title: rbohd_Highlight_2min_Systemic Leaf_rep_2

description:
Experiment2
Column name in processed data file: 2-36


title: LymeDisease Pt23 Visit7

status: Public on Dec 21 2018

type: SRA

city: Stanford

first: Lisa

middle: K

last: Blum

state: CA

address: 269 Campus Drive

country: USA

institute: Stanford University

description:
LD23_V7
Amplicon mixture

library_source: transcriptomic

data_processing:
Matching files from the two HiSeq lanes were concatenated together (e.g., Sample1_Read1_Lane1+Sample1_Read1_Lane2).
Reads were filtered and assembled within UMI groups using MIGEC.
Explanation of the cumulative quality score (CQS) in migec-processed fastq files, and the relationship between CQS and Phred scores is described in the initial migec publication (Shugay et al. 2014, Nature Methods), and further illustrated in Turchaninova et al. 2016, Nature Protocols).
Paired-ends were merged with MITOOLS.
Genome_build: NA
Supplementary_files_format_and_content: *fastq: Fastq files of stitched reads, assembled and collapsed by UMI read group. These processed fastq files represent sequences that were assembled based on unique molecular identifiers (UMIs). The Q scores in these files are calculated based on the number of reads per UMI, as well as the quality of each base in each read.

molecule: total RNA

organism: Homo sapiens

source_name: Peripheral Blood Mononuclear Cells

extract_protocol:
Total RNA from PBMCs was extracted with Trizol and purified using RNA Clean & Concentrator-5 (Zymo Research) according to the manufacturer’s procedure.
cDNA was tagged with unique-molecular identifier sequences during RT. After a preliminary amplification step (specific for immunoglobulin constant regions), samples were divided into two aliquots and tagged with sequencing adapters in opposing directions (i.e., P5-Gene-P7 and P5-eneG-P7 for each sample), to allow for high quality assembly of UMI contigs. Library was sequenced across two separate HiSeq2500 lanes.

tag: cell type

value: Peripheral Blood Mononuclear Cells

tag: timepoint

value: 2 years post-treatment

tag: disease group

value: Lyme disease

tag: treatment response

value: Responder


title: rbohd_Highlight_2min_Local Leaf_rep_2

city: Memphis

first: Soham

last: Sengupta

state: TN

address: 262 Danny Thomas Place

institute: St. Jude Children's Research Hospital

description:
Experiment2
Column name in processed data file: 2-35

data_processing:
Basecalling performed using Standard Illumina Base Caller (Bustard)
Quality control of reads were performed using FastQC v0.11.7
RNA-seq reads were aligned to Arabidopsis thaliana genome obtained from TAIR using STAR aligner v2.4.0.1
Differential gene expression analysis was performed using DeSeq2 v1.20.0
Genome_build: TAIR 10
Supplementary_files_format_and_content: tab-deliminated files included normalized counts for each sample

organism: Arabidopsis thaliana

source_name: rbohd_Highlight_2min_Local Leaf

growth_protocol: Arabidopsis thaliana Col (WT) and rbohD knockout plants were grown in peat pellets (Jiffy-7, Jiffy, http://www.jiffygroup.com/en/) at 23°C under short day growth conditions (8-hour light/16-hour dark, 50 µmol m−2 s−1).

extract_protocol:
Total RNA was isolated using Trizol (Invitrogen Life Technologies) according to the manufacturer’s instructions and purified using NucleoSpin RNA Clean-up kit (Macherey-Nagel).
TruSeqHT

treatment_protocol: Local leaves of 4– to 5-week-old Col (WT) and rbohD plants were exposed to a light intensity of 2000 µmol m-2 sec-1 for periods of 0, 2, 4 and 8 min using a gooseneck light source (ACE I; Schott)

tag: ecotype

value: Col

tag: stress

value: Highlight

tag: time (min)

tag: repeat

tag: genotype

value: rbohd mutant

tag: tissue

value: Local Leaf


title: rbohd_Highlight_8min_Local Leaf_rep_2

description:
Experiment2
Column name in processed data file: 2-39

source_name: rbohd_Highlight_8min_Local Leaf


title: A673 cells, Imazalil treated at 0.03uM, rep.1

type: RNA

city: Research Triangle Park

first: Michael

middle: B.

last: Black

state: North Carolina

address: 100 Capitola Dr., Suite 106

institute: Scitovation, LLC.

description:
Gene Expression data from A673 cell culture
BW_003_24h_193_P1_IMAZ-A673

hyb_protocol: Affymetrix, GeneChip® High Throughput 3' IVT PLUS Reagent Kit, page40-42 and GeneTitan® Instrument User Guide for Expression Array Plates

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan array scanner to generate CEL files with corresponding intensity values.

data_processing: Affymetrix CEL files were normalized by RMA using Partek Genomic's Suite 6.6 (each strain normalized independently)

label: biotin

source_name: ATCC (Manassas, VA)

growth_protocol: A673 cells were purchased from ATCC (Manassas, VA).   A673 cells were cultured in DMEM (hyclone) containing 10% FBS and 1X pen/strep and plated at 26,000 cells/well in a 96-well plate.

extract_protocol: Trizol® (ThermalFisher) organic extraction with Phase Lock Gel™ -Heavy- tubes (5Prime).  Aqueous phase placed in RB(QiaCube sample) tubes and loaded into QiaCube, the RNeasy Mini Protocol used.

treatment_protocol: Cells were exposed in 96-well plates 24hrs after plating to allow attachment.  2,4-dichlorophenoxyacetic acid, fenbuconazole, and imazalil were purchased from Sigma-Aldrich (St. Louis, MO).  Stock solutions of 2,4-D, fenbuconazole, and imazilil were diluted in DMSO and added to culture media to a final DMSO concentration of 0.2%.  The cells were exposed for 24hrs to the DMSO vehicle (0.2%) or one of the following chemical concentrations: 0.001, 0.003, 0.01, 0.03, 0.1, 0.3, 1, 3, and 10uM.

tag: cell line

value: Cell culture

tag: time of exposure

value: 24 hours

tag: agent

value: Imazalil

tag: dose (um)


title: A673 cells, Imazalil treated at 0.003uM, rep.3

description:
Gene Expression data from A673 cell culture
BW_0003_24h_251_P3_IMAZ-A673

label_protocol: Affymetrix, GeneChip® High Throughput 3' IVT PLUS Reagent Kit


title: A673 cells, Imazalil treated at 0.01uM, rep.2

description:
Gene Expression data from A673 cell culture
BW_001_24h_222_P2_IMAZ-A673


title: A673 cells, Imazalil treated at 0.01uM, rep.1

description:
Gene Expression data from A673 cell culture
BW_001_24h_194_P1_IMAZ-A673


title: A673 cells, Imazalil treated at 0.01uM, rep.3

description:
Gene Expression data from A673 cell culture
BW_001_24h_250_P3_IMAZ-A673


title: LymeDisease Pt24 Visit3

description:
LD24_V3
Amplicon mixture

value: 1 month post-treatment


title: rbohd_Control_0min_Systemic Leaf_rep_2

description:
Experiment2
Column name in processed data file: 2-34

source_name: rbohd_Control_0min_Systemic Leaf

value: Control

value: Systemic Leaf


title: LymeDisease Pt23 Visit3

description:
LD23_V3
Amplicon mixture


title: LymeDisease Pt23 Visit1

description:
LD23_V1
Amplicon mixture

value: Untreated


title: LymeDisease Pt23 Visit5

description:
LD23_V5
Amplicon mixture

value: 6 months post-treatment


title: A673 cells, Imazalil treated at 0.003uM, rep.2

description:
Gene Expression data from A673 cell culture
BW_0003_24h_223_P2_IMAZ-A673


title: rbohd_Highlight_4min_Local Leaf_rep_2

description:
Experiment2
Column name in processed data file: 2-37

source_name: rbohd_Highlight_4min_Local Leaf


title: A673 cells, Imazalil treated at 0.001uM, rep.3

description:
Gene Expression data from A673 cell culture
BW_0001_24h_252_P3_IMAZ-A673


title: rbohd_Highlight_8min_Local Leaf_rep_1

description:
Experiment2
Column name in processed data file: 2-31


title: rbohd_Control_0min_Local Leaf_rep_2

description:
Experiment2
Column name in processed data file: 2-33

source_name: rbohd_Control_0min_Local Leaf


title: A673 cells, Imazalil treated at 0.001uM, rep.2

description:
Gene Expression data from A673 cell culture
BW_0001_24h_224_P2_IMAZ-A673


title: LymeDisease Pt22 Visit5

description:
LD22_V5
Amplicon mixture


title: LymeDisease Pt22 Visit7

description:
LD22_V7
Amplicon mixture


title: Breast_tumor_sample_L_foci_1_methylation

type: genomic

city: Brussels

first: David

last: Brown

address: Boulevard de Waterloo 127

country: Belgium

institute: Institut Jules Bordet

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium HumanMethylation450 BeadChip using the standard Infinium HD Methylation assay protocol.

scan_protocol: Arrays were scanned using a HiScan Reader following recommended Illumina scanner settings.

data_processing:
Raw intensity values (Signal A and Signal B) were extracted using Illumina GenomeStudio software v2010.3 (Methylation Module v1.8.5). The data were then processed in two steps: (i) probes displaying a detection p-value lower than 0.05, cross-reactive probes (list based on GPL16304-47833 annotation), probes containing common SNPs (list based on GPL16304-47833 annotation and Illumina annotation Probe_SNPs and Probe_SNPs_10) were discarded; and (ii) the PBC within-array normalization method was applied on Beta-values, as described in Dedeurwaerder et al. (Epigenomics, 2011).
Signal_A is Unmethylated and Signal_B is Methylated Signal

label: Cy3 and Cy5

molecule: genomic DNA

source_name: Breast tumor

label_protocol: Standard Infinium HD Methylation assay protocol.

extract_protocol: Genomic DNA was extracted using DNeasy Blood & Tissue Kit (Qiagen) according to the manufacturers' instructions

tag: er

tag: pgr

tag: grade


title: A673 cells, Imazalil treated at 0.003uM, rep.1

description:
Gene Expression data from A673 cell culture
BW_0003_24h_195_P1_IMAZ-A673

tag: cell type


title: Breast_tumor_sample_L_foci_2_methylation


title: rbohd_Highlight_8min_Systemic Leaf_rep_1

description:
Experiment2
Column name in processed data file: 2-32

source_name: rbohd_Highlight_8min_Systemic Leaf


title: A673 common DMSO control 3, RMA normalized with IMAZ samples

description:
Gene Expression data from A673 cell culture
BW_0_24h_225_P3_DMSO-A673-IMAZ

value: control


title: Breast_tumor_sample_K_foci_2_methylation


title: A673 common DMSO control 2, RMA normalized with IMAZ samples

description:
Gene Expression data from A673 cell culture
BW_0_24h_197_P2_DMSO-A673-IMAZ


title: rbohd_Highlight_4min_Systemic Leaf_rep_1

description:
Experiment2
Column name in processed data file: 2-30

source_name: rbohd_Highlight_4min_Systemic Leaf


title: rbohd_Highlight_4min_Local Leaf_rep_1

description:
Experiment2
Column name in processed data file: 2-29


title: LymeDisease Pt22 Visit3

description:
LD22_V3
Amplicon mixture

value: Peripheral Blood Mononuclear Cells

tag: timepoint


title: LymeDisease Pt22 Visit1

description:
LD22_V1
Amplicon mixture

tag: disease group


title: rbohd_Highlight_2min_Systemic Leaf_rep_1

description:
Experiment2
Column name in processed data file: 2-28

source_name: rbohd_Highlight_2min_Systemic Leaf


title: A673 cells, Imazalil treated at 0.001uM, rep.1

description:
Gene Expression data from A673 cell culture
BW_0001_24h_196_P1_IMAZ-A673


title: LymeDisease Pt21 Visit7

description:
LD21_V7
Amplicon mixture

value: 2 years post-treatment

tag: treatment response


title: A673 common DMSO control 1, RMA normalized with IMAZ samples

description:
Gene Expression data from A673 cell culture
BW_0_24h_169_P1_DMSO-A673-IMAZ


title: rbohd_Highlight_2min_Local Leaf_rep_1

description:
Experiment2
Column name in processed data file: 2-27

tag: ecotype


title: Breast_tumor_sample_J_foci_2_methylation


title: Breast_tumor_sample_K_foci_1_methylation


title: Breast_tumor_sample_I_foci_2_methylation


title: Breast_tumor_sample_J_foci_1_methylation


title: rbohd_Control_0min_Local Leaf_rep_1

description:
Experiment2
Column name in processed data file: 2-25

tag: stress


title: A673 cells, Fenbuconazole treated at 3uM, rep.3

description:
Gene Expression data from A673 cell culture
BW_3_24h_236_P3_FENB-A673

value: Fenbuconazole


title: LymeDisease Pt21 Visit5

description:
LD21_V5
Amplicon mixture

value: Lyme disease

value: Responder


title: LymeDisease Pt21 Visit3

description:
LD21_V3
Amplicon mixture


title: LymeDisease Pt21 Visit1

description:
LD21_V1
Amplicon mixture


title: A673 cells, Fenbuconazole treated at 3uM, rep.1

description:
Gene Expression data from A673 cell culture
BW_3_24h_180_P1_FENB-A673


