title: BBN-NUMB_KO Verteporfin rep1

value: Verteporfin


title: BBN-NUMB_KO rep1

status: Public on Oct 11 2024

type: SRA

city: Milan

first: Salvatore

last: Pece

address: Via Adamello, 16

department: Experimental Oncology

country: Italy

institute: European Institute of Oncology IRCCS,

library_source: transcriptomic

data_processing:
Sequenced raw reads were processed with NF-CORE RNASeq pipeline, using the human GRCh38 and mouse GRCm39 as reference genomes. Transcript abundances were quantified using the Salmon pseudo-aligner.
Assembly: GRCh38, GRCm39
Supplementary files format and content: Tab-delimited text file containing Salmongene-level quantification for each sample, including feature length, effective length, TPM, and number of reads.

molecule: total RNA

organism: Mus musculus

source_name: urothelial bladder cancer

extract_protocol:
Total RNA was extracted with QIAzol™ Reagentand then purified using the RNeasy kit (Qiagen).
RNA libraries were prepared for sequencing using Illumina TruSeq Stranded Total RNA Goldkit according to the manufacturer’s protocol

tag: cell type

value: urothelial bladder cancer


title: PBS-treated K7M2 flank tumor

city: Columbus

first: Emily

middle: M.

last: Ringwalt

state: OH

address: 575 Children's Xrd

department: Center for Childhood Cancer

country: USA

institute: Nationwide Children's Hospital

description: PBS-treated K7M2 flank tumor

library_source: transcriptomic single cell

data_processing:
BCL files were converted to fastq files using cellranger mkfastq
Fastq files were processed using cellranger count
Further processing and analyses performed are outlined on GitHub (https://github.com/kidcancerlab/oHSV-trabectedin)
Assembly: The reference genome was built from mm10, hg19, and HSV-1 strain 17 (concatenated into one reference genome).
Supplementary files format and content: Tar files for each sample include the contents of the filtered_feature_bc_matrix folder output by Cellranger count (barcodes.tsv.gz  features.tsv.gz  matrix.mtx.gz)

molecule: polyA RNA

source_name: flank tumor (subQ)

extract_protocol:
Following dissociation into single cell suspension, single-cell 3’ RNA-Seq libraries were prepared using Chromium Single Cell 3′RNA-sequencing system (10x Genomics) with the Reagent Kit v3.1 (10XGenomics, PN-1000120) according to the manufacturer's instructions.
Libraries were constructed per 10x protocols

treatment_protocol: The Ewing sarcoma human xenografts were treated with either oHSV (1e7 pfu/mL) or PBS (as a control) intratumorally on Days 0 and 2 and/or trabectedin (0.15 mg/kg) on Day 0. Osteosarcoma mouse models were treated with either oHSV (1e8 pfu/mL) or PBS (as a control) intratumorally on Days 0 and 2 and/or trabectedin (0.15 mg/kg) on Day 0. Tumors were harvested on Day 3.

tag: tissue

value: flank tumor (subQ)

tag: cell line

value: Osteosarcoma

tag: treatment

value: PBS (control)


title: BBN-NUMB_KO rep2


title: BBN-WT rep2


title: BBN-WT rep1


title: Intranasal_FLAMOD_biol_rep4

city: Lille

first: Yasmine

last: Zeroual

state: Nord

address: 1 Rue du professeur Calmette, 59000 Lille (Institut pasteur de Lille)

country: France

institute: INSERM

data_processing:
STAR-2.7.10a
Genome index was generated using fasta file GRCm39.fa and annotation file gencode.vM30.chr_patch_hapl_scaff.annotation.gtf through STAR-2.7.10a (sjdbOverhang 149)
Sequence reads were mapped to generated genome using STAR-2.7.10a (--quantMode GeneCounts)
ReadsPerGene.out.tab file with four columns (gene ID, counts for unstranded RNA-seq, counts for the 1st read strand aligned with RNA, counts for the 2nd read strand aligned with RNA)  was generated by STAR for each sample
Assembly: GRCm39
Supplementary files format and content: TAB files include read counts for each sample (only first two columns were used :Gene ID and read counts for unstranded RNA-seq)

source_name: Lung

growth_protocol: Female BALB/cJRj mice (Janvier Laboratories, Saint Berthevin, France), 6-8 weeks old, were maintained (four by cage) in individually ventilated cages and handled in a vertical laminar flow cabinet.

extract_protocol:
RNA was harvested using NucleoSpin RNA kit by Macherey-Nagel
RNA libraries for RNA-seq were prepared using QIAseq stranded mRNA library kit (Qiagen). 200 ng of total RNA.

treatment_protocol:
Mice were treated intranasally with 30 µg of FLAMOD in 30 µl NaPi saline buffer per mouse , or by nebulization of 250 µg/ml FLAMOD (in 1ml NaPi buffer) using the Aerogen Solo mesh nebulizer connected to a custom made murine nebulization chamber containing 4 mice.
Control animals received NaPi buffer (the FLAMOD vehicle). Lungs were sampled 2 hours post-treatment and homogenized in 3 ml RA1 lysis buffer (NucleoSpin RNA kit by Macherey-Nagel) for subsequent RNA isolation

value: Lung

tag: genotype

value: BALB/c


title: Intranasal_FLAMOD_biol_rep3


title: BBN-WT rep3


title: Intransal_buffer_biol_rep2


title: Intransal_buffer_biol_rep3


title: Intranasal_FLAMOD_biol_rep1


title: Nebulized_FLAMOD_biol_rep2


title: Combination-treated K7M2 flank tumor

description: Combination-treated K7M2 flank tumor

value: oHSV+Trabectedin


title: Nebulized_FLAMOD_biol_rep4


title: Nebulized_FLAMOD_biol_rep1


title: Intransal_buffer_biol_rep1


title: Nebulized_FLAMOD_biol_rep3


title: Nebulized_buffer_biol_rep3


title: Nebulized_buffer_biol_rep2


title: LSD1cKO preosteoclast S5

city: Minneapolis

first: Kim

last: Mansky

state: MN

address: 515 Delaware St SE

institute: University of Minnesota

data_processing:
Sequencing reads were mapped to the mouse reference genome (GRCm38 v94) via Hisat2 (v2.1.0).
Quality control on raw sequence data for each sample was performed with FastQC
Gene quantification was done via Feature Counts for raw read counts
Genes differentially expressed between WT and conditional KO were determined using edgeR software package with an Absolute fold-change cutoff set at >2 and FDR < 0.05
Assembly: mouse (GRCm38 v94)
Supplementary files format and content: raw_counts.txt

source_name: bone marrow

growth_protocol: Bone marrow macrophages were isolated from 3 month old mice

extract_protocol:
RNA was isolated using RNA Plus Mini kit (Qiagen)
Libraries were constructed by UMN Genomic center

treatment_protocol: Cells were grown in alpha MEM without phenol red in the presence of M-CSF and RANKL for 48 hours

value: bone marrow

value: osteoclast

value: conditional knockout

value: M-CSF and RANKL


title: Nebulized_buffer_biol_rep1


title: scRNA-Seq CT-treated_3_TCR

city: London

first: Samar

last: Elorbany

address: Barbican

department: Tumour Microenvironment

country: United Kingdom

institute: Queen Mary University of London

description: 10X GENOMICS, dual indexing 5' prime V2 kit

data_processing:
Cell ranger multi software Suite (version 6.0.1) was used for de-multiplexing, alignment, barcode processing and unique molecular identifier (UM)I quantification, TCR/BCR  assembly, alignment, annotation and quantification of the reads.
Filtered feature barcode files were then imported in R for further processing using Seurat V4 and scRepertoire V1.7
Assembly: mm10-2020-A and vdj_GRCm38_alts_ensembl-5.0.0
Supplementary files format and content: For each mouse, 3 libraries exit, GEX, BCR and TCR. For GEX library processed data include 3 files, barcode.tsv, features.tsv and matrix.mtx.  For BCR and TCR libraries, one filtered_contig_annotation.csv file is submitted for each

source_name: Omentum

growth_protocol: tumours were harvested one week after the third dose of carboplatin and paclitaxel at day 70 for the treated mice.

extract_protocol:
Tumor samples were dissected and enzymatically digested in a mixture of collagenase and DNAse to obtain single-cell suspensions. Resulting cell suspensions were used enriched for live cells using Dead cell removal kit from Meltyni without any selection/enrichment for specific cell population to create single-cell RNA suspension.
For sample 1 and 4 , single cell 10X chromium 5' prime V1.0.0 kit with immunoprofiling(TCR and BCR) was used and for the remaining samples 10X chromium 5' prime V2 kit with immunprofiling was used

treatment_protocol: Fresh tissue was collected and placed in PBS and immediately processed

value: Omentum

value: Ovarian cancer cell line

value: C57/B6 WT

value: carboplatin+paclitaxel


title: scRNA-Seq CT-treated_3


title: MBP

city: St. Louis

first: Jonathan

last: Kipnis

state: MO

address: 4515 McKinley Ave

institute: Washington University in St. Louis

description: RNA was isolated from the lymph nodes of 3 mice

data_processing:
Illumina bcl2fastq software used for basecalling
UMI count matrices generated using the Cellranger count pipeline 6.0.0. The output from the cellranger count pipeline has been uploaded as a folder containing count, barcode, and gene matrices.
Assembly: mm10
Supplementary files format and content: Compressed folders containing the raw UMI count matrices for each sample, as well as matrices with gene symbols and barcodes.

source_name: Inguinal Lymph Node

extract_protocol:
10x Genomics Chromium single-cell preparation
NGS Illumina Next Seq

value: Inguinal Lymph Node

tag: gender

value: male

tag: age

value: 2-3 months

value: MOG+MBP


title: LSD1WT preosteoclast S3

value: wild type


title: scRNA-Seq CT-treated_2_BCR


title: scRNA-Seq CT-treated_2_TCR


title: Intranasal_FLAMOD_biol_rep2


title: scRNA-Seq CT-treated_1_TCR

description: 10X GENOMICS,5' prime V1 kit


title: scRNA-Seq CT-treated_2


title: scRNA-Seq CT-treated_1

description: 10X GENOMICS,5' prime V1 kit


title: scRNA-Seq CT-treated_1_BCR

description: 10X GENOMICS,5' prime V1 kit


title: scRNA-Seq control_3_BCR

value: saline IP


title: scRNA-Seq control_2_BCR


title: scRNA-Seq control_3


title: scRNA-Seq control_2


title: scRNA-Seq control_2_TCR


title: LSD1cKO preosteoclast S4


title: scRNA-Seq control_1

description: 10X GENOMICS,5' prime V1 kit


title: scRNA-Seq control_1_TCR

description: 10X GENOMICS,5' prime V1 kit


title: HK2 cells, AdSirt4+TGF 3

city: Shenzhen

first: Shu

last: Yang

address: 1017 Dongmen North Road, Luohu District, Shenzhen

country: China

institute: shenzhen people's hospital

data_processing:
Samples are sequenced on the platform to get image files, which are transformed by the software of the sequencing platform, and the original data in FASTQ format (Raw Data) is generated. Sequencing data contains a number of connectors, low-quality Reads, so we use fastp (v0.21.0) software to filter the sequencing data to get high quality sequence （ Clean Data ） for further analysis .
The reference genome and gene annotation files were downloaded from genome website. The filtered reads were mapping to the reference genome using HISAT2 v2.1.0.
We used StringTie(v2.1.5) statistics to compare the Read Count values on each gene as the original expression of the gene, and then used FPKM to standardize the expression. Then difference expression of genes was analyzed by DESeq2 (v1.30.1) with screened conditions as follows: expression difference multiple |log2FoldChange| > 1, significant padj≤0.05. At the same time, We used R language Pheatmap(1.0.8) software package to perform bi-directional clustering analysis of all different genes of samples. We geted heatmap according to the expression level of the same gene in different samples and the expression patterns of different genes in the same sample with Euclidean method to calculate the distance and Complete Linkage method to cluster.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Homo sapiens

source_name: Kidney

extract_protocol:
Total RNA was isolated using the Trizol Reagent (Invitrogen Life Technologies), after the total RNA was qualified and quantified as follows: (1) RNA purity and concentration were then examined using NanoDrop spectrophotometer (Thermo Scientific) and Qubit 4.0; (2) RNA integrity and quantity were measured using the Agilent 2100/4200 system.
Three micrograms of RNA were used as input material for the RNA sample preparations. Sequencing libraries were generated according to the following steps. Firstly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in fragmentation buffer. First strand strand was synthesized by random hexamers, and the second cDNA strand was synthesized by adding buffer, dNTPs, RNase H and DNA polymerase I. Double stranded cDNA was repaired and A was added to the 3 'end. Hieff NGS® DNA Selection Beads were used for purification and fragment Selection. After purification and fragment selection, the products were amplified and enriched by PCR. Qubit was used for quantitative .
The target region library of the duplex was denatured, cycled, and digested to yield a single-stranded circular DNA. Single-stranded circular DNA is amplified by a rolling circle amplification (RCA), known as DNA nano balls (DNB). After library construction, Qubit was used for quantitative.

value: Kidney

value: HK7 cells

value: Tubular epithelial cells

value: WT

value: TGF-beta1 stimulation


title: HK2 cells, AdCtrl+TGF 3

value: HK4 cells


title: scRNA-Seq control_1_BCR

description: 10X GENOMICS,5' prime V1 kit


title: HK2 cells, AdSirt4+TGF 1

value: HK5 cells


title: HK2 cells, AdSirt4+TGF 2

value: HK6 cells


title: scRNA-Seq CT-treated_3_BCR

value: Omentum

value: Ovarian cancer cell line


title: MOG

value: MOG


title: HK2 cells, AdCtrl+TGF 2

value: HK3 cells


title: MOCP_0162:ara:0.50000%:360min:CRISPRi-ssb:MOCP_0162_1:r1

city: Boston

first: Keith

last: Romano

address: 185 Cambridge St.

department: Molecular Biology

institute: Massachusetts General Hospital

data_processing:
BWA to align reads to reference
QC & filter samples with low counts and genes with low counts
DESeq2 to identify weak and robust transcriptional signals
VST function from DESeq2 for variance stabilization of counts
Calculate moderated z-scores using custom scripts, based on previously published scripts (Subramanian, A. et al. Cell. 2017. https://doi.org/10.1016/j.cell.2017.10.049)
Assembly: NC_0088463.1 (UCBPP-PA14)
Supplementary files format and content: comma separated file with counts for each sample
Supplementary files format and content: comma separated file with moderated z-score values for each treatment condition (replicates collapsed)

organism: Pseudomonas aeruginosa UCBPP-PA14

source_name: CRISPRi-ssb

growth_protocol: Bacterial cultures were grown with shaking (37°C, 250rpm) to mid-log phase, and 30uL of cultures were mixed with equal volume of 2X compound working solution, yielding final conditions containing 1x108 CFU/mL bacteria and with compounds (or vehicle) in 0.5% (v/v) DMSO or water in LB.

extract_protocol:
At the end of the incubation period, samples were mixed with 30uL of 3X RNAgem Blue Buffer (Zygem, Charlottesville VA), and chemically lysed by incubation in a thermocycler at 75°C for 10 minutes. Total RNA was then extracted using the Direct-zol kit (Zymo Research, Irvine CA), and RNA quality and quantity were analyzed using the RNA ScreenTape with the 2200 TapeStation (Agilent, Santa Clara CA).
RNA-Seq libraries were prepared using the RNA TagSeq protocol previously described (Shishkin, A. et al. Nature methods. 2015. https://doi.org/10.1038/nmeth.3313)

treatment_protocol: Cells were treated at 37°C without shaking in a humidity chamber.  In the case of the RNA-Seq Time Trial, cells were treated for 30, 60, 90, and 120 minutes. In the case of all other RNA-Seq experiments, cells were treated for 90 minutes.

