title: Alveolar Macrophage extracted from adult (wk6-12) mice via Bronchoalveolar lavage, biological replicate 2

description: Alveolar Macrophage extracted from wild type mice via Bronchoalveolar lavage

source_name: Alveolar macrophage (AMF), extracted from WT mice via BAL

value: Bronchoalveolar lavage


title: Monocyte extracted from E15.5 Fetal Liver, biological replicate 1

status: Public on Mar 01 2016

type: RNA

city: Zwijnaarde

first: Liesbet

last: Martens

address: Technologiepark 927

department: VIB Inflammation Research Center

country: Belgium

institute: VIB-University of Ghent

description: Monocyte extracted from Fetal Liver

hyb_protocol: Standard Affymetrix protocol. cDNA was hybrised on Affymetrix GeneChip Mouse Gene 1.0 ST Arrays (GPL6246).

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using Bioconductor. Normalisation was done by RMA.
MoGene-1_0-st-v1.r4.pgf
MoGene-1_0-st-v1.r4.mps

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Monocyte, extracted from Fetal Liver (FL)

label_protocol: Affymetrix WT Terminal Labeling Kit

growth_protocol: Tissues were isolated from the mice at the indicated ages.

extract_protocol: Single cell suspensions were prepared by organ digestion (yolk sac and fetal liver) with 1 mg/ml collagenase A and 10 U/ml DNA (30 and 5 minutes at 37oC), crushing (bones) or flushing of the lungs (broncholaveolar lavage). 2x104 cells were FACS purified into RLT buffer (Qiagen) containing 10 ml/ml 2-mercaptoethanol. RNA was isolated using the RNA isolation kit micro (Qiagen no74034).

treatment_protocol: not applicable

tag: strain

tag: tissue

value: Fetal Liver

tag: age


title: Macrophage extracted from E12.5 Yolk Sac, biological replicate 2

description: Macrophage extracted from Yolk Sac

source_name: Macrophage, extracted from Yolk Sac (YS)

value: Yolk Sac


title: Monocyte extracted from adult (wk6-12) Bone Marrow, biological replicate 1

description: Monocyte extracted from Bone Marrow

source_name: Monocyte, extracted from Bone Marrow (BM)

value: Bone Marrow


title: Macrophage extracted from E12.5 Yolk Sac, biological replicate 1

description: Macrophage extracted from Yolk Sac


title: Alveolar Macrophage extracted from adult (wk6-12) mice via Bronchoalveolar lavage, biological replicate 1


title: Monocyte extracted from E15.5 Fetal Liver, biological replicate 4

description: Monocyte extracted from Fetal Liver


title: Alveolar Macrophage extracted from adult (wk6-12) mice via Bronchoalveolar lavage, biological replicate 4


title: Monocyte extracted from adult (wk6-12) Bone Marrow, biological replicate 2

description: Monocyte extracted from Bone Marrow


title: Macrophage extracted from E12.5 Yolk Sac, biological replicate 4

description: Macrophage extracted from Yolk Sac


title: D105_10362_10

status: Public on Dec 31 2015

city: Shoham

first: jasmine

last: Jacob

state: -Select-

address: haChevel 33

country: Israel

institute: Sheba Medical Center at Tel HaShomer

description: microRNA expression data

hyb_protocol: FlashTag™ Biotin HSR RNA Labeling Kit  (Affymetrix) http://media.affymetrix.com/support/downloads/manuals/flashtag_user_guide.pdf

data_processing: RMA quantile normalization

organism: Homo sapiens

source_name: FFPE Human melanoma

growth_protocol: Melanoma samples were derived from metastatic melanoma patients  treated with ipilimumab.

extract_protocol: Total RNA was isolated using miRNeasy FFPE kit (Qiagen)  according to the manufacture guidelines.

treatment_protocol: Samples were prepared as Formalin fixed paraffin embedded (FFPE) tissues and stained with hematoxilin and eosin. Non-tumor tissue was removed.

value: tumor


title: D103_14146_07

description: microRNA expression data

scan_protocol: FlashTag™ Biotin HSR RNA Labeling Kit  (Affymetrix) http://media.affymetrix.com/support/downloads/manuals/flashtag_user_guide.pdf


title: D104_10001_10

description: microRNA expression data

label_protocol: FlashTag™ Biotin HSR RNA Labeling Kit  (Affymetrix) http://media.affymetrix.com/support/downloads/manuals/flashtag_user_guide.pdf


title: Monocyte extracted from E15.5 Fetal Liver, biological replicate 3

description: Monocyte extracted from Fetal Liver


title: Monocyte extracted from adult (wk6-12) Bone Marrow, biological replicate 3

description: Monocyte extracted from Bone Marrow


title: Alveolar Macrophage extracted from adult (wk6-12) mice via Bronchoalveolar lavage, biological replicate 3


title: Macrophage extracted from E12.5 Yolk Sac, biological replicate 3

description: Macrophage extracted from Yolk Sac


title: Monocyte extracted from E15.5 Fetal Liver, biological replicate 2

description: Monocyte extracted from Fetal Liver


title: D092_8929_08

description: microRNA expression data


title: D102_12663_10

description: microRNA expression data


title: D099_4719_10b

description: microRNA expression data


title: D101_5992_10

description: microRNA expression data


title: D096_2826_10

description: microRNA expression data


title: D100_196_11

description: microRNA expression data


title: H3K27Ac_ChIP_CTRLi

status: Public on Nov 12 2015

type: SRA

city: Stanford

first: Douglas

last: Porter

state: CA

address: 269 Campus Drive

department: Dermatology

country: USA

institute: Stanford

description: ChIP-seq in differentiated keratinocytes with control knockdown

library_source: genomic

data_processing:
Reads were trimmed for adaptor sequence, then mapped to UCSC hg19 using bowtie, duplicate fragments were then removed using Picard.ATACseq peaks were called using the MACS2 algorithm,ChIPseq peaks were called using MACS14.
Number of Raw reads in each peak was calculated using in house generated script, and data matrix was normalized using R
Genome_build: hg19
Supplementary_files_format_and_content: Peak files are in standard bed/whole bed format

molecule: genomic DNA

source_name: human keratinoctyes with control siRNA

growth_protocol: neonatal keratinocyte were isolated from discarded foreskin, cultured in KSF and 154 keratinocyte medium

extract_protocol:
For ATAC-seq, around 50,000 cells were used for each transposition reaction. Nuclei were prepared prior to transposition. For ChIP-seq, a mininum of 2 million cells were crosslinked with 1% formaldehyde, sonicated, and immunoprecipiated with antibodies recognizing Brg1/Brm (J1), H3K27Ac, H3K27me3, H3K4me1, p300, pol II, and p63.
For ATAC-seq, sequencing libraries were constructed using a modified version of the Illumina Nextera DNA Sample prep kit. For ChIP-seq, NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina were use for library construction

treatment_protocol: To induce differentiaiton, keratinocytes were seeded in confluence and cultured with the addition of 1.2mM of calcium to growth medium. 1nM of siRNA for each target were nucleofected (Lonza to keratinocytes)

tag: cell type

value: primary human neonatal keratinocytes

tag: knockdown

value: control

tag: chip antibody

value: H3K27Ac (Active Motif, cat#39134, lot#01613007) (Active Motif)


title: H3K4me1_ChIP_BAFi

description: ChIP-seq in differentiated keratinocytes with Brg1/Brm knockdown

source_name: human keratinoctyes with Brg1/Brm si

value: H3K4me1 (Abcam, cat#ab8895, lot#GR114265-2) (Active Motif)


title: H3K4me1_ChIP_CTRLi


title: pol2_ChIP_BAFi

value: Pol II (millipore, cat#05-623, lot#1776417) (millipore)


title: p300_ChIP_CTRLi

value: p300 (Active Motif, cat#61402. lot#01813001) (Active Motif)


title: Ctrli_rep2_RNAseq

library_source: transcriptomic

data_processing:
Reads were trimmed for adaptor sequence, then mapped to UCSC hg19 using bowtie, duplicate fragments were then removed using Picard.ATACseq peaks were called using the MACS2 algorithm,ChIPseq peaks were called using MACS14.
Number of Raw reads in each peak (or each gene for RNAseq) was calculated using in house generated script, and data matrix was normalized using R. For RNAseq, data normalization of significant analysis was performend using Deseq.
Genome_build: hg19
Supplementary_files_format_and_content: normalized read counts for each gene (RNA-seq) is in a text file.

extract_protocol:
For ATAC-seq, around 50,000 cells were used for each transposition reaction. Nuclei were prepared prior to transposition. For ChIP-seq, a mininum of 2 million cells were crosslinked with 1% formaldehyde, sonicated, and immunoprecipiated with antibodies recognizing Brg1/Brm (J1), H3K27Ac, H3K27me3, H3K4me1, p300, pol II, and p63. For RNA-seq, RNA were extracted using RNeasy Plus (Qiagen), rRNA were removed using using Ribo-Zero rRNA Removal Kit (Illumina).
For ATAC-seq, sequencing libraries were constructed using a modified version of the Illumina Nextera DNA Sample prep kit. For ChIP-seq, NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina was used for library construction. For RNA-seq, NEBNext Ultra RNA Library Prep Kit was used for library construction.

tag: genotype/variation

value: control knockdown


title: Ctrli_rep1_RNAseq


title: p63i_rep2_RNAseq

source_name: human keratinoctyes with p63 siRNA

value: p63 knockdown


title: p63i_rep1_RNAseq


title: H3K27me3_ChIP_CTRLi

value: H3K27me3 (millipore, cat#07-449, lot#1764447) (millipore)


title: pol2_ChIP_CTRLi


title: H3K27me3_ChIP_BAFi


title: p63_ChIP_CTRLi

value: H137 (Santa Cruz, cat#sc-8343, lot#A0614)


title: BAF_ChIPseq

description: ChIP-seq in differentiated keratinocytes

source_name: human keratinoctyes

value: J1 (gift from the Crabtree Lab (Khavari et al. Nature 1993))


title: p63_ChIP_BAFi

source_name: human keratinoctyes with Brg1/Brm siRNA


title: BAF_ChIP_63i

description: ChIP-seq in differentiated keratinocytes with p63 knockdown


title: BAFi_rep2_RNAseq

value: Brg1/Brm knockdown


title: BAFi_rep1_RNAseq


title: H3K27Ac_ChIP_BAFi


title: input_for_ChIPseq

description: input for ChIP-seq in differentiated keratinocytes

value: none (input)


title: D257_w011_SR

data_processing: LINEAR RMA SIGNALS (PARTEK)

source_name: Wilms tumor cells

label_protocol: RNA samples were used to prepare biotinylated target DNA, according to manufacturer’s recommendations. The target complementary DNA (cDNA) generated from each sample was processed as per manufacturer’s recommendation using an Affymetrix GeneChip Instrument System

growth_protocol: Total RNA was extracted from each of the 8 samples: 7 Wilms' Xns and a normal  fetal kidney  using TRIZOL .

extract_protocol: Total RNA was extracted from each sample using TRIZOL .

tag: developmental stage

value: adult

value: kidney


title: D259_w013_SR

treatment_protocol: RNA samples were used to prepare biotinylated target DNA, according to manufacturer’s recommendations. The target complementary DNA (cDNA) generated from each sample was processed as per manufacturer’s recommendation using an Affymetrix GeneChip Instrument System


title: D324_MINUS_---_xn cells


title: D322_US_US(un sorted)_xn cells


title: D178_AV04_FK

source_name: Fetal kidney

value: embryo


title: CTRL_ATAC_rep1

description:
ATAC-seq in differentiated keratinocytes with control knockdown
library strategy: ATAC-seq

source_name: human keratinoctyes with Ctrl si


title: CTRL_ATAC_rep2


title: p300_ChIP_BAFi


title: D258_w013_US


title: BAFi_ATAC_rep1

description:
ATAC-seq in differentiated keratinocytes with Brg1/Brm knockdown
library strategy: ATAC-seq


title: BAFi_ATAC_rep2


title: HMEC-Cont-shA

status: Public on Sep 30 2015

city: Suwon, Korea

first: Jung Woo

last: Eun

state: Korea

address: Department of Gastroenterology

country: South Korea

institute: Ajou University of Korea

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with GenPlex 3.0, and selected all Pcall on all arrays (P call = Detection P value < 0.1)

source_name: human mammary epithelial cell line

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: The culture of the immortalized human mammary epithelial cell line was carried out as described Elenbass et at. (Genes Dev, 15, 50-65)

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment and Quality control experiment performed

treatment_protocol: For TRIM29 level change, we generated stable cell line for kd of TRIM29. shTRIM29constructs were purchased from Sigma-Aldrich. For lentivirus production, MISSION lentiviral packaging mix was used. Infected derivative cells stably expressing shRNA were selected in the presence of 1.25 μg/mL puromycin for 21 days.

value: human mammary epithelial cells

tag: phenotype

value: TRIM29 wild-type


title: HMEC-TRIM29-shA

value: TRIM29 knock-down


title: 660T

status: Public on Sep 18 2015

hyb_protocol: This protocol uses directly isolated RNA without RNA target amplification, and ultimately reflects the cellular microRNA molar ratio, thus providing for the reliability of hybridization signals. The streptavidin conjugated dye stain (SA-S Dye) and the staining buffer (Buffer S) reagents are also included in this kit. Their preparation and use in the post-hybridization staining procedure is described below in the hybridization assay section.