title: A673 cells, Fenbuconazole treated at 3uM, rep.2

description:
Gene Expression data from A673 cell culture
BW_3_24h_208_P2_FENB-A673


title: rbohd_Control_0min_Systemic Leaf_rep_1

description:
Experiment2
Column name in processed data file: 2-26

value: Col

tag: time (min)


title: Breast_tumor_sample_H_foci_2_methylation


title: Breast_tumor_sample_I_foci_1_methylation


title: Col_Highlight_8min_Local Leaf_rep_3

description:
Experiment1
Column name in processed data file: M23

source_name: Col_Highlight_8min_Local Leaf

value: Highlight

tag: repeat

value: wild type


title: A673 cells, Fenbuconazole treated at 10uM, rep.3

description:
Gene Expression data from A673 cell culture
BW_10_24h_235_P3_FENB-A673

value: Cell culture


title: Col_Highlight_8min_Systemic Leaf_rep_3

description:
Experiment1
Column name in processed data file: M24

source_name: Col_Highlight_8min_Systemic Leaf

tag: genotype


title: LymeDisease Pt20 Visit5

description:
LD20_V5
Amplicon mixture


title: LymeDisease Pt20 Visit7

description:
LD20_V7
Amplicon mixture


title: Col_Highlight_4min_Systemic Leaf_rep_3

description:
Experiment1
Column name in processed data file: M22

source_name: Col_Highlight_4min_Systemic Leaf

tag: tissue


title: Breast_tumor_sample_H_foci_1_methylation


title: LymeDisease Pt20 Visit1

description:
LD20_V1
Amplicon mixture


title: A673 cells, Fenbuconazole treated at 1uM, rep.2

description:
Gene Expression data from A673 cell culture
BW_1_24h_209_P2_FENB-A673

tag: cell line

value: 24 hours


title: A673 cells, Fenbuconazole treated at 10uM, rep.1

description:
Gene Expression data from A673 cell culture
BW_10_24h_179_P1_FENB-A673

tag: time of exposure


title: Breast_tumor_sample_G_foci_2_methylation

data_processing: Raw intensity values (Signal A and Signal B) were extracted using Illumina GenomeStudio software v2010.3 (Methylation Module v1.8.5) and processed in three steps: (i) probes displaying a detection P-value lower than 0.05 were discarded, (ii) the 10% of probes displaying the highest average intensities were removed and (iii) a peak-based correction was applied on the resulting Beta-values in order to correct the Infinium type I / type II bias as described in Dedeurwaerder et al. (2011) Evaluation of the Infinium Methylation 450K technology. Epigenomics, 3(6): 771-84.

extract_protocol: Genomic DNA was extracted using DNeasy Blood & Tissue Kit according to the manufacturers' instructions

value: Breast tumor


title: Breast_tumor_sample_G_foci_1_methylation


title: LymeDisease Pt20 Visit3

description:
LD20_V3
Amplicon mixture

value: 1 month post-treatment


title: A673 cells, Fenbuconazole treated at 10uM, rep.2

description:
Gene Expression data from A673 cell culture
BW_10_24h_207_P2_FENB-A673

tag: agent


title: Col_Highlight_4min_Local Leaf_rep_3

description:
Experiment1
Column name in processed data file: M21

source_name: Col_Highlight_4min_Local Leaf

value: Local Leaf


title: RNAseq_PLZF

city: Marseille

first: Mathilde

last: Poplineau

address: 27 BOULEVARD LEI ROURE CS 30059

country: France

institute: INSERM

data_processing:
Reads were mapped to mm10 genome using subread-align (v1.5.0) with default parameters
Tag counts were obtained using featureCounts (v1.5.0) with default parameters
Counts were normalized by the size of each library (DESeq2, estimateSizeFactors function)
Genome_build: mm10

organism: Mus musculus

source_name: 416b cell line

growth_protocol: 416b cells (Cd34+) were grown in RPMI 10% FCS 1% P/S; GMPs (Lineage negative, C-kit+, Sca-1-, Cd34+, FcγR+) were purified from the different mouse models

extract_protocol:
For RNA-seq, total RNA were extracted with RNeasy Plus Mini kit (Qiagen). For ATAC-seq and ChIP-seq home-made protocols were used (see Materials and Methods)
ChIP-seq : MicroPlex Library Preparation Kit (Diagenode) ; ATAC-seq : Nextera DNA Library Prep Kit (Illumina) ; RNA-seq in GMPs : TruSeq Stranded Total RNA with Ribo Zero Gold kit (Illumina) ; RNA-seq in 416b : SMART-Seq v3 Ultra Low Input RNA kit for (Clontech)

treatment_protocol: 416b transduced by PLZF-Flag or empty vector

value: bone marrow-derived progenitor cells

value: 416b cell line

tag: culture properties

value: suspension

value: PLZF-Flag


title: Col_Control_0min_Systemic Leaf_rep_3

description:
Experiment1
Column name in processed data file: M18

source_name: Col_Control_0min_Systemic Leaf

value: Control

value: Systemic Leaf


title: A673 cells, Fenbuconazole treated at 1uM, rep.3

description:
Gene Expression data from A673 cell culture
BW_1_24h_237_P3_FENB-A673

value: Fenbuconazole

tag: dose (um)


title: LymeDisease Pt19 Visit5

description:
LD19_V5
Amplicon mixture

source_name: Peripheral Blood Mononuclear Cells

value: Peripheral Blood Mononuclear Cells

value: 6 months post-treatment

value: Lyme disease

value: Non-responder


title: Col_Highlight_2min_Systemic Leaf_rep_3

description:
Experiment1
Column name in processed data file: M20

source_name: Col_Highlight_2min_Systemic Leaf

value: Col

value: Highlight

value: wild type


title: A673 cells, Fenbuconazole treated at 1uM, rep.1

description:
Gene Expression data from A673 cell culture
BW_1_24h_181_P1_FENB-A673

value: Cell culture

value: 24 hours


title: RNAseq_Ctrl

value: Empty vector


title: LymeDisease Pt19 Visit7

description:
LD19_V7
Amplicon mixture

value: 2 years post-treatment


title: Col_Highlight_2min_Local Leaf_rep_3

description:
Experiment1
Column name in processed data file: M19

source_name: Col_Highlight_2min_Local Leaf

value: Local Leaf


title: Breast_tumor_sample_F_foci_1_methylation

value: Breast tumor

tag: er

tag: pgr


title: Breast_tumor_sample_F_foci_2_methylation

tag: grade


title: Breast_tumor_sample_E_foci_2_methylation


title: LymeDisease Pt19 Visit3

description:
LD19_V3
Amplicon mixture

tag: cell type

tag: timepoint

value: 1 month post-treatment


title: Input-PLZF_PLZF

library_source: genomic

data_processing:
basecalling was performed using Illumina CASAVA
Reads with Phred quality score less than 30 were filtered out
Replicate concurrency was verified by PCA plots, and sample replicates were merged into a single fastq file
Sequences were mapped to a hybride genome (concatenation of mouse and drosophila genome : mm10 and dm6) using Bowtie2 alignment tool (ref: PMID 22388286) with default parameters
Mapped sequences were filtered depending on the organism they belong to
For each mouse datasets, tag counts were normalized by the total number of drosophila mapped tags such that each file correspond to the same amount of drosophila reads.
bigwig files were generated from spiked in bam files using either a customed script or Deeptools 2.0 suite (bamCompare)
Peak callings were performed using MACS2 (in sharp mode for transcription factors; in broad mode for histone marks) using inputs as controls
Genome_build: mm10

value: bone marrow-derived progenitor cells

value: 416b cell line

value: suspension

value: PLZF-Flag


title: Col_Highlight_8min_Systemic Leaf_rep_2

description:
Experiment1
Column name in processed data file: M16

value: Systemic Leaf


title: ATRA+NIC

city: Xi'an

first: Jing

last: Li

state: Shaanxi

address: 157 Xi Wu Road

department: Dermatology

country: China

institute: Northwest Hospital, Xi'an Jiaotong University

hyb_protocol: Microarrays were hybridized at 42°C during 16 to 20h with 4 μg of Cy3 labeled ds-cDNA in NimbleGen hybridization buffer/hybridization component A in a hybridization chamber (Hybridization System - NimbleGen Systems, Inc., Madison, WI, USA).

scan_protocol: Following hybridization, washing was performed using the NimbleGen Wash Buffer kit (NimbleGen Systems, Inc., Madison, WI, USA). After being washed in an ozone-free environment, the slides were scanned using the Axon GenePix 4000B microarray scanner.

data_processing: Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis.

source_name: immortalized keratinocytes cell line

label_protocol: Expression Analysis protocol (NimbleGen Systems, Inc., USA). Briefly, ds-cDNA was incubated with 4 μg RNase A at 37°C for 10 min and cleaned using phenol:chloroform:isoamyl alcohol, followed by ice-cold absolute ethanol precipitation. The purified cDNA was quantified using a NanoDrop ND-1000. For Cy3 labeling of cDNA, the NimbleGen One-Color DNA labeling kit was used according to the manufacturer's guideline detailed in the Gene Expression Analysis protocol (NimbleGen Systems, Inc., Madison, WI, USA). One μg ds-cDNA was incubated for 10 min at 98°C with 1 OD of Cy3-9mer primer. Then, 100 pmol of deoxynucleoside triphosphates and 100U of the Klenow fragment (New England Biolabs, USA) were added and the mix incubated at 37°C for 2 hours. The reaction was stopped by adding 0.1 volume of 0.5 M EDTA, and the labeled ds-cDNA was purified by isopropanol / ethanol precipitation.

growth_protocol: HaCaT cells were grown in RPMI-1640 with 10% fetal bovine serum and 1% penicillin-streptomycin.  All cells were maintained in a 5% CO2 incubator at 37°C. Male BALB/c mice (8 weeks of age, about 100 25 g of body weight) were fed standard chow food and water ad libitum, and caged in a controlled environment (12 h light/dark cycle; temperature, 20-25°C; humidity, 45-55%). The mice were acclimatized for 3 days prior to any experiment

extract_protocol: The total RNA were extracted by Trizol after harvesting three treated cells according to the manufacturer’s instructions. RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: HaCaT cells were incubated with or without 1 μM ATRA for 36 h.

value: ATRA+NIC

value: HaCaT


title: A673 cells, Fenbuconazole treated at 0.3uM, rep.3

description:
Gene Expression data from A673 cell culture
BW_03_24h_238_P3_FENB-A673

source_name: ATCC (Manassas, VA)

value: Fenbuconazole


title: Col_Control_0min_Local Leaf_rep_3

description:
Experiment1
Column name in processed data file: M17

source_name: Col_Control_0min_Local Leaf

value: Col

value: Control


title: ATRA

value: ATRA


title: LymeDisease Pt18 Visit7

description:
LD18_V7
Amplicon mixture

value: Peripheral Blood Mononuclear Cells

tag: disease group

value: Lyme disease

tag: treatment response

value: Responder


title: Col_Highlight_8min_Local Leaf_rep_2

description:
Experiment1
Column name in processed data file: M15

tag: ecotype

tag: stress

value: Highlight

value: wild type

value: Local Leaf


title: Control


title: LymeDisease Pt19 Visit1

description:
LD19_V1
Amplicon mixture

value: Untreated

value: Non-responder


title: A673 cells, Fenbuconazole treated at 0.3uM, rep.2

description:
Gene Expression data from A673 cell culture
BW_03_24h_210_P2_FENB-A673

value: Cell culture

value: 24 hours


title: A673 cells, Fenbuconazole treated at 0.1uM, rep.3

description:
Gene Expression data from A673 cell culture
BW_01_24h_239_P3_FENB-A673


title: Breast_tumor_sample_C_foci_2_methylation

value: Breast tumor


title: A673 cells, Fenbuconazole treated at 0.3uM, rep.1

description:
Gene Expression data from A673 cell culture
BW_03_24h_182_P1_FENB-A673


title: A673 cells, Fenbuconazole treated at 0.1uM, rep.1

description:
Gene Expression data from A673 cell culture
BW_01_24h_183_P1_FENB-A673


title: Col_Highlight_4min_Systemic Leaf_rep_2

description:
Experiment1
Column name in processed data file: M14

tag: time (min)

tag: repeat

value: Systemic Leaf


title: PLZF_ChIPSeq_Ctrl

tag: tissue

value: bone marrow-derived progenitor cells

value: 416b cell line

value: suspension

tag: genotype

value: Empty vector


title: Col_Highlight_4min_Local Leaf_rep_2

description:
Experiment1
Column name in processed data file: M13

value: Col


title: LymeDisease Pt18 Visit3

description:
LD18_V3
Amplicon mixture

value: Peripheral Blood Mononuclear Cells

value: 1 month post-treatment


title: A673 cells, Fenbuconazole treated at 0.1uM, rep.2

description:
Gene Expression data from A673 cell culture
BW_01_24h_211_P2_FENB-A673

tag: cell line

tag: time of exposure

value: Fenbuconazole


title: Breast_tumor_sample_C_foci_1_methylation


title: LymeDisease Pt18 Visit1

description:
LD18_V1
Amplicon mixture

value: Lyme disease

value: Responder


title: Breast_tumor_sample_B_foci_2_methylation


title: Col_Highlight_2min_Systemic Leaf_rep_2

description:
Experiment1
Column name in processed data file: M12

value: Highlight

value: wild type


title: Breast_tumor_sample_E_foci_1_methylation


title: A673 cells, Fenbuconazole treated at 0.03uM, rep.3

description:
Gene Expression data from A673 cell culture
BW_003_24h_240_P3_FENB-A673

