title: Ethanol_NCY3290_ANAE_R1 [RNA-Seq_3strains]

description:
Grew strains from OD600 0.01 and collected at OD600 0.5, in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 4% in aerobic conditions, shaking in the incubator.  Additionally, we performed this experiment in the anaerobic chamber for the same three strains in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 3%.  Goal was to determine stress mechanisms of different types of alcohols, and how oxygen affect these mechanisms.
Ethanol_NCY3290_ANAE_R1


title: Isobutanol_Y7568_ANAE_R2 [RNA-Seq_3strains]

status: Public on Aug 04 2018

type: SRA

city: Madison

first: Audrey

last: Gasch

state: WI

address: 425G Henry mall

department: Genetics

country: USA

institute: University of Wisconsin

description:
Grew strains from OD600 0.01 and collected at OD600 0.5, in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 4% in aerobic conditions, shaking in the incubator.  Additionally, we performed this experiment in the anaerobic chamber for the same three strains in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 3%.  Goal was to determine stress mechanisms of different types of alcohols, and how oxygen affect these mechanisms.
Isobutanol_Y7568_ANAE_R2

library_source: transcriptomic

data_processing:
Alignment to  reference genome S288C R64-1-1 using BWA mem
Counts generated using HTSeq
RPKM Calculated
Genome_build: S288C R64-1-1
Supplementary_files_format_and_content: rpkm

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: Gasch Lab/ GLBRC

growth_protocol: Yeast grown in shaker flasks in aerobic conditions or in an anaerobi chamber

extract_protocol:
RNA extraction by hot acid-phenol extraction
Illumina TruSeq stranded library prep

treatment_protocol: Alcohol added to each culture for denoted times, if indicated

tag: agent

value: Isobutanol

tag: strain


title: Isobutanol_IL01_AER_R1 [RNA-Seq_3strains]

description:
Grew strains from OD600 0.01 and collected at OD600 0.5, in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 4% in aerobic conditions, shaking in the incubator.  Additionally, we performed this experiment in the anaerobic chamber for the same three strains in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 3%.  Goal was to determine stress mechanisms of different types of alcohols, and how oxygen affect these mechanisms.
Isobutanol_IL01_AER_R1


title: Ethanol_IL01_ANAE_R2 [RNA-Seq_3strains]

description:
Grew strains from OD600 0.01 and collected at OD600 0.5, in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 4% in aerobic conditions, shaking in the incubator.  Additionally, we performed this experiment in the anaerobic chamber for the same three strains in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 3%.  Goal was to determine stress mechanisms of different types of alcohols, and how oxygen affect these mechanisms.
Ethanol_IL01_ANAE_R2

value: Ethanol


title: Ethanol_NCY3290_ANAE_R2 [RNA-Seq_3strains]

description:
Grew strains from OD600 0.01 and collected at OD600 0.5, in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 4% in aerobic conditions, shaking in the incubator.  Additionally, we performed this experiment in the anaerobic chamber for the same three strains in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 3%.  Goal was to determine stress mechanisms of different types of alcohols, and how oxygen affect these mechanisms.
Ethanol_NCY3290_ANAE_R2


title: Isobutanol_Y7568_ANAE_R1 [RNA-Seq_3strains]

description:
Grew strains from OD600 0.01 and collected at OD600 0.5, in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 4% in aerobic conditions, shaking in the incubator.  Additionally, we performed this experiment in the anaerobic chamber for the same three strains in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 3%.  Goal was to determine stress mechanisms of different types of alcohols, and how oxygen affect these mechanisms.
Isobutanol_Y7568_ANAE_R1


title: Ethanol_IL01_AER_R2 [RNA-Seq_3strains]

description:
Grew strains from OD600 0.01 and collected at OD600 0.5, in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 4% in aerobic conditions, shaking in the incubator.  Additionally, we performed this experiment in the anaerobic chamber for the same three strains in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 3%.  Goal was to determine stress mechanisms of different types of alcohols, and how oxygen affect these mechanisms.
Ethanol_IL01_AER_R2


title: Ethanol_IL01_AER_R1 [RNA-Seq_3strains]

description:
Grew strains from OD600 0.01 and collected at OD600 0.5, in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 4% in aerobic conditions, shaking in the incubator.  Additionally, we performed this experiment in the anaerobic chamber for the same three strains in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 3%.  Goal was to determine stress mechanisms of different types of alcohols, and how oxygen affect these mechanisms.
Ethanol_IL01_AER_R1


title: Butanol_Y7568_ANAE_R2 [RNA-Seq_3strains]

description:
Grew strains from OD600 0.01 and collected at OD600 0.5, in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 4% in aerobic conditions, shaking in the incubator.  Additionally, we performed this experiment in the anaerobic chamber for the same three strains in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 3%.  Goal was to determine stress mechanisms of different types of alcohols, and how oxygen affect these mechanisms.
Butanol_Y7568_ANAE_R2

value: Butanol


title: Isobutanol_NCY3290_AER_R2 [RNA-Seq_3strains]

description:
Grew strains from OD600 0.01 and collected at OD600 0.5, in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 4% in aerobic conditions, shaking in the incubator.  Additionally, we performed this experiment in the anaerobic chamber for the same three strains in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 3%.  Goal was to determine stress mechanisms of different types of alcohols, and how oxygen affect these mechanisms.
Isobutanol_NCY3290_AER_R2


title: Ethanol_Y7568_ANAE_R1 [RNA-Seq_3strains]

description:
Grew strains from OD600 0.01 and collected at OD600 0.5, in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 4% in aerobic conditions, shaking in the incubator.  Additionally, we performed this experiment in the anaerobic chamber for the same three strains in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 3%.  Goal was to determine stress mechanisms of different types of alcohols, and how oxygen affect these mechanisms.
Ethanol_Y7568_ANAE_R1


title: Ethanol_Y7568_ANAE_R2 [RNA-Seq_3strains]

description:
Grew strains from OD600 0.01 and collected at OD600 0.5, in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 4% in aerobic conditions, shaking in the incubator.  Additionally, we performed this experiment in the anaerobic chamber for the same three strains in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 3%.  Goal was to determine stress mechanisms of different types of alcohols, and how oxygen affect these mechanisms.
Ethanol_Y7568_ANAE_R2


title: Ethanol_Y7568_AER_R1 [RNA-Seq_3strains]

description:
Grew strains from OD600 0.01 and collected at OD600 0.5, in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 4% in aerobic conditions, shaking in the incubator.  Additionally, we performed this experiment in the anaerobic chamber for the same three strains in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 3%.  Goal was to determine stress mechanisms of different types of alcohols, and how oxygen affect these mechanisms.
Ethanol_Y7568_AER_R1


title: Butanol_NCY3290_AER_R2 [RNA-Seq_3strains]

description:
Grew strains from OD600 0.01 and collected at OD600 0.5, in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 4% in aerobic conditions, shaking in the incubator.  Additionally, we performed this experiment in the anaerobic chamber for the same three strains in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 3%.  Goal was to determine stress mechanisms of different types of alcohols, and how oxygen affect these mechanisms.
Butanol_NCY3290_AER_R2


title: Butanol_NCY3290_AER_R1 [RNA-Seq_3strains]

description:
Grew strains from OD600 0.01 and collected at OD600 0.5, in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 4% in aerobic conditions, shaking in the incubator.  Additionally, we performed this experiment in the anaerobic chamber for the same three strains in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 3%.  Goal was to determine stress mechanisms of different types of alcohols, and how oxygen affect these mechanisms.
Butanol_NCY3290_AER_R1


title: Isobutanol_IL01_AER_R2 [RNA-Seq_3strains]

description:
Grew strains from OD600 0.01 and collected at OD600 0.5, in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 4% in aerobic conditions, shaking in the incubator.  Additionally, we performed this experiment in the anaerobic chamber for the same three strains in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 3%.  Goal was to determine stress mechanisms of different types of alcohols, and how oxygen affect these mechanisms.
Isobutanol_IL01_AER_R2


title: Isobutanol_Y7568_AER_R2 [RNA-Seq_3strains]

description:
Grew strains from OD600 0.01 and collected at OD600 0.5, in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 4% in aerobic conditions, shaking in the incubator.  Additionally, we performed this experiment in the anaerobic chamber for the same three strains in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 3%.  Goal was to determine stress mechanisms of different types of alcohols, and how oxygen affect these mechanisms.
Isobutanol_Y7568_AER_R2


title: Isobutanol_Y7568_AER_R1 [RNA-Seq_3strains]

description:
Grew strains from OD600 0.01 and collected at OD600 0.5, in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 4% in aerobic conditions, shaking in the incubator.  Additionally, we performed this experiment in the anaerobic chamber for the same three strains in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 3%.  Goal was to determine stress mechanisms of different types of alcohols, and how oxygen affect these mechanisms.
Isobutanol_Y7568_AER_R1


title: Isobutanol_NCY3290_AER_R1 [RNA-Seq_3strains]

description:
Grew strains from OD600 0.01 and collected at OD600 0.5, in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 4% in aerobic conditions, shaking in the incubator.  Additionally, we performed this experiment in the anaerobic chamber for the same three strains in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 3%.  Goal was to determine stress mechanisms of different types of alcohols, and how oxygen affect these mechanisms.
Isobutanol_NCY3290_AER_R1


title: Ethanol_NCY3290_AER_R1 [RNA-Seq_3strains]

description:
Grew strains from OD600 0.01 and collected at OD600 0.5, in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 4% in aerobic conditions, shaking in the incubator.  Additionally, we performed this experiment in the anaerobic chamber for the same three strains in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 3%.  Goal was to determine stress mechanisms of different types of alcohols, and how oxygen affect these mechanisms.
Ethanol_NCY3290_AER_R1


title: YPD_IL01_ANAE_R1 [RNA-Seq_3strains]

description:
Grew strains from OD600 0.01 and collected at OD600 0.5, in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 4% in aerobic conditions, shaking in the incubator.  Additionally, we performed this experiment in the anaerobic chamber for the same three strains in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 3%.  Goal was to determine stress mechanisms of different types of alcohols, and how oxygen affect these mechanisms.
YPD_IL01_ANAE_R1

value: YPD


title: Ethanol_NCY3290_AER_R2 [RNA-Seq_3strains]

description:
Grew strains from OD600 0.01 and collected at OD600 0.5, in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 4% in aerobic conditions, shaking in the incubator.  Additionally, we performed this experiment in the anaerobic chamber for the same three strains in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 3%.  Goal was to determine stress mechanisms of different types of alcohols, and how oxygen affect these mechanisms.
Ethanol_NCY3290_AER_R2


title: Ethanol_Y7568_AER_R2 [RNA-Seq_3strains]

description:
Grew strains from OD600 0.01 and collected at OD600 0.5, in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 4% in aerobic conditions, shaking in the incubator.  Additionally, we performed this experiment in the anaerobic chamber for the same three strains in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 3%.  Goal was to determine stress mechanisms of different types of alcohols, and how oxygen affect these mechanisms.
Ethanol_Y7568_AER_R2


title: YPD_Y7568_ANAE_R1 [RNA-Seq_3strains]

description:
Grew strains from OD600 0.01 and collected at OD600 0.5, in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 4% in aerobic conditions, shaking in the incubator.  Additionally, we performed this experiment in the anaerobic chamber for the same three strains in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 3%.  Goal was to determine stress mechanisms of different types of alcohols, and how oxygen affect these mechanisms.
YPD_Y7568_ANAE_R1


title: YPD_Y7568_ANAE_R2 [RNA-Seq_3strains]

description:
Grew strains from OD600 0.01 and collected at OD600 0.5, in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 4% in aerobic conditions, shaking in the incubator.  Additionally, we performed this experiment in the anaerobic chamber for the same three strains in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 3%.  Goal was to determine stress mechanisms of different types of alcohols, and how oxygen affect these mechanisms.
YPD_Y7568_ANAE_R2


title: Butanol_IL01_AER_R2 [RNA-Seq_3strains]

