title: SA_15h_6

city: Orenburg

first: Alexander

middle: S

last: Balkin

address: 11 Pionerskaya st.

country: Russia

institute: Institute for Cellular and Intracellular Symbiosis

description:
Salmonella were grown in PAS medium (with 10 μg mL^−1 gentamicin) at 25 °C for 15h.
SA15_6

data_processing:
Demultiplexed reads were trimmed against adapters with bbduk (https://sourceforge.net/projects/bbmap/)
Reads were mapped to the A. castellanii genome (GenBank accession number GCA_000313135) and then mapped against the S. Typhimurium 14028s genome (GCA_000022165.1) (Jarvik et al., 2010) using STAR aligner v2.7.11a (Dobin et al., 2013) (https://github.com/alexdobin/STAR) with ‘--outFilterMultimapNmax 1’, ‘--sjdbGTFfeatureExon gene’, ‘--sjdbGTFtagExonParentTranscript gene_id’, ‘--sjdbGTFtagExonParentGene old_locus_tag’, ‘ --quantMode GeneCounts’.
The featureCounts v1.4.6-p5 function of Rsubread package version 2.14.2 (Liao et al., 2014) (http://subread.sourceforge.net) was used to quantitate the number of reads mapped to each gene.
Assembly: GCA_000022165.1
Supplementary files format and content: A tab-delimited text file includes general statistics on the library depth and read alignment.
Supplementary files format and content: A tab-delimited text file include DESeq normalized trnascript coverage values for each sample.
Library strategy: Cappable-Seq

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

growth_protocol: Salmonella was grown in Luria broth at 37°C without antibiotics. A. castellanii axenic culture was grown for 5 d in PYG medium to a density of 4-5 × 105 cells/mL.

extract_protocol:
The Salmonella were collected by centrifugation. Total RNA was extracted using RNA Extract Reagent (Evrogen, Russia) according to the manufacturer's protocol. DNA contaminants were removed using RNase-free DNase I kit (Ambion, USA).
The integrity of the RNA was checked by Qsep100 bioanalyzer (BiOptic Inc.,Taiwan). Total RNA from Salmonella (5 μg) or Salmonella plus Acanthamoeba (10 μg) was capped with 3´ desthiobiotin-GTP using the Vaccinia Capping System (New England Biolabs, Ipswich, MA, USA). Capped RNA was then purified by Zymo Research Clean and Concentrator™-5 column using manufacturer instructions (Zymo Research, Irvine, CA, USA). Desthiobiotin-GTP-capped RNA was fragmented by polynucleotide kinase buffer and incubated for 5 min at 94 °C. The 3′-phosphates were removed from the fragmented RNA with polynucleotide kinase buffer and T4 polynucleotide kinase at 37 °C for 15 min. Streptavidin enrichment was performed by addition of capped RNA to 30 μL of prewashed hydrophilic streptavidin magnetic beads (New England Biolabs, Ipswich, MA, USA). The biotin-eluted RNA was collected by placing the tube on the magnetic rack. Eluted RNA was cleaned with AMPure XP beads (Beckman Coulter, Brea, CA, USA). Libraries were prepared from capped RNA using the NEBNext small RNA library prep kit (New England Biolabs, Ipswich, MA, USA) according to the manufacturer instructions. Library quality was assessed using a DNA high sensitivity chip on a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA) prior to sequencing.

treatment_protocol: ‘Rich medium’: bacterial cells were grown overnight in 10 mL LB, diluted 1:1000 into 10 mL LB, grown at 190 rpm and 37 °C in a 50 mL tubes until the middle of the exponential growth phase (A600 = 0.4). ‘Poor medium’: bacterial cells were grown overnight in 10 mL LB, diluted 1:1000 into 10 mL LB, grown at 190 rpm and 37°C in a 50 mL tubes until the middle of the exponential growth phase (A600 = 0.4). Then bacteria were washed thrice in sterile PAS by centrifugation at 1200× g for 5 min at 25 °C and were grown for 2 h at 25 °C in sterile PAS. ‘Peroxide shock’: bacterial cells were grown overnight in 10 mL LB, diluted 1:1000 into 10 mL LB, grown at 190 rpm and 37 °C in a 50 mL tubes until the middle of the exponential growth phase (A600 = 0.4) then H2O2 in the final concentration of 1 mM H2O2 for 10 min were added. Amoeba axenic culture was grown for 7 days in PYG medium to cell density 4-5×105 cells in 1 ml. Cells were collected by centrifugation at 800×g, washed twice with sterile Page’s Amoeba Saline (PAS) (Page, 1976) and suspended in 10 ml of fresh PAS medium. Salmonella were grown in LB broth at 37 °C to early stationary growth phase (A600 = 2.0). Cells were collected by centrifugation at 3000×g for 5 minutes, washed twice with PAS, then were added to Acanthamoeba at a bacteria:amoeba ratio of 100:1. After 1 hour of infection, extracellular bacteria were killed by adding media with gentamicin in final concentration 100 μg mL−1 and incubated for 1h at 25°C. The medium was then changed to ‘maintenance media’ containing 10 μg mL−1 gentamicin for the rest of the experiment.

tag: strain

value: Salmonella-Acanthamoeb coculture 15h


title: H524-JIB-04_1

status: Public on Oct 10 2024

type: SRA

city: Dallas

first: Luc

last: Girard

state: TX

address: 5323 Harry Hines Blvd

department: Hamon Center for Therapeutic Oncology Research

country: USA

institute: UT Southwestern Medical Center

description:
Gene_FPKM_uqnorm.txt
H524-JIB-04_1

library_source: transcriptomic

data_processing:
Illumina sequencer from UTSW Sequencing Core (single-end) or Novogene (paired-end)
fastq files were aligned to GRCh38 (human) reference genome using STAR v2.7.1a
bam files were processed to remove read duplicates using Picard MarkDuplicates from GATK v4.1.2. Mouse reads were filtered out from CLX samples
FPKM values were obtained using Cufflinks v2.2.1
FPKM values were upper-quartile normalized, then log-transformed
Assembly: GRCh38
Supplementary files format and content: Gene_FPKM_uqnorm.txt

molecule: total RNA

organism: Homo sapiens

growth_protocol: See publication

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen)
Library preparation was done with the TruSeq Stranded Total RNA LT Sample Prep Kit from Illumina or according to Novogene specifications (https://en.novogene.com)

treatment_protocol: See publication

tag: cell line

tag: cell type

value: SCLC

tag: xenograft

value: no

tag: treatment

tag: time

value: 24 hours


title: H524-JIB-04_2

description:
Gene_FPKM_uqnorm.txt
H524-JIB-04_2


title: RNAseq_ZT4_GFP_Cohort1_Rep1

city: New York

first: Benjamin

middle: H

last: Weekley

state: NY

address: 1470 Madison Ave

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Samples were demultiplexed using bcl2fastq2 (Illumina, v2.20).
Samples were aligned to the GRCm38 mouse genome using STAR (2.7.11b) alignReads in mode BAM SortedByCoordinate.
Gene counts were generated using htseq-count (HTSeq 2.0.5)  with the following parameters: --format=bam --minaqual=10 --type=exon --idattr=gene_name --stranded=yes --mode=union
Gene counts were normalized using DEseq2 (1.44.0) prior to analysis using JTKcycle (3.1)
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: Htseq-counts

molecule: polyA RNA

organism: Mus musculus

source_name: Brain-TMN

extract_protocol:
Tissue was resuspended in 800 uL of Trizol and homogenized using a small dounce homogenizer (30 strokes loose, 30 strokes tight) at room temperature. Chloroform was added and aqueos phase isolated. 70 % ethanol was added 1:1, and then passed over an RNAeasy mini-elute column. The Qiagen RNAeasy MicroKit protocol was followed, including all optional steps/DNAse treatment. RNA was eluted in 15 uL and quantitated using a nanodrop spectrophotometer. RNA quality was assessed using a tapestation RNA screentape. 100 ug of total RNA was used as input for library prep.
Illunia Stranded mRNA Prep, Ligation

treatment_protocol: Mice brains were collected every 4 hours across the zeitgeber time following IACUC protocols. They were flash-frozen using methylbutane and stored at -80 degrees celsius. Brains were sliced and TMN punched (1 mm punches) according to previously published coordinates. TMN were frozen at -80 degrees celsius until CUT&RUN was performed.

tag: tissue

value: Brain-TMN

tag: timepoint

tag: virus

value: GFP

tag: genotype

tag: cohort

tag: replicate


title: ChIP_seq_BDH1-FLAG_rep2

city: Valencia

first: Jaime

last: Pérez

address: Calle del Ingeniero Fausto Elio, s/n

country: Spain

institute: IBMCP

library_source: genomic

data_processing:
Reads were aligned to the TAIR10 genome reference using bowtie2 v2.5.2. Duplicates were marked using the markdup command from sambamba v.1.0
To retain uniquely mapped reads, alignments were filtered using samtools view with options -F 4 -F 1024 -q 5
Coverage files in bedgraph format were generated using the genomeCoverageBed command from bedtools v2.31.1 with options -bga -fs 200. These were converted to bigwig using the UCSC utility BedGraphToBigWig
Peak calling was performed using macs2 v2.2.9.1.
Assembly: TAIR10
Supplementary files format and content: bigwig, narrowPeak

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: Inflorescence

growth_protocol: Inflorescences of plants grown on soil in long days condition

extract_protocol:
The chromatin immunoprecipitation (ChIP) protocol was conducted according to previously described methods with minor adjustments (Diego-Martín et al. 2022). Briefly, 1 gram of inflorescences was ground in liquid nitrogen and cross-linked in Nuclei Isolation Buffer containing 1% formaldehyde for 10 minutes at room temperature. The cross-linking reaction was quenched with glycine, followed by nuclei isolation and chromatin shearing using a Bioruptor Pico (Diagenode). Chromatin was then immunoprecipitated overnight at 4°C with Anti-FLAG M2 antibody (5 μl/ChIP, F1804, Sigma). The immunocomplexes were captured using a 1:1 mixture of magnetic Protein A and Protein G Dynabeads (Invitrogen) for 3 hours at 4°C, followed by sequential washing with low salt, high salt, LiCl, and TE buffers for 10 minutes each at 4°C. Elution of the immunoprecipitated complexes was performed for 2 × 20 minutes at 65°C with elution buffer. Reverse cross-linking was carried out overnight at 65°C, followed by proteinase K treatment at 45°C for 5 hours. DNA was purified using phenol:chloroform:isoamyl alcohol 25:24:1 (Fisher Scientific) and precipitated with GlycoBlue (Invitrogen) and NaAc/EtOH overnight at -20°C. The purified DNA was resuspended in 75 μl of elution buffer. Libraries for sequencing were prepared using the Ovation Ultra Low System V2 1–16 kit (NuGEN) following the manufacturer's instructions. Libraries were sequenced in a HiSeq 2500asSE50reads.
Ovation Ultralow V2

value: Inflorescence

value: bdh1-1 BDH1-FLAG

tag: chip antibody

value: Anti-FLAG


title: ChIP_seq_BDH1-FLAG_rep1


title: SA_15h_3

description:
Salmonella were grown in PAS medium (with 10 μg mL^−1 gentamicin) at 25 °C for 15h.
SA15_3


title: ChIP_seq_WT

value: Wild type


title: SA_15h_1

description:
Salmonella were grown in PAS medium (with 10 μg mL^−1 gentamicin) at 25 °C for 15h.
SA15_1


title: RNAseq_ZT0_Q5A_Cohort2_Rep1


title: SA_8h_4

description:
Salmonella were grown in PAS medium (with 10 μg mL^−1 gentamicin) at 25 °C for 8h.
SA8_4

value: Salmonella-Acanthamoeb coculture 8h


title: KLtumors,vehicle,3weeks,rep9

city: Chicago

first: Lillian

middle: J

last: Eichner

state: IL

address: 303 E Superior St

department: Biochemistry and Molecular Genetics

institute: Northwestern University

description:
RNA-seq on KL GEMM tumors treated with vehicle
Veh_9_LJE9

data_processing:
Basecalls performed using RTA (Illumina)
Reads were aligned to the mouse genome (mm10) using STAR alignment tool (v2.5) for RNA-seq. In all cases, only reads that mapped to a unique genomic locations (MAPQ > 10) were used for downstream analysis.
For RNA-Seq, Reads Per Kilobase of exon per milion mapped reads were calculated using HOMER (http://homer.salk.edu/homer/) across annotated gene exons (RefSeq).
Assembly: mm10
Supplementary files format and content: tab delimited text file includes fpkm values for each sample

source_name: lung tumor

growth_protocol: Cell lines were incubated at 37ºC and maintained in 5% CO2. Cells were grown in DMEM + 10% fetal bovine serum

extract_protocol:
For RNA-seq, total RNA was isolated using Quick-RNA Miniprep Kit (Zymo Research).
RNA-Seq libraries were prepared using Illumina TruSeq RNA Library Prep Kit v2 following the manufacturer's instructions.