tag: agent


title: Input-PLZF_Ctrl

tag: culture properties


title: PLZF_ChIPSeq_PLZF

value: PLZF-Flag


title: LymeDisease Pt18 Visit5

description:
LD18_V5
Amplicon mixture

value: 6 months post-treatment


title: Col_Highlight_2min_Local Leaf_rep_2

description:
Experiment1
Column name in processed data file: M11

value: Local Leaf


title: LymeDisease Pt17 Visit7

description:
LD17_V7
Amplicon mixture

value: 2 years post-treatment

value: Non-responder


title: Input-Atac_PLZF

data_processing:
Reads were mapped and peaks were called as in ChIPseq analysis (MACS2, sharp mode, p 0.01)
Counts were normalized using the number of mouse mapped tags.
Genome_build: mm10

value: bone marrow-derived progenitor cells


title: Breast_tumor_sample_B_foci_1_methylation

value: Breast tumor

tag: er


title: Atac_PLZF

value: 416b cell line

value: suspension


title: Input-Atac_Ctrl

value: Empty vector


title: Atac_Ctrl


title: LymeDisease Pt17 Visit3

description:
LD17_V3
Amplicon mixture

value: Peripheral Blood Mononuclear Cells


title: Col_Control_0min_Systemic Leaf_rep_2

description:
Experiment1
Column name in processed data file: M10

value: Col

value: Control

value: Systemic Leaf


title: LymeDisease Pt17 Visit5

description:
LD17_V5
Amplicon mixture

value: Lyme disease


title: Input-histones_PLZF


title: LymeDisease Pt17 Visit1

description:
LD17_V1
Amplicon mixture

value: Untreated


title: Col_Control_0min_Local Leaf_rep_2

description:
Experiment1
Column name in processed data file: M9

value: wild type


title: LymeDisease Pt16 Visit5

description:
LD16_V5
Amplicon mixture


title: Input-histones_Ctrl


title: H3K4me3_ChIPSeq_PLZF

value: PLZF-Flag


title: Col_Highlight_8min_Local Leaf_rep_1

description:
Experiment1
Column name in processed data file: M7

value: Highlight


title: A673 cells, Fenbuconazole treated at 0.03uM, rep.1

description:
Gene Expression data from A673 cell culture
BW_003_24h_184_P1_FENB-A673

value: Cell culture

value: 24 hours

value: Fenbuconazole

tag: dose (um)


title: A673 cells, Fenbuconazole treated at 0.01uM, rep.3

description:
Gene Expression data from A673 cell culture
BW_001_24h_241_P3_FENB-A673


title: A673 cells, Fenbuconazole treated at 0.01uM, rep.1

description:
Gene Expression data from A673 cell culture
BW_001_24h_185_P1_FENB-A673


title: LymeDisease Pt16 Visit3

description:
LD16_V3
Amplicon mixture

value: 1 month post-treatment

value: Non-responder


title: A673 cells, Fenbuconazole treated at 0.03uM, rep.2

description:
Gene Expression data from A673 cell culture
BW_003_24h_212_P2_FENB-A673


title: Col_Highlight_4min_Systemic Leaf_rep_1

description:
Experiment1
Column name in processed data file: M6


title: H3K4me1_ChIPSeq_PLZF

value: bone marrow-derived progenitor cells

value: 416b cell line


title: A673 cells, Fenbuconazole treated at 0.01uM, rep.2

description:
Gene Expression data from A673 cell culture
BW_001_24h_213_P2_FENB-A673


title: LymeDisease Pt16 Visit1

description:
LD16_V1
Amplicon mixture


title: A673 cells, Fenbuconazole treated at 0.003uM, rep.2

description:
Gene Expression data from A673 cell culture
BW_0003_24h_214_P2_FENB-A673


title: H3K27ac_ChIPSeq_PLZF

value: suspension


title: Col_Highlight_2min_Systemic Leaf_rep_1

description:
Experiment1
Column name in processed data file: M4


title: Col_Highlight_2min_Local Leaf_rep_1

description:
Experiment1
Column name in processed data file: M3

value: Local Leaf


title: Col_Highlight_8min_Systemic Leaf_rep_1

description:
Experiment1
Column name in processed data file: M8

value: Col


title: LymeDisease Pt15 Visit7

description:
LD15_V7
Amplicon mixture

value: Peripheral Blood Mononuclear Cells

value: 2 years post-treatment


title: A673 cells, Fenbuconazole treated at 0.003uM, rep.3

description:
Gene Expression data from A673 cell culture
BW_0003_24h_242_P3_FENB-A673


title: Col_Highlight_4min_Local Leaf_rep_1

description:
Experiment1
Column name in processed data file: M5


title: Col_Control_0min_Systemic Leaf_rep_1

description:
Experiment1
Column name in processed data file: M2

value: Control

value: Systemic Leaf


title: LymeDisease Pt15 Visit3

description:
LD15_V3
Amplicon mixture

value: Lyme disease


title: LymeDisease Pt15 Visit5

description:
LD15_V5
Amplicon mixture

value: 6 months post-treatment


title: H3K4me1_ChIPSeq_Ctrl

value: Empty vector


title: H3K27ac_ChIPSeq_Ctrl


title: LymeDisease Pt15 Visit1

description:
LD15_V1
Amplicon mixture

value: Untreated


title: A673 cells, Fenbuconazole treated at 0.001uM, rep.3

description:
Gene Expression data from A673 cell culture
BW_0001_24h_243_P3_FENB-A673

value: Cell culture

value: 24 hours


title: Col_Control_0min_Local Leaf_rep_1

description:
Experiment1
Column name in processed data file: M1

value: wild type


title: A673 cells, Fenbuconazole treated at 0.003uM, rep.1

description:
Gene Expression data from A673 cell culture
BW_0003_24h_186_P1_FENB-A673

value: Fenbuconazole


title: H3K4me3_ChIPSeq_Ctrl

value: bone marrow-derived progenitor cells


title: A673 cells, Fenbuconazole treated at 0.001uM, rep.1

description:
Gene Expression data from A673 cell culture
BW_0001_24h_187_P1_FENB-A673


title: A673 cells, Fenbuconazole treated at 0.001uM, rep.2

description:
Gene Expression data from A673 cell culture
BW_0001_24h_215_P2_FENB-A673


title: A673 common DMSO control 3, RMA normalized with FENB samples

description:
Gene Expression data from A673 cell culture
BW_0_24h_225_P3_DMSO-A673-FENB

value: control


title: A673 common DMSO control 2, RMA normalized with FENB samples

description:
Gene Expression data from A673 cell culture
BW_0_24h_197_P2_DMSO-A673-FENB


title: M. smegmati WT+Gln

city: Chongqing

first: Xue

last: Huang

address: Tiansheng load, Beibei, Chongqing

description:
X9hao_1
Rif/gln

data_processing:
illumina Hiseq 4000 used for basecalling
Sequenced reads were filtered for Seqtk, and get clean Reads that can be used for data analysis, using the bowtie2 (version: 2-2.2.6), the Genome mapping was performed on post-pretreatment reads, which was more suitable for the sequencing data of the prokaryotic transcriptome. The comparison result generated by Mapping is the BAM file
Fragments Per Kilobase of exon model per Million mapped reads.We first apply HTSeq in TopHat than after each gene Fragments could count to count, and then use TMM (trimmed mean of M values) normalization method, finally calculated using perl script FPKM value of each gene.
Genome_build: ASM1500v1
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Mycolicibacterium smegmatis MC2 155

source_name: Mycobacterium smegmatis MC2 155

growth_protocol: M. smegmatis was cultured under starvation conditions in 250ml bottles.

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany).
Strand-specific libraries were prepared. ribosomal RNA was removed from total RNA using Ribo-Zero rRNA removal beads. Following purification, the mRNA is fragmented into small pieces. The cDNA fragments afterwards through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library.

treatment_protocol: For the antibiotic treatment, three 50ml cultures were was pelleted and washed twice with 1 x PBS followed by resuspending in M9 medium without glucose, in presence of rifampicin with or without glutamine about 12h

tag: genotype/variation

tag: culture condition

value: rifampicin+glutamine


title: M. smegmati WT

description:
X8hao_1
Rif

value: rifampicin


title: C-3

city: Wuhan

first: Yuanyuan

last: Chen

state: Hubei

address: Shizishan street 1

department: College of Fisheries

institute: Huazhong Agricultural University

description: treated with 3 µM Cu for 48 h

data_processing:
Illumina Casava1.8 software used for basecalling.
Clean the raw reads by clearing reads with the adapter, low sequence quality (> 30%), or a high percentage of unknown base (> 5%), then  use SOAPaligner / SOAP2 software to map clean data to the annotated genome of the M. aeruginosa NIES-843 ASM1062v1 and allow up to 5 nucleotides to mismatch.
The distribution of gene coverage is calculated using the alignment data. The gene expression levels were normalized as FPKM.  Differentially expressed genes were selected based on fold change > 2 (statistical power >0.8) and P value< 0.05.
Genome_build: M. aeruginosa NIES-843 ASM1062v1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Microcystis aeruginosa PCC 7806

source_name: Microcystis aeruginosa PCC 7806  grown in BG11-Cu treated with 3 µM

growth_protocol: The M. aeruginosa 7806 strain was grown in BG11 at 25 ℃ under continuous illumination (40 µmol photons m−2s−1).

extract_protocol:
Cultures were harvested after exposed 48 h for RNA extraction using Trizol reagent. TransZol Up Plus RNA Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: cultures were supplemented with 0.5 µM or 3µM CuSO4 for 48h.

tag: strain

tag: treatment

value: 3 microM Cu for 48 h


title: C-2

description: treated with 3 µM Cu for 48 h


title: CD8 normal 17

city: Bologna

first: Fabio

last: Fuligni

address: Via Massarenti 9

department: Department of Experimental, Diagnostic, and Specialty Medicine Bologna University Medical School

country: Italy

institute: University of Bologna

hyb_protocol: Standard Illumina Whole Genome DASL hybridization protocol.

scan_protocol: Illumina's BeadArray Reader was used to scan the BeadChips using the standard Illumina Whole Genome DASL scanning protocol.

data_processing: The data were log2-transformed and then quantile normalized using the lumi Bioconductor package. Normalized data coming from 2 different arrays (HumanRef-8 WG-DASL v3.0, HumanHT-12 WG-DASL V4.0 R2) were joined together considering only those genes in common to both versions of the array.

source_name: CD8 normal control cells

label_protocol: Standard Illumina Whole Genome DASL labeling protocol.

extract_protocol: RNA from FFPE samples was extracted with the Ambion RecoverAll Extraction Kit. Normal cells from healthy donors were isolated by the Qiagen RNeasy Mini kit.

tag: cell type

value: CD8 normal cells


title: CD4 normal 10

source_name: CD4 normal control cells

value: CD4 normal cells


title: CD8 normal 11


title: ATRA [Mouse]

data_processing:
Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis.
All Targets Value (Entities where at least 4 out of 4 samples have values greater than or equal to Lower cut-off: 50.0)

source_name: Mouse skin

growth_protocol: Male BALB/c mice (8 weeks of age, about 100 25 g of body weight) were fed standard chow food and water ad libitum, and caged in a controlled environment (12 h light/dark cycle; temperature, 20-25°C; humidity, 45-55%). The mice were acclimatized for 3 days prior to any experiment

extract_protocol: The total RNA were extracted by Trizol after harvesting four mouse skin according to the manufacturer’s instructions. RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: The skin on the back of the mice were divided into four groups, which were then treated with topical 0.1% ATRA cream (Chongqing Winbond Pharmaceutical co., China),an oil/water cream,topical 0.1% ATRA cream with NIC cream and NIC cream twice a day for five days.

value: ATRA

value: BALB/c

tag: age

value: 8 weeks


title: CD4 normal 12


title: B-3

description: treated with 0.5 µM Cu for 48 h

source_name: Microcystis aeruginosa PCC 7806  grown in BG11-Cu treated with 0.5 µM

value: 0.5 microM Cu for 48 h


title: A673 common DMSO control 1, RMA normalized with FENB samples

description:
Gene Expression data from A673 cell culture
BW_0_24h_169_P1_DMSO-A673-FENB


title: ATRA+NIC [Mouse]

value: ATRA+NIC


title: Eco FCE Hypothalamus 323

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

department: Genome Biology

country: Germany

institute: FBN Dummerstorf

description: Gene expression data from the hypothalamus.

hyb_protocol: Labelled DNA was hybridized for 16 hr at 42°C on Snowball Arrays (Freeman et al. in BMC Biol 2012, 10:90). Chips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning using the GeneChip scanner 3000 were performed according to Affymetrix protocols.

data_processing: Data were analysed with Affymetrix GCOS 1.1.1 software using global scaling to a target signal of 500 and BioConductor.

organism: Sus scrofa

source_name: Hypothalamus

label_protocol: Each RNA sample was transcribed to DNA using the Ambion WT Expression Kit (Ambion, Austin, TX, USA). DNA preparations were fragmented and labelled with the WT Terminal Labeling Kit (Affymetrix, Santa Clara, CA, USA).