value: CRISPRi-ssb

tag: pert id

value: ara

tag: pert iname

value: Arabinose

tag: pert dose

tag: pert dose_unit

tag: pert idose

tag: pert time

tag: pert time_unit

value: min

tag: pert itime

tag: pert type

value: poscon

tag: category

tag: project id

tag: replicate id

tag: project plate_id_384well

tag: strain id

tag: weak signal

value: FALSE


title: MOCP_0162:ara:0.50000%:360min:CRISPRi-rpsL:MOCP_0162_1:r2

source_name: CRISPRi-rpsL

tag: cell line

value: CRISPRi-rpsL


title: MOCP_0162:ara:0.50000%:360min:CRISPRi-rpoB:MOCP_0162_1:r2

source_name: CRISPRi-rpoB

value: CRISPRi-rpoB


title: MOCP_0162:ara:0.50000%:360min:CRISPRi-ssb:MOCP_0162_1:r3


title: MOCP_0162:ara:0.50000%:360min:CRISPRi-rpsL:MOCP_0162_1:r1


title: MOCP_0162:ara:0.50000%:360min:CRISPRi-ssb:MOCP_0162_1:r2


title: MOCP_0162:ara:0.50000%:360min:CRISPRi-rplJ:MOCP_0162_1:r3

source_name: CRISPRi-rplJ

value: CRISPRi-rplJ


title: MOCP_0162:ara:0.50000%:360min:CRISPRi-rpsL:MOCP_0162_1:r3


title: MOCP_0162:ara:0.50000%:360min:CRISPRi-pbpA:MOCP_0162_1:r3

source_name: CRISPRi-pbpA

value: CRISPRi-pbpA


title: MOCP_0162:ara:0.50000%:360min:CRISPRi-rpoB:MOCP_0162_1:r1


title: scRNA-Seq control_3_TCR

tag: tissue

tag: cell type

tag: genotype

value: C57/B6 WT

tag: treatment

value: saline IP


title: MOCP_0162:ara:0.50000%:360min:CRISPRi-pbpA:MOCP_0162_1:r2

tag: pert id

tag: pert iname

tag: pert dose

tag: pert dose_unit


title: MOCP_0162:ara:0.50000%:360min:CRISPRi-rplJ:MOCP_0162_1:r1

tag: pert idose

tag: pert time

tag: pert time_unit

tag: pert itime


title: MOCP_0162:ara:0.50000%:360min:CRISPRi-pbpA:MOCP_0162_1:r1

tag: pert type

tag: category

tag: project id

tag: replicate id


title: MOCP_0162:ara:0.50000%:360min:CRISPRi-parC:MOCP_0162_1:r1

source_name: CRISPRi-parC

tag: cell line

value: CRISPRi-parC

tag: project plate_id_384well

tag: strain id

tag: weak signal


title: MOCP_0162:ara:0.50000%:360min:CRISPRi-murA:MOCP_0162_1:r2

source_name: CRISPRi-murA

value: CRISPRi-murA


title: MOCP_0162:ara:0.50000%:360min:CRISPRi-murA:MOCP_0162_1:r3


title: MOCP_0162:ara:0.50000%:360min:CRISPRi-mreB:MOCP_0162_1:r2

source_name: CRISPRi-mreB

value: CRISPRi-mreB


title: MOCP_0162:ara:0.50000%:360min:CRISPRi-murA:MOCP_0162_1:r1


title: MOCP_0162:ara:0.50000%:360min:CRISPRi-mreB:MOCP_0162_1:r1


title: MOCP_0162:ara:0.50000%:360min:CRISPRi-lptE:MOCP_0162_1:r3

source_name: CRISPRi-lptE

value: CRISPRi-lptE

value: TRUE


title: MOCP_0162:ara:0.50000%:360min:CRISPRi-lptE:MOCP_0162_1:r2


title: MOCP_0162:ara:0.50000%:360min:CRISPRi-lpxC:MOCP_0162_1:r2

source_name: CRISPRi-lpxC

value: CRISPRi-lpxC


title: MOCP_0162:ara:0.50000%:360min:CRISPRi-mreB:MOCP_0162_1:r3

value: ara


title: MOCP_0162:ara:0.50000%:360min:CRISPRi-lptE:MOCP_0162_1:r1

value: Arabinose


title: MOCP_0162:ara:0.50000%:360min:CRISPRi-lpxC:MOCP_0162_1:r3

value: min


title: MOCP_0162:ara:0.50000%:360min:CRISPRi-lpxC:MOCP_0162_1:r1

value: poscon


title: MOCP_0162:ara:0.50000%:360min:CRISPRi-lptD-2:MOCP_0162_1:r2

value: FALSE


title: MOCP_0162:ara:0.50000%:360min:CRISPRi-lptA:MOCP_0162_1:r1

source_name: CRISPRi-lptA

value: CRISPRi-lptA


title: MOCP_0162:ara:0.50000%:360min:CRISPRi-lptA:MOCP_0162_1:r3


title: MOCP_0162:ara:0.50000%:360min:CRISPRi-rplJ:MOCP_0162_1:r2


title: MOCP_0162:ara:0.50000%:360min:CRISPRi-lptA:MOCP_0162_1:r2


title: MOCP_0162:ara:0.50000%:360min:CRISPRi-leuS:MOCP_0162_1:r3

source_name: CRISPRi-leuS

value: CRISPRi-leuS


title: MOCP_0162:ara:0.50000%:360min:CRISPRi-rpoB:MOCP_0162_1:r3

value: CRISPRi-rpoB


title: MOCP_0162:ara:0.50000%:360min:CRISPRi-parC:MOCP_0162_1:r2


title: MOCP_0162:ara:0.50000%:360min:CRISPRi-lptD-2:MOCP_0162_1:r3


title: MOCP_0162:ara:0.50000%:360min:CRISPRi-gyrB:MOCP_0162_1:r2

source_name: CRISPRi-gyrB

value: CRISPRi-gyrB


title: MOCP_0162:ara:0.50000%:360min:CRISPRi-leuS:MOCP_0162_1:r1


title: MOCP_0162:ara:0.50000%:360min:CRISPRi-leuS:MOCP_0162_1:r2


title: MOCP_0162:ara:0.50000%:360min:CRISPRi-gyrB:MOCP_0162_1:r1


title: MOCP_0162:ara:0.50000%:360min:CRISPRi-gyrB:MOCP_0162_1:r3


title: MOCP_0162:ara:0.50000%:360min:CRISPRi-gyrA:MOCP_0162_1:r1

source_name: CRISPRi-gyrA

value: CRISPRi-gyrA


title: MOCP_0162:ara:0.50000%:360min:CRISPRi-dxr:MOCP_0162_1:r3

source_name: CRISPRi-dxr

value: CRISPRi-dxr


title: MOCP_0162:ara:0.50000%:360min:CRISPRi-gyrA-2:MOCP_0162_1:r2


title: MOCP_0162:ara:0.50000%:360min:CRISPRi-gyrA-2:MOCP_0162_1:r1


title: MOCP_0162:ara:0.50000%:360min:CRISPRi-gyrA-2:MOCP_0162_1:r3


title: MOCP_0162:ara:0.50000%:360min:CRISPRi-dxr:MOCP_0162_1:r1


title: MOCP_0162:ara:0.50000%:360min:CRISPRi-dhfR:MOCP_0162_1:r3

source_name: CRISPRi-dhfR

value: CRISPRi-dhfR


title: MOCP_0162:ara:0.50000%:360min:CRISPRi-dxr:MOCP_0162_1:r2


title: MOCP_0162:ara:0.50000%:360min:CRISPRi-lptD-2:MOCP_0162_1:r1


title: MOCP_0162:ara:0.50000%:360min:CRISPRi-dhfR:MOCP_0162_1:r2


title: MOCP_0162:ara:0.50000%:360min:CRISPRi-C26:MOCP_0162_1:r3

value: negcon


title: MOCP_0162:ara:0.50000%:360min:CRISPRi-C26:MOCP_0162_1:r1


title: MOCP_0162:ara:0.50000%:360min:CRISPRi-C26:MOCP_0162_1:r2


title: MOCP_0162:ara:0.50000%:360min:CRISPRi-dhfR:MOCP_0162_1:r1


title: MOCP_0162:ara:0.12500%:360min:CRISPRi-ssb:MOCP_0162_1:r3

value: CRISPRi-ssb


title: MOCP_0162:ara:0.12500%:360min:CRISPRi-ssb:MOCP_0162_1:r2


title: MOCP_0162:ara:0.12500%:360min:CRISPRi-rpsL:MOCP_0162_1:r1

value: CRISPRi-rpsL


title: MOCP_0162:ara:0.12500%:360min:CRISPRi-rpoB:MOCP_0162_1:r3


title: MOCP_0162:ara:0.12500%:360min:CRISPRi-rpoB:MOCP_0162_1:r2


title: MOCP_0162:ara:0.12500%:360min:CRISPRi-ssb:MOCP_0162_1:r1

value: TRUE


title: MOCP_0162:ara:0.50000%:360min:CRISPRi-gyrA:MOCP_0162_1:r3


title: MOCP_0162:ara:0.12500%:360min:CRISPRi-rpsL:MOCP_0162_1:r2


title: MOCP_0162:ara:0.50000%:360min:CRISPRi-gyrA:MOCP_0162_1:r2


title: MOCP_0162:ara:0.12500%:360min:CRISPRi-rpsL:MOCP_0162_1:r3


title: MOCP_0162:ara:0.12500%:360min:CRISPRi-pbpA:MOCP_0162_1:r3

value: CRISPRi-pbpA


title: MOCP_0162:ara:0.12500%:360min:CRISPRi-rplJ:MOCP_0162_1:r3

value: CRISPRi-rplJ

value: ara


title: MOCP_0162:ara:0.12500%:360min:CRISPRi-rplJ:MOCP_0162_1:r2

value: Arabinose

value: min


title: MOCP_0162:ara:0.12500%:360min:CRISPRi-pbpA:MOCP_0162_1:r1

value: poscon

value: FALSE


title: MOCP_0162:ara:0.12500%:360min:CRISPRi-rplJ:MOCP_0162_1:r1


title: MOCP_0162:ara:0.12500%:360min:CRISPRi-parC:MOCP_0162_1:r1

value: CRISPRi-parC


title: MOCP_0162:ara:0.12500%:360min:CRISPRi-parC:MOCP_0162_1:r2


title: MOCP_0162:ara:0.12500%:360min:CRISPRi-murA:MOCP_0162_1:r2

value: CRISPRi-murA


title: MOCP_0162:ara:0.12500%:360min:CRISPRi-mreB:MOCP_0162_1:r3

value: CRISPRi-mreB


title: MOCP_0162:ara:0.12500%:360min:CRISPRi-murA:MOCP_0162_1:r3


title: MOCP_0162:ara:0.12500%:360min:CRISPRi-murA:MOCP_0162_1:r1


title: MOCP_0162:ara:0.12500%:360min:CRISPRi-mreB:MOCP_0162_1:r1


title: MOCP_0162:ara:0.12500%:360min:CRISPRi-mreB:MOCP_0162_1:r2


title: MOCP_0162:ara:0.12500%:360min:CRISPRi-lpxC:MOCP_0162_1:r3

value: CRISPRi-lpxC


title: MOCP_0162:ara:0.12500%:360min:CRISPRi-pbpA:MOCP_0162_1:r2


title: MOCP_0162:ara:0.12500%:360min:CRISPRi-lptE:MOCP_0162_1:r3

value: CRISPRi-lptE


title: MOCP_0162:ara:0.12500%:360min:CRISPRi-rpoB:MOCP_0162_1:r1

value: CRISPRi-rpoB


title: MOCP_0162:ara:0.12500%:360min:CRISPRi-lpxC:MOCP_0162_1:r1


title: MOCP_0162:ara:0.12500%:360min:CRISPRi-lptD-2:MOCP_0162_1:r1


title: MOCP_0162:ara:0.12500%:360min:CRISPRi-lptE:MOCP_0162_1:r1


title: MOCP_0162:ara:0.12500%:360min:CRISPRi-lptA:MOCP_0162_1:r2

value: CRISPRi-lptA


title: MOCP_0162:ara:0.12500%:360min:CRISPRi-lptA:MOCP_0162_1:r3


title: MOCP_0162:ara:0.12500%:360min:CRISPRi-lptD-2:MOCP_0162_1:r3


title: MOCP_0162:ara:0.12500%:360min:CRISPRi-lptA:MOCP_0162_1:r1


title: MOCP_0162:ara:0.12500%:360min:CRISPRi-lptD-2:MOCP_0162_1:r2


title: MOCP_0162:ara:0.12500%:360min:CRISPRi-leuS:MOCP_0162_1:r3

value: CRISPRi-leuS


title: MOCP_0162:ara:0.12500%:360min:CRISPRi-leuS:MOCP_0162_1:r1


title: MOCP_0162:ara:0.12500%:360min:CRISPRi-gyrB:MOCP_0162_1:r2

value: CRISPRi-gyrB


title: MOCP_0162:ara:0.12500%:360min:CRISPRi-leuS:MOCP_0162_1:r2

value: TRUE


title: MOCP_0162:ara:0.12500%:360min:CRISPRi-gyrB:MOCP_0162_1:r3


title: MOCP_0162:ara:0.12500%:360min:CRISPRi-gyrA:MOCP_0162_1:r3

value: CRISPRi-gyrA


title: MOCP_0162:ara:0.12500%:360min:CRISPRi-gyrB:MOCP_0162_1:r1


title: MOCP_0162:ara:0.12500%:360min:CRISPRi-gyrA:MOCP_0162_1:r2


title: MOCP_0162:ara:0.12500%:360min:CRISPRi-parC:MOCP_0162_1:r3


title: MOCP_0162:ara:0.12500%:360min:CRISPRi-gyrA-2:MOCP_0162_1:r2


title: MOCP_0162:ara:0.12500%:360min:CRISPRi-gyrA-2:MOCP_0162_1:r3


title: MOCP_0162:ara:0.12500%:360min:CRISPRi-dxr:MOCP_0162_1:r2

value: CRISPRi-dxr


title: MOCP_0162:ara:0.12500%:360min:CRISPRi-gyrA:MOCP_0162_1:r1

value: ara


title: MOCP_0162:ara:0.12500%:360min:CRISPRi-dxr:MOCP_0162_1:r1

value: Arabinose


title: MOCP_0162:ara:0.12500%:360min:CRISPRi-lptE:MOCP_0162_1:r2

value: min


title: MOCP_0162:ara:0.12500%:360min:CRISPRi-dxr:MOCP_0162_1:r3

value: poscon


title: MOCP_0162:ara:0.12500%:360min:CRISPRi-gyrA-2:MOCP_0162_1:r1


title: MOCP_0162:ara:0.12500%:360min:CRISPRi-C26:MOCP_0162_1:r2

value: negcon

value: FALSE


title: MOCP_0162:ara:0.12500%:360min:CRISPRi-dhfR:MOCP_0162_1:r2

value: CRISPRi-dhfR


title: MOCP_0162:ara:0.12500%:360min:CRISPRi-C26:MOCP_0162_1:r3


title: MOCP_0162:ara:0.12500%:360min:CRISPRi-dhfR:MOCP_0162_1:r1


title: MOCP_0162:ara:0.12500%:360min:CRISPRi-C26:MOCP_0162_1:r1


title: MOCP_0162:ara:0.00000%:360min:CRISPRi-ssb:MOCP_0162_1:r3

value: CRISPRi-ssb


title: MOCP_0162:ara:0.00000%:360min:CRISPRi-rpsL:MOCP_0162_1:r3

value: CRISPRi-rpsL


title: MOCP_0162:ara:0.00000%:360min:CRISPRi-rpsL:MOCP_0162_1:r1


title: MOCP_0162:ara:0.00000%:360min:CRISPRi-ssb:MOCP_0162_1:r2


title: MOCP_0162:ara:0.00000%:360min:CRISPRi-rpsL:MOCP_0162_1:r2


title: MOCP_0162:ara:0.00000%:360min:CRISPRi-rpoB:MOCP_0162_1:r3


title: MOCP_0162:ara:0.00000%:360min:CRISPRi-ssb:MOCP_0162_1:r1


title: MOCP_0162:ara:0.00000%:360min:CRISPRi-rpoB:MOCP_0162_1:r1


title: MOCP_0162:ara:0.00000%:360min:CRISPRi-rplJ:MOCP_0162_1:r3

value: CRISPRi-rplJ


title: MOCP_0162:ara:0.12500%:360min:CRISPRi-dhfR:MOCP_0162_1:r3


title: MOCP_0162:ara:0.00000%:360min:CRISPRi-pbpA:MOCP_0162_1:r1

value: CRISPRi-pbpA


title: MOCP_0162:ara:0.00000%:360min:CRISPRi-murA:MOCP_0162_1:r3

value: CRISPRi-murA


title: MOCP_0162:ara:0.00000%:360min:CRISPRi-parC:MOCP_0162_1:r2

value: CRISPRi-parC


title: MOCP_0162:ara:0.00000%:360min:CRISPRi-parC:MOCP_0162_1:r1


title: MOCP_0162:ara:0.00000%:360min:CRISPRi-rplJ:MOCP_0162_1:r2


title: MOCP_0162:ara:0.12500%:360min:CRISPRi-lpxC:MOCP_0162_1:r2

value: CRISPRi-lpxC


title: MOCP_0162:ara:0.00000%:360min:CRISPRi-murA:MOCP_0162_1:r1

value: TRUE


title: MOCP_0162:ara:0.00000%:360min:CRISPRi-mreB:MOCP_0162_1:r2

value: CRISPRi-mreB


title: MOCP_0162:ara:0.00000%:360min:CRISPRi-mreB:MOCP_0162_1:r3


title: MOCP_0162:ara:0.00000%:360min:CRISPRi-murA:MOCP_0162_1:r2


title: MOCP_0162:ara:0.00000%:360min:CRISPRi-mreB:MOCP_0162_1:r1


title: MOCP_0162:ara:0.00000%:360min:CRISPRi-lpxC:MOCP_0162_1:r3


title: MOCP_0162:ara:0.00000%:360min:CRISPRi-lpxC:MOCP_0162_1:r1


title: MOCP_0162:ara:0.00000%:360min:CRISPRi-pbpA:MOCP_0162_1:r3


title: MOCP_0162:ara:0.00000%:360min:CRISPRi-lpxC:MOCP_0162_1:r2


title: MOCP_0162:ara:0.00000%:360min:CRISPRi-rpoB:MOCP_0162_1:r2

value: CRISPRi-rpoB


title: MOCP_0162:ara:0.00000%:360min:CRISPRi-rplJ:MOCP_0162_1:r1

value: ara


title: MOCP_0162:ara:0.00000%:360min:CRISPRi-lptE:MOCP_0162_1:r2