value: lung tumor

value: Kras-mutant, Lkb1-/-


title: RNAseq_ZT0_Q5A_Cohort1_Rep4


title: KLtumors,vehicle,3weeks,rep8

description:
RNA-seq on KL GEMM tumors treated with vehicle
Veh_8_LJE8


title: RNAseq_ZT0_Q5A_Cohort1_Rep3


title: H524-DMSO_1

description:
Gene_FPKM_uqnorm.txt
H524-DMSO_1

value: DMSO


title: H446-JIB-04_3

description:
Gene_FPKM_uqnorm.txt
H446-JIB-04_3


title: RNAseq_ZT0_Q5A_Cohort1_Rep2


title: SA_8h_3

description:
Salmonella were grown in PAS medium (with 10 μg mL^−1 gentamicin) at 25 °C for 8h.
SA8_3


title: KLtumors,vehicle,3weeks,rep7

description:
RNA-seq on KL GEMM tumors treated with vehicle
Veh_7_LJE7


title: SA_8h_2

description:
Salmonella were grown in PAS medium (with 10 μg mL^−1 gentamicin) at 25 °C for 8h.
SA8_2


title: H446-JIB-04_2

description:
Gene_FPKM_uqnorm.txt
H446-JIB-04_2


title: RNAseq_ZT0_Q5A_Cohort1_Rep1


title: KLtumors,vehicle,3weeks,rep6

description:
RNA-seq on KL GEMM tumors treated with vehicle
Veh_6_LJE6


title: H446-JIB-04_1

description:
Gene_FPKM_uqnorm.txt
H446-JIB-04_1


title: SA_8h_1

description:
Salmonella were grown in PAS medium (with 10 μg mL^−1 gentamicin) at 25 °C for 8h.
SA8_1


title: RNAseq_ZT0_H3.3_Cohort2_Rep1


title: KLtumors,vehicle,3weeks,rep5

description:
RNA-seq on KL GEMM tumors treated with vehicle
Veh_5_LJE5


title: RNAseq_ZT0_Q5A_Cohort2_Rep2


title: S_P4

description:
Free-living Salmonella were grown overnight in 10 mL LB, diluted 1:1000 into 10 mL LB, grown at 190 rpm and 37°C in a 50 mL tubes until the middle of the exponential growth phase (A600 = 0.4). Then bacteria were washed thrice in sterile PAS by centrifugation at 1200× g for 5 min at 25 °C and were grown for 2 h at 25 °C in sterile PAS.
PAS4

value: Poor medium


title: SA_15h_2

description:
Salmonella were grown in PAS medium (with 10 μg mL^−1 gentamicin) at 25 °C for 15h.
SA15_2


title: H524-DMSO_3

description:
Gene_FPKM_uqnorm.txt
H524-DMSO_3


title: H524-DMSO_2

description:
Gene_FPKM_uqnorm.txt
H524-DMSO_2


title: H446-DMSO_3

description:
Gene_FPKM_uqnorm.txt
H446-DMSO_3


title: RNAseq_ZT0_H3.3_Cohort1_Rep4


title: KLtumors,vehicle,3weeks,rep4

description:
RNA-seq on KL GEMM tumors treated with vehicle
Veh_4_LJE4


title: H446-DMSO_2

description:
Gene_FPKM_uqnorm.txt
H446-DMSO_2


title: S_P3

description:
Free-living Salmonella were grown overnight in 10 mL LB, diluted 1:1000 into 10 mL LB, grown at 190 rpm and 37°C in a 50 mL tubes until the middle of the exponential growth phase (A600 = 0.4). Then bacteria were washed thrice in sterile PAS by centrifugation at 1200× g for 5 min at 25 °C and were grown for 2 h at 25 °C in sterile PAS.
PAS3


title: H446-DMSO_1

description:
Gene_FPKM_uqnorm.txt
H446-DMSO_1


title: RNAseq_ZT0_H3.3_Cohort1_Rep3


title: S_P2

description:
Free-living Salmonella were grown overnight in 10 mL LB, diluted 1:1000 into 10 mL LB, grown at 190 rpm and 37°C in a 50 mL tubes until the middle of the exponential growth phase (A600 = 0.4). Then bacteria were washed thrice in sterile PAS by centrifugation at 1200× g for 5 min at 25 °C and were grown for 2 h at 25 °C in sterile PAS.
PAS2


title: KLtumors,vehicle,3weeks,rep3

description:
RNA-seq on KL GEMM tumors treated with vehicle
Veh_3_LJE3


title: KLtumors,vehicle,3weeks,rep2

description:
RNA-seq on KL GEMM tumors treated with vehicle
Veh_2_LJE2


title: RNAseq_ZT0_H3.3_Cohort1_Rep2


title: S_P1

description:
Free-living Salmonella were grown overnight in 10 mL LB, diluted 1:1000 into 10 mL LB, grown at 190 rpm and 37°C in a 50 mL tubes until the middle of the exponential growth phase (A600 = 0.4). Then bacteria were washed thrice in sterile PAS by centrifugation at 1200× g for 5 min at 25 °C and were grown for 2 h at 25 °C in sterile PAS.
PAS1


title: HCC4001-JIB-04_3

description:
Gene_FPKM_uqnorm.txt
HCC4001-JIB-04_3


title: RNAseq_ZT0_H3.3_Cohort1_Rep1


title: S_L4

description:
Free-living Salmonella culture in LB medium until the middle of the exponential growth phase (A600 = 0.4).
LB4

value: Control


title: KLtumors,trametinib,3weeks,rep8

description:
RNA-seq on KL GEMM tumors treated with trametinib
Tram_9_LJE27

value: 1mg/kg tram


title: RNAseq_ZT0_GFP_Cohort1_Rep4


title: S_L3

description:
Free-living Salmonella culture in LB medium until the middle of the exponential growth phase (A600 = 0.4).
LB3


title: KLtumors,vehicle,3weeks,rep1

description:
RNA-seq on KL GEMM tumors treated with vehicle
Veh_1_LJE1


title: HCC4001-JIB-04_2

description:
Gene_FPKM_uqnorm.txt
HCC4001-JIB-04_2


title: KLtumors,trametinib,3weeks,rep7

description:
RNA-seq on KL GEMM tumors treated with trametinib
Tram_8_LJE26


title: S_L2

description:
Free-living Salmonella culture in LB medium until the middle of the exponential growth phase (A600 = 0.4).
LB2


title: HCC4001-DMSO_3

description:
Gene_FPKM_uqnorm.txt
HCC4001-DMSO_3


title: RNAseq_ZT0_GFP_Cohort1_Rep2


title: RNAseq_ZT0_GFP_Cohort1_Rep3


title: HCC4001-JIB-04_1

description:
Gene_FPKM_uqnorm.txt
HCC4001-JIB-04_1


title: KLtumors,trametinib,3weeks,rep6

description:
RNA-seq on KL GEMM tumors treated with trametinib
Tram_7_LJE25


title: S_L1

description:
Free-living Salmonella culture in LB medium until the middle of the exponential growth phase (A600 = 0.4).
LB1


title: KLtumors,trametinib,3weeks,rep5

description:
RNA-seq on KL GEMM tumors treated with trametinib
Tram_6_LJE24


title: HCC4001-DMSO_2

description:
Gene_FPKM_uqnorm.txt
HCC4001-DMSO_2


title: RNAseq_ZT0_GFP_Cohort1_Rep1


title: 6h_Mock_4

city: Padua

first: Graziano

last: Martello

address: viale Colombo 3

department: Department of Biology

country: Italy

institute: University of Padua

data_processing:
Alignment was performed with STAR (v. 2.7.6a); STAR parameters were set following Lexogen guidelines for data analysis.
Quantification was performed with Subread package featureCounts (v. 2.0.1); featureCounts was used with default parameters.
Assembly: Homo sapiens: GRCh38.p13 Ensembl release 100; SARS-CoV-2: NC_045512.2
Supplementary files format and content: raw_counts_table.txt is a TSV containing official gene symbols, EnsemblID, reference genome and raw counts for each condition

growth_protocol: Calu-3 cells (ATCC®, HB-55) were maintained in Dulbecco's Modified Eagle Medium: Nutrient Mixture F-12 (DMEM/F-12, Thermo Fisher Scientific). Media were supplemented with 10% (v/v) fetal bovine serum (FBS, Thermo Fisher Scientific) and penicillin/streptavidin (Thermo Fisher Scientific). Cell cultures were maintained at 37°C and 5% CO2 in humidified atmosphere and routinely tested for mycoplasma contamination (Euroclone, Cat: EMK090020). For seeding and subcultivation, cells were first washed with phosphate buffered saline (PBS) and then incubated in the presence of trypsin/EDTA solution (Gibco, Thermo Fisher Scientific) until cells detached. Upon seeding of Calu-3 cells, 10 μM ROCK inhibitor Y27632 (Axon Medchem, Cat #1683) was added for 24 h to the culture medium.

extract_protocol:
Total RNA purified with Total RNA Purification Kit (NorgenBiotek, Canada, Cat #48400), following manufacturer’s protocol.
Quant Seq 3' mRNA-seq Library Prep kit (Lexogen) was used for library construction.

treatment_protocol: Calu-3 cells were seeded (1.2x105/well) in 12 well plate, and after 24 h the cell culture supernatant was removed and replaced with virus inoculum (MOI of 1 PFU/cell). Following 1 h adsorption at 37 °C, the virus inoculum was removed, the cell monolayer was washed in PBS prior to medium replacement (10% FBS DMEM/F-12). Cells were harvested at 6, 9, 12 and 24 hours post infection.

tag: disease

value: lung adenocarcinoma

value: 6 h.p.i

value: uninfected control


title: HCC4001-DMSO_1

description:
Gene_FPKM_uqnorm.txt
HCC4001-DMSO_1

value: SCLC

value: no

value: 24 hours


title: S_H4

description:
Free-living Salmonella culture were grown overnight in 10 mL LB, diluted 1:1000 into 10 mL LB, grown at 190 rpm and 37 °C in a 50 mL tubes until the middle of the exponential growth phase (A600 = 0.4) then H2O2 in the final concentration of 1 mM H2O2 for 10 min were added.
H2O2_4

value: Peroxide shock


title: RRBP5 LKO - Tunicamycin - R4

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

data_processing:
Low-quality reads were filtered using the tool Trimmomatic
Reads were aligned to the mouse reference genome mm10 by STAR aligner
RNA FPKM values were quantified by Cufflinks
Assembly: mm10
Supplementary files format and content: TAB
Supplementary files format and content: supplementary files are for the FPKM value quantified by Cufflinks

source_name: liver

extract_protocol:
Total mRNA was isolated from mouse liver with PureLink RNA mini kit (Life Technologies) with additional on-column DNase digestion step to remove genomic DNA per the manufacturer’s instructions
The library is constructed using Bio-Red kit as illustrated in The samples were indexed by Bio Rad SEQuoia Dual Indexed Primers, followed by circularization using the Element Biosciences Adept Library Compatibility Kit.

value: liver

value: RRBP5 LKO

value: Tunicamycin


title: RRBP5 LKO - Tunicamycin - R3


title: H2171-JIB-04_3

description:
Gene_FPKM_uqnorm.txt
H2171-JIB-04_3


title: S_H3

description:
Free-living Salmonella culture were grown overnight in 10 mL LB, diluted 1:1000 into 10 mL LB, grown at 190 rpm and 37 °C in a 50 mL tubes until the middle of the exponential growth phase (A600 = 0.4) then H2O2 in the final concentration of 1 mM H2O2 for 10 min were added.
H2O2_3


title: S_H2

description:
Free-living Salmonella culture were grown overnight in 10 mL LB, diluted 1:1000 into 10 mL LB, grown at 190 rpm and 37 °C in a 50 mL tubes until the middle of the exponential growth phase (A600 = 0.4) then H2O2 in the final concentration of 1 mM H2O2 for 10 min were added.
H2O2_2


title: KLtumors,trametinib,3weeks,rep3

description:
RNA-seq on KL GEMM tumors treated with trametinib
Tram_4_LJE22


title: H2171-JIB-04_2

description:
Gene_FPKM_uqnorm.txt
H2171-JIB-04_2


title: KLtumors,trametinib,3weeks,rep2

description:
RNA-seq on KL GEMM tumors treated with trametinib
Tram_3_LJE21


title: RRBP5 LKO - Tunicamycin - R2


title: H2171-JIB-04_1

description:
Gene_FPKM_uqnorm.txt
H2171-JIB-04_1


title: H2171-DMSO_3

description:
Gene_FPKM_uqnorm.txt
H2171-DMSO_3


title: RRBP5 LKO - Tunicamycin - R1


title: KLtumors,trametinib,3weeks,rep1

description:
RNA-seq on KL GEMM tumors treated with trametinib
Tram_1_LJE19


title: S_H1

description:
Free-living Salmonella culture were grown overnight in 10 mL LB, diluted 1:1000 into 10 mL LB, grown at 190 rpm and 37 °C in a 50 mL tubes until the middle of the exponential growth phase (A600 = 0.4) then H2O2 in the final concentration of 1 mM H2O2 for 10 min were added.
H2O2_1


title: SA_15h_5

description: Salmonella were grown in PAS medium (with 10 μg mL^−1 gentamicin) at 25 °C for 15h.

data_processing:
Demultiplexed reads were trimmed against adapters with bbduk (https://sourceforge.net/projects/bbmap/)
Reads were mapped to the A. castellanii genome (GenBank accession number GCA_000313135) and then mapped against the S. Typhimurium 14028s genome (GCA_000022165.1) (Jarvik et al., 2010) using STAR aligner v2.7.11a (Dobin et al., 2013) (https://github.com/alexdobin/STAR) with ‘--outFilterMultimapNmax 1’, ‘--sjdbGTFfeatureExon gene’, ‘--sjdbGTFtagExonParentTranscript gene_id’, ‘--sjdbGTFtagExonParentGene old_locus_tag’, ‘ --quantMode GeneCounts’.
The featureCounts v1.4.6-p5 function of Rsubread package version 2.14.2 (Liao et al., 2014) (http://subread.sourceforge.net) was used to quantitate the number of reads mapped to each gene.
Assembly: GCA_000022165.1
Supplementary files format and content: A tab-delimited text file includes general statistics on the library depth and read alignment.
Supplementary files format and content: A tab-delimited text file include DESeq normalized trnascript coverage values for each sample.

