title: 91 high

city: Berlin

first: Chiara

last: Romagnani

address: Chariteplatz 1

institute: Deutsches Rheuma Forschungszentrum -      Leibniz-Gemeinschaft

description: Sorted as: DAPI- CD56- CD3- CD19- CD14- CD117- CD34bright

hyb_protocol: Cy3 labeled cRNAs were hybridized overnight (17 hours, 65°C) to an Agilent Whole Human Genome Oligo Microarrays (8x60K v2, Design ID 039494) using Agilent’s recommended hybridization chamber and oven.Finally, microarrays were washed once with wash buffer 1 for 1 min at RT followed by a second wash with wash buffer 2 for 1 min at 37°C.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA).

data_processing: The Agilent Feature Extraction Software (FES 10.7.3.1 ) was used to read out and process the microarray image files.

source_name: Naive Tonsil

label_protocol: 10 ng of total RNA was used for the samples: 7 c+, 7 NK, 8 high, 8 c+, 9 c+, 10 c+, 10 c -, 87 c+, for all other samples the complete available amount of RNA  was used as template to produce Cy3- labeled cRNA. The RNA samples were amplified and labeled using the Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol.

extract_protocol: RNA was isolated using the NucleoSpin® RNA kit (Macherey-Nagel)

treatment_protocol: ILC3, NK cells and the CD34+ HPC subsets were sorted by flow cytometry from tonsils of 6 distinct donors. The ILC3 and NK cells were sorted after MACS-depletion of CD34+ cells followed by CD56+ cell magnetic enrichment as DAPI- CD3- CD19- CD14- CD94- CD127hi CD56+ ILC3 and DAPI- CD3- CD19- CD14- CD94+ CD127lo/- CD56+ NK cells, respectively. The CD34+ HPC subsets were separated after MACH enrichment of CD34+ cells according to expression of CD34 and CD117 in DAPI- CD56- CD3- CD19- CD14- CD117+ CD34dim, DAPI- CD56- CD3- CD19- CD14- CD117- CD34dim and DAPI- CD56- CD3- CD19- CD14- CD117- CD34bright cells. All cell populations were sorted to purity above 95%, pelleted and stored at -80 °C.

value: Tonsil

tag: stimulation

value: Naive/Healthy

value: FACS sorted

tag: cell population


title: P500

status: Public on Nov 25 2014

type: genomic

city: HOUSTON

first: Christine

middle: R.

last: Beck

state: Texas

address: One Baylor Plaza

department: Molecular and Human Genetics

country: USA

institute: Baylor College of Medicine

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed following the manufacturer’s protocol.

scan_protocol: Scanned on an Agilent G2505C  scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1)

data_processing: Agilent Feature Extraction Software (version 10.7.3.1) was used for background subtraction and normalization.

molecule: genomic DNA

organism: Homo sapiens

source_name: DNA extracted from whole blood

label_protocol: 1.2 ug of genomic patient and reference DNA were digested with AluI (5 U) and RsaI (5 U) (Promega, R6281 and R6371) for 2 hr at 37°C. Labeling reactions were performed according to the manufacturer’s instructions (BioPrime Array CGH Genomic Labeling Module,Invitrogen Corporation, #18095-012; Perkin-Elmer Las Inc. Cyanine Smart Pack dCTP,  PerkinElmer, #NEL620001KT) with Cy5-dCTP for patient DNA and Cy3-dCTP for reference DNA.

extract_protocol: DNA was isolated from peripheral blood with a Puregene kit (Gentra Systems), following the manufacturer’s protocol

tag: disease

value: Pelizaeus-Merzbacher disease (MIM 312080)

tag: genotype/variation

value: Patient carries a 0.0.601 Mb duplication and a nested 1.031 Mb triplication spanning Xq22

source_name: Reference sample

tag: cell line


title: 91 NK

type: RNA

country: Germany

description: Sorted as: DAPI- CD3- CD19- CD14- CD94+ CD127lo/- CD56+

molecule: total RNA

tag: tissue

tag: treatment


title: Peripheral blood from CXMA-01-005

city: Cambridge

first: Tsun-Po

last: Yang

address: Wellcome Trust Genome Campus

department: Human Genetics

country: United Kingdom

institute: Wellcome Trust Sanger Institute

hyb_protocol: Bisulphite converted DNA was hybridised to Illumina Infinium HumanMethylation450 Beadchip using standard Illumina protocol

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

data_processing: GenomeStudio (2010.3) Methylation module (1.8.5)

label: Cy5 and Cy3

source_name: Peripheral blood

label_protocol: Standard Illumina protocol

extract_protocol: Genomic DNA was extracted from whole blood samples using Qiagen DNeasy Kit according to standard instructions

tag: smoking (0, 1 and 2, which represent never, former and current smokers)

tag: age

tag: gender

value: Male

value: blood


title: 91 c +

description: Sorted as: DAPI- CD56- CD3- CD19- CD14- CD117+ CD34dim


title: Peripheral blood from CXMA-01-008


title: 91 ILC3

description: Sorted as: DAPI- CD3- CD19- CD14- CD94- CD127hi CD56+


title: Peripheral blood from CXMA-01-004


title: 91 c -

description: Sorted as: DAPI- CD56- CD3- CD19- CD14- CD117- CD34dim


title: P154

value: Carrier Mother contains a complex rearrangement spanning Xq22 that includes duplication of the PLP1 gene.


title: P117

value: Affected Uncle carries a complex rearrangement spanning Xq22 that includes duplication of the PLP1 gene


title: P113

value: Patient carries a complex rearrangement spanning Xq22 that includes duplication of the PLP1 gene


title: Media_Medium_IPL_18hpi

city: Brisbane

first: Quan

middle: Hoang

last: Nguyen

state: Queensland

address: Queensland Bioscience Precinct (Building 80) The University of Queensland. 306 Carmody Road. St

department: Australian Institute for Bioengineering and Nanotechnology

country: Australia

institute: The University of Queensland

description: H.zea cultured in medium media IPL infected by HearSNPV virus at 18 hour post infection

hyb_protocol: Hybridization and washing was performed using the in situ Hybridization Plus kit (Agilent) and following the manufacturer's instructions.

scan_protocol: Arrays were scanned on an Axon GenePix AX AGP 4000B. Data were extracted from images using GenePix Pro version 6.0 with local background estimation.

data_processing: Normalization was performed between arrays using the Spike-in control method. Correction for multiple hypothesis testing in the linear model was performed using Benjamini-Hochberg method. The emperical bayes method within limma was used for significant events detection, with false discovery rate lower than 5%.

organism: Helicoverpa zea

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Low Input Quick Amp kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA) and assessed by Agilent 2100 bioanalyzer

growth_protocol: H.zea cells were typically cultivated in 250 ml Erlenmeyer flasks containing 50-100 ml of VPM3 medium at 28 degree C, and grown on an orbital shaker operating at 120 rpm. Cells were routinely passaged twice a week, with a seeding cell density of 2-4x1E5 cells/ml.

extract_protocol: 5x10^5 H. zea (HzAM1) cells infected with conditions described above in shaker-flask suspension cultures, were collected for total RNA extraction and DNA removal using the Qiagen RNAeasy extraction and on-column DNAse kit (Qiagen, Hilden, Germany).

treatment_protocol: Briefly, 5x10^9 caterpillar purified OB are digested with an alkaline solution for 30 minutes, neutralized by the addition of VPM3,  filter sterilized and inoculated to a total culture volume of 100 ml containing H.zea cells at 5x10^5 cells/ml. Passage 1, (P1), BV harvested at 4 d.p.i. was used for P2 virus production. The same P2 BV stock was used for the three P3 infection experiments conducted. The first setup included two cell clones in Sf900III medium (good clone, high OB/cell yield vs. bad clone, low OB/cell yield). The second setup was infection of the HzAM1 parental cells in three different media. The media are listed below in the order from low to high OB/cell yield: (i) Grace's medium with added 10% FBS (referred to as Media_B);  (ii) IPL41 with supplements of 1% chemically defined lipids, and a yeastolate ultrafiltrate (4 g/L) (referred to as Media_G_IPL); (iii) Sf900III with added FBS (Media_G_Sf). The third setup involved two infections of HzAM1 cells in Sf900III medium at a low cell density of 5x10^5 cells/ml (high OB/cell yield), and a high cell density of 2x10^6 cells/ml (low OB/cell yield). All infections were carried out at an MOI of 5 plaque forming units/cell and a T.O.I (Time of Infection), of 1x10^6 cells/ml (except for the low and high cell density infection experiment). For each infection condition, three biological replicates were performed.

tag: insect cell line

value: Helicoverpa zea cell line (HzAM1) isolated from pupal ovarian tissue by McIntosh and Ignoffo (1983)

tag: virus

value: Helicoverpa armigera single-capsid nucleopolyhedrovirus (HaSNPV). Strain:H25EA1 isolated by CSIRO. This is an Australian wildtype field isolate.


title: Peripheral blood from CXMA-01-002


title: Media_Poor_Grace_18hpi

description: H.zea cultured in poor media Grace infected by HearSNPV virus at 18 hour post infection


title: BAB4179

value: Grandmother contains no rearrangement on Xq22 including the PLP1 gene.