value: CRISPRi-lptE

value: Arabinose


title: MOCP_0162:ara:0.00000%:360min:CRISPRi-lptE:MOCP_0162_1:r3

value: min

value: poscon


title: MOCP_0162:ara:0.00000%:360min:CRISPRi-pbpA:MOCP_0162_1:r2

value: FALSE


title: MOCP_0162:ara:0.00000%:360min:CRISPRi-parC:MOCP_0162_1:r3


title: MOCP_0162:ara:0.00000%:360min:CRISPRi-lptD-2:MOCP_0162_1:r3


title: MOCP_0162:ara:0.00000%:360min:CRISPRi-lptA:MOCP_0162_1:r3

value: CRISPRi-lptA


title: MOCP_0162:ara:0.00000%:360min:CRISPRi-lptD-2:MOCP_0162_1:r2


title: MOCP_0162:ara:0.00000%:360min:CRISPRi-lptD-2:MOCP_0162_1:r1


title: MOCP_0162:ara:0.00000%:360min:CRISPRi-lptA:MOCP_0162_1:r2


title: MOCP_0162:ara:0.00000%:360min:CRISPRi-leuS:MOCP_0162_1:r3

value: CRISPRi-leuS


title: MOCP_0162:ara:0.00000%:360min:CRISPRi-leuS:MOCP_0162_1:r2


title: MOCP_0162:ara:0.00000%:360min:CRISPRi-gyrB:MOCP_0162_1:r1

value: CRISPRi-gyrB


title: MOCP_0162:ara:0.00000%:360min:CRISPRi-leuS:MOCP_0162_1:r1


title: MOCP_0162:ara:0.00000%:360min:CRISPRi-gyrB:MOCP_0162_1:r3


title: MOCP_0162:ara:0.00000%:360min:CRISPRi-gyrA:MOCP_0162_1:r3

value: CRISPRi-gyrA


title: MOCP_0162:ara:0.00000%:360min:CRISPRi-gyrA:MOCP_0162_1:r2


title: MOCP_0162:ara:0.00000%:360min:CRISPRi-gyrA-2:MOCP_0162_1:r1


title: MOCP_0162:ara:0.00000%:360min:CRISPRi-dxr:MOCP_0162_1:r3

value: CRISPRi-dxr


title: MOCP_0162:ara:0.00000%:360min:CRISPRi-gyrA-2:MOCP_0162_1:r2


title: MOCP_0162:ara:0.00000%:360min:CRISPRi-dxr:MOCP_0162_1:r2


title: MOCP_0162:ara:0.00000%:360min:CRISPRi-gyrB:MOCP_0162_1:r2


title: MOCP_0162:ara:0.00000%:360min:CRISPRi-gyrA:MOCP_0162_1:r1


title: MOCP_0162:ara:0.00000%:360min:CRISPRi-gyrA-2:MOCP_0162_1:r3


title: MOCP_0162:ara:0.00000%:360min:CRISPRi-lptE:MOCP_0162_1:r1


title: MOCP_0162:ara:0.00000%:360min:CRISPRi-C26:MOCP_0162_1:r1

value: negcon


title: MOCP_0162:ara:0.00000%:360min:CRISPRi-lptA:MOCP_0162_1:r1


title: MOCP_0162:ara:0.00000%:360min:CRISPRi-dhfR:MOCP_0162_1:r1

value: CRISPRi-dhfR


title: MOCP_0162:ara:0.00000%:360min:CRISPRi-dhfR:MOCP_0162_1:r2


title: MOCP_0110:fosmido:500.00000uM:90min:PA14:MOCP_0110_2:r3

value: fosmido

value: Fosmidomycin

value: uM


title: MOCP_0162:ara:0.00000%:360min:CRISPRi-dhfR:MOCP_0162_1:r3


title: MOCP_0162:ara:0.00000%:360min:CRISPRi-C26:MOCP_0162_1:r3


title: MOCP_0110:fosmido:500.00000uM:90min:PA14:MOCP_0110_2:r1

value: TRUE


title: MOCP_0110:fosmido:250.00000uM:90min:PA14:MOCP_0110_2:r3


title: MOCP_0110:fosmido:500.00000uM:90min:PA14:MOCP_0110_2:r2


title: MOCP_0162:ara:0.00000%:360min:CRISPRi-C26:MOCP_0162_1:r2

value: ara


title: MOCP_0110:fosmido:250.00000uM:90min:PA14:MOCP_0110_2:r1


title: MOCP_0110:fosmido:250.00000uM:90min:PA14:MOCP_0110_2:r2


title: MOCP_0110:ami:1.56000uM:90min:PA14:MOCP_0110_2:r2

value: ami

value: Amikacin


title: MOCP_0110:ami:1.56000uM:90min:PA14:MOCP_0110_2:r1

value: min


title: MOCP_0066:tobra:1.56250uM:90min:PA14:MOCP_0066_1:r3

value: tobra

value: Tobramycin

value: poscon


title: MOCP_0066:pol7080:0.02000uM:90min:lptD_kd:MOCP_0066_1:r3


title: MOCP_0066:tobra:1.56250uM:90min:PA14:MOCP_0066_1:r2


title: MOCP_0066:tobra:1.56250uM:90min:PA14:MOCP_0066_1:r1


title: MOCP_0066:ami:1.56250uM:90min:PA14:MOCP_0066_1:r3


title: MOCP_0066:cbr4830:15.62500uM:90min:PA14:MOCP_0066_1:r1


title: MOCP_0066:cbr4830:15.62500uM:90min:PA14:MOCP_0066_1:r3


title: MOCP_0066:pol7080:0.02000uM:90min:lptD_kd:MOCP_0066_1:r1


title: MOCP_0066:cbr4830:15.62500uM:90min:PA14:MOCP_0066_1:r2


title: MOCP_0066:ami:1.56250uM:90min:PA14:MOCP_0066_1:r2


title: MOCP_0162:ara:0.00000%:360min:CRISPRi-dxr:MOCP_0162_1:r1

value: Arabinose


title: MOCP_0066:ami:1.56250uM:90min:PA14:MOCP_0066_1:r1


title: MOC_1779:tun:50.00000uM:90min:PA14:MOC_1779_2:r3

value: tun

value: Tunicamycin


title: MOC_1779:tun:25.00000uM:90min:PA14:MOC_1779_1:r2


title: MOCP_0110:ami:1.56000uM:90min:PA14:MOCP_0110_2:r3


title: MOC_1779:tun:25.00000uM:90min:PA14:MOC_1779_1:r3


title: MOC_1779:tun:25.00000uM:90min:PA14:MOC_1779_1:r1


title: MOC_1779:tun:50.00000uM:90min:PA14:MOC_1779_2:r2


title: MOC_1779:tun:100.00000uM:90min:PA14:MOC_1779_2:r3


title: MOC_1779:tun:100.00000uM:90min:PA14:MOC_1779_2:r2


title: MOC_1779:tun:50.00000uM:90min:PA14:MOC_1779_2:r1


title: MOC_1779:thio:100.00000uM:90min:PA14:MOC_1779_1:r3

value: thio

value: Thiolactomycin


title: MOC_1779:tun:100.00000uM:90min:PA14:MOC_1779_2:r1


title: MOC_1779:rad:200.00000uM:90min:PA14:MOC_1779_2:r1

value: rad

value: Radicicol

value: FALSE


title: MOC_1779:thio:100.00000uM:90min:PA14:MOC_1779_1:r2

value: uM


title: MOC_1779:pip:200.00000uM:90min:PA14:MOC_1779_1:r3

value: pip

value: Piperacillin

value: TRUE


title: MOC_1779:rad:100.00000uM:90min:PA14:MOC_1779_1:r3


title: MOC_1779:rad:200.00000uM:90min:PA14:MOC_1779_2:r2


title: MOC_1779:rad:100.00000uM:90min:PA14:MOC_1779_1:r1


title: MOCP_0066:pol7080:0.02000uM:90min:lptD_kd:MOCP_0066_1:r2


title: MOC_1779:pip:200.00000uM:90min:PA14:MOC_1779_1:r2


title: MOC_1779:novo:100.00000uM:90min:PA14:MOC_1779_1:r2

value: novo

value: Novobiocin


title: MOC_1779:novo:100.00000uM:90min:PA14:MOC_1779_1:r3

value: min


title: MOC_1779:pip:200.00000uM:90min:PA14:MOC_1779_1:r1


title: MOC_1779:hu:800.00000uM:90min:PA14:MOC_1779_1:r2

value: hu

value: Hydroxyurea


title: MOC_1779:hu:800.00000uM:90min:PA14:MOC_1779_1:r3

value: poscon


title: MOC_1779:novo:100.00000uM:90min:PA14:MOC_1779_1:r1


title: MOC_1779:hu:800.00000uM:90min:PA14:MOC_1779_1:r1


title: MOC_1779:hu:1600.00000uM:90min:PA14:MOC_1779_2:r3


title: MOC_1779:hu:1600.00000uM:90min:PA14:MOC_1779_2:r1


title: MOC_1779:hu:1600.00000uM:90min:PA14:MOC_1779_2:r2


title: MOC_1779:gent:1.56000uM:90min:PA14:MOC_1779_1:r3

value: gent

value: Gentamicin


title: MOC_1779:thio:100.00000uM:90min:PA14:MOC_1779_1:r1

value: thio


title: MOC_1779:gent:1.56000uM:90min:PA14:MOC_1779_1:r1


title: MOC_1779:gent:1.56000uM:90min:PA14:MOC_1779_1:r2


title: MOC_1779:fusi:400.00000uM:90min:PA14:MOC_1779_2:r1

value: fusi

value: Fusidic acid


title: MOC_1779:fusi:200.00000uM:90min:PA14:MOC_1779_2:r3


title: MOC_1779:rad:200.00000uM:90min:PA14:MOC_1779_2:r3

value: rad

value: Radicicol


title: MOC_1779:fusi:400.00000uM:90min:PA14:MOC_1779_2:r2

value: uM

value: FALSE


title: MOC_1779:fusi:400.00000uM:90min:PA14:MOC_1779_2:r3


title: MOC_1779:fusi:200.00000uM:90min:PA14:MOC_1779_2:r1


title: MOC_1779:fusi:100.00000uM:90min:PA14:MOC_1779_1:r2


title: MOC_1779:fusi:200.00000uM:90min:PA14:MOC_1779_2:r2


title: MOC_1779:fusi:100.00000uM:90min:PA14:MOC_1779_1:r1


title: MOC_1779:rad:100.00000uM:90min:PA14:MOC_1779_1:r2


title: MOC_1779:ceftaz:200.00000uM:90min:PA14:MOC_1779_1:r1

value: ceftaz

value: Ceftazidime


title: MOC_1779:aztreo:800.00000uM:90min:PA14:MOC_1779_2:r3

value: aztreo

value: Aztreonam

value: TRUE


title: MOC_1779:fusi:100.00000uM:90min:PA14:MOC_1779_1:r3

value: min


title: MOC_1779:ceftaz:200.00000uM:90min:PA14:MOC_1779_1:r3


title: MOC_1779:ceftaz:200.00000uM:90min:PA14:MOC_1779_1:r2


title: MOC_1779:aztreo:800.00000uM:90min:PA14:MOC_1779_2:r1


title: MOC_1779:aztreo:200.00000uM:90min:PA14:MOC_1779_1:r1


title: MOC_1779:aztreo:1600.00000uM:90min:PA14:MOC_1779_2:r3


title: MOC_1779:aztreo:1600.00000uM:90min:PA14:MOC_1779_2:r2


title: MOC_1779:aztreo:200.00000uM:90min:PA14:MOC_1779_1:r3


title: MOC_1779:aztreo:1600.00000uM:90min:PA14:MOC_1779_2:r1


title: MOC_1779:azido:800.00000uM:90min:PA14:MOC_1779_2:r1

value: azido

value: Azidothymidine


title: MOC_1779:azido:800.00000uM:90min:PA14:MOC_1779_2:r2

value: poscon


title: MOC_1779:azido:400.00000uM:90min:PA14:MOC_1779_2:r3


title: MOC_1779:azido:400.00000uM:90min:PA14:MOC_1779_2:r2


title: MOC_1779:azido:400.00000uM:90min:PA14:MOC_1779_2:r1


title: MOC_1779:aztreo:200.00000uM:90min:PA14:MOC_1779_1:r2


title: MOC_1779:azido:200.00000uM:90min:PA14:MOC_1779_1:r1


title: MOC_1779:azido:200.00000uM:90min:PA14:MOC_1779_1:r3


title: MOC_1779:azido:200.00000uM:90min:PA14:MOC_1779_1:r2


title: MOC_1430:pol7080:0.25000uM:90min:PA14:MOC_1430_1:r3


title: MOC_1779:azido:800.00000uM:90min:PA14:MOC_1779_2:r3


title: MOC_1430:pol7080:0.25000uM:90min:PA14:MOC_1430_1:r1


title: MOC_1430:pol7080:0.25000uM:90min:PA14:MOC_1430_1:r2


title: MOC_1430:pol7080:0.25000uM:60min:PA14:MOC_1430_1:r3


title: MOC_1430:pol7080:0.25000uM:60min:PA14:MOC_1430_1:r1


title: MOC_1430:pol7080:0.25000uM:30min:PA14:MOC_1430_1:r2


title: MOC_1779:aztreo:800.00000uM:90min:PA14:MOC_1779_2:r2


title: MOC_1430:pol7080:0.25000uM:30min:PA14:MOC_1430_1:r1


title: MOC_1430:pol7080:0.25000uM:30min:PA14:MOC_1430_1:r3


title: MOC_1430:pol7080:0.25000uM:120min:PA14:MOC_1430_1:r3


title: MOC_1430:pol7080:0.25000uM:60min:PA14:MOC_1430_1:r2


title: MOC_1430:pol7080:0.25000uM:120min:PA14:MOC_1430_1:r2


title: MOC_1430:pol7080:0.25000uM:120min:PA14:MOC_1430_1:r1


title: MOC_1430:pol7001:0.20000uM:90min:PA14:MOC_1430_1:r1


title: MOC_1430:pol7001:0.20000uM:60min:PA14:MOC_1430_1:r2


title: MOC_1430:pol7001:0.20000uM:60min:PA14:MOC_1430_1:r1


title: MOC_1430:pol7001:0.20000uM:60min:PA14:MOC_1430_1:r3


title: MOC_1430:pol7001:0.20000uM:90min:PA14:MOC_1430_1:r3


title: MOC_1430:pol7001:0.20000uM:30min:PA14:MOC_1430_1:r3


title: MOC_1430:pol7001:0.20000uM:30min:PA14:MOC_1430_1:r1


title: MOC_1430:pol7001:0.20000uM:120min:PA14:MOC_1430_1:r3


title: MOC_1430:pol7001:0.20000uM:120min:PA14:MOC_1430_1:r2


title: MOC_1430:pol7001:0.20000uM:120min:PA14:MOC_1430_1:r1


title: MOC_1430:pip:37.50000uM:90min:PA14:MOC_1430_1:r2

value: pip

value: Piperacillin


title: MOC_1430:pol7001:0.20000uM:30min:PA14:MOC_1430_1:r2


title: MOC_1430:pip:37.50000uM:90min:PA14:MOC_1430_1:r3


title: MOC_1430:pip:37.50000uM:30min:PA14:MOC_1430_1:r3


title: MOC_1430:pip:37.50000uM:60min:PA14:MOC_1430_1:r3


title: MOC_1430:pip:37.50000uM:90min:PA14:MOC_1430_1:r1


title: MOC_1430:pip:37.50000uM:30min:PA14:MOC_1430_1:r1


title: MOC_1430:pip:37.50000uM:30min:PA14:MOC_1430_1:r2


title: MOC_1430:pip:37.50000uM:60min:PA14:MOC_1430_1:r1


title: MOC_1430:pip:37.50000uM:60min:PA14:MOC_1430_1:r2


title: MOC_1430:pip:37.50000uM:120min:PA14:MOC_1430_1:r2


title: MOC_1430:pip:37.50000uM:120min:PA14:MOC_1430_1:r3


title: MOC_1430:ceftaz:24.00000uM:60min:PA14:MOC_1430_1:r3


title: MOC_1430:fosfo:600.00000uM:30min:PA14:MOC_1430_1:r1

value: fosfo

value: Fosfomycin


title: MOC_1430:pip:37.50000uM:120min:PA14:MOC_1430_1:r1


title: MOC_1430:ceftaz:24.00000uM:60min:PA14:MOC_1430_1:r2


title: MOC_1430:fosfo:600.00000uM:30min:PA14:MOC_1430_1:r2


title: MOC_1430:pol7001:0.20000uM:90min:PA14:MOC_1430_1:r2


title: MOC_1430:fosfo:600.00000uM:30min:PA14:MOC_1430_1:r3


title: MOC_1430:ceftaz:24.00000uM:30min:PA14:MOC_1430_1:r3


title: MOC_1430:ceftaz:24.00000uM:30min:PA14:MOC_1430_1:r2


title: MOC_1430:ceftaz:24.00000uM:60min:PA14:MOC_1430_1:r1


title: MOC_1430:aztreo:37.50000uM:90min:PA14:MOC_1430_1:r2


title: MOC_1430:aztreo:37.50000uM:90min:PA14:MOC_1430_1:r1


title: MOC_1430:aztreo:37.50000uM:60min:PA14:MOC_1430_1:r2


title: MOC_1430:aztreo:37.50000uM:60min:PA14:MOC_1430_1:r1


title: MOC_1430:aztreo:37.50000uM:60min:PA14:MOC_1430_1:r3


title: MOC_1430:aztreo:37.50000uM:30min:PA14:MOC_1430_1:r2


title: MOC_1430:aztreo:37.50000uM:30min:PA14:MOC_1430_1:r1


title: MOC_1430:aztreo:37.50000uM:120min:PA14:MOC_1430_1:r2


title: MOC_1430:aztreo:37.50000uM:30min:PA14:MOC_1430_1:r3


title: MOC_1430:aztreo:37.50000uM:120min:PA14:MOC_1430_1:r1


title: MOCP_0110:water:0.50000uM:90min:PA14:MOCP_0110_2:r2

description:
moc1430_1779_0066_0110_2kd_counts_manuscript.csv
moc1430_1779_0066_0110_2kd_modzscore_ref_set.csv