extract_protocol: Total RNA was isolated using Qiazol reagent (Qiagen, Hilden, Germany) according to the manufacturer’s protocol. After DNaseI treatment, the RNA was column-purified using the RNeasy Kit (Qiagen, Hilden, Germany).

treatment_protocol: Animals differing in feed efficiency traits.

value: Hypothalamus

tag: feed efficiency (high

tag: Sex

value: female

tag: age (days post natum)

tag: pig identifier


title: CD4 normal 14


title: Control [Mouse]

value: Control


title: NIC [Mouse]

value: NIC


title: CD8 normal 15


title: CD8 normal 13


title: CD8 normal 4


title: Eco FCE Hypothalamus 318

tag: tissue


title: Eco FCE Hypothalamus 310


title: CD4 normal 16


title: Eco FCE Hypothalamus 317


title: Eco FCE Hypothalamus 304


title: Eco FCE Hypothalamus 309

value: male


title: Eco FCE Hypothalamus 307


title: Eco FCE Hypothalamus 324


title: CD4 normal 9


title: B-2

description: treated with 0.5 µM Cu for 48 h


title: C-1

description: treated with 3 µM Cu for 48 h


title: B-1

description: treated with 0.5 µM Cu for 48 h


title: A-3

description: untreated

source_name: Microcystis aeruginosa PCC 7806 grown in BG11-Cu untreated

value: untreated


title: A-2

description: untreated


title: A-1

description: untreated


title: t4 replicate 3

city: Bielefeld

first: Andreas

last: Albersmeier

address: Universitätsstr. 27

institute: Bielefeld University

data_processing:
Bcl2fastq v1.8.4
Bowtie2
Visualization and Read count in ReadXplorer
DESeq2
Genome_build: NC_007181.1
Supplementary_files_format_and_content: Raw reads in table containing all samples; DESeq2 result tables for different comparisons; both result forms contain start/stop position of the gene

organism: Sulfolobus acidocaldarius

source_name: cell culture

growth_protocol: S. acidocaldarius MW001 (wild type in this study) was grown aerobically at 75°C, 200 rpm, in Brocks basal medium supplemented with 0.1% (w/v) NZ-amine, 0.2 % (w/v) dextrin, and 10 µg/ml Uracil at pH 3.5

extract_protocol:
RNA isolation using TriZOL according to Hottes et al. 2004 (Transcriptional profiling of Caulobacter crescentus during growth on complex and minimal media)
Depletion of rRNA was performed using the Ribo-Zero rRNA Removal Kit (Bacteria) according to the manufacturerer's protocol with the following modifications: 1µg RNA and 90µl beads were used, 4µl of the ribbosomal removal solution were added to the mix, which had a final volume of 20µl. Libraries were prepared according to Illumina's instructions for TruSeq mRNA stranded samples, starting with resuspension of RNA in 17.5µl Fragment/Prime/Finish Mix after Ethanol precipitation. Libraries were sequenced on a HiSeq1500 in RAPID mode according to manufacturerer's protocol
TruSeq mRNA stranded

treatment_protocol: For starvation analysis, cells were harvested, timepoint zero was taken as reference timepoint, and remaining cells resuspended in basal Brock medium (pH 3.5) supplemented with 10 µg/ml Uracil but lacking any nutrients and samples were taken after 0.5,1.5,2 and 4 h after exposure to nutrient limitation. v

tag: timepoint

value: 240 min after exposure to nutrient limitation


title: t4 replicate 1


title: CD4 normal 8


title: Eco FCE Hypothalamus 308


title: CD4 normal 6


title: t2 replicate 3

value: 120 min after exposure to nutrient limitation


title: CD4 normal 5


title: Eco FCE Hypothalamus 303


title: PTCL/NOS 79

source_name: lymph node peripheral T-cell lymphoma not otherwise specified

tag: tumor type

value: PTCL/NOS


title: CD4 normal 3


title: PTCL/NOS 80


title: t2 replicate 1


title: t15 replicate 3

value: 90 min after exposure to nutrient limitation


title: Eco FCE Ileum 317

description: Gene expression data from ileal mucosa.

source_name: Ileum

value: Ileal mucosa


title: Eco FCE Hypothalamus 302


title: PTCL/NOS 78


title: Eco FCE Ileum 310

description: Gene expression data from ileal mucosa.


title: Eco FCE Ileum 318

description: Gene expression data from ileal mucosa.


title: PTCL/NOS 77


title: t1 replicate 3

value: 60 min after exposure to nutrient limitation


title: t1 replicate 1


title: t05 replicate 3

value: 30 min after exposure to nutrient limitation


title: Eco FCE Ileum 323

description: Gene expression data from ileal mucosa.


title: Eco FCE Ileum 309

description: Gene expression data from ileal mucosa.


title: PTCL/NOS 76


title: PTCL/NOS 75


title: PTCL/NOS 74


title: CD4 normal 1

value: CD4 normal cells


title: t15 replicate 1


title: t05 replicate 1


title: Eco FCE Ileum 307

description: Gene expression data from ileal mucosa.


title: Eco FCE Ileum 324

description: Gene expression data from ileal mucosa.


title: Eco FCE Hypothalamus 301


title: PTCL/NOS 73


title: Eco FCE Ileum 304

description: Gene expression data from ileal mucosa.


title: PTCL/NOS 72


title: Eco FCE Ileum 303

description: Gene expression data from ileal mucosa.


title: t0 replicate 3

value: before starvation


title: Eco FCE Ileum 308

description: Gene expression data from ileal mucosa.


title: 4h-NaAsO2-20 µM-Replicate 2

city: Ottawa

first: Eunnara

last: Cho

state: Ontario

address: 251 Sir Frederick Banting Driveway

country: Canada

institute: Health Canada

description:
SAMPLE 76
20 µM

data_processing:
Bio-Rad CFX Manager software was used to obtain raw Ct values.
The Ct values of the two housekeeping genes (GUSB and HPRT1) were averaged. Target gene signals were normalized to the average of the two housekeeping genes using the following equation:  2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKGavg)]. These values are reported in 'Sample table'.
Fold changes were calculated using the following equation: (2^-ΔCttest)/(2^-ΔCtcontrol). Fold Change worksheet reports test/vehicel control (e.g., NaAsO2/H2O) ratios

label: TaqMan probes

source_name: TK6 cell line

label_protocol: Complementary DNA was produced using the SuperScript IV First-Strand Synthesis System (Invitrogen, Burlington, ON, Canada).  In each 20 µL cDNA synthesis reaction, 500 ng of total RNA was input. For each of the 28 reference agents and seven vehicle controls, five cDNA synthesis reactions were performed, using 2.5 µg of RNA in total. The cDNA from the five reactions were pooled to 100 µL and diluted 1:10 in water to a final volume of 1 mL for each 96-well qPCR array. The 96-well arrays contained pre-designed, inventoried TaqMan Gene Expression Assays (FAM-labeled, MGB probe/primer sets, Applied Biosystems, Burlington, ON, Canada). Complementary DNA from two biological replicates of the 28 reference samples and the seven vehicle controls were prepared for qPCR with TaqMan Gene Expression Master Mix (Applied Biosystems) following the manufacturer’s instructions for 20 µl reactions. QPCR was performed on the CFX96 Real-Time System (Bio-Rad, Mississauga, ON, Canada) under settings for 96-well plates recommended by Applied Biosystems (Burlington, ON, Canada) (50°C for 2 minutes, 95°C for 10 minutes, and 40 cycles of 95°C for 15 seconds followed by 60°C for 1 minute).

growth_protocol: TK6 cells were obtained from American Type Culture Collection (ATCC# CRL-8015; ATCC, Manassas, VA) and cultured in RPMI 1640 medium with 10% fetal bovine serum.

extract_protocol: To extract and purify total RNA, the RNeasy Mini Kit (Qiagen, Toronto, ON, Canada) was used following the manufacturer’s protocol.

treatment_protocol: TK6 cells were treated with each agent and vehicle control in the exponential growth phase at a density of 4-5 × 105 cells/ml for 4 hours at 37°C before subsequent harvest and RNA extraction.

tag: agent

value: NaAsO2-20 microM

tag: group

value: Test - DDI

value: Lymphoblastoid

tag: cell line


title: PTCL/NOS 70


title: PTCL/NOS 71


title: PTCL/NOS 69


title: PTCL/NOS 68


title: t0 replicate 1


title: Eco FCE Ileum 302

description: Gene expression data from ileal mucosa.


title: Eco FCE Jejunum 324

description: Gene expression data from jejunal mucosa.

source_name: Jejunum

value: Jejunal mucosa

value: female


title: Eco FCE Ileum 301

description: Gene expression data from ileal mucosa.


title: Eco FCE Jejunum 318


title: 4h-Methylmethane sulfonate -40 µg/ml-Replicate 2

description:
SAMPLE 74
40 µg/ml

value: Methylmethane sulfonate -40 microg/ml


title: 4h-vehicle control-H2O (for NaAsO2)-Replicate 2

description:
SAMPLE 75
H2O (for NaAsO2)

value: vehicle control-H2O (for NaAsO2)

value: Vehicle control


title: PTCL/NOS 66


title: PTCL/NOS 67


title: Eco FCE Jejunum 323


title: 4h-vehicle control-MeOH (for MMS)-Replicate 2

description:
SAMPLE 73
MeOH (for MMS)

value: vehicle control-MeOH (for MMS)


title: Eco FCE Jejunum 317


title: 4h-Thapsigargin-250 nM-Replicate 2

description:
SAMPLE 70
250 nM

value: Thapsigargin-250 nM

value: Test - non-DDI


title: Eco FCE Jejunum 309

value: male


title: 4h-vehicle control-NaOH-Replicate 2

description:
SAMPLE 71
NaOH

value: vehicle control-NaOH


title: 4h-Methotrexate-100 µM-Replicate 2

description:
SAMPLE 72
100 µM

value: Methotrexate-100 microM


title: PTCL/NOS 65

value: PTCL/NOS


title: PTCL/NOS 63


title: PTCL/NOS 64


title: PTCL/NOS 62


title: Eco FCE Jejunum 310


title: 4h-vehicle control-Acetonitrile-Replicate 2

description:
SAMPLE 69
Acetonitrile

value: vehicle control-Acetonitrile


title: Eco FCE Jejunum 307


title: Eco FCE Jejunum 304


title: 4h-vehicle control-MeOH-Replicate 2

description:
SAMPLE 67
MeOH

value: vehicle control-MeOH


title: 4h-HC Toxin-20 ng/ml-Replicate 2

description:
SAMPLE 68
20 ng/ml

value: HC Toxin-20 ng/ml


title: 4h-Tunicamycin -2.5 µg/ml-Replicate 2

description:
SAMPLE 66
2.5 µg/ml

value: Tunicamycin -2.5 microg/ml


title: PTCL/NOS 61


title: PTCL/NOS 60


title: PTCL/NOS 58


title: Eco FCE Jejunum 301


title: PTCL/NOS 59


title: 4h-Colchicine-250 ng/ml-Replicate 2

description:
SAMPLE 64
250 ng/ml

value: Colchicine-250 ng/ml

value: Lymphoblastoid


title: 4h-vehicle control-EtOH-Replicate 2

description:
SAMPLE 63
EtOH

value: vehicle control-EtOH


title: Eco FCE Jejunum 308

value: Jejunal mucosa


title: Eco FCE Jejunum 303


title: PTCL/NOS 55


title: Eco FCE Jejunum 302


title: 4h-EtOH -4%-Replicate 2

description:
SAMPLE 62
4%

value: EtOH -4percent


title: Eco FCE Duodenum 324

description: Gene expression data from duodenal mucosa.