title: Media_Medium_IPL_0hpi

description: H.zea cultured in medium media IPL infected by HearSNPV virus at 0 hour post infection


title: Media_Rich_900III_18hpi

description: H.zea cultured in rich media Sf900III infected by HearSNPV virus at 18 hour post infection


title: 9 high

value: DAPI- CD56- CD3- CD19- CD14- CD117- CD34bright


title: BAB3700

value: Carrier mother contains a 0.380 Mb duplication and a nested 1.03 Mb triplication spanning Xq22.


title: 9 ILC3

value: DAPI- CD3- CD19- CD14- CD94- CD127hi CD56+


title: P088

value: Carrier Grandmother contains a complex rearrangement spanning Xq22 that includes duplication of the PLP1 gene.


title: 9 NK

value: Tonsil


title: 87 high

value: Naive/Healthy


title: 87 ILC3

value: FACS sorted


title: Peripheral blood from CXMA-01-003

value: Female


title: BAB3698

value: Pelizaeus-Merzbacher disease (MIM 312080)

value: Patient contains a 0.380 Mb duplication and a nested 1.03 Mb triplication spanning Xq22


title: BAB3699

value: Carrier sister contains a 0.380 Mb duplication and a nested 1.03 Mb triplication spanning Xq22.


title: 9 c +

value: DAPI- CD56- CD3- CD19- CD14- CD117+ CD34dim


title: 9 c -

value: DAPI- CD56- CD3- CD19- CD14- CD117- CD34dim


title: Media_Poor_Grace_0hpi

description: H.zea cultured in poor media Grace infected by HearSNPV virus at 0 hour post infection


title: 87 c -


title: Peripheral blood from CXMA-01-001

value: Male

value: blood


title: BAB2389

value: Patient carries a 3.936 Mb duplication and a nested 1.031 Mb triplication spanning Xq22


title: Media_Rich_900III_0hpi

description: H.zea cultured in rich media Sf900III infected by HearSNPV virus at 0 hour post infection

value: Helicoverpa zea cell line (HzAM1) isolated from pupal ovarian tissue by McIntosh and Ignoffo (1983)

value: Helicoverpa armigera single-capsid nucleopolyhedrovirus (HaSNPV). Strain:H25EA1 isolated by CSIRO. This is an Australian wildtype field isolate.


title: BAB1290

value: Patient carries a 0.795 Mb duplication and a nested 95 Kb triplication spanning Xq22


title: 85 NK


title: 85 c +


title: 87 NK


title: 85 ILC3

value: DAPI- CD3- CD19- CD14- CD94- CD127hi CD56+


title: 87 c +


title: 85 high

value: DAPI- CD56- CD3- CD19- CD14- CD117- CD34bright


title: HighDensity_18 hpi_replicate2

description: H.zea infected at high cell density (2*10^5cells/ml) by HearSNPV virus at 18 hour post infection replicate 2


title: HighDensity_0 hpi_replicate2

description: H.zea infected at high cell density (2*10^5cells/ml) by HearSNPV virus at 0 hour post infection replicate 2


title: LowDensity_18 hpi_replicate2

description: H.zea infected at low cell density (2*10^5cells/ml) by HearSNPV virus at 18 hour post infection replicate 2


title: HighDensity_0 hpi_replicate1

description: H.zea infected at high cell density (2*10^5cells/ml) by HearSNPV virus at 0 hour post infection replicate 1


title: LowDensity_18 hpi_replicate1

description: H.zea infected at low cell density (2*10^5cells/ml) by HearSNPV virus at 18 hour post infection replicate 1


title: LowDensity_0 hpi_replicate2

description: H.zea infected at low cell density (2*10^5cells/ml) by HearSNPV virus at 0 hour post infection replicate 2


title: Clone_HighYield_18 hpi_replicate 2

description: H.zea high yield clone infected by HearSNPV virus at 18 hour post infection replicate 2


title: 8 NK

description: Sorted as: DAPI- CD3- CD19- CD14- CD94+ CD127lo/- CD56+

value: Tonsil


title: LowDensity_0 hpi_replicate1

description: H.zea infected at low cell density (2*10^5cells/ml) by HearSNPV virus at 0 hour post infection replicate 1


title: 8 c +

description: Sorted as: DAPI- CD56- CD3- CD19- CD14- CD117+ CD34dim

value: Naive/Healthy


title: HighDensity_18 hpi_replicate1

description: H.zea infected at high cell density (2*10^5cells/ml) by HearSNPV virus at 18 hour post infection replicate 1


title: Clone_LowYield_18 hpi_replicate 2

description: H.zea low yield clone infected by HearSNPV virus at 18 hour post infection replicate 2


title: 85 c -

description: Sorted as: DAPI- CD56- CD3- CD19- CD14- CD117- CD34dim

value: FACS sorted


title: 8 ILC3

description: Sorted as: DAPI- CD3- CD19- CD14- CD94- CD127hi CD56+


title: Clone_LowYield_18 hpi_replicate 1

description: H.zea low yield clone infected by HearSNPV virus at 18 hour post infection replicate 1


title: Clone_HighYield_0 hpi_replicate 1

description: H.zea high yield clone infected by HearSNPV virus at 0 hour post infection replicate 1


title: Clone_HighYield_18 hpi_replicate 1

description: H.zea high yield clone infected by HearSNPV virus at 18 hour post infection replicate 1


title: Clone_HighYield_0 hpi_replicate 2

description: H.zea high yield clone infected by HearSNPV virus at 0 hour post infection replicate 2


title: Clone_LowYield_0 hpi_replicate 2

description: H.zea low yield clone infected by HearSNPV virus at 0 hour post infection replicate 2


title: Zn20-3

status: Public on Nov 24 2014

city: Marburg

first: Martin

last: Thanbichler

address: Hans-Meerwein-Straße 4

institute: Philipps University Marburg

description: Zn_20 min_rep2

hyb_protocol: RNA was suspended in a proprietary mRNA Hybridization Buffer (25 μl per array). Hybridization was performed automatically for 16 h at 45 °C using the Geniom RT Analyzer (febit).

scan_protocol: After a stringent wash, the bound antisense-RNAs were used as primers for an enzymatic elongation reaction with labeled nucleotides. The reaction was performed with Klenow Fragment and biotinylated nucleotides at 37°C for 15 minutes. Finally, the Biochip was washed automatically, and biotinylated hybrids were detected with streptavidin-phycoerythrin (SAPE) using a proprietary Signal Enhancement (CSE) procedure (febit). Feature recognition (with a Cy3 filter set) and signal calculation were performed automatically using the Geniom Technology (febit). The data correlated well with qPCR data. There was no photo-bleaching, enabling repeated measurements and multiple scanning of each Biochip.

data_processing: For each gene sequence, up to four specific oligonucleotides were synthesized directly on the Geniom biochips. For 181 genes, it was not possible to design specific probes. After background correction, the median of the signals measured for each set of gene‐specific probes was determined. These compressed background‐subtracted raw data were then normalized using variance‐stabilizing normalization (VSN) to account for technical variability between different arrays.

label: biotin

organism: Hyphomonas neptunium ATCC 15444

source_name: total bacterial cells

label_protocol: Probes for hybridization were generated from 1 µg of total RNA per array using the MessageAmp II-Bacteria Kit  (Ambion). In brief, mRNA was polyadenylated and reverse transcribed using an oligo (dT) primer containing a T7 promoter. The resulting cDNA was then transcribed with T7 RNA polymerase to generate hundreds to thousands of antisense-RNA copies for each RNA in the sample.

growth_protocol: A culture of H. neptunium was diluted into fresh Marine Broth (BD Biosciences) and grown overnight to an OD600 of 0.5. Subsequently, 2 ml of the culture were withdrawn (sample t0).

extract_protocol: Total RNA was  isolated using a phenol/chloroform/isoamyl alcohol-based extraction protocol. Contaminating DNA was removed using the Turbo DNA‐free Kit (Ambion), and RNasin (Promega) was added to inhibit RNases.

treatment_protocol: Heavy metal stock solution was added to obtain a final concentration of 0.5 mM CuSO4 or 0.5 mM ZnCl2, respectively. 20 min and 60 min after supplementation of the medium, further 2‐ml samples were taken (samples t20 and t60).

tag: heavy metal treatment

value: 0.5 mM ZnCl2 for 20 min


title: Clone_LowYield_0 hpi_replicate 1

description: H.zea low yield clone infected by HearSNPV virus at 0 hour post infection replicate 1


title: 8 high

description: Sorted as: DAPI- CD56- CD3- CD19- CD14- CD117- CD34bright


title: Zn0-3

description: Zn_before addition_rep2


title: 8 c -


title: 7 high


title: Zn60-2

description: Zn_60 min_rep1

value: 0.5 mM ZnCl2 for 60 min


title: 7 c +


title: 7 c -


title: Cu0-3

description: Cu_before addition_rep2


title: 10 high


title: Zn20-2

description: Zn_20 min_rep1


title: 7 NK


title: 7 ILC3


title: 10 ILC3


title: 10 c -


title: Cu20-3

description: Cu_20 min_rep2

value: 0.5 mM CuSO4 for 20 min


title: Cu60-3

description: Cu_60 min_rep2

value: 0.5 mM CuSO4 for 60 min


title: Zn0-2

description: Zn_before addition_rep1


title: 10 NK


title: Zn60-3

description: Zn_60 min_rep2


title: 10 c +

value: DAPI- CD56- CD3- CD19- CD14- CD117+ CD34dim


title: Cu60-2

description: Cu_60 min_rep1


title: Cu0-2

description: Cu_before addition_rep1


title: ALS 701-002

city: Boston

first: Oleg

last: Butovsky

state: MA

address: 77 Avenue Louis Pasteur, Office 614

department: Center of Neurologic Diseases

institute: Brigham and Women's Hospital, Harvard Medical School

data_processing: Data was proccessed using nSolver, normalized to Positive controls, Housekeeping genes and negative controls

