq samples, reads were aligned to the mm10 genome of the corresponding inbred strain using default parameter for bowtie (RNA-Star, respectively). Aligned read files were analyzed with HOMER (http://biowhat.ucsd.edu/homer/) to find peaks, calculate TPM from the gene bodies of RefSeq genes, perform motif-  and  other analyses in the study. Genetic variation analyses were performed using custom R scripts.
Genome_build: mm10, and DBA/2J from mm10 using published variants (Keane, T. M. et al., Nature 477, 289-294 (2011))
Supplementary_files_format_and_content: Processed files include BED-like files (ATAC-Seq peak positions), expression text files (RNA-Seq expression data, using default HOMER parameters).  All genomic coordinates are relative to mm10 (NCBI 38) mouse assembly.

source_name: alveolar macrophages

extract_protocol:
Lungs were incubated at 37oC for 15 minutes while on a rotator. Red blood cells were lysed using RBC lysis buffer (eBioscience) for a 5 minute incubation. The obtained cell suspension was filtered using a 70 micron filter, washed and cells were resuspended in PBS. Cells were then incubated with anti-Fc blocking mAb (anti CD16/32, clone 93, BioLegend) and viability dye Zombie Aqua (Biolegend) for 10 min. After this, cells where stained with an antibody cocktail containing APC Cy7-conjugated CD45, PE-conjugated F4/80, BV605-conjugated CD11c, v450-conjugated CD11b, PE Cy7-conjugated CD64, AF700-conjufgated Ly6c, FITC-conjugated Ly6g, AF647-conjugated SiglecF mAb for 30 minutes. All labeled cells were passed through a FACS Aria II flow cytometer (BD Biosciences) and after proper gating 4 subsets of lung MP were sorted
RNA-seq: PolyA enriched mRNA was fragmented, in 2x Superscript III first-strand buffer with 10mM DTT (Invitrogen), by incubation at 94°C for 9 minutes, then immediately chilled on ice before the next step. The 10 µL of fragmented mRNA, 0.5 µL of Random primer (Invitrogen), 0.5 µL of Oligo dT primer (Invitrogen), 0.5 µL of SUPERase-In (Ambion), 1 µL of dNTPs (10 mM) and 1 µL of DTT (10 mM) were heated at 50°C for three minutes. At the end of incubation, 5.8 µL of water, 1 µL of DTT (100 mM), 0.1 µL Actinomycin D (2 µg/µL), 0.2 µL of 1% Tween-20 (Sigma) and 0.2 µL of Superscript III (Invitrogen) were added and incubated in a PCR machine using the following conditions: 25°C for 10 minutes, 50°C for 50 minutes, and a 4°C hold. The product was then purified with RNAClean XP beads according to manufacture’s instruction and eluted with 10 µL nuclease-free water. The RNA/cDNA double-stranded hybrid was then added to 1.5 µL of Blue Buffer (Enzymatics), 1.1 µL of dUTP mix (10 mM dATP, dCTP, dGTP and 20 mM dUTP), 0.2 µL of RNAse H (5 U/µL), 1.05 µL of water, 1 µL of DNA polymerase I (Enzymatics) and 0.15 µL of 1% Tween-20. The mixture was incubated at 16°C for 1 hour. The resulting dUTP-marked dsDNA was purified using 28 µL of Sera-Mag Speedbeads (Thermo Fisher Scientific), diluted with 20% PEG8000, 2.5M NaCl to final of 13% PEG, eluted with 40 µL EB buffer (10 mM Tris-Cl, pH 8.5) and frozen -80°C. The purified dsDNA (40 µL) underwent end repair by blunting, A-tailing and adapter ligation as previously described44 using barcoded adapters (NextFlex, Bioo Scientific). Libraries were PCR-amplified for 14-16 cycles, size selected using 10% PAGE/TBE gels, eluted and quantified with Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific),
ATAC-seq: Sorted cells in FACS Buffer were pelleted by centrifugation at 400 RCF for 6 minutes at 4oC in a pre-cooled fixed-angle microfuge. Supernatant was carefully removed and cell pellet was resuspend in 47.5 ul lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630), 2.5ul of TDE1 (Cat# FC-121-1030, Illumina) by pipetting. Transposition reactions were incubated at 37°C for 30 minutes. Transposed DNA was purified using a Zymo ChIP DNA Clean & Concentrator kit (Cat# D5205) and purified DNA was eluted in 10 ul elution buffer (10 mM Tris-HCl, pH 8). Transposed fragments were amplified and purified as described previously (Buenostro et al) with modified primers.

treatment_protocol: no treatment


title: JS181210

value: +Tamoxifen

value: No


title: AM_LPS02h_nasalA171227

value: nasal LPS

tag: tissue


title: AM ATAC-seq DBA2J rep1


title: Genomic DNA from non-cancerous mucosa sample [MPC_N2]

description: SAMPLE 2

value: male


title: PROG_066

value: bladder cancer

value: FFPE

value: rec

value: Ta

value: UroB


title: JS181209

tag: cell type


title: PROG_067

value: prog

value: ScNE


title: 5Y_NHEG1_3

city: Wuhan

first: Qiangsong

last: Tong

state: Hubei

address: 1277 Jiefang Avenue

department: Department of Surgery

country: China

institute: Union Hospital of Tongji Medical College

description: Gene expression after stable transfection of NHEG1

hyb_protocol: Array hybridization and washing was performed using GeneChip Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US) in a Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US) and a Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) following the manufacturer's instructions.

scan_protocol: Arrays were scanned by Affymetrix GeneChip Scanncer 3000 (Cat#00-00213, Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Command Console Software (Affymetrix,Santa Clara, CA, US) was used to control the scanner and summarize probe cell intensity data (CEL file generation) with default settings.

source_name: SH-SY5Y stably transfected with NHEG1 repeat 3

label_protocol: Total RNA was amplified and labeled by Affymetrix WT PLUS Reagent Kit (Cat#902280，Affymetrix, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: Human neuroblastoma cell line SH-SY5Y was grown in RPMI1640 medium supplemented with 10% fetal bovine serum, penicillin (100 U/ml) and streptomycin (100 μg/ml), and maintained at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: The NHEG1 expression or empty vectors were transfected into tumor cells, and stable cell lines were screened by administration of neomycin.

value: neuroblastoma

tag: cell line

tag: vector


title: IMo_LPS20h_ipB161219

value: IP LPS

value: lung

value: inflammatory monocytes (iMo)


title: JS181208

value: lung adenocarcinoma (K-rasLA2-G12D/+; p53LSL/LSL; Rosa26-CreERT2+, KPR) cells

tag: infected with

value: sgRNA targeting the Pvt1 p53RE (gΔRE)

tag: s4u feed

value: Yes


title: IMo_LPS20h_ipA161219


title: 5Y_NHEG1_2

source_name: SH-SY5Y stably transfected with NHEG1 repeat 2


title: JS181207

value: +Tamoxifen


title: PROG_065

tag: tissue preparation

value: primary

value: GU


title: PROG_062

value: bladder cancer

tag: labeling batch


title: PROG_064

value: FFPE

tag: patient identifier

value: Ba/Sq


title: pMo ATAC-seq C57BL6J rep1

source_name: patrolling macrophages


title: IMo_LPS06h_ipB161219


title: PROG_063

tag: tumor number


title: 5Y_Mock_1

description: Gene expression after stable transfection of empty vector

source_name: SH-SY5Y stably transfected with empty vector repeat 1

value: empty


title: 5Y_Mock_2

source_name: SH-SY5Y stably transfected with empty vector repeat 2


title: PROG_061

tag: primary, recurrence, or progression

value: rec


title: 5Y_Mock_3

source_name: SH-SY5Y stably transfected with empty vector repeat 3


title: IMo_LPS06h_ipA161219


title: JS181206

value: control sgRNA (gCon)


title: PROG_060

tag: tumor stage


title: AM ATAC-seq C57BL6J rep2


title: IMo_LPS02h_ipB161219


title: pMo ATAC-seq C57BL6J rep2


title: IMo_LPS02h_ipA161219


title: IM RNA-seq DBA2J rep2

description: DBA_RNA_IM_rep2 TPM

source_name: interstital macrophages


title: JS181205


title: JS181204

value: -Tamoxifen


title: IM RNA-seq DBA2J rep1

description: DBA_RNA_IM_rep1 TPM


title: IM_LPS20h_ipA161219

value: interstitial macrophages (IM)


title: JS181203


title: JS181202


title: PROG_058

value: Ta

tag: grade (who1999)

value: UroA-Prog


title: PROG_057

value: prog

tag: molecular subtype


title: IM_LPS20h_ipB161219

tag: strain

value: IP LPS

value: lung


title: IM_LPS06h_ip160623

tag: treatment


title: AM ATAC-seq C57BL6J rep1


title: AM_LPS20h_ip160623

tag: treatment time

value: alveolar macrophages (AM)


title: IM_LPS02h_ip160623

tag: tissue


title: AM_LPS20h_ipA161219

tag: cell type


title: JS181201

value: lung adenocarcinoma (K-rasLA2-G12D/+; p53LSL/LSL; Rosa26-CreERT2+, KPR) cells

value: Yes


title: IM_LPS02h_ipA161219


title: PROG_056

value: primary

value: GU


title: AM_LPS06h_ip160623


title: PROG_054

value: bladder cancer

value: FFPE


title: RPF_control_rep2

city: Münster

first: Astrid

last: Haas

department: Biochemistry

country: Germany

institute: WWU Münster

description:
ribosome protected fragments (RPF)
siRNA_RPE_RPF_res.txt
siRNA_RPE_RPF_resLA.txt
siRNA_RPE_RPF_normalized.txt
siRNA_RPE_RPF_mRNA_res.txt

data_processing:
Library strategy: Ribosome profiling
Reads were demultiplexed with Illumina's bcl2fastq
for ribosome profiling: adapter sequences were clipped with the FASTX-Toolkit (Hannon Lab, version 0.0.13.)
for ribosome profiling: 4 randomized nucleotides were trimmer using the FASTX-Toolkit (Hannon Lab, version 0.0.13.)
for ribosome profiling: rRNA was depleted by mapping against human rRNA using bowtie version 1.0.0
mapping to UCSC cannonical ORFs was performed with bowtie version 1.0.0
count tables were created using a custom script and differential expression determined with DESeq2
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited txt files including standard DESeq2 output (baseMean, log2FoldChange (lfc), lfcSE, statx, pvalue, padj)
*normalized.txt: normalized reads
*resLA.txt: fully analyzed data; tested for significantly unchanged genes
*res.txt: fully analyzed data; tested for significantly changed genes
siRNA_RPE_RPF_mRNA_res.txt: combined file for RNA-seq and ribosome profiling fully analyzed data; tested for significantly changed genes

growth_protocol: hTERT-RPE-1 adherent cells were cultured at coated plastic (T75 flask, Greiner Bio-One or cell culture plates, 10 cm, Corning (Falcon)) in DMEM/Ham's F12 medium (Biochrom).