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. ATCC 14028

extract_protocol:
The Salmonella were collected by centrifugation. Total RNA was extracted using RNA Extract Reagent (Evrogen, Russia) according to the manufacturer's protocol. DNA contaminants were removed using RNase-free DNase I kit (Ambion, USA).
The integrity of the RNA was checked by Agilent 2100 bioanalyzer (USA). rRNA depletion performed using Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Illumina, USA). Barcoded RNA libraries were generated. NEBNext Ultra Directional RNA Library Prep Kit for Illumina was used to prepare RNA-seq libraries.

value: Salmonella-Acanthamoeb coculture 15h


title: RRBP5 LKO - Vehicle control - R4

value: Vehicle control


title: SA_15h_4


title: H2171-DMSO_2

description:
Gene_FPKM_uqnorm.txt
H2171-DMSO_2


title: H2171-DMSO_1

description:
Gene_FPKM_uqnorm.txt
H2171-DMSO_1


title: KLtumors,entinostat,3weeks,rep8

description:
RNA-seq on KL GEMM tumors treated with entinostat
Ent_8_LJE17

value: lung tumor

value: Kras-mutant, Lkb1-/-

value: 5mg/kg ent


title: KLtumors,trametinib,3weeks,rep4

description:
RNA-seq on KL GEMM tumors treated with trametinib
Tram_5_LJE23


title: SA_15h_3


title: RRBP5 LKO - Vehicle control - R3


title: KLtumors,entinostat,3weeks,rep6

description:
RNA-seq on KL GEMM tumors treated with entinostat
Ent_6_LJE15


title: KYSE510-siLIN00680

city: Xiamen

first: Jiancheng

last: Ding

state: Fujian

address: School of Pharmaceutical Sciences, Xiamen University Xiang`an South Road

country: China

institute: Xiamen University

data_processing:
Basecalling was performed using CASAVA version 1.4
Reads were aligned to the hg38 genome assembly using STAR.
Genome_build: hg38

source_name: esophagus

growth_protocol: The human ESCC cell lines (KYSE140, KYSE510) were preserved by our laboratory for years and were maintained in RPMI 1640 (Biological Industries) medium with 10% fetal bovine serum (Biological Industries) and 1% penicillin/streptomycin mixture (Biological Industries) as supplements. All cell lines were cultured in a humidified incubator containing 5% CO2 at 37 °C.

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen) following the manufacturer’s protocol.DNase I in column digestion was included to ensure the RNA quality.
RNA library preparation was performed by using NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina .Paired-end sequencing was performed with Illumina NovaSeq 6000.

treatment_protocol: Lipofectamine™2000 reagent (Invitrogen, USA) was used to transfect siRNAs according to the manufacturer’s instructions.

tag: condition


title: RRBP5 LKO - Vehicle control - R2


title: RRBP5 LKO - Vehicle control - R1


title: KLtumors,entinostat,3weeks,rep5

description:
RNA-seq on KL GEMM tumors treated with entinostat
Ent_5_LJE14


title: WT - Tunicamycin - R3

value: WT


title: SA_8h_5

description: Salmonella were grown in PAS medium (with 10 μg mL^−1 gentamicin) at 25 °C for 8h.

value: Salmonella-Acanthamoeb coculture 8h


title: KLtumors,entinostat,3weeks,rep4

description:
RNA-seq on KL GEMM tumors treated with entinostat
Ent_4_LJE13


title: SA_15h_1


title: KYSE140-siLIN00680


title: KYSE510-siCTL

value: siCTL


title: SA_8h_4


title: KLtumors,entinostat,3weeks,rep3

description:
RNA-seq on KL GEMM tumors treated with entinostat
Ent_3_LJE12


title: patient10-tumor

value: tumor


title: KLtumors,entinostat,3weeks,rep2

description:
RNA-seq on KL GEMM tumors treated with entinostat
Ent_2_LJE11


title: SA_8h_3


title: SA_8h_2


title: SA_15h_2


title: KLtumors,entinostat,3weeks,rep1

description:
RNA-seq on KL GEMM tumors treated with entinostat
Ent_1_LJE10


title: KLtumors,combination,3weeks,rep9

description:
RNA-seq on KL GEMM tumors treated with trametinib and entinostat
Combo_9_LJE36

value: 5mg/kg ent + 1mg/kg tram


title: WT - Vehicle control - R2


title: patient10-normal

value: normal


title: S_P4

description: Free-living Salmonella were grown overnight in 10 mL LB, diluted 1:1000 into 10 mL LB, grown at 190 rpm and 37°C in a 50 mL tubes until the middle of the exponential growth phase (A600 = 0.4). Then bacteria were washed thrice in sterile PAS by centrifugation at 1200× g for 5 min at 25 °C and were grown for 2 h at 25 °C in sterile PAS.

value: Poor medium


title: patient9-tumor


title: KLtumors,combination,3weeks,rep8

description:
RNA-seq on KL GEMM tumors treated with trametinib and entinostat
Combo_8_LJE35


title: WT - Vehicle control - R1


title: SA_8h_1


title: WT - Tunicamycin - R2


title: patient9-normal


title: KLtumors,entinostat,3weeks,rep7

description:
RNA-seq on KL GEMM tumors treated with entinostat
Ent_7_LJE16


title: patient8-tumor


title: KLtumors,combination,3weeks,rep7

description:
RNA-seq on KL GEMM tumors treated with trametinib and entinostat
Combo_7_LJE34


title: KLtumors,combination,3weeks,rep6

description:
RNA-seq on KL GEMM tumors treated with trametinib and entinostat
Combo_6_LJE33


title: Glu_PrrC170_rep1

city: Shinjuku-ku

first: Aa

middle: Haeruman

last: Azam

state: Tokyo

address: Toyama 1-23-1

department: Research Center for Therapeutic Drugs and Vaccines Development

country: Japan

institute: The National Institute of Infectious Diseases

data_processing:
Sequencing quality was examined by FastQC v0.11.7 software
3' adapter was trimmed from raw reads by cutadapt ver 1.17
Trimmed reads were aligned to the cytoplasmic mature-tRNA sequences getting from GtRNAdb and the mitocondrial mature-tRNA sequences from mitotRNAdb using BWA (0.7.12-r1039) software (maximum mismatch was set to 2).
The tRNAs expression profiling was calculated based on uniquely mapped reads and including mapped reads, respectively. The differentially expressed tRNAs were screened based on the count value with R package edgeR (3.5.1)
Assembly: the cytoplasmic mature-tRNA sequences (GtRNAdb) and the mitocondrial mature-tRNA sequences (mitotRNAdb)
Supplementary files format and content: unique read count file (XLSX format)

organism: Escherichia coli

source_name: bacterial cell

growth_protocol: An overnight culture of E. coli DH10B harboring plasmid with PrrC170 toxin was inoculated into 10 ml LB supplemented with chloramphenicol (20 μg/ml) until OD600 0.3.

extract_protocol:
Total RNA was extracted using miRNA isolation kit (QIAGEN, catalog number 217004), according to the manufacturer’s recommendation. Over 2g total RNA was resolved on Urea-PAGE and recovered within a size window of 60-100 nt for tRNA. Thereafter, purified tRNA was demethylated, alkaline-hydrolyzed by carbonate buffer, dephosphorylated by calf intestinal phosphatase (CIP), and re-phosphorylated by T4 polynucleotide kinase (T4 PNK).
Fragments of 19-35nt for partially hydrolyzed and re-phosphorylated tRNA were converted to small RNA sequencing libraries using NEBNext Multiplex Small RNA Library Prep Set for Illumina kit.
tRNA-seq

treatment_protocol: The bacteria were then induced with 0.2% arabinose (to induce PrrC170 expression) or 0.2% glucose (to repress PrrC170 expression) and cultured for 1h at 37°C with shaking at 200 rpm.  Following incubation, the culture was centrifuged at 6000 g for 5 minutes, and the pellet was washed twice with PBS buffer.

value: bacterial cell

value: early stationary (OD600 = 1.0)

value: treated with 0.2% glucose


title: patient8-normal


title: KYSE140-siCTL


title: S_P2


title: WT - Vehicle control - R3

value: liver


title: WT - Tunicamycin - R1

value: Tunicamycin


title: Ara_PrrC170_rep2

value: treated with 0.2% arabinose


title: S_P1


title: KLtumors,combination,3weeks,rep5

description:
RNA-seq on KL GEMM tumors treated with trametinib and entinostat
Combo_5_LJE32


title: KLtumors,entinostat,3weeks,rep9

description:
RNA-seq on KL GEMM tumors treated with entinostat
Ent_9_LJE18


title: S_L4

description: Free-living Salmonella culture in LB medium until the middle of the exponential growth phase (A600 = 0.4).

value: Control


title: patient7-normal


title: KLtumors,combination,3weeks,rep4

description:
RNA-seq on KL GEMM tumors treated with trametinib and entinostat
Combo_4_LJE31

value: lung tumor


title: Ara_PrrC170_rep1


title: Glu_PtuAB83_rep 2

growth_protocol: An overnight culture of E. coli DH10B harboring plasmid with PtuAB was inoculated into 10 ml LB supplemented with chloramphenicol (20 μg/ml) until OD600 0.3.

treatment_protocol: The bacteria were then induced with 0.2% arabinose (to induce PtuAB expression) or 0.2% glucose (to repress PtuAB expression) and cultured for 1h at 37°C with shaking at 200 rpm.  Following incubation, the culture was centrifuged at 6000 g for 5 minutes, and the pellet was washed twice with PBS buffer.


title: KLtumors,combination,3weeks,rep3

description:
RNA-seq on KL GEMM tumors treated with trametinib and entinostat
Combo_3_LJE30

value: Kras-mutant, Lkb1-/-


title: Glu_PrrC170_rep2


title: S_P3


title: Glu_PtuAB83_rep1


title: KLtumors,combination,3weeks,rep2

description:
RNA-seq on KL GEMM tumors treated with trametinib and entinostat
Combo_2_LJE29


title: Ara_PtuAB83_rep2


title: S_L3


title: patient6-normal


title: patient5-normal


title: patient5-tumor


title: S_H4

description: Free-living Salmonella culture were grown overnight in 10 mL LB, diluted 1:1000 into 10 mL LB, grown at 190 rpm and 37 °C in a 50 mL tubes until the middle of the exponential growth phase (A600 = 0.4) then H2O2 in the final concentration of 1 mM H2O2 for 10 min were added.

value: Peroxide shock


title: Ara_PtuAB83_rep1


title: KLtumors,combination,3weeks,rep1

description:
RNA-seq on KL GEMM tumors treated with trametinib and entinostat
Combo_1_LJE28


title: patient7-tumor


title: SK-N-BE, mutant (+13-Ala), 17-AAG, rep3

city: Genoa

first: Paolo

last: Uva

address: Via Gerolamo Gaslini, 5

institute: IRCCS Istituto Giannina Gaslini

data_processing:
Sequence reads were trimmed for adapter sequence/low-quality sequence using Trim Galore! (parameter - quality: 20)
Trimmed sequence reads were aligned to Ensembl transcripts (Homo_sapiens.GRCh38.cdna.all.fa.gz) and read counts were extracted using kallisto with default parameters
Read counts were summarized at gene level and normalized using DeSeq2 R package
Assembly: hg38
Supplementary files format and content: rlog nomalized values for each sample

source_name: SK-N-BE

growth_protocol: Human neuroblastoma SK-N-BE cells were plated in 35mm diameter dishes in triplicate and plasmids pcDNA3.1Myc-PHOX2B WT or pcDNA3.1Myc-(+13Ala) were transfected

extract_protocol:
Total RNA was extracted and purified with RNeasy Plus mini kit (Qiagen) and RNA samples thus obtained were quantified by NanoDrop
RNA libraries were prepared using TruSeq Stranded mRNA (TruSeq RNA-Seq v2) Library Preparation Kit following manufacturer's protocols.

treatment_protocol: At 24hrs, cells were treated with 17-AAG 300nM, or left untreated, and 24 hrs later RNAs were extracted from cell cultures for transcriptome analysis.