source_name: Whole spinal cord homogenate - post mortem

label_protocol: nCounter Human miRNA Assay Kit

extract_protocol: Total RNA was extracted using mirVanaTM miRNA isolation kit (Ambion) according to the manufacturer’s protocol

tag: cell type

tag: phenotype

value: ALS


title: ALS 701-004

hyb_protocol: according to the manufacturer’s protocol

value: Whole spinal cord homogenate - post mortem


title: ALS 701-013

scan_protocol: according to the manufacturer’s protocol


title: ALS 701-005


title: ALS 701-007


title: ALS 701-009


title: ALS 701-008


title: HC 200

value: non ALS


title: HC A13-17


title: HC A13-18


title: HC A13-14


title: HC A13-7


title: HC A12-241


title: HC A12-222


title: HC A12-5 112


title: HC A12-231


title: ALS 701-001


title: ALS 701-015


title: HC A12-243


title: WL402.1b

city: Oeiras

first: Raquel

last: Sá-Leão

address: Av da República

country: Portugal

institute: ITQB António Xavier

hyb_protocol: Samples were hybridised to the microarray slide using the NimbleGen Hybridization System and slides were washed using the NimbleGen Wash Buffer kit.

scan_protocol: Data was acquired on a NimbleGen MS 200 Scanner.

data_processing:
Normalisation and background correction of data were done done by quantile RMA analysis using the ArrayStar software (DNASTAR).
A cut-off of 512 was reached by drawing a graph of frequencies of signal intensities for all strains. Genes with signal intensities of 512 or above were considered present (assigned 1) and genes with signal intensities bellow that value were considered absent (assigned -1) from a given strain.

organism: Streptococcus pneumoniae

source_name: nasopharyngeal sample

label_protocol: 1ug of DNA from each strain was fluorescently labelled with Cy3 Random Nanomers using the Nimblegen One-Color DNA Labeling kit

growth_protocol: Pneumococcal strains were grown over night on blood agar plates supplemented 5% sheep blood at 37ºC, 5% CO2.

extract_protocol: Total genomic DNA was isolated using the Dneasy Blood & Tissue kit, Qiagen, Hilden, Germany, according to the manufacture's recommendations.

tag: strain


title: PT1718


title: PT673


title: DCC2787


title: PT6209b


title: PT1804b


title: WL977


title: WL165b


title: PT1493


title: WL108


title: PT5002


title: PT4812


title: DCC2648


title: WL850a


title: PT3201


title: PT4014


title: PT6210


title: PT5561


title: PT5727


title: DCC1795


title: PT1571b


title: WL352.1


title: DCC2879


title: PT5269


title: PT6318


title: WL1514


title: PT5838b


title: PT6317


title: WL992


title: PT2293b


title: DCC635


title: WL212


title: PT944


title: PT5899


title: Patient 33_NAT

city: New Lambton Heights

first: Kelly

last: Kiejda

state: NSW

address: HMRI

institute: University of Newcastle

description: miRNA expression

hyb_protocol: Labelled RNA was hybridised to Human miRNA microarrays (Sanger Release 14.0) according to the manufacturers’ instructions (Agilent Technologies)

scan_protocol: Slides were scanned immediately after washing on the Agilent High-resolution C Scanner using one color scan setting for miRNA array slides.

data_processing: Data from 15,000 probe features representing 904 unique miRNAs was extracted using Agilent Feature Extraction software (v10.7.3.1) using default parameters (protocol miRNA_107_09 and Grid: 029297_D_F_20100712) and converted to background subtracted signal intensities.

source_name: FFPE tissue specimen

label_protocol: 100ng of total RNA was dephosphorylated and directly labelled with Cy3 using the miRNA Complete Labelling and Hyb Kit (Agilent Technologies).

extract_protocol: Total RNA was extracted from 2mm punch biopsies of FFPE tissue using the miRNeasy FFPE kit (Qiagen, Doncaster, VIC, Australia).

value: Normal adjacent breast

tag: lymph node positive


title: Patient 31_LN

description: miRNA expression

value: Lymph node met


title: Patient 27_NAT

description: miRNA expression


title: Patient 24_IDC

description: miRNA expression

value: Breast tumour

value: no


title: Patient 28_IDC

description: miRNA expression

value: yes


title: Patient 33_IDC

description: miRNA expression


title: Patient 32_LN

description: miRNA expression


title: Patient 20_LN

description: miRNA expression


title: Patient 34_IDC

description: miRNA expression


title: Patient 22_IDC

description: miRNA expression


title: Patient 32_IDC

description: miRNA expression


title: Patient 25_NAT

description: miRNA expression


title: Patient 31_IDC

description: miRNA expression


title: Patient 30_LN

description: miRNA expression


title: Patient 27_IDC

description: miRNA expression


title: Patient 29_IDC

description: miRNA expression


title: Patient 34_NAT

description: miRNA expression


title: Patient 26_NAT

description: miRNA expression


title: Patient 28_LN

description: miRNA expression


title: Patient 21_LN

description: miRNA expression


title: Patient 21_IDC

description: miRNA expression


title: Patient 23_IDC

description: miRNA expression


title: Patient 19_LN

description: miRNA expression


title: Patient 19_IDC

description: miRNA expression


title: Patient 18_IDC

description: miRNA expression


title: Patient 20_IDC

description: miRNA expression


title: Patient 21_NAT

description: miRNA expression


title: Patient 18_LN

description: miRNA expression


title: Patient 13_IDC

description: miRNA expression


title: Patient 20_NAT

description: miRNA expression


title: Patient 16_NAT

description: miRNA expression


title: Patient 19_NAT

description: miRNA expression


title: Patient 9_NAT

description: miRNA expression


title: Patient 10_NAT

description: miRNA expression


title: Patient 15_IDC

description: miRNA expression


title: Patient 12_IDC

description: miRNA expression


title: Patient 14_IDC

description: miRNA expression


title: Patient 17_IDC

description: miRNA expression


title: Patient 15_NAT

description: miRNA expression


title: Patient 11_NAT

description: miRNA expression


title: Patient 12_NAT

description: miRNA expression


title: Patient 14_NAT

description: miRNA expression


title: Patient 11_IDC

description: miRNA expression


title: Patient 17_NAT

description: miRNA expression


title: Patient 16_IDC

description: miRNA expression


title: Patient 12_LN

description: miRNA expression


title: Patient 11_LN

description: miRNA expression


title: Patient 18_NAT

description: miRNA expression


title: Patient 13_NAT

description: miRNA expression


title: Patient 9_IDC

description: miRNA expression


title: Patient 8_IDC

description: miRNA expression


title: Patient 10_IDC

description: miRNA expression


title: ALS 701-006


title: Patient 6_NAT

description: miRNA expression


title: Patient 7_IDC

description: miRNA expression


title: Patient 6_IDC

description: miRNA expression


title: Patient 7_NAT

description: miRNA expression


title: Cu20-2

description: Cu_20 min_rep1


title: Patient 5_IDC

description: miRNA expression


title: Patient 3_NAT

description: miRNA expression


title: Patient 4_IDC

description: miRNA expression


title: Patient 3_IDC

description: miRNA expression


title: Patient 3_LN

description: miRNA expression


title: Patient 2_IDC

description: miRNA expression


title: Patient 1_LN

description: miRNA expression


title: Patient 5_NAT

description: miRNA expression


title: 101252_peripheral_CD4

city: Winston-Salem

first: Yongmei

last: Liu

state: NC

address: Medical Center Blvd.

institute: Wake Forest School of Medicine

description: human peripheral CD4+ cells

hyb_protocol: 700 ng of biotinylated cRNA was hybridized to a BeadChip at 580C for 16–17 hours.

scan_protocol: Illumina Bead Array Reader

data_processing:
Data corrected for local background were obtained from Illumina’s proprietary software GenomeStudio. QC analyses and bead type summarization (average bead signal for each type after outlier removal) were performed using the beadarray package (25). Detection P-values were computed using the negative controls on the array. The neqc function of the limma (26) package was used to perform a normal-exponential convolution model analysis to estimate non-negative signal, quantile normalization using all probes (gene and control, detected and not detected) and samples, addition of a recommended (small) offset, log2 transformation, and elimination of control probe data from the normalized expression matrix.
Sample data table cotains quantile normalized values - neqc function of the limma package was used to perform a normal-exponential convolution model analysis to estimate the quantile normalization using all probes/samples.

source_name: CD4+ cell

label_protocol: The Illumina TotalPrep-96 RNA Amplification Kit (Ambion/Applied Biosystems, DaeMStadt, Germany) was used for reverse transcription, and amplification with 500 ng of input total RNA (at 11ul).

growth_protocol: Not applicable

extract_protocol: Blood was initially collected in sodium heparin-containing Vacutainer CPTTM cell separation tubes (Becton Dickinson, Rutherford, NJ) to separate peripheral blood mononuclear cells from other elements within 2 hours from blood draw. Subsequently, T cells were isolated with the anti-CD4 coated magnetic beads, respectively, using AutoMACs automated magnetic separation unit (Miltenyi Biotec, Bergisch Gladbach, Germany).  DNA and RNA were isolated from samples simultaneously using the AllPrep DNA/RNA Mini Kit (Qiagen, Inc., Hilden, Germany).