scan_protocol: The SA-S dye stain signal can be detected using the GenePix 4000B scanner’s 635 nm wavelength (Cy5) channel.

data_processing: Genosensor (GenoExplorer™ microRNA probe set - human v14) standard protocol

source_name: Gastric cancer

label_protocol: This procedure is used to attach a biotin label to the 5’ ends of RNA molecules.Total 10ug amount of RNA used.

extract_protocol: Total RNA was extracted using TRIzol Reagent (Invitrogen). RNA quality control was performed with Bio-Rad Experion.

value: Gastric cancer tissue


title: 643T


title: 657T


title: 685T


title: 676T


title: 643N

source_name: Nontumor

value: non-cancerous gastric mucosal tissue


title: 660N


title: 685N


title: HMEC-TRIM29-shB


title: 657N


title: Liver expressing GFP from mouse #6

status: Public on Oct 30 2015

description: EGFP #6

hyb_protocol: Following fragmentation, 5.5 ug of ss-cRNA were hybridized with rotation at 60 rpm for 16 hr at 45°C. on GeneChip® Mouse Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G Plus.

data_processing: The data were analyzed with Robust Multichip Analysis (RMA) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: liver expressing GFP

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Mice were maintained in a SPF room

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

treatment_protocol: No treatment applied

tag: strain background

tag: gender

value: male

tag: mouse id

value: expressing GFP

value: liver


title: Liver expressing SHH from mouse #28

description: SHH #28

source_name: liver expressing SHH

value: expressing SHH


title: HMEC-Cont-shB


title: Liver expressing SHH from mouse #26

description: SHH #26


title: Liver expressing SHH from mouse #31

description: SHH #31


title: Liver expressing GFP from mouse #21

description: EGFP #21


title: Liver expressing GFP from mouse #13

description: EGFP #13


title: D323_PLUS_+_xn cells


title: 676N


title: D256_w011_US


title: BAF_ChIP_CTRLi

value: primary human neonatal keratinocytes

value: control


title: Ovarian sample56

status: Public on Jun 22 2015

city: Tampa

first: Chia-Ho

last: Cheng

address: 12902 USF Magnolia Drive

institute: Moffitt Cancer Center

description: Gene expression data from ovarian carcinoma tissue.

hyb_protocol: GeneChip microarrays are loaded with the fragmented target sample/hybridization buffer mix using standard manual techniques. Arrays are hybridized for 18 hours at 45C with vigorous mixing. Unbound sample is removed and staining is accomplished through the binding of streptavidin-conjugated phycoerythrin to the hybridized target. Excess label is removed. Washing and staining steps are performed by the Affymetrix FS450 Fluidics Station using standard protocols.

scan_protocol: Arrays are scanned using a GeneChip Scanner 3000 7G with a 48 array autoloader. The scanner maintains the optimal temperature for the arrays prior to and during scanning.

data_processing: Data were processed using the RMA algorithm (http://www.ncbi.nlm.nih.gov/pubmed/12582260).

label: Biotin

source_name: Ovarian carcinoma tissue

label_protocol: The final in vitro transcription incorporates biotin moieties that are later labeled with phycoerythrin. After amplification, samples are put through a controlled fragmentation to improve hybridization sensitivity and consistency. The labeled molecules are biotinylated-cRNA.

extract_protocol: Samples are processed in parallel in 96-well plates to minimize potential variation. Reaction purification is achieved using magnetic binding beads for cDNA and Qiagen RNeasy kits for cRNA purification.

value: primary ovarian carcinoma

value: surface epithelium

value: female


title: Ovarian sample55


title: Ovarian sample49


title: Ovarian sample52


title: Ovarian sample54


title: Ovarian sample53


title: Ovarian sample57


title: Ovarian sample45


title: Ovarian sample46


title: Ovarian sample48


title: Ovarian sample35


title: Ovarian sample47


title: Ovarian sample34


title: Ovarian sample38


title: Ovarian sample43


title: Ovarian sample40


title: Ovarian sample39


title: Ovarian sample37


title: Ovarian sample30


title: Ovarian sample41


title: Ovarian sample50


title: Ovarian sample44


title: Ovarian sample32


title: Ovarian sample42


title: Ovarian sample51


title: Ovarian sample36


title: Ovarian sample29


title: Ovarian sample33


title: Ovarian sample12


title: Ovarian sample19


title: Ovarian sample21


title: Ovarian sample31


title: Ovarian sample14


title: Ovarian sample26


title: Ovarian sample22


title: Ovarian sample24


title: Ovarian sample17


title: Ovarian sample15


title: Ovarian sample28


title: Ovarian sample10


title: Ovarian sample8


title: Ovarian sample9


title: Ovarian sample27


title: Ovarian sample25


title: Ovarian sample18


title: Ovarian sample3


title: Ovarian sample7


title: Ovarian sample13


title: Ovarian sample23


title: Ovarian sample16


title: Ovarian sample11


title: Ovarian sample20


title: Ovarian sample6


title: Ovarian sample4


title: Ovarian sample5


title: Ovarian sample2


title: Ovarian sample1


title: Normal-ovarian sample9

description: Gene expression data from normal ovarian tissue.

source_name: Normal ovarian tissue

value: normal ovary


title: Normal-ovarian sample11


title: Normal-ovarian sample6


title: Normal-ovarian sample7


title: Normal-ovarian sample2


title: Normal-ovarian sample8


title: Normal-ovarian sample12


title: Normal-ovarian sample3


title: Normal-ovarian sample4


title: Normal-ovarian sample10


title: Normal-ovarian sample5


title: Normal-ovarian sample1


title: Normal 16

status: Public on May 23 2015

description:
Non-disease control 9
Normal_16

data_processing:
The data were normalized using quantile normalization with GenPlex 3.0
The value was log2 transformed and remove the genes with detection p value >0.1 at all arrays after quantile normalization

source_name: normal control_blood

growth_protocol: Patients with ACS who underwent primary percutaneous coronary intervention (PCI) at the Seoul St. Mary’s Hospital in South Korea within 4 hours after the onset of chest pain were enrolled in an institutional review board–approved protocol.

extract_protocol: Total RNA from blood was extracted using the PAXgene blood RNA kit (Qiagen) and purified with RNeasy kit (Qiagen) according to the manufacturer’s instruction.

treatment_protocol: Blood samples were obtained from the arterial sheath before angiography and collected in PAXgene Blood RNA tube (Qiagen, Valencia, CA) for RNA isolation

tag: subject id

value: non-disease control 9

tag: subject status

value: healthy, normal

tag: subject group

value: Non-disease control

value: peripheral blood


title: STEMI 14

description:
STEMI patients 7
STEMI_14

value: patient 7

value: acute coronary syndrome (ACS) patient

value: patients with STEMI (before PCI)


title: UA_9

description: unstable angina 9

data_processing: The data were normalized using quantile normalization with GenPlex 3.0

source_name: Human blood

tag: disease

value: unstable angina


title: Normal 17

description:
Non-disease control 10
Normal_17

value: non-disease control 10


title: UA_7

description: unstable angina 7


title: STEMI 13

description:
STEMI patients 6
STEMI_13

value: patient 6


title: STEMI 11

description:
STEMI patients 4
STEMI_11

value: patient 4


title: UA_2

description: unstable angina 2


title: Normal 15

description:
Non-disease control 8
Normal_15

value: non-disease control 8


title: Normal 14

description:
Non-disease control 7
Normal_14

value: non-disease control 7


title: STEMI 12

description:
STEMI patients 5
STEMI_12

value: patient 5


title: Normal 12

description:
Non-disease control 5
Normal_12

value: non-disease control 5


title: UA_5

description: unstable angina 5


title: Normal 10

description:
Non-disease control 3
Normal_10

value: non-disease control 3


title: UA_3

description: unstable angina 3


title: UA_1

description: unstable angina 1


title: STEMI 9

description:
STEMI patients 2
STEMI_9

value: patient 2


title: Normal 11

description:
Non-disease control 4
Normal_11

value: non-disease control 4


title: STEMI_7

description: ST-elevation myocardial infarction patients 7


title: UA_4

description: unstable angina 4


title: Normal 9

description:
Non-disease control 2
Normal_9

value: non-disease control 2

value: healthy, normal


title: STEMI_4

description: ST-elevation myocardial infarction patients 4


title: UA_8

description: unstable angina 8


title: Normal 8

description:
Non-disease control 1
Normal_8

value: non-disease control 1

value: Non-disease control

value: peripheral blood


title: STEMI 10

description:
STEMI patients 3
STEMI_10

value: patient 3

value: acute coronary syndrome (ACS) patient

value: patients with STEMI (before PCI)


title: UA_6

description: unstable angina 6

value: unstable angina


title: STEMI_6

description: ST-elevation myocardial infarction patients 6


title: STEMI 8

description:
STEMI patients 1
STEMI_8

value: patient 1


title: Normal 13

description:
Non-disease control 6
Normal_13

value: non-disease control 6


title: STEMI_5

description: ST-elevation myocardial infarction patients 5


title: STEMI_3

description: ST-elevation myocardial infarction patients 3


title: NSTEMI_9

description: Non-ST-elevation MI patients 9

value: Non-ST-elevation MI patients


title: recovered STEMI 5

description:
Same STEMI patients 5 after PIC
r_STEMI-5

value: patient 5

value: patients with STEMI 7days after PCI


title: NSTEMI_7

description: Non-ST-elevation MI patients 7


title: NSTEMI_5

description: Non-ST-elevation MI patients 5


title: NSTEMI_10

description: Non-ST-elevation MI patients 10


title: NSTEMI_8

description: Non-ST-elevation MI patients 8


title: STEMI_2

description: ST-elevation myocardial infarction patients 2


title: recovered STEMI 2

description:
Same STEMI patients 2 after PIC
r_STEMI-2


title: recovered STEMI 3

description:
Same STEMI patients 3 after PIC
r_STEMI-3


title: recovered STEMI 6

description:
Same STEMI patients 6 after PIC
r_STEMI-6

value: patient 6


title: NSTEMI_6

description: Non-ST-elevation MI patients 6


title: recovered STEMI 1

description:
Same STEMI patients 1 after PIC
r_STEMI-1


title: Normal_6

description: Non-disease control 6


title: NSTEMI_1

description: Non-ST-elevation MI patients 1


title: NSTEMI_4

description: Non-ST-elevation MI patients 4


title: AF41

status: Public on Feb 18 2015

city: Athens

first: He

last: Fu

state: GA

address: 120 Cedar St

department: Microbiology

institute: University of Georgia

description:
AF41_GCCAAT_L007_R1_001
TableS2_GEO.xlsx

data_processing:
CLC Genomics Workbench (version 7.0)( Aarhus, Denmark) is used to perform all subsequent bioinformatic analysis.
Briefly, fastq files were imported as high-throughput data, and trimmed for quality (Quality: 0.001, Ambiguous: 2, Discard: min 30, max 100) and to remove adapter sequences.
After trimming, remaining reads that mapped to stable RNAs (16s, 23s, 5s rRNA and all tRNAs) were bioinformatically removed (similarity: 0.9, length: 0.85, mismtach: 2, insertion: 3, deletion: 3; global alignment and stand-alone read).
Remaining reads were then mapped to the genome for RNA-seq analyses (mapping parameters:  0.9, length: 0.85, mismatch: 2; insertion: 3; deletion: 3; maximum number of hits for a read: 10).
Expression analysis was set up in CLC before the data were normalized and statistical analysis were done using empirical analysis of DGE (digital gene expression), with total counter filter cutoff set as  5.0. From here, the xlsx files were generated.
genome build: ASM734v1
Supplementary_files_format_and_content: Excel files (xlsx) include normalized mean values for each sample

organism: Methanosarcina acetivorans C2A

growth_protocol: cells were grown to mid-exponential phase

extract_protocol:
The total RNA was isolated from early exponential phase cultures using TRIzol (Invitrogen, Carslbad, CA) and Zymo Direct-zol RNA MiniPrep kits (Zymo Research, Irvine, CA). The 16S- and 23S-rRNA were subtracted using sample-specific biotin-labeled 16S and 23S RNA probes
Fifty nanograms of rRNA-depleted messenger RNA were converted to indexed RNAseq libraries with the ScriptSeq™ v2 RNA-Seq Library Preparation Kit (Epicentre Biotechnologies, Madison, WI). The libraries were pooled in equimolar concentration and quantitated by qPCR with the Library Quantification kit Illumina compatible (Kapa Biosystems, Woburn, MA). The pooled libraries were sequenced for 101 cycles plus 7 cycles for the index read on a HiSeq2000 using TruSeq SBS version 3 reagents. The fastq files were generated and demultiplexed with Casava 1.8.2 (Illumina, San Diego, CA).