value: SK-N-BE

tag: genetic modification

value: mutant (+13Ala)


title: LJE1cells,NT,rep3

description:
RNA-seq on KL LJE1 cells transduced with sgNT
NT_R3_LJE18

value: Immortalized cell line derived from Kras-mutant, Lkb1-/- NSCLC lung tumor


title: patient4-normal


title: LJE1cells,NT,rep2

description:
RNA-seq on KL LJE1 cells transduced with sgNT
NT_R2_LJE17


title: SK-N-BE, mutant (+13-Ala), 17-AAG, rep2


title: S_H3


title: S_H2


title: patient4-tumor

value: tumor


title: LJE1cells,NT,rep1

description:
RNA-seq on KL LJE1 cells transduced with sgNT
NT_R1_LJE16


title: SK-N-BE, mutant (+13-Ala), 17-AAG, rep1


title: patient3-normal


title: S_H1


title: LJE1cells,p65sg2,rep3

description:
RNA-seq on KL LJE1 cells transduced with p65 sg2
p65g2_R3_LJE24

value: Kras-mutant, Lkb1-/-, p65-/-


title: patient6-tumor


title: S_L2


title: SK-N-BE, mutant (+13Ala), DMSO, rep3

value: vehicle (DMSO)


title: Rpb1-MNase, YPD, Input, Replicate 3

city: Evanston

first: Jason

last: Brickner

address: Hogan 1-500, 2205 Tech Drive

data_processing:
mapped with bowtie2.  Coverage counts were normalized for library size (CPM)
Supplementary files format and content: bigwig files contain CPM normalized coverage counts.  Repetitive regions are masked.
Assembly: S288C, R64.3.1

organism: Saccharomyces cerevisiae

extract_protocol:
Immunoprecipitation with Anti-Rpb1 (Clone 8WG16)
Diagenode MicroPlex Library Preparation Kit v3.  Illumina Nextera XT index adapters sequences

value: MATa his3delta1 leu2delta0 ura3delta0 met15delta0 RBP1-3FLAG-MNase:kanMX6


title: LJE1cells,p65sg2,rep2

description:
RNA-seq on KL LJE1 cells transduced with p65 sg2
p65g2_R2_LJE23


title: patient3-tumor


title: patient2-tumor


title: S_L1


title: SK-N-BE, mutant (+13Ala), DMSO, rep2


title: LJE1cells,p65sg2,rep1

description:
RNA-seq on KL LJE1 cells transduced with p65 sg2
p65g2_R1_LJE22


title: Rpb1-MNase, YPD, Input, Replicate 2


title: Rpb1-MNase, YPD, Input, Replicate 1


title: SK-N-BE, mutant (+13Ala), DMSO, rep1


title: LJE1cells,p65sg1,rep2

description:
RNA-seq on KL LJE1 cells transduced with p65 sg1
p65g1_R2_LJE20


title: patient2-normal

value: normal


title: BY4741, YPD, Input, Replicate 2

value: MATa his3delta1 leu2delta0 ura3delta0 met15delta0


title: SK-N-BE, wt, 17-AAG, rep3

value: wt


title: LJE1cells,p65sg1,rep3

description:
RNA-seq on KL LJE1 cells transduced with p65 sg1
p65g1_R3_LJE21


title: BY4741, YPD, Input, Replicate 3


title: patient1-tumor


title: SK-N-BE, wt, 17-AAG, rep1


title: IRI with MK8617 3

city: Guangzhou

first: Liting

last: Chen

state: Guangdong

address: 1838 North Guangzhou Blvd.

department: Division of Nephrology

institute: Nanfang Hospital, Southern Medical University

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts..In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

source_name: kidney

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: kidney

value: WT

value: IRI with MK8619


title: bdh_rep3

data_processing:
Reads were aligned to the TAIR10 genome using STAR v2.7.10b.
Gene counts were obtained using the featureCounts command from subread 2.0.3 with options -p --countReadPairs -Q 5 and providing the Araport11 annotation.
Differential expression analyses were carried out using DESeq2 v1.38.
Assembly: TAIR10
Supplementary files format and content: tab-delimited file of raw counts
Supplementary files format and content: tab-delimited file of differential expression analysis

source_name: 5-day etiolated seedlings

growth_protocol: Arabidopsis seedlings grown in 1/2 MS plates for 5 days in darkness at 22 degrees

extract_protocol:
Total RNA from etiolated seedlings of Col-0 and bdh.
Libraries for sequencing were prepared at BGI following the strand-specific mRNA libraries protocol for DNBSEQ platform.

value: 5-day etiolated seedlings

value: bdh1-1 bdh2-1


title: SK-N-BE, wt, 17-AAG, rep2


title: bdh_rep2


title: LJE1cells,p65sg1,rep1

description:
RNA-seq on KL LJE1 cells transduced with p65 sg1
p65g1_R1_LJE19


title: SK-N-BE, wt, DMSO, rep2


title: SK-N-BE, wt, DMSO, rep3


title: Rpb1-MNase, YPD,  IP, Replicate 3


title: IRI with MK8617 2

value: IRI with MK8618


title: SK-N-BE, wt, DMSO, rep1


title: Rpb1-MNase, YPD,  IP, Replicate 2


title: bdh_rep1


title: IRI with MK8617 1

value: IRI with MK8617


title: IRI 3

value: IRI


title: Rpb1-MNase, YPD,  IP, Replicate 1


title: WT_rep3

value: Wild type


title: Med8-MNase, SDC, Replicate 3

data_processing:
mapped with bowtie2.  Coverage counts were limited to the first base sequenced and normalized for library size (CPMn)
Supplementary files format and content: bigwig files contain CPMn noramlized coverage counts.  Repetitive regions are masked.
Assembly: S288C, R64.3.1
Library strategy: ChEC-seq2

extract_protocol:
Proteinase K digestion and phenol-choloroform extraction
Ligation and tagmentation.  Illumina Nextera XT index adapters sequences

value: MATa his3delta1 leu2delta0 ura3delta0 met15delta0 MED8-3FLAG-MNase:kanMX6


title: WT_rep2


title: patient1-normal


title: BY4741, YPD, IP, Replicate 3


title: Med8-MNase, SDC, Replicate 2


title: IRI 2


title: BY4741, YPD, Input, Replicate 1


title: WT_rep1


title: Med8-MNase, SDC, Replicate 1


title: BY4741, YPD, IP, Replicate 1


title: IRI 1


title: mMAC1 B

status: Public on Oct 09 2024

city: Badalona, Barcelona

first: Esteban

last: Ballestar

state: N/A = Not Applicable

address: Ctra de Can Ruti, Camí de les Escoles s/n

institute: Josep Carreras Research Institute (IJC)

description: LPS-activated macrophage at 1%O2

data_processing:
Fastq files were quality controlled with fastqc (v0.11.9) and multiqc (v1.0).
Fastq files were pseudoaligned to GRCh38 and quantified using Kallisto (v0.44)
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files include raw counts values for each sample.

source_name: peripheral blood

growth_protocol: Peripheral blood monocytes were purified using CD14 magnetic-activated cell sorting (MACS © MicroBeads, Miltenyi Biotec) and cultured in RPMI 1640 in the presence of 15ng/mL macrophage colony-stimulating factor (M-CSF) for 5 days in normoxia (21% O2) or hypoxia (1% O2). Cells were further stimulated with 10 ng/mL of lypopolysaccharide (LPS) or with PBS for 48h additional hours.

extract_protocol:
Total RNA was extracted and purified from monocytes or macrophages using the Maxwell RSC Cell DNA kit (Promega) according to standard instructions
RNA libraries for RNA-seq were prepared using the DNBseq Eukaryotic Strand-specific Transcriptome Resequencing protocol (P_Stranded Library/Seq (PE100))

value: peripheral blood

value: Monocyte-derived macrophage

tag: donor

value: B

tag: age

tag: Sex

value: F


title: mMAC1 C

description: LPS-activated macrophage at 1%O2

tag: cell type

value: C

value: M


title: iMAC1 D

description: Unstimulated macrophage at 1%O2

value: D


title: mMAC1 D

description: LPS-activated macrophage at 1%O2


title: mMAC1 A

description: LPS-activated macrophage at 1%O2

value: A


title: iMAC1 C

description: Unstimulated macrophage at 1%O2


title: mMAC21 B

description: LPS-activated macrophage at 21%O2


title: iMAC1 B

description: Unstimulated macrophage at 1%O2


title: iMAC21 C

description: Unstimulated macrophage at 21%O2


title: mMAC21 D

description: LPS-activated macrophage at 21%O2


title: mMAC21 A

description: LPS-activated macrophage at 21%O2


title: iMAC1 A

description: Unstimulated macrophage at 1%O2


title: BY4741, YPD, IP, Replicate 2

tag: cell line

value: MATa his3delta1 leu2delta0 ura3delta0 met15delta0


title: MO D

description: Blood monocytes (CD14+)

value: MO

value: Monocyte (CD14+)


title: MO A

description: Blood monocytes (CD14+)


title: iMAC21 A

description: Unstimulated macrophage at 21%O2


title: MO B

description: Blood monocytes (CD14+)


title: BLCA_Pall_261

type: RNA

city: Lund

first: Gottfrid

last: Sjodahl

address: Medicon Village

department: Department of Translational Medicine

country: Sweden

institute: Lund Univeristy

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

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Raw data from RMA was quantile normalized, adjusted for labeling batch using ComBat, and merged by median probe set values per gene symbol.
Platform design info was retrieved via bioconductor: pd.hugene.1.0.st.v1

label: biotin

source_name: FFPE tissue specimen

label_protocol: GeneChip WT Pico kit.

extract_protocol: Total RNA was extracted using the HighPure FFPET kit (Roche)

tag: labeling kit

value: GeneChip WT Pico kit

tag: labeling batch

tag: clinical tnm staging

tag: lundtax ihc subtype

value: BASQ

tag: lundtax rna subtype

tag: mibc consensus subtype

tag: previous curative treatment

value: No

tag: regimen type

value: Other

tag: ecog ps

tag: response

value: PR


title: MO C

description: Blood monocytes (CD14+)

tag: tissue

tag: condition


title: BLCA_Pall_260

value: Uro

value: UroA

value: LumP

value: GemCis


title: BLCA_Pall_246

value: UroC

value: LumNS


title: BLCA_Pall_234

value: MVAC


title: mMAC21 C

description: LPS-activated macrophage at 21%O2

value: peripheral blood

value: Monocyte-derived macrophage

tag: donor

value: C

value: M


title: BLCA_Pall_222

value: MES

value: Mes

value: SD


title: BLCA_Pall_228

value: GeneChip WT Pico kit

value: BASQ

value: Yes

value: PD


title: BLCA_Pall_213

value: GU

value: LumU

value: No

value: PR


title: BLCA_Pall_231

value: GemCis


title: BLCA_Pall_196


title: BLCA_Pall_202

value: CR


title: iMAC21 D

description: Unstimulated macrophage at 21%O2

value: peripheral blood

value: D

tag: age

value: F


title: BLCA_Pall_188

value: Uro

value: UroC

value: LumP

value: MVAC


title: BLCA_Pall_191

value: GeneChip WT Pico kit


title: BLCA_Pall_167

value: LumNS


title: BLCA_Pall_195

value: UroB

value: StromaRich

value: GemCarbo


title: BLCA_Pall_176

value: GU

value: PD


title: BLCA_Pall_198

value: No

value: PR


title: iMAC21 B

description: Unstimulated macrophage at 21%O2

value: Monocyte-derived macrophage

value: B

tag: Sex


title: BLCA_Pall_158

value: Yes

value: Other


title: BLCA_Pall_270

value: BASQ


title: tah-1_3

city: Tianjin

first: Jinyang

last: Li

address: No. 32, Xiqi Road, Tianjin Airport Economic Park

institute: Chinese Academy of Sciences

description: mRNA of the Δtah-1 mutant grown on lignosulfonate for 4 day, sample 3

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp v0.19.5.
Clear reads were mapped to Curvularia clavata YC1106 genome using HISAT2 (v2.1.0) with parameters --dta --phred64 unstranded --new-summary -x index -1 read_r1 -2 read_r2（PE).
The counts of reads uniquely mapped to only one gene for each gene were calculated by RSEM (v1.3.3) with default parameters.
The normalized expression values for each gene were calculated by the number of uniquely mapped transcripts per million (TPM) and differential gene expression was determined by DESeq2 package.
Assembly: ASM2392016v1
Supplementary files format and content: Tab-delimited text files include FPKM values for each sample

organism: Curvularia clavata

source_name: Mycelia

growth_protocol: Mycelia from the C. clavata strains were inoculated into 100 mL of Vogel’s minimal medium supplemented with 2% (w/v) glucose (MMG) or 2% lignosulfonate and 0.25% glucose (MML). The culture was incubated at 30°C with continuous shaking at 200 rpm for 4 days.

extract_protocol:
Total RNA from frozen samples was isolated using TRIzol reagent and an additional clean-up was performed for DNA degradation using the RNeasy mini kit (Qiagen).
RNA libraries for RNA-seq were prepared using standard Illumina protocols.

