title: C10 B

description: Table S6 Hypoxic RNA Seq.xlsx

data_processing:
Samples were prepared according to library kit manufacturer’s protocol, indexed, pooled, and sequenced on an Illumina HiSeq2000.
Reads were aligned to M. tuberculosis genome NC_000962 using MAQ 0.7.1-9.
Differential expression analysis was performed using DESeq
Genome_build: NC_000962
Supplementary_files_format_and_content: DESeq analysis is presented in an excel format comparing expression in the C10-treated samples to DMSO-treated samples. Column A: Identification column indicates gene identification number and product; Column B: baseMean; C: baseMeanA; Column D: baseMeanB; Column E: Linear fold change comparing gene expression levels in C10-treated samples vs DMSO-treated samples; Column F: Log2 fold change comparing gene expression levels in C10-treated samples vs DMSO-treated samples; Column G: p value; Column H: adjusted p value; Column I: resVarA; Column J: resVarB; Column K: Functional category based on Mycobrowser annotation.

growth_protocol: Stationary phase M. tuberculosis was inoculated 1:100 into Sauton's media containing 50 μM C10 and incubated in a sealed vessel for 2 weeks.

extract_protocol:
Bacteria were harvested from the culture by centrifugation, resuspended in Trizol and lysed by bead beating. RNA was extracted by chloroform extraction, followed by isopropanol precipitation, and the extracted RNA was resuspended in water. RNA integrity and concentration was measured with an Agilent Bioanalyzer.
RNA libraries were prepared using standard Illumina protocols.

tag: stress

value: hypoxia


title: C10 C

status: Public on May 31 2019

type: SRA

city: St. Louis

first: Gregory

middle: A

last: Harrison

state: MO

address: 660 South Euclid Avenue

department: Molecular Microbiology

country: USA

institute: Washington University School of Medicine

description: Table S6 Hypoxic RNA Seq.xlsx

library_source: transcriptomic

molecule: total RNA

organism: Mycobacterium tuberculosis

source_name: Bacterial cell extract

tag: strain

value: Erdman

tag: treatment


title: Planktonic A

growth_protocol: M. tuberculosis was cultured in 7H9 media supplemented with OADC to mid-logarithmic phase (OD600=0.4-0.7) before RNA was collected.

value: Aerobically growing in 7H9 medium (control)


title: Planktonic C


title: Planktonic B


title: DMSO C

description: Table S6 Hypoxic RNA Seq.xlsx

growth_protocol: Stationary phase M. tuberculosis was inoculated 1:100 into Sauton's media containing DMSO and incubated in a sealed vessel for 2 weeks.

value: DMSO


title: C10 A

description: Table S6 Hypoxic RNA Seq.xlsx


title: DMSO A

description: Table S6 Hypoxic RNA Seq.xlsx


title: DMSO A

data_processing:
Samples were prepared according to library kit manufacturer’s protocol, indexed, pooled, and sequenced on an Illumina HiSeq.
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read.
Reads were pseudo-aligned and quantified using Salmon
Data was imported into R from Salmon using tximport
Differential expression analysis was performed using DESeq2
Genome_build: NC_000962.3
Supplementary_files_format_and_content: DESeq2 expression profiles for both 5 μM C10 and 25 μM C10 compared to DMSO samples are presented in each excel file. Column A is the gene identification number based on H37Rv genome annotation; Column B is the base mean; Column C is the Log2 fold change in C10-treated vs DMSO-treated samples; Column D is the Linear fold change for C10-treated vs DMSO-treated samples; Column E is the Log2 fold change standard error; Column F is the Wald statistic; Column G is the p value; Column H is the adjusted p value; Column I is the functional annotation as annotated in Mycobrowser; Column J is the gene product as annotated in Mycobrowser; Column L is the predicted function as annotated in Mycobrowser

extract_protocol:
Bacteria were harvested from 60 mL of the culture by centrifugation, resuspended in 1 mL of Trizol and lysed by bead beating. RNA was extracted by chloroform extraction, followed by isopropanol precipitation, and the extracted RNA was resuspended in 50 μL of water. RNA integrity and concentration was measured with an Agilent Bioanalyzer.
RNA libraries were prepared using standard Illumina protocols.

treatment_protocol: Logarithmically growing Mycobacterium tuberculosis in Sauton's medium was inoculated into fresh Sauton's medium containing DMSO, 5 μM C10, or 25 μM C10 at an OD600 of 0.1 and incubated at 37°C for 48 hours.


title: wt_FAIRE_6h_rep1

city: Salt Lake City

first: Bruce

last: Edgar

state: UT

address: 2000 Cir of Hope Dr.

department: Department of Oncological Sciences

institute: University of Utah

library_source: genomic

data_processing:
FAIRE-Seq sequencing reads were aligned to  reference genome using Bowtie2. Merged bam files were generated for each genotype by combining replicates. The  Z-scores were calculated using the mean and standard deviation per chromosome arm
RNA-Seq sequencing reads were aligned to thereference genome using STAR and further counted using HTSeq
Genome_build: dm6
Supplementary_files_format_and_content: bigwig, count

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: wing

growth_protocol: female fly wings from wildtype or transgenic flies expressing flippase control, E2F1+DP (E2F) and CycD+Cdk4+E2F1+DP (CycD_E2F) were dissected at corresponding timepoints

extract_protocol:
For FAIRE- samples, fly wings were dissected in PBS and brifely fixed before sonication and pheno-chloroform extraction; For RNA collections, fly wings were dissected and harvested in Trizol
FAIRE-Seq libraries were constructed using the Rubicon Thruplex DNA-seq kit; RNA-Seq libraries  were generated using the stranded mRNA sequencing kit from KAPA Biosystems

tag: genotype/variation

value: wildtype

tag: Sex

value: female

tag: developmental stage

value: 6h APF


title: PntRNAi RNAseq [109]

city: London

first: Adam

last: Dobson

address: Gower Street

department: GEE

country: United Kingdom

institute: University College London

description:
109
PolyA RNA
processed data file: processedData_FxAxP.xlsx

data_processing:
UMIs clipped with Je.
Aligned with hisat2.
Sorted with SAMTOOLS.
Duplicates removed with Je.
Counted with featurecounts.
Analysed with DESeq2.
Genome_build: dmel 6.19
Supplementary_files_format_and_content: processedData_PntRNAi.xlsx: Excel file containing read counts and variance-stabilised reads for genes analysed in either tissue (i.e., where at least 1 read detected/gene).

source_name: gut

growth_protocol: Flies reared on 10% yeast, 5% sucrose.

extract_protocol:
Trizol-chloroform extraction, polyA enrichment using PerkinElmer NextFlex polyA beads.
PerkinElmer NextFlex qRNAseq v2 kit with 16 PCR cycles.

treatment_protocol: Mated 48h, separated from males, fed 200 µM RU486 for 6 days.

tag: tissue

value: Gut

tag: induction

value: +RU486 (expression induced)


title: wt_FAIRE_6h_rep2


title: DMSO B

description: Table S6 Hypoxic RNA Seq.xlsx


title: foxo*aop*foxo RNAseq [45F]

description:
45F
PolyA RNA
processed data file: processedData_FxAxP.xlsx

data_processing:
UMIs clipped with Je.
Aligned with hisat2.
Sorted with SAMTOOLS.
Duplicates removed with Je.
Counted with featurecounts.
Analysed with DESeq2.
Genome_build: dmel 6.19
Supplementary_files_format_and_content: processedData_FxAxP.xlsx: Excel file containing read counts and variance-stabilised reads for genes analysed in either tissue (i.e., where at least 1 read detected/gene).

source_name: adult female fly fat body

value: Female

tag: age

value: Adult

value: Fat body

tag: overexpression

value: overexpression (UAS) of pntP1


title: foxo*aop*foxo RNAseq [67G]

description:
67G
PolyA RNA
processed data file: processedData_FxAxP.xlsx

source_name: adult female fly gut


title: foxo*aop*foxo RNAseq [69F]

description:
69F
PolyA RNA
processed data file: processedData_FxAxP.xlsx


title: 2905_BG_t29_1

city: Marburg

first: Hannes

last: Link

state: Hessen

address: Karl-von-Frisch Straße 16

department: Dynamic Control of Metabolic Networks

country: Germany

institute: MPI Marburg

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Reads were aligned to the reference genome using the CLC Workbench Software (QIAGEN, Venlo, NL). TPMs were calculated using the same program
Genome_build: NC_000913
Supplementary_files_format_and_content: .csv file, exported from the analysis software CLC Workbench

organism: Escherichia coli

source_name: t29_whole cell

growth_protocol: E. coli BW25113 was cultivated in 1 L bioreactor with 500 mL of M9 minimal medium containing 5 g*L-1 glucose to an optical density at 600 nm (OD) of 2. Then the culture was centrifuged at 37 °C and 1800 rcf for 5 min. Pelleted cells were resuspended in M9 medium at 37°C without glucose and transferred back to the bioreactor. After 12 hours of starvation,  5 g*L-1 glucose was added again to the culture. Over this time course, total RNA was sampled. total RNA was sampled at different timepoints before starvation, during starvation and in the growth resumption phase. For detailed description of the sampling time points see Supplementary Material of the publication.

extract_protocol:
The total RNA of the cells was isolated using the Total RNA Isolation Mini Kit (Agilent, Santa Clara, CA).
Quality and Quantity of the extracted RNA were checked with a Agilent BioAnalyser. After an Ribosom depletion, the library was constructed using Directional RNAseq Library with NEBNext Ultra™ Directional RNA Library Prep Kit for Illumina (New England Biolabs).

treatment_protocol: 0.5 mL culture was transferred into reaction tubes and centrifuged at 11.000 rcf for 2 min, and the pellet was frozen in liquid nitrogen.

tag: timepoint

tag: replicate

tag: sample type

value: whole cell


title: 2905_BD_t27_2

source_name: t27_whole cell


title: 2905_BH_t29_2


title: foxo*aop*foxo RNAseq [67F]

description:
67F
PolyA RNA
processed data file: processedData_FxAxP.xlsx


title: 2905_BC_t27_1


title: FFPE tissue

type: RNA

city: Glasgow

first: Chiara

last: Braconi

address: Switchback road

department: Wolfson Wohl Cancer Research Centre

institute: University of Glasgow

hyb_protocol: RNA was hybridized to capture probes and detection probes using the NanoString nCounter system according to the manufacturer's protocol. Detection probes were provided by the manufacturer and were labeled with a proprietary fluorescent barcode system.

scan_protocol: Scanning was conducted using the NanoString confocal microscope scanner/Digital Analyzer according to manufacturer's instructions.

data_processing:
Data were collected as NanoString RCC files. Raw data were normalised using the NanoStringNorm R package version 1.1.21  following recommended parameters (geometric mean for technical variation correction, mean plus two standard deviation for background correction, and geometric mean of housekeeping genes for RNA contect correction) and median centred by genes.
Raw values are the number of copies of a feature-specific molecular barcode that is attached to a detection probe and counted by a confocal system.

organism: Homo sapiens

source_name: tumour tissue

label_protocol: RNA was not labeled; instead, RNA (33 ng/ul) was processed following the NanoString manufacturer's protocol

extract_protocol: RNA was isolated from FFPE tissue or fresh PDO culture

value: liver

value: male


title: PDO

source_name: tumour PDO


title: foxo*aop*foxo RNAseq [40G]

description:
40G
PolyA RNA
processed data file: processedData_FxAxP.xlsx


title: foxo*aop*foxo RNAseq [40F]

description:
40F
PolyA RNA
processed data file: processedData_FxAxP.xlsx


title: PorcineSubcutaneousPreadipocytes_GPR124-siRNA-transfection_differentiation_4d_rep2

city: Tsukuba

first: Masaaki

last: Taniguchi

state: Ibaraki

address: 2 Ikenodai

department: Division of Animal Breeding and Reproduction Research

country: Japan

institute: Institute of Livestock and Grassland Science National Agriculture Food Research Organization

hyb_protocol: The mixture of equal amounts of Cy3- and Cy5-labeled cRNA (850 ng each) was hybridized to each array in Agilent’s SureHyb Hybridization Chambers at 65°C for 17 h under constant rotation using a Gene Expression Hybridization Kit (Agilent). Each array was washed with Gene Expression Wash Pack (Agilent) according to the manufacturer’s instructions.

scan_protocol: Microarrays were scanned at 5 µm/pixel resolution using an Agilent DNA Microarray Scanner (G2505B).

data_processing: The raw data were processed using FEATURE EXTRACTION software (Agilent). Spot data considered to be greater than the background by the software were used for additional analyses.

organism: Sus scrofa

label_protocol: Each total RNA (400 ng) was used to synthesize cyanine (Cy) 3-labeled complementary RNA (cRNA) using a two-color, QuickAmp Labeling kit (Agilent technologies Inc. CA, USA) according to the manufacturer’s instructions. As an internal control, an equal amount of total RNA prepared from the no adipose differentiated nor siRNA transfected preadipocytes was used. The resulting cRNA was labeled using Cy5. Labeled cRNA was purified using an RNeasy Mini Kit (QIAGEN) according to the manufacturer’s instruction.

growth_protocol: DMEM growth medium containing a low glucose concentration (1.0 g/L) and 10% fetal bovine serum (FBS)

extract_protocol: Total RNA was extracted by ISOGEN II reagent (TOYOBO, Osaka, Japan)

treatment_protocol: Adipose conversion was carried out in high-glucose (4.5 g/L) DMEM containing 10% fetal bovine serum (FBS), 5 μg/mL insulin (Sigma-Aldrich, Basel, Switzerland), 0.25 μM dexamethasone (Sigma-Aldrich), 33 μM biotin (Wako Pure Chemicals, Osaka, Japan), 17 μM pantothenate (Sigma), and 5 mM octanoate (Sigma-Aldrich).