tag: genotype

value: Dhpt::(PmcrB-fC31 int-attP)

tag: growth medium

value: High Salt medium with 5 mM TMA supplemented with 20 mM MMPA


title: PK20

description:
PK20_ACTTGA_L00M_R1_001
TableS1_GEO.xlsx

tag: strain

value: wild type

value: High Salt medium with 125 mM MeOH


title: PK19

description:
PK19_CAGATC_L00M_R1_001
TableS1_GEO.xlsx


title: AF44

description:
AF44_GGCTAC_L007_R1_001
TableS2_GEO.xlsx

value: Dhpt DmsrH


title: PK21

description:
PK21_GATCAG_L00M_R1_001
TableS1_GEO.xlsx


title: recovered STEMI 4

description:
Same STEMI patients 4 after PIC
r_STEMI-4

value: patient 4

tag: tissue


title: AF42

description:
AF42_CAGATC_L007_R1_001
TableS2_GEO.xlsx


title: AF23

description:
AF23_GCCAAT_L001_R1_001
TableS1_GEO.xlsx

value: High Salt medium with 20 mM MMPA


title: NSTEMI_3

description: Non-ST-elevation MI patients 3


title: Normal_7

description: Non-disease control 7

value: Non-disease control


title: NSTEMI_2

description: Non-ST-elevation MI patients 2


title: Normal_3

description: Non-disease control 3


title: Normal_4

description: Non-disease control 4


title: Normal_1

description: Non-disease control 1


title: Normal_2

description: Non-disease control 2


title: AF40

description:
AF40_ACAGTG_L007_R1_001
TableS2_GEO.xlsx


title: AF21

description:
AF21_TGACCA_L001_R1_001
TableS1_GEO.xlsx


title: AF2

description:
AF2_TGACCA_L001_R1_001
TableS1_GEO.xlsx

value: High Salt medium with 9 mM DMS


title: AF22

description:
AF22_ACAGTG_L001_R1_001
TableS1_GEO.xlsx


title: AF10

description:
AF10_CAGATC_L001_R1_001
TableS1_GEO.xlsx

value: High Salt medium with 20 mM DMS


title: AF1

description:
AF1_CAGATC_L004_R1_001
TableS1_GEO.xlsx

value: High Salt medium with 10 mM MeSH


title: Normal_5

description: Non-disease control 5


title: AF43

description:
AF43_TAGCTT_L007_R1_001
TableS2_GEO.xlsx


title: recovered STEMI 7

description:
Same STEMI patients 7 after PIC
r_STEMI-7

value: patient 7

value: acute coronary syndrome (ACS) patient

value: peripheral blood


title: AF39

description:
AF39_TGACCA_L007_R1_001
TableS2_GEO.xlsx


title: Kidney_MV+SA_2

status: Public on Dec 31 2014

city: Seattle

first: Sina

last: Gharib

state: WA

address: 850 Republican St.

department: Medicine

institute: University of Washington

hyb_protocol: Following fragmentation, cRNA was hybridized to GeneChipMouse Genome 430 2.0 microarray per Affymetrix protocols.

scan_protocol: Microarrays were scanned using Affymetrix GeneChip Scanner and GeneChip Operating Software (GCOS) was used for image analysis.

data_processing: Two levels of data processing were performed. Initially, background adjustment and quantile normalization across all microarrays was performed using the Robust Multichip Average algorithm  (RMAExpress). These normalized results were used to compare the relative contribution of organ-type, experimental exposure, and biological replication to variability of gene expression using correspondence analysis. However, we observed that organ-specific gene expression dominated the overall transcriptional profiles. Therefore, we implemented RMA separately for each organ (liver, lung, kidney) for subsequent analyses.

source_name: Kidney

label_protocol: For each sample, biotinylated cRNA were prepared according the Affymetrix protocol from 1 ug total RNA.

extract_protocol: For each organ, total RNA was obtained using RNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer's protocol. For microarray experiments, integrity of purified total RNA samples was assessed qualitatively using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Mice in the treatment group were anesthetized, intubated and ~10^7 c.f.u. of S. aureus was deposited in the oropharynx followed by  mechanical ventilation for 6 hours prior to euthanasia by cardiac punture. Control mice were maintained in their cages and given an equivalent volume of PBS s.q. Lungs, kidneys, and liver were immediately recovered for subsequent RNA isolation and analysis.

tag: background strain

tag: tissue type

value: Kidney


title: Kidney_Control_2


title: Kidney_Control_3


title: Kidney_MV+SA_4


title: Lung_MV+SA_5

source_name: Lung

value: Lung


title: Kidney_MV+SA_5


title: Kidney_Control_5


title: Kidney_Control_4


title: Liver_MV+SA_4

source_name: Liver

value: Liver


title: Kidney_MV+SA_1


title: Liver_Control_3


title: Kidney_MV+SA_3


title: Kidney_Control_1


title: Liver_MV+SA_5


title: Lung_MV+SA_4


title: Lung_MV+SA_2


title: Lung_Control_3


title: Liver_Control_1


title: Lung_MV+SA_3


title: Liver_Control_2


title: Liver_MV+SA_3


title: Liver_MV+SA_2


title: Liver_MV+SA_1


title: Lung_Control_4


title: Lung_Control_2


title: Lung_Control_1


title: miR-20a

hyb_protocol: Affymetrix wt labeling protocol  as described in  https://www.affymetrix.com/support/downloads/manuals/wt_sensetarget_label_manual.pdf

scan_protocol: Affymetrix wt scanning protocol  as described in  https://www.affymetrix.com/support/downloads/manuals/wt_sensetarget_label_manual.pdf

data_processing: RMA (Partek)

source_name: miR-20a transfected PAG cells

label_protocol: Affymetrix biotin labeling_ wt kit  (Affymetrix)

growth_protocol: Stably transfected PAG (C81-61) cells were grown in Ham's F10 medium supplement with 15% FBS, Pen/Strep, 1µg/ml puromycine and 1× MITO + (BD Biosciences).

treatment_protocol: C81-61 melanoma cell line was stably transfected with the pQCXIP vector (i.e. either mock, miR-20a or miR-17). In details, 2×10^5 293T cells were seeded in a 6-well plate and cultured overnight in DMEM (Gibco/Invitrogen) containing 10% FBS (DMEM/FBS). On day 1, cells were transfected with a mixture of 1 µg GAG-POL, 1 µg Envelope, 2 µg of each of the pQCXIP constructs and 6 µl of Turbofect reagent (Fermentas). After six hours of incubation at 37°C, the cells were washed and re-cultured in fresh DMEM/FBS. On day 2, 5×10^4 melanoma cells were placed in each well of 6-well plates and cultured overnight in DMEM/FBS. On day 3, the melanoma cells were infected with 6 ml of 0.45 µm-filtered virion-containing medium of the 293T cells. After incubation at 37°C for 6 hours, the infected melanoma cells were washed and re-cultured with fresh DMEM./FBS. The aforementioned infection procedure was repeated the next day on the same melanoma culture. 48 hours after the second infection, selection was performed by addition of 1 µg/ml puromycine into culture medium.

tag: cell line

tag: cell type

value: Human melanoma

tag: transfected with

value: miR-20a (in pQCXIP vector)


title: Lung_MV+SA_1


title: miR-17

source_name: miR-17 transfected PAG cells

value: miR-17 (in pQCXIP vector)


title: Mock

source_name: mock transfected PAG cells

value: pQCXIP vector (mock)


title: STEMI_1

description: ST-elevation myocardial infarction patients 1


title: ALI AEC unstimulated replicate 2

status: Public on Dec 01 2014

hyb_protocol: Labeled RNA was processed for hybridization to Affymetrix Human Gene ST 1.0 microarrays at Fred Hutchinson Cancer Research Center’s Genomics Resources Facility according to the manufacturer’s instructions.

scan_protocol: Microarrays were scanned using Affymetrix GeneChip Scanner, and the GeneChip Operating Software (GCOS) was used for image analysis.

data_processing: Probe intensities were normalized using the RMA procedure as implemented in aroma.affymetrix package for R (http://www.aroma-project.org/).

source_name: Airway epithelial cells cultured in air-liquid interface (ALI)

label_protocol: Biotin labeled cRNA.

growth_protocol: Monolayer cells were grown on human placental collagen coated tissue culture plates with media changes every other day. Cells were grown until 90% confluent and then subcultured or harvested for cryopreservation. Monolayer cells were passaged no more than 3 times. To create ALI cultures, AECs were plated at 2.5 × 105 cells per cm2 directly onto collagen-coated semipermeable supports that were 12 mm diameter and 0.4 μm pore size (Corning Transwell, Cambridge, MA). After 24 hours incubation at 37ºC in a 5% CO2 incubator, the apical media was removed to create an air-liquid interface (ALI) and cells were continuously cultured in Grays’ Media with media changes every two days. Approximately 6 weeks after plating, cells became well differentiated, containing both ciliated and mucous producing goblet cells with a transepithelial resistance ≥ 500 Ω•cm2.

extract_protocol: Total RNA was isolated by Trizol reagent (Invitrogen), quantified by NanoDrop 2000 (Thermo Scientific, Wilmington, DE), assessed for quality by Bioanalyzer (Agilent Technologies, Fort Worth, TX), and transcribed to cDNA by Superscriptase II (Invitrogen).

treatment_protocol: When monolayer cultures reached ~ 90% confluency or the ALI cultures reached transepithelial electrical resistance > 500 Ω•cm2, the AECs were stimulated with 1 μg/ml flagellin (Invitrogen, Grand Island, NY) for 4 hours at 37°C.

tag: source

value: Cells obtained from trachea of adult lung transplant donor

value: Airway epithelial cells

tag: treatment

value: control


title: ALI AEC unstimulated replicate 1


title: ALI AEC stimulated with flagellin replicate 2

value: flagellin


title: ALI AEC stimulated with flagellin replicate 3


title: Monolayer AEC unstimulated replicate 2

source_name: Airway epithelial cells cultured as monolayer


title: ALI AEC stimulated with flagellin replicate 1


title: Monolayer AEC unstimulated replicate 1


title: Monolayer AEC stimulated with flagellin replicate 1


title: Female control fish 2 at 42d [449855]

city: Clemson

first: Qing

last: Liu

state: SC

address: Jordan Hall

department: Biological Sciences

institute: Clemson University

description:
Female control 2 _WK6
collected at 42 days

hyb_protocol: Cy3-labeled double strand DNA was hybridized to NimbleGen 12X135K array using NimbleGen hybridization kit, the hybridization was performed in NimbleGen Hybridization System (NimbleGen) at 42℃ for 16 hours. Arrays were washed with NimbleGen Wash buffers and 1M DTT, then spinned dry in a NimbleGen microarray drier.

scan_protocol: The arrays were scanned at 2µm on a NimbleGen MS200 scanner with auto-gain adjust.  The TIFF images were gridded and extracted using NimbleScan v. 2.6.

data_processing: Expression data were normalized using the Robust Multichip Average (RMA) algorithm. Differential gene expression were determined with Bayesian Estimation of Temporal Regulation (BETR) by Mev 4.0.

organism: Danio rerio

source_name: Female control, 42d

label_protocol: RNA of three male and female zebrafish was randomly selected for microarray experiments. cDNA was synthesized using Superscript Double-Stranded cDNA synthesis Kit (Invitrogen). 10ug total RNA of individual fish was denatured at 70℃ for 5min with oligo dT primer, then was reverse transcribed to the first stand cDNA at 42 ℃ for 60 min with SuperScript II enzyme. The second strand cDNA was synthesized at 16℃ with DNA ligase, DNA polymerase I and RNaseH for 2 hours. After digestion with RNase A solution, the double strand DNA was cleaned by Phase Lock tube (Fisher Scientific) with phenol: chloroform: isoamyl alcohol (25:24:1, Ambion), then precipitated in ice-cold ethanol with 7.5M ammonium acetate and 5mg/ml glycogen, dried to the pellet in a DNA 120 SpeedVac (Thermo). Then the DNA was cleaned using Qiaquick PCR purification kit (Qiagen). The quality of DNA was determined by Experion RNA HighSens chip (Bio-Rad). One ug double strand DNA was used for Cy3-labeling reaction with random primer and Klenow fragment (3’->5’ exo-) using One-Color DNA labeling Kit (NimbleGen), Cy3-labeled DNA was precipitated in ice-cold ethanol with 5M NaCl and dried to the pellet in a SpeedVac, then rehydrated in Nuclease-free water. The concentration of Cy3-labeled DNA was determined by the ND-1000 NanoDrop Spectrophotometer.

growth_protocol: All zebrafish were handled following Animal Care and Use Committee (ACUC) protocols of University of Wisconsin–Milwaukee. Juvenile wild-type zebrafish (stock originally purchased from EkkWill Waterlife Resources, Ruskin, FL) (0.16 g, 2.10 cm) were were reared in 28 °C dechlorinated, filtered municipal water (DFMW) in the NIEHS Children's Environmental Health Sciences Core Center (CEHSC) animal facility.