value: Mycelia

tag: strain

tag: genotype

tag: time

value: 4 day

tag: treatment

value: Lignosulfonate


title: tah-1_2

description: mRNA of the Δtah-1 mutant grown on lignosulfonate for 4 day, sample 2


title: rpn-4_3

description: mRNA of the Δrpn-4 mutant grown on lignosulfonate for 4 day, sample 3


title: Pa03c_Normoxia_0.5percentFBS_rep1

city: Baltimore

first: Peter

last: Espenshade

state: Maryland

address: 725 N Wolfe Street, Physiology 107

department: Cell Biology

institute: Johns Hopkins University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were quantile normalized and background corrected using the neqc function as implemented in the limma package in R

source_name: Pa03c Patient derived PDAC cell line

label_protocol: Biotinylated cRNA were prepared with the Ambion Total prep RNA amplification kit for Illumina arrays

growth_protocol: Cells were grown in DMEM 4.5 g/L glucose, L-glutamine, and sodium pyruvate] supplemented with and 1,000 U/mL penicillin-streptomycin, with different amount of FBS (as detailed in treatment protocol) in a 37 C CO2 incubator.

extract_protocol: Total RNA was isolated using Amsbio RNA Stat-60 reagent following manufacturer’s protocol.

treatment_protocol: Cells were grown in, either 0.5% FBS (treatment) or 10% FBS (control) for 16 h.

value: Pancreas

tag: metastasis site

value: Liver

value: 0.5% FBS (treatment) for 16hrs


title: tah-1_1

description: mRNA of the Δtah-1 mutant grown on lignosulfonate for 4 day, sample 1


title: BLCA_Pall_239

tag: labeling kit

value: GeneChip WT Pico kit

tag: labeling batch

tag: clinical tnm staging

tag: lundtax ihc subtype

value: ScNE

value: StromaRich

value: MVAC


title: BLCA_Pall_224

value: GU

tag: lundtax rna subtype

tag: mibc consensus subtype

value: LumU

tag: previous curative treatment

tag: regimen type

value: GemCis

value: CR


title: Pa03c_Normoxia_10percentFBS_rep1

tag: tissue

value: 10% FBS (control) for 16 hrs


title: rpn-4_1

description: mRNA of the Δrpn-4 mutant grown on lignosulfonate for 4 day, sample 1


title: WT_L_2

description: mRNA of the WT strain grown on lignosulfonate for 4 day, sample 2

value: WT


title: CclaeA_3

description: mRNA of the ΔCclaeA mutant grown on lignosulfonate for 4 day, sample 3

value: {delta}CclaeA


title: WT_L_3

description: mRNA of the WT strain grown on lignosulfonate for 4 day, sample 3

value: Mycelia


title: CclaeA_1

description: mRNA of the ΔCclaeA mutant grown on lignosulfonate for 4 day, sample 1

value: 4 day


title: rpn-4_2

description: mRNA of the Δrpn-4 mutant grown on lignosulfonate for 4 day, sample 2

value: Lignosulfonate


title: WT_G_2

description: mRNA of the WT strain grown on glucose for 4 day, sample 2

value: Glucose


title: WT_L_1

description: mRNA of the WT strain grown on lignosulfonate for 4 day, sample 1


title: WT_G_1

description: mRNA of the WT strain grown on glucose for 4 day, sample 1


title: WT_G_3

description: mRNA of the WT strain grown on glucose for 4 day, sample 3


title: CclaeA_2

description: mRNA of the ΔCclaeA mutant grown on lignosulfonate for 4 day, sample 2


title: vpsT_active_QrgB_30min_s2_RNA

city: Ann Arbor

first: Lydia

last: Freddolino

state: MI

address: 1136 Catherine St

department: Biological Chemistry

institute: University of Michigan

data_processing:
Adapter trimming, pseudo-alignment with kallisto, DE estimation using sleuth
Assembly: CP064350.1, CP064351.1, pBRP02
Supplementary files format and content: tsv files contain results of running differential expression analysis. Bedgraph files contain cpm for each of the minus and plus strands.

organism: Vibrio cholerae C6706

source_name: Bacterial culture

growth_protocol: For each biological replicate of each genotype, cells were grown in LB supplemented with a final concentration of 100 μg/ml ampicillin. Overnight cultures were diluted to an OD600 = 0.05 in 500 mL of LB pre-warmed to 35°C containing 100 μg/ml ampicillin. Cultures were incubated at 35°C with constant shaking to an OD600 = 1.0, at which time the 0 minute time point aliquots were collected. 200 μL of culture was mixed with 1 mL of DNA/RNA shield (Zymo Research Corporation) to be used for RNA extraction and 100 mL of culture was moved into a pre-warmed 250 mL flask containing sufficient rifampin to achieve final concentration of 75 μg/ml. IPTG was added to the remaining 400 mL of original culture to a final concentration of 1 mM. At 15, 30, and 60 minutes after IPTG addition, aliquots of culture were moved to DNA/RNA shield or a pre-warmed 250 mL flask containing rifampin as described above. For each timepoint, rifampin treatment was allowed to proceed under conditions of constant shaking at 35°C for 10 minutes, at which time 40mL of rifampin-treated culture was added to each of two 50 mL conical tubes containing 1080 μL of fresh formaldehyde. Crosslinking proceeded for 5 minutes at room temperature with constant shaking, at which time 8 mL of 2M glycine was added to quench excess formaldehyde. Tubes were incubated for 10 minutes at room temperature with constant shaking, placed on ice for 10 minutes, then cells were collected by centrifugation at 4°C. Twice, pellets were resuspended in 10 mL cold PBS and cells were collected by centrifugation at 4°C. A final resuspension of pellets was performed via addition of 400 μL of cold PBS and suspensions were split to three 1.8 mL tubes. Cells were collected via centrifugation for 5 minutes at 4°C, 10,000 x g. The supernatant was aspirated and pellets were flash frozen in an ethanol-dry ice bath, then stored at -80°C.

extract_protocol:
Total nucleic acid was extracted from cells, which had been lysed and preserved in DNA/RNA Shield and stored at -80°C, using an RNA Clean & Concentrator-96 kit (Zymo Research Corporation). Briefly, 300 μL of cell lysate was added to tubes containing 600 μL of RNA binding buffer and 900 μL of 100% ethanol, and vortexed. Each sample was bound to a filter (one well) of a 96 well spin column plate 700 μL at a time until all of the sample was bound. Washes were performed per manufacturer's protocol. Samples were eluted using 25 μL of water. DNA was removed by digestion with Baseline-ZERO DNase (LGC Biosearch Technologies). All of the samples (~23 μL each) were added to DNA lo-bind tubes containing 60 μL of water and 10 μL of 10X Baseline-ZERO DNase Buffer. After vortexing, 2 μL of  Murine RNase Inhibitor (NEB) and 5 μL of Baseline-ZERO DNase were added to each sample. After gentle mixing, tubes were incubated 37°C for 30 min. Reactions were cleaned again using a Zymo RNA Clean and Concentrate Kit-96 (Zymo Research) according to the manufacturer’s instructions, and eluted with 25 μL of water]. The QuantiFluor RNA System (Promega) was used to determine RNA concentration of samples. For each sample, 0.5 µg of RNA was diluted to 11 µL and used as input material for NEBNext rRNA Depletion Kit for Bacteria ( NEB). Depletion was performed per kit directions.
Library preparation was performed using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB) per kit directions for intact RNA (15 min fragmentation) except that diluted (1:100)  NEBNext Unique Dual Index UMI Adaptors DNA Set 1 were used instead of the NEBNext Adaptor for Illumina.

tag: cell type

value: Bacterial culture

value: vpsT KO, vpsL KO

value: 30 minutes inducing active QrgB


title: vpsT_active_QrgB_00min_s1_RNA

value: 00 minutes inducing active QrgB


title: vpsT_active_QrgB_60min_s1_RNA

value: 60 minutes inducing active QrgB


title: vpsT_active_QrgB_30min_s1_RNA


title: vpsT_active_QrgB_60min_s2_RNA


title: vpsT_inactive_QrgB_60min_s2_RNA

value: 60 minutes inducing inactive QrgB


title: vpsT_active_QrgB_00min_s2_RNA


title: vpsT_inactive_QrgB_60min_s1_RNA


title: vpsT_inactive_QrgB_30min_s2_RNA

value: 30 minutes inducing inactive QrgB


title: vpsT_active_QrgB_15min_s1_RNA

value: 15 minutes inducing active QrgB


title: vpsT_inactive_QrgB_15min_s1_RNA

value: 15 minutes inducing inactive QrgB


title: vpsT_inactive_QrgB_00min_s2_RNA

value: 00 minutes inducing inactive QrgB


title: vpsT_inactive_QrgB_30min_s1_RNA


title: vpsT_inactive_QrgB_15min_s2_RNA


title: vpsR_active_QrgB_60min_s1_RNA

value: vpsR KO, vpsL KO


title: vpsR_active_QrgB_30min_s2_RNA


title: vpsR_active_QrgB_30min_s1_RNA


title: vpsR_active_QrgB_15min_s2_RNA


title: vpsR_active_QrgB_00min_s1_RNA


title: vpsT_inactive_QrgB_00min_s1_RNA


title: vpsR_inactive_QrgB_60min_s2_RNA


title: vpsR_inactive_QrgB_30min_s2_RNA


title: vpsR_inactive_QrgB_60min_s1_RNA


title: vpsR_active_QrgB_00min_s2_RNA


title: vpsR_inactive_QrgB_15min_s2_RNA


title: vpsR_inactive_QrgB_15min_s1_RNA


title: vpsR_inactive_QrgB_30min_s1_RNA


title: vpsR_inactive_QrgB_00min_s1_RNA


title: vpsR_inactive_QrgB_00min_s2_RNA


title: wt_active_QrgB_30min_s2_RNA

value: vpsL KO


title: wt_active_QrgB_60min_s2_RNA


title: wt_active_QrgB_15min_s2_RNA


title: wt_active_QrgB_30min_s1_RNA


title: wt_active_QrgB_00min_s2_RNA


title: vpsR_active_QrgB_60min_s2_RNA


title: wt_inactive_QrgB_30min_s2_RNA


title: wt_inactive_QrgB_15min_s1_RNA


title: wt_inactive_QrgB_60min_s2_RNA


title: wt_active_QrgB_00min_s1_RNA


title: wt_inactive_QrgB_60min_s1_RNA


title: wt_inactive_QrgB_15min_s2_RNA


title: vpsT_active_QrgB_60min_s1_chip

data_processing:
Adapter trimming, alignment, fragment counting at 5-bp resolution
Assembly: CP064350.1, CP064351.1, pBRP02
Supplementary files format and content: Count bigwig files contain fragment counts for each sample at 5bp resolution.

extract_protocol:
Crosslinked cell pellets were resuspended in 630 μL of lysis buffer [10 mM Tris pH 8.0, 1x cOmplete™, EDTA-free Protease Inhibitor Cocktail (Roche), 50 mM NaCl, 52 units/mL Ready-Lyse (Epicentre)] and incubated 15 minutes at 30°C. Samples were placed on ice, then sonicated in ice bath at 25% amplitude for 20 seconds (5 seconds on, 5 seconds off). To each sample, 5.4 μL of 100 mM MnCl2, 4.5 μL 100 mM CaCl2, 12 μL of RNase A (10mg/mL) and 12 μL of DNase I (Fisher) was added and mixed. Samples were incubated on ice for 30 minutes before 50 μL of 500 mM EDTA was mixed in to stop DNase I digestion. Samples were clarified by centrifugation (16k r.c.f.,10 minutes, 4°C), then liquid was split into new microfuge tubes (50 μL for input; 350 μL for RNA polymerase ChIP; ~ 325 μL for other purposes). To each input sample, 450 μL of ChIP elution buffer (50 mM Tris pH 8.0, 10mM EDTA pH 8.0, 1% SDS) was added and mixed in. Inputs were maintained on ice until (at end of day) placed at 65C for 12 hours to reverse cross-links.After reversal of cross-links, all sample types were digested for 2 hours with RNaseA (100mg/sample) and then 2 hours with proteinase K (200mg/sample). This was followed by phenol/chloroform extraction [add 500μL of phenol/chloroform/isoamyl alcohol (25:24:1), mix, separate layers (2 minutes at 21,130 r.c.f.), transfer water layer to new tube with 500 μL of chloroform/isoamyl alcohol (24:1), mix, separate layers (2 minutes at 21130 r.c.f.), and then transfer water layer to new empty tube]. DNA from samples were precipitated by the addition of 1/25 volume of 5M NaCl, 2 μL of Glycoblue Coprecipitant (Invitrogen), and 3 volumes of 100% ethanol, mixed, incubating 1 hour at 4°C, then >2 hr at -20°C. DNA was pelleted via centrifugation (16,000 r.c.f., 15 minutes, 4°C), washed once with ice-cold 95% ethanol, and air dried. Pellets were brought up in 0.1X TE (100 μL for input, 20 μL for IPOD or RNApol ChIP). QuantiFluor dsDNA dye (Promega) was used to determine DNA concentration prior to sequencing library preparation.
For each sample (input and ChIP), 0.5 ng of DNA was diluted to 50 µL and used as input material for NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) with NEBNext® Multiplex Oligos for Illumina Dual Index Primers Sets 1 and 2 (NEB). Manufacturer’s instructions were followed except the post-ligation bead clean-up, which was replaced with Oligo Clean & Concentrator kit (Zymo Research Corporation; performed per manufacturer's protocol except DNA was eluted with 16.2 μL of 0.1X TE).