description:
Grew strains from OD600 0.01 and collected at OD600 0.5, in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 4% in aerobic conditions, shaking in the incubator.  Additionally, we performed this experiment in the anaerobic chamber for the same three strains in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 3%.  Goal was to determine stress mechanisms of different types of alcohols, and how oxygen affect these mechanisms.
Butanol_IL01_AER_R2


title: YPD_IL01_ANAE_R2 [RNA-Seq_3strains]

description:
Grew strains from OD600 0.01 and collected at OD600 0.5, in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 4% in aerobic conditions, shaking in the incubator.  Additionally, we performed this experiment in the anaerobic chamber for the same three strains in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 3%.  Goal was to determine stress mechanisms of different types of alcohols, and how oxygen affect these mechanisms.
YPD_IL01_ANAE_R2


title: Isobutanol_IL01_ANAE_R2 [RNA-Seq_3strains]

description:
Grew strains from OD600 0.01 and collected at OD600 0.5, in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 4% in aerobic conditions, shaking in the incubator.  Additionally, we performed this experiment in the anaerobic chamber for the same three strains in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 3%.  Goal was to determine stress mechanisms of different types of alcohols, and how oxygen affect these mechanisms.
Isobutanol_IL01_ANAE_R2


title: Isobutanol_IL01_ANAE_R1 [RNA-Seq_3strains]

description:
Grew strains from OD600 0.01 and collected at OD600 0.5, in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 4% in aerobic conditions, shaking in the incubator.  Additionally, we performed this experiment in the anaerobic chamber for the same three strains in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 3%.  Goal was to determine stress mechanisms of different types of alcohols, and how oxygen affect these mechanisms.
Isobutanol_IL01_ANAE_R1


title: Butanol_Y7568_AER_R2 [RNA-Seq_3strains]

description:
Grew strains from OD600 0.01 and collected at OD600 0.5, in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 4% in aerobic conditions, shaking in the incubator.  Additionally, we performed this experiment in the anaerobic chamber for the same three strains in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 3%.  Goal was to determine stress mechanisms of different types of alcohols, and how oxygen affect these mechanisms.
Butanol_Y7568_AER_R2


title: Butanol_NCY3290_ANAE_R1 [RNA-Seq_3strains]

description:
Grew strains from OD600 0.01 and collected at OD600 0.5, in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 4% in aerobic conditions, shaking in the incubator.  Additionally, we performed this experiment in the anaerobic chamber for the same three strains in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 3%.  Goal was to determine stress mechanisms of different types of alcohols, and how oxygen affect these mechanisms.
Butanol_NCY3290_ANAE_R1


title: YPD_NCY3290_AER_R1 [RNA-Seq_3strains]

description:
Grew strains from OD600 0.01 and collected at OD600 0.5, in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 4% in aerobic conditions, shaking in the incubator.  Additionally, we performed this experiment in the anaerobic chamber for the same three strains in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 3%.  Goal was to determine stress mechanisms of different types of alcohols, and how oxygen affect these mechanisms.
YPD_NCY3290_AER_R1


title: Isobutanol_NCY3290_ANAE_R2 [RNA-Seq_3strains]

description:
Grew strains from OD600 0.01 and collected at OD600 0.5, in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 4% in aerobic conditions, shaking in the incubator.  Additionally, we performed this experiment in the anaerobic chamber for the same three strains in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 3%.  Goal was to determine stress mechanisms of different types of alcohols, and how oxygen affect these mechanisms.
Isobutanol_NCY3290_ANAE_R2


title: YPD_IL_AER_R2 [RNA-Seq_3strains]

description:
Grew strains from OD600 0.01 and collected at OD600 0.5, in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 4% in aerobic conditions, shaking in the incubator.  Additionally, we performed this experiment in the anaerobic chamber for the same three strains in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 3%.  Goal was to determine stress mechanisms of different types of alcohols, and how oxygen affect these mechanisms.
YPD_IL_AER_R2


title: Mi1_d1_rep2

status: Public on Aug 05 2018

city: Bethesda

first: Fred

middle: P.

last: Davis

state: MD

address: 9000 Rockville Pike

department: NIAMS

institute: NIH

description:
QC: pass
s002

data_processing:
We trimmed five nucleotides from the 5’ end of reads using seqtk (https://github.com/lh3/seqtk) to remove potential contaminating adapter sequence from the NuGen Ovation kit. We estimated the abundance of annotated genes using kallisto (v 0.43.1; Bray et al., 2015) to pseudo-align trimmed reads to the fly transcriptome (cDNA and ncRNA transcript sequences from ENSEMBL release 91, based on FlyBase release 2017_04), ERCC spike-ins, and the INTACT construct sequences GAL4-DBD, p65-AD, and UNC84_2XGFP.
ERCC, INTACT tag constructs, and rRNA genes were removed from the abundance tables and the estimated abundances of the remaining genes were renormalized to one million total transcripts.
We further analyzed high-quality libraries passing three criteria: > 8,500 genes detected, > 3ug cDNA yield, r>= 0.85 pearson correlation between replicates
We modeled transcript abundance (in high-quality libraries) as arising from a gene-specific mixture of on and off log-normal components (See manuscript for details). We used this model to transform transcript abundance into probabilities of expression (probability of arising from on state).
Genome_build: dm6. ENSEMBL BDGP.r91

molecule: nuclear RNA

organism: Drosophila melanogaster

growth_protocol: Split-GAL4 and GAL4 driver lines were used to express the INTACT reporter (UNC84-2XGFP) in defined cell populations

extract_protocol:
INTACT protocol: Adult flies were entrained to a 12:12 light:dark cycle, anesthetized by CO2 at ZT8 - ZT12, flash frozen in liquid N2 and decapitated by vigorous vortexing. Heads or wings/appendages were then collected on cooled metal sieves (H&C Sieving Systems: 1296, 1297, 1298, 1301). Both flies and purified frozen material can be stored indefinitely at -80degrees C. In a typical experiment 100 to 500 frozen heads were added to 5mls of 20mM Beta-glycerophosphate pH7, 200mM NaCl, 2mM EDTA, 0.5% NP40, 0.5mM spermidine, 0.15mM spermine, 1mM DTT, 1X complete protease inhibitor (Sigma: 5056489001), 3mg/ml BSA (ThermoFisher: AM2618), 1mg/ml torula RNA (ThermoFisher: AM7118), 0.6mg/ml carboxyl coated Dynabeads (ThermoFisher: 14306D) and 2 microgram anti-GFP antibody (ThermoFisher: G10362). Homogenization was carried out on ice by 50 tractions in a Dounce homogenizer using the tight pestle followed by filtration over a 10 micrometer cup filter (Partec: 0400422314). Released chromatin and broken nuclei were adsorbed to carboxyl coated magnetic beads for 30 minutes at 4 degrees C with constant rotation. After which the beads were removed on a magnetic stand, the supernatant diluted to 50mls with 20mM Beta-glycerophosphate pH7, 200mM NaCl, 2mM EDTA, 0.5% NP40, 0.5mM spermidine, 0.15mM spermine, 1mM DTT and 1X complete protease inhibitor (Sigma: 5056489001), filtered over a 1 micrometer cup filter (Pluriselect: 435000103) and split into two equal volumes. A 40% Optiprep (Sigma: D1556), 20mM Beta-glycerophosphate pH7, 2mM EDTA and 0.5% NP40 solution was then carefully placed under each aliquot. Followed by a lower layer of 50% Optiprep, 20mM Beta-glycerophosphate pH7, 2mM EDTA and 0.5% NP40. Nuclei were then pelleted on to the 50% layer for 30 minutes at 2300Xg. Purified nuclei were passed over a 10 micrometer cup filter, diluted to 10mls with 20mM Beta-glycerophosphate pH7, 200mM NaCl, 2mM EDTA, 0.5% NP40, 0.5mM spermidine, 0.15mM spermine, 1mM DTT and 1X complete protease inhibitor and incubated with 30 microliters of protein G Dynabeads (ThermoFisher: 10004D) for 40 minutes on ice with occasional agitation. Bead-bound nuclei were recovered on a magnet stand followed by a 20 minute incubation on ice in 9mls of 20mM Beta-glycerophosphate pH7, 300mM NaCl, 1M urea, 0.5% NP40, 2mM EDTA, 0.5mM spermidine, 0.15mM spermine, 1mM DTT, 1X complete protease inhibitor, 0.075mg/ml torula RNA and 0.05Units/ml Superasin (ThermoFisher: AM2696). Nuclei were then recovered on a magnet stand, resuspended in 1ml of the previous buffer, passed over a 10 micrometer cup filter, a 5 microliter aliquot was withdrawn for quantitation and the remainder of the sample solubilized in Arcturus Picopure RNA extraction buffer (ThermoFisher: KIT0204).
TAPIN-seq protocol: 100 to 3000 frozen heads were added to 5mls of sodium acetate ph8.5, 2.5mM MgCl2, 250mM sucrose, 0.5% NP-40, 0.6mM spermidine, 0.2mM spermine, 1mM DTT, 1X complete protease inhibitor, 0.5mg/ml torula RNA, 0.6mg/ml carboxyl coated Dynabeads and 2microgram anti-GFP antibody. Homogenization was carried out on ice by 50 tractions in a Dounce homogenizer using the tight pestle followed by filtration over either a 10 or 20 micrometer cup filter (Partec: 0400422314, 040042315). Released chromatin and broken nuclei were adsorbed to carboxyl coated magnetic beads for 30 minutes at 4 degrees C with constant rotation. Unbound antibody was removed by incubating the sample on ice for 20 minutes with 100 microliters of washed UNOsphere SUPra resin (Biorad: 1560218). After the resin was removed on a 10 micrometer cup filter and the carboxyl beads on a magnet stand, the nuclei-containing supernatant was mixed with an equal volume of 500mM sodium acetate ph8.5, 250mM sucrose, 6mM EGTA, 6mM EDTA, 0.6mM spermidine, 0.2mM spermidine, 1mM DTT, 1X complete protease inhibitor, 0.25mg/ml torula RNA and 30 microliters Protein A Dynabeads (ThermoFisher: 10002D). A 2 hour incubation on ice with occasional agitation was used to recover tagged nuclei. Bead-bound nuclei were then recovered on a magnet stand and washed twice with 250mM sodium acetate ph8.5, 250mM sucrose and 0.1% NP40. Nuclei were then released at 37 degrees C for 1 hour by incubation in 50 microliters of 10mM Tris pH7.5, 2.5mM MgCl2, 0.5mM CaCl2, 250mM sucrose, 0.1% NP40, 1mg/ml torula RNA, 40 units RNAsin (Promega: N2515), 2 units DNAseI (NEB: M0303L), 320 units IdeZ protease (NEB: P0770S). The sample was diluted to 100 microliters with 10mM Tris pH7.5, 2.5mM MgCl2, 0.5mM CaCl2, 250mM sucrose and 0.1% NP40, EGTA was added to 1mM and the suspension was rapidly triturated 100 times. After returning the sample to a magnet stand, 90 microliters of buffer containing released nuclei was removed and added to 1.5 microliters of Protein G Dynabeads that were previously resuspended in 10 microliters of 10mM Tris pH7.5, 2.5mM MgCl2, 0.5mM CaCl2, 250mM sucrose and 0.1% NP40. The second binding reaction was run for 1 to 3 hours on ice with occasional agitation, followed by 2 X 250 microliters washes in 10mM Tris pH7.5, 2.5mM MgCl2, 0.5mM CaCl2, 250mM sucrose and 0.1% NP40. Prior to the last wash a 5 microliter aliquot was removed for quantitation and the remainder of the sample was solubilized in Arcturus Picopure RNA extraction buffer.