extract_protocol:
For ribosome proliferation RPE cells were incubated for 24 h after transfection with siRNA (Pdcd4 siRNA-2 or control siRNA (100 nM), reverse transfection with Lipofectamine RNAiMAX) and media was changed two hours before harvesting. To stabilize elongating ribosomes, cells were treated with 100 µg/mL cycloheximide (CHX) for 5 min at 37 °C, following a washing step with ice cold PBS (+ 100 µg/mL CHX). Cells were lysed in lysis buffer (10 mM Tris-HCl (pH=7.4), 10 mM MgCl2, 100 mM NaCl, 1% Triton, 1 mM DTT, 100 µg/mL CHX) per sample (sample = 8 dishes á 10 cm), and cell debris pelleted at 4 °C, 10 000 g for 3 min.  10 OD260 units of extract were treated with 900 U RNase I (Ambion)(+ 0.5 % deoxycholate) for 20 min at 22 °C, 800 rpm in a Thermomixer. The reaction was stopped by addition of 240 U SUPERase In (Ambion)(+ 0.5 % deoxycholate) and extracts were resolved by centrifugation at 4 °C, 35 000 rpm for 3 h in a SW-41 Ti swinging-bucket rotor (Beckman Coulter) on 10-50% sucrose density gradients (20 mM Tris-HCl (pH=7.5), 10 mM MgCl2, 100 mM NH4Cl, 2 mM DTT, 100 µg/mL CHX). Gradients were fractionated at 0.75 mL/min with continuous monitoring of OD254 values using a Biocomp Instruments Gradient Station (Teledyne Isco.). Monosome fractions were collected and, following addition of SDS 1%, flash-frozen and stored at -80 °C. RNA was isolated from gradient fractions by the hot acid phenol method (1-bromo-3-chloropropane used instead of chloroform), and ribosome footprints were purified from monosome RNA by size selection of 28-30 nt fragments (excluding major band around 31 nt) on 15 % polyacrylamide, 8 M urea, 1xTBE gels. rRNA depletion with RiboZero Kit was skipped, since contaminating reads were removed by aligning against a reference containing all the rRNA of the organism of interest
RNA libraries for ribosome profiling were prepared accoding to the protocol from Lecanda2016 (Lecanda A, Nilges BS, Sharma P, Nedialkova DD, Schwarz J, Vaquerizas JM, Leidel SA (2016). Dual randomization of oligonucleotides to reduce the bias in  ribosomeprofiling libraries. Methods 107:89–97)

treatment_protocol: hTERT-RPE-1 cells were reversely transfected with siRNA via Lipofectamine RNAiMAX reagent and cultured for 24 h (PDCD4-siRNA: GCUUCUUUCUGACCUUUGU; control-siRNA (targeting renilla luciferase): AAACAUGCAGAAAAUGCUG)

value: hTERT-immortalized retinal pigment epithelial cell line

value: control-siRNA (100 nM)

tag: passages


title: RPF_control_rep3


title: RPF_control_rep1


title: AM_LPS06h_ipA161219


title: RPF_PDCD4-KD_rep3

value: PDCD4-siRNA2 (100 nM)


title: AM_LPS02h_ip160623


title: AM_LPS06h_ipB161219


title: RPF_PDCD4-KD_rep2


title: AM_LPS00h_160623


title: AM_LPS02h_ipB161219


title: RPF_PDCD4-KD_rep1


title: IMo_LPS00h_B171227

value: inflammatory monocytes (iMo)


title: mRNA_control_rep2

description:
siRNA_RPE_mRNA_res.txt
siRNA_RPE_mRNA_resLA.txt
siRNA_RPE_mRNA_normalized.txt
siRNA_RPE_RPF_mRNA_res.txt

data_processing:
Reads were demultiplexed with Illumina's bcl2fastq
for ribosome profiling: adapter sequences were clipped with the FASTX-Toolkit (Hannon Lab, version 0.0.13.)
for ribosome profiling: 4 randomized nucleotides were trimmer using the FASTX-Toolkit (Hannon Lab, version 0.0.13.)
for ribosome profiling: rRNA was depleted by mapping against human rRNA using bowtie version 1.0.0
mapping to UCSC cannonical ORFs was performed with bowtie version 1.0.0
count tables were created using a custom script and differential expression determined with DESeq2
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited txt files including standard DESeq2 output (baseMean, log2FoldChange (lfc), lfcSE, statx, pvalue, padj)
*normalized.txt: normalized reads
*resLA.txt: fully analyzed data; tested for significantly unchanged genes
*res.txt: fully analyzed data; tested for significantly changed genes
siRNA_RPE_RPF_mRNA_res.txt: combined file for RNA-seq and ribosome profiling fully analyzed data; tested for significantly changed genes

extract_protocol:
RNA-seq: Total RNA samples were extracted with TRIzol
RNA libraries for RNA-seq were prepared for sequencing using the TruSeq Standard mRNA LT Kit from Illumina


title: IMo_LPS00h_A171227


title: PROG_052

value: rec


title: PROG_053

value: Ta


title: PROG_051

value: UroA-Prog


title: WT FoxA2 Negative FoxA2-RFP Rep 1 [ATAC-Seq]

city: Philadelphia

first: Gregory

last: Donahue

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

institute: The University of Pennsylvania

data_processing:
Alignment: paired-end ATAC-seq reads were mapped to the mouse mm10 genome with STAR-2.5.2a using the parameters --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --alignMatesGapMax 1000000 --alignIntronMax 1 (Dobin et al., 2013).
Post-processing: reads mapping to the mitochondria, unmapped contigs, and chromosome Y, and mate-pairs longer than 2 kb, and possible PCR duplicates were removed.
Peak-calling: we used MACS2 (Zhang et al., 2008) to call peaks with the parameters --nomodel --nolambda --keep-dup all --call-summits.  We extracted peaks with FDR < 0.01 and filtered out the peaks that were overlapped with the consensus excludable ENCODE blacklist and mitochondrial homologs (Buenrostro et al., 2015).
Genome_build: mm10
Supplementary_files_format_and_content: Peak files have MACS2 peaks called at FDR 0.1 for all samples post-filtering (see data processing); peak files represent the union of peaks taken across replicates

source_name: Mouse embryo E7.5

growth_protocol: All procedures were in accordance with the NIH Guide for the Care and Use of Laboratory Animals and were approved by an IACUC committee at University of Pennsylvania.  FoxA2WT-tagRFP/WT and FoxA2∆Hx-tagRFP/WT mice were generated by recombinase-mediated cassette exchange (RMCE) gene targeting in embryonic stem cells (Supplemental Figure 3A) (Chen et al., 2011).  For the FoxA2WT-tagRFP allele, the stop codon of FoxA2 was removed and a flexible linker (SGGGGS GGGGS GGGGS GGGGS) (Arai et al., 2004) plus tagRFP (Merzlyak et al., 2007) was inserted following the FoxA2 coding sequence.  For the FoxA2∆Hx-tagRFP allele, a 10-amino acid of the FoxA2 -helix region (LKAYEQVMHY) was removed from FoxA2WT-tagRFP allele.  These knock-in mice were maintained on a C57Bl6/J x CD-1 mixed background.  The PCR primers for genotyping FoxA2WT-tagRFP and FoxA2∆Hx-tagRFP knock-in alleles (generating 231 bp product) and non-modified allele (generating 197 bp product) are listed as below:  lox2272-F: AGT GTT GTC TTC TGC CTT TGA G   lox2272-R: GCT TAC CTT AGT CTC GGT CTT GG  The PCR primers for genotyping FoxA2WT-tagRFP allele (generating 300-bp product) and FoxA2∆Hx-tagRFP (generating 270-bp product) are listed as below:  tRFP-F: GCT CTT CGC CCT TAG ACA CC    tRFP-R: ATC AGC CCC ACA AAA TGG AC    Because none of the E7.5 embryonic phenotypes investigated in this study is evidently sex biased, embryos were not sexed, and a mixed population of male and female embryos was analyzed for RNA-seq and ATAC-seq.

extract_protocol:
ATAC-seq from two biological replicates was performed essentially as previously described (Buenrostro et al., 2015) with the following differences:  in total, 2,000-5,000 embryonic cells were used per ATAC-seq library and the transposition reaction was done in 5 ul instead of 50 ul reaction.  Also, the QIAGEN MinElute purification before PCR was eliminated and instead took the 5 ul reaction immediately after transposition directly into the 50 ul PCR.
The ATAC-seq libraries were quantified using the NEBNext Library Quant Kit for Illumina (NEB, #E7630S) and the size distribution of the libraries was validated using the High Sensitivity DNA Analysis Kit (Agilent, #5067-4626).  The libraries were pooled and paired-end sequenced on an Illumina NextSeq 500 with 2x38bp read lengths.

treatment_protocol: Females of 3-5 weeks old FoxA2WT-tagRFP/WT and FoxA2∆Hx-tagRFP/WT were superovulated by intraperitoneal injection of 7.5 IU pregnant mare serum gonadotropin (PMSG) (Prospec, #HOR-272) and, 48 hr later, followed by a second injection of 7.5 IU human chorionic gonadotropin (HCG) (Sigma, #G1063-1VL) and then bred to males of same genotype. E7.5 mouse embryos were dissected into phenol red-free DMEM/F12 (Invitrogen, # 11039-021) supplemented with 5% fetal bovine serum (FBS).  Extra-embryonic portion was removed and kept for PCR genotyping.  tagRFP intensity of embryos was evaluated by taking a fluorescence image (Nikon TE2000-U) in order to distinguish FoxA2WT-tagRFP and FoxA2∆Hx-tagRFP homozygous embryos from heterozygous and wild type embryos.  About 10 embryos of homozygous (for sorting), heterozygous (for setting a FACS gate), or wild type (for setting a FACS gate) were washed with PBS, dissociated with 200 ul of 0.05% Trypsin-EDTA (Invitrogen, #25300054) for 5 minutes at 37 ºC, and then stopped with 200 ul of DMEM/F12 supplemented with 20% FBS.  The embryos were pipetted up and down to obtain single cell suspension, spun down to remove supernatant, and re-suspend in DMEM/F12 supplemented with 10% FBS.  The cell suspensions were filtered through 35 um filter cap (BD Falcon #352253) and transfer to FACS tube (BD Falcon #352063).  Based on tagRFP intensity of wild type and heterozygous embryos, three sorting gates were set: “FoxA2-tagRFP-negative”, “FoxA2-tagRFP-middle” which were gated by avoiding autofluorescence of WT and including up to maximum tagRFP intensity of heterozygous (FoxA2tagRFP/WT) cells expressed, and “FoxA2-tagRFP-high” which exhibited higher tagRFP signal than heterozygous cells did (Supplemental Figure 6B).  These three populations of homozygous embryos were isolated on a BD Influx Cell Sorter.