extract_protocol:
At the end of the incubation period, samples were mixed with 30uL of 3X RNAgem Blue Buffer (Zygem, Charlottesville VA), and chemically lysed by incubation in a thermocycler at 75°C for 10 minutes. Total RNA was then extracted using the Direct-zol kit (Zymo Research, Irvin CA), and RNA quality and quantity were analyzed using the RNA ScreenTape with the 2200 TapeStation (Agilent, Santa Clara CA).
RNA-Seq libraries were prepared using the RNA TagSeq protocol previously described (Shishkin, A. et al. Nature methods. 2015. https://doi.org/10.1038/nmeth.3313)

value: water

value: negcon


title: MOCP_0110:pol7080:0.32000uM:90min:PA14:MOCP_0110_2:r3

value: uM


title: MOCP_0110:water:0.50000uM:90min:PA14:MOCP_0110_2:r3

value: FALSE


title: MOCP_0066:dmso:0.50000%:90min:dfhr-hypo:MOCP_0066_1:r3

source_name: dfhr-hypo

value: dfhr-hypo

value: dmso


title: MOCP_0110:pol7080:0.08000uM:90min:PA14:MOCP_0110_2:r3


title: MOCP_0110:pol7080:0.08000uM:90min:PA14:MOCP_0110_2:r2


title: MOCP_0110:pol7080:0.32000uM:90min:PA14:MOCP_0110_2:r2


title: MOCP_0110:pol7080:0.32000uM:90min:PA14:MOCP_0110_2:r1


title: MOCP_0110:pol7080:0.08000uM:90min:PA14:MOCP_0110_2:r1


title: MOCP_0110:pa69180:500.00000uM:90min:oprL-hypo:MOCP_0110_2:r2

description:
moc1430_1779_0066_0110_2kd_counts_manuscript.csv
pa69180_oprl_hypo_mod_nzscore.csv

source_name: oprL-hypo

value: oprL-hypo

value: test


title: MOC_1430:ceftaz:24.00000uM:30min:PA14:MOC_1430_1:r1

value: ceftaz

value: Ceftazidime

value: TRUE


title: MOC_1430:aztreo:37.50000uM:90min:PA14:MOC_1430_1:r3

value: aztreo

value: Aztreonam

value: min


title: MOCP_0110:pa69180:500.00000uM:90min:oprL-hypo:MOCP_0110_2:r1


title: MOCP_0110:pa69180:500.00000uM:90min:oprL-hypo:MOCP_0110_2:r3


title: MOCP_0110:doxy:25.00000uM:90min:PA14:MOCP_0110_2:r3

value: doxy

value: Doxycycline

value: poscon


title: MOCP_0110:pa69180:250.00000uM:90min:oprL-hypo:MOCP_0110_2:r1


title: MOCP_0110:doxy:25.00000uM:90min:PA14:MOCP_0110_2:r2


title: MOCP_0110:doxy:25.00000uM:90min:PA14:MOCP_0110_2:r1


title: MOC_1430:aztreo:37.50000uM:120min:PA14:MOC_1430_1:r3


title: MOCP_0110:pa69180:250.00000uM:90min:oprL-hypo:MOCP_0110_2:r2


title: MOCP_0110:doxy:100.00000uM:90min:PA14:MOCP_0110_2:r3


title: MOCP_0110:dmso:0.50000uM:90min:PA14:MOCP_0110_2:r3


title: MOCP_0110:doxy:100.00000uM:90min:PA14:MOCP_0110_2:r2


title: MOCP_0110:doxy:100.00000uM:90min:PA14:MOCP_0110_2:r1


title: MOCP_0110:water:0.50000uM:90min:PA14:MOCP_0110_2:r1

value: water


title: MOCP_0110:dmso:0.50000uM:90min:PA14:MOCP_0110_2:r2

value: negcon


title: MOCP_0110:cip:0.78000uM:90min:PA14:MOCP_0110_2:r3

value: cip

value: Ciprofloxacin

value: uM


title: MOCP_0110:cip:0.78000uM:90min:PA14:MOCP_0110_2:r2

value: FALSE


title: MOCP_0110:pa69180:250.00000uM:90min:oprL-hypo:MOCP_0110_2:r3

value: oprL-hypo


title: MOCP_0110:cip:0.78000uM:90min:PA14:MOCP_0110_2:r1


title: MOCP_0110:cip:0.19500uM:90min:PA14:MOCP_0110_2:r1


title: MOCP_0110:brd5750:62.50000uM:90min:PA14:MOCP_0110_2:r3

description:
moc1430_1779_0066_0110_2kd_counts_manuscript.csv
brd5750_modzscore.csv