tag: tissue

value: head

tag: genetic driver

tag: driver type

tag: external driver id

tag: intact reporter

tag: intact protocol

value: INTACT


title: YPD_NCY3290_ANAE_R2 [RNA-Seq_3strains]

description:
Grew strains from OD600 0.01 and collected at OD600 0.5, in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 4% in aerobic conditions, shaking in the incubator.  Additionally, we performed this experiment in the anaerobic chamber for the same three strains in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 3%.  Goal was to determine stress mechanisms of different types of alcohols, and how oxygen affect these mechanisms.
YPD_NCY3290_ANAE_R2


title: YPD_NCY3290_ANAE_R1 [RNA-Seq_3strains]

description:
Grew strains from OD600 0.01 and collected at OD600 0.5, in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 4% in aerobic conditions, shaking in the incubator.  Additionally, we performed this experiment in the anaerobic chamber for the same three strains in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 3%.  Goal was to determine stress mechanisms of different types of alcohols, and how oxygen affect these mechanisms.
YPD_NCY3290_ANAE_R1


title: YPD_Y7568_AER_R1 [RNA-Seq_3strains]

description:
Grew strains from OD600 0.01 and collected at OD600 0.5, in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 4% in aerobic conditions, shaking in the incubator.  Additionally, we performed this experiment in the anaerobic chamber for the same three strains in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 3%.  Goal was to determine stress mechanisms of different types of alcohols, and how oxygen affect these mechanisms.
YPD_Y7568_AER_R1


title: Butanol_IL01_AER_R1 [RNA-Seq_3strains]

description:
Grew strains from OD600 0.01 and collected at OD600 0.5, in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 4% in aerobic conditions, shaking in the incubator.  Additionally, we performed this experiment in the anaerobic chamber for the same three strains in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 3%.  Goal was to determine stress mechanisms of different types of alcohols, and how oxygen affect these mechanisms.
Butanol_IL01_AER_R1


title: Butanol_NCY3290_ANAE_R2 [RNA-Seq_3strains]

description:
Grew strains from OD600 0.01 and collected at OD600 0.5, in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 4% in aerobic conditions, shaking in the incubator.  Additionally, we performed this experiment in the anaerobic chamber for the same three strains in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 3%.  Goal was to determine stress mechanisms of different types of alcohols, and how oxygen affect these mechanisms.
Butanol_NCY3290_ANAE_R2


title: Butanol_Y7568_AER_R1 [RNA-Seq_3strains]

description:
Grew strains from OD600 0.01 and collected at OD600 0.5, in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 4% in aerobic conditions, shaking in the incubator.  Additionally, we performed this experiment in the anaerobic chamber for the same three strains in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 3%.  Goal was to determine stress mechanisms of different types of alcohols, and how oxygen affect these mechanisms.
Butanol_Y7568_AER_R1


title: Mouse-stomach-development-W1

city: Beijing

first: Xianju

last: Li

address: Life Science Park Road 38#

country: China

institute: National Center for Protein Sciences (The PHOENIX Center, Beijing)

data_processing:
Illumina HiSeq 4000 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mus musculus GRCm38.p2 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata.
FastQC from Simon Andrews et al.(https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)  were used to provide a simple way to do some quality control checks on raw sequence data
Fractions Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Mihaela Pertea et al., Nature Protocols,2016.
Genome_build: Mus musculus GRCm38.p2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …

organism: Mus musculus

source_name: stomach

growth_protocol: The aging by "embryonic days" relate to in the female presence of a vaginal plug indicating that the mating occurred.(https://embryology.med.unsw.edu.au/embryology/index.php/Mouse_Timeline_Detailed#Timed_Pregnancy)

extract_protocol:
Flash tissue frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina SBS regent (Hiseq 4000 SBS KIT) was used  for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: stomach

tag: age

value: Postnatal week1


title: Mouse-stomach-development-W2

value: Postnatal week2


title: Mouse-stomach-development-D1

value: Postnatal day1


title: Mouse-stomach-development-W6

value: Postnatal week6


title: Mouse-stomach-development-D3

value: Postnatal day3


title: Mouse-stomach-development-W3

value: Postnatal week3


title: Mouse-stomach-development-D5

value: Postnatal day5


title: Mouse-stomach-development-W8

value: Postnatal week8


title: FSPCre-PPARB KO ileum mucosa 1

type: RNA

city: Singapore

first: Eddie

middle: Han Pin

last: Tan

address: 60 Nanyang Drive

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

description:
Gene expression data from dissected mucosa from mouse ileum
Ileum_Mucosa_FSPPPARBKO1

hyb_protocol: 2 ug of cDNA were hybridized for 18hrs at 45C on GeneChip Mouse MTA-1_0 Array under gentle agitation in genechip hybridization oven 640. Genechip fluidics station 450 was then used for the washing and staining of the chips.

scan_protocol: Genechips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Partek genomic suite 6.0 was used to analyze samples by RMA.

label: biotin

source_name: FSPCre-PPARB KO ileum mucosa

label_protocol: Further sample processing of the RNA was carried out using GeneChip® WT Pico Kit

growth_protocol: Male FSPCre-PPARB -/- and PPARB flox/flox littermates were housed at 25 oC with regular light cycles of 12 light/12 dark hours, until sacrifice when 4 to 6 weeks-old.

extract_protocol: Mucosal tissue was dissected from colon or ileum sections

treatment_protocol: No treatment was administered

tag: background strain

tag: genotype/variation

value: FSPCre-PPARB -/-

tag: tissue source

value: Laser dissected tissue from sectioned tumors

value: Ileum Mucosa


title: Nicks, wild type rep1

type: genomic

city: Debrecen

first: Halasz

last: Laszlo

address: Egyetem tér 1

department: Department of Biochemistry and Molecular Biology

country: Hungary

institute: University of Debrecen

description: Nicks detected in wild-type yeast cells

hyb_protocol: The ChIP-on-Chip protocol of Agilent was followed.

scan_protocol: SureScan microarray scanner. Images were quantified, background subtracted and intra-array normalized using the Agilent Feature Extraction Software v9.5.1.1.

data_processing: Nick-ChIP enrichment was expressed as log10 anti-biotin ChIP/WCE ratios.

molecule: genomic DNA

source_name: Whole-cell extract

label_protocol: Two-thirds of the immunoprecipitated DNA was amplified by random primer extension followed by PCR amplification, incorporating amino-allyl dUTP for subsequent dye (Cy5 or Cy3) coupling.

growth_protocol: S. cerevisiae cells were grown in rich medium (YPD) to exponential phase and were fixed by 1% formaldehyde and embedded into 1% LMP agarose plugs.

extract_protocol: Nucleic acid preps were gel-purified and fragmented by sonication.

treatment_protocol: Single strand DNA breaks with 3'-OH termini were tagged by biotin-dCTP using E. coli DNA pol I holoenzyme.

tag: tag

value: biotin-dCTP, input

value: biotin dCTP, IP


title: Nickase

description: Nicks detected in nickase-digested wild-type yeast cells


title: Mouse-stomach-development-E18.5

value: Embryonic day18.5


title: Mouse-stomach-development-E17.5

value: Embryonic day17.5


title: Nicks, wild type rep2

description: Nicks detected in wild-type yeast cells


title: FSPCre-PPARB KO ileum mucosa 3

description:
Gene expression data from dissected mucosa from mouse ileum
Ileum_Mucosa_FSPPPARBKO3


title: Mouse-stomach-development-E16.5

value: Embryonic day16.5


title: PPARB floxed ileum mucosa 1

description:
Gene expression data from dissected mucosa from mouse ileum
Ileum_Mucosa_WT1

source_name: PPARB floxed ileum mucosa

value: PPARB flox/flox


title: Mouse-stomach-development-E14.5

value: stomach

value: Embryonic day14.5


title: Mouse-stomach-development-E13.5

value: Embryonic day13.5


title: PPARB floxed ileum mucosa 3

description:
Gene expression data from dissected mucosa from mouse ileum
Ileum_Mucosa_WT3


title: Mouse-stomach-development-E12.5

value: Embryonic day12.5


title: FSPCre-PPARB KO ileum mucosa 2

description:
Gene expression data from dissected mucosa from mouse ileum
Ileum_Mucosa_FSPPPARBKO2


title: PPARB floxed colon mucosa 3

description:
Gene expression data from dissected mucosa from mouse colons
Colon_Mucosa_WT3

source_name: PPARB floxed colon mucosa

value: Colon Mucosa


title: FSPCre-PPARB KO colon mucosa 2

description:
Gene expression data from dissected mucosa from mouse colons
Colon_Mucosa_FSPPPARBKO2

source_name: FSPCre-PPARB KO colon mucosa


title: H37Rv_12.5SMX_D1_rep3

city: Seattle

first: Shuyi

last: Ma

state: Washington

address: 1900 9th Avenue

department: Department of Pediatrics

institute: University of Washington

description: SMX.Expression.Rvgens.csv

data_processing:
Raw FASTQ read data processing was carried out using a custom processing pipeline that harnesses the Bowtie 2 utilities, which is available at https://github.com/sturkarslan/DuffyNGS, and https://github.com/sturkarslan/DuffyTools, as previously described (PMID: 25784701)
The pipeline consists of 2 stages: 1) a pre-alignment filtering step to remove unwanted transcripts such as rRNA, and 2) a genomic alignment step using Bowtie2 with the command line option 'very-sensitive.'
BAM files from step 2 are combined into read depth wiggle tracks that record both uniquely mapped and multiply mapped reads from each of the forward and reverse strangs of the genome. Multiply mapped reads are prorated over all highest-quality aligned locations. Transcript abundance is quantified by summing total reads landing inside annotated gene boundaries, expressed by RPKM.
Genome_build: MT_H37Rv_V3
Supplementary_files_format_and_content: Transcript abundance is quantified by summing total reads landing inside annotated gene boundaries, expressed by RPKM.

organism: Mycobacterium tuberculosis

source_name: H37Rv Mycobacterium tuberculosis

growth_protocol: Mycobacteria tuberculosis strain H37Rv (ATCC 27294) were grown on Middlebrook 7H9 medium (Difco) with 0.05% Tween 80 and ADC supplement.

extract_protocol:
RNA was isolated using published protocols (Rustad TR, Harrell MI, Liao R, Sherman DR (2008) The Enduring Hypoxic Response of Mycobacterium tuberculosis. PLoS ONE 3(1): e1502). In summary, frozen cell pellets Pellets were resuspended in Trizol, transferred to a tube containing Lysing Matrix B (QBiogene, Inc.), and vigorously shaken at max speed for 30 sec in a FastPrep 120 homogenizer (Qbiogene) three times, with cooling on ice between steps. This mixture was centrifuged at max speed for 1 min and the supernatant was transferred to a tube containing 300 mL chloroform and Heavy Phase Lock Gel (Eppendorf North America, Inc.), inverted for one minute, and centrifuged at max speed. The aqueous phase was then precipitated with 270 mL isopropanol and 270 mL high salt solution (0.8M Na citrate, 1.2M NaCl). RNA was cleaned using an RNeasy kit following manufacturer’s recommendations (Qiagen). Messenger RNA was enriched using the RiboZero rRNA removal (bacteria) magnetic kit (Illumina Inc.) according to manufacturer's instructions.
Libraries were prepared for Illumina sequencing using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs) according to manufacturer's instructions and using the AMPure XP reagent (Agencourt Bioscience Corporation) for size selection and cleanup of adaptor-ligated DNA. We used the NEBNext Multiplex Oligos for Illumina (Dual Index Primers Set 1) to barcode the libraries associated with each replicate and multiplexing up to 48 libraries per sequencing run. The prepared libraries were quantified using the Kapa qPCR quantification kit, and were sequenced at the University of Washington Northwest Genomics Center with the Illumina NextSeq 500 High Output v2 Kit (Illumina Inc).

treatment_protocol: Bacteria were harvested at 0, 1 days after being exposed to concentrations of sulfamethoxazole (0μM, 12.5μM) (as indicated in each sample title).