tag: genetic background

tag: rfp level

value: Negative

tag: replicate

value: Rep 1


title: IM_LPS00h_A171227

value: lung

value: interstitial macrophages (IM)


title: PROG_049

tag: tissue preparation

value: prog

value: UroC


title: IM_LPS06h_ipA161219

value: IP LPS


title: WT FoxA2 Negative FoxA2-RFP Rep 2 [ATAC-Seq]

value: Rep 2


title: WT FoxA2 Middle FoxA2-RFP Rep 1 [ATAC-Seq]

value: Middle


title: WT FoxA2 Middle FoxA2-RFP Rep 2 [ATAC-Seq]


title: PROG_050

value: bladder cancer

value: FFPE

tag: labeling batch

value: primary


title: WT FoxA2 High FoxA2-RFP Rep 2 [ATAC-Seq]

value: High


title: mRNA_PDCD4-KD_rep2

description:
siRNA_RPE_mRNA_res.txt
siRNA_RPE_mRNA_resLA.txt
siRNA_RPE_mRNA_normalized.txt
siRNA_RPE_RPF_mRNA_res.txt
didnt work well (too few reads); was not possible to consider

value: hTERT-immortalized retinal pigment epithelial cell line

value: PDCD4-siRNA2 (100 nM)


title: AM_LPS00h_D171227

value: alveolar macrophages (AM)


title: PROG_048

tag: patient identifier

value: rec

value: Ta


title: PROG_047

tag: tumor number


title: WT FoxA2 High FoxA2-RFP Rep 1 [ATAC-Seq]

value: Rep 1


title: mRNA_control_rep3

value: control-siRNA (100 nM)


title: IM_LPS00h_B171227

value: lung

value: interstitial macrophages (IM)


title: mRNA_control_rep1


title: AM_LPS00h_C171227


title: AM_LPS00h_A171227


title: mRNA_PDCD4-KD_rep3


title: mRNA_PDCD4-KD_rep1


title: Delta Helix Mutant FoxA2 Negative FoxA2-RFP Rep 1 [ATAC-Seq]

value: Negative


title: Delta Helix Mutant FoxA2 Middle FoxA2-RFP Rep 3 [ATAC-Seq]


title: ND_12_rep3

city: LOS ANGELES

first: Jesse

middle: R

last: Zamudio

address: 610 CHARLES E. YOUNG DRIVE EAST BOX 957239

department: MCDB

institute: University of California, Los Angeles

description:
RNAseq library prepared with TruSeq stranded mRNA kit (illumina)
edgeR_sg10_sgtom_dox_gene_summary_180601.txt

data_processing:
RNA-seq read files were merged from technical replicates.
Reads mapped to the mm10 genome assembly using Tophat (ver 2.0.14).
Additional transcripts were assembled using stringtie (1.2.4).
Reads within exon sequences counted using HTSeq (HTSeq-0.6.1).
Differential expression analysis was performed with EdgeR (3.22.3).
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files contain normalized read counts for exonic regions and output from edgeR.
Supplementary_files_format_and_content: The data represents merged replicates

source_name: mouse embryonic fibroblasts

growth_protocol: MEFs were grown  in Dulbecco’s Modified Essential Media supplemented with 15% fetal bovine serum (Gibco), 0.1 mM nonessential amino acids, 2 mM L-glutamine, Pen/Strep (50 U/ml) and 0.055 mM β-mercaptoethanol.

extract_protocol:
Total RNA was extracted with Qiagen RNAeasy kit
Strand-specific RNA sequencing libraries from purified polyadenylated RNA were prepared using the TruSeq Stranded mRNA kit (Illumina)

treatment_protocol: WT Mefs previously infected with an sgRNA targeting the PVT1 p53RE or a nontargeting control (sgtom) were untreated or grown in a 0.5uM concentration of doxorubicin for 24 hours to induce the DNA damage response.

value: mouse embryonic fibroblasts

tag: cell line name

value: Mefs sg10

value: 0.5uM Doxorubicin for 24h

tag: experimental series

value: PVT1 p53RE mutant doxorubicin timecourse


title: PROG_045

value: bladder cancer

value: FFPE

tag: primary, recurrence, or progression

tag: tumor stage

tag: grade (who1999)

value: UroA-Prog


title: Delta Helix Mutant FoxA2 Middle FoxA2-RFP Rep 2 [ATAC-Seq]

value: Middle


title: PROG_055

value: prog

tag: molecular subtype

value: UroC


title: Delta Helix Mutant FoxA2 Negative FoxA2-RFP Rep 2 [ATAC-Seq]

value: Rep 2


title: ND_10_rep3

value: Mefs sgtom

tag: treatment

value: PVT1 p53RE WT doxorubicin timecourse


title: ND_9_rep3

value: untreated


title: Delta Helix Mutant FoxA2 High FoxA2-RFP Rep 2 [ATAC-Seq]

value: High


title: ND_8_rep2


title: PROG_043

tag: tissue

value: primary

value: Ta


title: PROG_044

value: GU


title: PROG_046

value: Ba/Sq


title: PROG_041


title: Delta Helix Mutant FoxA2 High FoxA2-RFP Rep 1 [ATAC-Seq]

value: Rep 1


title: ND_11_rep3

tag: cell type

value: mouse embryonic fibroblasts

value: Mefs sg10

value: PVT1 p53RE mutant doxorubicin timecourse


title: PROG_040

value: bladder cancer

value: FFPE

value: UroA-Prog


title: WT FoxA2 Negative FoxA2-RFP Rep 3

data_processing:
Alignment: RNA-seq reads were mapped to the mouse mm10 genome with STAR-2.5.2a using the parameters --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 (Dobin et al., 2013).
Quantitation over exons: after alignment, the number of reads per transcript were estimated using HTSeq-0.6.1 (Love et al., 2015)
Library size adjustment and differential expression: DESeq2 (Love et al., 2014) was used to normalize read counts and call differentially expressed genes.
Genome_build: mm10
Supplementary_files_format_and_content: DESeq Processed Values.txt has the adjusted values for each sample from DESeq2 analysis

extract_protocol:
Three biological replicates of total RNA from 2,500-5,000 embryonic cells was isolated using the RNeasy Micro kit (QIAGEN, #74004) and genomic DNA was digested on column with the addition of RNase-free DNase I.  The RNA was eluted from the columns using RNase-free water.
RNA-seq libraries with the RNA equivalent of 1,000 cells were generated by SMART-Seq2 method as previously described (Picelli et al., 2014).  The RNA-seq libraries were quantified using the NEBNext Library Quant Kit for Illumina (NEB, #E7630S) and the size distribution of the libraries was validated using the High Sensitivity DNA Analysis Kit (Agilent, #5067-4626).  The libraries were pooled and single-end sequenced on an Illumina NextSeq 500 with 75-bp read length.

value: Negative

value: Rep 3


title: 23 70YM9 DMSO

city: Berlin

first: Eric

last: Seidel

state: Berlin

address: Augustenburger Platz 1

institute: Charite Berlin

description: HAC15 - mitotane resistant - DMSO - 9

hyb_protocol: Hybridization was done for 16 hr at 45°C on Human PrimeView array chip and washing was done using  Midi_euk2v3.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed via Expression Console, Data processing and normalization by the Robust Multi-array Adjustment method.

label: Biotin

source_name: HAC15 cell line

label_protocol: Biotinylated cRNA was prepared from 500 ng total RNA according to the standard Affymetrix protocol.

growth_protocol: Bulk HAC15 cells were grown in 2D cell culture and received long-term treatment with DMSO (nonresistant) or 70 µM mitotane (resistant) for 72 days followed by clonal selection.

extract_protocol: Total RNA was isolated using QIAzol Lysis Reagent, miRNeasy MiniKit and RNase-Free DNase set (all from Qiagen, Hilden, Germany)

treatment_protocol: Clones were treated with either DMSO or 50 µM mitotane for 18 h.

tag: cell line

value: DMSO, 18 h


title: ND_7_rep2


title: PROG_042

value: UroB


title: 24 70YM12 DMSO

description: HAC15 - mitotane resistant - DMSO - 12


title: WT FoxA2 Negative FoxA2-RFP Rep 2

tag: genetic background

value: Rep 2


title: 22 70YM8 DMSO

description: HAC15 - mitotane resistant - DMSO - 8


title: ND_6_rep2

value: Mefs sgtom

value: 0.5uM Doxorubicin for 24h

value: PVT1 p53RE WT doxorubicin timecourse


title: ND_5_rep2

value: untreated


title: 19 70YM5 DMSO

description: HAC15 - mitotane resistant - DMSO - 5


title: 21 70YM7 DMSO

description: HAC15 - mitotane resistant - DMSO - 7


title: PROG_036

value: rec

value: UroC


title: WT FoxA2 Negative FoxA2-RFP Rep 1

tag: rfp level

value: Rep 1


title: PROG_037

value: primary


title: WT FoxA2 Middle FoxA2-RFP Rep 3

value: Middle

tag: replicate


title: 20 70YM6 DMSO

description: HAC15 - mitotane resistant - DMSO - 6


title: WT FoxA2 Middle FoxA2-RFP Rep 2


title: ND_3_rep1

value: mouse embryonic fibroblasts

value: Mefs sg10

value: PVT1 p53RE mutant doxorubicin timecourse


title: PROG_038

value: bladder cancer

tag: tissue preparation

value: FFPE


title: PROG_039

tag: labeling batch

value: prog


title: WT FoxA2 Middle FoxA2-RFP Rep 1


title: ND_2_rep1


title: WT FoxA2 High FoxA2-RFP Rep 3

value: High

value: Rep 3


title: PROG_059

tag: patient identifier


title: 18 70YM12 MITOTAN

description: HAC15 - mitotane resistant - 70 µM mitotane - 12

value: 50 µM mitotane, 18 h


title: 5Y_NHEG1_1

source_name: SH-SY5Y stably transfected with NHEG1 repeat 1

value: neuroblastoma

tag: vector


title: ND_4_rep1

tag: cell line name

value: 0.5uM Doxorubicin for 24h


title: ND_1_rep1

value: Mefs sgtom

value: untreated

tag: experimental series

value: PVT1 p53RE WT doxorubicin timecourse


title: PROG_035

tag: tumor number

tag: primary, recurrence, or progression

value: Ta

value: UroA-Prog


title: 17 70YM9 MITOTAN

description: HAC15 - mitotane resistant - 70 µM mitotane - 9


title: 15 70YM7 MITOTAN

description: HAC15 - mitotane resistant - 70 µM mitotane - 7


title: MT100_3 (rep3)

city: yangzhou

first: hflx

middle: hflx

last: hflx

state: jiangsu

address: 88 University South Road

department: Agricultural College

institute: yangzhou 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 Oryza_sativa.IRGSP-1.0 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of transcript per Million fragments mapped (FPKM) were calculated using Cuffdiff.
Genome_build: Oryza_sativa.IRGSP-1.0
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

organism: Oryza sativa

source_name: seed

extract_protocol:
Rice seeds were sampled at 22 hours after sowing, and than removed in ultra low temperature freezer. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Nevogene protocols

value: seed

tag: Stage

value: 22 hours after sowing


title: PROG_034

value: rec

tag: tumor stage

tag: grade (who1999)

tag: molecular subtype

value: GU


title: MT100_2 (rep2)

tag: tissue


title: PROG_032

value: bladder cancer

value: primary


title: Delta Helix Mutant FoxA2 Negative FoxA2-RFP Rep 3

description:
FoxA2-∆Hx-tagRFP
delHx.Neg.3

value: Negative


title: 13 70YM5 MITOTAN

description: HAC15 - mitotane resistant - 70 µM mitotane - 5

tag: cell line

tag: treatment


title: PROG_030

value: FFPE

value: UroB


title: PROG_031


title: 12 K6 DMSO

description: HAC15 - nonresistant - DMSO - 6

value: DMSO, 18 h


title: WT FoxA2 High FoxA2-RFP Rep 2

tag: genetic background

tag: rfp level

value: High

value: Rep 2


title: NaCl_3 (rep3)


title: 11 K5 DMSO

description: HAC15 - nonresistant - DMSO - 5


title: Delta Helix Mutant FoxA2 Negative FoxA2-RFP Rep 2

description:
FoxA2-∆Hx-tagRFP
delHx.Neg.2

tag: replicate


title: Delta Helix Mutant FoxA2 Negative FoxA2-RFP Rep 1

description:
FoxA2-∆Hx-tagRFP
delHx.Neg.1

value: Rep 1


title: PROG_033

tag: tissue preparation

tag: labeling batch


title: 10 K4 DMSO

description: HAC15 - nonresistant - DMSO - 4


title: PROG_028

tag: patient identifier


title: NaCl_1 (rep1)