extract_protocol: Total RNA from individual fish was isolated using Trizol reagent (Invitrogen). One ml of Trizol was used for individual fish, which was homogenized by Power Gen 500 (Fisher), and 0.2 ml of chloroform was added for dissociation of nucleoprotein by shaking the tubes by hand for 15 seconds. The samples were centrifuged at 12000g for 15 minutes at 8℃. Upper aqueous phase was moved to a clean 1.5 ml Eppendorf tube, and 0.5 ml of isopropyl alcohol was added for precipitation of the RNA by incubating the samples at room temperature for 10 minutes. The samples were centrifuged at 12000g for 15 minutes at 8℃. Then the supernatant was removed and 1 ml of 75% ethanol was added for washing the pellet, and the samples were centrifuged at 12000g for 5 minutes at 8℃. The samples were air-dried then dissolved in RNase-free water. The concentration of RNA was determined by ND-1000 NanoDrop Spectrophotometer (Thermo Scientific, Wilmington, DE, USA). Further RNA-purification was performed using the RNeasy MiniElute cleanup kit (Qiagen) following the manufacturer’s protocol. Quality of zebrafish RNA was determined by Experion RNA StdSens chip (Bio-Rad).

treatment_protocol: Zebrafish were fed Biodiet starter (4% body weight per day) for 42 d with TCDD added at 0 ppb or 100 ppb (nominal concentration, ethanol used as vehicle).

tag: gender

value: Female

tag: agent

tag: tcdd dose

value: 0 ppb

tag: time

value: 42 days


title: ALI AEC unstimulated replicate 3


title: Female control fish 1 at 42d [440315]

description:
Female control 1b_WK6
collected at 42 days


title: Fetal kidney

status: Public on Dec 15 2014

data_processing: The analysis was performed with RMA algorithm in PARTEK  Genomic suite 6.6. The data was processed further for fold-change calculation.

source_name: kidney

extract_protocol: Total RNA was extracted from each of the four kidney samples: the index patient's kidney, a normal age-matched kidney, a normal fetal kidney and a normal adult kidney using TRIZOL .

tag: subject status

tag: developmental stage

value: embryo

tag: sample type

value: normal fetal kidney

value: kidney


title: Adult kidney

value: adult

value: normal adult kidney


title: Monolayer AEC stimulated with flagellin replicate 2


title: Male 100 ppb fish 3 at 42d [449855]

description:
Male 100 ppb 3_WK6
collected at 42 days

source_name: Male 100 ppb, 42d

value: Male

value: TCDD

value: 100 ppb


title: patient's kidney

value: patient with an ITGA3 mutation

value: child

value: patient kidney


title: Female control fish 3 at 42d [449855]

description:
Female control 3 _WK6
collected at 42 days


title: Immature Female 100 ppb fish 2 at 42d [449855]

description:
Immature Female 100 ppb 2_WK6
collected at 42 days

source_name: Immature Female 100 ppb, 42d


title: Female control fish 1 at 42d [449855]

description:
Female control 1a_WK6
collected at 42 days


title: Male control fish 2 at 42d [449855]

description:
Male control 2 _WK6
collected at 42 days

source_name: Male control, 42d


title: Male 100 ppb fish 1 at 42d [449855]

description:
Male 100 ppb 1_WK6
collected at 42 days


title: Age matched control kidney

value: normal age-matched kidney


title: Male control fish 3 at 42d [449855]

description:
Male control 3 _WK6
collected at 42 days

value: control


title: Immature Female 100 ppb fish 3 at 42d [449855]

description:
Immature Female 100 ppb 3_WK6
collected at 42 days


title: Male 100 ppb fish 2 at 42d [449855]

description:
Male 100 ppb 2_WK6
collected at 42 days


title: Immature Female 100 ppb fish 1 at 42d [449855]

description:
Immature Female 100 ppb 1_WK6
collected at 42 days


title: Immature Female 100 ppb fish 3 at 14d [449854]

description:
Immature Female 100 ppb 3_WK2
collected at 14 days

source_name: Immature Female 100 ppb, 14d

value: 14 days


title: Immature Female 100 ppb fish 2 at 14d [449854]

description:
Immature Female 100 ppb 2_WK2
collected at 14 days

value: Female


title: Female 100 ppb fish 3 at 14d [440311]

description:
Female 100 ppb 3_WK2
collected at 14 days

source_name: Female 100 ppb, 14d


title: Male 100 ppb fish 1 at 14d [440311]

description:
Male 100 ppb 1_WK2
collected at 14 days

source_name: Male 100 ppb, 14d


title: Female control fish 1 at 14d [440311]

description:
Female control 1 _WK2
collected at 14 days

source_name: Female control, 14d

value: 0 ppb


title: Female control fish 3 at 14d [440315]

description:
Female control 3b_WK2
collected at 14 days


title: Female control fish 3 at 14d [440311]

description:
Female control 3a _WK2
collected at 14 days


title: Male control fish 1 at 14d [440311]

description:
Male control 1 _WK2
collected at 14 days

source_name: Male control, 14d


title: Immature Female 100 ppb fish 1 at 14d [449854]

description:
Immature Female 100 ppb 1_WK2
collected at 14 days


title: Female 100 ppb fish 1 at 14d [440311]

description:
Female 100 ppb 1_WK2
collected at 14 days


title: Female 100 ppb fish 2 at 14d [440311]

description:
Female 100 ppb 2_WK2
collected at 14 days


title: Male control fish 3 at 14d [440311]

description:
Male control 3 _WK2
collected at 14 days


title: Immature female 100 ppb fish 3 at 7d [449854]

description:
Immature Female 100 ppb 3_WK1
collected at 7 days

source_name: Immature female 100 ppb, 7d

value: 7 days


title: Female control fish 2 at 7d [449901]

description:
Female control 2 _WK1
collected at 7 days

source_name: Female control, 7d


title: Female control fish 3 at 7d [449901]

description:
Female control 3 _WK1
collected at 7 days


title: Immature female 100 ppb fish 2 at 7d [449854]

description:
Immature Female 100 ppb 2_WK1
collected at 7 days


title: Male 100 ppb fish 2 at 14d [440311]

description:
Male 100 ppb 2_WK2
collected at 14 days


title: Male control fish 2 at 14d [440311]

description:
Male control 2 _WK2
collected at 14 days


title: Female control fish 1 at 7d [440315]

description:
Female control 1b_WK1
collected at 7 days


title: Female control fish 2 at 14d [440311]

description:
Female control 2 _WK2
collected at 14 days


title: Immature female 100 ppb fish 1 at 7d [449854]

description:
Immature Female 100 ppb 1_WK1
collected at 7 days


title: Male 100 ppb fish 3 at 14d [440311]

description:
Male 100 ppb 3_WK2
collected at 14 days


title: Female 100 ppb fish 1 at 7d [449901]

description:
Female 100 ppb 1_WK1
collected at 7 days

source_name: Female 100 ppb, 7d


title: Female 100 ppb fish 3 at 7d [449901]

description:
Female 100 ppb 3_WK1
collected at 7 days


title: Female control fish 1 at 7d [449901]

description:
Female control 1a _WK1
collected at 7 days


title: Female 100 ppb fish 2 at 7d [449901]

description:
Female 100 ppb 2_WK1
collected at 7 days


title: Male 100 ppb fish 3 at 7d [449901]

description:
Male 100 ppb 3_WK1
collected at 7 days

source_name: Male 100 ppb, 7d


title: Male control fish 3 at 7d [449901]

description:
Male control 3 _WK1
collected at 7 days

source_name: Male control, 7d


title: Male 100 ppb fish 1 at 7d [449901]

description:
Male 100 ppb 1_WK1
collected at 7 days


title: Male control fish 1 at 7d [449901]

description:
Male control 1 _WK1
collected at 7 days


title: Male control fish 1 at 42d [449855]

description:
Male control 1 _WK6
collected at 42 days

value: 42 days


title: Male control fish 2 at 7d [449901]

description:
Male control 2 _WK1
collected at 7 days


title: Male 100 ppb fish 2 at 7d [449901]

description:
Male 100 ppb 2_WK1
collected at 7 days


title: Female 0.1 ppb fish 1 at 28d [449701]

description:
collected at 28 days
Female 0.1  ppb 1_WK4
Female 0.1  ppb 1_WK4_449701_Cycle1.EXPRS

scan_protocol: The arrays were scanned at 2μm on a NimbleGen MS200 scanner with auto-gain adjust.  The TIFF images were gridded and extracted using NimbleScan v. 2.6.

source_name: female 0.1 ppb, 28d

treatment_protocol: Zebrafish were fed Biodiet starter (4% body weight per day) for 42 d with TCDD added at 0 ppb, 0.1 ppb, 1 ppb, 10 ppb or 100 ppb (nominal concentration, ethanol used as vehicle).

value: female

value: 0.1 ppb

value: 28 days


title: Female 10 ppb fish 3 at 28d [449701]

description:
collected at 28 days
Female 10 ppb 3_WK4
Female 10 ppb 3_WK4_449701_Cycle9.EXPRS

source_name: female 10 ppb, 28d

value: 10 ppb


title: Female control fish 2 at 28d [440315]

description:
collected at 28 days
Female control 2_WK4
Female control 2 _WK4_440315_Cycle8.EXPRS

source_name: female control, 28d


title: Female 100 ppb fish 3 at 28d [440315]

description:
collected at 28 days
Female 100 ppb 3_WK4
Female 100 ppb 3_WK4_440315_Cycle12.EXPRS

source_name: female 100 ppb, 28d


title: Female control fish 1 at 28d [449701]

description:
collected at 28 days
Female control 1_WK4
Female control 1 _WK4_449701_Cycle4.EXPRS


title: Female 100 ppb fish 2 at 28d [440315]

description:
collected at 28 days
Female 100 ppb 2_WK4
Female 100 ppb 2_WK4_440315_Cycle11.EXPRS


title: Female 0.1 ppb fish 3 at 28d [449701]

description:
collected at 28 days
Female 0.1  ppb 3_WK4
Female 0.1  ppb 3_WK4_449701_Cycle3.EXPRS


title: Male 100 ppb fish 1 at 28d [440315]

description:
collected at 28 days
Male 100 ppb 1_WK4
Male 100 ppb 1_WK4_440315_Cycle1.EXPRS

source_name: male 100 ppb, 28d

value: male


title: Female 1 ppb fish 3 at 28d [449701]

description:
collected at 28 days
Female 1 ppb 3_WK4
Female 1 ppb 3_WK4_449701_Cycle12.EXPRS

source_name: female 1 ppb, 28d

value: TCDD

value: 1 ppb


title: Female 1 ppb fish 2 at 28d [449701]

description:
collected at 28 days
Female 1 ppb 2_WK4
Female 1 ppb 2_WK4_449701_Cycle11.EXPRS


title: Female 0.1 ppb fish 2 at 28d [449701]

description:
collected at 28 days
Female 0.1  ppb 2_WK4
Female 0.1  ppb 2_WK4_449701_Cycle2.EXPRS


title: Female control fish 2 at 28d [449701]

description:
collected at 28 days
Female control 2_WK4
Female control 2 _WK4_449701_Cycle5.EXPRS


title: Female 1 ppb fish 1 at 28d [449701]

description:
collected at 28 days
Female 1 ppb 1_WK4
Female 1 ppb 1_WK4_449701_Cycle10.EXPRS


title: Female control fish 3 at 28d [440315]

description:
collected at 28 days
Female control 3_WK4
Female control 3 _WK4_440315_Cycle9.EXPRS


title: Female 100 ppb fish 1 at 28d [440315]

description:
collected at 28 days
Female 100 ppb 1_WK4
Female 100 ppb 1_WK4_440315_Cycle10.EXPRS

value: 100 ppb


title: Female control fish 3 at 28d [449701]

description:
collected at 28 days
Female control 3_WK4
Female control 3 _WK4_449701_Cycle6.EXPRS


title: Male 100 ppb fish 2 at 28d [440315]

description:
collected at 28 days
Male 100 ppb 2_WK4
Male 100 ppb 2_WK4_440315_Cycle2.EXPRS


title: Female 10 ppb fish 1 at 28d [449701]

description:
collected at 28 days
Female 10 ppb 1_WK4
Female 10 ppb 1_WK4_449701_Cycle7.EXPRS


title: Male 1 ppb fish 2 at 28d [449892]

description:
collected at 28 days
Male 1 ppb 2_WK4
Male 1 ppb 2 _WK4_449892_Cycle11.EXPRS

source_name: male 1 ppb, 28d


title: Male 10 ppb fish 2 at 28d [449892]

description:
collected at 28 days
Male 10 ppb 2_WK4
Male 10 ppb 2 _WK4_449892_Cycle5.EXPRS

source_name: male 10 ppb, 28d


title: Male 10 ppb fish 1 at 28d [449892]

description:
collected at 28 days
Male 10 ppb 1_WK4
Male 10 ppb 1 _WK4_449892_Cycle4.EXPRS


title: Male 1 ppb fish 3 at 28d [449892]

description:
collected at 28 days
Male 1 ppb 3_WK4
Male 1 ppb 3 _WK4_449892_Cycle12.EXPRS


title: Female 10 ppb fish 2 at 28d [449701]

description:
collected at 28 days
Female 10 ppb 2_WK4
Female 10 ppb 2_WK4_449701_Cycle8.EXPRS


title: Male 10 ppb fish 3 at 28d [449892]

description:
collected at 28 days
Male 10 ppb 3_WK4
Male 10 ppb 3 _WK4_449892_Cycle6.EXPRS