tag: gender

value: Subcutaneous tissue

tag: cell type

value: pre-adipocytes

tag: transfected with

value: GPR124 siRNA [designed by SIGMA]


title: PorcineSubcutaneousPreadipocytes_GPR124-siRNA-transfection_differentiation_4d_rep3


title: PorcineSubcutaneousPreadipocytes_neg.ctrl-transfection_differentiation_4d_rep2

value: negative control siRNA [AllStars Negative Control siRNA, QIAGEN]


title: PorcineSubcutaneousPreadipocytes_neg.ctrl-transfection_differentiation_4d_rep1


title: PorcineSubcutaneousPreadipocytes_GPR124-siRNA-transfection_differentiation_4d_rep1


title: 2905_BA_t26_1

source_name: t26_whole cell


title: 2905_BB_t26_2


title: PorcineSubcutaneousPreadipocytes_neg.ctrl-transfection_differentiation_4d_rep3


title: PorcineSubcutaneousPreadipocytes_F2RL2-siRNA-transfection_differentiation_4d_rep2

value: R2RL2 siRNA [designed by SIGMA]


title: foxo*aop*foxo RNAseq [69G]

description:
69G
PolyA RNA
processed data file: processedData_FxAxP.xlsx


title: PorcineSubcutaneousPreadipocytes_F2RL2-siRNA-transfection_differentiation_4d_rep1


title: PorcineSubcutaneousPreadipocytes_LGR4-siRNA-transfection_differentiation_4d_rep3

value: LGR4 siRNA [designed by SIGMA]


title: PorcineSubcutaneousPreadipocytes_LGR4-siRNA-transfection_differentiation_4d_rep2

value: female


title: 2905_BE_t28_1

source_name: t28_whole cell


title: 2905_AZ_t25_2

source_name: t25_whole cell


title: 2905_AX_t24_2

source_name: t24_whole cell


title: 2905_AW_t24_1


title: foxo*aop*foxo RNAseq [14F]

description:
14F
PolyA RNA
processed data file: processedData_FxAxP.xlsx


title: PorcineSubcutaneousPreadipocytes_F2RL2-siRNA-transfection_differentiation_4d_rep3


title: 2905_AV_t23_2

source_name: t23_whole cell


title: 2905_BF_t28_2


title: PorcineSubcutaneousPreadipocytes_LGR4-siRNA-transfection_differentiation_4d_rep1


title: foxo*aop*foxo RNAseq [14G]

description:
14G
PolyA RNA
processed data file: processedData_FxAxP.xlsx


title: foxo*aop*foxo RNAseq [10G]

description:
10G
PolyA RNA
processed data file: processedData_FxAxP.xlsx


title: 2905_AU_t23_1


title: 2905_AT_t22_2

source_name: t22_whole cell


title: foxo*aop*foxo RNAseq [64G]

description:
64G
PolyA RNA
processed data file: processedData_FxAxP.xlsx

value: overexpression (UAS) of foxo,pntP1


title: 2905_AS_t22_1


title: 2905_AQ_t21_1

source_name: t21_whole cell


title: 2905_AP_t20_2

source_name: t20_whole cell


title: foxo*aop*foxo RNAseq [64F]

description:
64F
PolyA RNA
processed data file: processedData_FxAxP.xlsx


title: foxo*aop*foxo RNAseq [62G]

description:
62G
PolyA RNA
processed data file: processedData_FxAxP.xlsx

value: Gut


title: 2905_AM_t19_1

source_name: t19_whole cell


title: 2905_AN_t19_2


title: foxo*aop*foxo RNAseq [39F]

description:
39F
PolyA RNA
processed data file: processedData_FxAxP.xlsx


title: 2905_AR_t21_2


title: foxo*aop*foxo RNAseq [37G]

description:
37G
PolyA RNA
processed data file: processedData_FxAxP.xlsx

value: +RU486 (expression induced)


title: 2905_AL_t18_2

source_name: t18_whole cell


title: 2905_AK_t18_1


title: foxo*aop*foxo RNAseq [37F]

description:
37F
PolyA RNA
processed data file: processedData_FxAxP.xlsx

value: Female


title: foxo*aop*foxo RNAseq [16F]

description:
16F
PolyA RNA
processed data file: processedData_FxAxP.xlsx

value: Adult


title: 2905_AJ_t17_2

source_name: t17_whole cell


title: foxo*aop*foxo RNAseq [02G]

description:
02G
PolyA RNA
processed data file: processedData_FxAxP.xlsx


title: foxo*aop*foxo RNAseq [05F]

description:
05F
PolyA RNA
processed data file: processedData_FxAxP.xlsx

source_name: adult female fly fat body

value: Fat body


title: foxo*aop*foxo RNAseq [61G]

description:
61G
PolyA RNA
processed data file: processedData_FxAxP.xlsx

source_name: adult female fly gut

value: overexpression (UAS) of foxo,aopACT,pntP1


title: foxo*aop*foxo RNAseq [62F]

description:
62F
PolyA RNA
processed data file: processedData_FxAxP.xlsx


title: 2905_AE_t15_1

source_name: t15_whole cell

value: whole cell


title: 2905_AF_t15_2


title: 2905_AC_t14_1

source_name: t14_whole cell


title: 2905_AB_t13_2

source_name: t13_whole cell


title: foxo*aop*foxo RNAseq [58F]

description:
58F
PolyA RNA
processed data file: processedData_FxAxP.xlsx


title: foxo*aop*foxo RNAseq [58G]

description:
58G
PolyA RNA
processed data file: processedData_FxAxP.xlsx


title: 2905_AA_t13_1


title: 2905_AG_t16_1

source_name: t16_whole cell


title: foxo*aop*foxo RNAseq [41G]

description:
41G
PolyA RNA
processed data file: processedData_FxAxP.xlsx


title: 2905_Z_t12_2

source_name: t12_whole cell


title: B6_rep3

city: Munich

first: Felix

last: Struebing

address: Feodor-Lynen-Str. 23

department: Center for Neuropathology and Prion Research

institute: Ludwig Maximilian University of Munich

data_processing:
Paired-end sequencing (100bp) was carried out by Hudson Alpha (Huntsville, AL)
FASTQC of the files was performed for quality control.
Reads from each replicate were not trimmed before mapping, as this was recently shown to decrease ability to map and correlation with microarray data
To avoid mapping issues arising from mouse strain heterogeneity, separate genome indices were built for the B6 and the D2 mouse genome. This was achieved by manually substituting the mm10 B6 reference genome (Ensembl version 86) with D2-specific SNPs and Indels (from dbSNP142).
Reads were then mapped to each genome using the two-pass mapping mode in RNA-STAR with default parameters. For each sample, strand-specific bam files were sorted and indexed with samtools. Counts per gene were tabulated with the “summarizeOverlaps” internal R function from uniquely mapped reads only.
Differential expression analysis was performed using a generalized linear model in edgeR after removing any genes with fewer than 0.5 cpm in more than 3 samples. All p-values were adjusted using the False Discovery Rate (FDR). Significance was assumed for genes with FDR<0.001 and a two-fold change between strains.
For comparison with microarray data, log2-transformed cpm counts were z-scaled and multiplied by 2 before a constant of 8 was added to avoid negative values. This is essentially the same normalization procedure that was applied to the microarray datasets hosted on GeneNetwork
Genome_build: mm10
Supplementary_files_format_and_content: Excel files include average Z-scaled values for each strain

organism: Mus musculus

source_name: Retina

extract_protocol:
Retinas from both eyes were quickly removed under a dissection microscope and directly placed into 160 U/ml Ribolock® (Thermo Scientific, Walton, MA, United States) in Hank’s Balanced Salt Solution (Sigma, St. Louis, MO, United States) on ice. Tissue was stored at -80°C. RNA was isolated in batches using a Qiacube and the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. The isolation included on-column DNase1 treatment to remove contaminating genomic DNA. All tissue was harvested between 10 am and noon to minimize circadian differences in gene expression. RNA integrity (RIN) was assessed on a Bioanalyzer 2100 (Agilent, Santa Clara, CA, United States). RIN-score for all samples ranged from 9.1 to 9.5. RNA was then quantified by spectrophotometry and 260/280 ratios for all samples were >2.1.
Six samples of purified retinal RNA underwent library preparation with the Illumina TruSeq Stranded Total RNA kit.

value: retina

value: post natal day 60-100

value: wild type


title: D2_rep2

value: DBA/2J (D2)


title: D2_rep1


title: skin of urushiol-induced group, biological rep3

city: Hangzhou

first: Chengyu

last: Yin

state: Zhejiang

address: 548 Binwen Road, Binjiang District, Hangzhou

department: The Third Clinical Medical College

country: China

institute: Zhejiang Chinese Medical University

description:
Whole tissue extract
Male C57BL/6 mice (6-8 weeks old)

hyb_protocol: standard Affymetrix protocol

scan_protocol: The samples were processed by Affymetrix GeneChip® Mouse Transcriptome Assay 1.0.

data_processing: The Affymetrix Mouse Transcriptome 1.0 CEL files were imported into Affymetrix Expression Console Software, version 1.4. The CEL files were analyzed using the Gene Level-SST RMA normalization method (Reference: User Manual Expression Console Software 1.4, PN 702387 Rev. 4). The Gene Level- SST RMA files (CHP files) were imported into the Affymetrix Transcriptome Analysis Console (TAC) 3.0 software (reference User Guide, Affymetrix Transcriptome Analysis Console (TAC) 3.0, PN 703150, Rev. 4) for further analysis.

label: biotin

source_name: allergic contact dermatitis_urushiol

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Mice were housed at facilities accredited by the Association for Assessment and Accreditation of Laboratory Animal Care in standard environmental conditions (12-hour light–dark cycle and 23⁰C).

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

treatment_protocol: Mice were sensitized by applying 2.0% urushiol  or oxazolone  to the shaved abdomen under ketamine/xylazine anesthesia. After 5d (day 0), mice were challenged on the shaved nape of neck by painting with 0.5% urushiol or oxazolone dissolved in acetone (40μl). On days 2, 4, 6, 8, mice were challenged with urushiol or oxazolone, in the same way as on day 0, for a total of 5  hallenges.

value: skin

tag: indication

value: allergic contact dermatitis

value: male

value: 6-8 weeks


title: B6_rep2


title: D2_rep3


title: B6_rep1


title: foxo*aop*foxo RNAseq [41F]

description:
41F
PolyA RNA
processed data file: processedData_FxAxP.xlsx


title: skin of urushiol-induced group, biological rep2


title: skin of control group, biological rep3

source_name: healthy skin

value: healthy


title: 2905_AI_t17_1


title: skin of urushiol-induced group, biological rep1


title: skin of oxazolone-induced group, biological rep2

source_name: allergic contact dermatitis_oxazolone


title: foxo*aop*foxo RNAseq [61F]

description:
61F
PolyA RNA
processed data file: processedData_FxAxP.xlsx


title: 2905_Y_t12_1


title: skin of control group, biological rep1


title: foxo*aop*foxo RNAseq [38G]

description:
38G
PolyA RNA
processed data file: processedData_FxAxP.xlsx


title: 2905_X_t11_2

source_name: t11_whole cell


title: skin of oxazolone-induced group, biological rep3


title: foxo*aop*foxo RNAseq [38F]

description:
38F
PolyA RNA
processed data file: processedData_FxAxP.xlsx


title: 2905_W_t11_1


title: skin of control group, biological rep2


title: foxo*aop*foxo RNAseq [17G]

description:
17G
PolyA RNA
processed data file: processedData_FxAxP.xlsx


title: skin of oxazolone-induced group, biological rep1


title: 2905_V_t10_2

source_name: t10_whole cell


title: foxo*aop*foxo RNAseq [17F]

description:
17F
PolyA RNA
processed data file: processedData_FxAxP.xlsx


title: foxo*aop*foxo RNAseq [08G]

description:
08G
PolyA RNA
processed data file: processedData_FxAxP.xlsx


title: 2905_T_t09_2

source_name: t09_whole cell


title: 2905_U_t10_1


title: foxo*aop*foxo RNAseq [72G]

description:
72G
PolyA RNA
processed data file: processedData_FxAxP.xlsx

value: overexpression (UAS) of foxo,aopACT


title: foxo*aop*foxo RNAseq [56F]

description:
56F
PolyA RNA
processed data file: processedData_FxAxP.xlsx


title: foxo*aop*foxo RNAseq [56G]

description:
56G
PolyA RNA
processed data file: processedData_FxAxP.xlsx

value: Gut


title: foxo*aop*foxo RNAseq [72F]

description:
72F
PolyA RNA
processed data file: processedData_FxAxP.xlsx

value: +RU486 (expression induced)


title: 2905_Q_t08_1

source_name: t08_whole cell


title: 2905_S_t09_1


title: 2905_P_t07_2

source_name: t07_whole cell


title: 2905_R_t08_2


title: foxo*aop*foxo RNAseq [46F]

description:
46F
PolyA RNA
processed data file: processedData_FxAxP.xlsx

value: Female


title: foxo*aop*foxo RNAseq [53G]

description:
53G
PolyA RNA
processed data file: processedData_FxAxP.xlsx

value: Adult


title: foxo*aop*foxo RNAseq [11G]

description:
11G
PolyA RNA
processed data file: processedData_FxAxP.xlsx


title: 2905_O_t07_1


title: 2905_N_t06_2

source_name: t06_whole cell


title: 2905_L_t05_2

source_name: t05_whole cell


title: foxo*aop*foxo RNAseq [11F]