title: Delta Helix Mutant FoxA2 Middle FoxA2-RFP Rep 2

description:
FoxA2-∆Hx-tagRFP
delHx.Mid.2

value: Middle


title: Delta Helix Mutant FoxA2 Middle FoxA2-RFP Rep 3

description:
FoxA2-∆Hx-tagRFP
delHx.Mid.3

value: Rep 3


title: PROG_027


title: 14 70YM6 MITOTAN

description: HAC15 - mitotane resistant - 70 µM mitotane - 6

value: 50 µM mitotane, 18 h


title: PROG_025

value: prog

value: UroC


title: PROG_026

value: UroA-Prog


title: 16 70YM8 MITOTAN

description: HAC15 - mitotane resistant - 70 µM mitotane - 8


title: PROG_029

value: rec

value: Ta


title: 8 K2 DMSO

description: HAC15 - nonresistant - DMSO - 2


title: 7 K1 DMSO

description: HAC15 - nonresistant - DMSO - 1


title: CK_3 (rep3)

value: seed

value: 22 hours after sowing


title: NaCl_2 (rep2)


title: CK_1 (rep1)


title: CK_2 (rep2)


title: Delta Helix Mutant FoxA2 Middle FoxA2-RFP Rep 1

description:
FoxA2-∆Hx-tagRFP
delHx.Mid.1


title: DL1777 Stationary Growth MFA Biological Repeat 3

city: Cambridge

first: Martin

middle: Andrew

last: White

state: MA

address: Northwest Building room 140, 52 Oxford Street

department: Molecular and Cellular Biology

institute: Harvard University

description: Chromosomal DNA isolated from a stationary phase culture of E. coli strain DL1777

data_processing:
Alignment: reads were aligned to an in-house generated draft sequence of strain DL1777 (DL1777ReferenceSequence.fasta) using the Burrows-Wheels Alignment software BWA-MEM.
Where multiple sequencing runs of the same library were carried out, the data from each of the runs was consolidated by merging BAM files using the merge function of SAMtools.
Read Counts: the number of reads mapped to each bp of the genome was quantified using the mpileup function of SAMtools (with parameters -BQ0 -d10000000).
Genomic positions lacking any mapped reads were assigned an arbitrary value of 0.1.
Genome_build: DL1777ReferenceSequence.fasta
Supplementary_files_format_and_content: Each CSV file contains a single headerless column of 4,625,919 rows corresponding to the 4,625,919 bp of the reference genome. The index of each row corresponds to the position on the reference genome. Values are the total number of reads mapped to the corresponding position on the reference genome.

organism: Escherichia coli K-12

source_name: E. coli cell lysates

growth_protocol: Cells were grown in LB media at 37°C with vigorous shaking.

extract_protocol:
Genomic DNA was isolated from cultures using the Promega Wizard® Genomic DNA purification kit. This was followed by further RNase treatment and phenol/chloroform purification.
Construction of libraries using the Illumina TruSeq DNA Sample Prep kit and DNA sequencing was carried out on an Illumina HiSeq 2000 platform by Edinburgh Genomics.

treatment_protocol: Cell density was maintained at a density of OD600 0.2 - 0.25 by serial dilution.

tag: strain identifier

tag: genotype

value: MG1655 fnr-267 lacIq lacZChi-

tag: population growth phase

value: Stationary Phase


title: Delta Helix Mutant FoxA2 High FoxA2-RFP Rep 2

description:
FoxA2-∆Hx-tagRFP
delHx.High.2


title: Delta Helix Mutant FoxA2 High FoxA2-RFP Rep 1

description:
FoxA2-∆Hx-tagRFP
delHx.High.1


title: DL1777 Stationary Growth MFA Biological Repeat 2


title: DL1777 Stationary Growth MFA Biological Repeat 1


title: PROG_023

value: bladder cancer

value: FFPE

tag: tumor number

tag: primary, recurrence, or progression

value: primary


title: NK_inf_2

city: Marburg

first: Leon

middle: Nicolas

last: Schulte

state: Hessen

address: Hans-Meerwein-Str. 2

department: Institute for Lung Research

institute: Philipps-Universität Marburg

description: NK cells from Salmonella-infected tissue models

data_processing:
RTA version 1.18.66.4 was used for basecalling
bcl2fastq version 1.8.4. was used for demultiplexing
Reads were mapped using the CLC genomics workbench version 10.01 and the GRCh38 GENCODE human genome annotation, fused to the S. Typhimurium SL1344 annotation (Vogel lab) with standard settings: mismatch cost = 2; insertion cost = 3; deletion cost = 3; length fraction = 0.8; similarity fraction = 0.8.
RPKMs were calculated for genes using the CLC genomics worbench version 10.01
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text-files including gene ID, chromosome, gene type, genomic position, unique read number, RPKM

source_name: Peripheral blood leukocytes

growth_protocol: intestinal tissue model in a trans-well setting, with natural porcine intestinal collagen matrix. Caco2 cells (apical), endothelial cells (basolateral) and peripheral blood cells (basolateral) were cultured in MEM (apical) and Vasculife / X-Vivo15 (basolateral) medium.

extract_protocol:
Cells were washed once with PBS and flow-sorted (endothelial and Caco2 cells were disattached by Accutase treatment and scraping). RNA was extracted using the Mirvana microRNA isolation kit, with the total RNA isolation protocol.
Strand-specific libraries were prepared following rRNA depletion (Ribo-Zero Gold rRNA Removal Kit (Epidemiology)), by Vertis Biotech AG, according to the companies protocols
strand-dpecific rRNA-depleted totalRNA-Seq

treatment_protocol: Cells were stimulated with Salmonella enterica serovar Typhimurium, added to the apical side (MOI 10, 24 h)

tag: cell type

value: CD56+ peripheral blood cell

tag: precursor

value: CD56+ peripheral NK cell

tag: disease

value: healthy

tag: ethnicity

value: caucasian


title: VT EBs, rep C

city: Vienna

first: Matthias

last: Horn

address: Althanstrasse 14

department: Division of Microbial Ecology

country: Austria

institute: University of Vienna

data_processing:
Filtering and trimming (in order shown): removal of first 11 bases, clipping of remaining adapter sequences and removal of reads <25 bases, all done using Trimmomatic.
Reads were mapped to the P. acanthamoebae UV-7 genome using BWA (default settings).
Strand-specific reads per predicted gene were counted via HTSeq (union mode).
Normalised gene expression values and differential gene expression were determined using DESeq2.
Genome_build: Parachlamydia acanthamoebae UV-7 (Accession number: NC_015702).
Supplementary_files_format_and_content: UV7_raw_counts: tab-delimited text file includes raw counts data by gene (rows) and sample (columns).
Supplementary_files_format_and_content: UV7_log2(TPM): tab-delimited text file includes log2(TPM) values by gene (rows) and sample (columns).

organism: Parachlamydia acanthamoebae UV-7

source_name: P. acanthamoebae UV-7

growth_protocol: Amoeba-endosymbiont cultures, originating from the same ancestral population, were maintained at 20°C in TSY (30 g/L trypticase soy broth, Oxoid, 10 g/L yeast extract; pH 7.3) for 14 months under two different experimental set-ups. In one, HT was the predominant mode of transmission, whereas in the other VT was the main mode of transmission. For the RNA-Seq infection experiment, uninfected amoebae were seeded at low density 3 days prior to infection and incubated at 20°C, before purified endosymbionts were added. These originated from the last passage of amoeba-endosymbiont cultures from the HT and VT set-ups, and extracellular endosymbionts were harvested from the medium supernatant after one week of incubation. Two hours after infection, cultures were washed 3x and infected cultures were harvested (2 hpi time point) or further incubated at 20°C in TSY for 24 hrs. Released EBs were collected 1 week after infection as the final time point.

extract_protocol:
After collection of cells, pellets were immediately resuspended in TRIzol reagent, followed by bead-beating (30s, 4.5 m/s, lysing matrix A tubes, MP Biomedicals). Subsequent RNA extraction was performed according to the TRIzol guidelines. Residual DNA was removed using the Turbo DNA-free Kit (Thermo Fisher Scientific).
The sequencing facility (Vienna BioCenter Core Facilities) removed ribosomal RNA using Illumina's Ribo-Zero Gold rRNA Removal Kit (Epidemiology). RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: At respective time points post infection infected amoebae were harvested, resuspended in sucrose buffer (35 mM Tris-HCl, 250 mM sucrose, 25 mM KCl, 10 mM MgCl2), supplemented with 50 µg/ml Rifampicin, and then disrupted by 1 min vortexing in the presence of glass beads. Suspensions were filtered through 5 µm filters, and bacteria were collected by 2 min high-speed centrifugation. Extracellular bacteria were pelleted, resuspended in sucrose buffer and treated like the other two time points.

tag: strain

tag: developmental stage of endosymbiont

value: released symbionts (EBs)

tag: multiplicity of infection


title: NK_mock_2

description: NK cells from mock-treated tissue models


title: PROG_024

source_name: FFPE tissue specimen

tag: tissue

tag: tumor stage

tag: grade (who1999)

tag: molecular subtype

value: UroB


title: VT EBs, rep B


title: DL2874 Exponential Growth MFA Biological Repeat 3

description:
Chromosomal DNA isolated from a culture of exponentially growing E. coli strain DL2874
MG1655 fnr-267 lacIq lacZχ- ΔsbcDC lacZ::pal246

value: MG1655 fnr-267 lacIq lacZChi- <delta>sbcDC lacZ::pal246

value: Exponential Growth


title: 6 K6 MITOTAN

description: HAC15 - nonresistant - 70 µM mitotane - 6

tag: cell line

tag: treatment

value: 50 µM mitotane, 18 h


title: PROG_022

tag: tissue preparation

tag: labeling batch

tag: patient identifier

value: prog

value: UroA-Prog


title: DL2874 Exponential Growth MFA Biological Repeat 2

tag: strain identifier

tag: genotype

tag: population growth phase


title: Mono_mock_2

description: Monocytes from mock-treated tissue models

tag: cell type

value: CD14+ peripheral blood cell

tag: precursor

value: CD14+ monocyte

tag: disease


title: PROG_019

tag: tumor number

tag: primary, recurrence, or progression


title: 3 K3 MITOTAN

description: HAC15 - nonresistant - 70 µM mitotane - 3


title: HT EBs, rep C

tag: strain

tag: developmental stage of endosymbiont

tag: multiplicity of infection


title: VT EBs, rep A


title: DL2874 Exponential Growth MFA Biological Repeat 1


title: PROG_020

tag: tissue

tag: tumor stage

tag: grade (who1999)

tag: molecular subtype

value: UroC


title: PROG_018

value: bladder cancer

tag: tissue preparation

tag: labeling batch


title: Endo_inf_2

description: Endothelial cells from Salmonella-infected tissue models

source_name: Human skin microvascular endothelium

value: Microvascular endothelial cell

tag: ethnicity


title: 1 K1 MITOTAN

description: HAC15 - nonresistant - 70 µM mitotane - 1

tag: cell line

tag: treatment


title: Mono_inf_2

description: Monocytes from Salmonella-infected tissue models

tag: cell type


title: HT EBs, rep B


title: DL2859 Exponential Growth MFA Biological Repeat 3

description: Chromosomal DNA isolated from a culture of exponentially growing E. coli strain DL2859