title: wt_inactive_QrgB_00min_s2_RNA


title: vpsT_active_QrgB_30min_s2_chip


title: vpsT_active_QrgB_30min_s1_chip


title: mMAC21 C

type: genomic

description: LPS-activated macrophage at 21%O2

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

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

data_processing: Data was processed with the minfi package in R

label: Cy3, Cy5

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from monocytes or macrophages using the Maxwell RSC Cell DNA kit (Promega) according to standard instructions

tag: donor

value: C

tag: age

value: M

tag: condition


title: vpsT_active_QrgB_00min_s1_chip

tag: genotype


title: mMAC1 A

description: LPS-activated macrophage at 1%O2

value: A

tag: Sex

value: F


title: vpsT_inactive_QrgB_60min_s2_chip

tag: treatment


title: vpsT_active_QrgB_15min_s2_chip


title: vpsT_active_QrgB_60min_s2_chip


title: iMAC1 D

description: Unstimulated macrophage at 1%O2

value: D


title: iMAC21 A

description: Unstimulated macrophage at 21%O2


title: wt_inactive_QrgB_30min_s1_RNA

value: Bacterial culture


title: iMAC21 B

description: Unstimulated macrophage at 21%O2

value: B


title: MO C

description: Blood monocytes (CD14+)

value: MO


title: vpsT_active_QrgB_15min_s1_chip

value: vpsT KO, vpsL KO


title: iMAC1 C

description: Unstimulated macrophage at 1%O2


title: vpsT_active_QrgB_00min_s2_chip

value: 00 minutes inducing active QrgB


title: MO A

description: Blood monocytes (CD14+)


title: wt_active_QrgB_15min_s1_RNA


title: vpsR_active_QrgB_30min_s2_chip

value: 30 minutes inducing active QrgB


title: vpsR_active_QrgB_60min_s1_chip

value: 60 minutes inducing active QrgB


title: iMAC1 B

description: Unstimulated macrophage at 1%O2


title: mMAC1 C

description: LPS-activated macrophage at 1%O2


title: vpsT_inactive_QrgB_60min_s1_chip

value: 60 minutes inducing inactive QrgB


title: iMAC21 D

description: Unstimulated macrophage at 21%O2


title: mMAC21 A

description: LPS-activated macrophage at 21%O2


title: mMAC1 B

description: LPS-activated macrophage at 1%O2


title: wt_inactive_QrgB_00min_s1_RNA


title: vpsT_inactive_QrgB_00min_s2_chip


title: vpsT_inactive_QrgB_30min_s2_chip

value: 30 minutes inducing inactive QrgB


title: mMAC21 B

description: LPS-activated macrophage at 21%O2


title: vpsT_inactive_QrgB_30min_s1_chip


title: vpsT_inactive_QrgB_15min_s2_chip

value: 15 minutes inducing inactive QrgB


title: vpsT_inactive_QrgB_15min_s1_chip


title: vpsR_active_QrgB_00min_s1_chip

value: vpsR KO, vpsL KO


title: vpsR_inactive_QrgB_15min_s2_chip


title: vpsR_active_QrgB_30min_s1_chip


title: vpsR_active_QrgB_60min_s2_chip


title: vpsR_inactive_QrgB_30min_s2_chip


title: vpsT_inactive_QrgB_00min_s1_chip

value: 00 minutes inducing inactive QrgB


title: mMAC21 D

description: LPS-activated macrophage at 21%O2


title: MO B

description: Blood monocytes (CD14+)


title: wt_active_QrgB_60min_s2_chip

value: vpsL KO


title: vpsR_active_QrgB_15min_s2_chip

value: 15 minutes inducing active QrgB


title: vpsR_active_QrgB_15min_s1_chip


title: mMAC1 D

description: LPS-activated macrophage at 1%O2


title: vpsR_active_QrgB_00min_s2_chip


title: vpsR_inactive_QrgB_60min_s1_chip


title: wt_active_QrgB_15min_s2_chip


title: iMAC1 A

description: Unstimulated macrophage at 1%O2

value: A


title: wt_inactive_QrgB_60min_s2_chip


title: vpsR_inactive_QrgB_00min_s2_chip


title: vpsR_inactive_QrgB_15min_s1_chip


title: vpsR_inactive_QrgB_00min_s1_chip


title: wt_active_QrgB_30min_s2_chip


title: vpsR_inactive_QrgB_30min_s1_chip


title: wt_active_QrgB_60min_s1_chip


title: wt_inactive_QrgB_00min_s1_chip


title: vpsT_active_QrgB_60min_s2_inp


title: wt_active_QrgB_30min_s1_chip


title: wt_active_QrgB_00min_s1_chip


title: wt_inactive_QrgB_00min_s2_chip


title: wt_inactive_QrgB_15min_s1_chip


title: vpsT_active_QrgB_60min_s1_inp


title: wt_inactive_QrgB_60min_s1_chip


title: vpsT_active_QrgB_15min_s2_inp


title: wt_inactive_QrgB_15min_s2_chip


title: vpsT_active_QrgB_00min_s2_inp


title: iMAC21 C

description: Unstimulated macrophage at 21%O2

value: C

value: M


title: vpsT_active_QrgB_30min_s2_inp

value: Bacterial culture


title: vpsT_active_QrgB_30min_s1_inp


title: vpsT_active_QrgB_00min_s1_inp


title: vpsT_inactive_QrgB_60min_s2_inp


title: vpsT_active_QrgB_15min_s1_inp


title: vpsT_inactive_QrgB_60min_s1_inp


title: vpsR_active_QrgB_60min_s2_inp


title: vpsT_inactive_QrgB_00min_s1_inp


title: vpsT_inactive_QrgB_30min_s1_inp


title: vpsR_active_QrgB_30min_s2_inp


title: vpsT_inactive_QrgB_15min_s2_inp


title: MO D

description: Blood monocytes (CD14+)

value: D

value: F


title: wt_inactive_QrgB_30min_s2_chip


title: vpsR_active_QrgB_15min_s2_inp


title: vpsR_active_QrgB_00min_s2_inp


title: vpsR_active_QrgB_00min_s1_inp


title: vpsR_inactive_QrgB_60min_s1_inp


title: vpsR_inactive_QrgB_30min_s2_inp


title: vpsR_active_QrgB_15min_s1_inp


title: vpsR_inactive_QrgB_30min_s1_inp


title: vpsR_active_QrgB_60min_s1_inp


title: vpsR_inactive_QrgB_15min_s2_inp


title: vpsR_inactive_QrgB_00min_s2_inp


title: vpsR_active_QrgB_30min_s1_inp


title: wt_active_QrgB_60min_s1_inp


title: wt_active_QrgB_60min_s2_inp


title: vpsR_inactive_QrgB_00min_s1_inp


title: wt_active_QrgB_00min_s1_inp


title: wt_active_QrgB_30min_s2_inp


title: wt_active_QrgB_30min_s1_inp


title: wt_active_QrgB_00min_s2_inp


title: wt_inactive_QrgB_60min_s2_inp


title: wt_active_QrgB_15min_s1_inp


title: wt_active_QrgB_15min_s2_inp


title: wt_inactive_QrgB_60min_s1_inp


title: wt_inactive_QrgB_30min_s1_inp


title: wt_inactive_QrgB_15min_s1_inp


title: wt_inactive_QrgB_15min_s2_inp


title: wt_inactive_QrgB_30min_s2_inp


title: wt_inactive_QrgB_00min_s2_inp


title: vpsR_inactive_QrgB_15min_s1_inp


title: wt_inactive_QrgB_00min_s1_inp


title: WX-02-43,Stim,Rep2

first: Jahan

last: Rahman

state: New York

address: 417 E 68th St

department: Center for Hematologic Malignancies

institute: Memorial Sloan Kettering

data_processing:
Raw FASTQ files were trimmed using Trim_Galore (v0.6.4) to remove sequencing adapters and any low quality (Q<15) reads. Trimmed sequencing reads were next aligned to the human Hg19 reference genome (GENCODE, GRCh37.p13) with STAR (v2.7.5) using a two-pass alignment mode with the following parameters: --twopassMode Basic --twopass1readsN -1. SAM files were subsequently converted to BAM files, sorted, and indexed using samtools (v1.9). For visualization of RNA-seq in Integrated Genomics Viewer (IGV; Broad Institute), BAM files were used to generate bigwig files using bamCoverage (part of the Deeptools package; v3.3.1). For differential gene expression analysis, read counting across genomic features (exons) was performed using featureCounts (part of the subread package; v1.5.0) using the following parameters: -p -T 20 -O -F GTF -t exon. Differential gene expression analysis was performed using the edgeR (v3.32.1), DESeq2 (v1.30.1), and limma voom (v3.46.0) R packages. Data visualization and figure generation was performed in Rstudio (v1.3.1073). For quantification of alternative RNA splicing, processed BAM files were used as the input for rMATS (v4.1.1) and against the GENCODE (v35) GTF annotation for GRCh37.p13 using the following parameters: -t paired –libType fr-unstranded –readLength 150 –novelSS. Enumeration of isoform counts was performed using only reads that span the splice junction directly. To identify high confidence AS events, events were considered significant if (i) the inclusion level difference was greater than 20% compared to DMSO, (ii) the False Discovery Rate (FDR) was smaller than 0.05. For comparison of splicing events between conditions, we further limited to highly covered events where at least an average of 50 junctional reads for all conditions. Data analysis and visualization was performed using custom scripts in Rstudio (v1.3.1073) using the following packages: ggplot2 (v3.3.5), ggrepel (v0.9.1), maser (v1.8.0). The processed data can be found in Supplementary Table 2S. The prcomp() and autoplot() functions were used to generate Principal Component Analysis (PCA) plots using gene expression counts as an input.
Assembly: Hg19
Supplementary files format and content: RNA raw gene count matrix:  RNA_seq_counts.txt

source_name: PBMC

growth_protocol: Studies using primary human T cells were carried out with samples from healthy donors following protocols approved by The Scripps Research Institute and The Rockefeller University Internal Review Board. Blood from de-identified healthy donors was obtained from Scripps Research Normal Blood Donor Services, NYBC, STEMCELL Technologies or Rockefeller Hospital. Peripheral blood mononuclear cells (PBMCs) were isolated using a Lymphoprep gradient (STEMCELL Technologies) following a slightly modified protocol compared to manufacturer’s instructions. Briefly, freshly isolated blood (25 mL) was layered on top of cold Lymphoprep (12.5 mL) in a 50 mL Falcon tube without disturbing the Lymphoprep layer. Tubes were spun down (930 g, 20 min, 23 °C) in a benchtop centrifuge with brake off. The plasma and Lymphoprep layers, containing PBMCs, were transferred to new Falcon tubes with 2-fold dilution with PBS and pelleted by centrifugation (520 g, 8 min, 4 °C). Cells were re-combined into one Falcon tube using PBS and pelleted (520 g, 8 min, 4 °C). Pan T cells were isolated from PBMCs using EasySep Human T Cell Isolation Kit (STEMCELL Technologies, negative selection) following manufacturer’s instructions.

extract_protocol:
Following this incubation period, the cells were pelleted (600 g, 5 min, 4 °C), washed with PBS, transferred to 1.5 mL Eppendorf tubes, flash-frozen, and stored at -80 °C until further analysis. Total RNA was extracted from cells using Direct-zol RNA MicroPrep Kit (Zymo research) according to manufacturer’s instructions, and RNA concentration was determined using NanoDrop. RNA (0.5 μg/treatment) was reverse-transcribed into complementary DNA (cDNA) using iScript cDNA Synthesis Kit (Bio-Rad) according to manufacturer’s instructions.
Small aliquots of T cells from TMT-exp unenriched proteomics experiments (8 x 106 cells/condition) were collected, pelleted (600 g, 5 min, 4 °C), transferred to new Eppendorf tubes in cold PBS (1 mL), pelleted (600 g, 5 min, 4 °C), flash frozen and stored at -80 °C until the RNA isolation step. Total RNA isolation and on column DNA digestion was carried out from compound or DMSO treated cells using the RNeasy Mini Kit (QIAGEN) following cell homogenization with the QIAshredder kit (QIAGEN) according to the manufacturer’s protocol. RNA concentration was determined using NanoDrop and the samples were stored at -80 °C until sequencing analysis.

treatment_protocol: Expanded primary human T cells were pelleted (600 g, 5 min, 4 °C) and re-suspended in fresh T cell media at 2 x 106 cells/mL for compound treatment. T cells were treated with WX-02-23 (5 µM), WX-02-43 (5 µM), PladB (10 nM)) or DMSO control in 6-well plates (2 mL/well, 4 x 106 cells/treatment) with or without CD3/CD28 stimulation for 8 h. For treatment conditions that required T cell activation, plates were pre-coated with 1.5 mL PBS containing CD3 (5 µg/mL, BioXCell) and CD28 (2 µg/mL, BioXCell) overnight at 4 °C or for 2 h at 37 °C and washed with PBS (3 mL, 3 times) prior to treatment.