tag: drug dose

tag: days post drug


title: E: RWV ColI

city: Temple

first: Carl

middle: A

last: Gregory

state: Texas

address: 5701 Airport Road

department: Molecular and Cellular Medicine

institute: Texas A&M Health Sciences Center

description: RWV ColI

scan_protocol: Chips were read on an Illumina Hiscan scanner and analyzed according to standard manufacturer’s protocols using GenomeStudio version 3 (Illumina).

data_processing: Background correction, quality control, and quantile normalization were performed in accordance with Illumina standard operating procedures.

organism: Homo sapiens

source_name: RWV ColI

label_protocol: Biotin-UTP labeled antisense copy RNA (cRNA) was generated from 200 ng of total RNA using a commercially available kit (Illumina TotalPrep RNA Amplification Kit, Life Technologies, Carlsbad, CA). Labeled cRNA was hybridized to a HumanHT-v4.0 Expression BeadChip (Illumina, San Diego, CA) and visualized with biotin-Cy3 (Amersham, Piscataway, NJ, USA).

growth_protocol: Two million human mesenchymal stem cells (hMSC) were grown as monolayers or attached to spherical microcarriers on 50 cm^2 growth area ofr 8 days in alpha MEM with 20% bovine serum in the presence of ostegenic supplements 5 mM beta glycerophosphate and 50 microM ascorbate

extract_protocol: After 8 days, the cell-laden beads were recovered by brief centrifugation, washed in PBS and subjected to total RNA purification with a ROche Highpure minifilter.  Resultant total RNA yields ranged from 4.5-13.5 microg at a concentration of 150-450 microg mL-1 with OD260/280 ratios ranging from between 1.85-2.0. RNA integrity was confirmed by analysis using an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA) and RNA integrity scores were 10 in each case.

treatment_protocol: Some cultures were grown on collagen I coating and some were grown on an extracellular matrix derived from osteogenic hMSCs

value: Mesenchymal stem cells


title: H37Rv_12.5SMX_D0_rep3

description: SMX.Expression.Rvgens.csv


title: PPARB floxed colon mucosa 2

description:
Gene expression data from dissected mucosa from mouse colons
Colon_Mucosa_WT2


title: G: Monolayer hMatrix

description: Monolayer hMatrix

hyb_protocol: Labeled cRNA was hybridized to a HumanHT-v4.0 Expression BeadChip (Illumina, San Diego, CA) and visualized with biotin-Cy3 (Amersham, Piscataway, NJ, USA).

source_name: Monolayer hMatrix


title: H: Monolayer hMatrix

description: Monolayer hMatrix


title: H37Rv_12.5SMX_D1_rep2

description: SMX.Expression.Rvgens.csv


title: C: RWV hMatrix

description: RWV hMatrix

source_name: RWV hMatrix


title: H37Rv_12.5SMX_D0_rep1

description: SMX.Expression.Rvgens.csv


title: H37Rv_12.5SMX_D1_rep1

description: SMX.Expression.Rvgens.csv


title: B: RWV hMatrix

description: RWV hMatrix


title: H37Rv_12.5SMX_D0_rep2

description: SMX.Expression.Rvgens.csv


title: A: RWV hMatrix

description: RWV hMatrix


title: F: RWV ColI

description: RWV ColI


title: PPARB floxed colon mucosa 1

description:
Gene expression data from dissected mucosa from mouse colons
Colon_Mucosa_WT1


title: D: RWV ColI

description: RWV ColI


title: L: Monolayer colI

description: Monolayer colI

source_name: Monolayer colI


title: K: Monolayer colI

description: Monolayer colI


title: J: Monolayer colI

description: Monolayer colI


title: FSPCre-PPARB KO colon mucosa 1

description:
Gene expression data from dissected mucosa from mouse colons
Colon_Mucosa_FSPPPARBKO1


title: H37Rv_0SMX_D0_rep3

description: SMX.Expression.Rvgens.csv

value: 0 uM


title: H37Rv_0SMX_D1_rep3

description: SMX.Expression.Rvgens.csv


title: Isobutanol_NCY3290_ANAE_R1 [RNA-Seq_3strains]

description:
Grew strains from OD600 0.01 and collected at OD600 0.5, in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 4% in aerobic conditions, shaking in the incubator.  Additionally, we performed this experiment in the anaerobic chamber for the same three strains in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 3%.  Goal was to determine stress mechanisms of different types of alcohols, and how oxygen affect these mechanisms.
Isobutanol_NCY3290_ANAE_R1

value: Isobutanol


title: YPD_NCY3290_AER_R2 [RNA-Seq_3strains]

description:
Grew strains from OD600 0.01 and collected at OD600 0.5, in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 4% in aerobic conditions, shaking in the incubator.  Additionally, we performed this experiment in the anaerobic chamber for the same three strains in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 3%.  Goal was to determine stress mechanisms of different types of alcohols, and how oxygen affect these mechanisms.
YPD_NCY3290_AER_R2

value: YPD


title: H37Rv_0SMX_D1_rep2

description: SMX.Expression.Rvgens.csv


title: FSPCre-PPARB KO colon mucosa 3

description:
Gene expression data from dissected mucosa from mouse colons
Colon_Mucosa_FSPPPARBKO3

value: FSPCre-PPARB -/-

value: Laser dissected tissue from sectioned tumors


title: PPARB floxed ileum mucosa 2

description:
Gene expression data from dissected mucosa from mouse ileum
Ileum_Mucosa_WT2

value: Ileum Mucosa


title: triple-2

city: New York

first: Duncan

last: Smith

state: NY

address: 1009 Silver Center, 100 Washington Sq E

department: Dept. of Biology/Center for Genomics and Systems Biology

institute: New York University

library_source: genomic

data_processing:
bowtie2 (version 2.2.3) was used to align paired-end fastq files to the S. cerevisiae reference genome
sam files were converted to bam files using samtools then reads were sorted
bam files were converted to bed files using bedtools paired end function
Printed columns for the chromosome, position of the start and stop of mate 1 and mate 2, name, and strand information for mate 1 and mate 2 into output bedpe files
Genome_build: Yeast S288C, build R64-1-1
Supplementary_files_format_and_content: bedpe files, chromosome,start and stop positions of mate 1 and mate 2, name, and strand information for mate 1 and mate 2

growth_protocol: Stains were grown at 30ºC in YPD.

extract_protocol:
Okazaki fragments were enriched and purified as described previously (Smith, D. J., and Whitehouse, I. (2012). Intrinsic coupling of lagging-strand synthesis to chromatin assembly. Nature 483, 434-438)
Libraries were generated as previously described (Smith, D. J., and Whitehouse, I. (2012). Intrinsic coupling of lagging-strand synthesis to chromatin assembly. Nature 483, 434-438)

treatment_protocol: Rapamycin was added to a final concentration of 1 mg/ml for the depletion of CDC9 and the nucleases.

tag: strain background

value: W303 tor1-1::HIS3, fpr1::NatMX4, RPL13A-2xFKBP12::TRP1, CDC9-FRB::KanMX6

tag: genotypic variation

tag: molecule subtype

value: DNA, Okazaki fragments


title: triple-1


title: rad27;exo1-2


title: Mouse-stomach-development-E15.5

tag: strain

value: Embryonic day15.5


title: H37Rv_0SMX_D1_rep1

description: SMX.Expression.Rvgens.csv


title: H37Rv_0SMX_D0_rep1

description: SMX.Expression.Rvgens.csv


title: rad27;exo1-1


title: rad27;dna2-2


title: dna2;exo1-2


title: rad27;dna2-1


title: dna2;exo1-1


title: H37Rv_4LZD_D0_rep4

description: LZD.Expression.Rvgens.csv

treatment_protocol: Bacteria were harvested at 0, 1 days after being exposed to concentrations of linezolid (0μM, 4μM) (as indicated in each sample title).

value: 4 uM


title: H37Rv_4LZD_D1_rep4

description: LZD.Expression.Rvgens.csv


title: H37Rv_4LZD_D1_rep3

description: LZD.Expression.Rvgens.csv


title: H37Rv_4LZD_D0_rep3

description: LZD.Expression.Rvgens.csv


title: H37Rv_0SMX_D0_rep2

description: SMX.Expression.Rvgens.csv


title: H37Rv_4LZD_D1_rep2

description: LZD.Expression.Rvgens.csv


title: rad27-1


title: exo1-2


title: H37Rv_4LZD_D1_rep1

description: LZD.Expression.Rvgens.csv


title: H37Rv_4LZD_D0_rep1

description: LZD.Expression.Rvgens.csv


title: YPD_Y7568_AER_R2 [RNA-Seq_3strains]

description:
Grew strains from OD600 0.01 and collected at OD600 0.5, in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 4% in aerobic conditions, shaking in the incubator.  Additionally, we performed this experiment in the anaerobic chamber for the same three strains in YPD, YPD + Butanol 0.8%, YPD + Isobutanol 1%, YPD + Ethanol 3%.  Goal was to determine stress mechanisms of different types of alcohols, and how oxygen affect these mechanisms.
YPD_Y7568_AER_R2

tag: agent


title: H37Rv_4LZD_D0_rep2

description: LZD.Expression.Rvgens.csv


title: rad27-2


title: dna2-2


title: H37Rv_0LZD_D1_rep4

description: LZD.Expression.Rvgens.csv


title: H37Rv_0LZD_D0_rep4

description: LZD.Expression.Rvgens.csv


title: WT-2

source_name: wild type CDC9-FRB

value: WT


title: H37Rv_0LZD_D1_rep3

description: LZD.Expression.Rvgens.csv


title: H37Rv_0LZD_D0_rep2

description: LZD.Expression.Rvgens.csv


title: H37Rv_0LZD_D0_rep3

description: LZD.Expression.Rvgens.csv


title: WT-1


title: dna2-1


title: H37Rv_0LZD_D1_rep1

description: LZD.Expression.Rvgens.csv


title: KMST6_MYC_CUG_rep3

city: La Jolla

first: Kuniaki

last: Sato

state: CA

address: 3855 Health Sciences Dr Room 2345

department: Moores Cancer Center

institute: University of California San Diego

data_processing:
The in-house pipeline Genomon 2.5.0  (https://genomon-project.github.io/GenomonPagesR)  was used for quality control and mapping.
The sequencing reads were trimmed for adaptor sequence, and low-complexity or low-quality reads were removed. Subsequently, the sequencing reads were aligned to the human reference GRCh38 genome with Gencode v27 annotations by STAR v2.5.2a with following parameters; --runThreadN 6 --outSAMstrandField intronMotif --outSAMunmapped Within --alignMatesGapMax 500000 --alignIntronMax 500000 --alignSJstitchMismatchNmax -1 -1 -1 -1 --outSJfilterDistToOtherSJmin 0 0 0 0 --outSJfilterOverhangMin 12 12 12 12 --outSJfilterCountUniqueMin 1 1 1 1 --outSJfilterCountTotalMin 1 1 1 1 --chimSegmentMin 12 --chimJunctionOverhangMin 12.
Read counts per gene were quantified using the HTSeq Python package.
Genome_build: GRCh38 with Gencode v27 annotations
Supplementary_files_format_and_content: tab-delimited text files of read counts per gene from HTSeq

source_name: Fibroblast cell line

extract_protocol:
Total RNA was extracted from the cells using ISOGEN II (Nippon Gene).
After the total RNA extraction and DNase I treatment, magnetic beads with Oligo (dT) are used to isolate mRNA. Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. Then cDNA is synthesized using the mRNA fragments as templates. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters. The suitable fragments are selected for the PCR amplification as templates. During the quality checking steps, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used in quantification and qualification of the sample library.

tag: wt cell line name

tag: source of wt cell line

value: RIKEN BRC Cat# RCB1955

tag: expression

value: CUG-initiated c-Myc


title: KMST6_MYC_CUG_rep1


title: KMST6_MYC_AUG_rep2

value: AUG-initiated c-Myc


title: KMST6_MYC_AUG_rep3


title: H37Rv_0LZD_D0_rep1

description: LZD.Expression.Rvgens.csv


title: KMST6_MYC_CUG_rep2


title: H37Rv_25DDS_D1_rep4

description: DDS.Expression.Rvgens.csv

treatment_protocol: Bacteria were harvested at 0, 1 days after being exposed to concentrations of dapsone (0μM, 25μM) (as indicated in each sample title).