description:
11F
PolyA RNA
processed data file: processedData_FxAxP.xlsx

source_name: adult female fly fat body

value: Fat body


title: 2905_M_t06_1


title: 2905_K_t05_1


title: foxo*aop*foxo RNAseq [68G]

description:
68G
PolyA RNA
processed data file: processedData_FxAxP.xlsx

source_name: adult female fly gut

value: overexpression (UAS) of foxo


title: 2905_I_t04_1

source_name: t04_whole cell

value: whole cell


title: 2905_H_t03_2

source_name: t03_whole cell


title: foxo*aop*foxo RNAseq [07F]

description:
07F
PolyA RNA
processed data file: processedData_FxAxP.xlsx


title: foxo*aop*foxo RNAseq [59G]

description:
59G
PolyA RNA
processed data file: processedData_FxAxP.xlsx


title: foxo*aop*foxo RNAseq [68F]

description:
68F
PolyA RNA
processed data file: processedData_FxAxP.xlsx


title: 2905_J_t04_2


title: 2905_F_t02_2

source_name: t02_whole cell


title: 2905_D_t01_4

source_name: t01_whole cell


title: foxo*aop*foxo RNAseq [49G]

description:
49G
PolyA RNA
processed data file: processedData_FxAxP.xlsx


title: foxo*aop*foxo RNAseq [47G]

description:
47G
PolyA RNA
processed data file: processedData_FxAxP.xlsx


title: 2905_B_t01_2


title: 2905_E_t02_1


title: 2905_G_t03_1


title: foxo*aop*foxo RNAseq [59F]

description:
59F
PolyA RNA
processed data file: processedData_FxAxP.xlsx


title: 2905_C_t01_3


title: 2905_A_t01_1


title: foxo*aop*foxo RNAseq [47F]

description:
47F
PolyA RNA
processed data file: processedData_FxAxP.xlsx


title: foxo*aop*foxo RNAseq [06F]

description:
06F
PolyA RNA
processed data file: processedData_FxAxP.xlsx


title: SG-exosome

city: Taipei

first: Hsieh

last: Chia-Hsin

address: No.155, Sec.2, Linong Stree

country: Taiwan

institute: National Yang-Ming University

data_processing:
ConDeTri was implemented to trim or remove the reads according to the quality score.
Qualified reads after filtering low-quality data were analyzed using miRDeep2 to clip the 3' adapter sequence and discarding reads shorter than 18 nucleotides, before aligning reads to the ____Human&Mouse___ genome from UCSC
Genome_build: GRCh38
Supplementary_files_format_and_content: text files include RPKM values for each Sample ...

source_name: SG cell secreted exosome

extract_protocol:
Total RNA was extracted by Trizol® Reagent (Invitrogen, USA) according to the instruction manual. RNA purified was quantified at OD260nm by using a ND-1000 spectrophotometer (Nanodrop Technology, USA) and qualitated by using a Bioanalyzer 2100 (Agilent Technology, USA) with RNA 6000 labchip kit (Agilent Technologies, USA).
TruSeq Small RNA Library Preperation Kit

value: human gingival mucosa cells


title: foxo*aop*foxo RNAseq [07G]

description:
07G
PolyA RNA
processed data file: processedData_FxAxP.xlsx


title: foxo*aop*foxo RNAseq [02F]

description:
02F
PolyA RNA
processed data file: processedData_FxAxP.xlsx


title: foxo*aop*foxo RNAseq [05G]

description:
05G
PolyA RNA
processed data file: processedData_FxAxP.xlsx


title: NelfE_kD_rep3

city: Dallas

first: Xiaoying

last: Bai

state: TEXAS

address: 5323 Harry Hines Blvd.

department: OB/GYN

institute: UT Southwestern Medical Center

description: run-on nascent transcripts

data_processing:
The GRO-seq reads were aligned to the hg19 human reference genome using the BWA aligner (Li and Durbin, 2010) .
Mapped reads were further converted to “bigWig” files counting reads in non-overlapping 200-bp windows across the genome by using the writeWiggle function in the GRO-seq package  for presentation as genome browser tracks  (Quinlan et al, 2010).
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

source_name: human CD34+, mobilzed adult peripheral blood

growth_protocol: Human hematopoietic CD34+ progenitor cells isolated from peripheral blood of GCSF-mobilized healthy volunteers were obtained from the Fred Hutchinson Cancer Research Center. Cells were expended in StemSpan SFEM II medium (StemCell Technologies Inc.) with  1X CC100 cytokine mix (StemCell Technologies Inc.) and 2% penicillin-streptomycin (P/S) for 5 days.  For differeatiation, expended cells were reseeded in differentiation medium containing IMDM supplemented with 2% P/S, 10% FBS, 100ng/ml IL-3 and 100ng/ml SCF for two days, followed by addition of 10ng/ml G-CSF on day 3.

extract_protocol:
Cells were pelleted, washed twice with ice-cold PBS and kept on ice. Lysis buffer (10 mM Tris-HCl, pH 7.4, 0.5% NP-40, 10% glycerol, 3 mM CaCl2, 2mM MgCl2, 1mM DTT, 1X protease inhibitor cocktail and SUPERase-In) was added and cells were pipetted up and down through 1 ml tips to release nuclei. The nuclei were washed twice with lysis buffer and resuspended in 100ul freezing buffer (50 mM Tris-HCl, pH 8.3, 40% glycerol, 5 mM MgCl2, 0.1mM EDTA, and 4 units of SUPERase-In per mL). 8 x 106 nuclei were used for each library. Nuclear run-on performed as previously described (Franco et al., 2015)
library construction were performed as previously described  (Franco et al., 2015)
GRO-seq

treatment_protocol: siRNA transfection was done on day 2 of expension.

value: transfected by NE-siRNA

tag: collection stage

value: 3 days post transfection


title: foxo*aop*foxo RNAseq [66G]

description:
66G
PolyA RNA
processed data file: processedData_FxAxP.xlsx

tag: strain

value: overexpression (UAS) of aopACT,pntP1


title: NelfE_kD_rep2

description: run-on nascent transcripts

tag: treatment


title: NelfE_kD_rep1

description: run-on nascent transcripts


title: foxo*aop*foxo RNAseq [49F]

description:
49F
PolyA RNA
processed data file: processedData_FxAxP.xlsx


title: foxo*aop*foxo RNAseq [65G]

description:
65G
PolyA RNA
processed data file: processedData_FxAxP.xlsx


title: foxo*aop*foxo RNAseq [06G]

description:
06G
PolyA RNA
processed data file: processedData_FxAxP.xlsx


title: Reo-2 V+m

city: San Diego

first: Nathan

middle: E.

last: Lewis

state: CA

address: 9500 Gilman Dr.

department: Pediatrics

institute: University of California, San Diego

data_processing:
RNA-Seq quality was assessed using FastQC. Adapter sequences and low-quality bases were trimmed using Trimmomatic (Bolger et al. 2014).
Sequence alignment was accomplished using STAR (Dobin et al. 2013) against the CHO genome (GCF_000419365.1_C_griseus_v1.0) with default parameters.
HTSeq (Anders et al. 2015) was used to quantify the expression of each gene. We performed differential gene expression analysis using DESeq2 (Anders and Huber 2010).
Genome_build: CHO genome (GCF_000419365.1, C_griseus_v1.0)
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample ...

organism: Cricetulus griseus

source_name: Ovary

growth_protocol: Cells were seeded in cell culture plates (3x105 and 1.2x106 cells/well in 96-well and 6-well plates, respectively) and grown overnight in RPMI-1040 supplemented with 10% FBS, 2mM L-glutamine, 100 U/ml penicillin and 100 µg/ml streptomycin, 10 mM Hepes, 1x non-essential amino acids and 1 mM sodium pyruvate (RPMI-10).

extract_protocol:
Cell cultures were resuspended in RLT buffer (Qiagen) and kept at -80°C until RNA was extracted using the RNeasy kit (Qiagen) and on-column DNAse digestion.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: IFNα/β (human IFNα (Avonex) and IFNβ (Roferon), mouse IFNα (vendor)) as well as innate immune modulators (LPS (TLR4) (Calbiochem), CpG-oligodeoxynucleotide (ODN) D-ODN, 5’-GGTGCATCGATGCAGGGGG-3’ (Puig et al. 2012) and ODN-1555, 5’-GCTAGACGTTAGCGT-3’ (TLR9) (custom-synthesized at the Center for Biologics Evaluation and Research facility, FDA), imidazoquinoline R837 (TLR7/8) (Sigma) and poly I:C-Low molecular weight/LyoVec (poly I:C) (Invivogen) were added to the cultures 16-24 h prior to testing or virus infection, at the concentrations indicated in the figures.

value: Ovary

tag: pretreatment

value: No pretreatment

tag: virus infection

value: Reo infection


title: Reo-2 poly

value: Poly I:C

value: No virus infection


title: Reo-2 ifn

value: IFN


title: NelfB_kD_rep1

description: run-on nascent transcripts

value: transfected by NB-siRNA


title: Reo-2 m


title: Reo-2 V+poly


title: Reo-1 V+ifn


title: Gra-d3-rep2

description: run-on nascent transcripts

value: day 3 granulocytes


title: Reo-2 V+ifn


title: foxo*aop*foxo RNAseq [65F]

description:
65F
PolyA RNA
processed data file: processedData_FxAxP.xlsx

tag: Sex

value: Female

value: +RU486 (expression induced)


title: foxo*aop*foxo RNAseq [50G]

description:
50G
PolyA RNA
processed data file: processedData_FxAxP.xlsx

value: Adult

tag: tissue

value: Gut


title: Reo-1 V+poly


title: foxo*aop*foxo RNAseq [48F]

description:
48F
PolyA RNA
processed data file: processedData_FxAxP.xlsx

value: Fat body

tag: induction


title: foxo*aop*foxo RNAseq [48G]

description:
48G
PolyA RNA
processed data file: processedData_FxAxP.xlsx

tag: age


title: Gra-d3-rep1

description: run-on nascent transcripts


title: Reo-1 V+m


title: foxo*aop*foxo RNAseq [66F]

description:
66F
PolyA RNA
processed data file: processedData_FxAxP.xlsx

tag: overexpression


title: foxo*aop*foxo RNAseq [15F]

description:
15F
PolyA RNA
processed data file: processedData_FxAxP.xlsx


title: CD34_con3

description: run-on nascent transcripts

value: untransfected


title: foxo*aop*foxo RNAseq [13G]

description:
13G
PolyA RNA
processed data file: processedData_FxAxP.xlsx


title: CD34_con2

description: run-on nascent transcripts

value: transfected by con-siRNA


title: CD34_con1

description: run-on nascent transcripts

value: 3 days post transfection


title: NelfB_kD_rep3

description: run-on nascent transcripts


title: Reo-1 m


title: foxo*aop*foxo RNAseq [13F]

description:
13F
PolyA RNA
processed data file: processedData_FxAxP.xlsx

value: overexpression (UAS) of aopACT,pntP1


title: NelfB_kD_rep2

description: run-on nascent transcripts


title: EMCV-2 V+ifn

value: Ovary

value: EMCV infection


title: EMCV-2 V+poly


title: foxo*aop*foxo RNAseq [63F]

description:
63F
PolyA RNA
processed data file: processedData_FxAxP.xlsx

value: overexpression (UAS) of aopACT


title: foxo*aop*foxo RNAseq [63G]

description:
63G
PolyA RNA
processed data file: processedData_FxAxP.xlsx


title: EMCV-2 ifn


title: Cg_E_2_24h

city: College Station

first: Katy

last: Kao

state: Texas

address: 3122 TAMU Room 200

department: Chemical Engineering

institute: Texas A&M University

description: Cg monoculture rep 2

data_processing:
Illumina software used for base-calling
RNA-sequencing analysis was done using the Galaxy interface, through the Texas A&M High Performance Research Computing Center. In Galaxy, raw reads were trimmed of adapter sequences using Trimmomatic  In Trimmomatic, TruSeq3 adapter sequences were used and selected operations were MINLEN (20), LEADING (3), TRAILING (3). MINLEN drops reads below a specified length (in this case 20 bp), and LEADING/TRAILING cuts off bases from the start/end of the read if the quality is below a certain threshold (set to default of 3).
Reads were mapped to the reference genome using Tophat2. In Tophat2, intron length was set to 10 – 1500 bp as previously described and all other parameters were set to default
After mapping, HTseq-counts was used to count how many reads mapped to each feature of the genome using the aligned sequencing reads and a list of genomic features as the input
The Bioconductor DEseq2 package was used to analyze HTseq-count data for differentially expressed genes
Genome_build: C_albicans_SC5314_version_A22-s07-m01-r06 (for *Ca_counts.xlsx files) and C_glabrata_CBS138_version_s02-m07-r08 (for *Cg_counts.xlsx files)
Supplementary_files_format_and_content: Excel format data sheets, raw count data for each file name/sample.

organism: Nakaseomyces glabratus

source_name: Candida biofilms

growth_protocol: Prior to the experiments, strains were cultured on Yeast Peptone Dextrose (YPD) agar plates for 48 hours at 30°C. For all experiments, single colonies were isolated from YPD agar plates and inoculated into 25 mL YNB medium (50 mM glucose and pH 7, Amresco). Cultures were grown overnight at 30°C and 170 rpm for 12 hours prior to experiments. Cultures were washed twice in PBS and adjusted to a cell density of  ~10^7 cells/mL. A final volume of 4 mL was used per well. Biofilms were grown for 6, 12, and 24 hours on glass coverslips (pre-incubated in HI FBS) in 6-well tissue culture plates.