value: test


title: MOCP_0110:brd5750:62.50000uM:90min:PA14:MOCP_0110_2:r2


title: MOCP_0110:brd5750:62.50000uM:90min:PA14:MOCP_0110_2:r1


title: MOCP_0110:brd5750:250.00000uM:90min:PA14:MOCP_0110_2:r2


title: MOCP_0110:brd5750:250.00000uM:90min:PA14:MOCP_0110_2:r1


title: MOCP_0110:cip:0.19500uM:90min:PA14:MOCP_0110_2:r3


title: MOCP_0110:ami:6.25000uM:90min:PA14:MOCP_0110_2:r3

value: ami

value: Amikacin


title: MOCP_0110:ami:6.25000uM:90min:PA14:MOCP_0110_2:r2


title: MOCP_0110:ami:6.25000uM:90min:PA14:MOCP_0110_2:r1


title: MOCP_0110:a22:800.00000uM:90min:PA14:MOCP_0110_2:r2


title: MOCP_0110:a22:200.00000uM:90min:PA14:MOCP_0110_2:r2


title: MOCP_0066:water:0.50000%:90min:PA14:MOCP_0066_1:r2


title: MOCP_0110:a22:200.00000uM:90min:PA14:MOCP_0110_2:r1


title: MOCP_0110:brd5750:250.00000uM:90min:PA14:MOCP_0110_2:r3


title: MOCP_0066:water:0.50000%:90min:PA14:MOCP_0066_1:r1


title: MOCP_0110:dmso:0.50000uM:90min:PA14:MOCP_0110_2:r1

value: dmso


title: MOCP_0066:water:0.50000%:90min:PA14:MOCP_0066_1:r3


title: MOCP_0066:water:0.50000%:90min:murA-hypo:MOCP_0066_1:r3

source_name: murA-hypo

value: murA-hypo


title: MOCP_0066:water:0.50000%:90min:murA-hypo:MOCP_0066_1:r2


title: MOCP_0066:water:0.50000%:90min:dxr_kd:MOCP_0066_1:r3


title: MOCP_0066:water:0.50000%:90min:dxr_kd:MOCP_0066_1:r2


title: MOCP_0066:water:0.50000%:90min:dxr_kd:MOCP_0066_1:r1


title: MOCP_0110:cip:0.19500uM:90min:PA14:MOCP_0110_2:r2


title: MOCP_0066:water:0.50000%:90min:murA-hypo:MOCP_0066_1:r1


title: MOCP_0066:tobra:6.25000uM:90min:PA14:MOCP_0066_1:r3

value: tobra

value: Tobramycin


title: MOCP_0066:tobra:6.25000uM:90min:PA14:MOCP_0066_1:r1

value: min


title: MOCP_0066:tmp:400.00000uM:90min:PA14:MOCP_0066_1:r3

value: tmp

value: Trimethoprim


title: MOCP_0066:tmp:400.00000uM:90min:dfhr-hypo:MOCP_0066_1:r3

value: dfhr-hypo

value: poscon


title: MOCP_0066:tmp:400.00000uM:90min:PA14:MOCP_0066_1:r1


title: MOCP_0110:a22:800.00000uM:90min:PA14:MOCP_0110_2:r3


title: MOCP_0066:tmp:400.00000uM:90min:PA14:MOCP_0066_1:r2


title: MOCP_0066:tobra:6.25000uM:90min:PA14:MOCP_0066_1:r2


title: MOCP_0066:tmp:400.00000uM:90min:dfhr-hypo:MOCP_0066_1:r2


title: MOCP_0066:tmp:100.00000uM:90min:PA14:MOCP_0066_1:r3


title: MOCP_0110:a22:800.00000uM:90min:PA14:MOCP_0110_2:r1


title: MOCP_0066:tmp:100.00000uM:90min:PA14:MOCP_0066_1:r2


title: MOCP_0066:tmp:400.00000uM:90min:dfhr-hypo:MOCP_0066_1:r1


title: MOCP_0066:tmp:100.00000uM:90min:dfhr-hypo:MOCP_0066_1:r3


title: MOCP_0066:tmp:100.00000uM:90min:PA14:MOCP_0066_1:r1


title: MOCP_0066:pol7080:0.32000uM:90min:PA14:MOCP_0066_1:r3


title: MOCP_0066:pol7080:0.32000uM:90min:PA14:MOCP_0066_1:r2


title: MOCP_0066:pol7080:0.32000uM:90min:dfhr-hypo:MOCP_0066_1:r2


title: MOCP_0066:pol7080:0.32000uM:90min:dfhr-hypo:MOCP_0066_1:r3


title: MOCP_0066:tmp:100.00000uM:90min:dfhr-hypo:MOCP_0066_1:r2


title: MOCP_0066:pol7080:0.08000uM:90min:PA14:MOCP_0066_1:r2


title: MOCP_0066:pol7080:0.08000uM:90min:PA14:MOCP_0066_1:r3


title: MOCP_0066:pol7080:0.08000uM:90min:PA14:MOCP_0066_1:r1


title: MOCP_0066:pol7080:0.08000uM:90min:lptD_kd:MOCP_0066_1:r3


title: MOCP_0066:pol7080:0.32000uM:90min:dfhr-hypo:MOCP_0066_1:r1


title: MOCP_0066:pol7080:0.08000uM:90min:lptD_kd:MOCP_0066_1:r1


title: MOCP_0066:pol7080:0.08000uM:90min:lptD_kd:MOCP_0066_1:r2


title: MOCP_0066:pol7080:0.08000uM:90min:dfhr-hypo:MOCP_0066_1:r2


title: MOCP_0066:pf3299:1.56250uM:90min:PA14:MOCP_0066_1:r3


title: MOCP_0066:pol7080:0.08000uM:90min:dfhr-hypo:MOCP_0066_1:r1


title: MOCP_0066:pf3299:1.56250uM:90min:PA14:MOCP_0066_1:r2


title: MOCP_0066:pf3299:1.56250uM:90min:lpxC-hypo:MOCP_0066_1:r3

source_name: lpxC-hypo

value: lpxC-hypo


title: MOCP_0066:pf3299:1.56250uM:90min:PA14:MOCP_0066_1:r1


title: MOCP_0066:pf3299:1.56250uM:90min:lpxC-hypo:MOCP_0066_1:r1


title: MOCP_0066:pf3299:1.56250uM:90min:gyrA-hypo:MOCP_0066_1:r3

source_name: gyrA-hypo

value: gyrA-hypo


title: MOCP_0066:pf3299:1.56250uM:90min:lpxC-hypo:MOCP_0066_1:r2

value: uM


title: MOCP_0066:pf3299:1.56250uM:90min:gyrA-hypo:MOCP_0066_1:r2

value: FALSE


title: MOCP_0066:pf3299:0.39100uM:90min:PA14:MOCP_0066_1:r3


title: MOCP_0066:tmp:100.00000uM:90min:dfhr-hypo:MOCP_0066_1:r1


title: MOCP_0066:pf3299:1.56250uM:90min:gyrA-hypo:MOCP_0066_1:r1


title: MOCP_0066:pol7080:0.32000uM:90min:PA14:MOCP_0066_1:r1


title: MOCP_0066:pf3299:0.39100uM:90min:lpxC-hypo:MOCP_0066_1:r3


title: MOCP_0066:pf3299:0.39100uM:90min:lpxC-hypo:MOCP_0066_1:r1


title: MOCP_0066:pf3299:0.39100uM:90min:PA14:MOCP_0066_1:r1


title: MOCP_0066:pf3299:0.39100uM:90min:gyrA-hypo:MOCP_0066_1:r1


title: MOCP_0066:pol7080:0.08000uM:90min:dfhr-hypo:MOCP_0066_1:r3


title: MOCP_0066:mrl494:50.00000uM:90min:PA14:MOCP_0066_1:r2


title: MOCP_0066:pf3299:0.39100uM:90min:gyrA-hypo:MOCP_0066_1:r2


title: MOCP_0066:mrl494:50.00000uM:90min:bamA-hypo:MOCP_0066_1:r3

source_name: bamA-hypo

value: bamA-hypo


title: MOCP_0066:mrl494:25.00000uM:90min:PA14:MOCP_0066_1:r3


title: MOCP_0066:pf3299:0.39100uM:90min:gyrA-hypo:MOCP_0066_1:r3


title: MOCP_0066:mrl494:50.00000uM:90min:bamA-hypo:MOCP_0066_1:r2


title: MOCP_0066:mrl494:25.00000uM:90min:PA14:MOCP_0066_1:r2


title: MOCP_0066:mrl494:50.00000uM:90min:PA14:MOCP_0066_1:r1


title: MOCP_0066:mrl494:50.00000uM:90min:bamA-hypo:MOCP_0066_1:r1


title: MOCP_0066:mrl494:50.00000uM:90min:PA14:MOCP_0066_1:r3


title: MOCP_0066:mrl494:25.00000uM:90min:bamA-hypo:MOCP_0066_1:r3


title: MOCP_0066:ll37:6.25000uM:90min:PA14:MOCP_0066_1:r3


title: MOCP_0066:mrl494:25.00000uM:90min:bamA-hypo:MOCP_0066_1:r1


title: MOCP_0066:ll37:6.25000uM:90min:PA14:MOCP_0066_1:r2


title: MOCP_0066:mrl494:25.00000uM:90min:bamA-hypo:MOCP_0066_1:r2


title: MOCP_0066:ll37:6.25000uM:90min:PA14:MOCP_0066_1:r1


title: MOCP_0066:ll37:12.50000uM:90min:PA14:MOCP_0066_1:r2


title: MOCP_0066:ll37:12.50000uM:90min:PA14:MOCP_0066_1:r1


title: MOCP_0066:imi:6.25000uM:90min:PA14:MOCP_0066_1:r3

value: imi

value: Imipenem


title: MOCP_0066:pf3299:0.39100uM:90min:lpxC-hypo:MOCP_0066_1:r2


title: MOCP_0066:imi:1.56250uM:90min:PA14:MOCP_0066_1:r3


title: MOCP_0066:imi:1.56250uM:90min:PA14:MOCP_0066_1:r2


title: MOCP_0066:imi:6.25000uM:90min:PA14:MOCP_0066_1:r1


title: MOCP_0066:ll37:12.50000uM:90min:PA14:MOCP_0066_1:r3


title: MOCP_0066:mrl494:25.00000uM:90min:PA14:MOCP_0066_1:r1


title: MOCP_0066:imi:1.56250uM:90min:PA14:MOCP_0066_1:r1


title: MOCP_0066:fosmido:500.00000uM:90min:PA14:MOCP_0066_1:r1

value: fosmido

value: Fosmidomycin


title: MOCP_0066:fosmido:500.00000uM:90min:dxr_kd:MOCP_0066_1:r2


title: MOCP_0066:fosmido:500.00000uM:90min:dxr_kd:MOCP_0066_1:r1


title: MOCP_0066:fosmido:500.00000uM:90min:dxr_kd:MOCP_0066_1:r3


title: MOCP_0066:fosmido:250.00000uM:90min:PA14:MOCP_0066_1:r2


title: MOCP_0066:fosmido:250.00000uM:90min:PA14:MOCP_0066_1:r1


title: MOCP_0066:fosmido:250.00000uM:90min:dxr_kd:MOCP_0066_1:r2


title: MOCP_0066:fosmido:250.00000uM:90min:dxr_kd:MOCP_0066_1:r1


title: MOCP_0066:fosfo:800.00000uM:90min:PA14:MOCP_0066_1:r3

value: fosfo

value: Fosfomycin


title: MOCP_0066:fosfo:800.00000uM:90min:PA14:MOCP_0066_1:r1


title: MOCP_0066:fosfo:200.00000uM:90min:murA-hypo:MOCP_0066_1:r1

value: murA-hypo


title: MOCP_0066:doxy:25.00000uM:90min:murA-hypo:MOCP_0066_1:r2

value: doxy

value: Doxycycline

value: min


title: MOCP_0066:doxy:25.00000uM:90min:murA-hypo:MOCP_0066_1:r1


title: MOCP_0066:fosfo:200.00000uM:90min:murA-hypo:MOCP_0066_1:r2


title: MOCP_0066:fosfo:800.00000uM:90min:murA-hypo:MOCP_0066_1:r3


title: MOCP_0066:pf3299:0.39100uM:90min:PA14:MOCP_0066_1:r2


title: MOCP_0066:fosfo:3200.00000uM:90min:PA14:MOCP_0066_1:r3


title: MOCP_0066:doxy:25.00000uM:90min:PA14:MOCP_0066_1:r3


title: MOCP_0066:fosfo:200.00000uM:90min:murA-hypo:MOCP_0066_1:r3


title: MOCP_0066:fosfo:800.00000uM:90min:murA-hypo:MOCP_0066_1:r1


title: MOCP_0066:doxy:25.00000uM:90min:PA14:MOCP_0066_1:r2


title: MOCP_0066:fosfo:3200.00000uM:90min:PA14:MOCP_0066_1:r2


title: MOCP_0066:fosmido:500.00000uM:90min:PA14:MOCP_0066_1:r3


title: MOCP_0066:fosfo:800.00000uM:90min:murA-hypo:MOCP_0066_1:r2


title: MOCP_0066:imi:6.25000uM:90min:PA14:MOCP_0066_1:r2


title: MOCP_0066:fosfo:3200.00000uM:90min:PA14:MOCP_0066_1:r1


title: MOCP_0066:doxy:25.00000uM:90min:lptD_kd:MOCP_0066_1:r1


title: MOCP_0066:doxy:25.00000uM:90min:lptD_kd:MOCP_0066_1:r3


title: MOCP_0066:doxy:25.00000uM:90min:lpxC-hypo:MOCP_0066_1:r3


title: MOCP_0066:fosmido:250.00000uM:90min:PA14:MOCP_0066_1:r3


title: MOCP_0066:doxy:25.00000uM:90min:gyrA-hypo:MOCP_0066_1:r3


title: MOCP_0066:doxy:25.00000uM:90min:lptD_kd:MOCP_0066_1:r2


title: MOCP_0066:fosmido:250.00000uM:90min:dxr_kd:MOCP_0066_1:r3


title: MOCP_0066:fosfo:800.00000uM:90min:PA14:MOCP_0066_1:r2


title: MOCP_0066:doxy:25.00000uM:90min:gyrA-hypo:MOCP_0066_1:r1


title: MOCP_0066:doxy:25.00000uM:90min:PA14:MOCP_0066_1:r1


title: MOCP_0066:doxy:25.00000uM:90min:murA-hypo:MOCP_0066_1:r3


title: MOCP_0066:doxy:25.00000uM:90min:lpxC-hypo:MOCP_0066_1:r1


title: MOCP_0066:doxy:25.00000uM:90min:dfhr-hypo:MOCP_0066_1:r3

value: dfhr-hypo


title: MOCP_0066:doxy:25.00000uM:90min:dfhr-hypo:MOCP_0066_1:r1

value: poscon


title: MOCP_0066:doxy:25.00000uM:90min:dxr_kd:MOCP_0066_1:r3


title: MOCP_0066:doxy:100.00000uM:90min:PA14:MOCP_0066_1:r2


title: MOCP_0066:doxy:25.00000uM:90min:bamA-hypo:MOCP_0066_1:r1


title: MOCP_0066:doxy:25.00000uM:90min:bamA-hypo:MOCP_0066_1:r3


title: MOCP_0066:doxy:25.00000uM:90min:dxr_kd:MOCP_0066_1:r1


title: MOCP_0066:doxy:100.00000uM:90min:lpxC-hypo:MOCP_0066_1:r1

value: lpxC-hypo


title: MOCP_0066:doxy:100.00000uM:90min:PA14:MOCP_0066_1:r3


title: MOCP_0066:doxy:25.00000uM:90min:lpxC-hypo:MOCP_0066_1:r2


title: MOCP_0066:doxy:100.00000uM:90min:lpxC-hypo:MOCP_0066_1:r2


title: MOCP_0066:doxy:100.00000uM:90min:murA-hypo:MOCP_0066_1:r3


title: MOCP_0066:doxy:100.00000uM:90min:murA-hypo:MOCP_0066_1:r2


title: MOCP_0066:doxy:25.00000uM:90min:dfhr-hypo:MOCP_0066_1:r2


title: MOCP_0066:doxy:100.00000uM:90min:lptD_kd:MOCP_0066_1:r2


title: MOCP_0066:doxy:100.00000uM:90min:lptD_kd:MOCP_0066_1:r1


title: MOCP_0066:doxy:100.00000uM:90min:gyrA-hypo:MOCP_0066_1:r2

value: gyrA-hypo


title: MOCP_0066:doxy:100.00000uM:90min:murA-hypo:MOCP_0066_1:r1

value: uM


title: MOCP_0066:doxy:100.00000uM:90min:gyrA-hypo:MOCP_0066_1:r3

value: FALSE


title: MOCP_0066:doxy:100.00000uM:90min:PA14:MOCP_0066_1:r1


title: MOCP_0066:doxy:100.00000uM:90min:gyrA-hypo:MOCP_0066_1:r1


title: MOCP_0066:doxy:100.00000uM:90min:lpxC-hypo:MOCP_0066_1:r3


title: MOCP_0066:doxy:25.00000uM:90min:dxr_kd:MOCP_0066_1:r2


title: MOCP_0066:doxy:100.00000uM:90min:dxr_kd:MOCP_0066_1:r1


title: MOCP_0066:doxy:100.00000uM:90min:dxr_kd:MOCP_0066_1:r2


title: MOCP_0066:doxy:25.00000uM:90min:bamA-hypo:MOCP_0066_1:r2

value: bamA-hypo


title: MOCP_0066:doxy:100.00000uM:90min:dfhr-hypo:MOCP_0066_1:r3


title: MOCP_0066:doxy:25.00000uM:90min:gyrA-hypo:MOCP_0066_1:r2


title: MOCP_0066:doxy:100.00000uM:90min:dfhr-hypo:MOCP_0066_1:r2


title: MOCP_0066:doxy:100.00000uM:90min:lptD_kd:MOCP_0066_1:r3


title: MOCP_0066:dmso:0.50000%:90min:PA14:MOCP_0066_1:r3

value: dmso

value: negcon


title: MOCP_0066:doxy:100.00000uM:90min:bamA-hypo:MOCP_0066_1:r1


title: MOCP_0066:doxy:100.00000uM:90min:bamA-hypo:MOCP_0066_1:r3


title: MOCP_0066:doxy:100.00000uM:90min:bamA-hypo:MOCP_0066_1:r2


title: MOCP_0066:dmso:0.50000%:90min:PA14:MOCP_0066_1:r1


title: MOCP_0066:dmso:0.50000%:90min:lpxC-hypo:MOCP_0066_1:r1


title: MOCP_0066:dmso:0.50000%:90min:lptD_kd:MOCP_0066_1:r2


title: MOCP_0066:dmso:0.50000%:90min:lptD_kd:MOCP_0066_1:r1


title: MOCP_0066:dmso:0.50000%:90min:PA14:MOCP_0066_1:r2


title: MOCP_0066:dmso:0.50000%:90min:dfhr-hypo:MOCP_0066_1:r2


title: MOCP_0066:dmso:0.50000%:90min:lptD_kd:MOCP_0066_1:r3


title: MOCP_0066:dmso:0.50000%:90min:gyrA-hypo:MOCP_0066_1:r3


title: MOCP_0066:dmso:0.50000%:90min:gyrA-hypo:MOCP_0066_1:r2


title: MOCP_0066:dmso:0.50000%:90min:bamA-hypo:MOCP_0066_1:r2


title: MOCP_0066:dmso:0.50000%:90min:lpxC-hypo:MOCP_0066_1:r2


title: MOCP_0066:dmso:0.50000%:90min:bamA-hypo:MOCP_0066_1:r3


title: MOCP_0066:dmso:0.50000%:90min:lpxC-hypo:MOCP_0066_1:r3


title: MOCP_0066:col:3.12500uM:90min:PA14:MOCP_0066_1:r3

value: col

value: Colistin


title: MOCP_0066:doxy:100.00000uM:90min:dxr_kd:MOCP_0066_1:r3


title: MOCP_0066:dmso:0.50000%:90min:gyrA-hypo:MOCP_0066_1:r1


title: MOCP_0066:doxy:100.00000uM:90min:dfhr-hypo:MOCP_0066_1:r1


title: MOCP_0066:col:3.12500uM:90min:PA14:MOCP_0066_1:r1


title: MOCP_0066:dmso:0.50000%:90min:dfhr-hypo:MOCP_0066_1:r1


title: MOCP_0066:col:12.50000uM:90min:PA14:MOCP_0066_1:r3


title: MOCP_0066:dmso:0.50000%:90min:bamA-hypo:MOCP_0066_1:r1


title: MOCP_0066:col:3.12500uM:90min:PA14:MOCP_0066_1:r2


title: MOCP_0066:col:12.50000uM:90min:PA14:MOCP_0066_1:r1


title: MOCP_0066:col:12.50000uM:90min:PA14:MOCP_0066_1:r2


title: MOCP_0066:clari:50.00000uM:90min:PA14:MOCP_0066_1:r3

value: clari

value: Clarithromycin


title: MOCP_0066:clari:200.00000uM:90min:PA14:MOCP_0066_1:r3


title: MOCP_0066:cip:0.78125uM:90min:PA14:MOCP_0066_1:r3

value: cip

value: Ciprofloxacin


title: MOCP_0066:clari:200.00000uM:90min:PA14:MOCP_0066_1:r1


title: MOCP_0066:clari:50.00000uM:90min:PA14:MOCP_0066_1:r2


title: MOCP_0066:cip:0.78125uM:90min:PA14:MOCP_0066_1:r2


title: MOCP_0066:cip:0.78125uM:90min:PA14:MOCP_0066_1:r1


title: MOCP_0066:cip:0.78125uM:90min:murA-hypo:MOCP_0066_1:r3

value: murA-hypo


title: MOCP_0066:cip:0.78125uM:90min:murA-hypo:MOCP_0066_1:r2

value: min


title: MOCP_0066:cip:0.78125uM:90min:murA-hypo:MOCP_0066_1:r1


title: MOCP_0066:cip:0.78125uM:90min:lpxC-hypo:MOCP_0066_1:r1


title: MOCP_0066:clari:200.00000uM:90min:PA14:MOCP_0066_1:r2


title: MOCP_0066:cip:0.78125uM:90min:lpxC-hypo:MOCP_0066_1:r3


title: MOCP_0066:cip:0.78125uM:90min:lptD_kd:MOCP_0066_1:r2


title: MOCP_0066:cip:0.78125uM:90min:dxr_kd:MOCP_0066_1:r2


title: MOCP_0066:cip:0.78125uM:90min:gyrA-hypo:MOCP_0066_1:r2


title: MOCP_0066:clari:50.00000uM:90min:PA14:MOCP_0066_1:r1


title: MOCP_0066:cip:0.78125uM:90min:dxr_kd:MOCP_0066_1:r3


title: MOCP_0066:cip:0.78125uM:90min:gyrA-hypo:MOCP_0066_1:r1