tag: strain identifier

tag: genotype

value: MG1655 fnr-267 lacIq lacZChi- lacZ::pal246

tag: population growth phase


title: Endo_mock_2

description: Endothelial cells from mock-treated tissue models

tag: precursor

tag: disease


title: DL2859 Exponential Growth MFA Biological Repeat 2


title: HT EBs, rep A

tag: strain

tag: developmental stage of endosymbiont


title: 2 K2 MITOTAN

description: HAC15 - nonresistant - 70 µM mitotane - 2


title: Delta Helix Mutant FoxA2 High FoxA2-RFP Rep 3

description:
FoxA2-∆Hx-tagRFP
delHx.High.3

tag: genetic background

tag: rfp level

value: High

tag: replicate

value: Rep 3


title: 4 K4 MITOTAN

description: HAC15 - nonresistant - 70 µM mitotane - 4


title: VT 24 hpi, rep C

value: 24 hr post infection

tag: multiplicity of infection


title: DL2859 Exponential Growth MFA Biological Repeat 1


title: PROG_015

tag: tissue

tag: tissue preparation

value: FFPE

tag: patient identifier

tag: tumor number

tag: primary, recurrence, or progression

value: primary

tag: tumor stage

tag: grade (who1999)

tag: molecular subtype


title: Caco2_GFP+_2

description: Caco2 cells from Salmonella-infected tissue models (FACS-purified GFP+ fraction)

source_name: Human colorectal adenocarcinoma

tag: cell line

value: colorectal adenocarcinoma

tag: ethnicity

value: caucasian

value: colon adenocarcinoma patient


title: VT 24 hpi, rep B


title: Caco2_mock_2

description: Caco2 cells from mock-treated tissue models

tag: precursor

tag: disease


title: PROG_021

tag: labeling batch

value: rec


title: PROG_016


title: DL2151 Exponential Growth MFA Biological Repeat 2

description:
Chromosomal DNA isolated from a culture of exponentially growing E. coli strain DL2151
MG1655 fnr-267 lacIq lacZχ- ΔsbcDC

tag: strain identifier

tag: genotype

value: MG1655 fnr-267 lacIq lacZChi- <delta>sbcDC

tag: population growth phase

value: Exponential Growth


title: NK_inf_1

tag: cell type

value: CD56+ peripheral blood cell

value: CD56+ peripheral NK cell

value: healthy


title: PROG_017

tag: tissue

value: bladder cancer

value: UroA-Prog


title: PROG_014

tag: tissue preparation

value: prog

value: UroC


title: Caco2_GFP-_2

description: Caco2 cells from Salmonella-infected tissue models (FACS-purified GFP- fraction)


title: VT 24 hpi, rep A

tag: strain

tag: developmental stage of endosymbiont

tag: multiplicity of infection


title: HT 24 hpi, rep C


title: PROG_013

tag: patient identifier

tag: tumor number

tag: primary, recurrence, or progression

tag: tumor stage

value: ScNE


title: DL2151 Exponential Growth MFA Biological Repeat 1


title: MT100_1 (rep1)

value: seed

tag: Stage

value: 22 hours after sowing


title: NK_mock_1

tag: precursor

tag: ethnicity


title: PROG_010

value: FFPE

tag: labeling batch

value: primary

tag: grade (who1999)

tag: molecular subtype


title: PROG_009


title: DL1777 Exponential Growth MFA Biological Repeat 3

description: Chromosomal DNA isolated from a culture of exponentially growing E. coli strain DL1777

tag: strain identifier

tag: genotype

value: MG1655 fnr-267 lacIq lacZChi-

tag: population growth phase


title: HT 24 hpi, rep B

value: 24 hr post infection


title: DL2151 Exponential Growth MFA Biological Repeat 3


title: Mono_inf_1

tag: cell type

value: CD14+ peripheral blood cell

value: CD14+ monocyte

tag: disease

value: caucasian


title: DL1777 Exponential Growth MFA Biological Repeat 1

value: Exponential Growth


title: Mono_mock_1


title: PROG_012

tag: tissue

tag: tissue preparation

value: GU


title: VT 2 hpi, rep C

tag: strain

tag: developmental stage of endosymbiont

value: 2 hr post infection

tag: multiplicity of infection


title: Endo_inf_1

value: Microvascular endothelial cell

value: healthy


title: S.tm_input_2

description: Salmonella pre-infection inoculum

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

source_name: Salmonella Typhimurium

value: Salmonella enterica serovar Typhimurium (SL1344), constitutively expressing GFP


title: Endo_mock_1


title: PROG_008

value: bladder cancer

tag: patient identifier

tag: tumor number

tag: primary, recurrence, or progression

value: rec

tag: tumor stage

value: UroC


title: PROG_011

tag: labeling batch

value: prog


title: PROG_006

value: FFPE

tag: grade (who1999)


title: VT 2 hpi, rep A


title: S.tm_input_1

description: Salmonella pre-infection inoculum

tag: precursor

value: Salmonella enterica serovar Typhimurium (SL1344)


title: PROG_007

tag: molecular subtype


title: HT 2 hpi, rep C


title: Caco2_GFP-_1

tag: cell line

value: colorectal adenocarcinoma

tag: ethnicity

value: colon adenocarcinoma patient


title: DL1777 Exponential Growth MFA Biological Repeat 2

tag: strain identifier

tag: genotype

value: MG1655 fnr-267 lacIq lacZChi-

tag: population growth phase


title: Caco2_GFP+_1

tag: disease


title: Day 50 NM organoid 4

first: Cornelius

last: Fischer

address: Robert-Rössle-Straße 10

department: Berlin Institute for Medical Systems Biology

institute: Max Delbrück Center for Molecular Medicine (MDC)

data_processing:
HiSeq 4000 data was demultiplexed using bcl2fastq v1.9
Fastq data from different lanes and appropriate indexes was merged.
Alignment, filtering, UMI counting, barcode counting and filtering and gene-barcode matrix generation was performed with 10X Cell Ranger (v3.0.2, 10X Genomics).
the biological read is read 2 (R2, 98 bp, read 2 is used to sequence the cDNA fragment) the cell-barcode/UMI read is read 1 (R1, 28 bp, read 1 is used to sequence the 16 bp 10x Barcode and 10 bp UMI) the sample index is read I (I1, 8 bp)
Cell Ranger R kit version 2.0.0 and Seurat version 3.0.3 was used for downstream analysis. For clustering, principal-component analysis was performed for dimension reduction and t-SNE was used for clustering visualization. sSeq integrated in the Cell Ranger R kit was used for modeling the gene expression with negative binomial distribution to identify genes whose expression was enriched in specific clusters
Genome_build: GRCh38
Supplementary_files_format_and_content: Cell Ranger output, see readme.txt

source_name: Neuromuscular organoid

growth_protocol: Neuromesodermal progenitors generated from human PSCs were dissociated using accutase to generate a single cell suspension. On day 0 of organoid formation, NMP cells (4,500 – 9,000 /well depending on the line) were plated on an ultra-low binding 96-we plate (Corning) in Neurobasal medium with 50uM Rho-associated protein kinase ROCK inhibitor, 10ng/ml bFGF and 2ng/ml IGF1 and HGF (peprotech). The initial volume in each well was 100ul. At day2, 50ul of the medium was removed and 100ul of NB medium supplemented with 2ng/ml IGF1 and HGF was added. After day 4 the organoids were maintained in NB medium without the addition of growth factors. On day 10 the organoids were transferred in p6 plates and after 1 month in p10 plates. During the whole period organoids were maintained on an orbital shaker rotating at 75rpm.

extract_protocol: Organoids were dissociated mechanically using accutase solution and incubation at 37C. After single cell formation, the cell suspension was run through a 70μm strainer to remove any residual cell and debris clumps. A small volume of the cell suspension was removed for cell counts. The remaining cells were diluted 4-fold in 1X dPBS and then centrifuged at 200g for 5  minutes. The cell pellet was then resuspended in dPBS containing 0.04% BSA to give a final concentration of 206 cells/μl. PolyA selection based RNA capture (Chromium Single Cell 3’ Reagent Kit , v3 Chemistry, 10X Genomics) was done as per the manufacturer's instructions provided by 10X Genomics platform.   RNA-Seq libraries were prepared as per manufacturer's insturctions provided by 10X Genomics platform (https://www.10xgenomics.com/single-cell/)

treatment_protocol: Collection of D5 organoids and D50 organoids. The condiions of cultured are described in detail in the growth protocol.

tag: tissue

value: Neuromuscular organoid. Time point:50 days differentiated.


title: HT 2 hpi, rep B

tag: strain

tag: developmental stage of endosymbiont


title: HT 24 hpi, rep A

value: 24 hr post infection

tag: multiplicity of infection


title: PROG_005

tag: tissue preparation

tag: patient identifier

tag: tumor number

value: Ba/Sq


title: Day 5 NM organoids

description: Cellranger output files (multiple flies)

data_processing:
HiSeq 4000 data was demultiplexed using bcl2fastq v1.9
Fastq data from different lanes and appropriate indexes was merged.
Alignment, filtering, UMI counting, barcode counting and filtering and gene-barcode matrix generation was performed with 10X Cell Ranger (v2.1.0, 10X Genomics).
the biological read is read 2 (R2, 98 bp, read 2 is used to sequence the cDNA fragment) the cell-barcode/UMI read is read 1 (R1, 26 bp, read 1 is used to sequence the 16 bp 10x Barcode and 10 bp UMI) the sample index is read I (I1, 8 bp)
Cell Ranger R kit version 2.0.0 and Seurat version 2.3 was used for downstream analysis. For clustering, principal-component analysis was performed for dimension reduction and t-SNE was used for clustering visualization. sSeq integrated in the Cell Ranger R kit was used for modeling the gene expression with negative binomial distribution to identify genes whose expression was enriched in specific clusters
Genome_build: GRCh38
Supplementary_files_format_and_content: Cell Ranger output, see readme.txt

extract_protocol:
Organoids were dissociated mechanically using accutase solution and incubation at 37C. After single cell formation, the cell suspension was run through a 70μm strainer to remove any residual cell and debris clumps. A small volume of the cell suspension was removed for cell counts. The remaining cells were diluted 4-fold in 1X dPBS and then centrifuged at 200g for 5  minutes. The cell pellet was then resuspended in dPBS containing 0.04% BSA to give a final concentration of 206 cells/μl. PolyA selection based RNA capture (Chromium Single Cell 3’ Reagent Kit , v2 Chemistry, 10X Genomics) was done as per the manufacturer's instructions provided by 10X Genomics platform.   RNA-Seq
Libraries were prepared as per manufacturer's insturctions provided by 10X Genomics platform (https://www.10xgenomics.com/single-cell/)

value: Neuromuscular organoid. Time point:5 days differentiated. 10 Day 5 NM organoids labelled with two indexes (pooled 5+5).


title: Caco2_mock_1

value: caucasian


title: HT 2 hpi, rep A

value: 2 hr post infection


title: PROG_003

tag: labeling batch

tag: primary, recurrence, or progression

tag: tumor stage

value: UroA-Prog


title: THP1_LPS_MTS

status: Public on Jan 19 2020

city: Edinburgh

first: Elisa

last: Barbieri

address: 5 Little France Drive

country: United Kingdom

institute: University of Edinburgh

description:
nascent RNA
nascent-RNA profiling with fastGRO was performed in LPS treated THP1 cells

data_processing:
Image analysis: Firecrest (Illumina pipeline 1.9, default parameters)
base calling: Bustard (Illumina pipeline 1.9, default parameters)
Quality Control FastQC
Adapter Trimming TRIM-GALORE
alignment (RNAseq, chromatin RNA-seq) STAR
tag density files deepTools package was used to generate BigWiggle files
Genome_build: hg19
Supplementary_files_format_and_content: strand specific bigWig, compatible with UCSC Genome Browser, were generated using the deepTools package (bamCoverage function, with RPGC [reads per genome coverage] normalization)

source_name: THP1 cell line

growth_protocol: THP1 cells were maintained in RPMI-1640 medium supplemented with 10% (v/v) of FBS and 2 mM of L-glutamine.