extract_protocol:
Biofilms were washed off of the coverslip with pre-chilled sterile MilliQ water and cells were collected by centrifugation (2000 x g, 5 minutes, 4 °C). Supernatant was removed and cell pellets were flash-frozen in liquid nitrogen prior to lyophilization for 24 hours. Acid-washed glass beads (Sigma-Aldrich) were added to the dried cell pellets and disrupted in the Disruptor Genie for 2 minute cycles for up to 10 minutes. Lysis buffer from the GE Illustra RNAspin Mini kit was added to the disrupted cell powder and RNA was extracted using the kit protocol with on-column DNase I treatment. RNA quality and concentration were determined using a Nanodrop® and Qubit™, respectively.
RNA libraries were constructed using TruSeqRNA kit and processed (125SE) on an Illumina HiSeq 2500 v4 High Output instrument

tag: cg strain

value: ATCC 2001

tag: cg genotype

value: GFP labeled

tag: culture condition

value: Cg monoculture

tag: time


title: Cg_E_1_12h

description: Cg monoculture rep 1


title: Cg_E_2_6h

description: Cg monoculture rep 2


title: Cg_E_1_24h

description: Cg monoculture rep 1


title: EMCV-2 V+m

value: No pretreatment


title: Cg_E_2_12h

description: Cg monoculture rep 2


title: Reo-1 ifn

value: IFN

value: No virus infection


title: EMCV-2 m


title: foxo*aop*foxo RNAseq [54G]

description:
54G
PolyA RNA
processed data file: processedData_FxAxP.xlsx

value: Female

value: +RU486 (expression induced)


title: EMCV-2 poly

value: Poly I:C


title: foxo*aop*foxo RNAseq [54F]

description:
54F
PolyA RNA
processed data file: processedData_FxAxP.xlsx

value: Adult

value: Fat body


title: EMCV-1 V+ifn


title: Cg_E_1_6h

description: Cg monoculture rep 1


title: foxo*aop*foxo RNAseq [52G]

description:
52G
PolyA RNA
processed data file: processedData_FxAxP.xlsx

value: Gut


title: Reo-1 poly


title: Ca_Cg_D_2_24h

description: Ca:Cg 1:3, rep 2

organism:
Candida albicans
Nakaseomyces glabratus

source_name: Candida biofilms, co-culture

tag: ca strain

tag: ca genotype

value: Ca:Cg 1:3,  co-culture


title: foxo*aop*foxo RNAseq [18F]

description:
18F
PolyA RNA
processed data file: processedData_FxAxP.xlsx


title: EMCV-1 V+poly


title: foxo*aop*foxo RNAseq [12G]

description:
12G
PolyA RNA
processed data file: processedData_FxAxP.xlsx


title: EMCV-1 ifn


title: EMCV-1 V+m


title: Ca_Cg_D_2_12h

description: Ca:Cg 1:3, rep 2


title: Ca_Cg_D_1_12h

description: Ca:Cg 1:3, rep 1


title: foxo*aop*foxo RNAseq [55G]

description:
55G
PolyA RNA
processed data file: processedData_FxAxP.xlsx


title: foxo*aop*foxo RNAseq [55F]

description:
55F
PolyA RNA
processed data file: processedData_FxAxP.xlsx


title: Ca_Cg_D_2_6h

description: Ca:Cg 1:3, rep 2


title: EMCV-1 poly


title: foxo*aop*foxo RNAseq [12F]

description:
12F
PolyA RNA
processed data file: processedData_FxAxP.xlsx


title: EMCV-1 m


title: VSV-2 V+ifn

value: VSV infection


title: Proline control strain

city: Bielefeld

first: Fernando

last: Pérez-García

address: Universitaetsstr. 25

institute: University of Bielefeld

description:
PRC
DESeq-PRC-vs-PRO.txt, where A = PRC and B = PRO.

data_processing:
The reads were trimmed to a minimal length of 20 base pairs and in paired end mode with the Trimmotatic ver. 0.33 (Bolger et al., 2014). Trimmed reads were mapped to the reference genome of C. glutamicum ATCC13032 (Kalinowski et al., 2003) using the software Bowtie (Langmead et al., 2009). In order to perform differential gene expression analysis (DEseq) (Anders and Huber, 2010), we used the software for visualization of mapped sequences ReadXplorer (Hilker et al., 2014).
Genome_build: reference genome of C. glutamicum ATCC13032 (Kalinowski et al., 2003)
Supplementary_files_format_and_content: DEseq analysis results

organism: Corynebacterium glutamicum

source_name: Bacterial cells

growth_protocol: Bacterial cell pellets grown under the experimental conditions were harvested at mid-exponential phase.

extract_protocol:
Harvesting procedure was done according to (Irla et al., 2015) and cell pellets were kept at -80 °C for further RNA isolation. The pellets were thawed in ice and RNA was isolated individually for each sample using NucleoSpin RNA isolation kit (Macherey-Nagel, Düren, Germany). RNA samples with genomic DNA contamination were treated with the RNase-free DNase set (Qiagen, Hilden, Germany) (Brito et al., 2017).
The preparation and sequencing of the libraries were performed as described elsewhere (Irla et al., 2015; Mentz et al., 2013)
The extracted RNA samples were pooled in equal parts and the pool of total RNA was subsequently used for the preparation of the cDNA libraries

tag: reference

value: Jensen and Wendisch, 2013


title: Proline producer

description:
PRO
DESeq-PRC-vs-PRO.txt, where A = PRC and B = PRO.


title: VSV-2 V+poly

value: Ovary


title: Pipecolic acid producer

description:
PIP
DESeq-PIC-vs-PIP.txt, where A = PIC and B = PIP.

value: Pérez-García et al., 2016


title: Pipecolic control strain

description:
PIC
DESeq-PIC-vs-PIP.txt, where A = PIC and B = PIP.


title: Ca_Cg_D_1_24h

description: Ca:Cg 1:3, rep 1

value: ATCC 2001


title: Ca_A_2_6h

description: Ca monoculture rep 2

organism: Candida albicans

value: Ca monoculture


title: VSV-2 ifn


title: Ca_Cg_C_1_24h

description: Ca:Cg 1:1, rep 1

value: GFP labeled

value: Ca:Cg 1:1,  co-culture


title: Ca_A_1_6h

description: Ca monoculture rep 1


title: VSV-2 poly


title: Ca_Cg_D_1_6h

description: Ca:Cg 1:3, rep 1


title: Ca_Cg_C_1_12h

description: Ca:Cg 1:1, rep 1


title: Ca_Cg_C_2_24h

description: Ca:Cg 1:1, rep 2


title: Ca_Cg_C_2_12h

description: Ca:Cg 1:1, rep 2


title: Ca_Cg_C_2_6h

description: Ca:Cg 1:1, rep 2


title: 2D_Soft_rep3

city: Boston

first: Sundari

last: Chetty

state: MA

address: 185 Cambridge Street

department: Harvard Medical School

institute: Massachusetts General Hospital, Harvard University

description:
MCF10A cells cultured on soft 2D matrices
tagAlign.counts.for.naive.overlap.merged.peaks.txt
2D_soft_ppr.IDR0.1.filt.narrowPeak.gz
2D_soft_ppr.naive_overlap.filt.narrowPeak.gz
2D_Soft_CAGAGAGG_R1.PE2SE.nodup.tn5_pooled.pf.fc.signal.bigwig
2D_Soft_CAGAGAGG_R1.PE2SE.nodup.tn5_pooled.pf.pval.signal.bigwig

data_processing:
FASTQ files for each sample were processed through the ENCODE DCC ATAC-seq pipeline (https://github.com/ENCODE-DCC/atac-seq-pipeline/) version 1.3.0
A merged peak set was generated by concatenating the optimal naive overlap peaks for all samples, truncating the concatenated peak set to 200 bp around the summit, sorting and merging the resulting peaks. This yielded a merged peak set of 221,510 peaks.
Read counts for each replicate for each peak were obtained by running bedtools coverage on the the filtered tagAlign file generated by the ENCODE DCC pipeline over the set of 221,510 merged peaks.
Differential accessibility across each pair of samples was obtained via DESeq2 on the count matrix.
Genome_build: hg19
Supplementary_files_format_and_content: fold change bigWigs for individual replicates and pooled across replicates;
Supplementary_files_format_and_content: pval bigWigs for individual replicates and pooled across replicates;
Supplementary_files_format_and_content: Tab-delimited text file including un-normalized read counts from each replicate for each peak in the merged naive overlap peak set.
Supplementary_files_format_and_content: Naive overlap optimal narrowPeak calls

source_name: MCF10A mammary epithelial cells

growth_protocol: MCF10A cells were grown in alginate-recombinant basement membrane hydrogels of 100 Pa or 2000 Pa elastic modulus, or on 2D polyacrylamide (100 Pa) or on tissue culture plastic. Standard MCF10A growth media was used.

extract_protocol:
Cells were extracted from matrices by incubating gels in ice cold 50 mM EDTA in PBS for 10 minutes with pipette mixing. The suspensions were centrifuged at 500 g at 4oC for 10 mins to pellet cells. The pellets were incubated in 1 ml of 0.25% trypsin/2.21 mM EDTA at 37oC for 5 minutes to digest any remaining rBM, then centrifuged at 500 g for 10 mins again.
Libraries were prepared using Illumina Nextera Tn5 Transposase (FC-121-1030)

treatment_protocol: Some groups were treated with 1 uM suberoylanilide hydroxamic acid

tag: stiffness

tag: tissue culture substrate

value: 2D matrix

tag: cell line


title: Ca_A_1_24h

description: Ca monoculture rep 1


title: Ca_A_2_24h

description: Ca monoculture rep 2


title: VSV-2 m

tag: strain

tag: pretreatment

value: No pretreatment

value: No virus infection


title: 2D_Soft_rep2

tag: treatment


title: Ca_Cg_C_1_6h

description: Ca:Cg 1:1, rep 1


title: Ca_A_2_12h

description: Ca monoculture rep 2


title: Ca_Cg_B_2_24h

description: Ca:Cg 3:1, rep 2

value: Ca:Cg 3:1,  co-culture


title: VSV-1 V+ifn

tag: tissue

value: IFN

tag: virus infection


title: 2D_Soft_rep1


title: VSV-1 V+poly

value: Poly I:C


title: PF3_1

city: Fullerton

first: M. S.

last: Ramirez

address: 800 N. State College Blvd

institute: California State University Fullerton

data_processing:
Low-quality reads were removed using Trimmomatic v0.32
Reads were aligned witth Burrows Wheeler Alignment software (BWA)
Bigwig files were generated with custom bash scripts and BEDtools
RNA-seq differential expression analysis was performed using DESeq
Genome_build: assembly of Acintetobacter baumannii A118 (that was performed in RAST)
Supplementary_files_format_and_content: raw counts and tsv file generated by DESeq provides gene ID, base mean reads, fold-change, log2 fold-change, p-value and adjusted p-value for the expression of each gene.

organism: Acinetobacter baumannii

growth_protocol: Bacteria were grown in a rotary shaker with agitation at 37oC.

extract_protocol:
Total RNA was extracted using the TRI REAGENT® Kit
Illumina RNA-seq

treatment_protocol: Bacteria were cultured in Luria Bertani broth (LB) with or without PF for 18 h.

tag: condition

value: LB + 4% Pleural Fluid

tag: biological replicate


title: PF4_1


title: PF1_1


title: PF2_1


title: Ca_A_1_12h

description: Ca monoculture rep 1


title: LB4_1

value: LB


title: Ca_Cg_B_1_24h

description: Ca:Cg 3:1, rep 1

tag: cg strain


title: VSV-2 V+m


title: pBRplac-OxyS; hfq-

city: Busan

first: Kwang-sun

last: Kim

address: 63 beon-gil 2, Jangjeon-dng, Geumjeong-gu

department: Chemistry

country: South Korea

institute: Pusan National University

description: pBR OxyS_dhfq fold change.xlsx

data_processing:
CLRNASeq V.1.00 (From ChunLab, Inc.)
Trimmed Mean of M-value of library size were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Elimination of <100 reads in either pBRplac or pBRplac-OxyS
Supplementary_files_format_and_content: tab-delimited excel files include TMM values for each Sample

organism: Escherichia coli K-12

source_name: pBRplac-OxyS

growth_protocol:
growth in the presence of 0.1 mM IPTG and ampicillin
Growth in LB media to OD600=1.0

extract_protocol:
RNA was extracted from OD600=1.0 using RNA Protect Bacteria (Qiagen). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: IPTG (0.1 mM) was added to OD600=0.2

tag: overexpression

value: OxyS overexpression

tag: genotype

value: hfq-


title: pBRplac; hfq-

description: pBR OxyS_dhfq fold change.xlsx

source_name: pBRplac


title: pBRplac-OxyS; wild type

description: pBR OxyS_fold change.xlsx

value: wild type (MG1655)


title: VSV-1 poly

value: Ovary


title: VSV-1 V+m

value: VSV infection


title: VSV-1 ifn


title: Ca_Cg_B_1_12h

description: Ca:Cg 3:1, rep 1

value: ATCC 2001

tag: cg genotype

tag: culture condition

tag: time


title: Ca_Cg_B_1_6h

description: Ca:Cg 3:1, rep 1

tag: ca strain

tag: ca genotype


title: VSV-1 m


title: Ca_Cg_B_2_6h

description: Ca:Cg 3:1, rep 2


title: pBRplac; wild type

description: pBR OxyS_fold change.xlsx


title: LB2_1


title: LB1_1


title: LB3_1


title: Ca_Cg_B_2_12h

description: Ca:Cg 3:1, rep 2


title: TCF1_CUT&RUN_EILP_rep4_GB6244_tech2

status: Public on May 30 2019

city: Bethesda

first: Keji

last: Zhao

state: MD

address: 9000 Rockville Pike

department: Systems Biology Center

institute: NHLBI,NIH

description:
small cell ChIC-seq
EILP_TCF1_peaks.txt
EILP_TCF1-W50-normalized.wig.gz

data_processing:
Library strategy: Cut&Run
Basecalling by RTA 1.18.66.3, Illumina instrument run time analysis software
Sequencing reads were aligned to mouse genome (mm9) with default parameters.
Reads from replicates were merged and redundant reads were removed from further analysis.
Peak calling were performed using MACS2 with default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: Called peaks generated by MACS2. Wig files contain normalized tag density, which can be uploaded to UCSC genome browser for visulization.