title: MOCP_0066:cip:0.78125uM:90min:bamA-hypo:MOCP_0066_1:r3


title: MOCP_0066:cip:0.78125uM:90min:bamA-hypo:MOCP_0066_1:r1


title: MOCP_0066:cip:0.78125uM:90min:dxr_kd:MOCP_0066_1:r1


title: MOCP_0066:cip:0.78125uM:90min:bamA-hypo:MOCP_0066_1:r2


title: MOCP_0066:cip:0.19500uM:90min:PA14:MOCP_0066_1:r1


title: MOCP_0066:cip:0.19500uM:90min:PA14:MOCP_0066_1:r3


title: MOCP_0066:cip:0.78125uM:90min:lptD_kd:MOCP_0066_1:r3


title: MOCP_0066:cip:0.19500uM:90min:lpxC-hypo:MOCP_0066_1:r3


title: MOCP_0066:cip:0.19500uM:90min:murA-hypo:MOCP_0066_1:r2


title: MOCP_0066:cip:0.19500uM:90min:murA-hypo:MOCP_0066_1:r3


title: MOCP_0066:cip:0.19500uM:90min:lpxC-hypo:MOCP_0066_1:r1


title: MOCP_0066:cip:0.19500uM:90min:lpxC-hypo:MOCP_0066_1:r2


title: MOCP_0066:cip:0.19500uM:90min:murA-hypo:MOCP_0066_1:r1


title: MOCP_0066:cip:0.19500uM:90min:lptD_kd:MOCP_0066_1:r3


title: MOCP_0066:cip:0.19500uM:90min:lptD_kd:MOCP_0066_1:r2


title: MOCP_0066:cip:0.19500uM:90min:lptD_kd:MOCP_0066_1:r1


title: MOCP_0066:cip:0.19500uM:90min:gyrA-hypo:MOCP_0066_1:r3


title: MOCP_0066:cip:0.19500uM:90min:gyrA-hypo:MOCP_0066_1:r2


title: MOCP_0066:cip:0.19500uM:90min:dxr_kd:MOCP_0066_1:r2


title: MOCP_0066:cip:0.19500uM:90min:dxr_kd:MOCP_0066_1:r3


title: MOCP_0066:cip:0.78125uM:90min:lptD_kd:MOCP_0066_1:r1


title: MOCP_0066:cip:0.78125uM:90min:gyrA-hypo:MOCP_0066_1:r3


title: MOCP_0066:chir090:3.12500uM:90min:PA14:MOCP_0066_1:r2


title: MOCP_0066:cip:0.19500uM:90min:PA14:MOCP_0066_1:r2


title: MOCP_0066:cip:0.19500uM:90min:dxr_kd:MOCP_0066_1:r1


title: MOCP_0066:chir090:0.78125uM:90min:PA14:MOCP_0066_1:r2


title: MOCP_0066:cip:0.19500uM:90min:bamA-hypo:MOCP_0066_1:r1


title: MOCP_0066:chir090:3.12500uM:90min:PA14:MOCP_0066_1:r1


title: MOCP_0066:chir090:0.78125uM:90min:PA14:MOCP_0066_1:r3


title: MOCP_0066:chir090:3.12500uM:90min:PA14:MOCP_0066_1:r3


title: MOCP_0066:cip:0.78125uM:90min:lpxC-hypo:MOCP_0066_1:r2


title: MOCP_0066:cip:0.19500uM:90min:bamA-hypo:MOCP_0066_1:r3


title: MOCP_0066:cbr4830:62.50000uM:90min:PA14:MOCP_0066_1:r3


title: MOCP_0066:chir090:0.78125uM:90min:PA14:MOCP_0066_1:r1


title: MOCP_0066:carb:6400.00000uM:90min:PA14:MOCP_0066_1:r3

value: carb

value: Carbenicillin


title: MOCP_0066:cbr4830:62.50000uM:90min:PA14:MOCP_0066_1:r2

value: poscon


title: MOCP_0066:carb:1600.00000uM:90min:PA14:MOCP_0066_1:r3


title: MOCP_0066:carb:6400.00000uM:90min:PA14:MOCP_0066_1:r1


title: MOCP_0066:carb:1600.00000uM:90min:PA14:MOCP_0066_1:r2


title: MOCP_0066:carb:1600.00000uM:90min:PA14:MOCP_0066_1:r1


title: MOCP_0066:carb:6400.00000uM:90min:PA14:MOCP_0066_1:r2


title: MOCP_0066:cip:0.19500uM:90min:gyrA-hypo:MOCP_0066_1:r1

value: gyrA-hypo


title: MOCP_0066:cbr4830:62.50000uM:90min:PA14:MOCP_0066_1:r1

value: uM


title: MOCP_0066:ami:6.25000uM:90min:PA14:MOCP_0066_1:r2

value: ami

value: Amikacin

value: FALSE


title: MOCP_0066:a22:800.00000uM:90min:PA14:MOCP_0066_1:r3


title: MOCP_0066:cip:0.19500uM:90min:bamA-hypo:MOCP_0066_1:r2

value: bamA-hypo


title: MOCP_0066:ami:6.25000uM:90min:PA14:MOCP_0066_1:r3


title: MOCP_0066:a22:800.00000uM:90min:PA14:MOCP_0066_1:r2


title: MOCP_0066:a22:200.00000uM:90min:PA14:MOCP_0066_1:r3


title: MOCP_0066:a22:800.00000uM:90min:PA14:MOCP_0066_1:r1


title: MOCP_0066:a22:200.00000uM:90min:PA14:MOCP_0066_1:r2


title: MOCP_0066:a22:200.00000uM:90min:PA14:MOCP_0066_1:r1


title: MOCP_0066:ami:6.25000uM:90min:PA14:MOCP_0066_1:r1


title: MOC_1779:water:0.50000%:90min:PA14:MOC_1779_2:r2

value: water

value: negcon


title: MOC_1779:water:0.50000%:90min:PA14:MOC_1779_2:r1


title: MOC_1779:water:0.50000%:90min:PA14:MOC_1779_1:r3


title: MOC_1779:water:0.50000%:90min:PA14:MOC_1779_2:r3


title: MOC_1779:tmp:800.00000uM:90min:PA14:MOC_1779_2:r3

value: tmp

value: Trimethoprim


title: MOC_1779:water:0.50000%:90min:PA14:MOC_1779_1:r1


title: MOC_1779:water:0.50000%:90min:PA14:MOC_1779_1:r2


title: MOC_1779:tmp:400.00000uM:90min:PA14:MOC_1779_2:r3


title: MOC_1779:tmp:400.00000uM:90min:PA14:MOC_1779_2:r1


title: MOC_1779:tmp:800.00000uM:90min:PA14:MOC_1779_2:r2


title: MOC_1779:tmp:400.00000uM:90min:PA14:MOC_1779_2:r2


title: MOC_1779:tmp:100.00000uM:90min:PA14:MOC_1779_1:r3


title: MOC_1779:thio:400.00000uM:90min:PA14:MOC_1779_2:r1

value: thio

value: Thiolactomycin


title: MOC_1779:tmp:100.00000uM:90min:PA14:MOC_1779_1:r2


title: MOC_1779:thio:400.00000uM:90min:PA14:MOC_1779_2:r3


title: MOC_1779:thio:200.00000uM:90min:PA14:MOC_1779_2:r2


title: MOC_1779:thio:400.00000uM:90min:PA14:MOC_1779_2:r2


title: MOC_1779:thio:200.00000uM:90min:PA14:MOC_1779_2:r1


title: MOC_1779:thio:200.00000uM:90min:PA14:MOC_1779_2:r3


title: MOC_1779:rif:50.00000uM:90min:PA14:MOC_1779_1:r3

value: rif

value: Rifampicin


title: MOC_1779:rif:50.00000uM:90min:PA14:MOC_1779_1:r2

value: min


title: MOC_1779:rif:50.00000uM:90min:PA14:MOC_1779_1:r1


title: MOC_1779:rif:200.00000uM:90min:PA14:MOC_1779_2:r3


title: MOC_1779:rif:400.00000uM:90min:PA14:MOC_1779_2:r3


title: MOC_1779:rad:400.00000uM:90min:PA14:MOC_1779_2:r2

value: rad

value: Radicicol


title: MOC_1779:rif:400.00000uM:90min:PA14:MOC_1779_2:r1

value: poscon


title: MOC_1779:rif:400.00000uM:90min:PA14:MOC_1779_2:r2

value: uM


title: MOC_1779:rad:400.00000uM:90min:PA14:MOC_1779_2:r1


title: MOC_1779:rif:200.00000uM:90min:PA14:MOC_1779_2:r1


title: MOC_1779:tmp:800.00000uM:90min:PA14:MOC_1779_2:r1


title: MOC_1779:pol7080:0.64000uM:90min:PA14:MOC_1779_2:r3


title: MOC_1779:rad:400.00000uM:90min:PA14:MOC_1779_2:r3


title: MOC_1779:pol7080:0.64000uM:90min:PA14:MOC_1779_2:r1


title: MOC_1779:pol7080:0.32000uM:90min:PA14:MOC_1779_2:r2


title: MOC_1779:tmp:100.00000uM:90min:PA14:MOC_1779_1:r1


title: MOC_1779:pol7080:0.08000uM:90min:PA14:MOC_1779_1:r3


title: MOC_1779:pol7080:0.64000uM:90min:PA14:MOC_1779_2:r2


title: MOC_1779:pol7080:0.08000uM:90min:PA14:MOC_1779_1:r2


title: MOC_1779:pol7080:0.32000uM:90min:PA14:MOC_1779_2:r1


title: MOC_1779:pol7080:0.08000uM:90min:PA14:MOC_1779_1:r1


title: MOC_1779:pol7001:3.20000uM:90min:PA14:MOC_1779_2:r3


title: MOC_1779:pol7001:3.20000uM:90min:PA14:MOC_1779_2:r2


title: MOC_1779:pol7001:1.60000uM:90min:PA14:MOC_1779_2:r3


title: MOC_1779:pol7001:1.60000uM:90min:PA14:MOC_1779_2:r1


title: MOC_1779:pol7001:0.40000uM:90min:PA14:MOC_1779_1:r1


title: MOC_1779:rif:200.00000uM:90min:PA14:MOC_1779_2:r2


title: MOC_1779:pip:800.00000uM:90min:PA14:MOC_1779_2:r3

value: pip

value: Piperacillin


title: MOC_1779:pip:800.00000uM:90min:PA14:MOC_1779_2:r1

value: FALSE


title: MOC_1779:pip:1600.00000uM:90min:PA14:MOC_1779_2:r3


title: MOC_1779:pip:1600.00000uM:90min:PA14:MOC_1779_2:r2


title: MOC_1779:pf1090:3.12500uM:90min:PA14:MOC_1779_2:r2


title: MOC_1779:pip:800.00000uM:90min:PA14:MOC_1779_2:r2


title: MOC_1779:pol7080:0.32000uM:90min:PA14:MOC_1779_2:r3


title: MOC_1779:pf1090:3.12500uM:90min:PA14:MOC_1779_2:r3


title: MOC_1779:pf1090:3.12500uM:90min:PA14:MOC_1779_2:r1


title: MOC_1779:pip:1600.00000uM:90min:PA14:MOC_1779_2:r1


title: MOC_1779:pf1090:1.56000uM:90min:PA14:MOC_1779_2:r2


title: MOC_1779:pf1090:0.39000uM:90min:PA14:MOC_1779_1:r3


title: MOC_1779:novo:800.00000uM:90min:PA14:MOC_1779_2:r3

value: novo

value: Novobiocin


title: MOC_1779:novo:400.00000uM:90min:PA14:MOC_1779_2:r3


title: MOC_1779:novo:800.00000uM:90min:PA14:MOC_1779_2:r1


title: MOC_1779:novo:800.00000uM:90min:PA14:MOC_1779_2:r2


title: MOC_1779:pf1090:1.56000uM:90min:PA14:MOC_1779_2:r1


title: MOC_1779:pf1090:0.39000uM:90min:PA14:MOC_1779_1:r1


title: MOC_1779:novo:400.00000uM:90min:PA14:MOC_1779_2:r2


title: MOC_1779:pol7001:0.40000uM:90min:PA14:MOC_1779_1:r3


title: MOC_1779:pol7001:3.20000uM:90min:PA14:MOC_1779_2:r1


title: MOC_1779:novo:400.00000uM:90min:PA14:MOC_1779_2:r1


title: MOC_1779:pf1090:1.56000uM:90min:PA14:MOC_1779_2:r3


title: MOC_1779:pol7001:0.40000uM:90min:PA14:MOC_1779_1:r2


title: MOC_1779:pol7001:1.60000uM:90min:PA14:MOC_1779_2:r2


title: MOC_1779:pf1090:0.39000uM:90min:PA14:MOC_1779_1:r2


title: MOC_1779:nitro:50.00000uM:90min:PA14:MOC_1779_1:r2

value: nitro

value: Nitrofurantoin


title: MOC_1779:nitro:50.00000uM:90min:PA14:MOC_1779_1:r3


title: MOC_1779:nitro:50.00000uM:90min:PA14:MOC_1779_1:r1


title: MOC_1779:nitro:200.00000uM:90min:PA14:MOC_1779_2:r3


title: MOC_1779:nitro:200.00000uM:90min:PA14:MOC_1779_2:r1


title: MOC_1779:nitro:100.00000uM:90min:PA14:MOC_1779_2:r2


title: MOC_1779:nitro:100.00000uM:90min:PA14:MOC_1779_2:r3


title: MOC_1779:mero:6.25000uM:90min:PA14:MOC_1779_1:r3

value: mero

value: Meropenem


title: MOC_1779:mero:6.25000uM:90min:PA14:MOC_1779_1:r2


title: MOC_1779:mero:6.25000uM:90min:PA14:MOC_1779_1:r1


title: MOC_1779:nitro:100.00000uM:90min:PA14:MOC_1779_2:r1


title: MOC_1779:mero:50.00000uM:90min:PA14:MOC_1779_2:r3


title: MOC_1779:mero:50.00000uM:90min:PA14:MOC_1779_2:r2


title: MOC_1779:mero:50.00000uM:90min:PA14:MOC_1779_2:r1


title: MOC_1779:mero:25.00000uM:90min:PA14:MOC_1779_2:r3


title: MOC_1779:mero:25.00000uM:90min:PA14:MOC_1779_2:r2


title: MOC_1779:imi:12.50000uM:90min:PA14:MOC_1779_2:r3

value: imi

value: Imipenem


title: MOC_1779:imi:6.25000uM:90min:PA14:MOC_1779_2:r2


title: MOC_1779:imi:6.25000uM:90min:PA14:MOC_1779_2:r1


title: MOC_1779:imi:1.56000uM:90min:PA14:MOC_1779_1:r3


title: MOC_1779:imi:1.56000uM:90min:PA14:MOC_1779_1:r2


title: MOC_1779:hu:3200.00000uM:90min:PA14:MOC_1779_2:r3

value: hu

value: Hydroxyurea


title: MOC_1779:imi:12.50000uM:90min:PA14:MOC_1779_2:r1

value: min


title: MOC_1779:hu:3200.00000uM:90min:PA14:MOC_1779_2:r2


title: MOC_1779:nitro:200.00000uM:90min:PA14:MOC_1779_2:r2


title: MOC_1779:imi:12.50000uM:90min:PA14:MOC_1779_2:r2


title: MOC_1779:gent:6.25000uM:90min:PA14:MOC_1779_2:r1

value: gent

value: Gentamicin


title: MOC_1779:imi:1.56000uM:90min:PA14:MOC_1779_1:r1

value: uM

value: poscon


title: MOC_1779:hu:3200.00000uM:90min:PA14:MOC_1779_2:r1


title: MOC_1779:mero:25.00000uM:90min:PA14:MOC_1779_2:r1


title: MOC_1779:gent:12.50000uM:90min:PA14:MOC_1779_2:r3


title: MOC_1779:fosfo:800.00000uM:90min:PA14:MOC_1779_1:r1

value: fosfo

value: Fosfomycin


title: MOC_1779:fosfo:800.00000uM:90min:PA14:MOC_1779_1:r3

value: FALSE


title: MOC_1779:gent:12.50000uM:90min:PA14:MOC_1779_2:r1


title: MOC_1779:gent:12.50000uM:90min:PA14:MOC_1779_2:r2


title: MOC_1779:fosfo:6400.00000uM:90min:PA14:MOC_1779_2:r3


title: MOC_1779:fosfo:800.00000uM:90min:PA14:MOC_1779_1:r2


title: MOC_1779:fosfo:3200.00000uM:90min:PA14:MOC_1779_2:r3


title: MOC_1779:fosfo:6400.00000uM:90min:PA14:MOC_1779_2:r1


title: MOC_1779:imi:6.25000uM:90min:PA14:MOC_1779_2:r3


title: MOC_1779:fosfo:3200.00000uM:90min:PA14:MOC_1779_2:r2


title: MOC_1779:fosfo:3200.00000uM:90min:PA14:MOC_1779_2:r1


title: MOC_1779:doxy:25.00000uM:90min:PA14:MOC_1779_1:r3

value: doxy

value: Doxycycline


title: MOC_1779:doxy:25.00000uM:90min:PA14:MOC_1779_1:r2


title: MOC_1779:gent:6.25000uM:90min:PA14:MOC_1779_2:r3


title: MOC_1779:doxy:25.00000uM:90min:PA14:MOC_1779_1:r1


title: MOC_1779:doxy:200.00000uM:90min:PA14:MOC_1779_2:r3


title: MOC_1779:doxy:200.00000uM:90min:PA14:MOC_1779_2:r1


title: MOC_1779:gent:6.25000uM:90min:PA14:MOC_1779_2:r2


title: MOC_1779:doxy:200.00000uM:90min:PA14:MOC_1779_2:r2


title: MOC_1779:doxy:100.00000uM:90min:PA14:MOC_1779_2:r2


title: MOC_1779:dox:50.00000uM:90min:PA14:MOC_1779_2:r3

value: dox

value: Doxorubicin


title: MOC_1779:dox:25.00000uM:90min:PA14:MOC_1779_2:r2


title: MOC_1779:dox:25.00000uM:90min:PA14:MOC_1779_2:r3


title: MOC_1779:doxy:100.00000uM:90min:PA14:MOC_1779_2:r1


title: MOC_1779:dox:25.00000uM:90min:PA14:MOC_1779_2:r1


title: MOC_1779:doxy:100.00000uM:90min:PA14:MOC_1779_2:r3


title: MOC_1779:dox:12.50000uM:90min:PA14:MOC_1779_1:r3


title: MOC_1779:fosfo:6400.00000uM:90min:PA14:MOC_1779_2:r2


title: MOC_1779:dmso:0.50000%:90min:PA14:MOC_1779_2:r3

value: dmso

value: negcon


title: MOC_1779:dmso:0.50000%:90min:PA14:MOC_1779_1:r3


title: MOC_1779:dox:12.50000uM:90min:PA14:MOC_1779_1:r2


title: MOC_1779:dox:50.00000uM:90min:PA14:MOC_1779_2:r1


title: MOC_1779:dmso:0.50000%:90min:PA14:MOC_1779_1:r1


title: MOC_1779:col:3.12500uM:90min:PA14:MOC_1779_1:r3

value: col

value: Colistin


title: MOC_1779:dmso:0.50000%:90min:PA14:MOC_1779_2:r2


title: MOC_1779:dmso:0.50000%:90min:PA14:MOC_1779_1:r2


title: MOC_1779:col:3.12500uM:90min:PA14:MOC_1779_1:r2


title: MOC_1779:col:3.12500uM:90min:PA14:MOC_1779_1:r1


title: MOC_1779:dox:12.50000uM:90min:PA14:MOC_1779_1:r1


title: MOC_1779:dox:50.00000uM:90min:PA14:MOC_1779_2:r2


title: MOC_1779:col:25.00000uM:90min:PA14:MOC_1779_2:r3


title: MOC_1779:col:25.00000uM:90min:PA14:MOC_1779_2:r2


title: MOC_1779:dmso:0.50000%:90min:PA14:MOC_1779_2:r1


title: MOC_1779:col:12.50000uM:90min:PA14:MOC_1779_2:r3


title: MOC_1779:col:12.50000uM:90min:PA14:MOC_1779_2:r2


title: MOC_1779:col:25.00000uM:90min:PA14:MOC_1779_2:r1


title: MOC_1779:clari:400.00000uM:90min:PA14:MOC_1779_2:r3

value: clari

value: Clarithromycin


title: MOC_1779:clari:50.00000uM:90min:PA14:MOC_1779_1:r3

value: min


title: MOC_1779:clari:50.00000uM:90min:PA14:MOC_1779_1:r1


title: MOC_1779:col:12.50000uM:90min:PA14:MOC_1779_2:r1


title: MOC_1779:clari:50.00000uM:90min:PA14:MOC_1779_1:r2


title: MOC_1779:clari:200.00000uM:90min:PA14:MOC_1779_2:r3


title: MOC_1779:clari:400.00000uM:90min:PA14:MOC_1779_2:r1


title: MOC_1779:cisp:50.00000uM:90min:PA14:MOC_1779_1:r3

value: cisp

value: Cisplatin


title: MOC_1779:cisp:50.00000uM:90min:PA14:MOC_1779_1:r2

value: uM

value: poscon


title: MOC_1779:clari:400.00000uM:90min:PA14:MOC_1779_2:r2


title: MOC_1779:clari:200.00000uM:90min:PA14:MOC_1779_2:r2


title: MOC_1779:clari:200.00000uM:90min:PA14:MOC_1779_2:r1


title: MOC_1779:cisp:400.00000uM:90min:PA14:MOC_1779_2:r2


title: MOC_1779:cisp:400.00000uM:90min:PA14:MOC_1779_2:r3


title: MOC_1779:cisp:200.00000uM:90min:PA14:MOC_1779_2:r2


title: MOC_1779:cisp:200.00000uM:90min:PA14:MOC_1779_2:r3


title: MOC_1779:cisp:400.00000uM:90min:PA14:MOC_1779_2:r1


title: MOC_1779:cisp:200.00000uM:90min:PA14:MOC_1779_2:r1


title: MOC_1779:cip:0.78000uM:90min:PA14:MOC_1779_2:r3

value: cip