value: 25 uM


title: exo1-1


title: H37Rv_25DDS_D0_rep4

description: DDS.Expression.Rvgens.csv


title: H37Rv_25DDS_D0_rep3

description: DDS.Expression.Rvgens.csv


title: H37Rv_25DDS_D1_rep3

description: DDS.Expression.Rvgens.csv


title: KMST6_control_rep3

value: empty vector


title: KMST6_MYC_AUG_rep1


title: HCT116 control

description: transfected with pCDF1-MCS2-EF1-Puro

source_name: Colorectal cancer cell line

value: RIKEN BRC Cat# RCB2979

tag: transfection


title: H37Rv_25DDS_D1_rep2

description: DDS.Expression.Rvgens.csv


title: KMST6_control_rep1


title: HCT116 5MP1

description: transfected with pCDF1-5MP1-EF1-Puro


title: H37Rv_25DDS_D0_rep2

description: DDS.Expression.Rvgens.csv


title: H37Rv_25DDS_D1_rep1

description: DDS.Expression.Rvgens.csv


title: KMST6_control_rep2


title: H37Rv_25DDS_D0_rep1

description: DDS.Expression.Rvgens.csv


title: H37Rv_0DDS_D1_rep4

description: DDS.Expression.Rvgens.csv

value: 0 uM


title: H37Rv_0DDS_D0_rep4

description: DDS.Expression.Rvgens.csv


title: H37Rv_0DDS_D1_rep3

description: DDS.Expression.Rvgens.csv


title: H37Rv_0DDS_D1_rep2

description: DDS.Expression.Rvgens.csv


title: H37Rv_0DDS_D0_rep3

description: DDS.Expression.Rvgens.csv


title: H37Rv_0DDS_D1_rep1

description: DDS.Expression.Rvgens.csv


title: MLL-AF9 Evi1 Tg, replicate 3

city: Miyazaki

first: Yusuke

last: Saito

address: 5200 Kihara Kiyotake-cho

country: Japan

institute: University of Miyazaki

description: Evi1 Tg 3

hyb_protocol: 2.3 μg of labeled cDNA were hybridized to Affymetrix Mouse Gene ST 2.0 microarrays.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000 and the GeneChip Command Console software v3.0.

data_processing: The data were analyzed with GeneSpring GX using default analysis settings.

source_name: Whole leukemia cells from MLL-AF9 Evi1-Tg

label_protocol: Biotinylated cDNA were prepared using GeneChip WT PLUS Reagent Kit (Thermo Fisher Scientific).

growth_protocol: Leukemia cells were plated in MethoCult M3234 (StemCell Technologies, Vancouver, Canada) medium supplemented with 20 ng/ml SCF, 10 ng/ml GM-CSF, 10 ng/ml IL-3, and 10 ng/ml IL-6, according to the manufacturer’s instructions, and used for colony forming assays.

extract_protocol: 10,000 whole leukemia cells (GFP+) were into Tri Regent by cell sorter.

treatment_protocol: Untreated

tag: strain/background

value: Evi1 Tg

tag: cell type

value: Whole AML cells


title: AZA-3

city: Paris

first: Franck

last: Letourneur

address: 22 rue mechain

country: France

institute: INSERM

hyb_protocol: biotynilated single stranded sense  cDNA is then hybridized to GeneChip® Human Gene2.0 (Affymetrix) at 45°C for 17 hours

scan_protocol: After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G

data_processing: Data were normalized using RMA and statistical analysis was realized on Partek Genomics Suite. Brain array CDF file V21 was used for annotation.

label: Biotin

source_name: AZA

label_protocol: 250 ng of total RNA is reverse transcribed  following the Genechip Whole transcript (WTplus) Sense Target labelling assay kit (Affymetrix). Briefly, the resulting double strand cDNA is used for in vitro transcription with T7 RNA pol. This cRNA is reverse transcribed in single stranded sens DNA which is fragmented and biotin labelled

extract_protocol: not provided

tag: tissue

value: Hematopoietic

tag: cell line


title: NT-3

source_name: NT


title: MLL-AF9 Evi1 Tg, replicate 2

description: Evi1 Tg 2

tag: genotype/variation


title: AZA-2


title: AZA-1


title: MLL-AF9 WT, replicate 3

description: WT 3

source_name: Whole leukemia cells from MLL-AF9 WT


title: H37Rv_0DDS_D0_rep1

description: DDS.Expression.Rvgens.csv


title: H37Rv_2.45EMB_D1_rep4

description: Expression.MTB.GeneData.EMB.csv

treatment_protocol: Bacteria were harvested at 0, 1 days after being exposed to concentrations of ethambutol (0μM, 2.45μM) (as indicated in each sample title).

tag: ethambutol dose


title: H37Rv_0DDS_D0_rep2

description: DDS.Expression.Rvgens.csv

tag: drug dose


title: H37Rv_2.45EMB_D0_rep3

description: Expression.MTB.GeneData.EMB.csv

tag: days post drug


title: H37Rv_2.45EMB_D1_rep2

description: Expression.MTB.GeneData.EMB.csv


title: H37Rv_2.45EMB_D0_rep2

description: Expression.MTB.GeneData.EMB.csv


title: H37Rv_2.45EMB_D1_rep3

description: Expression.MTB.GeneData.EMB.csv


title: H37Rv_2.45EMB_D0_rep1

description: Expression.MTB.GeneData.EMB.csv


title: H37Rv_0EMB_D1_rep4

description: Expression.MTB.GeneData.EMB.csv


title: H37Rv_2.45EMB_D1_rep1

description: Expression.MTB.GeneData.EMB.csv


title: H37Rv_2.45EMB_D0_rep4

description: Expression.MTB.GeneData.EMB.csv


title: NT-2


title: I: Monolayer hMatrix

description: Monolayer hMatrix

value: Mesenchymal stem cells


title: MLL-AF9 WT, replicate 2

description: WT 2


title: H37Rv_0EMB_D0_rep4

description: Expression.MTB.GeneData.EMB.csv


title: MLL-AF9 Evi1 Tg, replicate 1

description: Evi1 Tg 1


title: APR-AZA-3

source_name: APR-AZA


title: MLL-AF9 WT, replicate 1

description: WT 1


title: Bone marrow with Stearate, biological rep-2

city: Würzburg

first: Hao

last: Wu

address: versbacherstr 7-9

country: Germany

institute: institute for systemsimmunology, wurzburg university

description: Gene expression data from Stearete polarized bone marrow Gr1- myeloid cells in the presence of GM-CSF

hyb_protocol: The resultant biotinylated cDNA was fragmented and hybridized to the GeneChip Mouse Gene 2.0 ST Array. The arrays were washed, stained, and scanned using the Affymetrix Model 450 Fluidics Station

scan_protocol: The arrays were scanned using the Affymetrix Model 450 Fluidics Station and Affymetrix Model 3000 scanner according to the manufacturer's protocols by the University of Iowa DNA Core Facility.

data_processing: Expression values were generated by using Microarray Suite (MAS) v5.0 software (Affymetrix). Each sample and hybridization underwent a quality control evaluation, including cDNA amplification of >4-fold, percentage of probe sets reliably detecting between 40 % and 60 % present call, and 3'-5' ratio of GAPDH gene <3.

source_name: Balb/c bone marrow

label_protocol: Ten micrograms of total RNA were processed for use on the microarray by using the Affymetrix GeneChip one-cycle target labeling kit (Affymetrix, Santa Clara, CA) according to the manufacturer's protocols.

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

treatment_protocol: Bone marrow cells were isolated and cultured in the non-treated petri dish for overnight in the presence of 40 ng/ml GM-CSF. All the cells were harvested for red cell lysis on the second day. Cells were washed and seeded into 6 well plate in the concentration of 4 million cells per well. Forty ng/ml GM-CSF plus 0.2 mM stearate (SS), oleate (SO) or corresponding dose of BSA control were added into the medium. Refresh the medium every other day. On day 7, cells were harvested for Gr1 negtive sorting. Gr1- cells were used for expression assay.

tag: background strain

value: Balb/c

tag: gender

value: female

tag: age

value: 6-10 weeks

value: bone marrow

value: Gr1- myeloid cells


title: NT-1


title: Bone marrow with Oleate, biological rep-2

description: Gene expression data from Oleate polarized bone marrow Gr1- myeloid cells in the presence of GM-CSF


title: H37Rv_0EMB_D0_rep3

description: Expression.MTB.GeneData.EMB.csv


title: H37Rv_0EMB_D1_rep2

description: Expression.MTB.GeneData.EMB.csv


title: H37Rv_0EMB_D1_rep1

description: Expression.MTB.GeneData.EMB.csv


title: APR-AZA-2


title: H37Rv_0EMB_D0_rep1

description: Expression.MTB.GeneData.EMB.csv


title: vena_porta3_vSMC

status: Public on Aug 03 2018

city: Utrecht

first: Frank

last: van Steenbeek

state: Select State/Province

address: Yalelaan 104

country: Netherlands

institute: Utrecht University

description:
readCounts_raw.txt
processed data file column: SMCvpISO5

data_processing:
RNA-seq reads were aligned to the reference genome using STAR version 2.4.2a
Read groups were added to the BAM files with Picard's AddOrReplaceReadGroups
The BAM files are sorted with Sambamba v0.4.5 and transcript abundances were quantified with HTSeq-count version 0.6.1p1, using the union mode.
Genome_build: canfam3.1
Supplementary_files_format_and_content: readCounts_raw.txt

organism: Canis lupus familiaris

extract_protocol:
cells were trypsinized and stored in RLT. Total RNA was isolated using a RNeasy Mini Kit (Qiagen).
Sequencing libraries were prepared using the Rapid Directional RNA-Seq Kit (NEXTflex)

value: vascular smooth muscle cell


title: H37Rv_0EMB_D0_rep2

description: Expression.MTB.GeneData.EMB.csv


title: APR-AZA-1


title: H37Rv_0EMB_D1_rep3

description: Expression.MTB.GeneData.EMB.csv


title: vena_cava3_vSMC

description:
readCounts_raw.txt
processed data file column: SMCvcISO5


title: vena_porta1_vSMC

description:
readCounts_raw.txt
processed data file column: SMCvpISO1


title: vena_cava2_vSMC

description:
readCounts_raw.txt
processed data file column: SMCvcISO2


title: aorta2_vSMC

description:
readCounts_raw.txt
processed data file column: SMCaoISO2

value: aorta


title: aorta3_vSMC

description:
readCounts_raw.txt
processed data file column: SMCaoISO5


title: vena_cava1_vSMC

description:
readCounts_raw.txt
processed data file column: SMCvcISO1


title: APR-2

source_name: APR


title: vena_porta2_EC

description:
readCounts_raw.txt
processed data file column: ECvp537

value: endothelial cell


title: vena_porta3_EC

description:
readCounts_raw.txt
processed data file column: ECvp840


title: aorta1_vSMC

description:
readCounts_raw.txt
processed data file column: SMCaoISO1


title: APR-1


title: vena_porta1_EC

description:
readCounts_raw.txt
processed data file column: ECvp482


title: vena_cava2_EC

description:
readCounts_raw.txt
processed data file column: ECvc537


title: aorta2_EC

description:
readCounts_raw.txt
processed data file column: ECao537


title: vena_cava1_EC

description:
readCounts_raw.txt
processed data file column: ECvc482


title: vena_cava3_EC

description:
readCounts_raw.txt
processed data file column: ECvc840


title: vena_porta2_vSMC

description:
readCounts_raw.txt
processed data file column: SMCvpISO2


title: APR-3


title: aorta3_EC

description:
readCounts_raw.txt
processed data file column: ECao840


title: Bone marrow with Stearate, biological rep-1

description: Gene expression data from Stearete polarized bone marrow Gr1- myeloid cells in the presence of GM-CSF


title: aorta1_EC

description:
readCounts_raw.txt
processed data file column: ECao482


title: Bone marrow with BSA, biological rep-1

description: Gene expression data from BSA polarized bone marrow Gr1- myeloid cells in the presence of GM-CSF


title: normoxia_48h_rep3

city: Guangzhou

first: Fei

last: Liu

address: No. 1838 North Guangzhou Avenue

institute: Southern Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hs19 whole genome using HISAT2 (version 2.0.4)
Read counts were calculated by HTSeq
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw read counts

source_name: human dental pulp cells

growth_protocol: Primary human dental pulp cells were collected from the pulp tissues of extracted third molars (aged from 15 to 25 years old). Culture cells in an incubator containing 21% oxygen, 5% carbon dioxide, 37 °C.