growth_protocol: Samples were isolated by cell sorting from bone marrow single cell suspensions

extract_protocol:
Cells were fixed by adding 1:15 volume of 16%w/v formaldehyde solution (Thermo Fisher Scientific) and incubating at RT for 10 minutes. Reaction was terminated by adding 1:10 volume. 1ml RIPA buffer (10 mM Tris-Cl, 1 mM EDTA, 0.1% sodium deoxycholate, 0.2% sodium dodecyl sulfate, 1% Triton X-100) added to each sorted 500 ALP, EILP, and ILCP cells, and incubated at room temperature for 30 minutes. Cells were rinsed with 500 μl binding buffer (10 mM Tris-Cl, 1 mM EDTA, 150 mM sodium chloride, 0.1% Triton X-100) twice and re-suspended in 50 μl binding buffer. To prepare TCF1 bounded PA-MNase (Ab+PA-MNase), TCF1 and the PA-MNase at a molecular ratio of 1:2 were pre-incubated at 4 °C for 30 minutes in 50 μl binding buffer. TCF1+PA-MNase were add to 50 μl binding buffer re-suspended cells and incubated one hour at 4 °C with rotation. Cells were washed using 200 μl wash buffer (10 mM Tris-Cl, 1 mM EDTA, 150 mM sodium chloride, 0.1%w/v SDS, 0.1%w/v sodium deoxycholate and 1%v/v Triton X-100) three times and pelleted by centrifugation at 600g for 2 minutes. Next, cells were rinsed using 200 μl rinsing buffer (10 mM Tris-Cl and 10 mM sodium chloride, 0.1%v/v Triton X-100). The MNase digestion was initiated by re-suspending the rinsed cells in 40 μl reaction solution buffer (10 mM Tris-Cl, 10 mM sodium chloride, 0.1%v/v Triton X-100, 2 mM CaCl2) and incubated at 37 °C for 3 minutes. The reaction was stopped by adding 80 μl stop buffer (20 mM Tris-Cl (pH 8.0), 10 mMethylenedioxy-bis-(ethylenenitrilo)-tetraacetic acid (EGTA), 20 mM sodium chloride, 0.2%w/v SDS) and 1 μl proteinase K (SigmaAldrich), then incubating at 65 °C for overnight. DNAs were purified by using phenol-chloroform extraction and ethanol precipitation. The purified DNA is ready for library preparation.
DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3’ to 5’ exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. The ligation reaction was performed by adding 2 μM Illumina's adapters to each sample and incubated at RT one hour. After adapter ligation DNA was PCR amplified with Illumina primers for 16 cycles and library fragments from 180bp to 300bp were isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Hi-seq3000 following the manufacturer's protocols.

tag: genotype/variation

value: bone marrow

tag: cell type

value: EILP

tag: sorting profile

value: Lin- Kit+ 2B4+ a4b7+ Tcf7+ Thy1-

tag: antibody

value: TCF1/TCF7 (C46C7) Rabbit mAb #2206 from CST


title: TCF1_CUT&RUN_EILP_rep3_GB6244_tech1

tag: strain


title: IgG_CUT&RUN_EILP_rep2_GB3051

description:
small cell ChIC-seq
EILP_IgG-W50-normalized.wig.gz

tag: tissue


title: TCF1_CUT&RUN_EILP_rep4_GB6236_tech2


title: IgG_CUT&RUN_EILP_rep1_GB3042


title: TCF1_CUT&RUN_EILP_rep3_GB6248_tech1


title: TCF1_CUT&RUN_EILP_rep3_GB6236_tech1


title: TCF1_CUT&RUN_EILP_rep4_GB6248_tech2


title: IgG_CUT&RUN_EILP_rep3_GB6240_tech1


title: IgG_CUT&RUN_EILP_rep4_GB6240_tech2


title: TCF1_CUT&RUN_EILP_rep2_GB3048


title: TCF1_CUT&RUN_EILP_rep1_GB3039


title: breast cancer sample, replicate 1 [Anon_15J_R1]

city: Houston

first: Bruno

middle: Valentin

last: Sinn

state: TX

address: 2130 W Holcombe Blvd

department: Translational Molecular Pathology

institute: University of Texas - MD Anderson Cancer Center

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized overnight at 46C on Affymetrix U133A arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the diagnostic-grade Affymetrix scanner 3000DX.

data_processing: Probe intensities were quantified with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. CEL files were normalized using global scaling with a trimmed mean target intensity of each array arbitrarily set to 600 using the MAS5 algorithm from the simpleaffy package (http://bioconductor.org/packages/2.4/bioc/html/simpleaffy.html).

source_name: breast cancer sample, replicate 1

label_protocol: A single-round T7 amplification was used to generate biotin-labeled cRNA for hybridization. At least 1 ug of RNA is required for cRNA synthesis.

extract_protocol: Total RNA was extracted from tissue using Qiagen RNeasy columns.

treatment_protocol: Patients prospectively consented to a fine-needle aspiration.

value: Breast cancer

tag: replicate

tag: cohort

value: Training

tag: set er_pr rnaseq

tag: set er_pr u133a


title: breast cancer sample, replicate 1 [Anon_15D_R1]


title: breast cancer sample, replicate 3 [Anon_15A_R3]

source_name: breast cancer sample, replicate 3


title: breast cancer sample, replicate 2 [Anon_15C_R2]

source_name: breast cancer sample, replicate 2


title: breast cancer sample, replicate 2 [Anon_15E_R2]


title: breast cancer sample, replicate 2 [Anon_15F_R2]

value: Validation


title: breast cancer sample, replicate 2 [Anon_15D_R2]


title: breast cancer sample, replicate 1 [Anon_15F_R1]


title: breast cancer sample, replicate 1 [Anon_15I_R1]


title: breast cancer sample, replicate 1 [Anon_15E_R1]


title: breast cancer sample, replicate 2 [Anon_15J_R2]


title: breast cancer sample, replicate 2 [Anon_15I_R2]


title: breast cancer sample, replicate 2 [Anon_15A_R2]


title: breast cancer sample, replicate 3 [Anon_14Z_R3]


title: breast cancer sample, replicate 2 [Anon_14U_R2]


title: breast cancer sample, replicate 2 [Anon_14Z_R2]


title: breast cancer sample, replicate 1 [Anon_14U_R1]


title: breast cancer sample, replicate 2 [Anon_14S_R2]


title: breast cancer sample, replicate 1 [Anon_15C_R1]


title: breast cancer sample, replicate 2 [Anon_14N_R2]


title: breast cancer sample, replicate 1 [Anon_14V_R1]


title: breast cancer sample, replicate 1 [Anon_14O_R1]


title: breast cancer sample, replicate 1 [Anon_14N_R1]


title: breast cancer sample, replicate 2 [Anon_14M_R2]


title: breast cancer sample, replicate 1 [Anon_14Z_R1]


title: breast cancer sample, replicate 1 [Anon_15A_R1]


title: breast cancer sample, replicate 2 [Anon_14V_R2]


title: breast cancer sample, replicate 1 [Anon_14M_R1]


title: breast cancer sample, replicate 2 [Anon_14O_R2]


title: breast cancer sample, replicate 2 [Anon_14C_R2]


title: breast cancer sample, replicate 1 [Anon_14I_R1]


title: breast cancer sample, replicate 1 [Anon_14E_R1]


title: breast cancer sample, replicate 2 [Anon_14F_R2]


title: breast cancer sample, replicate 1 [Anon_13V_R1]


title: breast cancer sample, replicate 2 [Anon_13V_R2]


title: breast cancer sample, replicate 2 [Anon_14G_R2]


title: breast cancer sample, replicate 1 [Anon_14F_R1]


title: breast cancer sample, replicate 2 [Anon_14E_R2]


title: breast cancer sample, replicate 2 [Anon_14B_R2]


title: breast cancer sample, replicate 1 [Anon_14G_R1]


title: breast cancer sample, replicate 2 [Anon_13U_R2]


title: breast cancer sample, replicate 1 [Anon_14B_R1]


title: breast cancer sample, replicate 1 [Anon_14C_R1]


title: breast cancer sample, replicate 2 [Anon_13Q_R2]


title: breast cancer sample, replicate 1 [Anon_13S_R1]


title: breast cancer sample, replicate 2 [Anon_13M_R2]


title: breast cancer sample, replicate 2 [Anon_13T_R2]


title: breast cancer sample, replicate 1 [Anon_14S_R1]


title: breast cancer sample, replicate 2 [Anon_13S_R2]


title: breast cancer sample, replicate 1 [Anon_13N_R1]


title: breast cancer sample, replicate 2 [Anon_14I_R2]


title: breast cancer sample, replicate 1 [Anon_13Q_R1]


title: breast cancer sample, replicate 1 [Anon_13U_R1]


title: breast cancer sample, replicate 2 [Anon_13O_R2]


title: breast cancer sample, replicate 1 [Anon_13T_R1]


title: breast cancer sample, replicate 1 [Anon_13O_R1]


title: breast cancer sample, replicate 2 [Anon_13N_R2]


title: breast cancer sample, replicate 2 [Anon_13A_R2]


title: breast cancer sample, replicate 2 [Anon_13J_R2]


title: breast cancer sample, replicate 1 [Anon_13E_R1]


title: breast cancer sample, replicate 1 [Anon_13G_R1]


title: breast cancer sample, replicate 1 [Anon_13D_R1]


title: breast cancer sample, replicate 1 [Anon_13C_R1]


title: breast cancer sample, replicate 1 [Anon_13M_R1]


title: breast cancer sample, replicate 1 [Anon_13J_R1]


title: breast cancer sample, replicate 2 [Anon_13G_R2]


title: breast cancer sample, replicate 2 [Anon_12Z_R2]


title: breast cancer sample, replicate 2 [Anon_12Y_R2]


title: breast cancer sample, replicate 1 [Anon_13K_R1]


title: breast cancer sample, replicate 2 [Anon_13K_R2]


title: breast cancer sample, replicate 2 [Anon_13D_R2]


title: breast cancer sample, replicate 1 [Anon_12Z_R1]


title: breast cancer sample, replicate 1 [Anon_13A_R1]


title: breast cancer sample, replicate 2 [Anon_13C_R2]


title: breast cancer sample, replicate 2 [Anon_12X_R2]


title: breast cancer sample, replicate 1 [Anon_12V_R1]


title: breast cancer sample, replicate 2 [Anon_12U_R2]


title: breast cancer sample, replicate 2 [Anon_13E_R2]


title: breast cancer sample, replicate 1 [Anon_12X_R1]


title: breast cancer sample, replicate 2 [Anon_12W_R2]


title: breast cancer sample, replicate 2 [Anon_12V_R2]


title: breast cancer sample, replicate 1 [Anon_12W_R1]


title: breast cancer sample, replicate 1 [Anon_12U_R1]


title: breast cancer sample, replicate 1 [Anon_12T_R1]


title: breast cancer sample, replicate 2 [Anon_12T_R2]


title: breast cancer sample, replicate 1 [Anon_12Y_R1]


title: breast cancer sample, replicate 2 [Anon_12S_R2]


title: breast cancer sample, replicate 1 [Anon_12S_R1]


title: breast cancer sample, replicate 1 [Anon_12Q_R1]


title: breast cancer sample, replicate 1 [Anon_12O_R1]


title: breast cancer sample, replicate 2 [Anon_12R_R2]


title: breast cancer sample, replicate 2 [Anon_12J_R2]


title: breast cancer sample, replicate 2 [Anon_12G_R2]


title: breast cancer sample, replicate 1 [Anon_12P_R1]


title: breast cancer sample, replicate 2 [Anon_12P_R2]


title: breast cancer sample, replicate 2 [Anon_12N_R2]


title: breast cancer sample, replicate 2 [Anon_12H_R2]


title: breast cancer sample, replicate 1 [Anon_12M_R1]


title: breast cancer sample, replicate 2 [Anon_12M_R2]


title: breast cancer sample, replicate 2 [Anon_12F_R2]


title: breast cancer sample, replicate 1 [Anon_12A_R1]


title: breast cancer sample, replicate 1 [Anon_12G_R1]


title: breast cancer sample, replicate 2 [Anon_12O_R2]


title: breast cancer sample, replicate 1 [Anon_12F_R1]


title: breast cancer sample, replicate 2 [Anon_12Q_R2]


title: breast cancer sample, replicate 1 [Anon_11Z_R1]


title: breast cancer sample, replicate 2 [Anon_12D_R2]


title: breast cancer sample, replicate 1 [Anon_12H_R1]


title: breast cancer sample, replicate 1 [Anon_12N_R1]


title: breast cancer sample, replicate 2 [Anon_11Y_R2]


title: breast cancer sample, replicate 2 [Anon_12A_R2]


title: breast cancer sample, replicate 1 [Anon_11Y_R1]


title: breast cancer sample, replicate 1 [Anon_12D_R1]


title: breast cancer sample, replicate 2 [Anon_11Z_R2]


title: breast cancer sample, replicate 1 [Anon_12J_R1]


title: breast cancer sample, replicate 2 [Anon_11X_R2]


title: Sample_110_tissue

source_name: breast cancer sample, surgical tissue

treatment_protocol: Patients prospectively consented to a surgical tissue sample.