treatment_protocol: Not applicable

tag: ChIP

tag: well

value: G

tag: age (yrs)

tag: racegendersite

tag: bcell

tag: mono

tag: nkcell

tag: neutro


title: 101196_peripheral_CD4

description: human peripheral CD4+ cells


title: Patient 5_LN

description: miRNA expression

tag: tissue


title: 101228_peripheral_CD4

description: human peripheral CD4+ cells

value: H


title: Patient 1_NAT

description: miRNA expression


title: 101247_peripheral_CD4

description: human peripheral CD4+ cells

value: K


title: 101163_peripheral_CD4

description: human peripheral CD4+ cells

value: A


title: Patient 1_IDC

description: miRNA expression


title: 101261_peripheral_CD4

description: human peripheral CD4+ cells


title: 101240_peripheral_CD4

description: human peripheral CD4+ cells


title: 101264_peripheral_CD4

description: human peripheral CD4+ cells

value: L


title: 101202_peripheral_CD4

description: human peripheral CD4+ cells

value: D


title: 101227_peripheral_CD4

description: human peripheral CD4+ cells

value: F


title: 101212_peripheral_CD4

description: human peripheral CD4+ cells


title: 101225_peripheral_CD4

description: human peripheral CD4+ cells


title: 101250_peripheral_CD4

description: human peripheral CD4+ cells

value: J


title: 101223_peripheral_CD4

description: human peripheral CD4+ cells


title: 101160_peripheral_CD4

description: human peripheral CD4+ cells

value: B


title: 101150_peripheral_CD4

description: human peripheral CD4+ cells


title: 101199_peripheral_CD4

description: human peripheral CD4+ cells


title: 101173_peripheral_CD4

description: human peripheral CD4+ cells


title: 101119_peripheral_CD4

description: human peripheral CD4+ cells


title: 101167_peripheral_CD4

description: human peripheral CD4+ cells


title: 101136_peripheral_CD4

description: human peripheral CD4+ cells

value: I


title: 101102_peripheral_CD4

description: human peripheral CD4+ cells


title: 101111_peripheral_CD4

description: human peripheral CD4+ cells

value: C


title: 101097_peripheral_CD4

description: human peripheral CD4+ cells


title: 101248_peripheral_CD4

description: human peripheral CD4+ cells


title: 101074_peripheral_CD4

description: human peripheral CD4+ cells


title: 101101_peripheral_CD4

description: human peripheral CD4+ cells


title: 101077_peripheral_CD4

description: human peripheral CD4+ cells


title: 101054_peripheral_CD4

description: human peripheral CD4+ cells


title: 101061_peripheral_CD4

description: human peripheral CD4+ cells


title: 101075_peripheral_CD4

description: human peripheral CD4+ cells


title: 101003_peripheral_CD4

description: human peripheral CD4+ cells


title: 101007_peripheral_CD4

description: human peripheral CD4+ cells


title: 101045_peripheral_CD4

description: human peripheral CD4+ cells


title: 101057_peripheral_CD4

description: human peripheral CD4+ cells


title: 101038_peripheral_CD4

description: human peripheral CD4+ cells


title: 101033_peripheral_CD4

description: human peripheral CD4+ cells


title: 100977_peripheral_CD4

description: human peripheral CD4+ cells


title: 101015_peripheral_CD4

description: human peripheral CD4+ cells


title: 101064_peripheral_CD4

description: human peripheral CD4+ cells

value: E


title: 100978_peripheral_CD4

description: human peripheral CD4+ cells


title: 101095_peripheral_CD4

description: human peripheral CD4+ cells


title: 101079_peripheral_CD4

description: human peripheral CD4+ cells


title: 101046_peripheral_CD4

description: human peripheral CD4+ cells


title: 101022_peripheral_CD4

description: human peripheral CD4+ cells


title: 100975_peripheral_CD4

description: human peripheral CD4+ cells


title: 100988_peripheral_CD4

description: human peripheral CD4+ cells


title: 101027_peripheral_CD4

description: human peripheral CD4+ cells


title: 101018_peripheral_CD4

description: human peripheral CD4+ cells


title: 100949_peripheral_CD4

description: human peripheral CD4+ cells


title: 100971_peripheral_CD4

description: human peripheral CD4+ cells


title: 100966_peripheral_CD4

description: human peripheral CD4+ cells


title: 100969_peripheral_CD4

description: human peripheral CD4+ cells


title: 100935_peripheral_CD4

description: human peripheral CD4+ cells


title: 100928_peripheral_CD4

description: human peripheral CD4+ cells


title: 100927_peripheral_CD4

description: human peripheral CD4+ cells


title: 100905_peripheral_CD4

description: human peripheral CD4+ cells


title: 100859_peripheral_CD4

description: human peripheral CD4+ cells


title: 100866_peripheral_CD4

description: human peripheral CD4+ cells


title: 100879_peripheral_CD4

description: human peripheral CD4+ cells


title: 100852_peripheral_CD4

description: human peripheral CD4+ cells


title: 100934_peripheral_CD4

description: human peripheral CD4+ cells


title: 100832_peripheral_CD4

description: human peripheral CD4+ cells


title: 100851_peripheral_CD4

description: human peripheral CD4+ cells


title: 100913_peripheral_CD4

description: human peripheral CD4+ cells


title: 100922_peripheral_CD4

description: human peripheral CD4+ cells


title: 100896_peripheral_CD4

description: human peripheral CD4+ cells


title: 100890_peripheral_CD4

description: human peripheral CD4+ cells


title: 100844_peripheral_CD4

description: human peripheral CD4+ cells


title: 100841_peripheral_CD4

description: human peripheral CD4+ cells


title: 100865_peripheral_CD4

description: human peripheral CD4+ cells


title: 100842_peripheral_CD4

description: human peripheral CD4+ cells


title: 100829_peripheral_CD4

description: human peripheral CD4+ cells


title: 100909_peripheral_CD4

description: human peripheral CD4+ cells


title: 100846_peripheral_CD4

description: human peripheral CD4+ cells


title: 100849_peripheral_CD4

description: human peripheral CD4+ cells


title: 100855_peripheral_CD4

description: human peripheral CD4+ cells


title: 100827_peripheral_CD4

description: human peripheral CD4+ cells


title: 100800_peripheral_CD4

description: human peripheral CD4+ cells


title: 100821_peripheral_CD4

description: human peripheral CD4+ cells


title: 100899_peripheral_CD4

description: human peripheral CD4+ cells


title: 100817_peripheral_CD4

description: human peripheral CD4+ cells


title: 100668_peripheral_CD4

description: human peripheral CD4+ cells


title: 100794_peripheral_CD4

description: human peripheral CD4+ cells


title: 100744_peripheral_CD4

description: human peripheral CD4+ cells


title: 100782_peripheral_CD4

description: human peripheral CD4+ cells


title: 100798_peripheral_CD4

description: human peripheral CD4+ cells


title: 100677_peripheral_CD4

description: human peripheral CD4+ cells


title: 100689_peripheral_CD4

description: human peripheral CD4+ cells


title: 100675_peripheral_CD4

description: human peripheral CD4+ cells


title: 100751_peripheral_CD4

description: human peripheral CD4+ cells


title: 100764_peripheral_CD4

description: human peripheral CD4+ cells


title: 100659_peripheral_CD4

description: human peripheral CD4+ cells


title: 100788_peripheral_CD4

description: human peripheral CD4+ cells


title: 100774_peripheral_CD4

description: human peripheral CD4+ cells


title: 100683_peripheral_CD4

description: human peripheral CD4+ cells


title: 100721_peripheral_CD4

description: human peripheral CD4+ cells


title: 100611_peripheral_CD4

description: human peripheral CD4+ cells


title: 100628_peripheral_CD4

description: human peripheral CD4+ cells


title: 100760_peripheral_CD4

description: human peripheral CD4+ cells


title: 100629_peripheral_CD4

description: human peripheral CD4+ cells


title: 100657_peripheral_CD4

description: human peripheral CD4+ cells


title: 100762_peripheral_CD4

description: human peripheral CD4+ cells


title: 100722_peripheral_CD4

description: human peripheral CD4+ cells


title: 100608_peripheral_CD4

description: human peripheral CD4+ cells


title: 100606_peripheral_CD4

description: human peripheral CD4+ cells


title: 100747_peripheral_CD4

description: human peripheral CD4+ cells


title: 100603_peripheral_CD4

description: human peripheral CD4+ cells


title: 100664_peripheral_CD4

description: human peripheral CD4+ cells


title: 100593_peripheral_CD4

description: human peripheral CD4+ cells


title: 100945_peripheral_CD4

description: human peripheral CD4+ cells


title: 100587_peripheral_CD4

description: human peripheral CD4+ cells


title: 100547_peripheral_CD4

description: human peripheral CD4+ cells


title: 100519_peripheral_CD4

description: human peripheral CD4+ cells


title: 100513_peripheral_CD4

description: human peripheral CD4+ cells


title: 100578_peripheral_CD4

description: human peripheral CD4+ cells


title: 100570_peripheral_CD4

description: human peripheral CD4+ cells


title: 100500_peripheral_CD4

description: human peripheral CD4+ cells


title: 100590_peripheral_CD4

description: human peripheral CD4+ cells


title: 100464_peripheral_CD4

description: human peripheral CD4+ cells


title: 100521_peripheral_CD4