extract_protocol: NEBNext ChIP-Seq ULTRAII RNA Sample Prep Kit (New England Biolabs, inc.)

treatment_protocol: THP1 cells were treated with 5 µg/ml of LPS

value: THP1 cell line

tag: protocol

tag: experiment

value: fastGRO


title: PROG_004

value: bladder cancer

value: rec

tag: grade (who1999)

tag: molecular subtype


title: 5 K5 MITOTAN

description: HAC15 - nonresistant - 70 µM mitotane - 5

tag: cell line

tag: treatment

value: 50 µM mitotane, 18 h


title: PROG_002

value: FFPE

value: ScNE


title: THP1_LPS_Ribodepl

description:
ribodepleted RNA
ribodepleted RNA-seq performed in LPS THP1 cells

extract_protocol: KAPA RNA HyperPrep Kit (Illumina)/SENSE mRNA-Seq Library Prep Kit V2 (Lexogen)


title: THP1_CTRL_Ribodepl

description:
ribodepleted RNA
ribodepleted RNA-seq performed in untreated THP1 cells


title: HeLa_EGF_20mln

description:
nascent RNA
nascent-RNA profiling with fastGRO was performed in EGF treated HeLa cells

source_name: HeLa cell line

growth_protocol: HeLa cells were maintained in DMEM medium supplemented with 10% (v/v) of SCS and 2 mM of L-glutamine.

treatment_protocol: HeLa cells were treated with 100 ng/ml of rEGF for 15 minutes

value: HeLa cell line


title: THP1_LPS_polyA

description: PolyA RNA-seq performed in LPS THP1 cells

extract_protocol: SENSE mRNA-Seq Library Prep Kit V2 (Lexogen)


title: THP1_CTRL_polyA

description: PolyA RNA-seq performed in untreated THP1 cells


title: HeLa_EGF_2-5mln_MTS


title: HeLa_EGF_2-5mln_HPDP


title: HeLa_EGF_5mln_HPDP


title: HeLa_EGF_0-5mln_MTS


title: HeLa_EGF_1mln_MTS


title: WT FoxA2 High FoxA2-RFP Rep 1

tag: genetic background

tag: rfp level

value: High

tag: replicate

value: Rep 1


title: HeLa_20mln_shortSonication

description:
nascent RNA
nascent-RNA profiling with fastGRO was performed in HeLa cells


title: 9 K3 DMSO

description: HAC15 - nonresistant - DMSO - 3

value: DMSO, 18 h


title: HeLa_20mln_mediumSonication


title: Rh4 shscr BRD4 48h

city: Bethesda

first: Javed

last: Khan

state: MD

address: 37 Convent Dr.

department: Genetics Branch

institute: NCI, NIH

data_processing:
ChIP enriched DNA reads were mapped to reference genome using BWA version 0.7.10
The ChIP-seq peaks were called by MACS2 version 2.1.0.  Duplicates were allowed
Enrichment of known and de novo motifs were found using HOMER version 4.8.2
Genome_build: Hg19
Supplementary_files_format_and_content: peak files are tab delimited text files (BED coordinates) for each sample.

growth_protocol: Cells were maintained in DMEM with 10% FBS and Penn/Strep at 37 °C incubation until harvesting for ChIP.

extract_protocol:
ChIP samples harvested after 1% formaldehyde fixation for 12 minutes, sonicated, processed and ChIP-enriched via standard protocols (Active Motif ChIP-IT HS kit).  ChIP enriched DNA was treated with Proteinase K at 55 ˚C for 30 minutes followed by reversal of crosslinks by heating to 80 ˚C for 2 hours, and DNA purification by column (MiniElute PCR purification kit, Qiagen).
DNA was extracted from ChIP-seq samples prepared following the Active Motif ChIP-IT High Sensitivity kit protocol.
Standard Illumina barcodes were introduced during library preparation with the Illumina TruSeq ChIP Sample Prep Kit 48 Samples - Set A Cat# IP-202-1012

tag: antibody

value: BRD4, Bethyl Lab (A301-985A100)

tag: enrichment target

tag: condition

value: Epigenetic regulator

tag: shRNA/target function

value: shRNA-scramble


title: Rh4 shCHD4 H3K27ac 48h

value: H3K27ac, Active Motif (cat39133)

value: Active Histone Mark


title: Rh4 shscr H3K27ac 48h


title: PROG_001

data_processing:
Data were processed using Bioconductor R package Affy. Probe intensities were normalized in labeling batches using RMA.
The file Processed_data_supplement.txt is available on the series record and contains the full dataset of 200 CEL files. These CEL files were normalized using RMA by labeling batches. Batches were combined and RMA normalized. The data was filtered for probes with signal intensity less than the median of negative control probes for >80% of the values. Gene symbols and EntrezID were appended using Bioconductor (hugene10stprobeset.db Version 8.6.0). Probes not mapping to a gene symbol were removed. The probes were median merged by gene symbol and log-transformed. Batch correction was performed using ComBat, and the final data set was median centered.

extract_protocol: High Pure FFPET RNA isolation kit (Roche)

tag: tissue

tag: tissue preparation

tag: patient identifier

tag: tumor number

value: primary

value: UroC


title: VT 2 hpi, rep B

tag: strain

tag: developmental stage of endosymbiont

value: 2 hr post infection

tag: multiplicity of infection


title: HeLa_20mln_longSonication

tag: protocol

tag: experiment

value: fastGRO


title: Day 50 NM organoids 1-3

data_processing:
HiSeq 4000 data was demultiplexed using bcl2fastq v1.9
Fastq data from different lanes and appropriate indexes was merged.
Alignment, filtering, UMI counting, barcode counting and filtering and gene-barcode matrix generation was performed with 10X Cell Ranger (v3.0.2, 10X Genomics).
the biological read is read 2 (R2, 98 bp, read 2 is used to sequence the cDNA fragment) the cell-barcode/UMI read is read 1 (R1, 26 bp, read 1 is used to sequence the 16 bp 10x Barcode and 10 bp UMI) the sample index is read I (I1, 8 bp)
Cell Ranger R kit version 2.0.0 and Seurat version 3.0.3 was used for downstream analysis. For clustering, principal-component analysis was performed for dimension reduction and t-SNE was used for clustering visualization. sSeq integrated in the Cell Ranger R kit was used for modeling the gene expression with negative binomial distribution to identify genes whose expression was enriched in specific clusters
Genome_build: GRCh38
Supplementary_files_format_and_content: Cell Ranger output, see readme.txt

extract_protocol: Organoids were dissociated mechanically using accutase solution and incubation at 37C. After single cell formation, the cell suspension was run through a 70μm strainer to remove any residual cell and debris clumps. A small volume of the cell suspension was removed for cell counts. The remaining cells were diluted 4-fold in 1X dPBS and then centrifuged at 200g for 5  minutes. The cell pellet was then resuspended in dPBS containing 0.04% BSA to give a final concentration of 206 cells/μl. PolyA selection based RNA capture (Chromium Single Cell 3’ Reagent Kit , v2 Chemistry, 10X Genomics) was done as per the manufacturer's instructions provided by 10X Genomics platform.   RNA-Seq libraries were prepared as per manufacturer's instructions provided by 10X Genomics platform  (https://www.10xgenomics.com/single-cell/)

value: Neuromuscular organoid. Time point:50 days differentiated. Day 50 NM organoids 1, 2 and 3, labelled with different indexes.


title: Snf2h_nFGO_KO_RNAseq_rep1

city: Cincinnati

first: Zhiyuan

last: Chen

state: Ohio

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

data_processing:
RNA-seq datasets
Low quality bases and sequencing adaptors of raw RNA-seq reads were trimmed using Trim Galore (version 0.4.5) with parameters “-q 20 –length 35bp”. Reads after trimming were then aligned to the mm10 reference genome using HISAT2 (version 2.1.0) with parameters “--sp 1000,1000 --dta-cufflinks --no-unal”.
Following reads mapping, uniquely aligned reads were retrieved by selecting the alignment records with “NH:i:1” tag and mapping quality greater than 30.
BamCoverage from deepTools (version 3.0.2) was used to generate bigwig tracks with parameters “--skipNonCoveredRegions --binSize 10 --scaleFactor 1/DESeq’s size Factor”.
Genome_build: mm10
Supplementary_files_format_and_content: RPKM values were computated using Cuffnorm from Cufflinks (version 2.2.1), read counts were counted using TEtranscript (version 1.5.1), and differential gene expression was analyzed using DESeq package (version 1.34.1)

source_name: mouse oocytes

extract_protocol:
As all libraries generated in this study involved low-input techniques, samples collected were directly put into lysis buffer for further library construction.
Twenty oocytes at Growing1 (GO1), Growing2 (GO2), and fullly grown (FGO, with or without hormone stimulation) stages from WT and CKO female mice were used for RNA-seq library preparation. Briefly, reverse transcription and cDNA amplification were performed using SMARTer Ultra Low Input RNA cDNA preparation kit (Clontech) following the manufacturer’s instructions. Nextera XT DNA Library Preparation Kit (Illumina) was used for cDNA fragmentation, adaptor-ligation, and amplification according to the manufacturer’s instructions. Single-end 100 bp sequencing was performed on a HiSeq2500 sequencer (Illumina).

tag: genotype

value: ZP3-Cre, Snf2h(fl/fl)

tag: cell type

value: oocytes


title: Snf2h_nFGO_KO_RNAseq_rep2


title: Snf2h_nFGO_WT_RNAseq_rep2


title: Snf2h_KO_GO1_ATAC_rep2

description: Chromatin accessibility

data_processing:
After quality trimming using Trim Galore version (0.4.5), the ATAC-seq reads were aligned to the mm10 reference genome using Bowtie2 (version 2.2.9) with default parameter.
Following alignment, uniquely mapped reads (reads without “XS” tag and mapping quality > 30) were retrieved and PCR duplicates were removed using MarkDuplicates command from Picard tools (version 2.8.0) (https://broadinstitute.github.io/picard/). ATAC-seq bigwig tracks were generated using bamcoverage from deeptools (version 3.0.2) (Ramirez et al., 2014) with parameters “--binSize 20 -e 250 --minMappingQuality 30 --scaleFactor 1 --normalizeUsing RPKM”.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files that can be uploaded on a genome browser to view RNA levels and ATAC-seq peaks at different genomic locations.

extract_protocol:
As all libraries generated in this study involved low-input techniques, samples collected were directly put into lysis buffer for further library construction.
Briefly, 100 fully grown oocytes nuclei or growing oocytes were collected. After washing with 0.2%BSA/PBS, oocytes or nuclei were added into 8 µL Tagmentation Mix (33 mM Tris-Acetate, 66 mM K-Acetate, 10 mM Mg-Acetate, 16% DMF, and 0.02% Digitonin) containing 0.5 µL of Assembled Tn5/Adapter (760 µg/mL unassembled Tn5 enzyme with 0.143 vol of 100 µM Tn5MEDS-A/B oligonucleotides). After tagmentation at 37 °C for 30 min, the reaction was stopped with freshly made Stop buffer (100 mM Tris pH8.0, 100 mM NaCl, 0.4% SDS, 40 µg/mL Proteinase K) and incubated at 55 °C for 16 hours. After quenching SDS by adding 5 µL 25% Tween-20, PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 5 minutes; 98 °C for 5 minutes; thermocycling at 98 °C for 20 seconds, 63 °C for 30 seconds, 72 °C for 60 seconds; followed by 72 °C 5 minutes. After the PCR reaction, libraries were purified with the 1.6× SPRI beads (Beckman).