value: Ciprofloxacin


title: MOC_1779:cip:1.56000uM:90min:PA14:MOC_1779_2:r3

value: FALSE


title: MOC_1779:cip:0.78000uM:90min:PA14:MOC_1779_2:r1


title: MOC_1779:cip:0.19500uM:90min:PA14:MOC_1779_1:r3


title: MOC_1779:cip:0.78000uM:90min:PA14:MOC_1779_2:r2


title: MOC_1779:ceftaz:800.00000uM:90min:PA14:MOC_1779_2:r2

value: ceftaz

value: Ceftazidime


title: MOC_1779:ceftaz:1600.00000uM:90min:PA14:MOC_1779_2:r3


title: MOC_1779:ceftaz:1600.00000uM:90min:PA14:MOC_1779_2:r2


title: MOC_1779:ceftaz:800.00000uM:90min:PA14:MOC_1779_2:r1


title: MOC_1779:carb:6400.00000uM:90min:PA14:MOC_1779_2:r3

value: carb

value: Carbenicillin


title: MOC_1779:ceftaz:1600.00000uM:90min:PA14:MOC_1779_2:r1


title: MOC_1779:carb:6400.00000uM:90min:PA14:MOC_1779_2:r1


title: MOC_1779:carb:6400.00000uM:90min:PA14:MOC_1779_2:r2


title: MOC_1779:cisp:50.00000uM:90min:PA14:MOC_1779_1:r1


title: MOC_1779:carb:1600.00000uM:90min:PA14:MOC_1779_1:r3


title: MOC_1779:carb:1600.00000uM:90min:PA14:MOC_1779_1:r1


title: MOC_1779:carb:12800.00000uM:90min:PA14:MOC_1779_2:r2


title: MOC_1779:carb:1600.00000uM:90min:PA14:MOC_1779_1:r2


title: MOC_1779:a22:800.00000uM:90min:PA14:MOC_1779_2:r2


title: MOC_1779:a22:800.00000uM:90min:PA14:MOC_1779_2:r3


title: MOC_1779:carb:12800.00000uM:90min:PA14:MOC_1779_2:r1


title: MOC_1779:a22:800.00000uM:90min:PA14:MOC_1779_2:r1


title: MOC_1779:cip:1.56000uM:90min:PA14:MOC_1779_2:r2


title: MOC_1779:cip:1.56000uM:90min:PA14:MOC_1779_2:r1


title: MOC_1779:a22:400.00000uM:90min:PA14:MOC_1779_2:r3


title: MOC_1779:cip:0.19500uM:90min:PA14:MOC_1779_1:r2


title: MOC_1779:cip:0.19500uM:90min:PA14:MOC_1779_1:r1


title: MOC_1779:a22:200.00000uM:90min:PA14:MOC_1779_1:r3


title: MOC_1779:ceftaz:800.00000uM:90min:PA14:MOC_1779_2:r3


title: MOC_1779:a22:200.00000uM:90min:PA14:MOC_1779_1:r2


title: MOC_1430:water:0.50000%:90min:PA14:MOC_1430_1:r3

value: water

value: negcon


title: MOC_1430:water:0.50000%:90min:PA14:MOC_1430_1:r2


title: MOC_1430:water:0.50000%:90min:PA14:MOC_1430_1:r1


title: MOC_1430:water:0.50000%:60min:PA14:MOC_1430_1:r3


title: MOC_1430:water:0.50000%:60min:PA14:MOC_1430_1:r2


title: MOC_1430:water:0.50000%:60min:PA14:MOC_1430_1:r1


title: MOC_1779:carb:12800.00000uM:90min:PA14:MOC_1779_2:r3


title: MOC_1430:water:0.50000%:30min:PA14:MOC_1430_1:r2


title: MOC_1430:water:0.50000%:30min:PA14:MOC_1430_1:r1


title: MOC_1430:water:0.50000%:120min:PA14:MOC_1430_1:r3


title: MOC_1430:water:0.50000%:120min:PA14:MOC_1430_1:r2


title: MOC_1430:water:0.50000%:120min:PA14:MOC_1430_1:r1


title: MOC_1430:tmp:375.00000uM:90min:PA14:MOC_1430_1:r2

value: tmp

value: Trimethoprim


title: MOC_1430:tmp:375.00000uM:90min:PA14:MOC_1430_1:r3


title: MOC_1779:a22:400.00000uM:90min:PA14:MOC_1779_2:r2


title: MOC_1430:tmp:375.00000uM:60min:PA14:MOC_1430_1:r2


title: MOC_1430:tmp:375.00000uM:60min:PA14:MOC_1430_1:r3


title: MOC_1779:a22:400.00000uM:90min:PA14:MOC_1779_2:r1


title: MOC_1430:tmp:375.00000uM:90min:PA14:MOC_1430_1:r1


title: MOC_1430:tmp:375.00000uM:60min:PA14:MOC_1430_1:r1


title: MOC_1430:tmp:375.00000uM:30min:PA14:MOC_1430_1:r3


title: MOC_1430:tmp:375.00000uM:30min:PA14:MOC_1430_1:r1


title: MOC_1779:a22:200.00000uM:90min:PA14:MOC_1779_1:r1


title: MOC_1430:tmp:375.00000uM:120min:PA14:MOC_1430_1:r3


title: MOC_1430:tmp:375.00000uM:120min:PA14:MOC_1430_1:r2


title: MOC_1430:tmp:375.00000uM:30min:PA14:MOC_1430_1:r2


title: MOC_1430:tet:108.00000uM:90min:PA14:MOC_1430_1:r3

value: tet

value: Tetracyclin


title: MOC_1430:tmp:375.00000uM:120min:PA14:MOC_1430_1:r1

value: min


title: MOC_1430:tet:108.00000uM:90min:PA14:MOC_1430_1:r1


title: MOC_1430:tet:108.00000uM:60min:PA14:MOC_1430_1:r1


title: MOC_1430:tet:108.00000uM:60min:PA14:MOC_1430_1:r2


title: MOC_1430:tet:108.00000uM:30min:PA14:MOC_1430_1:r3


title: MOC_1430:water:0.50000%:30min:PA14:MOC_1430_1:r3


title: MOC_1430:tet:108.00000uM:30min:PA14:MOC_1430_1:r2


title: MOC_1430:tet:108.00000uM:30min:PA14:MOC_1430_1:r1


title: MOC_1430:tet:108.00000uM:120min:PA14:MOC_1430_1:r1


title: MOC_1430:tet:108.00000uM:120min:PA14:MOC_1430_1:r3


title: MOC_1430:pg1:6.00000uM:90min:PA14:MOC_1430_1:r3


title: MOC_1430:tet:108.00000uM:120min:PA14:MOC_1430_1:r2


title: MOC_1430:pg1:6.00000uM:90min:PA14:MOC_1430_1:r1


title: MOC_1430:pg1:6.00000uM:60min:PA14:MOC_1430_1:r2


title: MOC_1430:pg1:6.00000uM:90min:PA14:MOC_1430_1:r2


title: MOC_1430:pg1:6.00000uM:60min:PA14:MOC_1430_1:r3


title: MOC_1430:pg1:6.00000uM:60min:PA14:MOC_1430_1:r1


title: MOC_1430:pg1:6.00000uM:30min:PA14:MOC_1430_1:r1


title: MOC_1430:pg1:6.00000uM:30min:PA14:MOC_1430_1:r2


title: MOC_1430:pf3299:1.20000uM:90min:PA14:MOC_1430_1:r3


title: MOC_1430:pg1:6.00000uM:120min:PA14:MOC_1430_1:r1


title: MOC_1430:pg1:6.00000uM:120min:PA14:MOC_1430_1:r3


title: MOC_1430:pf3299:1.20000uM:90min:PA14:MOC_1430_1:r2


title: MOC_1430:pg1:6.00000uM:120min:PA14:MOC_1430_1:r2


title: MOC_1430:pf3299:1.20000uM:60min:PA14:MOC_1430_1:r3


title: MOC_1430:tet:108.00000uM:90min:PA14:MOC_1430_1:r2


title: MOC_1430:pg1:6.00000uM:30min:PA14:MOC_1430_1:r3


title: MOC_1430:pf3299:1.20000uM:60min:PA14:MOC_1430_1:r2


title: MOC_1430:pf3299:1.20000uM:60min:PA14:MOC_1430_1:r1


title: MOC_1430:pf3299:1.20000uM:90min:PA14:MOC_1430_1:r1


title: MOC_1430:pf3299:1.20000uM:30min:PA14:MOC_1430_1:r1


title: MOC_1430:tet:108.00000uM:60min:PA14:MOC_1430_1:r3


title: MOC_1430:pf3299:1.20000uM:30min:PA14:MOC_1430_1:r2


title: MOC_1430:pf3299:1.20000uM:120min:PA14:MOC_1430_1:r3


title: MOC_1430:pf3299:1.20000uM:120min:PA14:MOC_1430_1:r2


title: MOC_1430:pf3299:1.20000uM:120min:PA14:MOC_1430_1:r1


title: MOC_1430:pf3299:1.20000uM:30min:PA14:MOC_1430_1:r3


title: MOC_1430:pf1090:1.20000uM:90min:PA14:MOC_1430_1:r3


title: MOC_1430:pf1090:1.20000uM:90min:PA14:MOC_1430_1:r2


title: MOC_1430:pf1090:1.20000uM:90min:PA14:MOC_1430_1:r1


title: MOC_1430:pf1090:1.20000uM:60min:PA14:MOC_1430_1:r3


title: MOC_1430:pf1090:1.20000uM:60min:PA14:MOC_1430_1:r1


title: Brain tissue after MCAO, ketogenic diet, sample 9

city: Moscow

first: Anastasiya

last: Zharikova

address: Leninskie gory 1/73

country: Russia

institute: MSU

data_processing:
Basecalling was performed using bcl2fastq v2.20
Quality control assessments of raw reads of sequencing results were performed using FastQC (v0.11.8) and MultiQC (v1.15)
Raw reads were aligned to mRatBN7 genome using HISAT2 v2.0.5 with parameters --no-softclip --dta-cufflinks; splice sites were obtained from gene annotation Ensemble (v. mRatBN7.2.106)
Gene counts per gene were calculated using htseq-count (version 0.7.2.) with gene annotation Ensemble (v. mRatBN7.2.106) and parameters -m intersection-strict --stranded=yes -t gene.
Normalized counts were obtained using DESeq2 v1.42.0
Assembly: mRatBN7
Supplementary files format and content: Tab-delimited text files with raw counts for each sample

organism: Rattus norvegicus

source_name: brain

extract_protocol:
RNA was extracted from intact brain tissue or from ischemic lesions 14 days after MCAO using RNeasy Micro Kit Qiagen (Qiagen, USA) following the manufacturer’s protocol and stored at −70 °C.
cDNA libraries were constructed using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (New England Biolabs, USA).

tag: tissue

value: brain


title: Brain tissue after MCAO, ketogenic diet, sample 5


title: Brain tissue after MCAO, ketogenic diet, sample 43


title: Brain tissue after MCAO, ketogenic diet, sample 41


title: MOC_1430:pf1090:1.20000uM:30min:PA14:MOC_1430_1:r3

tag: pert id

value: uM


title: MOC_1430:pf1090:1.20000uM:60min:PA14:MOC_1430_1:r2

tag: pert iname

value: poscon


title: MOC_1430:pf1090:1.20000uM:30min:PA14:MOC_1430_1:r2

tag: pert dose


title: MOC_1430:pf1090:1.20000uM:30min:PA14:MOC_1430_1:r1

tag: pert dose_unit


title: Brain tissue after MCAO, ketogenic diet, sample 39


title: MOC_1430:pf1090:1.20000uM:120min:PA14:MOC_1430_1:r2

tag: pert idose


title: Brain tissue after MCAO, ketogenic diet, sample 37


title: MOC_1430:pf1090:1.20000uM:120min:PA14:MOC_1430_1:r1

tag: pert time


title: MOC_1430:pf1090:1.20000uM:120min:PA14:MOC_1430_1:r3

tag: pert time_unit


title: MOC_1430:pa0918:250.00000uM:90min:PA14:MOC_1430_1:r3

description:
moc1430_1779_0066_0110_2kd_counts_manuscript.csv
pa0918_modzscore.csv

tag: pert itime

value: test


title: MOC_1430:pa0918:250.00000uM:90min:PA14:MOC_1430_1:r2

tag: pert type


title: Brain tissue after MCAO, ketogenic diet, sample 29


title: MOC_1430:pa0918:250.00000uM:90min:PA14:MOC_1430_1:r1

tag: category


title: Brain tissue after MCAO, ketogenic diet, sample 27


title: Brain tissue after MCAO, ketogenic diet, sample 25


title: Brain tissue after MCAO, ketogenic diet, sample 23


title: MOC_1430:pa0918:250.00000uM:60min:PA14:MOC_1430_1:r3

tag: project id


title: MOC_1430:pa0918:250.00000uM:60min:PA14:MOC_1430_1:r2

tag: replicate id


title: Brain tissue after MCAO, ketogenic diet, sample 21


title: Brain tissue after MCAO, ketogenic diet, sample 19


title: MOC_1430:pa0918:250.00000uM:30min:PA14:MOC_1430_1:r3

tag: cell line


title: Brain tissue after MCAO, ketogenic diet, sample 15


title: MOC_1430:pa0918:250.00000uM:30min:PA14:MOC_1430_1:r2

tag: project plate_id_384well


title: Brain tissue after MCAO, ketogenic diet, sample 13


title: Brain tissue after MCAO, ketogenic diet, sample 11


title: Brain tissue after MCAO, ketogenic diet, sample 33


title: MOC_1430:pa0918:250.00000uM:30min:PA14:MOC_1430_1:r1

tag: strain id


title: MOC_1430:pa0918:250.00000uM:120min:PA14:MOC_1430_1:r3


title: Brain tissue after MCAO, ketogenic diet, sample 31


title: Brain tissue after MCAO, ketogenic diet, sample 3


title: Brain tissue after MCAO, ad libitum diet, sample 82


title: MOC_1430:pa0918:250.00000uM:120min:PA14:MOC_1430_1:r2


title: MOC_1430:pa0918:250.00000uM:120min:PA14:MOC_1430_1:r1


title: Brain tissue after MCAO, ad libitum diet, sample 71


title: Brain tissue after MCAO, ad libitum diet, sample 78


title: Brain tissue after MCAO, ad libitum diet, sample 70


title: MOC_1430:novo:750.00000uM:90min:PA14:MOC_1430_1:r3

value: novo

value: Novobiocin


title: MOC_1430:novo:750.00000uM:90min:PA14:MOC_1430_1:r1

value: FALSE


title: Brain tissue after MCAO, ad libitum diet, sample 69


title: MOC_1430:novo:750.00000uM:90min:PA14:MOC_1430_1:r2


title: Brain tissue after MCAO, ad libitum diet, sample 67


title: MOC_1430:novo:750.00000uM:60min:PA14:MOC_1430_1:r3


title: Brain tissue after MCAO, ad libitum diet, sample 66


title: Brain tissue after MCAO, ad libitum diet, sample 65


title: MOC_1430:novo:750.00000uM:60min:PA14:MOC_1430_1:r2


title: Brain tissue after MCAO, ad libitum diet, sample 64


title: MOC_1430:novo:750.00000uM:60min:PA14:MOC_1430_1:r1


title: MOC_1430:novo:750.00000uM:30min:PA14:MOC_1430_1:r2


title: MOC_1430:novo:750.00000uM:30min:PA14:MOC_1430_1:r3


title: Brain tissue after MCAO, ad libitum diet, sample 62


title: Brain tissue after MCAO, ketogenic diet, sample 7


title: Brain tissue after MCAO, ad libitum diet, sample 61


title: MOC_1430:pa0918:250.00000uM:60min:PA14:MOC_1430_1:r1


title: MOC_1430:novo:750.00000uM:30min:PA14:MOC_1430_1:r1


title: Intact brain tissue, ketogenic diet, sample 55


title: Intact brain tissue, ketogenic diet, sample 59


title: Intact brain tissue, ketogenic diet, sample 57


title: MOC_1430:novo:750.00000uM:120min:PA14:MOC_1430_1:r2


title: MOC_1430:novo:750.00000uM:120min:PA14:MOC_1430_1:r3


title: Intact brain tissue, ketogenic diet, sample 53


title: MOC_1430:mino:37.50000uM:90min:PA14:MOC_1430_1:r2

value: mino

value: Minocycline


title: Intact brain tissue, ketogenic diet, sample 51


title: Intact brain tissue, ketogenic diet, sample 49


title: Intact brain tissue, ketogenic diet, sample 47


title: MOC_1430:mino:37.50000uM:90min:PA14:MOC_1430_1:r1


title: MOC_1430:mino:37.50000uM:60min:PA14:MOC_1430_1:r3


title: MOC_1430:mino:37.50000uM:60min:PA14:MOC_1430_1:r2


title: Intact brain tissue, ketogenic diet, sample 45


title: MOC_1430:mino:37.50000uM:60min:PA14:MOC_1430_1:r1


title: Intact brain tissue, ad libitum diet, sample 90


title: MOC_1430:mino:37.50000uM:30min:PA14:MOC_1430_1:r3


title: Intact brain tissue, ad libitum diet, sample 89


title: Intact brain tissue, ad libitum diet, sample 88


title: MOC_1430:mino:37.50000uM:120min:PA14:MOC_1430_1:r3


title: Intact brain tissue, ad libitum diet, sample 85


title: Intact brain tissue, ad libitum diet, sample 87


title: Intact brain tissue, ad libitum diet, sample 86


title: MOC_1430:mino:37.50000uM:90min:PA14:MOC_1430_1:r3


title: MOC_1430:mino:37.50000uM:30min:PA14:MOC_1430_1:r2


title: MOC_1430:novo:750.00000uM:120min:PA14:MOC_1430_1:r1


title: Intact brain tissue, ad libitum diet, sample 83


title: MOC_1430:mero:2.40000uM:90min:PA14:MOC_1430_1:r2

value: mero

value: Meropenem


title: MOC_1430:mero:2.40000uM:90min:PA14:MOC_1430_1:r3


title: Intact brain tissue, ad libitum diet, sample 84


title: MOC_1430:mero:2.40000uM:90min:PA14:MOC_1430_1:r1


title: Tas1r3 KO-WD_2

city: Seoul

first: Keon-Hee

last: Lee

address: 1, Gwanak-ro, Gwanak-gu, Seoul, Republic of Korea

department: Food and Nutrition

country: South Korea

institute: Seoul National University

data_processing:
Raw data were trimmed and filtered into FASTQ files by removing adpater sequence and low-quality reads.
High quality reads were mapped and aligned by using STAR algorithm to generate BAM file.
Aligned reads in gene transcript levels were quantified to RefSeq Transcripts using Partek's E/M method, normalized as fragments per kilobase of transcripts per million mapped reads (FPKM) by using a mixed-model approach in Partek® Flow® v7.0 Copyright ©; 2018 (Partek Inc., Saint Louis, MO, USA).
Assembly: mm39, Refseq transcripts 93
Supplementary files format and content: Excel files include FPKM values for each Sample

source_name: Hippocampus

extract_protocol:
Total RNA from hippocampus was isolated with RNAqueousTM-4PCR Total RNA Isolation Kit (Invitrogen, Carlsbad, CA, USA). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Ion Total-RNA Seq Kit v2 (Life Technologies, Carlsbad, CA, USA).