description: human peripheral CD4+ cells


title: 100542_peripheral_CD4

description: human peripheral CD4+ cells


title: 100456_peripheral_CD4

description: human peripheral CD4+ cells


title: 100581_peripheral_CD4

description: human peripheral CD4+ cells


title: 100528_peripheral_CD4

description: human peripheral CD4+ cells


title: 100505_peripheral_CD4

description: human peripheral CD4+ cells


title: 100556_peripheral_CD4

description: human peripheral CD4+ cells


title: 100569_peripheral_CD4

description: human peripheral CD4+ cells


title: 100439_peripheral_CD4

description: human peripheral CD4+ cells


title: 100518_peripheral_CD4

description: human peripheral CD4+ cells


title: 100428_peripheral_CD4

description: human peripheral CD4+ cells


title: 100555_peripheral_CD4

description: human peripheral CD4+ cells


title: 100496_peripheral_CD4

description: human peripheral CD4+ cells


title: 100427_peripheral_CD4

description: human peripheral CD4+ cells


title: 100534_peripheral_CD4

description: human peripheral CD4+ cells


title: 100413_peripheral_CD4

description: human peripheral CD4+ cells


title: 100436_peripheral_CD4

description: human peripheral CD4+ cells


title: 100507_peripheral_CD4

description: human peripheral CD4+ cells


title: 100404_peripheral_CD4

description: human peripheral CD4+ cells


title: 100401_peripheral_CD4

description: human peripheral CD4+ cells


title: 100376_peripheral_CD4

description: human peripheral CD4+ cells


title: 100349_peripheral_CD4

description: human peripheral CD4+ cells


title: 100323_peripheral_CD4

description: human peripheral CD4+ cells


title: 100319_peripheral_CD4

description: human peripheral CD4+ cells


title: 100383_peripheral_CD4

description: human peripheral CD4+ cells


title: 100316_peripheral_CD4

description: human peripheral CD4+ cells


title: 100330_peripheral_CD4

description: human peripheral CD4+ cells


title: 100281_peripheral_CD4

description: human peripheral CD4+ cells


title: 100302_peripheral_CD4

description: human peripheral CD4+ cells


title: 100312_peripheral_CD4

description: human peripheral CD4+ cells


title: 100301_peripheral_CD4

description: human peripheral CD4+ cells


title: 100277_peripheral_CD4

description: human peripheral CD4+ cells


title: 100307_peripheral_CD4

description: human peripheral CD4+ cells


title: 100365_peripheral_CD4

description: human peripheral CD4+ cells


title: 100282_peripheral_CD4

description: human peripheral CD4+ cells


title: 100265_peripheral_CD4

description: human peripheral CD4+ cells


title: 100787_peripheral_CD4

description: human peripheral CD4+ cells


title: 100252_peripheral_CD4

description: human peripheral CD4+ cells


title: 100263_peripheral_CD4

description: human peripheral CD4+ cells


title: 100250_peripheral_CD4

description: human peripheral CD4+ cells


title: 100251_peripheral_CD4

description: human peripheral CD4+ cells


title: 100269_peripheral_CD4

description: human peripheral CD4+ cells


title: 100329_peripheral_CD4

description: human peripheral CD4+ cells


title: 100300_peripheral_CD4

description: human peripheral CD4+ cells


title: 100297_peripheral_CD4

description: human peripheral CD4+ cells


title: 100268_peripheral_CD4

description: human peripheral CD4+ cells


title: 100266_peripheral_CD4

description: human peripheral CD4+ cells


title: 100218_peripheral_CD4

description: human peripheral CD4+ cells


title: 100145_peripheral_CD4

description: human peripheral CD4+ cells


title: 100181_peripheral_CD4

description: human peripheral CD4+ cells


title: 100212_peripheral_CD4

description: human peripheral CD4+ cells


title: 100210_peripheral_CD4

description: human peripheral CD4+ cells


title: 100824_peripheral_CD4

description: human peripheral CD4+ cells


title: 100235_peripheral_CD4

description: human peripheral CD4+ cells


title: 100140_peripheral_CD4

description: human peripheral CD4+ cells


title: 100135_peripheral_CD4

description: human peripheral CD4+ cells


title: 100096_peripheral_CD4

description: human peripheral CD4+ cells


title: 100144_peripheral_CD4

description: human peripheral CD4+ cells


title: 100100_peripheral_CD4

description: human peripheral CD4+ cells


title: 100169_peripheral_CD4

description: human peripheral CD4+ cells


title: 100142_peripheral_CD4

description: human peripheral CD4+ cells


title: 100111_peripheral_CD4

description: human peripheral CD4+ cells


title: 100094_peripheral_CD4

description: human peripheral CD4+ cells


title: 100073_peripheral_CD4

description: human peripheral CD4+ cells


title: 100107_peripheral_CD4

description: human peripheral CD4+ cells


title: 100077_peripheral_CD4

description: human peripheral CD4+ cells


title: 100049_peripheral_CD4

description: human peripheral CD4+ cells


title: 100193_peripheral_CD4

description: human peripheral CD4+ cells


title: 100126_peripheral_CD4

description: human peripheral CD4+ cells


title: 100085_peripheral_CD4

description: human peripheral CD4+ cells


title: 100066_peripheral_CD4

description: human peripheral CD4+ cells


title: 100105_peripheral_CD4

description: human peripheral CD4+ cells


title: 100279_peripheral_CD4

description: human peripheral CD4+ cells


title: 100133_peripheral_CD4

description: human peripheral CD4+ cells


title: 100113_peripheral_CD4

description: human peripheral CD4+ cells


title: 100044_peripheral_CD4

description: human peripheral CD4+ cells


title: 100057_peripheral_CD4

description: human peripheral CD4+ cells


title: SOD 155 -/- (2)

organism: Mus musculus

source_name: Lumbar spinal cord homogenate

label_protocol: nCounter Mouse miRNA Assay Kit

value: Lumbar spinal cord homogenate

tag: strain/genotype

value: Mouse -B6/SJL-mSOD1G93A-miR-155-/-

tag: gender

value: female


title: 100043_peripheral_CD4

description: human peripheral CD4+ cells


title: 100042_peripheral_CD4

description: human peripheral CD4+ cells


title: 100039_peripheral_CD4

description: human peripheral CD4+ cells


title: SOD 155 -/- (1)


title: WT 155+/- (1)

value: Mouse -B6/SJL-miR-155+/-


title: SOD 155+/- (1)

value: Mouse -B6/SJL-mSOD1G93A-miR-155+/-


title: 100038_peripheral_CD4

description: human peripheral CD4+ cells


title: 100037_peripheral_CD4

description: human peripheral CD4+ cells


title: 100036_peripheral_CD4

description: human peripheral CD4+ cells


title: 100023_peripheral_CD4

description: human peripheral CD4+ cells


title: 100040_peripheral_CD4

description: human peripheral CD4+ cells


title: 100021_peripheral_CD4

description: human peripheral CD4+ cells


title: 100018_peripheral_CD4

description: human peripheral CD4+ cells


title: SOD 155+/- (2)


title: 100035_peripheral_CD4

description: human peripheral CD4+ cells


title: 100004_peripheral_CD4

description: human peripheral CD4+ cells


title: 100007_peripheral_CD4

description: human peripheral CD4+ cells


title: 100001_peripheral_CD4

description: human peripheral CD4+ cells


title: 100022_peripheral_CD4

description: human peripheral CD4+ cells


title: 100028_peripheral_CD4

description: human peripheral CD4+ cells


title: WT 155+/- (2)


title: 100014_peripheral_CD4

description: human peripheral CD4+ cells


title: SigH-FLAG_wt_stat_2nd

city: Kyoto

first: Masayuki

last: Inui

address: 9-2 Kizugawadai, Kizugawa

country: Japan

institute: Research institute of Innovative Technology for the Earth (RITE)

hyb_protocol: Hybridization was performed using Agilent Oligo aCGH Hybridization kit according to the manufacture’s manual (Agilent). Equal amount (2.5 μg) of each labeled DNA were mixed and hybridized to microarrays in an Agilent Technologies Microarray chamber at 65˚C for 24 h in a rotating Agilent hybridization oven at 20 rpm. After hybridization, microarrays were washed 5 min at room temperature with Oligo aCGH/ChIP-on-chip Wash Buffer 1 (Agilent), 5 min with 31˚C Oligo aCGH/ChIP-on-chip Wash buffer 2 (Agilent Technologies), 10 sec with acetonitrile, and 30 sec with Stabilization and Drying Solution (Agilent) at room temperature.

scan_protocol: Slides were scanned immediately after washing and placement within an Agilent Ozone Barrier Slide cover (Agilent) the Agilent DNA Microarray Scanner (G2505C) using two color scan setting for 4x44k array Scan resolution 5 microns. Scanning was done in both channels and PMT is set to 100% for both Cy3\cy5 channels.

data_processing: Feature extraction software provided by Agilent (version 10.5.1.1, Agilent Technologies, Palo Alto, CA, USA) was used to quantify the intensity of the fluorescent images and to normalize the results by subtracting local background fluorescence, according to the manufacturer’s instructions.

organism: Corynebacterium glutamicum R

source_name: wild type_stationary_SigH-FLAG ChIP DNA

label_protocol: DNA samples were blunted with T4 DNA polymerase, ligated to linkers, and amplified by PCR. Amplified DNA from reference DNA and immunoprecipitated DNA were differentially labeled with Cy3 and Cy5, respectively, by using CGH labeling kit (Invitrogen) according to the manufacture’s instruction.