value: mouse oocytes


title: Snf2h_KO_GO1_ATAC_rep1

description: Chromatin accessibility


title: Snf2h_nFGO_WT_RNAseq_rep1


title: Snf2h_KO_FGO_ATAC_rep1

data_processing:
After quality trimming using Trim Galore version (0.4.5), the ATAC-seq reads were aligned to the mm10 reference genome using Bowtie2 (version 2.2.9) with default parameter.
Following alignment, uniquely mapped reads (reads without “XS” tag and mapping quality > 30) were retrieved and PCR duplicates were removed using MarkDuplicates command from Picard tools (version 2.8.0) (https://broadinstitute.github.io/picard/). ATAC-seq bigwig tracks were generated using bamcoverage from deeptools (version 3.0.2) (Ramirez et al., 2014) with parameters “--binSize 20 -e 250  --minMappingQuality 30  --scaleFactor 1 --normalizeUsing RPKM”.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files that can be uploaded on a genome browser to view RNA levels and ATAC-seq peaks at different genomic locations.

extract_protocol:
Briefly, 100 GV nuclei were removed and collected from oocytes after incubation in M2 medium containing 0.2 mM IBMX, 10 mg/ml cytochalasin B and 0.1 mg/ml colcemid for 15 min. After washing with 0.2%BSA/PBS, GV nuclei were added into 8 µL Tagmentation Mix (33 mM Tris-Acetate, 66 mM K-Acetate, 10 mM Mg-Acetate, 16% DMF, and 0.02% Digitonin) containing 0.5 µL of Assembled Tn5/Adapter (760 µg/mL unassembled Tn5 enzyme with 0.143 vol of 100 µM Tn5MEDS-A/B oligonucleotides). After tagmentation at 37 °C for 30 min, the reaction was stopped with freshly made Stop buffer (100 mM Tris pH8.0, 100 mM NaCl, 0.4% SDS, 40 µg/mL Proteinase K) and incubated at 55 °C for 16 hours. After quenching SDS by adding 5 µL 25% Tween-20, PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 5 minutes; 98 °C for 5 minutes; thermocycling at 98 °C for 20 seconds, 63 °C for 30 seconds, 72 °C for 60 seconds; followed by 72 °C 5 minutes. After the PCR reaction, libraries were purified with the 1.6× SPRI beads (Beckman).
As all libraries generated in this study involved low-input techniques,  samples collected were directly put into lysis buffer for further library construction.


title: Snf2h_WT_FGO_ATAC_rep2


title: Snf2h_WT_GO1_ATAC_rep2

description: Chromatin accessibility


title: Snf2h_WT_GO1_ATAC_rep1

description: Chromatin accessibility


title: Snf2h_KO_FGO_ATAC_rep2


title: Snf2h_KO_FGO_RNAseq_rep1

data_processing:
Low quality bases and sequencing adaptors of raw RNA-seq reads were trimmed using Trim Galore (version 0.4.5) with parameters “-q 20 –length 35bp”.  Reads after trimming were then aligned to the mm10 reference genome using HISAT2 (version 2.1.0)  with parameters “--sp 1000,1000  --dta-cufflinks --no-unal”.
Following reads mapping, uniquely aligned reads were retrieved by selecting the alignment records with “NH:i:1” tag and mapping quality greater than 30.
BamCoverage from deepTools (version 3.0.2) was used to generate bigwig tracks with parameters “--skipNonCoveredRegions --binSize 10 --scaleFactor 1/DESeq’s size Factor”.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files that can be uploaded on a genome browser to view RNA levels and ATAC-seq peaks at different genomic locations.
RPKM values were computated using Cuffnorm from Cufflinks (version 2.2.1), read counts were counted using TEtranscript (version 1.5.1), and differential gene expression was analyzed using DESeq package (version 1.34.1)

extract_protocol:
Twenty oocytes at Growing1 (GO1), Growing2 (GO2), and fullly grown (FGO) stages from WT and CKO female mice were used for RNA-seq library preparation. Briefly, reverse transcription and cDNA amplification were performed using SMARTer Ultra Low Input RNA cDNA preparation kit (Clontech) following the manufacturer’s instructions. Nextera XT DNA Library Preparation Kit (Illumina) was used for cDNA fragmentation, adaptor-ligation, and amplification according to the manufacturer’s instructions.  Single-end 100 bp sequencing was performed on a HiSeq2500 sequencer (Illumina).
As all libraries generated in this study involved low-input techniques,  samples collected were directly put into lysis buffer for further library construction.


title: Snf2h_KO_FGO_RNAseq_rep2


title: Snf2h_WT_FGO_RNAseq_rep1


title: Snf2h_WT_FGO_RNAseq_rep2


title: Snf2h_WT_FGO_ATAC_rep1


title: Snf2h_KO_GO2_RNAseq_rep1


title: Snf2h_WT_GO2_RNAseq_rep1


title: Snf2h_WT_GO2_RNAseq_rep2


title: Snf2h_KO_GO1_RNAseq_rep1


title: 265 PBA + Tg 4h

city: São Paulo

first: Maristela

middle: Martins de

last: Camargo

state: SP

address: Av. Prof. Lineu Prestes 1730

department: Immunology

country: Brazil

institute: University of São Paulo

description:
test
PBA + Tg 4h

data_processing: Target DCq values were normalized against Gapdh DCq levels. Target gene signals normalized to housekeeping gene; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_GAPDH)]. Replicates were averaged and filtered for SE < 0.5 for removal os low-abundance measurements. A ratio of Treated (x) / Untreated (NT) was calculated and log2-transformed.

label: FAM

source_name: EBV-immortalized B cell

label_protocol: All RNA samples were normalized to 30 ng/ul before proceeding. cDNA was generated using 300 ng of total RNA and the High-Capacity RNA-to-cDNA kit (Thermo Scientific). cDNA was ketp at -20˚C until processing. Thirty-three nL of TaqMan OpenArray Real-Time PCR Master Mix (Thermo Scientific) were loaded into custom-made TaqManOpenArray slides by an automated Accufill system (Thermo Scientific) and amplified in triplicate reactions for quantification of specific transcipts using a QuantStudio 12K Flex real-Time PCR System (Thermo Scientific) for up to 40 cycles.

growth_protocol: EBV-B cells were cultured in RPMI-1640 GlutaMAX media containing 100U/ml penicollon, 100ug/ml streptomycin and 10% heat-inactivated fetal bovine serum (all from Thermo Scientific) at 37˚C and 5% CO2. Cells were split every 3 days, and harvested for experiments between the 3rd and 10th splits. Cell vioability was determined by Trypan blue staining using an automatic counter Countess II (Thermo Scientific).

extract_protocol: Samples were harvested in RNAlater (Thermo Scientific) and kept at -20˚C until processing. Total RNA was isolated using Purelink Mini (thermo Scientific) and kept at -80˚C until processing. Purified RNA was quali- and quantified by spectrometry in a Nanodrop and by fluorometry in a Qubit, respectively.

treatment_protocol: Cells were plated as triplicates at 3x10e5 cells/well (96 round bottom plate) in media containing chemical chaperones (final concentrations were 1 mM PBA, 5 mM TUDCA, or 1 mM DMSO) and/or ER stressors (final concentrations were 1uM Thapsigargin (Tg) or 10 ug/ml Tunicamycin (Tm). Cells were stimulated for 1, 2, 3 and 4 hours (h) or left untreated.

tag: time

value: 4 hours

tag: treatment

value: 4-PBA plus Thapsigargin

tag: cell lineage origin

value: Patient P2


title: 264 PBA + Tg 4h

description:
test
PBA + Tg 4h


title: Snf2h_WT_GO1_RNAseq_rep2


title: Rh4 shCHD4 BRD4 48h

tag: antibody

tag: enrichment target


title: Snf2h_WT_GO1_RNAseq_rep1


title: 263 PBA + Tg 4h

description:
test
PBA + Tg 4h


title: 262 PBA + Tg 3h

description:
test
PBA + Tg 3h

value: 3 hours


title: 261 PBA + Tg 3h

description:
test
PBA + Tg 3h


title: 259 PBA + Tg 2h

description:
test
PBA + Tg 2h

value: 2 hours


title: 260 PBA + Tg 3h

description:
test
PBA + Tg 3h


title: 252 PBA 4h

description:
test
PBA 4h


title: 251 PBA 4h

description:
test
PBA 4h


title: 256 PBA + Tg 1h

description:
test
PBA + Tg 1h

value: 1 hour


title: Snf2h_KO_GO2_RNAseq_rep2


title: 254 PBA + Tg 1h

description:
test
PBA + Tg 1h


title: 255 PBA + Tg 1h

description:
test
PBA + Tg 1h


title: 257 PBA + Tg 2h

description:
test
PBA + Tg 2h


title: 258 PBA + Tg 2h

description:
test
PBA + Tg 2h


title: 253 PBA 4h

description:
test
PBA 4h


title: NTX28214CTC_33

first: Annika

last: Fendler

address: Robert-Roessle-Str. 10

department: Signal Transduction in Development and Cancer

institute: Max Delbrueck Center for Molecular Medicine in the Helmholtz Association

data_processing:
Conversion and demultiplexing with BCL2FASTQ (v2.20)
Demultiplexing, alignment and generation of a UMI count matrix with CELSEQ2
Normalisation and cluster analysis with Seurat (V2.2.0)
Genome_build: UCSC hg19
Supplementary_files_format_and_content: Raw UMI  read counts in a .csv format generated with CELSEQ2

source_name: CXCR4+MET+CD44+ CSC of patient NTX28214

extract_protocol:
Single CXCR4+MET+CD44+ cells were sorted into 96-well plates into lysis buffer.
SuperScript II double-stranded cDNA Synthesis kit (Thermo Fisher) was used for reverse transcription. ERCC spike-in (Thermo Fisher) was added to the primer mix. AmPure XP kit (Beckman Coulter) was used for RNA clean-up. In vitro transcription was performed using the MEGAscript T7 transcription kit  (Thermo Fisher). aRNA was transcribed to cDNA using random hexamer primers and SuperscriptII polymerase (Invitrogen) and amplified using RP1 Illumina Primers.