value: PBMC

value: Primary Human T Cell


title: WX-02-43,Stim,Rep1


title: WX-02-43,Stim,Rep3


title: WX-02-43,No Stim,Rep3


title: WX-02-23,Stim,Rep3


title: WX-02-23,Stim,Rep2


title: WX-02-23,Stim,Rep1


title: WX-02-43,No Stim,Rep1


title: WX-02-23,No Stim,Rep3


title: Heat shocked nucleoli, Rep2

city: Miami

first: Stephen

last: Lee

state: FL

department: Biochemistry & Molecular Biology

institute: University of Miami

description:
Combined HS alignment counts
HS_allreadsaligned.bam.tdf

data_processing:
barcodes removed using lima with isoseq and peek-guess settings
refined using Isoseq3 with require-polya setting
clustered using Isoseq3 cluster with verbose and use-qvs settings
Clustered bam files from both flow cells were combined using samtools merge
pbmm2 align using preset ISOSEQ, sort, log-level INFO settings
Assembly: GRCh38.primary_assembly.genome.fa
Supplementary files format and content: Resultant bam files from the alignment of each condition were combined into a single file for increase depth.
Library strategy: ISO-seq

source_name: Breast

growth_protocol: Cells were propagated in DMEM (HyClone) with 10% FBS (Omega Scientific) and 1% penicillin-streptomycin (HyClone). Cells were maintained at 37C in a 5% CO2 humidified incubator

extract_protocol:
Trizol extraction
Library prep was performed on total RNA by polyadenylating RNA (poly(A) polymerase tailing kit Lucigen), cDNA synthesis (Low input RNA synthesis and amplification kit, NEB). Samples were barcoded and prepared for sequencing using (SMRTbell Express Template Prep Kit and Barcoded Overhang Adapter A/B Kits)

treatment_protocol: Cells were subjected to heat shock by translocation to a 5% CO2 humidified incubator maintained at 43C and incubated there for 1 hour

value: Breast

tag: cell line

value: Epithelial

value: Heat Shocked at 43C for 1 hour


title: Heat shocked nucleoli, Rep3


title: WX-02-23,No Stim,Rep1


title: PladB,Stim,Rep3


title: Heat shocked nucleoli, Rep1


title: WX-02-23,No Stim,Rep2


title: Unstressed nucleoli, Rep2

description:
Combined UN alignment counts
UN_allreadsaligned.bam.tdf

value: Unstressed, maintained at 37C


title: PladB,Stim,Rep2


title: PladB,Stim,Rep1


title: WX-02-43,No Stim,Rep2


title: PladB,No Stim,Rep2


title: Unstressed nucleoli, Rep3


title: PladB,No Stim,Rep3


title: Unstressed nucleoli, Rep1


title: scRNA-seq_Post1

city: Koto-ku

first: Reo

last: Maruyama

department: Cancer Institute

institute: Japanese Foundation For Cancer Research

library_source: transcriptomic single cell

data_processing:
Fastq files were generated by RTA in Illumina NextSeq 550.
Raw data produced from the 10x Genomic platform were processed by Cell Ranger (v6.1.2).
Assembly: GRCH38
Supplementary files format and content: A cell x gene data matrix in AnnData format

source_name: Breast Cancer Tissue

extract_protocol:
Breast cancer specimens were obtained by core needle biopsy for diagnosis or from surgically removed tumors. Specimens were dissociated into single cells using a MACS Tumor Dissociation Kit and a gentle MACS dissociator (Miltenyi Biotec) according to the manufacturer’s instructions. Single cells were cryopreserved using the Banbanker.
10x Genomics Chromium was used for single cell capture and cDNA preparations according to the Single Cell 3' v3 Protocol recommended by the manufacturer.

value: Breast Cancer Tissue


title: scRNA-seq_Meta

source_name: Mesenteric metastasis

value: Mesenteric metastasis


title: DMSO,Stim,Rep3

city: New York


title: scRNA-seq_Pre


title: DMSO,Stim,Rep2


title: brain tumor

city: Melbourne

first: Saskia

last: Freytag

state: Victoria (V)

address: 1G Royal Parade

country: Australia

institute: WEHI

data_processing:
Data was aligned with STAR (version 2.7.3a) with reference to mouse mm10 genome sequences.
Assembly: mm10
Supplementary files format and content: Count data was produced with STAR (version 2.7.3a).
Supplementary files format and content: tab-deliminted text file with raw counts

source_name: tumor

extract_protocol:
RNeasy RNA extraction kit (Qiagen 74104, Qiagen, Germantown, MD, USA) and then analyzed by using a 2200 Tapestation Analyzer (Agilent, Santa Clara, CA, USA).
An input of 500 ng of RNA was used to generate libraries (TruSeq RNA Library Prep v2, Illumina, San Diego, CA, USA). Sequencing was performed on the NextSeq System (Illumina) to produce 132bp single-end reads

value: tumor


title: wt_active_QrgB_15min_s1_chip

value: vpsL KO


title: DMSO,Stim,Rep1


title: brain healthy

source_name: brain

value: brain


title: DMSO,No Stim,Rep2


title: DMSO,No Stim,Rep3


title: RNA_CM_SRF_KO_day3_rep2

city: Berlin

first: Pavel

last: Tsaytler

address: Ihnestrasse  63-73

country: Germany

institute: MPI Molecular Genetics

description: processed data linked to rep1 sample

data_processing:
RNA-seq reads were subjected to quality control using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and trimmed using cutadapt (version 2.9) (https://doi.org/10.14806/ej.17.1.200) to remove adapter sequences. Alignment was performed using Hisat2 [Kim, 2019] (version 2.1.0) with the following arguments: --no-mixed --no-discordant. The index files for Hisat2 were built using mm10 reference genome containing chromosomes 1-19, X, Y and M, and splice sites and exon data from refSeq mm10 annotations. The resulting sam format files were then converted to bam format, sorted and indexed using samtools [Li, 2009] (version 1.9). FPKM values were calculated using Cuffdiff [Trapnell, 2010] (version 2.2.1) with the following arguments: -u -no-effective-length-correction -b.
genome build/assembly: mm10
processed data files format and content: bigWig files representing read density

extract_protocol:
At day 3 or day 4 of CM differentiation, Srf-flex1 cells carrying H2B-mCherry (WT) or H2B-Venus-T2A-Cre (SRF KO) were trypsinized, resuspended in 3% BSA in PBS, and 40,000 cells (per replicate) expressing fluorescent reporter (mCherry or Venus) were sorted on a FACS Aria II (Becton Dickinson). Total RNA was extracted from 40,000 differentiated cells using Trizol reagent (ThermoFisher; 15596026) following the manufacturer’s instructions and purified using the RNeasy Micro kit (Qiagen). Residual genomic DNA was digested on a column. The RNA was quantified using Qubit RNA HS assay (Life Technologies), and the integrity of the RNA was assessed using Bioanalyzer RNA pico chips (Agilent).
Strand-specific RNA-seq libraries were generated from 100 ng of total RNA using the ScriptSeq v2 (Epicentre) low input library preparation kit according to manufacturer’s instructions. The library was amplified using 15 PCR cycles. RNA-seq libraries were quantified using the Qubit HS DNA assay (Life Technologies) and the size distribution was assessed using the DNA HS Bioanalyzer chips (Agilent).

value: embryonic stem cells

value: SRF KO

value: cardiac mesoderm differentiation


title: RNA_CM_SRF_KO_day4


title: RNA_CM_WT_day4

value: WT


title: scRNA-seq_Post2


title: RNA_CM_WT_day3_rep2

description: processed data linked to rep1 sample


title: RNA_CM_SRF_KO_day3_rep1


title: 3-A549 cells, 20μM T-96, 24h

city: Beijing

first: Lina

last: Wang

address: No. 2, Bei Yi Street, Zhongguancun, Haidian District, Beijing

institute: Institute of Chemistry, Chinese Academy of Sciences

data_processing:
Base quality analysis, FastQC (0.11.2)
Data quality control, fastp (0.14.0)
Read alignmnent, Hisat2 (2.1.0)
Assembly and quantification, StringTie (1.3.3b)
Assembly: hg38
Supplementary files format and content: excel file include raw counts for each sample
Supplementary files format and content: excel file include FPKM values for each sample

extract_protocol:
The cells were collected and lysed with 1mL TRIzol reagent (15596-026, Invitrogen Life Technologies). The RNA extraction was performed following the manufacturer’s instructions for the TRIzol reagent.
RNA-seq libraries were generated and sequenced by CapitalBio Technology (Beijing, China). The NEB Next Ultra RNA Library Prep Kit for Illumina (NEB) was used to construct the libraries for sequencing.


title: ChIP_ES_input

data_processing:
The ChIP-seq reads were aligned to the reference genome using bowtie2 (version 2.2.4) with the following arguments: -3 5 -I 100 -X 500 --no-discordant --no-mixed. Sam files containing mapped paired-end reads were converted to bam files, sorted and indexed using samtools. For visualization, the data were normalized and converted to bigWig (bw) format using bamCoverage tool from deepTools with the following arguments: --normalizeUsing CPM --extendReads 200 --smoothLength 9 -bs 3 -ignore chrM.
genome build/assembly: mm10
processed data files format and content: bigWig files representing read density

extract_protocol:
ChIP experiments were carried out as previously described [Koch, 2017]. SRF ChIP-seq was performed in WT ESCs and in CM cells on differentiation day 4. Control SRF ChIP-seq was performed in SRF KO ES cells after 48 of treatment with 250 nM dTAG13. SRF ChIP-qPCR was performed in CTCF KO ES cells after 24 hours of treatment with 250 nM dTAG13. CTCF ChIP-qPCR was performed in SRF KO ES cells after 24 hours of treatment with 250 nM dTAG13. Crosslinking was performed directly on cells in the medium with the addition of 1/10th volume of crosslinking solution (11% formaldehyde, 50 mM Hepes pH 7.8, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) for 10minutes at room temperature, while shaking. The crosslinking reaction was quenched with the addition of 1/10th volume of 2.5 M glycine and 5minutes incubation. Cells were washed twice with cold PBS, scraped in cold PBS containing 0.05% Triton X-100, and pelleted in aliquots of 5x107. For sonication, complete protease inhibitors without EDTA (Roche) at 1x final concentration was added to all lysis buffers (LB) prior to use. Each pellet was resuspended in 2.5 ml LB1 (50 mM Hepes pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.75% NP-40, 0.25% triton X-100) and rotated at 4°C for 20minutes. The cell suspension was homogenized using a douncer. The chromatin was pelleted by centrifugation at 1400g and 4°C for 5minutes and resuspended in 2.5 ml LB2 (10 mM Tris pH8, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA). After 10minutes rotation at 4°C, the centrifugation step was repeated and each pellet was resuspended in 1.5 ml LB3 (10 mM Tris pH 8, 1 mM EDTA, 0.5 mM EGTA, 100 mM NaCl, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine), transferred to 15 ml Falcon tubes and sonicated using a W-450D Digital Sonifier (Branson) sonicator for 14 cycles of 10s on/50s off in a 4°C cold room with tubes chilled in ice water. After sonication, 150 μl of Triton X-100 was added per tube, transferred to two 1.5 ml Eppendorf tubes and debris was pelleted by centrifugation at 20,000g and 4°C for 10minutes. The solubilized chromatin was then pooled and mixed thoroughly. The chromatin was distributed into 1.5 ml aliquots, snap frozen and stored at-80°C until use. 100 μl protein G-coated Dynal beads (Life Technologies) were washed 3x with 1 ml of blocking buffer (PBS, 0.5% BSA), resuspended in 500 μl of blocking solution containing 5 μg primary ChIP antibody (listed in the Key resources table) and rotated overnight at 4°C. Beads were then washed 3x with 1 ml of blocking buffer and resuspended in 100 μl blocking buffer. Chromatin equivalent to 5x107 cells was added and rotated overnight at 4°C. The following day, 5 washing steps with 1 ml RIPA buffer (50 mM Hepes pH 7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate) and one washing step with 1 ml of TEN (10 mM Tris pH 8, 1 mM EDTA, 50 mM NaCl) were performed. The elution was performed in two subsequent steps using 100 μl of 1x elution buffer (50 mM Tris pH 8, 10 mM EDTA, 1% SDS) and incubation at 65°C while shaking for 10minutes each. The eluates were combined and incubated for 13-15 hours at 65°C. 200 μl of TE were added and the ChIP DNA was purified as described for the input above. ChIP DNA was quantified using the Qubit (Life Technologies) DNA HS assay.
The ChIP-seq libraries were generated using the TruSeq ChIP library kit (Illumina) with the previously described modifications (Koch, 2017). After adapter ligation, 0.95x of AMPure XP beads (Beckman Coulter) were used for a single purification and the DNA was eluted using 14 μl of resuspension buffer (RSB, Illumina). After the addition of 1 μl primer mix (25 mM each) and 15 μl 2x Kapa HiFi HotStart Ready Mix (Kapa Biosystems), amplification was performed for 45 seconds at 98°C, 5 cycles of [15 seconds at 98°C, 30 seconds at 63°C and 30 seconds at 72°C] and a final 1 minute incubation at 72°C. The PCR products were purified using 0.95x of beads and eluted using 21 μl of RSB. Ligation products were then separated using a 1.5% agarose gel. Post-run staining was performed using SYBR Gold under agitation for 30 minutes. Gel slices corresponding to 250-400 bp fragment size were cut out. using a Dark Reader Transilluminator.  The gel extraction was performed using 5 gel volumes of QG buffer (Qiagen) with the addition of one gel volume of isopropanol. The MinElute (Qiagen) columns were washed once with QG buffer and twice with PE buffer, air-dried for at least 10minutes and eluted using 21 μl of EB buffer. 19 μl of the eluate was used in the final amplification, with the addition of 1 μl primer mix and 20 μl 2x Kapa HiFi Hotstart premix. The same protocol as for the pre-amplification was used, with the exception of using 13 amplification cycles. The libraries were quantified using the Qubit DNA HS assay and the library size was validated using DNA HS Bioanalyzer chips.