growth_protocol: C. glutamicum are grown in 100 ml of nutrient rich A medium containing 1% glucose in  500 ml flask at 33˚C

extract_protocol: C. glutamicum cultures at the late exponential phase and the onset of the stationary phase (at the OD610 of up to 2.5 and 7.0, respectively) were treated with formaldehyde (at the final concentration of 1%) and incubate for 20 min at room temperature. The cross-linking was quenched by addition of glycine (at the final concentration of 125 mM) and incubation for 10 min at room temperature. Cells were then collected by centrifugation, washed twice with Tris-buffered saline (20 mM Tris-HCl pH 7.5, 150 mM NaCl) and stored at -80˚C. Pellets were resuspended in 2 ml IP buffer (50 mM HEPES-KOH pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, Roche Antiprotease mini). The cells were mechanically disrupted for nine cycles of 25 s at a speed rating of 6.5 with a FastPrep™ FP120 (BIO 101, Thermo Savant) at room temperature with intermittent cooling on ice for 5 min. The supernatant after centrifugation was sonicated on ice to shear DNA to an average size to 600-1,000 bp. A 50 μl fraction of the supernatant was saved for later analysis (reference DNA). The remainder was subjected to immunoprecipitation with 100μl of magnetic beads coated with Protein G (Invitrogen), which was coupled to the monoclonal anti-FLAG-tag antibody (Sigma). The mixture was incubated overnight on a rotating platform at 4˚C. The beads were washed once with IP buffer, twice with IP buffer containing 400 mM NaCl, eight times with RIPA buffer (50 mM HEPES pH7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Sodium deoxycholate), and twice with TE buffer with 50 mM NaCl. Immunoprecipitated complexes were eluted from the beads by treatment with 210 μl elution buffer (50 mM Tris-HCl pH8.0, 10 mM EDTA, 1% SDS) at 65˚C for 20 min. Cross-links of immunoprecipitated samples and of total DNA samples were reversed by incubation overnight at 65˚C. Samples were then treated with RNase A and proteinase K for 2 h at 55˚C. DNA was extracted with phenol-chloroform and purified with QIAquick PCR purification mini Elute kit (Qiagen).

tag: genotype/variation

value: wild type carrying FLAG-tagged sigH

tag: growth phase

value: stationary phase

source_name: wild type_stationary_Reference DNA (no IP)


title: SigH-FLAG_wt_stat_1st


title: SigH-FLAG_rshA_stat_2nd

source_name: rshA deletant_stationary_SigH-FLAG ChIP DNA

value: ΔrshA mutant carrying FLAG-tagged sigH

source_name: rshA deletant_stationary_Reference DNA (no IP)


title: SigH-FLAG_rshA_stat_3rd


title: SigH-FLAG_rshA_exp_3rd

source_name: rshA deletant_exponential_SigH-FLAG ChIP DNA

value: exponential phase

tag: chip antibody

value: monoclonal ANTI-FLAG M2 antibody (produced in mouse)

tag: chip antibody vendor

value: SIGMA,

tag: chip antibody cat. #

tag: chip antibody lot #

source_name: rshA deletant_exponential_Reference DNA (no IP)


title: rshA mutant at the exponential phase_5th

hyb_protocol: Hybridization was performed using Gene Expression Hybridization Kit according to the manufacture’s manual (Agilent). The labeled cDNA was hybridized to microarrays in an Agilent Technologies Microarray chamber at 65˚C for 17 h in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), and 1 minute with 37˚C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) at a resolution of 5 µm using single color scan setting for 4x44k array slides. PMT is set to 100% for Cy3 channels.

data_processing: The scanned images were analyzed quantified with Feature Extraction Software 10.5.5.1 (Agilent) using default parameters (protocol GE1_105_Dec08). Feature extracted data were analyzed using GeneSpring GX v 12.0 software from Agilent. Normalization of the data was done in GeneSpring GX using the recommended Percentile shift normalization (50th percentile).

source_name: rshA mutant_exponential phase

label_protocol: The cDNAs were synthesized from RNA by using reverse transcriptase from 10 μg of total RNAs and labeled with cyanine 3 (Cy3) using the SuperScript Indirect cDNA Labeling system (Life Technologies).

growth_protocol: C. glutamicum strains are grown in 100 ml of nutrient rich A medium containing 1% glucose in  500 ml flask at 33˚C

extract_protocol: Total RNA was extracted from C. glutamicum cells using the Qiagen RNeasy Mini kit (Qiagen) according to the manufacture's manual.

value: ΔrshA


title: Naïve MG-SC

source_name: Mouse -B6/SJL-miR-155+/-

label_protocol: nCounter Mouse Inflammation Kit

tag: cell type

value: Spinal FACS sorted adult FCRLS+ microglia


title: SigH-FLAG_wt_exp_1st

source_name: wild type_exponential_SigH-FLAG ChIP DNA

source_name: wild type_exponential_Reference DNA (no IP)


title: wt at the exponential phase_4th

source_name: WT_exponential phase

value: wild type


title: MG-SC (SOD1/miR155+/-)-1

source_name: Mouse -B6/SJL-mSOD1G93A-miR-155+/-

value: B6SJL-Tg(SOD1-G93A)1Gur/J / miR-155+/-


title: Ly6CHi-SPL (SOD1/miR155+/-)-2

value: Splenic FACS sorted Ly6CHi monocytes


title: Ly6CHi-SPL (SOD1/miR155-/-)-3

source_name: Mouse -B6/SJL-mSOD1G93A-miR-155-/-


title: MG-SC (SOD1/miR155+/-)-3


title: Ly6CHi-SPL (SOD1/miR155+/-)-1


title: MG-SC (SOD1/miR155+/-)-2


title: rshA mutant at the exponential phase_3rd


title: SigH-FLAG_wt_exp_2nd


title: rshA mutant at the exponential phase_2nd


title: SigH-FLAG_rshA_exp_2nd


title: SigH-FLAG_rshA_stat_1st


title: wt at the exponential phase_1st


title: rshA mutant at the exponential phase_4th


title: wt at the exponential phase_3rd


title: SigH-FLAG_rshA_exp_1st


title: Ly6CHi-SPL (SOD1/miR155+/-)-3


title: Naïve Ly6CHi-Spl MO


title: MG-SC(SOD1/miR155-/-)-2


title: Ly6CHi-SPL (SOD1/miR155-/-)-2


title: wt at the exponential phase_5th


title: MG-SC (SOD1/miR155-/-)-1


title: rshA mutant at the exponential phase_1st


title: Ly6CHi-SPL (SOD1/miR155-/-)-1


title: wt at the exponential phase_2nd


title: ALS-701-006

source_name: Whole spinal cord homogenate - post mortem

label_protocol: nCounter® GX Human Immunology Kit

tag: phenotype

value: ALS


title: ALS-701-009

value: Whole spinal cord homogenate - post mortem


title: ALS-701-015


title: ALS-701-013


title: ALS-701-005


title: ALS-701-008


title: ALS-701-002


title: HC-200

value: non-ALS


title: ALS-701-001


title: ALS-701-007


title: ALS-701-004


title: HC-A13-14


title: HC-A13-18


title: HC-A13-7


title: HC-A13-17


title: HC-A12-243


title: HC-A12-5 112


title: WT 140d

label_protocol: MG400 custom Nanostring codesets

value: Spinal cord FACS sorted adult FCRLS+ microglia

value: female

tag: age


title: SOD 140d


title: WT 120d


title: WT 60d


title: SOD 60d


title: HC-A12-231


title: SOD 90d


title: HC-A12-241


title: WT 90d


title: SOD 120d


title: HC-A12-222


title: 101264_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells

hyb_protocol: The resuspended samples were hybridized on HumanMethylation 450 BeadChips at 48°C for 16 h.

scan_protocol: Illumina HiScan reader

data_processing: Bead-level methylation data were summarized in GenomeStudio.  Because a two-channel system and both Infinium I and II assays were used, normalization was performed in several steps using the lumi package (27). We first adjusted for color bias using “smooth quantile normalization”. Next, the data were background adjusted by subtracting the median intensity value of the negative control probes.  Lastly, data were normalized across all samples by standard quantile normalization applied to the bead-type intensities and combined across Infinium I and II assays and both colors.

label_protocol: The Illumina HumanMethylation450 BeadChip and HiScan reader were used to perform the epigenome-wide methylation analysis. The EZ-96 DNA MethylationTM Kit (Zymo Research, Orange, CA) was used for bisulfate conversation with 1ug of input DNA (at 45 ul). 4 ul of bisulfite-converted DNA were used for DNA methylation assays, following the Illumina Infinium HD Methylation protocol. This consisted of a whole genome amplification step followed by enzymatic end-point fragmentation, precipitation, and resuspension.