extract_protocol:
Human dental pulp cells were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: All hypoxia experiments were performed at 3% oxygen concentration.

value: dental pulp

tag: sample id

tag: oxygen status

value: normoxia

tag: time


title: hypoxia_48h_rep3

value: hypoxia


title: normoxia_48h_rep2


title: hypoxia_48h_rep2


title: Bone marrow with Oleate, biological rep-1

description: Gene expression data from Oleate polarized bone marrow Gr1- myeloid cells in the presence of GM-CSF


title: hypoxia_4h_rep1


title: normoxia_48h_rep1


title: hypoxia_4h_rep2


title: Bone marrow with BSA, biological rep-2


title: normoxia_4h_rep2


title: normoxia_4h_rep1


title: normoxia_4h_rep3


title: MEF_WM2474_240h_2: WM-2474 treated mouse embryonic fibroblast (240 hours, replicate 2)

city: Parkville

first: Alexandra

last: Garnham

state: Victoria

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
FastQ files were output using standard Illumina protocols and software
Reads were aligned to the mouse genome by Rsubread version 1.28.0
Reads counts were summarized by Entrez Gene ID using the Rsubread featureCounts function and Rsubread's built-in NCBI annotation
Genome_build: mm10 (NCBI build 38.1)
Supplementary_files_format_and_content: tab-delimited text files; columns represent Entrez Gene ID, gene length (total base count of all exons) and the number of read pairs mapping to that gene

source_name: Embryonic fibroblast

growth_protocol: Mouse embryonic fibroblasts (MEFs) were isolated from E13.5 wild type embryos. MEFs were cultured in DMEM + 10% FBS in 3% O2 / 5%CO2/balance N2.

extract_protocol:
RNeasy RNA isolation kit (Qiagen), according to manufacturer’s instructions.
Uniquely indexed libraries were generated per sample with the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina), according to manufacturer’s instructions.

treatment_protocol: MEFs were treated with 10 µM WM-2474 (inactive control) or DMSO (vehicle control) for 96 h or 240 h.

tag: strain

value: Male

value: embryonic fibroblasts

tag: treatment

tag: treatment time (hours)


title: MEF_WM2474_96h_3: WM-2474 treated mouse embryonic fibroblast (96 hours, replicate 3)


title: MEF_WM2474_240h_1: WM-2474 treated mouse embryonic fibroblast (240 hours, replicate 1)


title: MEF_DMSO_240h_1: DMSO treated mouse embryonic fibroblast (240 hours, replicate 1)

value: DMSO


title: MEF_DMSO_240h_2: DMSO treated mouse embryonic fibroblast (240 hours, replicate 2)


title: MEF_DMSO_240h_3: DMSO treated mouse embryonic fibroblast (240 hours, replicate 3)


title: MEF_WM2474_240h_3: WM-2474 treated mouse embryonic fibroblast (240 hours, replicate 3)


title: MEF_WM2474_96h_2: WM-2474 treated mouse embryonic fibroblast (96 hours, replicate 2)


title: MEF_DMSO_96h_3: DMSO treated mouse embryonic fibroblast (96 hours, replicate 3)


title: MEF_DMSO_96h_2: DMSO treated mouse embryonic fibroblast (96 hours, replicate 2)


title: Lym_DMSO_6D_3: DMSO treated EMRK1184luc lymphoma cells (6 days, replicate 3)

description: Eµ-Myc

source_name: EMRK1184luc lymphoma cell line

growth_protocol: EMRK1184luc cells were cultured in high-glucose DMEM supplemented with 10% FBS (Gibco), 50 mM ß-mercaptoethanol (Sigma-Aldrich), 100 mM asparagine (Sigma-Aldrich), 100 U/mL penicillin, and 100 mg/mL streptomycin (Gibco) at 37°C and 10% CO2, as previously described.

treatment_protocol: A lymphoma cell line, EMRK1184, derived from a female Eμ-Myc transgenic mouse, was infected with a luciferase-expressing lentiviral imaging construct to allow quantitation of tumor burden throughout treatment. The EMRK1184luc cells were then treated with 5 µM WM-1119 (MYST inhibitor) or DMSO (vehicle control) for 3 days or 6 days.

value: E<mu>-Myc

value: B cell lymphoma cell line

tag: treatment time (days)


title: Lym_DMSO_3D_3: DMSO treated EMRK1184luc lymphoma cells (3 days, replicate 3)

description: Eµ-Myc


title: MEF_WM2474_96h_1: WM-2474 treated mouse embryonic fibroblast (96 hours, replicate 1)


title: hypoxia_4h_rep3


title: hypoxia_48h_rep1


title: Lym_WM1119_6D_2: WM-1119 treated EMRK1184luc lymphoma cells (6 days, replicate 2)

description: Eµ-Myc


title: Lym_DMSO_3D_1: DMSO treated EMRK1184luc lymphoma cells (3 days, replicate 1)

description: Eµ-Myc


title: Lym_WM1119_6D_1: WM-1119 treated EMRK1184luc lymphoma cells (6 days, replicate 1)

description: Eµ-Myc


title: Lym_WM1119_3D_3: WM-1119 treated EMRK1184luc lymphoma cells (3 days, replicate 3)

description: Eµ-Myc


title: Lym_WM1119_6D_3: WM-1119 treated EMRK1184luc lymphoma cells (6 days, replicate 3)

description: Eµ-Myc


title: Lym_WM1119_3D_2: WM-1119 treated EMRK1184luc lymphoma cells (3 days, replicate 2)

description: Eµ-Myc


title: Lym_DMSO_3D_2: DMSO treated EMRK1184luc lymphoma cells (3 days, replicate 2)

description: Eµ-Myc


title: WM-8014 treated mouse embryonic fibroblast (240 hours) culture 6

data_processing:
FASTQ files were output using standard Illumina protocols and software.
Reads were aligned to the mouse genome by Rsubread version 1.20.6
Read counts were summarized by Entrez Gene ID using the Rsubread featureCounts function and NCBI annotation
Genome_build: mm10 (NCBI build 38.1)
Supplementary_files_format_and_content: tab-delimited text file; columns represent Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene

growth_protocol: Mouse embryonic fibroblasts were isolated from E13.5 wild type embryos. MEFS were cultured in DMEM + 10% FBS in 3% O2 / 5%CO2/balance N2.

treatment_protocol: MEFs were treated with 10 µM WM-8014 (MYST inhibitor) or 10 µM WM-2474 (inactive control) for 96 h or 240 h.

value: Female

tag: culture

value: 240 hours of treatment

tag: cell type

value: Embryonic fibroblast


title: WM-8014 treated mouse embryonic fibroblast (96 hours) culture 6

value: 96 hours of treatment


title: MEF_DMSO_96h_1: DMSO treated mouse embryonic fibroblast (96 hours, replicate 1)

tag: tissue


title: WM-8014 treated mouse embryonic fibroblast (96 hours) culture 7


title: WM-8014 treated mouse embryonic fibroblast (240 hours) culture 7


title: Lym_DMSO_6D_2: DMSO treated EMRK1184luc lymphoma cells (6 days, replicate 2)

description: Eµ-Myc


title: Lym_DMSO_6D_1: DMSO treated EMRK1184luc lymphoma cells (6 days, replicate 1)

description: Eµ-Myc


title: WM-2474 treated mouse embryonic fibroblast (96 hours) culture 5


title: Wild type mouse embryonic fibroblasts replicate 3

source_name: Wild type mouse embryonic fibroblasts

growth_protocol: Mouse embryonic fibroblasts were isolated from E13.5 Kat6a+/+ and Kat6a–/– embryos. MEFS were cultured in DMEM + 10% FBS in 3% O2 / 5%CO2/balance N2.

tag: genotype


title: WM-2474 treated mouse embryonic fibroblast (240 hours) culture 7


title: WM-2474 treated mouse embryonic fibroblast (240 hours) culture 6


title: Kat6a knock-out mouse embryonic fibroblasts replicate 1


title: WM-8014 treated mouse embryonic fibroblast (96 hours) culture 5


title: Kat6a knock-out mouse embryonic fibroblasts replicate 3


title: WM-2474 treated mouse embryonic fibroblast (96 hours) culture 6


title: vehicle_13

city: Charlottesville

first: Christopher

last: Overall

state: Virginia

address: 409 Lane Road

department: Neuroscience

institute: University of Virginia

description: da_mesquita_visudyne_before_mwm_raw_counts.tsv

data_processing:
Raw FASTQ sequencing reads were chastity filtered to remove clusters having outlying intensity corresponding to bases other than the called base.
Filtered reads were assessed for quality using FastQC.
Transcript-level abundances were calculated using Salmon.
Transcript-level abundances were summarized into gene-level counts with tximport.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file with the raw counts.

source_name: Total RNA from hippocampus

growth_protocol: All C57BL/6J mice were bred and maintained in standard vivarium conditions

extract_protocol:
RNA was extracted using the RNeasy mini kit (Qiagen)
The Illumina TruSeq Stranded Total RNA Library Prep Kit was used for cDNA library preparation.

treatment_protocol: Intra-cisterna magna injection of Visudyne (verteporfin for injection), or vehicle as control, and photoconversion with 689-nm wavelength non-thermal red light above the intact skull. Procedure was repeated 2 weeks after.

value: Brain whole hippocampus

value: 2 months

value: Wild type

value: Vehicle


title: WM-2474 treated mouse embryonic fibroblast (96 hours) culture 7


title: Wild type mouse embryonic fibroblasts replicate 2


title: Lym_WM1119_3D_1: WM-1119 treated EMRK1184luc lymphoma cells (3 days, replicate 1)

description: Eµ-Myc


title: WM-8014 treated mouse embryonic fibroblast (240 hours) culture 5


title: Kat6a knock-out mouse embryonic fibroblasts replicate 2


title: vehicle_10


title: vehicle_1


title: visudyne_9

value: Visudyne


title: vehicle_7


title: visudyne_15


title: vehicle_4


title: visudyne_6


title: visudyne_3


title: visudyne_12


title: Pillar_3

city: Omaha

first: David

middle: ZZ

last: He

state: Nebraska

address: 2500 California Plaza

department: Biomedical Sciences

institute: Creighton University

description:
This biological replicate has paired-end sequencing and two associated raw reads files.
Pillars - 7_CBA_1m_pillar_2_TAAGGCGA-AGAGTAGA_L001_R1_001

data_processing:
CLC Genomics Workbench software (CLC bio, Waltham, MA, USA) was used to map the reads to the  mouse genome (mm10, build name GRCm38) and generate gene expression values in the normalized form of reads per kilobase of transcript per million mapped reads (RPKM) values
Genome_build: mm10, build name GRCm38
Supplementary_files_format_and_content: Normalized RPKM gene expression values

source_name: Pillar cells, organ of Corti

growth_protocol: Adult CBA/J mice (28 to 32 days old) were used for the study.