value: untreated


title: PladB,No Stim,Rep1


title: DMSO,No Stim,Rep1


title: 2-A549 cells, 20μM T-96, 24h

growth_protocol: The cells were collected and lysed with 1mL TRIzol reagent (15596-026, Invitrogen Life Technologies). The RNA extraction was performed following the manufacturer’s instructions for the TRIzol reagent.


title: 1-A549 cells, 20μM T-96, 24h


title: RNA_CM_WT_day3_rep1


title: wt_active_QrgB_00min_s2_chip

value: Bacterial culture

value: 00 minutes inducing active QrgB


title: ChIP_ES_SRF_KO_SRF_control


title: ChIP_ES_WT_SRF


title: 2-A549 cells, DMSO, 24h

value: DMSO


title: 1-A549 cells, DMSO, 24h


title: input_mMAC1B

description: LPS-activated macrophage at 1%O2

data_processing:
Read trimming using Cutadapt 1.18
Alignment to the GRCh38 genome using the BWA-MEM algorithm (bwa 0.7.17)
MAPQ lower than 30 were filtered using samtools (1.6)
Peak calling was performed using MACS2 (2.2.6) with the options (--nomodel –extsize 200)
Assembly: GRCh38
Supplementary files format and content: NarrowPeak (except for input)

growth_protocol: Peripheral blood monocytes were purified using CD14 magnetic-activated cell sorting (MACS © MicroBeads, Miltenyi Biotec) and cultured in RPMI 1640 in the presence of 10ng/mL macrophage colony-stimulating factor (M-CSF) for 5 days in normoxia (21% O2) or hypoxia (1% O2). Cells were further stimulated with 10 ng/mL of lypopolysaccharide (LPS) or with PBS for 2h additional hours.

extract_protocol:
Cells were directly fixed in the cell plate for 10 min with 1% formaldehyde methanol-free and chromatin was prepared for sonication following the Covaris truChIP Shearing kit instructions. Chromatin in Shearing D3 Buffer was sonicated using the Covaris M220 sonicator. Chromatin size distribution was checked using an agarose gel electrophoresis (250-150bp).
ChIP-seq libraries were prepared for sequencing using the Illumina TruSeq ChIP Library Preparation Kit.

value: peripheral blood

value: Monocyte-derived macrophage

value: B

tag: chip antibody

value: input


title: 19456X18 Ctrl 21

city: Salt Lake City

first: Kathryn

middle: Anne

last: Peterson

state: Utah

address: 30 N Mario Capecchi Dr

department: Internal Medicine

institute: University of Utah

data_processing:
The human GRCh38 genome and gene annotation files were downloaded from Ensembl release 102
Trimmed reads were aligned to the reference database using STAR version 2.7.6a in two pass mode to output a BAM file sorted by coordinates
Mapped reads were assigned to annotated genes using featureCounts version 1.6.3
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.30.0
Assembly: GRCh38
Supplementary files format and content: FeatureCount output files combined into a single tab-delimited raw count matrix

source_name: esophageal

extract_protocol:
Total RNA from esophageal biopsies was isolated from 5 scrolls per sample of 10-micron, formalin-fixed, paraffin-embedded tissue with the High Pure FFPET RNA isolation kit (Roche Diagnostics) that includes on-column DNase digestion
RNA libraries for RNA-seq were prepared using Illumina TruSeq RNA Exome library kit following manufacturer's protocols

value: esophageal

value: male

tag: disease state

value: control

tag: tissue location

value: distal


title: 19456X14 Baseline Remission 8

value: EoE

value: elimination diet


title: 19456X13 Baseline Remission 9

value: female


title: input_iMAC1B

description: LPS-activated macrophage at 1%O2


title: 19456X12 Baseline Remission 7

value: mid


title: input_mMAC21B

description: LPS-activated macrophage at 21%O2


title: 19456X8 Baseline Remission 2

value: proximal


title: 19456X7 Baseline Remission 10


title: 3-A549 cells, DMSO, 24h


title: 19456X4 Recurring Low Eos 10

value: trigger food reintroduction


title: ChIP_CM_WT_SRF

value: embryonic stem cells

value: WT

value: untreated


title: input_iMAC21A

description: Unstimulated macrophage at 21%O2

value: peripheral blood

value: A


title: 19456X2 Recurring Low Eos 9


title: mMAC1_HIF1A_A

description: LPS-activated macrophage at 1%O2

value: Monocyte-derived macrophage


title: mMAC1_HIF1A_B

description: LPS-activated macrophage at 1%O2

value: B


title: 19456X1 Recurring High Eos 9

value: esophageal


title: 18483X44 Recurring Low Eos 8

value: male


title: iMAC1_HIF1A_A

description: Unstimulated macrophage at 1%O2


title: input_mMAC1A

description: Unstimulated macrophage at 1%O2

value: input


title: 18483X42 Recurring High Eos 8

value: distal


title: mMAC21_HIF1A_B

description: LPS-activated macrophage at 21%O2


title: 18483X38 Recurring Low Eos 7

value: EoE


title: mMAC21_HIF1A_A

description: LPS-activated macrophage at 21%O2


title: 18483X33 Recurring Low Eos 6


title: input_iMAC1A

description: Unstimulated macrophage at 1%O2


title: 18483X26 Recurring High Eos 5


title: input_mMAC21A

description: Unstimulated macrophage at 21%O2


title: 19456X3 Recurring High Eos 10


title: mMAC1_p65_B

description: LPS-activated macrophage at 1%O2


title: iMAC1_p65_B

description: Unstimulated macrophage at 1%O2


title: input_iMAC21B

description: LPS-activated macrophage at 21%O2


title: mMAC1_p65_A

description: LPS-activated macrophage at 1%O2


title: 18483X20 Ctrl 15

value: control


title: iMAC21_HIF1A_A

description: Unstimulated macrophage at 21%O2


title: iMAC1_HIF1A_B

description: Unstimulated macrophage at 1%O2


title: 18483X25 Recurring Low Eos 5

value: female


title: 18483X18 Ctrl 13


title: 18483X15 Recurring Low Eos 4


title: 18483X14 Recurring Low Eos 2


title: mMAC21_p65_B

description: LPS-activated macrophage at 21%O2


title: iMAC1_p65_A

description: Unstimulated macrophage at 1%O2


title: 18483X40 Recurring High Eos 7


title: 18483X34 Recurring High Eos 6

value: mid


title: mMAC21_p65_A

description: LPS-activated macrophage at 21%O2


title: 18483X13 Recurring Low Eos 3


title: 18483X7 Recurring High Eos 4


title: iMAC21_HIF1A_B

description: Unstimulated macrophage at 21%O2


title: 18483X10 Recurring High Eos 1


title: 18483X6 Recurring High Eos 2


title: iMAC21_p65_A

description: Unstimulated macrophage at 21%O2


title: HCT116_8h_Tg_3_25_22_S17

city: Ottawa

first: John

last: Stead

state: ON

address: 1125 Colonel By Drive

department: Department of Neuroscience

country: Canada

institute: Carleton University

data_processing:
Base calling was performed by bcl2fastq v 2.20
Quality trimming was performed using fastp v0.23.2
Alignment was performed using STAR v2.7.10a
Gene counts were performed with RSEM v1.3.3
Normalization was performed with DESeq2 v1.31.15
Assembly: Genome Reference Consortium Human Build 38 reference genome version 107
Supplementary files format and content: count_table.csv is a genes by samples count matrix of raw counts from the STAR alignments

growth_protocol: HCT116 and HCT116 ATF4 deficient cells were grown in McCoys medium, supplmented with Newborn Calf Serum (NBCS) and Fetal Bovine Serum (FBS) is a 3:1 ratio to give 12% serum, and 90 units/ml penicillin, 90µg/ml streptomycin

extract_protocol:
EZ-10 DNAaway RNA Miniprep (Bio Basic)
The Illumina Stranded mRNA prep, Ligation Reference Guide (1000000124518) was used. The Illumina Poly(A) Capture (2004893), cDNA synthesis (2004895) and RNA PRE Ligation (20040897) kits were used to purify polyadenylated mRNA and synthesize first and second strand cDNA. Anchors were ligated using the IDT for Illumina RNA index Anchors (200040899), and samples were indexed using the IDT for Illumina DNA/RNA UD Indexes Set A (20026121).

treatment_protocol: Cells were treated for 2 or 8 hours with 30µM Isoginkgetin, 2µM Thapsigargin, an equivalent volume of DMSO or left untreated.

tag: duration of_chemical_exposure

value: 8 hours

tag: chemical

value: Thapsigargin

tag: batch

tag: technical control

value: FALSE

tag: reference rna

tag: solvent control

tag: chemical exposure_date

tag: cell seeding_date

tag: library well


title: 18483X5 Recurring High Eos 3

tag: tissue

value: trigger food reintroduction


title: HCT116_8h_Tg_3_31_22_S29

tag: genotype


title: HCT116_8h_Tg_3_23_22_S45


title: HCT116_8h_Tg_3_18_22_S35


title: C10

first: Junchao

last: Jiang

address: Dongdan Santiao, Doncheng District

institute: Peking Union Medical College

data_processing:
CLC Genomics Workbench V11.0.1
Assembly: mm10
Supplementary files format and content: Text files include RPKM values

source_name: lung tissue

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3ug of total RNA was used for the construction of sequencing library.
RNA library for RNA-seq was prepared using SMARTER Mrna-Seq Library Prep Kit following manufacturer's protocols.

value: lung tissue


title: 18483X2 Recurring low Eos 1

tag: Sex


title: HCT116_8h_ND_3_31_22_S24

tag: treatment

value: TRUE


title: HCT116_8h_ND_3_25_22_S43

tag: cell line


title: C9


title: C8


title: HCT116_8h_ND_3_18_22_S48


title: C6


title: HCT116_8h_ND_3_23_22_S1


title: C5


title: HCT116_8h_I30_3_31_22_S37

value: Isoginkgetin


title: iMAC21_p65_B

description: Unstimulated macrophage at 21%O2

value: peripheral blood

tag: condition

tag: cell type

value: Monocyte-derived macrophage

tag: donor

tag: age

tag: chip antibody


title: C4


title: HCT116_8h_I30_3_25_22_S13

tag: duration of_chemical_exposure

tag: chemical

tag: batch


title: C3


title: HCT116_8h_I30_3_23_22_S32

tag: technical control

tag: reference rna

tag: solvent control


title: HCT116_8h_I30_3_18_22_S22

tag: chemical exposure_date

tag: cell seeding_date

tag: library well


title: C2

tag: tissue


title: C1


title: wt_inactive_QrgB_30min_s1_chip

value: Bacterial culture

tag: genotype

value: vpsL KO

tag: treatment

value: 30 minutes inducing inactive QrgB


title: E13


title: E11


title: HCT116_8h_DMSO_3_31_22_S3

tag: cell line

value: DMSO


title: HCT116_8h_DMSO_3_25_22_S39


title: HCT116_8h_DMSO_3_23_22_S20


title: E10


title: HCT116_8h_DMSO_3_18_22_S26


title: HCT116_2h_Tg_3_31_22_S5

value: 2 hour


title: E9


title: E6


title: HCT116_2h_Tg_3_25_22_S6


title: E4


title: E3


title: HCT116_2h_DMSO_3_31_22_S44

value: 2 hours


title: S10


title: HCT116_2h_Tg_3_18_22_S8


title: HCT116_2h_Tg_3_23_22_S28


title: E2


title: E1


title: S7


title: S9


title: HCT116_2h_DMSO_3_18_22_S4


title: S5


title: S6


title: S8


title: 2-1-25_8h_Tg_3_25_22_S23

source_name: HCT116 ATF4 deficient

value: HCT116 ATF4 deficient


title: 2-1-25_8h_Tg_3_31_22_S12


title: HCT116_2h_DMSO_3_23_22_S47


title: 2-1-25_8h_Tg_3_23_22_S2


title: S1


title: S4


title: 2-1-25_8h_ND_3_31_22_S41


title: 2-1-25_8h_ND_3_25_22_S15


title: S3


title: 2-1-25_8h_Tg_3_18_22_S19


title: 2-1-25_8h_ND_3_23_22_S25


title: H10


title: H9


title: HCT116_2h_DMSO_3_25_22_S27


title: 2-1-25_8h_ND_3_18_22_S40


title: 2-1-25_8h_I30_3_31_22_S30


title: H8


title: H7


title: 2-1-25_8h_I30_3_25_22_S42


title: H5


title: 2-1-25_8h_I30_3_23_22_S7


title: H6


title: 2-1-25_8h_DMSO_3_31_22_S36


title: 2-1-25_8h_I30_3_18_22_S33


title: 2-1-25_8h_DMSO_3_25_22_S34


title: H2