tag: chip id

tag: well id

tag: age (yrs)

tag: racegendersite


title: 101248_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells

tag: bcell

tag: mono

tag: nkcell

tag: neutro


title: 101252_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 101261_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 101250_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 101247_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 101228_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 101240_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: WT 30d

tag: strain/genotype

tag: gender


title: SOD 30d


title: 101223_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 101227_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 101225_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 101212_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 101199_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 101196_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 101202_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 101173_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 101167_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 101111_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 101163_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 101150_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 101119_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 101160_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 101136_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 101102_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 101097_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 101077_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 101079_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 101064_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 101074_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 101061_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 101075_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 101057_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 101054_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 101045_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 101046_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 101038_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 101033_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 101101_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 101022_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 101015_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 101018_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 101007_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 101003_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 101027_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100988_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100978_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 101095_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100977_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100975_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100971_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100949_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100969_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100922_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100927_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100935_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100909_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100913_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100934_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100905_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100890_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100855_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100899_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100859_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100896_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100849_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100846_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100879_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100851_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100945_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100844_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100842_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100865_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100966_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100852_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100824_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100832_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100829_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100827_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100866_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100928_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100817_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100821_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100841_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100788_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100800_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100798_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100794_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100787_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100782_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100751_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100774_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100762_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100764_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100747_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100760_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100722_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100744_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100677_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100721_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100689_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100683_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100657_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100668_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100664_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100629_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100675_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100659_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100628_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100611_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100608_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100603_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100593_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100581_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100587_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100590_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100578_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100570_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100569_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100556_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100542_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100528_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100547_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100555_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100534_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100513_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100519_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100518_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100505_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100507_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100464_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100496_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100439_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100456_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100427_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100428_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100436_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100606_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100413_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: MG-SC(SOD1/miR155-/-)-3


title: 100404_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100383_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100365_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100376_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100521_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100330_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100323_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100319_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100316_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100307_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100329_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100500_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100349_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100302_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100300_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100297_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100282_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100269_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100281_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100279_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100266_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100268_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100265_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100277_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100401_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100263_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100250_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100252_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100235_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100212_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100210_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100193_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100181_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100301_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100144_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100142_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100140_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100145_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100126_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100113_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100251_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100111_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100107_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100096_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100312_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100077_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100066_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100218_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100073_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100057_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100049_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100044_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100043_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100169_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100135_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100042_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100040_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100039_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100037_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100038_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100036_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100133_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100035_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100028_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100023_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100105_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100100_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100085_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100094_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100018_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100014_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100021_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100007_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100004_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100001_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100022_peripheral_CD4 [methylation]

description: human peripheral CD4+ cells


title: 100012_PBMC_WNV

city: New Haven

first: Hailong

last: Meng

state: CT

address: 300 George Str

institute: Yale University

hyb_protocol: Hybridization buffer from the BeadChip kit (Illumina) was mixed with 1500 ng of biotin-labeled cRNA, heated to 65°C for 5 minutes, and then loaded onto the BeadChip. The BeadChips were sealed in a hybridization chamber and placed in an oven at 58°C with a rocker for 16-20 hours. After the hybridization, the BeadChips were washed and stained in a series of washes and stains as outlined in the Illumina protocol.

scan_protocol: The BeadChips were scanned on the Illumina Iscan.

data_processing: The data were normalised using quantile normalisation with lumi in R.

source_name: PBMC, severe disease, WNV

label_protocol: Preparation of cDNA, cRNA, and labeling were carried out by the Yale Center for Genomic Analysis using the standard Illumina protocols.

extract_protocol: Total RNA from PBMC and macrophage samples was extracted using the RNeasy mini kit (Qiagen, CA).

value: peripheral blood mononuclear cells (PBMCs)

tag: treatment

value: West Nile virus (WNV)

value: male

tag: batch

value: severe disease


title: 100035_PBMC_WNV


title: 110448_PBMC_WNV

source_name: PBMC, asymptomatic, WNV

value: asymptomatic


title: 100039_PBMC_WNV


title: 100034_PBMC_WNV


title: 100013_PBMC_WNV


title: 100016_PBMC_WNV


title: 110452_PBMC_WNV


title: 110141_PBMC_WNV


title: 110457_PBMC_WNV


title: 110460_PBMC_WNV


title: 110471_PBMC_WNV


title: 100014_PBMC_WNV


title: 100032_PBMC_WNV


title: 100017_PBMC_WNV


title: 110482_PBMC_WNV


title: 110485_PBMC_WNV


title: 110483_PBMC_WNV


title: 100019_PBMC_WNV


title: 100011_PBMC_WNV


title: 110440_PBMC_WNV


title: 100031_PBMC_WNV


title: 100015_PBMC_WNV


title: 100037_PBMC_WNV


title: 100033_PBMC_WNV


title: 110463_PBMC_WNV


title: 100022_PBMC_WNV


title: 110451_PBMC_WNV


title: 110139_PBMC_WNV


title: 110140_PBMC_WNV


title: 110137_PBMC_WNV


title: 100033_Macrophage_WNV

source_name: Macrophage, severe disease, WNV

value: macrophages


title: 100031_Macrophage_WNV


title: 110136_PBMC_WNV


title: 100035_Macrophage_WNV


title: 110134_PBMC_WNV


title: 100022_Macrophage_WNV


title: 110135_PBMC_WNV


title: 100014_Macrophage_WNV


title: 110039_PBMC_WNV


title: 110460_Macrophage_WNV


title: 110138_PBMC_WNV


title: 110054_PBMC_WNV


title: 100016_Macrophage_WNV


title: 100017_Macrophage_WNV


title: 110457_Macrophage_WNV


title: 100032_Macrophage_WNV


title: 100034_Macrophage_WNV


title: 100039_Macrophage_WNV


title: 100019_Macrophage_WNV


title: 100013_Macrophage_WNV


title: 100011_Macrophage_WNV


title: 100038_PBMC_WNV


title: 110485_Macrophage_WNV

source_name: Macrophage, asymptomatic, WNV


title: 100037_Macrophage_WNV


title: 110482_Macrophage_WNV


title: 110483_Macrophage_WNV


title: 100043_PBMC_WNV


title: 100015_Macrophage_WNV


title: 100012_Macrophage_WNV


title: 110138_Macrophage_WNV


title: 110440_Macrophage_WNV


title: 110136_Macrophage_WNV


title: 110139_Macrophage_WNV


title: 110452_Macrophage_WNV


title: 110463_Macrophage_WNV


title: 110460_Macrophage_PolyICH

source_name: Macrophage, severe disease, polyICH

value: PolyICH


title: 110451_Macrophage_WNV


title: 110137_Macrophage_WNV


title: 110448_Macrophage_WNV


title: 110039_Macrophage_WNV


title: 110140_Macrophage_WNV


title: 110471_Macrophage_WNV


title: 110134_Macrophage_WNV


title: 100043_Macrophage_WNV


title: 100037_Macrophage_PolyICH


title: 110054_Macrophage_WNV


title: 100034_Macrophage_PolyICH


title: 110141_Macrophage_WNV


title: 110135_Macrophage_WNV


title: 100038_Macrophage_WNV


title: 100019_Macrophage_PolyICH


title: 100013_Macrophage_PolyICH


title: 110457_Macrophage_PolyICH


title: 100032_Macrophage_PolyICH


title: 100031_Macrophage_PolyICH


title: 100035_Macrophage_PolyICH


title: 100033_Macrophage_PolyICH


title: 100039_Macrophage_PolyICH


title: 100022_Macrophage_PolyICH


title: 100017_Macrophage_PolyICH


title: 100014_Macrophage_PolyICH


title: 100015_Macrophage_PolyICH


title: 110483_Macrophage_PolyICH

source_name: Macrophage, asymptomatic, polyICH


title: 100012_Macrophage_PolyICH


title: 100016_Macrophage_PolyICH


title: 100011_Macrophage_PolyICH


title: 110485_Macrophage_PolyICH


title: 110482_Macrophage_PolyICH


title: 110440_Macrophage_PolyICH


title: 110448_Macrophage_PolyICH


title: 110451_Macrophage_PolyICH


title: 110141_Macrophage_PolyICH


title: 110054_Macrophage_PolyICH


title: 110136_Macrophage_PolyICH


title: 110460_Macrophage_MOCK

source_name: Macrophage, severe disease, mock

value: mock


title: 100038_Macrophage_PolyICH


title: 110452_Macrophage_PolyICH


title: 110135_Macrophage_PolyICH


title: 110039_Macrophage_PolyICH


title: 110140_Macrophage_PolyICH


title: 110134_Macrophage_PolyICH


title: 100037_Macrophage_MOCK


title: 110463_Macrophage_PolyICH


title: 110138_Macrophage_PolyICH


title: 100034_Macrophage_MOCK


title: 100013_Macrophage_MOCK


title: 100043_Macrophage_PolyICH


title: 100035_Macrophage_MOCK


title: 100039_Macrophage_MOCK


title: 100033_Macrophage_MOCK


title: 100031_Macrophage_MOCK


title: 100032_Macrophage_MOCK


title: 110139_Macrophage_PolyICH


title: 100022_Macrophage_MOCK


title: 110137_Macrophage_PolyICH


title: 100011_Macrophage_MOCK


title: 100016_Macrophage_MOCK


title: 100019_Macrophage_MOCK


title: 100012_Macrophage_MOCK


title: 100015_Macrophage_MOCK


title: 110483_Macrophage_MOCK

source_name: Macrophage, asymptomatic, mock


title: 100014_Macrophage_MOCK


title: 110471_Macrophage_MOCK


title: 110448_Macrophage_MOCK


title: 110482_Macrophage_MOCK


title: 110140_Macrophage_MOCK


title: 110485_Macrophage_MOCK


title: 110452_Macrophage_MOCK


title: 110440_Macrophage_MOCK


title: 110141_Macrophage_MOCK


title: 110451_Macrophage_MOCK


title: 110463_Macrophage_MOCK


title: 110138_Macrophage_MOCK


title: SOD1/miR155+/-

value: Spinal FACS sorted adult FCRLS+ microglia

tag: genotype/strain


title: Ly6CHi-SPL-SOD1/miR155+/-


title: Ly6CHi-SPL-SOD1/miR155-/-


title: Ly6CHi-SPL-WT


title: SOD1/miR155-/-


title: Non-Tg/miR155+/-


title: 110136_Macrophage_MOCK


title: 110139_Macrophage_MOCK


title: 110134_Macrophage_MOCK


title: fALS 701-013

source_name: Whole spinal cord homogenate - post mortem obtained from  ALS donor

label_protocol: MG447 microglial custom Nanostring codesets


title: 100043_Macrophage_MOCK


title: sALS 701-015


title: sALS 701-007


title: 110054_Macrophage_MOCK


title: 100038_Macrophage_MOCK


title: 110039_Macrophage_MOCK


title: 110457_Macrophage_MOCK


title: 110137_Macrophage_MOCK


title: sALS 701-001


title: HC A12-200

source_name: Whole spinal cord homogenate - post mortem obtained from non ALS donor