value: Hippocampus

tag: genotype

value: KO

tag: treatment

value: western diet for 18 weeks


title: Tas1r3 KO-WD_1

tag: tissue


title: MOC_1430:mero:2.40000uM:60min:PA14:MOC_1430_1:r3

tag: pert id

tag: pert iname


title: Tas1r3 WT-WD_2

value: WT


title: MOC_1430:mero:2.40000uM:60min:PA14:MOC_1430_1:r2

tag: pert dose

tag: pert dose_unit


title: Tas1r3 WT-WD_1


title: MOC_1430:mero:2.40000uM:60min:PA14:MOC_1430_1:r1

tag: pert idose

tag: pert time


title: MOC_1430:mero:2.40000uM:30min:PA14:MOC_1430_1:r3

tag: pert time_unit

tag: pert itime


title: MOC_1430:mero:2.40000uM:30min:PA14:MOC_1430_1:r2

tag: pert type

tag: category


title: MOC_1430:mero:2.40000uM:30min:PA14:MOC_1430_1:r1

tag: project id

tag: replicate id


title: MOC_1430:mino:37.50000uM:120min:PA14:MOC_1430_1:r1

tag: cell line

tag: project plate_id_384well


title: MOC_1430:mino:37.50000uM:120min:PA14:MOC_1430_1:r2

tag: strain id


title: Clodronate 3

type: RNA

city: Gainesville

first: Sadeem

last: Qdaisat

address: 1333 Center Dr.

institute: University of Florida

hyb_protocol: Nanostring NS_Mm_CancerImm_C3400 kit protocol nCounter, NS_Mm_Glial_v1.0

scan_protocol: nCounter FLEX High sensitivity scan

data_processing: Rosalind

label: biotin

source_name: Glioma tumors in C57Bl/6

label_protocol: Nanostring NS_Mm_CancerImm_C3400 kit on a BIO-RAD T100 Thermal Cycler, NS_Mm_Glial_v1.0

growth_protocol: In vivo

extract_protocol: TriZol followed by RNA purification

tag: strain

value: Glioma tumors

tag: treatment

value: Clodronate


title: Clodronate 2

tag: tissue


title: MOC_1430:mero:2.40000uM:120min:PA14:MOC_1430_1:r2

tag: pert id

tag: pert iname

value: min


title: MOC_1430:mero:2.40000uM:120min:PA14:MOC_1430_1:r1

tag: pert dose

tag: pert dose_unit

value: uM


title: MOC_1430:levo:4.50000uM:90min:PA14:MOC_1430_1:r3

value: levo

value: Levofloxacin

tag: pert idose

tag: pert time

value: poscon


title: UT 2

value: UT


title: seedlhp1_rep2

city: Norwich

first: William

last: Bezodis

address: Norwich Research Park, Colney Lane

department: Crop Genetics

institute: John Innes Centre

data_processing:
Raw RNA-seq reads were trimmed using cutadapt-1.9.1
mapped to Arabidopsis thaliana TAIR10 reference genome using STAR-2.5.a
featureCounts (Liao et al., 2014) was used to count the numbers of reads mapped to each gene
Assembly: TAIR10
Supplementary files format and content: TPM values for each gene

organism: Arabidopsis thaliana

source_name: Seed

growth_protocol: Arabidopsis plants were grown in 22°C till bolting, then transferred to 16°C or 22°C as indicated. The Day 0 (0DAP) was identified by the first emergence of petals from the buds.  At bent-cotyledon stage, Col16 (14-15DAP), Col22(6-7DAP), lhp1(14-15DAP) siliques were manually dissected under microscope. Separated fruits and seeds from 3-5 siliques were collected as one biological replicate.

extract_protocol:
RNA was extracted using RNeasy Plant Mini Kit (Qiagen, 74904).
Fruits and seeds RNA samples were sequenced at BGI (China) using DNBSEQ, 100-bp paired-end sequences with minimum 25 million reads acquired per sample

value: Seed

tag: genotype


title: UT 1


title: MOC_1430:levo:4.50000uM:90min:PA14:MOC_1430_1:r2

tag: pert time_unit

tag: pert itime

tag: pert type

value: FALSE


title: fruitlhp1_rep2

source_name: Fruit

value: Fruit


title: fruitlhp1_rep3


title: MOC_1430:levo:4.50000uM:60min:PA14:MOC_1430_1:r3

tag: category

tag: project id

tag: replicate id


title: fruitlhp1_rep1


title: MOC_1430:levo:4.50000uM:60min:PA14:MOC_1430_1:r2

tag: cell line

tag: project plate_id_384well

tag: strain id


title: MOC_1430:levo:4.50000uM:60min:PA14:MOC_1430_1:r1


title: seedlhp1_rep1

tag: tissue


title: MOC_1430:levo:4.50000uM:90min:PA14:MOC_1430_1:r1

tag: pert id


title: MOC_1430:mino:37.50000uM:30min:PA14:MOC_1430_1:r1

value: mino

tag: pert iname

value: Minocycline


title: seedCol-0_rep3


title: seedCol-0_rep2


title: MOC_1430:levo:4.50000uM:30min:PA14:MOC_1430_1:r3

tag: pert dose


title: Clodronate 1

tag: strain

tag: treatment


title: seedCol-0_rep1


title: UT 3


title: fruitCol-0_rep3


title: MOC_1430:mero:2.40000uM:120min:PA14:MOC_1430_1:r3

value: mero

value: Meropenem

tag: pert dose_unit

tag: pert idose

tag: pert time


title: seedlhp1_rep3

tag: genotype


title: MOC_1430:levo:4.50000uM:30min:PA14:MOC_1430_1:r1

tag: pert time_unit

tag: pert itime

tag: pert type


title: MOC_1430:levo:4.50000uM:120min:PA14:MOC_1430_1:r3

tag: category

tag: project id

tag: replicate id


title: LECs, OE-4

city: Shanghai

first: Liming

last: Chen

state: Shanghai

address: 180 Fenglin Road, Xuhui District

institute: Zhongshan Hospital, Fudan University

data_processing:
fastp software was used to process raw reads in fastq format.
we removed reads containing sequencing adapters or reads of poor quality in raw datam using trim-galore
Transcriptional reads were mapped to the human genome (GRCh38) using HISAT2 using hisat2
Gene expression volume (FPKM) was calculated. The reads of each gene were obtained by HTSeq-count
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include count and FPKM values for each sample

source_name: LEC

growth_protocol: LECs were maintained in DMEM/F12 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humified atmosphere

extract_protocol:
Total RNA was extracted using UNIQ-10 Column Trizol Total RNA Isolation Kit (Sangon Biotech, China)
Sequencing libraries were built on the Illumina Novaseq platform (Genedenovo, Shanghai, China).

treatment_protocol: LECs were transfected with Ad-NC or Ad-Efnb2  before hypoxia

tag: cell line

value: LEC

tag: cell type

value: lymphatic endothelial cells

value: EphrinB2 overexpression

value: hypoxia


title: fruitCol-0_rep2

tag: tissue


title: MOC_1430:levo:4.50000uM:120min:PA14:MOC_1430_1:r2

tag: pert id

tag: pert iname

value: min

tag: project plate_id_384well

tag: strain id


title: LECs, OE-3

tag: treatment


title: LECs, OE-2


title: MOC_1430:levo:4.50000uM:120min:PA14:MOC_1430_1:r1

tag: pert dose

tag: pert dose_unit

value: uM

tag: pert idose


title: MOC_1430:imi:9.00000uM:90min:PA14:MOC_1430_1:r3

value: imi

value: Imipenem

tag: pert time

tag: pert time_unit


title: fruitCol-0_rep1

tag: genotype


title: LECs, OE-1


title: MOC_1430:imi:9.00000uM:60min:PA14:MOC_1430_1:r2

tag: pert itime

tag: pert type

value: poscon

tag: category


title: LECs, NC-1

tag: cell line

value: WT


title: MOC_1430:imi:9.00000uM:90min:PA14:MOC_1430_1:r2

tag: project id

tag: replicate id


title: LECs, NC-2

tag: cell type


title: LECs, NC-3


title: MOC_1430:imi:9.00000uM:60min:PA14:MOC_1430_1:r1

tag: pert id

tag: pert iname


title: MOC_1430:imi:9.00000uM:30min:PA14:MOC_1430_1:r3

tag: project plate_id_384well

tag: strain id


title: MOC_1430:imi:9.00000uM:60min:PA14:MOC_1430_1:r3

tag: pert dose


title: CD8+ T cell, PSA stimulated, ATLAS, V(D)J

city: Philadelphia

first: Siwei

last: Luo

state: Pennsylvania

address: 3401 Civic Center Blvd.

institute: Children’s Hospital of Philadelphia

description: 10X Single Cell V(D)J Library

library_source: other

data_processing:
The barcoded processing, V(D)J clonotye analysis, gene counting and aggregation from 10X Single Cell V(D)J libraries and 5' Single Cell GEX libraries were made using the Cell Ranger software v6.0.1 (https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/using/pipelines-overview)
Assembly: GRCh38
Supplementary files format and content: csv files contain single-cell V(D)J clonotype annotations
Supplementary files format and content: tsv and mtx files contain filtered feature-barcode matrices of single-cell gene expressions
Library strategy: scTCR-seq

molecule: other

source_name: Blood

extract_protocol:
After the cell sorting in ATLAS-seq or Dextramer staining, collected T cell suspension was transferred to laminar wash plate (~80μl in each well) and incubated at room temperature for 30min, followed by washing 5 times with DPBS in Laminar Wash HT2000. Then, the protocol of 10X Genomics Chromium Next GEM Single Cell 5’ Kits were used to resuspend T cells into a proper concentration to achieve targeted cell recovery and prepare the V(D)J library for single-cell TCR sequencing and GEx library for single-cell mRNA sequencing.
Followed the protocol of 10X Genomics Chromium Next GEM Single Cell 5’ Kits

tag: tissue

value: Blood

value: CD8+ T cell


title: MOC_1430:levo:4.50000uM:30min:PA14:MOC_1430_1:r2

value: levo

value: Levofloxacin

tag: pert dose_unit

tag: pert idose

value: FALSE


title: CD8+ T cell, PSA stimulated, ATLAS, GEX

description: 10X 5' Single Cell GEX Library

data_processing:
The barcoded processing, V(D)J clonotye analysis, gene counting and aggregation from 10X Single Cell V(D)J libraries and 5' Single Cell GEX libraries were made using the Cell Ranger software v6.0.1 (https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/using/pipelines-overview)
Assembly: GRCh38
Supplementary files format and content: csv files contain single-cell V(D)J clonotype annotations
Supplementary files format and content: tsv and mtx files contain filtered feature-barcode matrices of single-cell gene expressions


title: donor2, CD8+ T cell, CMV stimulated, Dextramer, GEX

description: 10X 5' Single Cell GEX Library


title: donor2, CD8+ T cell, CMV stimulated, Dextramer, V(D)J

description: 10X Single Cell V(D)J Library


title: MOC_1430:imi:9.00000uM:30min:PA14:MOC_1430_1:r1

tag: pert time

tag: pert time_unit


title: MOC_1430:imi:9.00000uM:120min:PA14:MOC_1430_1:r3

tag: pert itime


title: donor2, CD8+ T cell, CMV stimulated, ATLAS, GEX

description: 10X 5' Single Cell GEX Library


title: donor2, CD8+ T cell, CMV stimulated, ATLAS, V(D)J

description: 10X Single Cell V(D)J Library


title: MOC_1430:imi:9.00000uM:120min:PA14:MOC_1430_1:r2

tag: pert type


title: MOC_1430:imi:9.00000uM:120min:PA14:MOC_1430_1:r1

tag: category


title: MOC_1430:gent:6.00000uM:90min:PA14:MOC_1430_1:r3

tag: cell line

value: gent

value: Gentamicin


title: donor2, CD8+ T cell, unstimulated, GEX

description: 10X 5' Single Cell GEX Library


title: MOC_1430:imi:9.00000uM:90min:PA14:MOC_1430_1:r1

tag: project id


title: donor2, CD8+ T cell, unstimulated, V(D)J

description: 10X Single Cell V(D)J Library


title: MOC_1430:gent:6.00000uM:90min:PA14:MOC_1430_1:r2

tag: replicate id


title: SUM44PE_CMexpt_CM_antiIL6_3

city: Edinburgh

first: Esme

last: Bullock

address: Edinburgh Cancer Research Centre, IGC, Western General Hospital, Crewe Road

institute: University of Edinburgh

data_processing:
For the SUM44PE + CAF CM experiment (samples with CMexpt in library name), alignment and counting was carried out using the Lexogen Illumina Bluebee pipeline and all other data (IL6expt in library name) were analysed using Lexogen QuantSeq FWD data analysis pipeline. Both Bluebee and Lexogen QuantSeq FWD pipelines used Bbduk from the bbmap suite trimming, STAR alignment with modified ENCODE settings and gene counts using HTSeq-count with QuantSeq FWD-specific options.
Assembly: GRCh38
Supplementary files format and content: tab delimited text file with raw counts

source_name: breast

extract_protocol:
Qiagen RNeasy Mini kit
QuantSeq 3’ mRNA-Seq Library Prep Kit (FWD) for Illumina (Lexogen Inc, #015)

treatment_protocol: Cells were grown in phenol-red free media for 24 hours (SUM44PE and MDA-MB-134VI) or 48 hours (HCI-013 and HCI-018) before stimulation with recombinant human IL-6 (10 ng/ml, Biolegend 570804) for 24 hours. For CAF CM experiment, SUM44PE cells were grown in phenol-red free media for 24 hours and then stimulated with ED26 CAF conditioned media (characterised here:https://doi.org/10.3390/cancers14040904) +/- anti-IL-6 (1 μg/ml, Biolegend 501125). CAF conditioned media was generated by growing ED26 ILC CAFs on collagen coated T75 flasks in DMEM/F12 + 10% FBS until confluent, then replacing media with phenol-red free and FBS-free media for 72 hours. Media was centrifuged at 1000xg to remove debris then filtered through a 0.22μm filter and stored at -80°C until used. Conditioned media was diluted 1:1 in phenol-red free growth factor free SUM44PE media for stimulation.

value: breast

tag: cell type

value: Invasive lobular carcinoma

tag: treatment

value: CAF CM + anti-IL6


title: MOC_1430:gent:6.00000uM:90min:PA14:MOC_1430_1:r1

tag: pert id

tag: pert iname


title: SUM44PE_CMexpt_CM_antiIL6_1


title: SUM44PE_CMexpt_CM_4

value: CAF CM


title: SUM44PE_CMexpt_CM_antiIL6_2


title: SUM44PE_CMexpt_CM_1


title: MOC_1430:gent:6.00000uM:60min:PA14:MOC_1430_1:r3

value: min

tag: project plate_id_384well

tag: strain id


title: MOC_1430:imi:9.00000uM:30min:PA14:MOC_1430_1:r2

tag: pert dose

value: uM


title: SUM44PE_CMexpt_ctrl_4

tag: tissue

value: Control


title: HBO_DAPT_JAGGED_2

city: Atlanta

first: Steven

middle: L

last: Goudy

state: GA

address: 2174 N Druid Hills Rd, 1st Floor

institute: Emory University

data_processing:
Sequencing and data processing was perfomed by the Molecular Evolution core at the Georgia Institute of Technology. Paired-end 150 base pairs (PE150) sequencing was performed on the Illumina NovaSeq 6000 instrument to obtain a sequencing depth of 30 million reads per sample. The transcripts obtained were aligned using the hg38 genome reference database along with elimination of duplicate reads, using the DNAStar Lasergene 17.3 application. The RNA levels were calculated in reads per kilobase per million mapped reads (RPKM). Genes expressed at > 1.5 RPKM were retained for further analyses.
Assembly: hg38 genome reference database
Supplementary files format and content: processed raw count matrix in comma separated value (.csv) file

source_name: Human bone-derived osteoblast-like

extract_protocol:
RNA was extracted using Qiagen Rneasy kit (Qiagen, 74106) according to manufacturer's protocols.
The samples were submitted to the Molecular Evolution core at the Georgia Institute of Technology for sequencing. Quality Control (QC) was performed using an Agilent Bioanalyzer 2100 to determine the RNA Integrity Number (RIN) of the samples. mRNA was enriched using the New England Biolab’s (NEB) NEBNext Poly(A) mRNA isolation module for samples with RINs greater than 7 and libraries were prepared using the NEBNext Ultra II directional RNA library preparation kit (NEB, E7760). QC was then performed on these libraries using an Agilent Bioanalyzer 2100 and the libraries were quantified using fluorometric methods.

value: Human bone-derived osteoblast-like

tag: genotype


title: HBO_DAPT_JAGGED_1


title: SUM44PE_CMexpt_ctrl_3


title: HBO_DAPT_JAGGED_3


title: SUM44PE_CMexpt_ctrl_2


title: SUM44PE_CMexpt_CM_2


title: MOC_1430:gent:6.00000uM:60min:PA14:MOC_1430_1:r2

tag: pert dose_unit

tag: pert idose

tag: pert time

value: poscon


title: SUM44PE_CMexpt_ctrl_1