tag: sample number

tag: tissue type

value: tissue

tag: immunohistochemistry subtype


title: breast cancer sample, replicate 2 [Anon_11H_R2]


title: breast cancer sample, replicate 1 [Anon_11O_R1]


title: Sample_114_tissue


title: breast cancer sample, replicate 1 [Anon_11V_R1]


title: breast cancer sample, replicate 1 [Anon_11U_R1]


title: breast cancer sample, replicate 2 [Anon_11U_R2]


title: breast cancer sample, replicate 1 [Anon_11X_R1]


title: Sample_109_tissue


title: Sample_112_tissue


title: Sample_99_tissue


title: breast cancer sample, replicate 2 [Anon_11D_R2]


title: breast cancer sample, replicate 1 [Anon_11D_R1]


title: Sample_108_tissue


title: Sample_97_tissue


title: breast cancer sample, replicate 2 [Anon_11V_R2]


title: Sample_96_tissue


title: breast cancer sample, replicate 2 [Anon_11O_R2]


title: Sample_89_tissue


title: Sample_30_tissue


title: Sample_105_tissue


title: Sample_87_tissue


title: Sample_88_tissue


title: Sample_111_tissue


title: Sample_86_tissue


title: Sample_116_tissue


title: Sample_77_tissue


title: Sample_106_tissue


title: breast cancer sample, replicate 1 [Anon_11H_R1]


title: Sample_60_tissue


title: Sample_65_tissue


title: Sample_44_tissue


title: Sample_54_tissue


title: Sample_29_tissue


title: Sample_15_tissue


title: Sample_20_tissue


title: Sample_21_tissue


title: Sample_28_tissue


title: Sample_16_tissue


title: Sample_22_tissue


title: Sample_13_tissue


title: Sample_14_tissue


title: Sample_9_tissue


title: Sample_8_tissue


title: Sample_3_tissue


title: Sample_116_scrape

source_name: breast cancer sample, scrape cytology

value: scrape


title: Sample_68_tissue


title: Sample_112_scrape


title: Sample_96_scrape


title: Sample_86_scrape


title: Sample_4_tissue


title: Sample_97_scrape


title: Sample_105_scrape


title: Sample_99_scrape


title: Sample_6_tissue


title: Sample_114_scrape


title: Sample_24_tissue


title: Sample_111_scrape


title: Sample_65_scrape


title: Sample_88_scrape


title: Sample_68_scrape


title: Sample_89_scrape


title: Sample_106_scrape


title: Sample_87_scrape


title: Sample_108_scrape


title: Sample_110_scrape


title: Sample_60_scrape


title: Sample_77_scrape


title: Sample_30_scrape


title: Sample_20_scrape


title: Sample_24_scrape


title: Sample_22_scrape


title: Sample_109_scrape


title: Sample_54_scrape


title: Sample_28_scrape


title: Sample_15_scrape


title: Sample_19_scrape


title: Sample_21_scrape


title: Sample_29_scrape


title: Sample_9_scrape


title: Sample_16_scrape


title: Sample_13_scrape


title: Sample_14_scrape


title: Sample_44_scrape


title: Sample_6_scrape


title: Sample_103_tissue


title: Sample_3_scrape


title: Sample_104_tissue


title: Sample_8_scrape


title: Sample_113_tissue


title: breast cancer sample, replicate 1 [Anon_12R_R1]