title: Male 100 ppb fish 3 at 28d [440315]

description:
collected at 28 days
Male 100 ppb 3_WK4
Male 100 ppb 3_WK4_440315_Cycle3.EXPRS


title: Female control fish 1 at 28d [440315]

description:
collected at 28 days
Female control 1_WK4
Female control 1 _WK4_440315_Cycle7.EXPRS


data_processing:
Image analysis and base calling were performed with Illumina’s RTA 1.12 software, followed by demultiplexing and FASTQ format file generation with Illumina’s CASAVA 1.8 software. After removing reads that did not pass Illumina’s base call quality filter, alignment to UCSC’s hg19 genome build was performed using TopHat 1.3.1.  Gene counts were generated using htseq-count 0.5.1, (http://www-huber.embl.de/users/anders/HTSeq/doc/count.html).
Genome_build: UCSC hg19
Supplementary_files_format_and_content: A single tab-delimited text file of raw gene counts for each sample (n = 8)

source_name: Airway epithelial cells cultured in air-liquid interface (ALI)

extract_protocol:
Total RNA was isolated by Trizol reagent (Invitrogen), quantified by NanoDrop 2000 (Thermo Scientific, Wilmington, DE), assessed for quality by Bioanalyzer (Agilent Technologies, Fort Worth, TX), and transcribed to cDNA by Superscriptase II (Invitrogen).
Illumina’s TruSeq RNA protocol (Illumina, San Diego, CA)

value: Cells obtained from trachea of adult lung transplant donor

value: Airway epithelial cells

value: flagellin


title: ALI AEC unstimulated replicate 2

value: control


title: ALI AEC unstimulated replicate 1


title: Male 0.1 ppb fish 3 at 28d [449892]

description:
collected at 28 days
Male 0.1 ppb 3_WK4
Male 0.1 ppb 3 _WK4_449892_Cycle3.EXPRS

source_name: male 0.1 ppb, 28d


source_name: Airway epithelial cells cultured as monolayer


title: Male 1 ppb fish 1 at 28d [449892]

description:
collected at 28 days
Male 1 ppb 1_WK4
Male 1 ppb 1 _WK4_449892_Cycle10.EXPRS


title: Male 0.1 ppb fish 2 at 28d [449892]

description:
collected at 28 days
Male 0.1 ppb 2_WK4
Male 0.1 ppb 2 _WK4_449892_Cycle2.EXPRS


title: Monolayer AEC unstimulated replicate 2


title: Male control fish 3 at 28d [449854]

description:
collected at 28 days
Male control 3_WK4
Male control 3 _WK4_449854_Cycle6.EXPRS

source_name: male control, 28d


title: Male control fish 3 at 28d [449892]

description:
collected at 28 days
Male control 3_WK4
Male control 3 _WK4_449892_Cycle9.EXPRS


title: Monolayer AEC unstimulated replicate 1


title: Male 0.1 ppb fish 1 at 28d [449892]

description:
collected at 28 days
Male 0.1 ppb 1_WK4
Male 0.1 ppb 1 _WK4_449892_Cycle1.EXPRS


title: Male control fish 2 at 28d [449892]

description:
collected at 28 days
Male control 2_WK4
Male control 2 _WK4_449892_Cycle8.EXPRS


title: Male control fish 1 at 28d [449854]

description:
collected at 28 days
Male control 1_WK4
Male control 1 _WK4_449854_Cycle4.EXPRS


title: Male control fish 1 at 28d [449892]

description:
collected at 28 days
Male control 1_WK4
Male control 1 _WK4_449892_Cycle7.EXPRS


title: Male control fish 2 at 28d [449854]

description:
collected at 28 days
Male control 2_WK4
Male control 2 _WK4_449854_Cycle5.EXPRS


title: MAFB_differentiated

status: Public on Nov 11 2014

description: Primary human epidermal keratinocytes isolated from foreskin.

data_processing:
Raw reads were mapped to the human reference genome (hg19) using bowtie.
Peaks for each sample were called using MACs algorithm.
Genome_build: GRCh37
Supplementary_files_format_and_content: The processed file is in bed format with called peak summits.

source_name: human epidermal keratinocytes, MAFB ChIP

growth_protocol: Human primary keratinocytes were cultured in 50/50 growth media and induced to differentiate for three days as previously described (Zarnegar et al., 2012).

extract_protocol:
The isolated DNA was RNase treated and purified using Qiagen columns.
We used the NEB Next ChIP-seq library prep kit; for sequencing libraries we followed Illumina's protocol.

treatment_protocol: ChIP-qPCR and ChIP-seq were carried out following the Farnham protocol (O'Geen et al., 2011) in differentiated primary human keratinocytes.

value: foreskin

value: primary human epidermal keratinocytes

tag: chip antibody

value: MAFB (Santa Cruz, cat.# SC-7866, lot# G0312)


title: MAF_differentiated

source_name: human epidermal keratinocytes, MAF ChIP

value: MAF (Santa Cruz, cat.# SC-10022, lot# B1513)


title: ZNF750_differentiated

status: Public on Sep 11 2014

data_processing:
Raw reads were mapped to human reference genome(hg19) using bowtie
Peaks for each sample were called using MACs algorithm
Genome_build: hg19
Supplementary_files_format_and_content: The processed file is in bed format with called peak summits

source_name: human epidermal keratinocytes

growth_protocol: Human primary keratinocytes were cultured in 50/50 growth media and induced to differentiate with confluence and calcium for three days (Sen et al. 2012)

extract_protocol:
The isolated DNA was purified using Qiagen columns.
We used the NuGen Mondrian for library preparation for Illumina sequencing

treatment_protocol: ChIP-seq was carried out following the Farnham protocol (O'Geen et al., 2011) in differentiated primary human keratinocytes

value: human epidermal keratinocytes

value: primary human epidermal keratinocytes isolate from foreskin

value: Sigma HPA023012 Lot # A41703


title: LSD1_differentiated


title: RCOR1_differentiated

value: Santa Cruz SC-30189 Lot # C2511


title: KLF4_differentiated


title: Epidermis__d2_rep1

description: replicate 1

hyb_protocol: Affymetrix GeneChip Hybridization, Wash, and Stain Kit

scan_protocol: Affymetrix GeneChip Scanner 3000 7G

data_processing: RMA normalization using justRMA package in R 2.11.1

label_protocol: Ambion MessageAmpIII RNA Amplification kit

growth_protocol: Primary human keratinocytes isolated from foreskin were placed on devitalized human dermis for epidermal regeneration as described (Ridky et al, 2010)

extract_protocol: Trizol and qiagen RNeasy kits were used to isolate total RNA.

treatment_protocol: For time-course, cell were not treated; for MAF/MAFB experiments, cells were nucleofected with scrambled control siRNA or MAF and MAFB siRNA

value: primary keratinocytes isolated from foreskin


title: Epidermis__MAFi_MAFBi_rep2

description: replicate 2


title: Epidermis__MAFi_MAFBi_rep3

description: replicate 3


title: Epidermis__d4_rep2

description: replicate 2


title: Epidermis__d6_rep2

description: replicate 2


title: Epidermis__d7_rep1

description: replicate 1


title: Epidermis__MAFi_MAFBi_rep1

description: replicate 1


title: Epidermis__d5_rep1

description: replicate 1


title: Epidermis__d0_rep2

description: replicate 2


title: Epidermis__d1_rep2

description: replicate 2


title: Epidermis__d4_rep1

description: replicate 1


title: Epidermis__d3_rep1

description: replicate 1


title: Epidermis__d5_rep2

description: replicate 2


title: Epidermis__CTRi_rep1

description: replicate 1


title: Epidermis__d1_rep1

description: replicate 1


title: PEC-deprived cells isolate replicate 1

status: Public on Aug 01 2014

hyb_protocol: Labeled RNA was processed for hybridization to Affymetrix Rat GeneChip 1.0ST microarrays at University of Washington’s Center for Array Technology according to the manufacturer’s instructions.

data_processing: Background adjustment and quantile normalization using the Robust Multichip Average algorithm (http://www.bioconductor.org) using Log2 transformed intensities.

organism: Rattus norvegicus

source_name: Decapsulated glomeruli

growth_protocol: No culturing of cells was performed

extract_protocol: Total RNA was extracted from capsulated and decapsulated glomeruli using TRIzol protocol per manufacturer's instructions. RNA quality was confirmed by a Bioanalyzer 2100.

treatment_protocol: After discarding medulla and papilla, minced cortices were passed through differential stainless steel sieves. In order to obtain capsulated glomeruli enriched in PECs, minced cortices were first pressed through a 180um-sized mesh sieve and then washed through sequential sieves with sizes of 106um, 90um. In order to obtain decapsulated glomeruli deprived of PECs, the 90μm sieve was removed and decapsulated glomeruli were collected on the 75μm sieve. Glomeruli were centrifuged at 80G at 4oC and quantification of glomeruli was performed in aliquots of the glomerular suspension by phase microscopy.

tag: age

value: Adult

value: male

tag: strain

value: Sprague-Dawley


title: PEC-deprived cells isolate replicate 2


title: PEC-deprived cells isolate replicate 3


title: Epidermis__CTRi_rep2

description: replicate 2

tag: tissue


title: Epidermis__d6_rep1

description: replicate 1


title: Epidermis__d3_rep2

description: replicate 2


title: PEC-enriched cells isolate replicate 2

source_name: Capsulated glomeruli


title: Epidermis__d2_rep2

description: replicate 2


title: Epidermis__d7_rep2

description: replicate 2


title: Epidermis__d0_rep1

description: replicate 1


title: PEC-enriched cells isolate replicate 3


title: E14.5 WT FEMALE

status: Public on Dec 31 2013

description: Gene expression data from WT female fetal liver cells at 14.5 day of gestation

data_processing: RMA

source_name: Mouse embryos at E14.5 age

growth_protocol: Pregnant females at different pregnancy time were sacrficed and embryos were extracted. The embryos were genotyped by PCR and fetal liver cells were extracted from the different genotypes. Single cell suspension was prepared.

treatment_protocol: Wt, Gata1s and ERG Tg females were placed with males for timed mating and embryos were dissected. PCR genotyping was performed proir to fetal liver extraction and preparation of single cell suspension.

tag: Stage

value: E14.5 fetal liver cells

value: female

tag: genotype/variation

value: wild type


title: E14.5 ERG Tg FEMALE

description: Gene expression data from ERG Tg female fetal liver cells at 14.5 day of gestation

value: ERG Tg


title: E14.5 WT MALE

description: Gene expression data from WT male fetal liver cells at 14.5 day of gestation


title: E14.5 ERG/GATA1s FEMALE

description: Gene expression data from ERG/GATA1s female fetal liver cells at 14.5 day of gestation


title: E12.5 ERG/GATA1s MALE

description: Gene expression data from ERG/GATA1s male fetal liver cells at 12.5 day of gestation

source_name: Mouse embryos at E12.5 age

value: E12.5 fetal liver cells


title: PEC-enriched cells isolate replicate 1


title: E14.5 ERG/GATA1s MALE

description: Gene expression data from ERG/GATA1s male fetal liver cells at 14.5 day of gestation


title: E12.5 ERG/GATA1s FEMALE

description: Gene expression data from ERG/GATA1s female fetal liver cells at 12.5 day of gestation


title: E14.5 WT/GATA1s MALE

description: Gene expression data from WT/GATA1s male fetal liver cells at 14.5 day of gestation


title: E14.5 WT/GATA1s FEMALE

description: Gene expression data from WT/GATA1s female fetal liver cells at 14.5 day of gestation


title: E14.5 ERG Tg MALE

description: Gene expression data from ERG Tg male fetal liver cells at 14.5 day of gestation


title: E12.5 WT MALE

description: Gene expression data from WT male fetal liver cells at 12.5 day of gestation


title: E12.5 WT/GATA1s MALE

description: Gene expression data from WT/GATA1s male fetal liver cells at 12.5 day of gestation


title: E12.5 WT/GATA1s FEMALE

description: Gene expression data from WT/GATA1s female fetal liver cells at 12.5 day of gestation


title: E12.5 WT FEMALE

description: Gene expression data from WT female fetal liver cells at 12.5 day of gestation


title: E12.5 ERG Tg FEMALE

description: Gene expression data from ERG Tg female fetal liver cells at 12.5 day of gestation


title: E12.5 ERG Tg MALE

description: Gene expression data from ERG Tg male fetal liver cells at 12.5 day of gestation


title: PBL_Pre_18

hyb_protocol: Affymetrix standard protocol

scan_protocol: GeneChip Operating System (GCOS)

data_processing: RMA algorithm with quantile normalization and background correction

source_name: Peripheral blood leukocytes

label_protocol: Affymetrix standard protocol

extract_protocol: RNeasy Mini Kit (Qiagen, Valencia, CA)

treatment_protocol: PBLs were isolated at baseline and following CPAP treatment of subjects and immediately processed using LeukoLOCK™ Total RNA Isolation System (Applied Biosystems, Carlsbad, CA)

tag: subject

value: none, baseline


title: PBL_Pre_16


title: PBL_Post_14

value: CPAP


title: PBL_Pre_14


title: PBL_Post_13


title: PBL_Post_16


title: PBL_Pre_17


title: PBL_Post_17


title: PBL_Post_18


title: PBL_Pre_15


title: PBL_Pre_13


title: PBL_Post_15


title: PBL_Post_12


title: PBL_Post_11


title: PBL_Pre_12


title: PBL_Pre_11


title: PBL_Pre_8


title: PBL_Post_8


title: PBL_Pre_10


title: PBL_Post_9


title: PBL_Post_10


title: PBL_Post_7


title: PBL_Post_6


title: PBL_Pre_5


title: PBL_Post_4


title: PBL_Pre_6


title: PBL_Pre_9


title: PBL_Post_5


title: PBL_Pre_7


title: PBL_Pre_3


title: PBL_Post_2


title: PBL_Pre_1


title: PBL_Pre_2


title: PBL_Post_1


title: PBL_Pre_4


title: PBL_Post_3


title: N-2D-6

status: Public on Aug 16 2013

description: To export to gene expression data based on unique gene, we use Illumina BeadStudio software.