extract_protocol:
The basilar membrane together with the organ of Corti was isolated and transferred to a small Petri dish with an enzymatic digestion medium. After 5 min incubation at room temperature, the tissue was transferred to a small plastic chamber containing enzyme-free culture medium. Cells were separated after gentle trituration of the tissue with a small pipette. Morphologically distinct cells were individually collected with suction pipette technique. Approximately 1,000 cells of each type were separately suspended in RNALater (~100 µL in total volume) and total RNA, including small RNAs (> ~18 nucleotides), were extracted and purified using the Qiagen RNeasy mini plus Kit (Qiagen, Germantown, MD). On-column DNase digestion was performed to eliminate DNA contamination in the collected RNA.
Libraries were prepared using the SMARTer Low Input RNA kit (Clontech Laboratories, Mountain View, CA) to generate cDNA in combination with the Nextera Library preparation kit (Illumina, San Diego, CA). Library size and concentration were assessed using an Agilent 2100 Bioanalyzer and a Quibit fluorometer (Invitrogen, Thermo Fisher Scientific) to ensure the inserts were the appropriate size and determine concentration prior to sequencing. Transcriptome libraries were sequenced using the HiSeq 2500 Sequencing System (Illumina).

tag: strain/ age

value: CBA/J

value: adult; 28 to 32 days old

tag: sample size

value: ~1,000 isolated cells

value: Pillar cell


title: Pillar_5

description:
This biological replicate has paired-end sequencing and two associated raw reads files.
Pillars - 7_CBA_1m_pillar_3_TCCTGAGC-TATCCTCT_L001_R1_001


title: Pillar_2

description:
This biological replicate has paired-end sequencing and two associated raw reads files.
Pillars - 7_CBA_1m_pillar_1_AGGCAGAA-AGAGTAGA_L002_R1_001-1


title: Pillar_4

description:
This biological replicate has paired-end sequencing and two associated raw reads files.
Pillars - 7_CBA_1m_pillar_2_TAAGGCGA-AGAGTAGA_L002_R1_001


title: WM-2474 treated mouse embryonic fibroblast (240 hours) culture 5


title: Pillar_1

description:
This biological replicate has paired-end sequencing and two associated raw reads files.
Pillars - 7_CBA_1m_pillar_1_AGGCAGAA-AGAGTAGA_L001_R1_001-1


title: Deiters_4

description:
This biological replicate has paired-end sequencing and two associated raw reads files.
Deiters - 8_CBA_1m_deiters_2_CGTACTAG-GCGTAAGA_L002_R1_001

source_name: Deiters cells, organ of Corti

value: Deiters' cell


title: Deiters_6

description:
This biological replicate has paired-end sequencing and two associated raw reads files.
Deiters - 8_CBA_1m_deiters_3_GGACTCCT-AGAGTAGA_L002_R1_001


title: Deiters_5

description:
This biological replicate has paired-end sequencing and two associated raw reads files.
Deiters - 8_CBA_1m_deiters_3_GGACTCCT-AGAGTAGA_L001_R1_001


title: Deiters_2

description:
This biological replicate has paired-end sequencing and two associated raw reads files.
Deiters - 8_CBA_1m_deiters_1_TCCTGAGC-GCGTAAGA_L002_R1_001


title: Deiters_1

description:
This biological replicate has paired-end sequencing and two associated raw reads files.
Deiters - 8_CBA_1m_deiters_1_TCCTGAGC-GCGTAAGA_L001_R1_001


title: Pillar_6

description:
This biological replicate has paired-end sequencing and two associated raw reads files.
Pillars - 7_CBA_1m_pillar_3_TCCTGAGC-TATCCTCT_L002_R1_001


title: Deiters_3

description:
This biological replicate has paired-end sequencing and two associated raw reads files.
Deiters - 8_CBA_1m_deiters_2_CGTACTAG-GCGTAAGA_L001_R1_001


title: SJEPD037_D

city: Memphis

first: ji

last: wen

state: Tennessee

address: 262 Danny Thomas Place

department: pathology

institute: st jude children's research hospital

description: RMA normalized gene expression data

hyb_protocol: Of the 15 ug of biotin modified aRNA that was fragmented, 12.5 ug was hybridized per array for 16 hours at 45° C while rotating at 60 rpm.

scan_protocol: The U133v2 arrays were then stained and washed on the Affymetrix GeneChip Fluidics Station 450 per Affymetrix protocol.  The arrays were then scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: RMA summarization via affymetrix Expression Console

source_name: frozen ependymal tumor tissue_PFA1

label_protocol: Biotinylated aRNA was prepared according to the standard Affymetrix 3’ IVT Express protocol with an initial input of 200 ng of total RNA. (GeneChip  3’ IVT Express Kit: 901229).

extract_protocol: Trizol reagent, following manufacturer's instructions. Ispropyl alcohol precipitation of RNA from aqueous phase.

tag: age (yrs)

value: Frozen ependymal tumor tissue


title: SJEPD025_D

description: RMA normalized gene expression data

value: Male


title: SJEPD039_D

description: RMA normalized gene expression data

source_name: frozen ependymal tumor tissue_PFA2


title: SJEPD018276_D1

description: RMA normalized gene expression data


title: SJEPD018275_R1

description: RMA normalized gene expression data


title: SJEPD018271_D1

description: RMA normalized gene expression data


title: SJEPD018267_D1

description: RMA normalized gene expression data


title: SJEPD028_D

description: RMA normalized gene expression data


title: SJEPD035_D

description: RMA normalized gene expression data


title: SJEPD018270_D1

description: RMA normalized gene expression data


title: SJEPD030_D

description: RMA normalized gene expression data


title: SJEPD014_D

description: RMA normalized gene expression data


title: SJEPD018274_D1

description: RMA normalized gene expression data


title: SJEPD019_D

description: RMA normalized gene expression data


title: SJEPD013_D

description: RMA normalized gene expression data


title: SJEPD018268_D1

description: RMA normalized gene expression data


title: SJEPD012_D

description: RMA normalized gene expression data


title: SJEPD038_D

description: RMA normalized gene expression data


title: SJEPD002_D

description: RMA normalized gene expression data


title: SJEPD016_D

description: RMA normalized gene expression data


title: SJEPD015_D

description: RMA normalized gene expression data


title: SJEPD010_D

description: RMA normalized gene expression data


title: SJEPD009_D

description: RMA normalized gene expression data


title: SJEPD018266_D1

description: RMA normalized gene expression data


title: SJEPD011_D

description: RMA normalized gene expression data


title: SJEPD018273_D1

description: RMA normalized gene expression data


title: SJEPD018269_D1

description: RMA normalized gene expression data


title: H3 day 3

city: Glasgow

first: Katherine

last: West

address: University of Glasgow

department: College of Medical, Veterinary and Life Sciences

country: United Kingdom

institute: University of Glasgow

data_processing:
Base calling was performed using CASAVA
Unfiltered reads were aligned to mm9 using Bowtie.
Reads aligning to more than three positions, and duplicate reads, were discared.
Aligned data was converted to BED and BigBed files for further analysis.
Statistically enriched regions compared to a background control (peak finding) were identified using MACS with parameters p = 1e-3; bandwidth = 200; genome = mm9; fold enrichment = 10,30; and input control was used as a background.
Genome_build: mm9
Supplementary_files_format_and_content: Bigbed, bigWig

source_name: day 3 neuronal cells

growth_protocol: Undifferentiated P19 cells were maintained in advanced DMEM/F12 (Thermo Fisher Scientific 12634-010)  containing 10% NBCS and 1X GlutaMAX.

extract_protocol:
Cells were crosslinked with 5% formaldehyde for 5 mins. Nuclei were extracted, chromatin sonicated, and ChIP was performed using protein G agarose using standard procedures.
NEB ultra DNA library prep kit

treatment_protocol: For neural induction, cells were seeded onto laminin coated plates in DMEM/F12 basal media containing sodium pyruvate and NEAA supplemented with 1 X N2 supplement, 200 mM L-glutamine, 500 nM retinoic acid, 10 ng/ml FGF8 and 10 µM DAPT, and harvested after 3 days.

tag: chip antibody


title: SJEPD004_D

description: RMA normalized gene expression data

tag: gender


title: SJEPD001526_D1

description: RMA normalized gene expression data


title: SJEPD001528_D1

description: RMA normalized gene expression data


title: SJEPD001534_D1

description: RMA normalized gene expression data


title: SJEPD001530_D1

description: RMA normalized gene expression data


title: Hmgn2 day3


title: SJEPD005_D

description: RMA normalized gene expression data


title: SJEPD001539_D1

description: RMA normalized gene expression data


title: H3K4me1 day3


title: SJEPD001538_R1

description: RMA normalized gene expression data


title: totalFly-LCA-30days-replicate1

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

institute: University of Lübeck

hyb_protocol: Microarray analysis was performed at Source Bioscience (Nottingham, UK). RNA quality was assessed by using an Agilent Bioanalyzer 2100 applying the RNA 6000 Nano Assay.  cDNA were hybridized  for 16h at 45°C using Hybridization Wash and Stain Kit (Affymetrix).

scan_protocol: Arrays were washed and stained with GeneChip Fluidics Station 450 and scanned with GeneChip Scanner 3000 using the GeneChip Operating Software (Affymetrix).

data_processing: R/Bioconductor

source_name: total fly_LCA diet_age 30d

label_protocol: Biotinylated cRNA was generated from 1.5 µg total RNA using the One-Cycle Target Labeling Assay (Affymetrix).

growth_protocol: The Drosophila melanogaster wild type strain W1118 (Bloomington Drosophila Stock Center #5905) was used for all experiments and grown over 30 days.

extract_protocol: Total RNA was extracted from whole flies by using TriFastTM (Peqlab, Nuernberg, Germany) according to manufacturer’s instructions. Prior to RNA extraction, 10 flies per group were homogenized in TriFastTM in a TissueLyser II (Qiagen, Hilden, Germany). RNA concentration and purity was detected via a NanoDrop (NanoDrop2000c; ThermoScientific, Waltham, MA, USA).

treatment_protocol: For RNA isolation flies were maintained either on a control or lithocholic acid (LCA)-supplemented medium for 30 days.

tag: genotype/variation

value: wild type

value: male

tag: age

value: 30 days

tag: diet

value: lithocholic acid (LCA) supplemented (50 µmol/l) diet

value: whole fly


title: totalFly-LCA-30days-replicate3


title: totalFly-LCA-30days-replicate2


title: totalFly-control-30days-replicate1

source_name: total fly_control diet_age 30d

value: Control


title: IgG day3

value: IgG


title: totalFly-control-30days-replicate2


title: SJEPD001527_R1

description: RMA normalized gene expression data

value: Female


title: SJEPD001535_R1

description: RMA normalized gene expression data


title: SJEPD001522_R1

description: RMA normalized gene expression data


title: SJEPD001525_D1

description: RMA normalized gene expression data


title: H3K4me1 undiff

source_name: undifferentiated P19 EC cells


title: H3 undiff


title: H3K27ac day3


title: Hmgn2 undiff


title: IgG undiff


title: input undiff


title: input day3


title: H3K27ac undiff


title: Snail-OE replicate 4

city: Lausanne

first: Nadine

last: Fournier

state: Vaud

address: Agora Cancer Research Center, Bugon 25A

country: Switzerland

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

description: Gene expression data of murine lung adenocarcinoma with Snail overexpression

hyb_protocol: Affymetrix mouse gene 2.0ST arrays (Affymetrix, Santa Clara , CA, USA) were hybridized with 3.7μg of fragmented target, at 45°C for 16 hours washed and stained according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual (Fluidics protocol FS450_0002)

scan_protocol: The arrays were scanned with the GeneChip® Scanner 3000 7G (Affymetrix).

data_processing: R/Bioconductor package oligo (v 1.42.0), robust multi-array average (RMA) algorithm.