title: Sample_102_tissue


title: Sample_101_tissue


title: Sample_115_tissue


title: Sample_100_tissue


title: Sample_4_scrape


title: Sample_93_tissue


title: Sample_27_tissue


title: Sample_19_tissue


title: Sample_94_tissue


title: Sample_25_tissue


title: Sample_26_tissue


title: Sample_92_tissue


title: Sample_95_tissue


title: Sample_18_tissue


title: Sample_91_tissue


title: Sample_17_tissue


title: Sample_11_tissue


title: Sample_12_tissue


title: Sample_107_tissue


title: Sample_90_tissue


title: Sample_98_tissue


title: Sample_23_tissue


title: Sample_5_tissue


title: Sample_10_tissue


title: Sample_7_tissue


title: Sample_1_tissue


title: Sample_107_scrape


title: Sample_103_scrape


title: Sample_102_scrape


title: Sample_115_scrape


title: Sample_100_scrape


title: Sample_95_scrape


title: Sample_2_tissue


title: Sample_93_scrape


title: Sample_98_scrape


title: Sample_94_scrape


title: Sample_104_scrape


title: Sample_113_scrape


title: Sample_27_scrape


title: Sample_26_scrape


title: Sample_91_scrape


title: Sample_25_scrape


title: Sample_90_scrape


title: Sample_101_scrape


title: Sample_12_scrape


title: Sample_23_scrape


title: Sample_17_scrape


title: Sample_92_scrape


title: Sample_7_scrape


title: Sample_11_scrape


title: Sample_2_scrape


title: Sample_18_scrape


title: Sample_5_scrape


title: Sample_10_scrape


title: Sample_1_scrape


title: Sample_42_scrape


title: Sample_37_scrape


title: Sample_41_scrape


title: Sample_34_scrape


title: Sample_40_scrape


title: Sample_36_scrape


title: Sample_33_scrape


title: Sample_82_scrape


title: Sample_31_scrape


title: Sample_79_scrape


title: Sample_85_scrape


title: Sample_53_scrape


title: Sample_45_scrape


title: Sample_46_scrape


title: Sample_59_scrape


title: Sample_51_scrape


title: Sample_52_scrape


title: Sample_75_scrape


title: Sample_84_scrape


title: Sample_39_scrape


title: Sample_49_scrape


title: Sample_67_scrape


title: Sample_48_scrape


title: Sample_32_scrape


title: Sample_83_scrape


title: Sample_58_scrape


title: Sample_42_tissue


title: Sample_39_tissue


title: Sample_41_tissue


title: Sample_43_scrape


title: Sample_38_tissue


title: Sample_40_tissue


title: Sample_37_tissue


title: Sample_75_tissue


title: Sample_74_tissue


title: Sample_84_tissue


title: Sample_85_tissue


title: Sample_38_scrape


title: Sample_58_tissue


title: Sample_74_scrape


title: Sample_52_tissue


title: Sample_34_tissue


title: Sample_67_tissue


title: Sample_79_tissue


title: Sample_31_tissue


title: Sample_32_tissue


title: Sample_33_tissue


title: Sample_82_tissue


title: Sample_43_tissue


title: Sample_83_tissue


title: Sample_36_tissue


title: Sample_51_tissue


title: Sample_53_tissue


title: Sample_49_tissue


title: Sample_47_scrape


title: Sample_59_tissue


title: Sample_35_scrape


title: Sample_47_tissue


title: Sample_81_scrape


title: Sample_45_tissue


title: Sample_56_scrape


title: Sample_80_scrape


title: Sample_72_scrape


title: Sample_73_scrape


title: Sample_78_scrape


title: Sample_70_scrape


title: Sample_69_scrape


title: Sample_76_scrape


title: Sample_66_scrape


title: Sample_48_tissue


title: Sample_46_tissue


title: Sample_64_scrape


title: Sample_61_scrape


title: Sample_63_scrape


title: Sample_71_scrape


title: Sample_62_scrape


title: Sample_80_tissue


title: Sample_81_tissue


title: Sample_35_tissue


title: Sample_57_scrape


title: Sample_78_tissue


title: Sample_55_scrape


title: Sample_50_scrape


title: Sample_71_tissue


title: Sample_76_tissue


title: Sample_69_tissue


title: Sample_63_tissue


title: Sample_66_tissue


title: Sample_50_tissue


title: Sample_55_tissue


title: Sample_1_Full replicate

source_name: breast cancer sample, technical replicate

treatment_protocol: Patients prospectively consented to a surgical tissue sample

tag: level of repetition

value: Full replicate


title: Sample_56_tissue


title: Sample_70_tissue


title: Sample_1_Original

value: Original


title: Sample_1_Full replicate re-scan

value: Full replicate re-scan


title: Sample_19_cRNA synthesis replicate

value: cRNA synthesis replicate


title: Sample_62_tissue


title: Sample_20_cRNA synthesis replicate


title: Sample_20_Original


title: Sample_57_tissue


title: Sample_1_cDNA synthesis replicate

value: cDNA synthesis replicate


title: Sample_61_tissue


title: Sample_20_cDNA synthesis replicate


title: Sample_20_RNA extraction replicate

value: RNA extraction replicate


title: Sample_1_cRNA synthesis replicate


title: Sample_73_tissue


title: Sample_64_tissue


title: Sample_19_Original


title: Sample_19_RNA extraction replicate


title: Sample_19_cDNA synthesis replicate


title: Sample_18_cRNA synthesis replicate


title: Sample_18_cDNA synthesis replicate


title: Sample_18_RNA extraction replicate


title: Sample_17_RNA extraction replicate


title: Sample_17_cRNA synthesis replicate


title: Sample_18_Original


title: Sample_17_Original


title: Sample_16_cDNA synthesis replicate


title: Sample_16_cRNA synthesis replicate


title: Sample_17_cDNA synthesis replicate


title: Sample_1_RNA extraction replicate


title: Sample_16_RNA extraction replicate


title: Sample_16_Original


title: Sample_15_RNA extraction replicate


title: Sample_20_Full replicate


title: Sample_20_Full replicate re-scan


title: Sample_19_Full replicate


title: Sample_15_Original


title: Sample_15_cDNA synthesis replicate


title: Sample_17_Full replicate


title: Sample_18_Full replicate


title: Sample_15_Full replicate re-scan


title: Sample_16_Full replicate


title: Sample_15_Full replicate


title: Sample_14_cRNA synthesis replicate


title: Sample_19_Full replicate re-scan


title: Sample_18_Full replicate re-scan


title: Sample_16_Full replicate re-scan


title: Sample_14_cDNA synthesis replicate


title: Sample_15_cRNA synthesis replicate


title: Sample_14_RNA extraction replicate


title: Sample_17_Full replicate re-scan


title: Sample_14_Original


title: Sample_13_cDNA synthesis replicate


title: Sample_13_cRNA synthesis replicate


title: Sample_13_RNA extraction replicate


title: Sample_13_Original


title: Sample_14_Full replicate


title: Sample_12_RNA extraction replicate


title: Sample_11_cDNA synthesis replicate


title: Sample_14_Full replicate re-scan


title: Sample_11_RNA extraction replicate


title: Sample_12_Original


title: Sample_11_Full replicate


title: Sample_11_cRNA synthesis replicate


title: Sample_13_Full replicate


title: Sample_10_RNA extraction replicate


title: Sample_12_Full replicate


title: Sample_11_Original


title: Sample_10_Original


title: Sample_12_Full replicate re-scan


title: Sample_12_cRNA synthesis replicate


title: Sample_9_RNA extraction replicate


title: Sample_10_cDNA synthesis replicate


title: Sample_11_Full replicate re-scan


title: Sample_9_cDNA synthesis replicate


title: Sample_9_cRNA synthesis replicate


title: Sample_10_cRNA synthesis replicate


title: Sample_13_Full replicate re-scan


title: Sample_9_Original


title: Sample_12_cDNA synthesis replicate


title: Sample_10_Full replicate


title: Sample_9_Full replicate


title: Sample_7_cRNA synthesis replicate


title: Sample_8_Original


title: Sample_8_RNA extraction replicate


title: Sample_7_Full replicate re-scan


title: Sample_10_Full replicate re-scan


title: Sample_8_cRNA synthesis replicate


title: Sample_72_tissue


title: Sample_9_Full replicate re-scan


title: Sample_8_Full replicate


title: Sample_7_cDNA synthesis replicate


title: Sample_8_cDNA synthesis replicate


title: Sample_7_RNA extraction replicate


title: Sample_6_Original


title: Sample_5_RNA extraction replicate


title: Sample_8_Full replicate re-scan


title: Sample_5_cDNA synthesis replicate


title: Sample_3_cDNA synthesis replicate


title: Sample_6_cRNA synthesis replicate


title: Sample_6_RNA extraction replicate


title: Sample_5_Full replicate re-scan


title: Sample_6_cDNA synthesis replicate


title: Sample_3_cRNA synthesis replicate


title: Sample_7_Full replicate


title: Sample_5_cRNA synthesis replicate


title: Sample_6_Full replicate


title: Sample_5_Full replicate


title: Sample_7_Original


title: Sample_6_Full replicate re-scan


title: Sample_4_cRNA synthesis replicate


title: Sample_3_Original


title: Sample_5_Original


title: Sample_4_cDNA synthesis replicate


title: Sample_12_Area_C

source_name: breast cancer sample

tag: tumor area

value: C


title: Sample_4_Full replicate re-scan


title: Sample_2_cDNA synthesis replicate


title: Sample_10_Area_C


title: Sample_10_Area_A

value: A


title: Sample_4_Original


title: Sample_10_Area_B

value: B


title: Sample_11_Area_B


title: Sample_2_Full replicate re-scan


title: Sample_3_Full replicate


title: Sample_3_Full replicate re-scan


title: Sample_2_Original


title: Sample_4_RNA extraction replicate


title: Sample_12_Area_A


title: Sample_11_Area_A


title: Sample_4_Area_C


title: Sample_11_Area_C


title: Sample_2_Full replicate


title: Sample_4_Area_A


title: Sample_12_Area_B


title: Sample_3_Area_C


title: Sample_4_Full replicate


title: Sample_2_cRNA synthesis replicate


title: Sample_2_RNA extraction replicate


title: Sample_4_Area_B


title: Sample_3_Area_B


title: Sample_3_Area_A


title: Sample_2_Area_B


title: Sample_2_Area_C


title: Sample_3_RNA extraction replicate


title: Sample_1_Area_C


title: Sample_49_Area_A


title: Sample_49_Area_C


title: Sample_20_Area_C


title: Sample_22_Area_C


title: Sample_22_Area_A


title: Sample_22_Area_B


title: Sample_41_Area_C


title: Sample_49_Area_B


title: Sample_20_Area_B


title: Sample_50_Area_C


title: Sample_50_Area_A


title: Sample_50_Area_B


title: Sample_1_Area_B


title: Sample_44_Area_B


title: Sample_41_Area_A


title: Sample_13_Area_C


title: Sample_34_Area_A


title: Sample_44_Area_C


title: Sample_6_Area_C


title: Sample_34_Area_B


title: Sample_1_Area_A


title: Sample_20_Area_A


title: Sample_41_Area_B


title: Sample_13_Area_B


title: Sample_13_Area_A


title: Sample_6_Area_B


title: Sample_44_Area_A


title: Sample_6_Area_A


title: Sample_40_Area_B


title: Sample_51_Area_B


title: Sample_8_Area_B


title: Sample_27_Area_A


title: Sample_40_Area_C


title: Sample_40_Area_A


title: Sample_27_Area_B


title: Sample_51_Area_A


title: Sample_21_Area_B


title: Sample_17_Area_B


title: Sample_27_Area_C


title: Sample_2_Area_A


title: Sample_51_Area_C


title: Sample_34_Area_C


title: Sample_18_Area_A


title: Sample_18_Area_B


title: Sample_21_Area_C


title: Sample_18_Area_C


title: Sample_8_Area_A


title: Sample_17_Area_C


title: Sample_21_Area_A


title: Sample_28_Area_A


title: Sample_16_Area_B


title: Sample_8_Area_C


title: Sample_28_Area_B


title: Sample_28_Area_C


title: Sample_15_Area_C


title: Sample_16_Area_A


title: Sample_16_Area_C


title: Sample_17_Area_A


title: Sample_15_Area_B


title: Sample_14_Area_C


title: Sample_7_Area_C


title: Sample_7_Area_B


title: Sample_5_Area_A


title: Sample_48_Area_A


title: Sample_48_Area_B


title: Sample_46_Area_C


title: Sample_48_Area_C


title: Sample_47_Area_A


title: Sample_47_Area_B


title: Sample_15_Area_A


title: Sample_9_Area_C


title: Sample_7_Area_A


title: Sample_47_Area_C


title: Sample_5_Area_B


title: Sample_9_Area_A


title: Sample_9_Area_B


title: Sample_45_Area_C


title: Sample_45_Area_B


title: Sample_14_Area_B


title: Sample_42_Area_C


title: Sample_14_Area_A


title: Sample_43_Area_C


title: Sample_5_Area_C


title: Sample_43_Area_B


title: Sample_45_Area_A


title: Sample_46_Area_A


title: Sample_46_Area_B


title: Sample_42_Area_A


title: Sample_37_Area_B


title: Sample_38_Area_B


title: Sample_38_Area_C


title: Sample_38_Area_A


title: Sample_36_Area_A


title: Sample_35_Area_A


title: Sample_35_Area_B


title: Sample_37_Area_C


title: Sample_36_Area_C


title: Sample_35_Area_C


title: Sample_33_Area_B


title: Sample_31_Area_A


title: Sample_32_Area_C


title: Sample_32_Area_B


title: Sample_33_Area_A


title: Sample_37_Area_A


title: Sample_43_Area_A


title: Sample_32_Area_A


title: Sample_33_Area_C


title: Sample_30_Area_B


title: Sample_42_Area_B


title: Sample_31_Area_B


title: Sample_31_Area_C


title: Sample_39_Area_A


title: Sample_30_Area_C


title: Sample_30_Area_A


title: Sample_36_Area_B


title: Sample_29_Area_B


title: Sample_29_Area_C


title: Sample_26_Area_B


title: Sample_23_Area_A


title: Sample_24_Area_B


title: Sample_29_Area_A


title: Sample_26_Area_A


title: Sample_25_Area_C


title: Sample_26_Area_C


title: Sample_25_Area_A


title: Sample_19_Area_C


title: Sample_19_Area_B


title: Sample_24_Area_A


title: Sample_23_Area_B


title: Sample_85_u133a

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized overnight at 46C on Affymetrix U133A or U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

source_name: breast cancer sample profiled on U133A microarray

tag: microarray


title: Sample_19_Area_A


title: Sample_24_Area_C


title: Sample_23_Area_C


title: Sample_25_Area_B


title: Sample_88_u133a


title: Sample_79_u133a


title: Sample_83_u133a


title: Sample_73_u133a


title: Sample_80_u133a


title: Sample_84_u133a


title: Sample_74_u133a


title: Sample_66_u133a


title: Sample_86_u133a


title: Sample_46_u133a


title: Sample_50_u133a


title: Sample_75_u133a


title: Sample_19_u133a


title: Sample_14_u133a


title: Sample_41_u133a


title: Sample_39_Area_B


title: Sample_15_u133a


title: Sample_22_u133a


title: Sample_65_u133a


title: Sample_4_u133a


title: Sample_13_u133a


title: Sample_82_u133a


title: Sample_12_u133a


title: Sample_81_u133a


title: Sample_16_u133a


title: Sample_77_u133a


title: Sample_3_u133a


title: Sample_17_u133a


title: Sample_71_u133a


title: Sample_69_u133a


title: Sample_6_u133a


title: Sample_87_u133a


title: Sample_68_u133a


title: Sample_32_u133a


title: Sample_72_u133a


title: Sample_78_u133a


title: Sample_21_u133a


title: Sample_20_u133a


title: Sample_58_u133a


title: Sample_10_u133a


title: Sample_39_Area_C


title: Sample_27_u133a


title: Sample_5_u133a


title: Sample_2_u133a


title: Sample_29_u133a


title: Sample_70_u133a


title: Sample_31_u133a


title: Sample_63_u133a


title: Sample_24_u133a


title: Sample_8_u133a


title: Sample_64_u133a


title: Sample_7_u133a


title: Sample_28_u133a


title: Sample_62_u133a


title: Sample_23_u133a


title: Sample_30_u133a


title: Sample_1_u133a


title: Sample_59_u133a


title: Sample_57_u133a


title: Sample_26_u133a


title: Sample_25_u133a


title: Sample_52_u133a


title: Sample_45_u133a


title: Sample_9_u133a


title: Sample_67_u133a


title: Sample_40_u133a


title: Sample_37_u133a


title: Sample_56_u133a


title: Sample_35_u133a


title: Sample_44_u133a


title: Sample_39_u133a


title: Sample_33_u133a


title: Sample_54_u133a


title: Sample_36_u133a


title: Sample_34_u133a


title: Sample_60_u133a


title: Sample_53_u133a


title: Sample_11_u133a


title: Sample_51_u133a


title: Sample_48_u133a


title: Sample_43_u133a


title: Sample_61_u133a


title: Sample_55_u133a


title: Sample_49_u133a


title: Sample_42_u133a


title: Sample_47_u133a


title: Breast cancer sample [631_mda_set_ep]

source_name: breast cancer, hormone receptor-positive

treatment_protocol: Patients prospectively consented to a research biopsy by fine needle aspiration (FNA), core biopsy or surgical tissue sample.

tag: ajcc stage

value: Fine needle aspiration


title: Breast cancer sample [549_mda_set_ep]

value: IIIB

value: Core biopsy


title: Breast cancer sample [550_mda_set_ep]

value: Breast cancer

value: IIA


title: Breast cancer sample [577_mda_set_ep]


title: Breast cancer sample [548_mda_set_ep]


title: Breast cancer sample [629_mda_set_ep]


title: Sample_76_u133a


title: Breast cancer sample [535_mda_set_ep]


title: Breast cancer sample [630_mda_set_ep]


title: Breast cancer sample [547_mda_set_ep]


title: Breast cancer sample [534_mda_set_ep]


title: Sample_38_u133a


title: Breast cancer sample [528_mda_set_ep]

value: Surgical tissue


title: Breast cancer sample [532_mda_set_ep]


title: Breast cancer sample [526_mda_set_ep]


title: Breast cancer sample [531_mda_set_ep]

value: IIIC


title: Breast cancer sample [527_mda_set_ep]


title: Breast cancer sample [533_mda_set_ep]

value: IA


title: Breast cancer sample [525_mda_set_ep]


title: Breast cancer sample [521_mda_set_ep]


title: Breast cancer sample [357_mda_set_ep]


title: Breast cancer sample [530_mda_set_ep]


title: Breast cancer sample [523_mda_set_ep]


title: Breast cancer sample [358_mda_set_ep]


title: Breast cancer sample [420_mda_set_ep]

value: IIB


title: Breast cancer sample [524_mda_set_ep]


title: Breast cancer sample [418_mda_set_ep]


title: Breast cancer sample [522_mda_set_ep]


title: Breast cancer sample [355_mda_set_ep]


title: Breast cancer sample [394_mda_set_ep]


title: Breast cancer sample [356_mda_set_ep]


title: Breast cancer sample [392_mda_set_ep]

value: IIIA


title: Breast cancer sample [354_mda_set_ep]


title: Breast cancer sample [494_mda_set_ep]


title: Sample_18_u133a


title: Breast cancer sample [529_mda_set_ep]


title: Breast cancer sample [338_mda_set_ep]


title: Breast cancer sample [352_mda_set_ep]


title: Breast cancer sample [353_mda_set_ep]


title: Breast cancer sample [332_mda_set_ep]


title: Breast cancer sample [316_mda_set_ep]


title: Breast cancer sample [326_mda_set_ep]


title: Breast cancer sample [261_mda_set_ep]


title: Breast cancer sample [260_mda_set_ep]


title: Breast cancer sample [259_mda_set_ep]


title: Breast cancer sample [258_mda_set_ep]

value: IV


title: Breast cancer sample [282_mda_set_ep]


title: Breast cancer sample [288_mda_set_ep]


title: Breast cancer sample [252_mda_set_ep]


title: Breast cancer sample [255_mda_set_ep]


title: Breast cancer sample [253_mda_set_ep]


title: Breast cancer sample [256_mda_set_ep]


title: Breast cancer sample [254_mda_set_ep]


title: Breast cancer sample [246_mda_set_ep]


title: Breast cancer sample [250_mda_set_ep]


title: Breast cancer sample [243_mda_set_ep]


title: Breast cancer sample [249_mda_set_ep]


title: Breast cancer sample [247_mda_set_ep]


title: Breast cancer sample [248_mda_set_ep]


title: Breast cancer sample [242_mda_set_ep]


title: Breast cancer sample [244_mda_set_ep]


title: Breast cancer sample [241_mda_set_ep]


title: Breast cancer sample [236_mda_set_ep]


title: Breast cancer sample [239_mda_set_ep]


title: Breast cancer sample [238_mda_set_ep]


title: Breast cancer sample [251_mda_set_ep]


title: Breast cancer sample [235_mda_set_ep]


title: Breast cancer sample [233_mda_set_ep]


title: Breast cancer sample [295_mda_set_ep]


title: Breast cancer sample [257_mda_set_ep]


title: Breast cancer sample [234_mda_set_ep]


title: Breast cancer sample [231_mda_set_ep]


title: Breast cancer sample [216_mda_set_ep]


title: Breast cancer sample [219_mda_set_ep]


title: Breast cancer sample [218_mda_set_ep]


title: Breast cancer sample [227_mda_set_ep]


title: Breast cancer sample [215_mda_set_ep]


title: Breast cancer sample [228_mda_set_ep]


title: Breast cancer sample [214_mda_set_ep]


title: Breast cancer sample [222_mda_set_ep]


title: Breast cancer sample [230_mda_set_ep]


title: Breast cancer sample [226_mda_set_ep]


title: Breast cancer sample [224_mda_set_ep]


title: Breast cancer sample [232_mda_set_ep]


title: Breast cancer sample [220_mda_set_ep]


title: Breast cancer sample [245_mda_set_ep]


title: Breast cancer sample [211_mda_set_ep]


title: Breast cancer sample [221_mda_set_ep]


title: Breast cancer sample [209_mda_set_ep]


title: Breast cancer sample [204_mda_set_ep]


title: Breast cancer sample [208_mda_set_ep]


title: Breast cancer sample [206_mda_set_ep]


title: Breast cancer sample [202_mda_set_ep]


title: Breast cancer sample [162_mda_set_ep]


title: Breast cancer sample [203_mda_set_ep]


title: Breast cancer sample [210_mda_set_ep]


title: Breast cancer sample [161_mda_set_ep]


title: Breast cancer sample [160_mda_set_ep]


title: Breast cancer sample [158_mda_set_ep]


title: Breast cancer sample [207_mda_set_ep]


title: Breast cancer sample [159_mda_set_ep]


title: Breast cancer sample [157_mda_set_ep]


title: Klu-Dam replicate 3

city: Novato

first: Tal

last: Ronnen Oron

address: 8001 Redwood blvd.