source_name: rat liver tissue

growth_protocol: Animals were handled humanely in accordance with the IACUC (Institutional Animal Care and Use Committee) guidelines and observed at least once daily for signs of overt toxicity and for readily apparent clinical symptoms.

extract_protocol: Total RNA was isolated from tissues using TRIzol Reagent (Invitrogen) according to the manufacturer's protocol, followed by clean up on Ambion columns (Illumina Total-Prep RNA Amplification Kit, Ambion). RNA quality control was performed with Bio-Rad Experion.

treatment_protocol: The five drugs that induce three patterns of DILI, that is, pyrazinamide (PZA), ranitidine Hcl (RAN), enalapril maleate (ENA), carbamazepine (CBZ), and chlorpromazine hydrochloride (CPZ) were obtained from Sigma–Aldrich (St. Louis, MO, USA). All these DILI-causing drugs were administered to 7-week-old male Sprague-Dawley rats (Charles River Laboratories, Inc.). Animals were housed in a controlled environment in the institutional animal facility with free access to food and water throughout the experiment. PZA (CAS number, 98-96-4; Sigma P7136), RAN (CAS number, 66357-35-5; Sigma R101), ENA (CAS number, 75847-73-3; Sigma E6888), CBZ (CAS number, 298-46-4; Sigma C4024), and CPZ (CAS number, 50-53-3; Sigma C8138) were prepared following the manufacturer’s protocol. Dosage levels used in the study were 5% (low dose), 10% (middle dose) and 50% (high dose) of the published LD50s for each DILI-causing drug; and three animals were treated with a single oral administration of PZA (150, 300, 1500 mg/kg), RAN (209.5, 419, 2095 mg/kg), ENA (148.65, 297.3, 1486.5 mg/kg), CBZ (97.85, 195.7, 978.5 mg/kg) or CPZ (7.1, 14.2, 71 mg/kg) with vehicle (corn oil). At the indicated time points (2, 3, and 10 days after administration), the rats were sacrificed

value: liver

value: vehicle (corn oil)


title: N-10D-1


title: N-3D-2


title: N-10D-4


title: N-2D-1


title: N-3D-6


title: N-2D-3


title: N-3D-1


title: N-3D-5


title: N-10D-3


title: N-3D-3


title: N-10D-2


title: CPZ-10D-H-6

value: 10 days after CPZ treatment (high dose)


title: N-2D-5


title: CPZ-10D-H-5


title: CPZ-10D-H-3


title: CPZ-10D-H-4


title: N-3D-4


title: N-2D-4


title: CPZ-10D-H-1


title: N-2D-2


title: CPZ-10D-M-6

value: 10 days after CPZ treatment (middle dose)


title: CPZ-10D-M-3


title: CPZ-10D-M-4


title: CPZ-10D-M-1


title: CPZ-10D-L-6

value: 10 days after CPZ treatment (low dose)


title: CPZ-10D-M-5


title: CPZ-10D-L-5


title: CPZ-10D-L-4


title: CPZ-3D-H-4

value: 3 days after CPZ treatment (high dose)


title: CPZ-10D-H-2


title: CPZ-10D-L-3


title: CPZ-10D-L-1


title: CPZ-3D-H-5


title: CPZ-3D-H-6


title: CPZ-3D-H-1


title: CPZ-3D-H-3


title: CPZ-3D-M-6

value: 3 days after CPZ treatment (middle dose)


title: CPZ-10D-L-2


title: CPZ-10D-M-2


title: CPZ-3D-M-2


title: CPZ-3D-L-1

value: 3 days after CPZ treatment (low dose)


title: CPZ-3D-H-2


title: CPZ-3D-L-2


title: CPZ-3D-M-3


title: CPZ-3D-L-5


title: CPZ-3D-M-1


title: CPZ-3D-M-4


title: CPZ-3D-M-5


title: CPZ-2D-H-2

value: 2 days after CPZ treatment (high dose)


title: CPZ-2D-H-3

value: Sprague-Dawley


title: CPZ-2D-H-6


title: CPZ-2D-H-4


title: CPZ-2D-H-1


title: CPZ-2D-M-1

value: 2 days after CPZ treatment (middle dose)


title: CPZ-3D-L-4


title: CPZ-2D-M-2


title: CPZ-2D-M-4


title: CPZ-3D-L-6


title: CPZ-2D-M-5


title: CPZ-2D-H-5


title: CPZ-2D-M-6


title: CPZ-2D-L-1

value: 2 days after CPZ treatment (low dose)


title: CPZ-2D-L-2


title: CPZ-2D-L-6


title: CBZ-10D-H-6

value: 10 days after CBZ treatment (high dose)


title: CPZ-3D-L-3


title: CPZ-2D-L-4


title: CBZ-10D-H-3


title: CBZ-10D-H-5


title: CPZ-2D-L-3


title: CPZ-2D-L-5


title: CBZ-10D-H-2


title: CPZ-2D-M-3


title: CBZ-10D-M-4

value: 10 days after CBZ treatment (middle dose)


title: CBZ-10D-H-4


title: CBZ-10D-M-3


title: CBZ-10D-M-5


title: CBZ-10D-L-5

value: 10 days after CBZ treatment (low dose)


title: CBZ-10D-M-1


title: CBZ-10D-H-1


title: CBZ-10D-L-6


title: CBZ-10D-M-2


title: CBZ-10D-L-2


title: CBZ-3D-H-2

value: 3 days after CBZ treatment (high dose)


title: CBZ-10D-L-4


title: CBZ-3D-H-4


title: CBZ-10D-L-1


title: CBZ-3D-H-1


title: CBZ-3D-H-5


title: CBZ-3D-M-3

value: 3 days after CBZ treatment (middle dose)


title: CBZ-3D-H-3

value: liver


title: CBZ-3D-M-6


title: CBZ-10D-L-3


title: CBZ-3D-M-2


title: CBZ-3D-M-5


title: CBZ-3D-H-6


title: CBZ-3D-M-1


title: CBZ-3D-L-6

value: 3 days after CBZ treatment (low dose)


title: CBZ-3D-L-5


title: CBZ-3D-L-3


title: CBZ-2D-H-6

value: 2 days after CBZ treatment (high dose)


title: CBZ-3D-L-1


title: CBZ-3D-L-4


title: CBZ-3D-L-2


title: CBZ-2D-H-5


title: CBZ-3D-M-4


title: CBZ-2D-H-3


title: CBZ-2D-M-2

value: 2 days after CBZ treatment (middle dose)


title: CBZ-2D-M-5


title: CBZ-2D-H-2


title: CBZ-2D-M-3


title: CBZ-2D-M-1


title: CBZ-2D-L-6

value: 2 days after CBZ treatment (low dose)


title: CBZ-2D-L-3


title: CBZ-2D-H-4


title: CBZ-2D-L-5


title: CBZ-2D-M-6


title: ENA-10D-H-3

value: 10 days after RAN treatment (high dose)


title: ENA-10D-H-1


title: ENA-10D-H-2


title: CBZ-2D-L-2


title: CBZ-2D-M-4


title: ENA-10D-H-5


title: ENA-10D-H-4


title: ENA-10D-M-6

value: 10 days after RAN treatment (middle dose)


title: CBZ-2D-H-1


title: ENA-10D-H-6


title: CBZ-2D-L-4


title: CBZ-2D-L-1


title: ENA-10D-M-2


title: ENA-10D-L-6

value: 10 days after RAN treatment (low dose)


title: ENA-10D-M-1


title: ENA-10D-M-4


title: ENA-10D-M-5


title: ENA-10D-M-3


title: ENA-10D-L-5


title: ENA-10D-L-4


title: ENA-10D-L-3


title: ENA-3D-H-6

value: 3 days after RAN treatment (high dose)


title: ENA-10D-L-1

value: Sprague-Dawley


title: ENA-3D-H-4


title: ENA-3D-H-1


title: ENA-3D-H-3


title: ENA-3D-M-2

value: 3 days after RAN treatment (middle dose)


title: ENA-3D-L-2

value: 3 days after RAN treatment (low dose)


title: ENA-3D-M-1


title: ENA-3D-M-6


title: ENA-3D-L-6


title: ENA-3D-L-3


title: ENA-3D-M-3


title: ENA-3D-M-4


title: ENA-3D-H-2


title: ENA-3D-M-5


title: ENA-10D-L-2


title: ENA-3D-H-5


title: ENA-2D-H-5

value: 2 days after RAN treatment (high dose)


title: ENA-3D-L-1


title: ENA-2D-H-6


title: ENA-2D-H-4


title: ENA-3D-L-5


title: ENA-3D-L-4


title: ENA-2D-H-3


title: ENA-2D-M-6

value: 2 days after RAN treatment (middle dose)


title: ENA-2D-M-4


title: ENA-2D-M-5


title: ENA-2D-H-1


title: ENA-2D-H-2


title: ENA-2D-L-5

value: 2 days after RAN treatment (low dose)


title: ENA-2D-M-3


title: ENA-2D-M-1


title: RAN-10D-H-5


title: RAN-10D-H-4


title: RAN-10D-M-6


title: ENA-2D-L-2


title: RAN-10D-H-3


title: ENA-2D-L-4


title: ENA-2D-L-1


title: RAN-10D-H-6


title: ENA-2D-M-2


title: RAN-10D-M-5


title: RAN-10D-H-1


title: RAN-10D-M-2


title: RAN-10D-M-3


title: RAN-10D-H-2


title: RAN-10D-M-4


title: ENA-2D-L-3


title: RAN-10D-M-1


title: RAN-10D-L-4


title: RAN-10D-L-3


title: RAN-10D-L-5


title: RAN-10D-L-1


title: RAN-3D-H-5


title: RAN-10D-L-6


title: RAN-3D-H-2


title: RAN-3D-H-3


title: RAN-10D-L-2


title: RAN-3D-H-6


title: RAN-3D-H-4


title: RAN-3D-M-6


title: RAN-3D-H-1


title: RAN-3D-M-5


title: RAN-3D-L-6


title: RAN-3D-M-3


title: RAN-3D-L-5


title: RAN-3D-M-4


title: RAN-2D-H-6


title: RAN-3D-M-1


title: RAN-3D-L-3


title: RAN-3D-L-1


title: RAN-2D-H-5


title: RAN-2D-H-4


title: RAN-3D-L-4


title: RAN-3D-L-2


title: RAN-2D-H-3


title: RAN-2D-H-2


title: RAN-3D-M-2


title: RAN-2D-M-6


title: RAN-2D-M-5


title: RAN-2D-L-2


title: RAN-2D-H-1


title: RAN-2D-M-1


title: RAN-2D-M-3


title: RAN-2D-L-5


title: RAN-2D-L-6


title: RAN-2D-M-4


title: RAN-2D-L-1


title: PZA-10D-H-4

value: 10 days after PZA treatment (high dose)


title: PZA-10D-H-6


title: RAN-2D-M-2


title: PZA-10D-H-3


title: PZA-10D-H-1

value: 10 days after PZA treatment (middle dose)


title: RAN-2D-L-3

value: liver


title: PZA-10D-L-3-RE


title: PZA-10D-H-5


title: PZA-10D-M-4


title: RAN-2D-L-4


title: PZA-10D-M-5


title: PZA-10D-M-3


title: PZA-10D-L-3

value: 10 days after PZA treatment (low dose)


title: PZA-10D-L-2


title: PZA-3D-M-6

value: 3 days after PZA treatment (middle dose)


title: PZA-10D-L-6


title: PZA-10D-M-2


title: PZA-10D-M-6


title: PZA-10D-L-5


title: PZA-10D-H-2


title: PZA-3D-H-1

value: 3 days after PZA treatment (high dose)


title: PZA-3D-H-3


title: PZA-10D-M-1


title: PZA-3D-H-2


title: PZA-3D-M-3


title: PZA-3D-M-1


title: PZA-3D-L-6

value: 3 days after PZA treatment (low dose)


title: PZA-3D-M-4


title: PZA-3D-L-4


title: PZA-3D-M-2


title: ENA-2D-L-6


title: PZA-10D-L-1


title: PZA-10D-L-4


title: PZA-3D-H-5


title: PZA-3D-M-5


title: PZA-3D-H-4


title: PZA-3D-L-3


title: PZA-3D-L-5


title: PZA-3D-H-6


title: PZA-3D-L-1


title: PZA-3D-L-2


title: PZA-2D-M-3

value: 2 days after PZA treatment (middle dose)


title: PZA-2D-H-3

value: 2 days after PZA treatment (high dose)


title: PZA-2D-H-4


title: PZA-2D-M-2


title: PZA-2D-M-1


title: PZA-2D-L-5

value: 2 days after PZA treatment (low dose)


title: PZA-2D-H-2


title: PZA-2D-M-5


title: PZA-2D-H-1


title: PZA-2D-H-5


title: PZA-2D-M-4


title: PZA-2D-H-6


title: PZA-2D-L-6


title: PZA-2D-M-6


title: PZA-2D-L-4


title: PZA-2D-L-3


title: PZA-2D-L-1


title: PZA-2D-L-2


title: Tg 6496

status: Public on Aug 13 2013

source_name: Transgenic ERG #6496

growth_protocol: ERG transgenic animals were kept in the animal facility and were sacrified when leukemia  signs  appeared.