value: CXCR4+MET+CD44+ CSC

tag: patient id


title: NTX28214CTC_25


title: 250 Tn 4h

description:
test
Tn 4h

value: Tunicamycin


title: 249 Tn 4h

description:
test
Tn 4h


title: 247 PBA 3h

description:
test
PBA 3h


title: NTX28214bulk_17

source_name: Unsorted ccRCC tumor cells of patient NTX28214

value: Unsorted ccRCC tumor cells


title: NTX28214bulk_9


title: 248 Tn 4h

description:
test
Tn 4h


title: Snf2h_KO_GO1_RNAseq_rep2

tag: tissue


title: NTX28214bulk_1


title: NTX28214sc_96

source_name: Single Cell data of patient NTX28214

value: clear cell renal cell cancer


title: NTX28214sc_95


title: 245 PBA 3h

description:
test
PBA 3h


title: 244 Tn 3h

description:
test
Tn 3h


title: NTX28214sc_94


title: 246 PBA 3h

description:
test
PBA 3h


title: NTX28214sc_93


title: NTX28214CTC_41


title: 241 PBA 2h

description:
test
PBA 2h


title: 242 Tn 3h

description:
test
Tn 3h


title: 240 PBA 2h

description:
test
PBA 2h


title: 239 PBA 2h

description:
test
PBA 2h


title: NTX28214sc_89


title: NTX28214sc_90


title: 238 Tn 2h

description:
test
Tn 2h


title: 235 PBA 1h

description:
test
PBA 1h


title: NTX28214sc_87


title: NTX28214sc_92


title: 237 Tn 2h

description:
test
Tn 2h


title: 236 Tn 2h

description:
test
Tn 2h


title: 233 PBA 1h

description:
test
PBA 1h


title: 234 PBA 1h

description:
test
PBA 1h


title: NTX28214sc_88


title: NTX28214sc_84


title: NTX28214sc_83


title: 232 Tn 1h

description:
test
Tn 1h


title: NTX28214sc_82


title: 243 Tn 3h

description:
test
Tn 3h


title: 231 Tn 1h

description:
test
Tn 1h


title: 230 Tn 1h

description:
test
Tn 1h


title: NTX28214sc_80


title: NTX28214sc_81


title: NTX28214sc_79


title: 228 Tg 4h

description:
test
Tg 4h

value: Thapsigargin


title: NTX28214sc_91


title: 227 Tg 4h

description:
test
Tg 4h


title: 223 Tg 3h

description:
test
Tg 3h


title: NTX28214sc_86


title: 224 NT 4h

description:
control
NT 4h

value: no treatment


title: NTX28214sc_75


title: NTX28214sc_73


title: NTX28214sc_77


title: NTX28214sc_85


title: 222 Tg 3h

description:
test
Tg 3h


title: NTX28214sc_70


title: 220 NT 3h

description:
control
NT 3h


title: 218 NT 3h

description:
control
NT 3h


title: 221 Tg 3h

description:
test
Tg 3h


title: 229 Tg 4h

description:
test
Tg 4h


title: NTX28214sc_78


title: NTX28214sc_72


title: NTX28214sc_71


title: 217 Tg 2h

description:
test
Tg 2h


title: NTX28214sc_69


title: 215 Tg 2h

description:
test
Tg 2h


title: 216 Tg 2h

description:
test
Tg 2h


title: NTX28214sc_68


title: NTX28214sc_67


title: 214 NT 2h

description:
control
NT 2h


title: NTX28214sc_66


title: NTX28214sc_65


title: NTX28214sc_76


title: NTX28214sc_74


title: 219 NT 3h

description:
control
NT 3h


title: NTX28214sc_63


title: NTX28214sc_64


title: NTX28214sc_61


title: 210 Tg 1h

description:
test
Tg 1h


title: 211 Tg 1h

description:
test
Tg 1h


title: 212 NT 2h

description:
control
NT 2h


title: NTX28214sc_60


title: 207 NT 1h

description:
control
NT 1h


title: 204 point zero

description:
control
point zero

value: 0 hour (fresh)


title: 205 point zero

description:
control
point zero


title: NTX28214sc_59


title: 203 point zero

description:
control
point zero


title: 206 NT 1h

description:
control
NT 1h


title: 202 TUDCA 4h

description:
test
TUDCA 4h

value: TUDCA

value: Patient P1


title: NTX28214sc_57


title: NTX28214sc_58


title: NTX28214sc_62


title: 200 TUDCA 4h

description:
test
TUDCA 4h


title: NTX28214sc_54


title: NTX28214sc_55


title: NTX28214sc_56


title: 201 TUDCA 4h

description:
test
TUDCA 4h


title: 199 DMSO + Tg 4h

description:
test
DMSO + Tg 4h

value: DMSO plus Thapsigargin


title: NTX28214sc_53


title: 213 NT 2h

description:
control
NT 2h


title: 197 DMSO + Tg 4h

description:
test
DMSO + Tg 4h


title: NTX28214sc_52


title: 196 TUDCA 3h

description:
test
TUDCA 3h


title: NTX28214sc_51


title: NTX28214sc_50


title: 194 TUDCA 3h

description:
test
TUDCA 3h


title: NTX28214sc_49


title: 195 TUDCA 3h

description:
test
TUDCA 3h


title: NTX28214sc_47


title: NTX28214sc_46


title: 192 DMSO + Tg 3h

description:
test
DMSO + Tg 3h


title: 191 DMSO + Tg 3h

description:
test
DMSO + Tg 3h


title: NTX28214sc_45


title: 190 TUDCA 2h

description:
test
TUDCA 2h


title: 189 TUDCA 2h

description:
test
TUDCA 2h


title: NTX28214sc_42


title: NTX28214sc_44


title: 187 DMSO + Tg 2h

description:
test
DMSO + Tg 2h


title: NTX28214sc_40


title: 186 DMSO + Tg 2h

description:
test
DMSO + Tg 2h


title: 185 DMSO + Tg 2h

description:
test
DMSO + Tg 2h


title: NTX28214sc_38


title: NTX28214sc_37


title: NTX28214sc_39


title: 184 TUDCA 1h

description:
test
TUDCA 1h


title: NTX28214sc_36


title: NTX28214sc_48


title: NTX28214sc_35


title: NTX28214sc_34


title: 182 TUDCA 1h

description:
test
TUDCA 1h


title: 193 DMSO + Tg 3h

description:
test
DMSO + Tg 3h


title: 181 DMSO + Tg 1h

description:
test
DMSO + Tg 1h


title: 198 DMSO + Tg 4h

description:
test
DMSO + Tg 4h


title: 180 DMSO + Tg 1h

description:
test
DMSO + Tg 1h


title: NTX28214sc_32


title: NTX28214sc_31


title: NTX28214sc_43


title: 188 TUDCA 2h

description:
test
TUDCA 2h


title: 175 PBA + Tg 4h

description:
test
PBA + Tg 4h


title: 176 DMSO 4h

description:
test
DMSO 4h

value: DMSO


title: 178 DMSO 4h

description:
test
DMSO 4h

value: 4 hours


title: NTX28214sc_29


title: NTX28214sc_30


title: NTX28214sc_28


title: NTX28214sc_26


title: NTX28214sc_27


title: 174 PBA + Tg 4h

description:
test
PBA + Tg 4h

value: 4-PBA plus Thapsigargin


title: 173 DMSO 3h

description:
test
DMSO 3h


title: 183 TUDCA 1h

description:
test
TUDCA 1h


title: 172 DMSO 3h

description:
test
DMSO 3h


title: NTX28214sc_24


title: NTX28214sc_23


title: 171 DMSO 3h

description:
test
DMSO 3h


title: NTX28214sc_22


title: 168 PBA + Tg 3h

description:
test
PBA + Tg 3h


title: 170 PBA + Tg 3h

description:
test
PBA + Tg 3h


title: 169 PBA + Tg 3h

description:
test
PBA + Tg 3h


title: NTX28214sc_20


title: NTX28214sc_21


title: 179 DMSO + Tg 1h

description:
test
DMSO + Tg 1h


title: NTX28214sc_19


title: 166 DMSO 2h

description:
test
DMSO 2h


title: 165 DMSO 2h

description:
test
DMSO 2h


title: 167 DMSO 2h

description:
test
DMSO 2h


title: 164 PBA + Tg 2h

description:
test
PBA + Tg 2h


title: 163 PBA + Tg 2h

description:
test
PBA + Tg 2h


title: NTX28214sc_18


title: 162 PBA + Tg 2h

description:
test
PBA + Tg 2h


title: 161 DMSO 1h

description:
test
DMSO 1h


title: 160 DMSO 1h

description:
test
DMSO 1h


title: 159 DMSO 1h

description:
test
DMSO 1h


title: NTX28214sc_8


title: NTX28214sc_14


title: NTX28214sc_10


title: NTX28214sc_11


title: NTX28214sc_7


title: NTX28214sc_13


title: 157 PBA + Tg 1h

description:
test
PBA + Tg 1h


title: NTX28214sc_15


title: NTX28214sc_12


title: 158 PBA + Tg 1h

description:
test
PBA + Tg 1h


title: 156 PBA + Tg 1h

description:
test
PBA + Tg 1h


title: 155 PBA 4h

description:
test
PBA 4h


title: NTX28214sc_16


title: NTX28214sc_4


title: NTX28214sc_6


title: NTX9415bulk_96

source_name: Unsorted ccRCC tumor cells of patient NTX9415


title: NTX28214sc_3


title: 151 PBA 3h

description:
test
PBA 3h


title: 152 PBA 3h

description:
test
PBA 3h


title: 153 PBA 3h

description:
test
PBA 3h


title: NTX9415bulk_88


title: 149 Tn 3h

description:
test
Tn 3h


title: 148 Tn 3h

description:
test
Tn 3h


title: NTX9415bulk_80


title: 147 PBA 2h

description:
test
PBA 2h


title: NTX9415CTC_72

source_name: CXCR4+MET+CD44+ CSC of patient NTX9415


title: NTX9415CTC_64


title: 144 Tn 2h

description:
test
Tn 2h


title: 146 PBA 2h

description:
test
PBA 2h


title: 143 Tn 2h

description:
test
Tn 2h


title: NTX9415CTC_56


title: 141 PBA 1h

description:
test
PBA 1h


title: NTX9415sc_94

source_name: Single Cell data of patient NTX9415


title: NTX9415sc_93


title: NTX9415sc_95


title: NTX9415sc_90


title: 142 Tn 2h

description:
test
Tn 2h


title: NTX9415sc_91


title: 150 Tn 3h

description:
test
Tn 3h


title: NTX28214sc_2


title: NTX9415sc_92


title: 140 PBA 1h

description:
test
PBA 1h


title: 138 Tn 1h

description:
test
Tn 1h


title: 139 PBA 1h

description:
test
PBA 1h


title: 137 Tn 1h

description:
test
Tn 1h


title: NTX9415sc_87


title: NTX9415sc_89


title: 136 Tn 1h

description:
test
Tn 1h


title: 145 PBA 2h

description:
test
PBA 2h


title: 134 Tg 4h

description:
test
Tg 4h


title: NTX9415sc_84


title: NTX9415sc_83


title: 133 Tg 4h

description:
test
Tg 4h


title: NTX9415sc_82


title: 132 NT 4h

description:
control
NT 4h


title: NTX9415sc_81


title: NTX9415sc_79


title: 131 NT 4h

description:
control
NT 4h


title: 225 NT 4h

description:
control
NT 4h

value: Patient P2


title: NTX9415sc_78


title: 129 Tg 3h

description:
test
Tg 3h

value: 3 hours


title: 128 Tg 3h

description:
test
Tg 3h


title: 127 Tg 3h

description:
test
Tg 3h


title: 126 NT 3h

description:
control
NT 3h


title: NTX9415sc_77


title: 124 NT 3h

description:
control
NT 3h


title: NTX9415sc_76


title: NTX9415sc_86


title: 123 Tg 2h

description:
test
Tg 2h

value: 2 hours


title: NTX9415sc_85


title: NTX9415sc_71


title: NTX9415sc_73


title: NTX9415sc_75


title: 135 Tg 4h

description:
test
Tg 4h


title: NTX9415sc_74


title: 120 NT 2h

description:
control
NT 2h


title: 122 Tg 2h

description:
test
Tg 2h


title: NTX9415sc_69


title: NTX9415sc_70


title: 130 NT 4h

description:
control
NT 4h


title: 119 NT 2h

description:
control
NT 2h


title: NTX9415sc_67


title: 117 Tg 1h

description:
test
Tg 1h

value: 1 hour


title: NTX9415sc_66


title: 118 NT 2h

description:
control
NT 2h


title: NTX9415sc_65


title: NTX9415sc_63


title: 113 NT 1h

description:
control
NT 1h


title: 112 NT 1h

description:
control
NT 1h


title: 111 point zero

description:
control
point zero


title: NTX9415sc_62


title: 116 Tg 1h

description:
test
Tg 1h


title: 110 point zero

description:
control
point zero