department: Bioinformatics Core

institute: Buck Institute for Research on Aging

description: PCR-Amplified Dam-methylated DNA

data_processing:
Library strategy: DamID-seq
damid_seq pipeline, Marshall, O. J. & Brand, A. H. damidseq_pipeline: an automated pipeline for processing DamID sequencing datasets. Bioinformatics 31, 3371–3373 (2015), was used to map reads to dm6 genome, create bedgraphs, and to call peaks in low FDR threshold of 0.1
use idr method, https://github.com/nboley/idr, to filter for reproducible peaks between pair of replicates.
use MOMER mergepeaks utility, http://homer.ucsd.edu/homer/ngs/mergePeaks.html, to merge between the pairwise reproducible peak sets
Genome_build: dm6
Supplementary_files_format_and_content: peaks, bed files

source_name: Dam-methylated DNA amplified from whole midgut in which Klu-Dam was expressed in Esg-positive stem-progenitors from Drosophila midgut

growth_protocol: Flies were kept at 18ºC and induced for Dam-expression for 24 hours prior to dissection

extract_protocol:
Isolation of methylated GATC-sequences and subsequent amplification was done according to the protocol published by Marshall et al (doi:10.1038/nprot.2016.084), until step 34 (Library construction, see below)
TruSeq nano DNA kit LT

treatment_protocol: Genomic DNA was isolated from 30-40 midguts for each replicate. Replicate sets were isolated on different dates

tag: genotype

value: esgts, UAS-Flp, UAS-Klu Dam

tag: treatment

value: 24 hr Shift-induction of UAS-Flp and Dam

value: midgut (30-40 midguts/sample)


title: Klu-Dam replicate 2

description: PCR-Amplified Dam-methylated DNA


title: Klu-Dam replicate 1

description: PCR-Amplified Dam-methylated DNA


title: Control Dam-only replicate 3

description: PCR-Amplified Dam-methylated DNA

source_name: Dam-methylated DNA amplified from whole midgut in which Dam alone was expressed in Esg-positive stem-progenitors from Drosophila midgut

value: esgts, UAS-Flp, UAS-Dam control


title: Breast cancer sample [155_mda_set_ep]


title: Wound 466

city: Indianapolis

first: Brad

last: Griesenauer

state: Indiana

address: 635 Barnhill Dr, MS 420

department: Microbiology and Immunology

institute: Indiana University School of Medicine

description:
Sample 7
Human_Raw_Read_Counts.txt

data_processing:
For the human samples, the sequence data were mapped to the human reference genome hg19 with STAR-2.5.2b
For the bacterial samples, the sequence data were mapped to the regerene genome Haemophilu ducreyi 35000hp ASM794v1  with bowtie 2 (version 2.3.2)
featureCounts (subread-1.6.0) was used to quantify gene expression (parameters applied: "“-s 2 –p –Q 10")
Differential expression analysis was performed using edgeR
Genome_build: Haemophilu ducreyi 35000hp reference genome  ASM794v1 and human reference genome hg19
Supplementary_files_format_and_content: Two files (one for H. ducreyi and one for human) containing raw counts of sequencing reads

source_name: Wound control from humans

growth_protocol: For samples 1-4, RNA was directly extracted from H. ducreyi-infected pustules on human volunteers. For samples 5-8, RNA was directly extracted from human wound-control sites. For samples 9-12, H. ducreyi was grown under GMP conditions to mid-log phase in a proteose peptone broth-based medium with 1% IsoVitaleX, 5% heat-inactivated fetal calf serum, and 50 ug/ml hemin and grown at 33°C for 5-6 hours.

extract_protocol:
Biopsy samples immediately after collection and the extra inocula immediately after inoculation were placed in 2 mL RNAlater, incubated for 30 minutes at room temperature, and stored in RNAlater for one day at -80°C. Using a mini-Beadbeater (Biospec Products), we next homogenized the samples and extracted total RNA using a RNeasy Fibrous Tissue Mini kit according to manufacturer’s instructions along with addition of lysozyme (20 ug/mL) added at the proteinase K step. The RNA was treated twice with TURBO DNA-free DNase (Ambion) following manufacturer’s instructions. RNA concentrations and integrities were measured using a NanoPhotometer P330 (Implen). RNA samples were stored at -80°C until all samples were ready for sequencing. We removed 23S, 16S, and 5S rRNA before RNA-seq using the Ribo-Zero Gold rRNA Removal Kit (Epidemiology) (Epicentre Biotechnologies) following manufacturer’s instructions and confirmed their removal using the Agilent 2100 Bioanalyzer.
Twelve libraries (four mid-log phase growth H. ducreyi cultures, four infected sites, and four wounded sites) were constructed using the TruSeq Stranded Total RNA Library kit (Illumina) following manufacturer’s instructions.

tag: time

value: 6-8 days post-inoculation

value: 6 mm skin


title: Wound 467

description:
Sample 8
Human_Raw_Read_Counts.txt


title: Wound 462

description:
Sample 5
Human_Raw_Read_Counts.txt


title: Wound 465

description:
Sample 6
Human_Raw_Read_Counts.txt


title: Breast cancer sample [146_mda_set_ep]


title: Breast cancer sample [154_mda_set_ep]


title: Breast cancer sample [151_mda_set_ep]


title: Control Dam-only replicate 1

description: PCR-Amplified Dam-methylated DNA


title: Control Dam-only replicate 2

description: PCR-Amplified Dam-methylated DNA


title: Breast cancer sample [152_mda_set_ep]


title: Breast cancer sample [145_mda_set_ep]


title: Breast cancer sample [153_mda_set_ep]


title: Breast cancer sample [147_mda_set_ep]


title: Breast cancer sample [142_mda_set_ep]


title: Breast cancer sample [144_mda_set_ep]


title: MERS-CoV-infected-rIFN-treated-2dpi-sacrifice-4dpi [2T1]

city: Iowa City

first: Stanley

last: Perlman

state: Iowa

address: Dept. Microbiology, BSB 3-712, 51 Newton Road

institute: University of Iowa

description:
2T1
processed data file: Channappanavar_Raw_Data.txt
processed data file: Processed_files_2C_vs_2T_101genes_2XFC_FDR_0.05.xlsx

data_processing:
Sample Quality Assessment: RNA isolates were quantified using a fluorimetric RiboGreen assay. Total RNA integrity was assessed using capillary electrophoresis (e.g., Agilent BioAnalyzer 2100), generating an RNA Integrity Number (RIN). For samples to pass the initial QC step, they need to quantify higher than 500 nanograms and have a RIN of 8 or greater, before they are converted to Illumina sequencing libraries.
Cluster generation and sequencing: TruSeq libraries were hybridized to a NextSeq (single Read). Clustering occurred on-board where the bound library molecules are clonally amplified and sequenced using Illumina’s SBS chemistry. NextSeq uses 2-color chemistry to image the clusters. Upon completion of read 1, a 7 base paired index read is performed in the case of single indexed libraries. If dual indexing was used during library preparation, 2 separate 8 or 10 base pair index reads were performed. Finally, clustered library fragments were re-synthesized in the reverse direction thus producing the template for paired end read 2.
Primary analysis and de-multiplexing: Base call (.bcl) files for each cycle of sequencing are generated by Illumina Real Time Analysis (RTA) software. The base call files and run folders are streamed to servers maintained at the Minnesota Supercomputing Institute. Primary analysis and de-multiplexing are performed using Illumina’s bcl2fastq software 2.20.  The end result of the bcl2fastq workflow is de-multiplexed FASTQ files that are released.
RNA Sequencing data analyses: 75bp FastQ single-end reads (n=11.7 Million per sample) were trimmed using Trimmomatic (v 0.33) enabled with the optional “-q” option; 3bp sliding-window trimming from 3’ end requiring minimum Q30. Quality control checks on raw sequence data for each sample were performed with FastQC (v0.11.7). Read mapping was performed via Hisat2 (2.1.0) using the mouse UCSC genome (mm10) as reference. Gene quantification was done via Subreads (Feature Counts v1.4.6) for raw read counts. Differentially expressed genes were identified using the edgeR (negative binomial) feature in CLCGWB v10.1.2 (Qiagen, Valencia, CA) using raw read counts. We filtered the generated list based on a minimum 1.5 X Absolute Fold Change and FDR corrected p < 0.001.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Channappanavar_Raw_Data.txt
Supplementary_files_format_and_content: Processed_files_1C_vs._1T_314genes_2XFC_FDR_0.05.xlsx
Supplementary_files_format_and_content: Processed_files_2C_vs_2T_101genes_2XFC_FDR_0.05.xlsx

source_name: Lung

extract_protocol:
Total lung RNA extracted from lungs at different times p.i. using Trizol (Invitrogen) was treated with RQ1 RNase-free DNase (Promega) for 10-15 minutes at 37°C to remove genomic DNA contamination.
Total RNA samples were converted to Illumina sequencing libraries using Illumina’s TruSeq Stranded mRNA Sample Preparation Kit (Cat. # RS-122-2103. Please see www.illumina.com for a detailed list of kit contents and methods). In summary, 500 nanograms of total RNA were oligo-dT purified using oligo-dT coated magnetic beads, fragmented and then reverse transcribed into cDNA. The cDNA was adenylated, ligated to dual-indexed (barcoded) adaptors and amplified using 15 cycles of PCR. Final library size distribution is validated using capillary electrophoresis and quantified using fluorimetry (PicoGreen). Indexed libraries were then normalized, pooled and then size selected to 320bp +/- 5% using the Pippin HT instrument.

treatment_protocol: IFN treated lungs after MERS-CoV infection.

tag: strain/background

value: hDPP4 knock-in C57BL/6

tag: cell type

value: Total lung cells

tag: infection

value: MERS-CoV

value: rIFN-treated 2dpi

tag: sacrifice


title: MERS-CoV-infected-untreated-sacrifice-4dpi [2C2]

description:
2C2
processed data file: Channappanavar_Raw_Data.txt
processed data file: Processed_files_2C_vs_2T_101genes_2XFC_FDR_0.05.xlsx

value: Untreated


title: MERS-CoV-infected-rIFN-treated-2dpi-sacrifice-4dpi [2T3]

description:
2T3
processed data file: Channappanavar_Raw_Data.txt
processed data file: Processed_files_2C_vs_2T_101genes_2XFC_FDR_0.05.xlsx


title: MERS-CoV-infected-rIFN-treated-2dpi-sacrifice-4dpi [2T2]

description:
2T2
processed data file: Channappanavar_Raw_Data.txt
processed data file: Processed_files_2C_vs_2T_101genes_2XFC_FDR_0.05.xlsx


title: MERS-CoV-infected-rIFN-treated-1dpi-sacrifice-3dpi [1T4]

description:
1T4
processed data file: Channappanavar_Raw_Data.txt
processed data file: Processed_files_1C_vs._1T_314genes_2XFC_FDR_0.05.xlsx

value: rIFN-treated 1dpi


title: MERS-CoV-infected-untreated-sacrifice-4dpi [2C4]

description:
2C4
processed data file: Channappanavar_Raw_Data.txt
processed data file: Processed_files_2C_vs_2T_101genes_2XFC_FDR_0.05.xlsx


title: Breast cancer sample [141_mda_set_ep]

tag: tissue

value: Breast cancer

value: Surgical tissue


title: MERS-CoV-infected-rIFN-treated-1dpi-sacrifice-3dpi [1T3]

description:
1T3
processed data file: Channappanavar_Raw_Data.txt
processed data file: Processed_files_1C_vs._1T_314genes_2XFC_FDR_0.05.xlsx


title: MERS-CoV-infected-rIFN-treated-2dpi-sacrifice-4dpi [2T4]

description:
2T4
processed data file: Channappanavar_Raw_Data.txt
processed data file: Processed_files_2C_vs_2T_101genes_2XFC_FDR_0.05.xlsx


title: MERS-CoV-infected-rIFN-treated-1dpi-sacrifice-3dpi [1T2]

description:
1T2
processed data file: Channappanavar_Raw_Data.txt
processed data file: Processed_files_1C_vs._1T_314genes_2XFC_FDR_0.05.xlsx


title: MERS-CoV-infected-untreated-sacrifice-4dpi [2C3]

description:
2C3
processed data file: Channappanavar_Raw_Data.txt
processed data file: Processed_files_2C_vs_2T_101genes_2XFC_FDR_0.05.xlsx


title: MERS-CoV-infected-untreated-sacrifice-4dpi [2C1]

description:
2C1
processed data file: Channappanavar_Raw_Data.txt
processed data file: Processed_files_2C_vs_2T_101genes_2XFC_FDR_0.05.xlsx


title: MERS-CoV-infected-rIFN-treated-1dpi-sacrifice-3dpi [1T1]

description:
1T1
processed data file: Channappanavar_Raw_Data.txt
processed data file: Processed_files_1C_vs._1T_314genes_2XFC_FDR_0.05.xlsx


title: MERS-CoV-infected-untreated-sacrifice-3dpi [1C4]

description:
1C4
processed data file: Channappanavar_Raw_Data.txt
processed data file: Processed_files_1C_vs._1T_314genes_2XFC_FDR_0.05.xlsx


title: Breast cancer sample [139_mda_set_ep]

value: IIB


title: Breast cancer sample [137_mda_set_ep]

value: IIA


title: MERS-CoV-infected-untreated-sacrifice-3dpi [1C3]

description:
1C3
processed data file: Channappanavar_Raw_Data.txt
processed data file: Processed_files_1C_vs._1T_314genes_2XFC_FDR_0.05.xlsx


title: Breast cancer sample [129_mda_set_ep]


title: MERS-CoV-infected-untreated-sacrifice-3dpi [1C2]

description:
1C2
processed data file: Channappanavar_Raw_Data.txt
processed data file: Processed_files_1C_vs._1T_314genes_2XFC_FDR_0.05.xlsx


title: Breast cancer sample [133_mda_set_ep]

value: IA