source_name: Murine lung adenocarcinoma with Snail overexpression

label_protocol: cDNA was generated from RNA using Ambion WT Expression kit (4411973, Life Tech). cDNA was fragmented and labeled with GenChip WT Terminal Labeling Kit (901525, Affymetrix)

extract_protocol: RNA was extracted using Trizol Reagent and purified using Ethanol precipitation (using NaOAc, glycogen).

treatment_protocol: Twelve week old KPR mice (Jackson, 2005; Meylan, 2009) were infected with Pgk-Cre_TRE-Snail lentiviral constructs. Mice were fed with doxycycline diet for 16 weeks, sacrificed and lung tumors collected. Tumors were snap-frozen.

value: lung tumors

tag: group

value: Snail overexpression

value: 28 weeks


title: Snail-KD replicate 1

description: Gene expression data of murine lung adenocarcinoma with Snail knockdown

source_name: Murine lung adenocarcinoma with Snail knockdown

treatment_protocol: Twelve week old KPR mice (Jackson, 2005; Meylan, 2009) were infected with Pgk-Cre_U6-shSnail or Pgk-Cre_U6-shp53 (control) lentiviral constructs. Mice were sacrificed after 33 weeks and lung tumors collected. Tumors were snap-frozen.

tag: strain

value: Snail-KD

value: 45 weeks


title: Snail-KD replicate 2


title: Control replicate 6

description: Gene expression data of murine lung adenocarcinoma as control

source_name: Murine lung adenocarcinoma

value: control


title: Snail-KD replicate 5


title: Control replicate 2


title: Control replicate 3 [KP_36]


title: Snail-OE replicate 3


title: Snail-KD replicate 3


title: Control replicate 4


title: Control replicate 5


title: Snail-OE replicate 2


title: AEC donor 2, +Spores, 24hr

city: Oklahoma City

first: J.

middle: Leland

last: Booth

state: OK

address: 800 N. Research Parkway

department: Internal Medicine Dept., Pulmonary and Critical Care Div.

institute: Oklahoma University Health Sciences Center

hyb_protocol: Hybridization cocktails were created using standard array format with components from the GeneChip Hybridization, Wash, and Stain Kit (Affymetrix). Cocktails were incubated on GeneChip HuGene 2.0 ST Array, Format 100 (Affymetrix) for 18 h at 45 °C with rotation.  Arrays were then washed and stained using components of the GeneChip Hybridization, Wash, and Stain Kit and a Fluidics Station 450 (Affymetrix).

scan_protocol: Arrays were scanned using a GeneChip Scanner 3000 7G (Affymetrix) and Affymetrix GeneChip Command Console to generate intensity data.

data_processing: The data were normalized using RMA [PMID: 12925520]. Probes were annotated on a transcript level using hugene20sttranscriptcluster v. 8.4.0 Bioconductor package. Quality control included hierarchical clustering, principal components analysis. Only protein-coding genes were analyzed. Differentially expressed genes were detected using limma R package v. 3.28.21 [PMID: 25605792] controlling for the “Amp group” variability. Functional enrichment analysis (Gene Ontology Molecular Function, Biological Process, Cellular Component pathways) was performed using GOStats R package v. 2.42.0 [PMID: 17098774]. Volcano plots and heatmap visualization was performed in R/Bioconductor environment v. 3.3.1.

source_name: primary human type I AEC_anthrax spores_24 hrs

label_protocol: 5 μg cDNA per sample were fragmented and biotinylated (Encore Biotin Module, NuGEN) following manufacturer’s instructions for hybridization with microarrays.

growth_protocol: Human lungs from deceased donors and rejected for transplant were obtained under a protocol approved by the University of Oklahoma Health Sciences Institutional Review Board. After perfusion with PBS and lavage with 150 mM NaCl solution, approximately 60g of lung tissue was digested in 200ml HBSS containing 8 U/ml porcine elastase and 150 KU/ml DNase for 60 min at 37°C.  After inactivation of the elastase with FBS, the softened tissue was minced into a slurry and passed sequentially through gauze and increasingly smaller pore size nylon mesh until a single cell dispersion was obtained.  Type II AEC were purified from this mixture by 3 sequential enrichment protocols: 1) Total cells were panned in flasks coated with human IgG.  2) Unattached cells were concentrated, then separated by Percoll gradient; and, 3) Cells in the interface band were negatively selected against anti-CD45 coated magnetic microbeads.  The isolated AEC II were added to 6-well BioCoat plates pre-coated with collagen I extracellular matrix and overlaid with human fibronectin in DMEM supplemented with 10% FBS, 1% solution of penicillin/streptomycin/amphotericin B, 5.0 μg/liter vancomycin, and 10.0 μg/liter ceftazidime at a concentration of 20,000 cells/cm2.  This initial cell density was optimized to drive differentiation toward a type I-like AEC phenotype.  The medium was changed every other day and by day 10 of culture, plated type II AEC had morphologically differentiated into confluent, type I-like AEC monolayers.

extract_protocol: When Thawed, the QIAzol cell lysates were bead mill homogenized in a TissueLyser II, then purified by the QIAcube automated workstation using miRNeasy Mini Purification Kits (all from Qiagen, Inc.) following the manufacturer's instructions. Product RNA was eluted in water, with final aliquots being stored in 10 mM Tris Cl, pH 8.0.  The resulting total RNA yields and purities were determined using a NanoDrop 2000c (Thermo Scientific).  RNA was reverse transcribed to cDNA and amplified using Ovation Pico WTA Systems V2 (NuGEN) following manufacturer’s instructions. Final amplified cDNA was purified using Agencourt RNAClean XP Beads, and the final yields and purities were determined by NanoDrop.

treatment_protocol: After differentiation in 6-well plates, the type I AEC from the three donors were infected with 1 × 106 cfu/ml (MOI ≈ 2) B. anthracis, Sterne strain 7702 (pX01+, pX02-) endospores in fresh DMEM-10 and incubated for 4 and 24 h at 37°C in 5% CO2.  A volume of spore diluent (sterile di-water) equal to that of the spores was used as a negative control.  At the end of incubation, the cell monolayers were washed twice with 2 ml PBS, lysed by addition of 700 μl/well QIAzol Lysis Reagent (Qiagen Inc.), and immediately stored at -80°C.

tag: subject id

value: donor 2

tag: race

value: caucasian

tag: Cause of death

value: trauma, anoxia, secondary cardiovascular failure

value: primary human type I alveolar epithelial cells (AECs)

tag: treated with

value: B. anthracis, Sterne strain 7702 (pX01+, pX02-) endospores for 24hrs


title: Snail-OE replicate 1


title: AEC donor 2, +Spores, 4hr

source_name: primary human type I AEC_anthrax spores_4 hrs

value: male

tag: cell type

value: B. anthracis, Sterne strain 7702 (pX01+, pX02-) endospores for 4hrs


title: AEC donor 1, +Spores, 24hr

value: donor 1

value: stroke


title: AEC donor 3, Mock, 4hr

source_name: primary human type I AEC_mock_4 hrs

value: donor 3

value: female

value: hispanic

value: spore diluent (mock) for 4hrs


title: Control replicate 2 [KP_33]

tag: tissue

value: lung tumors

value: 28 weeks


title: AEC donor 2, Mock, 24hr

source_name: primary human type I AEC_mock_24 hrs

value: spore diluent (mock) for 24hrs


title: AEC donor 1, +Spores, 4hr


title: AEC donor 3, Mock, 24hr


title: Snail-KD replicate 4

value: Snail-KD

value: 45 weeks


title: Control replicate 1

value: control


title: AEC donor 1, Mock, 24hr

value: caucasian


title: Control replicate 1 [KP_27]


title: AEC donor 3, +Spores, 4hr

value: primary human type I alveolar epithelial cells (AECs)


title: AEC donor 3, +Spores, 24hr

value: B. anthracis, Sterne strain 7702 (pX01+, pX02-) endospores for 24hrs


title: Control replicate 4 [KP_46]


title: Control replicate 3


title: 6h_High_light_BiorepA

city: Colchester

first: Philip

middle: Mark

last: Mullineaux

address: Wivenhoe Park

institute: University of Essex

description: Randomized loop design providing dye-swaps between treatments, time points and bioreps

hyb_protocol: The order in which the 200 slides were hybridized and scanned was randomized to minimize the impact on differences between samples of any potential variation in the processing conditions. According to this randomized experimental design combinations of labelled samples were hybridized to slides overnight at 42 oC.

scan_protocol: Following hybridization, slides were washed and scanned using an Affymetrix 428 array scanner at 532nm (Cy3) and 635nm (Cy5).

data_processing:
Cy3 and Cy5 scans for each slide were combined and processed in ImaGene version 8.0 (BioDiscovery) to extract raw intensity and background corrected data values for each spot on the array
Quantified microarray data were Lowess normalized within print-tip groups and within arrays, then variation due to arrays and dyes was removed by a random effects model, and averaged, in log space, using a modified version of R/MAANOVA (MicroArray ANalysis Of VAriance) (Wu et al. 2003).

label: Cy3, Cy5

organism: Arabidopsis thaliana

label_protocol: Cy3 and Cy5 labelled cDNA probes were prepared by reverse transcribing 5µg of aRNA with Cy3- or Cy5- dCTP (GE Healthcare) and a modified dNTP mix (10mM each dATP, dGTP and dTTP; 2mM dCTP) using random primers (Invitrogen) and SuperScript II reverse transcriptase (Invitrogen), with the inclusion of RNase inhibitor (RNaseOUT, Invitrogen) and DTT. Labelled probes were purified using QiaQuick PCR Purification columns (Qiagen), freeze-dried, and resuspended in 50µl hybridization buffer (25% formamide, 5xSSC, 0.1% SDS, 0.5µg/µl yeast tRNA [Invitrogen]).

growth_protocol: Arabidopsis thaliana plants (Col-0) were obtained from the European Arabidopsis Stock Centre, and were grown under a 8:16-h light:dark cycle at 23°C, 60% relative humidity, and light intensity of 150 µmol m-2 s-1. Arabidopsis seed was stratified for 3 d in 0.1% agarose at 4°C before sowing individual seeds onto a soil mix (Scotts Levingtons F2+S compost : fine grade vermiculite in a ratio of 6:1:) in pots (7cm x 7cm x 9 cm) . For the HL time series and LL parallel controls, two consecutive sowings, 24 hours apart, were grown to 42 days post sowing on the same growth room shelf and randomized across the shelf every day. Leaf 7 (Boyes et al., 2001) was tagged at 37 days post sowing.

extract_protocol: Total RNA was isolated from four individual leaves from each sampled time point from the 2 days (arbitrarily labelled as biological replicates A, B, C and D) using TRIzol reagent (Invitrogen), purified with RNeasy columns (Qiagen) and amplified using the MessageAmp II aRNA Amplification kit (Ambion) in accordance with the kit protocol with a single round of amplification.

treatment_protocol: The HL exposure was a light intensity of 1500 (± 100) µmol m-2 s-1 from a white light emitting diode (LED) array (Isolight; Technologica Ltd, Colchester UK).  We used the 24 h staging of plant growth and 3 light Isolight arrays to treat 27 plants each day, allowing a maximum of 54 plants to be exposed over the two days of the experiment. The same number of plants were selected to be LL controls. The HL exposure began 1h after subjective dawn and was completed 1h before subjective dusk and was carried out in the chamber the plants were grown in. Each set of tagged leaves (4) at each time point and their LL controls (4) were sampled within 5 min at time 0 and each 0.5 h interval for the 6 h exposure. Two HL experiments were conducted with duplicate samplings of a full range of time points on each day. During the time series HL experiments, an individual plant from under each LED array and not destined to be sampled was monitored for  its response to HL by non-invasively determining the chlorophyll fluoerescence parameters Fq’/Fm’, Fq’/Fv’ and Fv’/Fm’  from leaf 7  in situ under each isolight using PAM-2000 portable fluorometers (Walz GmbH, Effeltrich, Germany).

tag: ecotype

tag: treatment

value: high light (HL)

tag: time (hour)

value: leaf


title: 5h_High_light_BiorepC