source_name: Duodenum

value: Duodenal mucosa

value: female


title: PTCL/NOS 57


title: PTCL/NOS 56


title: Eco FCE Duodenum 318


title: PTCL/NOS 54


title: Eco FCE Duodenum 317


title: Eco FCE Duodenum 323


title: 4h-EtOH -2%-Replicate 2

description:
SAMPLE 61
2%

value: EtOH -2percent


title: 4h-Heat Shock-47°C-Replicate 2

description:
SAMPLE 60
47°C

value: Heat Shock-47degreeC

value: Test - non-DDI


title: PTCL/NOS 52


title: PTCL/NOS 53


title: 4h-Gamma ray-4 Gy-Replicate 2

description:
SAMPLE 59
4 Gy

value: Gamma ray-4 Gy

value: Test - DDI


title: 4h-Antimycin A-100 µM-Replicate 2

description:
SAMPLE 65
100 µM

value: Antimycin A-100 microM


title: Eco FCE Duodenum 309

value: male


title: PTCL/NOS 51

value: PTCL/NOS


title: 4h- Cisplatin-80 µM-Replicate 2

description:
SAMPLE 57
80 µM

value: Cisplatin-80 microM


title: 4h-Oxamflatin-1 µM-Replicate 2

description:
SAMPLE 56
1 µM

value: Oxamflatin-1 microM


title: 4h-Etoposide-200 nM-Replicate 2

description:
SAMPLE 54
200 nM

value: Etoposide-200 nM


title: PTCL/NOS 50


title: 4h-Camptothecin-125 nM-Replicate 2

description:
SAMPLE 53
125 nM

value: Camptothecin-125 nM

value: Lymphoblastoid


title: PTCL/NOS 48


title: PTCL/NOS 47


title: Eco FCE Duodenum 308


title: Eco FCE Duodenum 310


title: Eco FCE Duodenum 307


title: PTCL/NOS 49


title: PTCL/NOS 46


title: 4h-vehicle control-Media-Replicate 2

description:
SAMPLE 58
Media

value: vehicle control-Media

value: Vehicle control


title: PTCL/NOS 44


title: Eco FCE Duodenum 302

value: Duodenal mucosa


title: Eco FCE Duodenum 301


title: Eco FCE Duodenum 304

value: female


title: Eco FCE Duodenum 303


title: 4h-Trichostatin A-20 ng/ml-Replicate 2

description:
SAMPLE 51
20 ng/ml

value: Trichostatin A-20 ng/ml


title: 4h- 5-Fluorouracil-25 µg/ml-Replicate 2

description:
SAMPLE 55
Fluorouracil

value: 5-Fluorouracil-25 microg/ml


title: 4h-Vinblastine-200 ng/ml-Replicate 2

description:
SAMPLE 50
200 ng/ml

value: Vinblastine-200 ng/ml

value: Test - non-DDI


title: PTCL/NOS 43


title: LY6D- prostate basal epithelial cells from mouse #5

city: Boston

first: Zhe

state: MA

address: 77 Avenue Louis Pasteur, Room 466

department: Medicine, Genetics Division

institute: Brigham and Women's Hospital

description: Gene expression data for LY6D- cells sorted from the lineage-negative;Sca1-intermediate;CD49f-positive basal gate from mouse #5

hyb_protocol: The biotinylated cDNA was added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C

scan_protocol: Each cDNA bound at its complementary oligonucleotide was excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions were captured

data_processing:
The raw CEL files were imported and processed with genepattern AffySTExpressionFileCreator tool from Broad institiute
Expression data was generated by AffySTExpressionFileCreator tool using the Robust Multi-array Average (RMA) algorithm as provided by the 'oligo' package in Bioconductor.

label_protocol: Labeling, hybridization and scan were performed by the Dana-Farber Cancer Institute Molecular Biology Core Facilities. The NuGEN Ovation V2 Amplification System was used to amplify and label the samples, according to manufacturer's protocol.

growth_protocol: Wild-type male mice were used.

extract_protocol: RNeasy kit (Qiagen, #73504) was used on sorted prostate epithelial cells according to manufacturer's protocol

treatment_protocol: Different subpopulation of prostate epithelial cells were sorted from hormone-naïve male mice.

tag: gender


title: 4h-Apicidin-1 µg/ml-Replicate 2

description:
SAMPLE 52
1 µg/ml

value: Apicidin-1 microg/ml


title: LY6D- prostate basal epithelial cells from mouse #3

description: Gene expression data for LY6D- cells sorted from the lineage-negative;Sca1-intermediate;CD49f-positive basal gate from mouse #3


title: LY6D+ prostate basal epithelial cells from mouse #3

description: Gene expression data for LY6D+ cells sorted from the lineage-negative;Sca1-intermediate;CD49f-positive basal gate from mouse #3


title: LY6D- Sca1-high prostate epithelial cells from mouse #5

description: Gene expression data for LY6D- cells sorted from the lineage-negative;Sca1-high;CD49f-positive gate from mouse #5


title: PTCL/NOS 45


title: PTCL/NOS 42


title: 4h-Paclitaxel-50 nM-Replicate 2

description:
SAMPLE 49
50 nM

value: Paclitaxel-50 nM


title: LY6D+ prostate basal epithelial cells from mouse #5

description: Gene expression data for LY6D+ cells sorted from the lineage-negative;Sca1-intermediate;CD49f-positive basal gate from mouse #5

value: male


title: PTCL/NOS 41

value: PTCL/NOS


title: 4h-H2O2-80 µM-Replicate 2

description:
SAMPLE 46
80 µM

value: H2O2-80 microM

value: Test - DDI


title: 4h-vehicle control-DMSO-Replicate 2

description:
SAMPLE 47
DMSO

value: vehicle control-DMSO


title: 4h- 2-Deoxyglucose-20 µM-Replicate 2

description:
SAMPLE 45
Deoxyglucose

value: 2-Deoxyglucose-20 microM


title: LY6D- Sca1-high prostate epithelial cells from mouse #1

description: Gene expression data for LY6D- cells sorted from the lineage-negative;Sca1-high;CD49f-positive gate from mouse #1


title: PTCL/NOS 40


title: PTCL/NOS 39


title: PTCL/NOS 38


title: LY6D+ Sca1-high prostate epithelial cells from mouse #5

description: Gene expression data for LY6D+ cells sorted from the lineage-negative;Sca1-high;CD49f-positive gate from mouse #5


title: LY6D+ Sca1-high prostate epithelial cells from mouse #1

description: Gene expression data for LY6D+ cells sorted from the lineage-negative;Sca1-high;CD49f-positive gate from mouse #1


title: PTCL/NOS 37


title: LY6D- prostate luminal epithelial cells from mouse #4

description: Gene expression data for LY6D- cells sorted from the lineage-negative;Sca1-low;CD49f-low luminal gate from mouse #4


title: 4h-Hydroxyurea-0.5 mM-Replicate 2

description:
SAMPLE 44
0.5 mM

value: Hydroxyurea-0.5 mM

value: Lymphoblastoid


title: PTCL/NOS 36


title: 4h-Arabinofuranosyl Cytidine-50 µM-Replicate 2

description:
SAMPLE 43
50 µM

value: Arabinofuranosyl Cytidine-50 microM


title: 4h-Docetaxel-50 nM-Replicate 2

description:
SAMPLE 48
50 nM

value: Docetaxel-50 nM


title: LY6D- prostate luminal epithelial cells from mouse #5

description: Gene expression data for LY6D- cells sorted from the lineage-negative;Sca1-low;CD49f-low luminal gate from mouse #5


title: 4h-CdCl2-50 µM-Replicate 2

description:
SAMPLE 41
50 µM

value: CdCl2-50 microM


title: PTCL/NOS 35


title: PTCL/NOS 34


title: 4h-K2CrO4-100 µM-Replicate 2

description:
SAMPLE 40
100 µM

value: K2CrO4-100 microM


title: PTCL/NOS 33


title: 4h-vehicle control-H2O -Replicate 2

description:
SAMPLE 39
H2O

value: vehicle control-H2O

value: Vehicle control


title: 4h-Bleomycin-10 µg/ml-Replicate 2

description:
SAMPLE 42
10 µg/ml

value: Bleomycin-10 microg/ml


title: 4h-NaAsO2-20 µM-Replicate 1

description:
SAMPLE 38
20 µM

value: NaAsO2-20 microM


title: LY6D+ prostate luminal epithelial cells from mouse #4

description: Gene expression data for LY6D+ cells sorted from the lineage-negative;Sca1-low;CD49f-low luminal gate from mouse #4


title: PTCL/NOS 32


title: 4h-vehicle control-H2O (for NaAsO2)-Replicate 1

description:
SAMPLE 37
H2O (for NaAsO2)

value: vehicle control-H2O (for NaAsO2)


title: LY6D+ prostate luminal epithelial cells from mouse #5

description: Gene expression data for LY6D+ cells sorted from the lineage-negative;Sca1-low;CD49f-low luminal gate from mouse #5

value: male


title: Enchytraeus crypticus cocoons_16 mgCd/kg_rep2

city: Aveiro

first: Susana

middle: Isabel Lopes

last: Gomes

address: Campus Universitário de Santiago, Departement of Biology, University of Aveiro

department: Biology

country: Portugal

institute: CESAM & University of Aveiro

description: E. crypticus cocoons_16 mg/kg Cd_2

hyb_protocol: The cRNA samples were hybridized on the Custom Gene Expression Agilent Microarrays (4 x 44k format) developed for Enchytraeus crypticus. Hybridizations were performed using the Agilent Gene Expression Hybridization Kit (Agilent Technologies, Palo Alto, CA, USA) and each biological replicate was individually hybridized on one array. The arrays were hybridized at 65ºC with a rotation of 10 rpm, during 17h. After that the microarrays were washed using Agilent Gene Expression Wash Buffer Kit (Agilent Technologies, Palo Alto, CA, USA)

scan_protocol: Scanning was performed using the Agilent DNA microarray scanner G2505B (Agilent Technologies). Fluorescence intensity data was obtained with Feature Extraction (10.5.1.1) Software (Agilent Technologies).

data_processing: Background correction was provided by Agilent Feature Extraction software and only gene probes with good signal quality (flag IsPosAndSignif = True) in all samples were employed in the analyses.

organism: Enchytraeus crypticus

source_name: E. crypticus cocoons_16 mg/kg Cd

label_protocol: Labelling and hybridizations followed the protocol “One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling” from Agilent Technologies (Agilent Technologies, Palo Alto, CA, USA)). Briefly, 500 ng of total RNA was amplified and labelled with Agilent Low Input Quick Amp Labelling Kit (Agilent Technologies, Palo Alto, CA, USA). Positive controls were added with the Agilent one-colour RNA Spike-In Kit (Agilent Technologies, Palo Alto, CA, USA). Purification of the amplified and labelled cRNA was performed with the RNeasy columns (Qiagen, Valencia, CA, USA).

extract_protocol: Total RNA was extracted using SV Total RNA Isolation System (Promega Corporation, USA).The quantity and purity of the RNA samples was checked using the ND-1000 spectrophotometer (Nanodrop®, USA) through measurement of the 260nm/280nm and 260nm/230nm absorbance. For all used samples these ratios were approximately 2. To verify the integrity of the RNA samples, a denaturating formaldehyde agarose gel electrophoresis was performed.

tag: stage of development

value: cocoons with 1-2 days old (after laying)

tag: exposed to

value: LUFA 2.2 soil spiked with Cadmium at 16 mg Cd/kg

value: Whole cocoons extracts (300 cocoons)


title: Enchytraeus crypticus cocoons_5 mgCd/kg_rep3

description: E. crypticus cocoons_5 mg/kg Cd_3

source_name: E. crypticus cocoons_5 mg/kg Cd

value: LUFA 2.2 soil spiked with Cadmium at 5 mg Cd/kg


title: 4h-Methylmethane sulfonate -40 µg/ml-Replicate 1

description:
SAMPLE 36
40 µg/ml

value: Methylmethane sulfonate -40 microg/ml

value: Test - DDI


title: PTCL/NOS 31

value: PTCL/NOS


title: Enchytraeus crypticus cocoons_5 mgCd/kg_rep2

description: E. crypticus cocoons_5 mg/kg Cd_2


title: Enchytraeus crypticus cocoons_16 mgCd/kg_rep1

description: E. crypticus cocoons_16 mg/kg Cd_1


title: PTCL/NOS 29


title: Enchytraeus crypticus cocoons_16 mgCd/kg_rep3

description: E. crypticus cocoons_16 mg/kg Cd_3


title: pif4_29C_3

city: Shanghai

first: Lan

last: Ding

address: No.2005 in Songhu Road

department: School of Life Science

institute: Fudan University

description: genes.fpkm

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: http://plants.ensembl.org/Arabidopsis_thaliana/Info/Index
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: seedlings

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

tag: strain

value: Columbia

value: seedlings day 7

tag: genotype

tag: temperature


title: 4h-Methotrexate-100 µM-Replicate 1

description:
SAMPLE 34
100 µM

value: Methotrexate-100 microM

tag: cell type

value: Lymphoblastoid


title: 4h-vehicle control-NaOH-Replicate 1

description:
SAMPLE 33
NaOH

value: vehicle control-NaOH


title: pif4_29C_2

description: genes.fpkm

tag: age


title: Enchytraeus crypticus cocoons_5 mgCd/kg_rep1

description: E. crypticus cocoons_5 mg/kg Cd_1


title: PTCL/NOS 27


title: PTCL/NOS 28


title: Enchytraeus crypticus cocoons_Control_rep2

description: E. crypticus cocoons_Control_2

source_name: E. crypticus cocoons_control

value: un-spiked soil for 1 day


title: PTCL/NOS 26


title: Enchytraeus crypticus cocoons_Control_rep1

description: E. crypticus cocoons_Control_ 1


title: pif4_29C_1

description: genes.fpkm


title: 4h-vehicle control-MeOH (for MMS)-Replicate 1

description:
SAMPLE 35
MeOH (for MMS)

value: vehicle control-MeOH (for MMS)

value: Vehicle control


title: 4h-HC Toxin-20 ng/ml-Replicate 1

description:
SAMPLE 30
20 ng/ml

value: HC Toxin-20 ng/ml

value: Test - non-DDI


title: 4h-vehicle control-Acetonitrile-Replicate 1

description:
SAMPLE 31
Acetonitrile

value: vehicle control-Acetonitrile


title: 4h-Thapsigargin-250 nM-Replicate 1

description:
SAMPLE 32
250 nM

value: Thapsigargin-250 nM


title: Enchytraeus crypticus cocoons_Control_rep3

description: E. crypticus cocoons_Control_3

value: cocoons with 1-2 days old (after laying)

value: Whole cocoons extracts (300 cocoons)


title: PTCL/NOS 30


title: pif4_22C_3

description: genes.fpkm


title: pif4_22C_2

description: genes.fpkm


title: ERCC6 GC NSC UV rep1

city: Beijing

first: Zunpeng

last: Liu

address: Beichen West Road

department: Institute of Zoology, Chinese Academy of Sciences

institute: State Key Laboratory of Stem Cell and Reproductive Biology

data_processing:
Reads were trimmed to remove the adapter sequences and low quality bases.
Clean reads were aligned to hg19 genome using hisat2 software.
Reads were counted by Htseq-count.
Differentially expressed genes were calculated by DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: The fomat of processed data is tab seprated file. And, the content is HTseq reads count.