extract_protocol: RNA was extracted using TriZol, according to the manufacturer's instructions and cleaned with Phenol/chlorophorm/Isoamyl alcohol in Phase lock gel (PLG) tubes.

treatment_protocol: Bone marrow was extracted from mouse femur, washed with PBS and then either taken directly for RNA extraction or first lineage depleted using a lineage depletion kit (Miltenyi Biotec).


title: WT 2

source_name: Wild type bone marrow #2


title: Tg 64960

source_name: Transgenic ERG #64960


title: Tg 70248

source_name: Transgenic ERG #70248


title: WT 1

source_name: Wild type bone marrow #1


title: WT 1 Lin-

source_name: Wild type lineage negative bone marrow #1


title: WT 3 Lin-

source_name: Wild type lineage negative bone marrow #3


title: WT 3

source_name: Wild type bone marrow #3


title: c828_NCAM1 plus cells

status: Public on Jul 23 2013

description: Gene expression from human NCAM1 plus subpopulation

data_processing: RMA PARTEK suite6.6 Quantile norm.

source_name: NCAM1 plus subpopulation isolated from total human fetal kidney cells

growth_protocol: Normal human fetal kidney (hFK) samples were were collected from fetuses that were aborted electively. Fetal gestational age ranged from 15 to 23 weeks. The samples were minced in HBSS, soaked in collagenase for 2 hours and then cultured in IMDM medium supplemented with 10% fetal bovine serim (FBS), 1% L-glutamine, 1% penicillin-streptomycin  and the following growth factors: 50ng/ml bFGF, 50ng/ml EGF and 5ng/ml SCF

treatment_protocol: CD56 (NCAM1) microbeads (Miltenyi Biotec) were used for single marker cell separation. Positive and negative fractions were separated using Mini or MidiMACS cell columns (Miltenyi Biotech) according to the manufacturer's protocol.

tag: cell type

value: Normal human fetal kidney (hFK)


title: WT 2 Lin-

source_name: Wild type lineage negative bone marrow #2


title: C598_AK72_minus

description: Gene expression from human adult renal cells cultured as monolayer

growth_protocol: Normal human adult kidney (hAK) samples were retrieved from borders of renal cell carcinoma tumors from partial and total nephrectomy patients. The samples were minced in HBSS, soaked in collagenase for 2 hours and then cultured in IMDM medium supplemented with 10% fetal bovine serim (FBS), 1% L-glutamine, 1% penicillin-streptomycin  and the following growth factors: 50ng/ml bFGF, 50ng/ml EGF and 5ng/ml SCF

value: Normal human adult kidney (hAK)

tag: cell fraction

value: Negative NCAM fraction


title: c827_Total cells

description: Gene expression from human fetal kidney cells

source_name: total human fetal kidney cells


title: C597_AK72_plus

description: Gene expression from human adult renal cells cultured in suspention in low attachment conditions

value: positive NCAM fraction


title: MRL  mouse digit at day 7, biological rep 2

status: Public on Jul 01 2013

description: anterior 1/2 of hindlimb middle digit

hyb_protocol: Hybridization and scanning of nicroarrays was performed by the Cornell Microarray Facility. The biotinylated cDNA was fragmented and hybridized to the Affymetrix GeneChip Mouse Exon 1.0 ST arrays for analysis of over 80,000 transcripts on a single array.  The hybridized arrays were washed and stained in a Fluidics station.

data_processing:
Data were processed using Affymetrix Expression Console . Gene level expression were summarized from the corrected intensities and then RMA normalized.
MoEx-1_0-st-v1.r2.qcc
MoEx-1_0-st-v1.r2.dt1.mm8.core.ps

source_name: MRL digit, day 7

label_protocol: Samples were enzymatically fragmented and biotinylated using the Affymetrix WT Terminal Labeling Kit according to the manufacturer's instructions.

growth_protocol: Mouse hindlimb digits dissected from C57Bl/6 or MRL mice

extract_protocol: The second phalanx of both middle digits was isolated from C57Bl/6 or MRL mice hindlimbs.  Total RNA was isolated from the digits using Trizol (Gibco) and further purified using an RNeasy Mini Column kit (Qiagen).  cDNA synthesis and amplification was performed using the WT cDNA synthesis and amplification kit (Affymetrix).

treatment_protocol: digit amputation at day 0; regenerating digits isolated at various timepoints post-amputation

value: day 7

value: 3-4 months

value: second phalanx on the middle digit

tag: genotype

value: wild-type

tag: genetic background

value: MRL/MpJ


title: C57BL/6 mouse digit at day 14, biological rep 2

description: anterior 1/2 of hindlimb middle digit

source_name: B6 digit, day 14

value: day 14


title: C57BL/6 mouse digit at day 7, biological rep 3

description: anterior 1/2 of hindlimb middle digit

source_name: B6 digit, day 7


title: C57BL/6 mouse digit at day 14, biological rep 1

description: anterior 1/2 of hindlimb middle digit


title: C57BL/6 mouse digit at day 7, biological rep 1

description: anterior 1/2 of hindlimb middle digit


title: MRL  mouse digit at day 14, biological rep 3

description: anterior 1/2 of hindlimb middle digit

source_name: MRL digit, day 14


title: MRL  mouse digit at day 3, biological rep 1

description: anterior 1/2 of hindlimb middle digit

source_name: MRL digit, day 3

value: day 3


title: MRL  mouse digit at day 7, biological rep 3

description: anterior 1/2 of hindlimb middle digit


title: MRL  mouse digit at day 7, biological rep 1

description: anterior 1/2 of hindlimb middle digit


title: C57BL/6 mouse digit at day 14, biological rep 3

description: anterior 1/2 of hindlimb middle digit


title: C57BL/6 mouse digit at day 3, biological rep 2

description: anterior 1/2 of hindlimb middle digit

source_name: B6 digit, day 3


title: C57BL/6 mouse digit at day 7, biological rep 2

description: anterior 1/2 of hindlimb middle digit


title: K562_control

status: Public on Jun 17 2013

description: scrambled siRNA was used as control

data_processing:
Alignment: Alignment of RNA-seq reads was done using TopHat (Trapnell et al. 2009), a splicing-aware aligner. The reads were mapped to the human reference genome (hg19). Mismatches were not allowed adjacent to the splice junction, and a splice-junction anchor of at least 12 bases was used. The alignment was done with respect to known Ensembl transcripts (using Ensembl62 transcripts GTF file), and unknown splice-junction detection was set to 'off'. Therefore, unknown splice variants could not be detected, and all results shown in this study are based on known variants. Using SAMtools (Li et al.2009), only paired-end reads were retained, where both ends aligned in a proper orientation and with less than 100,000 bases between them.
Differential expression (DE) analysis was done using AltAnalyze (Emig et al. 2010; Salomonis et al. 2010) by counting the reads for each constitutive exon in Ensembl genes (Ensembl62) and using AltAnalyze quantile normalization.
Alternative splicing analysis: RNA-seq AS analysis was done using AltAnalyze (Emig et al. 2010; Salomonis et al. 2010) based on alignment and junctions obtained by TopHat (Trapnell et al. 2009).
Genome_build: hg19
Supplementary_files_format_and_content: HepG2_AS_region: HepG2 reads mapping and splice junctions were  resulted from TopHat. Quantile normalization and alternative splicing (AS) analysis were done using AltAnalyze. AltAnlayze  AS results format in xls file (from left column to right column)- Ensembl-ID, Splicing-Index,gene symbol,description, exons,regulation_call, junctionID, fold, adjfold, up_exons, down_exons, functional_prediction, uniprot-ens_feature_predictions, peptide_predictions, ens_overlapping_domains, constitutive_baseline_exp, gene-expression-change, transcript_cluster_ID, ensembl_exons, consitutive_probeset(yes/no), exon-region-ID,exon_annotations, Junction_location
Supplementary_files_format_and_content: K562_AS_region: K562 reads mapping and splice junctions were resulted from TopHat. Quantile normalization and alternative splicing (AS) analysis were done using AltAnalyze. AltAnalyze AS results format in xls file (from left column to right col column)- Ensembl-ID, Splicing-Index,gene symbol,description,exons, regulation_call, junctionID, fold, adjfold, up_exons, down_exons, functional_prediction, uniprot-ens_feature_predictions, peptide_predictions, ens_overlapping_domains, constitutive_baseline_exp, gene-expression-change, transcript_cluster_ID, ensembl_exons, consitutive_probeset(yes/no), exon-region-ID,exon_annotations, Junction_location
Supplementary_files_format_and_content: HepG2_DE_2_fold: HepG2 reads mapping were resulted from TopHat. Quantile normalization and differential expression (DE) analysis were done using AltAnalyze. 2 fold change was taken as cutoff for this list. Format of xls file (from left colum to righ colum) - GeneID, gene_symbol, full_name, avg-ADARkd, avg-control, log_fold-ADARkd_vs_control, fold-ADARkd_vs_control
Supplementary_files_format_and_content: K562_DE_2_fold: K562 reads mapping and junctions were resulted from TopHat. Quantile normalization and differential expression (DE) analysis were done using AltAnalyze.2 fold change was taken as cutoff for this list. Format of xls file (from left column to right column) - GeneID, gene_symbol, full_name, avg-ADARkd, avg-control, log_fold-ADARkd_vs_control, fold-ADARkd_vs_control

source_name: K562 cells

growth_protocol: HepG2 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Beit-Haemek, Israel)).  K562 cells were cultured in RPMI 1640 medium (Beit-Haemek, Israel). Both media were supplemented with 10% fetal calf serum (FCS) (Beit-Haemek, Israel), 2 mM glutamine, 100 mg/ml streptomycin and 100 units/ml penicillin (Beit-Haemek, Israel), at 370c in a humidified incubator with 5% CO2.

extract_protocol:
RNA was purified using TRIzol.
Libraries were prepared according to Illumina's instructions. Libraries were sequenced on the Genome Analyzer 2x following the manufacturer's protocols. 76 base paired-end reads were sequenced in Illumina GAIIX with two technical replicates for each sample (2 × control and 2 × ADAR KD for HepG2 and K562).

treatment_protocol: HepG2 and K562 cell lines were stably transfected with plasmids containing siRNA designed to specifically knock down ADAR expression (ADAR KD). Different types of siRNA were tested, and the one yielding the best ADAR reduction was chosen. The same cells transected with a plasmid containing the scrambled siRNA (SCR) were used as a control.

tag: cell line

tag: transfected with

value: scrambled siRNA (control)


title: K562_ADARkd

description: siRNA against ADAR1 (ADARkd)

value: siRNA against ADAR1 (ADAR knock down)


title: C57BL/6 mouse digit at day 3, biological rep 3

description: anterior 1/2 of hindlimb middle digit

tag: time


title: HepG2_control

description: scrambled siRNA was used as control

source_name: HepG2 cells


title: MRL  mouse digit at day 14, biological rep 2

description: anterior 1/2 of hindlimb middle digit


title: MRL  mouse digit at day 14, biological rep 1

description: anterior 1/2 of hindlimb middle digit


title: MRL  mouse digit at day 3, biological rep 3

description: anterior 1/2 of hindlimb middle digit


title: MRL  mouse digit at day 3, biological rep 2

description: anterior 1/2 of hindlimb middle digit


title: MRL  mouse digit at day 0, biological rep 2

description: anterior 1/2 of hindlimb middle digit

source_name: MRL digit, day 0

value: day 0


title: MRL  mouse digit at day 0, biological rep 3

description: anterior 1/2 of hindlimb middle digit


title: C57BL/6 mouse digit at day 3, biological rep 1

description: anterior 1/2 of hindlimb middle digit


title: C57BL/6 mouse digit at day 0, biological rep 2

description: anterior 1/2 of hindlimb middle digit

source_name: B6 digit, day 0


title: HepG2_ADARkd

description: siRNA against ADAR1 (ADARkd)


title: C57BL/6 mouse digit at day 0, biological rep 3

description: anterior 1/2 of hindlimb middle digit


title: C57BL/6 mouse digit at day 0, biological rep 1

description: anterior 1/2 of hindlimb middle digit


title: MRL  mouse digit at day 0, biological rep 1

description: anterior 1/2 of hindlimb middle digit


title: B637_HEPG2_SCR

status: Public on Jun 15 2013

data_processing:
RMA
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: HepG2 cell lines

extract_protocol: RNA was purified using TRIzol.

value: control


title: B640_K562_SCR

source_name: K562 cell lines


title: B641_K562_1105

value: siRNA against ADAR1 (ADARkd)

value: knock down ADAR expression (ADAR KD


title: B638_HEPG2_1105


title: Female 50ppm fish 2

status: Public on Jun 01 2013

description: collected at six weeks

scan_protocol: The arrays were scanned at 2um on a NimbleGen MS200 scanner with auto-gain adjust.  The TIFF images were gridded and extracted using NimbleScan v. 2.6.

data_processing: Expression data were normalized using the Robust Multichip Average (RMA) algorithm as described by Irizarry, et al. (Nucleic Acids Res. 2003; 31:e15 and Biostatistics 2003; 4:249). Differential gene expression were determined with SAM  by Mev 4.0.

source_name: female 50ppm

growth_protocol: All zebrafish were handled following Animal Care and Use Committee (ACUC) protocols of University of Wisconsin–Milwaukee. Three-month old EkkWill (EK) zebrafish were used for is experiment and were reared in 28 ℃ dechlorinated, filtered municipal water (DFMW) in the NIEHS Children's Environmental Health Sciences Core Center (CEHSC) animal facility.

treatment_protocol: Zebrafish were fed Biodiet starter (Bio-Oregon) (4% body weight per day) with MeHg added at 0ppm, 0.5ppm, 5ppm and 50ppm (with ethanol as vehicle) for six weeks.

value: individual female fish from 50ppm group

tag: gender

value: female

value: whole fish

value: 3 mo

tag: treatment

value: 50ppm MeHg


title: Male 5ppm fish 3

description: collected at six weeks

source_name: male 5ppm

tag: sample type

value: individual male fish from 5 ppm group

value: male

value: 5ppm MeHg


title: Female 0.5ppm fish 2

description: collected at six weeks

source_name: female 0.5ppm

value: individual female fish from 0.5ppm group

value: 0.5ppm MeHg


title: Female control fish 3

description: collected at six weeks

source_name: female control

value: individual female fish from control group


title: Male 0.5ppm fish 2

description: collected at six weeks

source_name: male 0.5ppm

value: individual male fish from 0.5 ppm group


title: Female 5ppm fish 1

description: collected at six weeks

source_name: female 5ppm

value: individual female fish from 5ppm group


title: Female control fish 2

description: collected at six weeks


title: Female 50ppm fish 1

description: collected at six weeks


title: Male 5ppm fish 2

description: collected at six weeks


title: 0.5 ppm MeHg 5 fish vs. common reference of 11

description: collected at six weeks

hyb_protocol: Labeled DNAs were hybridized to prewarmed microarrays at 50°C for 16 hours. Following the first hybridization, arrays were washed in 2X SSC, 0.2% SDS solution at 50 ℃ 1 x 15 min, 2X SSC 1 x 15 min at room temperature, then 0.2X SSC for 1 x 15 min at room temperature. The fluorescent labeling hybridization (50 ℃ for 4hr) utilized the Genisphere 3DNA Cy3 and Cy5 capture reagents in formamide hybridization buffer. The slides were washed as described above, and the arrays were dried by centrifugation.

scan_protocol: Microarrays were scanned using the ScanArray Express (PerkinElmer) at 10 um resolution. The TIFF images of arrays were generated with ScanArray Express software and the intensities of raw data of two-channel arrays were collected by the ImaGene 6.0 (BioDiscovery).

data_processing: Statistical analysis of microarray data was performed using scripts written in R language. These scripts included functions of background correction and array normalization. Background correction was done using background subtraction by the function “backgroundCorrect” and normalization was done by the function  “normalizeBetweenArrays” with “lowess” method, which was implemented in the package LIMMA (version 2.18.3) from the Bioconductor project (version 2.4). Bayesian analysis generated p-values using the eBayes function.

organism: Oncorhynchus mykiss

source_name: common reference

label_protocol: RNA of ten fish from control group was pooled as a common reference, and total RNA of five individual fish from control and MeHg-treated groups were randomly selected for comparison to the common reference.  cDNA was synthesized from 1 μg pooled RNA using SuperScript II Reverse Transcriptase (Invitrogen) according to the manufacturer’s protocol . The common reference cDNA targets were labeled with Cy3 and cDNA of individual fish from each group was labeled with Cy5 using the Array 900 Expression Array Detection kit (Genisphere) according to the manufacturer’s protocol. Briefly, cDNA was denatured at 80 ℃ for 5 min in the presence of oligo (dT) primers with 3’ unique capture sequences (used in the Cy3 or Cy5 labeling reactions, respectively), then reverse transcribed at 42 ℃ (2.5 hours). The capture sequence-labeled cDNAs for each comparison were combined and incubated at 50 ℃ until applied to microarray hybridization.

growth_protocol: All rainbow trout were handled following Animal Care and Use Committee (ACUC) protocols of University of Wisconsin–Milwaukee. Eyed trout eggs were ordered from Fish and Wildlife Service of Ennis National Fish Hatchery (MT), reared in 10 ℃ dechlorinated, filtered municipal water (DFMW) in the NIEHS Children's Environmental Health Sciences Core Center (CEHSC) animal facility.  , and 45 days after hatching MeHg dietary exposures were initiated.

extract_protocol: Total RNA from individual fish was isolated using Trizol reagent (Invitrogen). One ml of Trizol was used for individual fish, which was homogenized by Power Gen 500 (Fisher), and 0.2 ml of chloroform was added for dissociation of nucleoprotein by shaking the tubes by hand for 15 seconds. The samples were centrifuged at 12000g for 15 minutes at 8℃. Upper aqueous phase was moved to a clean 1.5 ml Eppendorf tube, and 0.5 ml of isopropyl alcohol was added for precipitation of the RNA by incubating the samples at room temperature for 10 minutes. The samples were centrifuged at 12000g for 15 minutes at 8℃. Then the supernatant was removed and 1 ml of 75% ethanol was added for washing the pellet, and the samples were centrifuged at 12000g for 5 minutes at 8℃. The samples were air-dried then dissolved in RNase-free water. The concentration of RNA was determined by ND-1000 NanoDrop Spectrophotometer (Thermo Scientific, Wilmington, DE, USA). Further RNA-purification was performed using the RNeasy MiniElute cleanup kit (Qiagen) following the manufacturer’s protocol.

treatment_protocol: Fish were fed Biodiet starter (Bio-Oregon) (4% body weight per day) with MeHg added at 0ppm, 0.5ppm, 5ppm and 50ppm (with ethanol as vehicle) for six weeks.

value: pooled RNA of 10 fish from control group

tag: developmental stage

value: juevenile

source_name: 5 fish from 0.5ppm group

value: RNA of 5 fish from 0.5ppm group

value: 0.5 ppm MeHg

value: jeuvenile


title: Female 0.5ppm fish 1

description: collected at six weeks

value: female

tag: age


title: 5 ppm MeHg 5 fish vs. common reference of 12

description: collected at six weeks

value: control

value: whole fish

source_name: 5 fish from 5ppm group

value: RNA of 5 fish from 5ppm group

value: 5 ppm MeHg


title: Male control fish 3

description: collected at six weeks

source_name: male control

value: individual male fish from control group

value: male

value: 3 mo


title: Male 0.5ppm fish 1

description: collected at six weeks

value: 0.5ppm MeHg


title: Male 50ppm fish 2

description: collected at six weeks

source_name: male 50ppm

value: individual male fish from 50 ppm group

value: 50ppm MeHg


title: 50 ppm MeHg 5 fish vs. common reference of 12

description: collected at six weeks

source_name: 5 fish from 50ppm group

value: RNA of 5 fish from 50ppm group

value: 50 ppm MeHg


title: Female 50ppm fish 3

description: collected at six weeks

value: individual female fish from 50ppm group


title: Female control fish 1

description: collected at six weeks

value: individual female fish from control group


title: Male 0.5ppm fish 3

description: collected at six weeks

value: individual male fish from 0.5 ppm group


title: Male 5ppm fish 1

description: collected at six weeks

value: individual male fish from 5 ppm group

value: 5ppm MeHg


title: Female 0.5ppm fish 3

description: collected at six weeks

value: individual female fish from 0.5ppm group

value: female


title: Male control fish 2

description: collected at six weeks

value: whole fish

value: control


title: Male 50ppm fish 3

description: collected at six weeks


title: Male 50ppm fish 1

description: collected at six weeks


title: Male control fish 1

description: collected at six weeks

value: individual male fish from control group


title: day6_WT_rep2

status: Public on Apr 01 2013

description: replicate 2

hyb_protocol: 10ug of cDNA in 200ul Hybridization Cocktil use affymitrx Hybridization Oven 640 for 16hours at 45C

scan_protocol: scanned by Affymetix Genechip Scanner 3000 7G

source_name: mouse tissue, day6, wildtype, replicate2

label_protocol: a MessageAmp III kit for cDNA was used

extract_protocol: Qiagen RNeasy kit following tissue maceration

tag: background strain

value: C57BL/6 and 129 mixed background strain

tag: time point

tag: agent

value: topical 4OHT

value: wildtype


title: day0_WT_rep1

description: replicate 1

source_name: mouse tissue, day0, wildtype, replicate1


title: day6_IQGAP1_Null_rep1

description: replicate 1

source_name: mouse tissue, day6, IQGAP1 knockout, replicate1

value: IQGAP1 knockout


title: Airwayepithelial_Injured_WT_replicate3

status: Public on Nov 01 2012

hyb_protocol: Standard hybridization protocol was used as recommended by Affymterix.

label: Biotin labeled cRNA

source_name: Airway epithelial cell injured

label_protocol: For microarray hybridization, RNA was processed for hybridization to Affymetrix Affymetrix Mouse Genome 430A 2.0 oligonucleotide microarrays at University of Washington’s Center for Array Technology according to the manufacturer’s instructions.

extract_protocol: Total RNA was isolated using the Trizol protocol (Invitrogen; Carlsbad, CA). RNA quality was confirmed by a Bioanalyzer 2100 (Agilent; Santa Clara, CA).

treatment_protocol: Cells were cultured for 24 hours in serum-free medium before RNA isolation. Injury was created by 3 parallel scratches with a sterile p-200 pipet tip.

tag: strain

value: C57BL/6 mice

value: WT

tag: tissue

value: Airway epithelium

tag: culture

value: Air-liquid interface


title: Airwayepithelial_Injured_WT_replicate4


title: day0_IQGAP1_Null_rep2

description: replicate 2

source_name: mouse tissue, day0, IQGAP1 knockout, replicate2


title: day6_WT_rep1

description: replicate 1

source_name: mouse tissue, day6, wildtype, replicate1


title: Female 5ppm fish 3

description: collected at six weeks

value: individual female fish from 5ppm group

value: 3 mo


title: Rh30-CONT-72H

status: Public on Dec 12 2012

hyb_protocol: Biotin-labeled cRNA (15 µg) was hybridized to a GeneChip Human Genome U133 Plus 2.0 oligonucleotide arrays (HG-U133, Affymetrix, Santa Clara, CA, USA).

scan_protocol: Analysis was conducted with a GeneChip Scanner 3000.

data_processing: Differential gene expression was evaluated with the Microarray Suite 5.0 software (Affymetrix).

source_name: prostate carcinoma cell lines

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

growth_protocol: The P69 and M12 prostate cancer-derived cell lines were cultured in RPMI-1640 medium containing 10 ng/ml EGF, 0.1 nM dexamethasone, 5 µg/ml insulin, 5 µg/ml transferrin, and 5 ng/ml selenium.

extract_protocol: Total RNA was prepared from 5-Aza-treated and untreated P69 and M12 cells using the Trizol reagent (InVitrogen, Carlsbad, CA, USA), according to the manufacturer’s instructions.

treatment_protocol: Cells were treated with the demethylating agent 5'-Aza-2'-deoxycytidine (5-Aza) for 72 h, with daily medium changes. At the end of the incubation period the cells were harvested and total RNA was prepared for cDNA microarray analysis.


title: Primary neonatal keratinocytes_ACTL6a_i_rep2

status: Public on Nov 30 2012

description: replicate 2

source_name: Primary neonatal keratinocytes

label_protocol: Affymetrix 3' IVT Express Kit

growth_protocol: Keratinocytes were grown in subconfluent condition with the medium composed of 50% complete Keratinocyte-SFM (Life Technologies) and 50% Medium 154 (Life Technologies).

extract_protocol: Qiagen RNeasy Plus kits were used to isolate total RNA.

treatment_protocol: shRNA knock down

tag: genotype/variation

value: ACTL6a knock down


title: day6_IQGAP1_Null_rep2

description: replicate 2

source_name: mouse tissue, day6, IQGAP1 knockout, replicate2

tag: genotype


title: Primary neonatal keratinocytes_control_rep2

description: replicate 2


title: day0_IQGAP1_Null_rep1

description: replicate 1

source_name: mouse tissue, day0, IQGAP1 knockout, replicate1