source_name: ERCC6 GC NSC upon UV irradiation

growth_protocol: The derived iPSC lines were cultured on mitomycin C-treated MEF feeder cells in human ESC medium or on Matrigel-coated plates in mTeSR medium (STEMCELL Technology). The ESC medium consists of DMEM/F12 (Invitrogen) supplemented with 20% Knockout Serum Replacement (Invitrogen), 0.1 mM non-essential amino acids (NEAA, Invitrogen), 2 mM GlutaMAX (Invitrogen), 55 mM β-mercaptoethanol (Invitrogen), and 10 ng/ml bFGF (Joint Protein Central).MSCs were cultured in αMEM (Invitrogen) medium supplemented with 10% FBS (Gemcell), 1% penicillin/streptomycin (Gibco), 0.1mM non-essential amino acids (Gibco), and 1 ng/ml bFGF (JPC). NSCs were cultured in NSC maintenance medium containing 50% Neurobasal Medium (Invitrogen), 50% Advanced DMEM/F12 (Invitrogen), 1× N2 Supplement (Invitrogen), 1× B27 Supplement (Invitrogen), 2 mM GlutaMAX, 3 μM CHIR99021 (Selleck), 2 μM SB431542 (Selleck) and 10 ng/ml human leukemia inhibitory factor (hLIF, Millipore).

extract_protocol:
Total cellular RNA was extracted using TRIzol (Thermo Fisher Scientific) and genomic DNA was removed using a DNA-free kit (Thermo Fisher Scientific). Quality control and sequencing was done by CapitalBio Technology Co.Ltd.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

treatment_protocol: ERCC6 mut MSCs and ERCC6 GC MSCs were treated or not treated with 10j/m2 UV irradiation, 12 hours later the cells were collected for RNA extraction. ERCC6 mut MSCs and ERCC6 GC MSCs were passaged for 28 passage (under replicative stress) and the RNA were extracted. ERCC6 mut MSCs and ERCC6 GC MSCs were treated or not treated with 5j/m2 UV irradiation, 12 hours later the cells were collected for RNA extraction. Normally cultured iPSCs were also collected for RNA extraction. Two replicatives for each samples were prepared.

value: NSC

tag: treatment

value: ERCC6 GC NSC upon UV irradiation (5j/m2)


title: ERCC6 mut NSC UV rep1

source_name: ERCC6 mut NSC upon UV irradiation

value: ERCC6 mut NSC upon UV irradiation (5j/m2)


title: ERCC6 GC NSC Ctrl rep1

source_name: directed differentiation from ERCC6 GC iPSC


title: ERCC6 GC NSC Ctrl rep2

value: directed differentiation from ERCC6 GC iPSC


title: ERCC6 mut NSC UV rep2


title: pif4_22C_1

description: genes.fpkm

value: Columbia

value: seedlings day 7


title: 4h-vehicle control-MeOH-Replicate 1

description:
SAMPLE 29
MeOH

value: vehicle control-MeOH

value: Lymphoblastoid


title: ERCC6 mut NSC Ctrl rep2

source_name: directed differentiation from ERCC6 mut iPSC


title: 4h-Tunicamycin -2.5 µg/ml-Replicate 1

description:
SAMPLE 28
2.5 µg/ml

value: Tunicamycin -2.5 microg/ml


title: 4h-Antimycin A-100 µM-Replicate 1

description:
SAMPLE 27
100 µM

value: Antimycin A-100 microM


title: dm_29C_3

description: genes.fpkm


title: ERCC6 mut NSC Ctrl rep1

value: directed differentiation from ERCC6 mut iPSC


title: Neuron 2

city: Edinburgh

first: Iain

last: Williamson

address: Crewe Road

department: Chromosomes and Gene Expression

country: United Kingdom

institute: IGMM MRC Human Genetics Unit

data_processing:
The sequencing data was processed through a Torrent 5C data transformation pipeline on Galaxy (https://main.g2.bx.psu.edu/). The data was mapped against a customized reference file with TMAP. The reference file contained a list of all possible contacts between Forward and Reverse 5C primers covering our regions.
The data was then filtered to remove low-quality reads (MAQ quality score of lower than 30), reads aligning more than two nucleotides away from the reference sequence start site, and reads which do not contain EcoRI restriction sites.
5C data was normalized by dividing the number of reads of each 5C contact in the neuron cells by a normalisation factor derived from a gene desert region. The normalisation factor was defined by calculating the log10 ratio of each corresponding pairwise interaction frequencies. These ratios were averaged and returned to base 10 notation. This value was used to divide the neuron cells dataset.
Genome_build: hg19
Supplementary_files_format_and_content: This analysis generates a matrix file containing the interaction frequencies;
The column header names for the tabular files are:
region, primer name, assembly, chromosome, start position, end position, region, primer name, assembly, chromosome, start position, end position, genomic distance, 5C count.

growth_protocol: Neuroblastoma SH-SY5Y cells were maintained in Dulbecco’s Modified Eagle Medium with 4.5 g/l glucose (DMEM, Sigma) supplemented with 2 mM L-Glutamine (LifeTechnologies), 2 mM Sodium Pyruvate (Sigma), 10% Foetal Calf Serum (Thermo Scientific), 100 U/L Pencillin and 0.1mg Streptomycin (LifeTechnologies) at 37°C in humidified air with 5% CO2 atmosphere. Neural differentiation was induced 48 hours after plating at a density of 12x103 cells/cm2 with a differentiation cocktail including 50% DMEM/F12 (Sigma) and 50% Neurobasal (Thermo-Fisher) cell culture medium complemented with 2 mM L-Glutamine, 12.5 μg/ml Insulin (Sigma), 50 μg/ml Apo-Transferrin (Sigma), 37.5 μg/ml Bovine Serum Albumin (Sigma), 9.9 ng/ml Progesterone, 8 μg/ml Putrescine (Sigma), 12 nM Sodium Selenite (Sigma) and 10 μM Retinoic Acid (Sigma). Differentiation was complete after 14 days. Pre-adipocyte SGBS cells were maintained in DMEM/F12 supplemented with 33 μM Pantothenic Acid (Sigma), 17 μM Biotin (Sigma) 10% Foetal Calf Serum (Thermo Scientific), 100 U/L Pencillin and 0.1mg Streptomycin (LifeTechnologies) at 37°C in humidified air with 5% CO2 atmosphere. For differentiation, cells were plated at a density of 5000 cells/cm2 and grown to near confluency. To induce differentiation, cells were cultured in serum-free culture medium supplemented with 100 nM Insulin (Sigma), 100 nM Cortisol (Sigma), 0.2 nM triiodothyronine (Sigma), 25 nM Dexamethasone (Sigma), 250 μM IBMX (Sigma), 2 μM Rosiglitazone (Sigma), and 0.01 mg/ml Apo-Transferrin (Sigma). After four days, cells were incubated in differentiation medium lacking Dexamethasone, IBMX and Rosiglitazone for a further 10 days.

extract_protocol:
3-10 million fixed cells were incubated for 15 min on ice in 200 ml of lysis buffer (10 mM Tris pH 8.0, 10 mM NaCl, 0.2% NP40, supplemented with fresh protease inhibitor cocktail).  Cells were then disrupted on ice with a dounce homogenizer (pestle B; 2 x 20 strokes), cell suspensions transferred to eppendorf tubes and centrifuged 5 min at 2000 g.  Supernatants were removed, the cell pellets washed twice with 100 ml of 1X CutSmart buffer (NEB) and the cell pellet resuspended in 100 ml of 1X CutSmart buffer, and divided into two eppendorf tubes.  1X CutSmart buffer (337 ml) was added to each tube, and the mixture was incubated 10 min at 65°C with 0.1% SDS.  44 ml of 10% Triton X-100 were added before overnight digestion with 400 Units EcoRI.  The restriction enzyme was then inactivated by adding 86 ml of 10% SDS, and incubation for 30 min at 65°C.  Samples were then individually diluted into 7.62 ml of ligation mix (750 ml 10% Triton X-100, 750 ml 10X ligation buffer, 80 ml 10 mg/ml of BSA, 80 ml 100 mM ATP and 3000 Cohesive end Units of T4 DNA ligase) and incubated at 16°C for 2 hours. 3C libraries were incubated overnight at 65°C with 50 ml Proteinase K (10 mg/ml), and with an additional 50 ml Proteinase K the following day for 2 hours.  The DNA was purified by one phenol and one phenol-chloroform extraction, and precipitated with 0.1 volume (800 ml) of 3 M NaOAc pH 5.2 and 2.5 volumes of cold EtOH (20 ml).  After at least 1 h at -80°C, the DNA was centrifuged for 25 min at 20,000 g at 4°C, and the pellets washed with cold 70% EtOH. DNA was resuspended in 400 ml of TE pH 8.0, and transferred to eppendorf tubes for another phenol-chloroform extraction and precipitation with 40 ml of 3 M NaOAc pH 5.2 and 1.1 ml of cold EtOH.  DNA was recovered by centrifugation, and washed eight times with cold 70% EtOH.  Pellets were then dissolved in 100 ml TE pH 8.0, and incubated with RNAse A (1 ml at 10 mg/ml) for 15 min at 37°C.
3C libraries were denatured and annealed to 5C primers. 5C oligonucleotide were designed upstream (FORWARD) or downstream (REVERSE) EcoRI restriction sites. Annealing was followed by ligation with Taq DNA ligase. Ligated 5C primers were then amplified with the A-key and P1-key primers to generate the 5C libraries. 5C libraries were then prepared for sequencing onto Ion 316™ Chips with an Ion PGM™ Sequencer following either the Ion Xpress™ Template Kit v2.0, and Ion Sequencing Kit v2.0 protocols, or the Ion PGM™ Template OT2 200 Kit, and Ion PGM™ Sequencing 200 Kit v2.0 protocols as recommended by the manufacturer’s instructions (Life TechnologiesTM). Libraries were prepared according to Ion Torrent's instructions

treatment_protocol: Cells were fixed with 1% formaldehyde for 10 min at room temperature. Crosslinking was stopped with glycine (125 mM final concentration), and incubated for 5 min at room temperature followed by 15 min on ice. Cells were centrifuged at 400 g for 10 min at 4°C. Supernatants were removed and cell pellets were flash frozen on dry ice.

tag: tissue source

value: Bone marrow biopsy of metatastic neuroblastoma

tag: undifferentiated source

value: neuroblastoma


title: dm_29C_2

description: genes.fpkm


title: dm_29C_1

description: genes.fpkm


title: Adipocyte 2

source_name: SGBS

value: Adipose tissue from a patient with Simpson-Golabi-Behemel Syndrome (SGBS)

value: pre-adipocyte


title: ERCC6 GC MSC RS rep2

source_name: ERCC6 GC MSC upon replicative stress

value: MSC

value: ERCC6 GC MSC upon replicative stress


title: Neuron 1


title: 4h-Colchicine-250 ng/ml-Replicate 1

description:
SAMPLE 26
250 ng/ml

value: Colchicine-250 ng/ml

value: Test - non-DDI


title: dm_22C_3

description: genes.fpkm


title: 4h-vehicle control-EtOH-Replicate 1

description:
SAMPLE 25
EtOH

value: vehicle control-EtOH

value: Vehicle control


title: ERCC6 mut MSC RS rep2

source_name: ERCC6 mut MSC upon replicative stress

value: ERCC6 mut MSC upon replicative stress


title: dm_22C_2

description: genes.fpkm

value: Columbia

value: seedlings day 7


title: Adipocyte 1


title: ERCC6 mut MSC RS rep1


title: 4h-EtOH -2%-Replicate 1

description:
SAMPLE 23
2%

value: EtOH -2percent

value: Lymphoblastoid


title: 4h-EtOH -4%-Replicate 1

description:
SAMPLE 24
4%

value: EtOH -4percent


title: 4h-Heat Shock-47°C-Replicate 1

description:
SAMPLE 22
47°C

value: Heat Shock-47degreeC


title: WT_29C_3

description: genes.fpkm

value: wild type


title: dm_22C_1

description: genes.fpkm


title: ERCC6 GC MSC UV rep2

source_name: ERCC6 GC MSC upon UV irradiation

value: ERCC6 GC MSC upon UV irradiation (10j/m2)


title: WT_29C_2

description: genes.fpkm


title: ERCC6 GC MSC UV rep1


title: ERCC6 mut MSC UV rep2

source_name: ERCC6 mut MSC upon UV irradiation

value: ERCC6 mut MSC upon UV irradiation (10j/m2)


title: WT_29C_1

description: genes.fpkm


title: ERCC6 mut MSC UV rep1


title: 4h-Gamma ray-4 Gy-Replicate 1

description:
SAMPLE 21
4 Gy

value: Gamma ray-4 Gy

value: Test - DDI


title: 4h-vehicle control-Media-Replicate 1

description:
SAMPLE 20
Media

value: vehicle control-Media


title: WT_22C_3

description: genes.fpkm


title: ERCC6 GC MSC RS rep1

value: MSC

value: ERCC6 GC MSC upon replicative stress


title: WT_22C_2

description: genes.fpkm


title: 4h-Oxamflatin-1 µM-Replicate 1

description:
SAMPLE 18
1 µM

value: Oxamflatin-1 microM

value: Test - non-DDI


title: ERCC6 GC MSC Ctrl rep2

value: directed differentiation from ERCC6 GC iPSC


title: 4h- 5-Fluorouracil-25 µg/ml-Replicate 1

description:
SAMPLE 17
Fluorouracil

value: 5-Fluorouracil-25 microg/ml


title: WT_22C_1

description: genes.fpkm

value: Columbia

value: seedlings day 7


title: ERCC6 GC NSC UV rep2

value: NSC

value: ERCC6 GC NSC upon UV irradiation (5j/m2)


title: ERCC6 mut MSC Ctrl rep2

value: directed differentiation from ERCC6 mut iPSC


title: 4h-Etoposide-200 nM-Replicate 1

description:
SAMPLE 16
200 nM

value: Etoposide-200 nM

value: Lymphoblastoid


title: ERCC6 mut MSC Ctrl rep1


title: ERCC6 GC iPSC rep2

source_name: gene corrected cell line from ERCC6 mut iPSC

value: iPSC


title: ERCC6 GC iPSC rep1

value: gene corrected cell line from ERCC6 mut iPSC


title: 4h-Camptothecin-125 nM-Replicate 1

description:
SAMPLE 15
125 nM

source_name: TK6 cell line

value: Camptothecin-125 nM

value: Test - DDI


title: t4 replicate 2

source_name: cell culture

value: 240 min after exposure to nutrient limitation


title: 4h-Apicidin-1 µg/ml-Replicate 1

description:
SAMPLE 14
1 µg/ml

value: Apicidin-1 microg/ml


title: 4h-Trichostatin A-20 ng/ml-Replicate 1

description:
SAMPLE 13
20 ng/ml

value: Trichostatin A-20 ng/ml


title: ERCC6 mut iPSC rep2

source_name: reprogramming from ERCC6 mut fibroblast

value: reprogramming from ERCC6 mut fibroblast


title: ERCC6 mut iPSC rep1


title: t2 replicate 2

value: 120 min after exposure to nutrient limitation


title: 4h- Cisplatin-80 µM-Replicate 1

description:
SAMPLE 19
80 µM

value: Cisplatin-80 microM


title: 4h-Vinblastine-200 ng/ml-Replicate 1

description:
SAMPLE 12
200 ng/ml

value: Vinblastine-200 ng/ml

value: Test - non-DDI


title: t15 replicate 2

value: 90 min after exposure to nutrient limitation


title: Unhealthy centenarian rep3

city: Providence

first: Nicola

last: Neretti

state: RI

address: 70 Ship St

department: Department of Molecular Biology, Cell Biology & Biochemistry

institute: Brown University

data_processing:
Paired-end reads were aligned to hs37d5 genome using BWA-MEM 0.7.12
Reads mapping to the mitochondrial, X and Y chromosomes were removed.
Duplicate reads were discarded using picard-tools-1.88.
DANPOS2 was used to assess the nucleosome signals at TSS, TTS, CTCF and subcompartments. BAM files of triplicates from each age group were merged using SAMTools (Li et al. 2009) and used to identify fragment sizes using picard-tools-1.88
Genome_build: hs37d5
Supplementary_files_format_and_content: 100kb.Fnor.smooth.wig and 10bp.Fnor.smooth.wig are the nucleosome occupancy values with 100kb and 10bp spanning step, respectively.

source_name: Unhealthy centenarian_blood plasma

extract_protocol:
cfDNA was isolated from 3 to 4 mL of plasma using the QIAamp Circulating Nucleic Acid Kit (Qiagen, Hilden, Germany). At least 20 ng of total DNA from each sample was extracted and quantified using Qubit fluorometer (Thermo Fisher Scientific, Waltham, MA, USA).
Sequencing libraries were prepared from the purified DNA using Ovation® Ultralow Library Systems V2 library preparation kit (NuGen Technologies, San Carlos, CA, USA). Sequencing was performed on HiseqX-Ten Illumina platform at BGI Beijing Genomics Institute, Hong Kong.

value: 100 years old

value: Female

tag: tissue

value: Blood plasma


title: Unhealthy centenarian rep2


title: 4h-Paclitaxel-50 nM-Replicate 1

description:
SAMPLE 11
50 nM

value: Paclitaxel-50 nM

value: Lymphoblastoid


title: 4h-Docetaxel-50 nM-Replicate 1

description:
SAMPLE 10
50 nM

value: Docetaxel-50 nM


title: 4h-vehicle control-DMSO-Replicate 1

description:
SAMPLE 9
DMSO

value: vehicle control-DMSO

value: Vehicle control


title: ERCC6 GC MSC Ctrl rep1

value: MSC

value: directed differentiation from ERCC6 GC iPSC


title: Unhealthy centenarian rep1


title: t05 replicate 2

tag: timepoint

value: 30 min after exposure to nutrient limitation


title: 4h-H2O2-80 µM-Replicate 1

description:
SAMPLE 8
80 µM

value: H2O2-80 microM

value: Test - DDI


title: t1 replicate 2

value: 60 min after exposure to nutrient limitation


title: Healthy centenarian rep3

source_name: Healthy centenarian_blood plasma

value: Male


title: 4h- 2-Deoxyglucose-20 µM-Replicate 1

description:
SAMPLE 7
Deoxyglucose

value: 2-Deoxyglucose-20 microM

value: Test - non-DDI


title: t0 replicate 2

value: before starvation


title: Healthy centenarian rep1

value: 100 years old

value: Female


title: Zbhaa1∆_Cu_R3

city: Lisbon

first: Isabel

last: Sá-Correia

address: Avenida Rovisco Pais, 1

department: Department of Bioengineering

institute: Instituto Superior Técnico

data_processing:
Quality trimming of the sequences performed using BBDuk
Sequence reads were aligned to the Z. bailii IST302 genome assembly using the alignment algorithm STAR v2.5.2a, using the recommended parameters in QuantSeq 3' mRNA-Seq Integrated Data Analysis Pipeline on Bluebee platform
Quantification of reads per gene was performed using the htseq-count script of the HTSeq suite, in the intersection nonempty mode
Differential gene expression analysis was conducted using the Bioconductor software package edgeR
Genome_build: GCA_900162805.1 assembly deposited in ENA
Supplementary_files_format_and_content: text file with logFC,  logCPM,  FDR

organism: Zygosaccharomyces bailii

source_name: Yeast cells

growth_protocol: Yeast strains were batch cultured at 30°C, with orbital agitation (250 rpm), in liquid mineral medium (MM) containing: 0.17% (w/v) yeast nitrogen base (YNB) and 2% (v/v) glucose, at pH 4.0, and supplemented with CuSO4 (0.08 mM final concentration).

extract_protocol:
RNA extraction was performed by using a modified hot phenol method, described in Amin-ul Mannan et., Analytical Biochemistry, 2009.
Libraries were prepared using the QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina.

value: Zbhaa1delta deletion mutant


title: 4h-Arabinofuranosyl Cytidine-50 µM-Replicate 1

description:
SAMPLE 5
50 µM

value: Arabinofuranosyl Cytidine-50 microM

value: Lymphoblastoid


title: 4h-Hydroxyurea-0.5 mM-Replicate 1

description:
SAMPLE 6
0.5 mM

value: Hydroxyurea-0.5 mM


title: 4h-Bleomycin-10 µg/ml-Replicate 1

description:
SAMPLE 4
10 µg/ml

value: Bleomycin-10 microg/ml


title: Wt_Cu_R3

description:
Wt_Cu.txt
Mut_Wt_Cu.txt

value: wild-type


title: Old rep1

source_name: Old_blood plasma

value: 70 years old

value: Blood plasma


title: Zbhaa1∆_Cu_R1


title: Old rep2


title: Zbhaa1∆_Cu_R2


title: Wt_Cu_R2

description:
Wt_Cu.txt
Mut_Wt_Cu.txt


title: 4h-CdCl2-50 µM-Replicate 1

description:
SAMPLE 3
50 µM

value: CdCl2-50 microM


title: Young rep3

source_name: Young_blood plasma

value: 25 years old


title: Old rep3


title: 4h-vehicle control-H2O -Replicate 1

description:
SAMPLE 1
H2O

value: vehicle control-H2O

value: Vehicle control


title: Young rep2


title: 4h-K2CrO4-100 µM-Replicate 1

description:
SAMPLE 2
100 µM

value: K2CrO4-100 microM

value: Test - DDI


title: Zbhaa1∆_AA_R3

growth_protocol: Yeast strains were batch cultured at 30°C, with orbital agitation (250 rpm), in liquid mineral medium (MM) containing: 0.17% (w/v) yeast nitrogen base (YNB) and 2% (v/v) glucose, at pH 4.0, and supplemented with acetic acid (140 mM final concentration).


title: Wt_Cu_R1

description:
Wt_Cu.txt
Mut_Wt_Cu.txt


title: J4211-SanCI-Erm-LL

city: Oklahoma City

first: William

middle: Michael

last: McShan

state: OK

address: 1110 N. Stonewall Ave.

department: Pharmaceutical Sciences

institute: University of Oklahoma Health Sciences Center

description:
strain OKSan3 contains chromosomal island and mutated strA
Whole bacterial cell
J4211-SanCl-Erm-LL_S4

data_processing:
Genesifter software was used for base-calling and alignment.
BWA Reseq PE (Targeted, GATKv3) pipeline was used to align with Streptococcus anginosus  reference genome (NZ_CP012805). Pairwise analyses were done using Genesifter software and gene lists were exported as tab delimited files.
Pairwise settings were as follows: normalize to mapped reads, statistical analysis using t-test, differential genes originally shown if 1.5fold or more, narrowed to 3 fold min for final analysis, data correct using Benjamini Hochberg method.
Genome_build: NZ_CP012805
Supplementary_files_format_and_content: Genesifter output

organism: Streptococcus anginosus

source_name: J4211(SanCI ∆strA::ermB) LL

growth_protocol: Incubator with 5% CO2

extract_protocol:
Lysozyme followed by Trizol reagent (Life Technologies)
RNA libraries were prepared for sequencing using standard Illumina protocols with TruSeq V2 chemistry and methods.

treatment_protocol: Cells stored in RNA-Later until RNA extraction

value: J4211(SanCI delta_strA::ermB)

tag: growth stage

value: Late logarithmic

value: 37 degrees C

tag: growth medium

value: Todd Hewitt Broth


title: Zbhaa1∆_AA_R2

value: Zbhaa1delta deletion mutant


title: J4211-SanCI-LL

description:
strain OKSan4 contains chromosomal island +strA
Whole bacterial cell
Sanc1LL_S4

source_name: J4211(SanCI) LL


title: Healthy centenarian rep2

value: 100 years old

value: Female


title: Zbhaa1∆_AA_R1


title: Young rep1


title: pilR deletion mutant, replicate 3

city: Hamilton

first: Sara

middle: LN

last: Kilmury

state: ON

address: 1280 Main St. W Room 4H13

department: Biochemistry

institute: McMaster University

data_processing:
Paired end reads were concatenated in Rockhopper
Reads were aligned to the PAO1 reference genome
Raw fastq files from Illumina were used as input for Rockhopper analyses. Default parameters were used, with reverse complementation of reads
Raw transcript levels, normalized transcript levels, RPKM transcript levels, and expression transcript levels (transcript levels normalized by the upper quartile of gene expression) were obtained using Rockhopper software (McClure et al., 2013)

organism: Pseudomonas aeruginosa PAK

source_name: P. aeruginosa ΔpilR cells

growth_protocol: All cells were grown on Lennox Broth (LB) plates with 1.5% agar, for 16h at 37 degrees C

extract_protocol:
RNA from a half petri dish worth of cells was extracted using the RNeasy mini kit (Qiagen) with both on column and in solution DNase digestion
rRNA was depleted using a ribo-zero rRNA depletion kit. RNA libraries were prepared using standard Illumina protocols.

value: PAK

value: deletion of pilR (PA4547)


title: J4211-SanCI-EL

description:
strain OKSan4 contains chromosomal island +strA
Whole bacterial cell
Sanc1EL_S3

source_name: J4211(SanCI) EL

value: Early logarithmic


title: SSF_D15_rep3

city: Marseille

first: Marie-Noëlle

last: Rosso

address: 163 avenue de Luminy

department: Biodiversity and Biotechnology of Fungi - BBF

institute: INRAE - Aix Marseille University

data_processing:
QCed reads from each library were aligned to the genome Polyporus brumalis BRFM 1820 (https://genome.jgi.doe.gov/Polbr1/Polbr1.home.html) using TopHat (Kim et al., 2013) with only unique mapping allowed.
R was used for data manipulations (R Core Team, 2013). Raw read counts obtained from HTSeq were normalized using ddsNorm from the DESeq Bioconductor package (version 1.5) (Love et al. 2014).
Genome_build: Polyporus brumalis BRFM 1820 v1.0
Supplementary_files_format_and_content: The processed data file includes raw read counts calculated with HTSeq  for proteinID. The sequence and annotations of all Protein IDs can be retrieved from the Mycocosm portal dedicated to the genome of Polyporus brumalis v1.0 BRFM 1820  publicaly available at https://genome.jgi.doe.gov/Polbr1/Polbr1.home.html

organism: Lentinus brumalis

source_name: mycelium

growth_protocol: P. brumalis BRFM 985 was obtained from the International Center of Microbial Resources (CIRM; https://www6.inra.fr/cirm_eng/Filamentous-Fungi). After 6-day growth on 2% malt extract, solid state fermentations were performed in packed-bed bioreactors (glass columns) on 20 g dw (dry weight) sterilized wheat straw (≈ 4 mm) impregnated with 10 mL of P. brumalis inoculum (12 ± 1 mg dw mycelium/mL) and 1 mL of metal solution (CuSO4, FeSO4, and MnSO4 0.9 μmol each/g dw substrate). The bioreactors were incubated at 28°C for 4, 10 or 15 days. Air stream was filtered, wetted and flow rate set to 0.5 v.v-1.min-1. Control mycelium was grown for 10 days on 2% malt extract. Assays were performed in triplicate.

extract_protocol:
Total RNA was extracted from snap frozen mycelium  or fermented wheat straw. Frozen material was ground using the SamplePrep 6770 FreezerMill (Spex). RNA extraction was done from one hundred milligram of ground mycelium in 1 mL TRIZOL (Ambion). RNAs were precipitated with isopropanol, treated with DNAse I (QIAGEN) and resuspended in 25 µL RNAse Free water. RNA purity and integrity were analyzed on NanoDrop Spectrophotometer and on Agilent 2100 BioAnalyser.
cDNA libraries were prepared using the TruSeq RNA-Seq Sample Prep Kit V2 (Illumina Inc., San Diego, CA), and submitted to sequencing using Illumina HiSeq 2x75 bp technology (Beckman Coulter Genomics).

value: BRFM 985

tag: growth condition

value: SSF on wheat straw

tag: time point

value: Day 15


title: J4211-SanCI-Erm-EL

description:
strain OKSan3 contains chromosomal island and mutated strA
Whole bacterial cell
J4211-SanCl-Erm-EL_S3

source_name: J4211(SanCI ∆strA::ermB) EL


title: pilR deletion mutant, replicate 2


title: J4211LL (Set two)

description:
J4211 WT samples with no chromosomal island
Whole bacterial cell
J4211LL_S2

source_name: WT used for comparison to SanCI-LL

value: WT


title: SSF_D15_rep2


title: Wt_AA_R3

description:
Wt_AA.txt
Mut_Wt_AA.txt

value: wild-type


title: J4211-LL (Set one)

description:
J4211 WT samples with no chromosomal island
Whole bacterial cell
J4211-LL_S2

source_name: WT used for comparison to SanCI-Erm-LL


title: Zbhaa1∆_R2

growth_protocol: Yeast strains were batch cultured at 30°C, with orbital agitation (250 rpm), in liquid mineral medium (MM) containing: 0.17% (w/v) yeast nitrogen base (YNB) and 2% (v/v) glucose, at pH 4.0.


title: J4211EL (Set two)

description:
J4211 WT samples with no chromosomal island
Whole bacterial cell
J4211EL_S1

source_name: WT used for comparison to SanCI-EL


title: pilA deletion mutant, replicate 2

source_name: P. aeruginosa ΔpilA cells

value: deletion of pilA (PA4525)


title: Wild type PAK, replicate 1

source_name: WT P. aeruginosa cells

value: wild type


title: Wild type PAK, replicate 3


title: pilA deletion mutant, replicate 3


title: J4211-EL (Set one)

description:
J4211 WT samples with no chromosomal island
Whole bacterial cell
J4211-EL_S1

source_name: WT used for comparison to SanCI-Erm-EL


title: Wt_AA_R2

description:
Wt_AA.txt
Mut_Wt_AA.txt


title: SSF_D10_rep2

value: Day 10


title: SSF_D4_rep1

value: Day 4


title: Zbhaa1∆_R3


title: pilA deletion mutant, replicate 1


title: Zbhaa1∆_R1


title: Wt_R2

description:
Mut_Wt.txt
Wt_AA.txt
Wt_Cu.txt


title: SSF_D10_rep1


title: OA-treated

city: nanjing

first: Cheng

last: Chi

address: weigang road

institute: Nanjing Agricultural University

data_processing:
The library preparation and Illumina sequencing were performed by Beijing Genomics Institute (BGI) (Hongkong, China). For cluster generation, the qualified and quantified libraries were firstly amplified within the flow cell on the cBot instrument (HiSeq® 4000 PE Cluster Kit, Illumina). For paired-end sequencing, the clustered flow cell was then loaded onto the HiSeq 4000 Sequencer (HiSeq® 4000 SBS Kit, Illumina) with 100bp which was recommended read lengths.
The resulting sequences assembled using Trinity (version: v2.0.6; parameters: --min_contig_length 150  --CPU 8 --min_kmer_cov 3 --min_glue 3 --bfly_opts '-V 5 --edge-thr=0.1 --stder) was referred to as transcripts.
Gene family clustering was then carried out using TGICL (version: v2.0.6; parameters: -l 40 -c 10 -v 25 -O '-repeat_stringency 0.90 -minmatch 35 -minscore 35') to obtain the final unigenes.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Supplementary_files_format_and_content: Excel files includes RPKM values and fasta files include unigene sequences for each group.

organism: Argopecten irradians

source_name: gill

extract_protocol:
Gills were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. RNA integrity was measured using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system
RNA libraries were prepared for sequencing using standard Illumina protocols

value: gill

value: okadaic acid at a concentration of 500 nM for 48 h.


title: SSF_D10_rep3


title: W83-Gal-grown-3

city: Gainesville

first: Zachary

middle: Daniel

last: Moye

state: Florida

address: 1395 Center Drive

institute: University of Florida

data_processing:
The cleaned and initially processed data files were downloaded from the Illumina website.
Files were analyzed using Rockhopper version 100.0 on the default setting.
All functional RNA messages were eliminated. Of the remaining transcripts, only genes with changes to expression (in RPKM) with a fold change of >1.5 and a P <0.01 were retained.
Genome_build: GCF_000007585.1: Porphyromonas gingivalis W8 (NCBI Reference Sequence: NC_002950.2)
Supplementary_files_format_and_content: Microsoft Excel spreadsheet

organism: Porphyromonas gingivalis W83

source_name: bacteria grown with galactose

growth_protocol: Cultures of P. gingivalis W83 were grown in TSBHK to mid-exponential phase. Cultures were supplemented with 0.1% galactose or water as a control and grown anaerobically for three additional hours.

extract_protocol:
The Direct-zol RNA MiniPrep Kit (Zymo Research) kit was used for RNA extraction. Samples were next treated in two separate rounds with DNase I to digest gDNA. After washing the column, total RNA was eluted using nuclease free water. This elution was repeated a second time to concentrate samples.
Only samples with an RNA integrity number (RIN) of 7.0 or greater were processed. The Illumina Ribo-Zero magnetic kit for bacterial RNA was used to reduce ribosomal RNA. 5 μL of samples were fragmented and used to perform first strand synthesis with random priming. The NEBNext Ultra RNA library prep kit for Illumina (New England Biolabs) was used to prepare libraries. Samples were enriched by rounds of PCR and purified using the Agencourt AMPure XP system.

treatment_protocol: We tested the impact of 0.1% galactose on gene expression in exponentially grown cultures of P. gingivalis W83.

value: TSBHK + 0.1% galactose


title: pilR deletion mutant, replicate 1


title: SSF_D15_rep1


title: W83-Gal-grown-2


title: W83-Gal-grown-1


title: Wt_AA_R1

description:
Wt_AA.txt
Mut_Wt_AA.txt

source_name: Yeast cells


title: W83-Control-3

source_name: control bacterial culture

value: TSBHK


title: Wt_R3

description:
Mut_Wt.txt
Wt_AA.txt
Wt_Cu.txt


title: Wild type PAK, replicate 2


title: W83-Control-2


title: SSF_D4_rep2


title: control_rep3

value: malt 2 percent


title: control_rep2


title: W83-Control-1


title: control_rep1


title: GM12878 cell 3051

status: Public on Dec 20 2018

city: Stanford

first: Paul

last: Khavari

address: 269 Campus Drive, CCSR 2150

institute: Stanford University

description:
GBC_290-92-Ad1-16-Ad2-65_S569
GBC_counts_GM12878_experiment2.txt

data_processing:
Library strategy: Perturb-ATAC-seq
For GBC mapping, any read not containing the expected 27 nt sequence prior to the GBC was discarded, allowing for a maximum Levenshtein distance of 2 to account for sequencing errors. The subsequent 22 nt sequence was then compared to a list of GBC sequences, allowing for a maximum Levenshtein distance of 3 to be considered a match. Note that the minimum Levenshtein distance between any two of our GBC sequences was 10. This generated a counts-per-cell table for each GBC sequence and cell. For sgRNA mapping, raw reads for sgRNA sequencing were matched to a list of sgRNA sequences used in the experiment. We required strict matching of the 20bp variable sequence along with 18bp of the standard sgRNA backbone. This resulted in the counts-per-cell table for each sgRNA.
Genome_build: hg19
Supplementary_files_format_and_content: Table of raw GBC or sgRNA counts per cell. Each row represents an individual cell and each column represents a distinct GBC or sgRNA considered in the experiment.

source_name: GM12878 cell line

growth_protocol: GM1878 cells were grown in RPMI 1640 with 10% FBS and 1% pen/strep. Human primary keratinocytes were cultured in 50/50 growth media and induced to differentiated for three or six days as previously described (Zarnegar et al., 2012)

extract_protocol: Single cells were captured using the C1 Single-Cell Auto Prep IFC microfluidic chips and assayed using the transcript-indexed single-cell ATAC-seq protocol. In a 96-well plate, 6.5 µL from a total of 15ul of harvested libraries were amplified in a 20 µL PCR for an additional 17 cycles (1uM each V1 primer, 1x NEBnext High-Fidelity PCR Master Mix) using the following PCR conditions: 98°C for 30 s, and cycling at 98°C for 10 s, 63°C for 30 s, and 72°C for 45 s. Then 2ul of the previous V1 PCR reaction were transferred to a nested V2 PCR reaction with V2 primers at the same concentration and using same cycling parameters as the V1 reaction, for 15 cycles. Next 2ul of the previous V2 PCR reaction were transferred to a cell barcoding V3 PCR reaction with V3 primers at the same concentration and using the same cycling parameters as the V2 reaction, for 15 cycles. Finally V3 reactions were pooled, purified, sized selected via PAGE, and quantified by qPCR prior to sequencing.

value: GM12878 cell line


title: GM12878 cell 3055

description:
GBC_290-96-Ad1-16-Ad2-70_S574
GBC_counts_GM12878_experiment2.txt


title: GM12878 cell 3052

description:
GBC_290-93-Ad1-16-Ad2-64_S568
GBC_counts_GM12878_experiment2.txt


title: GM12878 cell 3056

description:
GBC_290-9-Ad1-10-Ad2-61_S421
GBC_counts_GM12878_experiment2.txt


title: GM12878 cell 3053

description:
GBC_290-94-Ad1-16-Ad2-72_S576
GBC_counts_GM12878_experiment2.txt


title: GM12878 cell 3047

description:
GBC_290-89-Ad1-15-Ad2-71_S551
GBC_counts_GM12878_experiment2.txt


title: GM12878 cell 3048

description:
GBC_290-8-Ad1-10-Ad2-62_S422
GBC_counts_GM12878_experiment2.txt


title: GM12878 cell 3054

description:
GBC_290-95-Ad1-16-Ad2-71_S575
GBC_counts_GM12878_experiment2.txt


title: GM12878 cell 3041

description:
GBC_290-83-Ad1-14-Ad2-71_S527
GBC_counts_GM12878_experiment2.txt


title: GM12878 cell 3040

description:
GBC_290-82-Ad1-14-Ad2-72_S528
GBC_counts_GM12878_experiment2.txt


title: GM12878 cell 3044

description:
GBC_290-86-Ad1-15-Ad2-65_S545
GBC_counts_GM12878_experiment2.txt


title: GM12878 cell 3042

description:
GBC_290-84-Ad1-14-Ad2-70_S526
GBC_counts_GM12878_experiment2.txt


title: GM12878 cell 3045

description:
GBC_290-87-Ad1-15-Ad2-64_S544
GBC_counts_GM12878_experiment2.txt


title: GM12878 cell 3043

description:
GBC_290-85-Ad1-15-Ad2-66_S546
GBC_counts_GM12878_experiment2.txt


title: GM12878 cell 3039

description:
GBC_290-81-Ad1-14-Ad2-64_S520
GBC_counts_GM12878_experiment2.txt


title: Wt_R1

description:
Mut_Wt.txt
Wt_AA.txt
Wt_Cu.txt


title: Control

value: control


title: GM12878 cell 3037

description:
GBC_290-7-Ad1-10-Ad2-63_S423
GBC_counts_GM12878_experiment2.txt


title: GM12878 cell 3038

description:
GBC_290-80-Ad1-14-Ad2-65_S521
GBC_counts_GM12878_experiment2.txt


title: GM12878 cell 3036

description:
GBC_290-79-Ad1-14-Ad2-66_S522
GBC_counts_GM12878_experiment2.txt