value: non ALS


title: fALS 701-006


title: sALS 701-002


title: sALS 701-005


title: 110471_Macrophage_PolyICH


title: HC A13-7


title: 110135_Macrophage_MOCK


title: HC A12-243


title: HC A13-14


title: HC A13-18


title: HC A12-5-112


title: HC A12-241


title: HC A13-17


title: 100017_Macrophage_MOCK


title: AHR_knockdown_BaP+FL_treated_2hpd_replicate2

city: Durham

first: Nishad

last: Jayasundara

address: A346, Research Drive, LSRC

department: Nicholas School of the Environment

institute: Duke University

description: Raw data file received truncated at 3393 rows of data

hyb_protocol: Standard Aglient protocol by Cogenics – Beckman Coulter Genomics

data_processing: Agilent Feature Extraction Software was used for background subtraction and LOWESS normalization.

organism: Danio rerio

source_name: Embryonic heart_AHR_Knockdown__2hpd

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: AB zebrafish (cmlc2::GFP)  were maintained according to Nusslein-Volhard (2002), and embryos were obtained for morpholino injections at 24 hpf and exposed to control (DMSO), BaP, FL and BaP+FL at 36 hpf. Hearts were extracted at 2, 6, 12, and 18 hours post dosing.

tag: tissue

tag: knockdown

tag: time extracted

value: BaP+FL

source_name: Pooled RNA from embryonic fibroblast cell line, Zf4 cells derived from one-day old zebrafish embryos

value: Fiberblast_Zf4 cells

value: 24h embryos


title: AHR_knockdown_BaP+FL_treated_2hpd_replicate1

scan_protocol: Standard Aglient protocol by Cogenics – Beckman Coulter Genomics

tag: age


title: AHR_knockdown_BaP+FL_treated_2hpd_replicate3

label_protocol: Standard Aglient protocol by Cogenics – Beckman Coulter Genomics


title: Control_BaP+FL_treated_2hpd_replicate2

description: Raw data file received truncated at 22226 rows of data

source_name: Embryonic heart_control_2hpd


title: Control_BaP+FL_treated_2hpd_replicate1


title: Control_FL_treated_2hpd_replicate3

value: FL


title: AHR_knockdown_FL_treated_2hpd_replicate3


title: AHR_knockdown_BaP_treated_2hpd_replicate2

description: Raw data file received truncated at 6873 rows of data

value: BaP


title: Control_FL_treated_2hpd_replicate4


title: Control_BaP+FL_treated_2hpd_replicate4


title: Control_DMSO_treated_6hpd_replicate1

source_name: Embryonic heart_control_6hpd

value: DMSO


title: AHR_knockdown_BaP_treated_2hpd_replicate4


title: Control_BaP+FL_treated_2hpd_replicate3


title: AHR_knockdown_BaP+FL_treated_2hpd_replicate4


title: Control_BaP_treated_2hpd_replicate3


title: AHR_knockdown_FL_treated_2hpd_replicate2


title: AHR_knockdown_BaP_treated_2hpd_replicate1


title: Control_BaP_treated_2hpd_replicate4


title: Control_FL_treated_2hpd_replicate1

description: Raw data file received truncated at 1801 rows of data


title: AHR_knockdown_BaP_treated_2hpd_replicate3


title: Control_FL_treated_2hpd_replicate2


title: sALS 701-004

tag: cell type

value: Whole spinal cord homogenate - post mortem

tag: phenotype

value: ALS


title: Control_BaP_treated_2hpd_replicate1


title: Control_BaP_treated_2hpd_replicate2


title: AHR_knockdown_FL_treated_2hpd_replicate1


title: AHR_knockdown_DMSO_treated_2hpd_replicate3


title: AHR_knockdown_DMSO_treated_2hpd_replicate1


title: AHR_knockdown_DMSO_treated_2hpd_replicate2


title: Control_DMSO_treated_2hpd_replicate4


title: Control_DMSO_treated_2hpd_replicate2


title: Control_DMSO_treated_2hpd_replicate1


title: Control_DMSO_treated_2hpd_replicate3


title: AHR_knockdown_FL_treated_18hpd_replicate2

source_name: Embryonic heart_AHR_Knockdown__18hpd


title: Control_BaP+FL_treated_18hpd_replicate4

source_name: Embryonic heart_control_18hpd


title: Control_BaP+FL_treated_18hpd_replicate3


title: AHR_knockdown_BaP_treated_18hpd_replicate1


title: Control_FL_treated_18hpd_replicate1


title: Control_BaP_treated_18hpd_replicate3


title: AHR_knockdown_BaP+FL_treated_18hpd_replicate2


title: Control_FL_treated_18hpd_replicate2


title: AHR_knockdown_BaP_treated_18hpd_replicate3


title: AHR_knockdown_BaP+FL_treated_18hpd_replicate1


title: AHR_knockdown_BaP+FL_treated_18hpd_replicate3


title: Control_BaP_treated_18hpd_replicate4


title: Control_FL_treated_18hpd_replicate3


title: AHR_knockdown_FL_treated_18hpd_replicate1


title: Control_BaP+FL_treated_18hpd_replicate1


title: Control_BaP_treated_18hpd_replicate1


title: AHR_knockdown_FL_treated_18hpd_replicate3


title: Control_BaP_treated_18hpd_replicate2


title: AHR_knockdown_BaP_treated_18hpd_replicate2


title: Control_BaP+FL_treated_18hpd_replicate2


title: AHR_knockdown_DMSO_treated_18hpd_replicate1


title: AHR_knockdown_DMSO_treated_18hpd_replicate2


title: AHR_knockdown_DMSO_treated_18hpd_replicate3


title: Control_DMSO_treated_18hpd_replicate2


title: Control_DMSO_treated_18hpd_replicate1


title: Control_DMSO_treated_18hpd_replicate3


title: AHR_knockdown_BaP+FL_treated_12hpd_replicate3

source_name: Embryonic heart_AHR_Knockdown__12hpd


title: AHR_knockdown_BaP+FL_treated_12hpd_replicate2


title: Control_BaP+FL_treated_12hpd_replicate3

source_name: Embryonic heart_control_12hpd


title: Control_BaP+FL_treated_12hpd_replicate2


title: Control_BaP+FL_treated_12hpd_replicate4


title: AHR_knockdown_FL_treated_12hpd_replicate3


title: AHR_knockdown_BaP_treated_12hpd_replicate2


title: AHR_knockdown_BaP+FL_treated_12hpd_replicate1


title: AHR_knockdown_BaP_treated_12hpd_replicate1


title: AHR_knockdown_FL_treated_12hpd_replicate1


title: Control_BaP+FL_treated_12hpd_replicate1


title: AHR_knockdown_DMSO_treated_12hpd_replicate3


title: Control_BaP_treated_12hpd_replicate2

description: Raw data file received truncated at 1820 rows of data


title: Control_DMSO_treated_12hpd_replicate4


title: AHR_knockdown_BaP_treated_12hpd_replicate3


title: Control_BaP_treated_12hpd_replicate1


title: Control_FL_treated_12hpd_replicate2


title: Control_BaP_treated_12hpd_replicate3


title: AHR_knockdown_FL_treated_12hpd_replicate2


title: Control_DMSO_treated_12hpd_replicate3


title: Control_FL_treated_12hpd_replicate3


title: Control_DMSO_treated_12hpd_replicate2

description: Raw data file received truncated at 13180 rows of data


title: AHR_knockdown_DMSO_treated_12hpd_replicate1


title: AHR_knockdown_DMSO_treated_12hpd_replicate2


title: Control_FL_treated_12hpd_replicate4


title: AHR_knockdown_BaP+FL_treated_6hpd_replicate3

source_name: Embryonic heart_AHR_Knockdown__6hpd


title: AHR_knockdown_BaP+FL_treated_6hpd_replicate2

description: Raw data file received truncated at 2864 rows of data


title: Control_BaP_treated_12hpd_replicate4


title: Control_FL_treated_12hpd_replicate1


title: Control_BaP+FL_treated_6hpd_replicate4


title: Control_DMSO_treated_12hpd_replicate1


title: Control_BaP+FL_treated_6hpd_replicate2

description: Raw data file received truncated at 3697 rows of data


title: Control_BaP+FL_treated_6hpd_replicate1


title: AHR_knockdown_BaP+FL_treated_6hpd_replicate1


title: AHR_knockdown_FL_treated_6hpd_replicate3


title: AHR_knockdown_FL_treated_6hpd_replicate2

description: Raw data file received truncated at 608 rows of data


title: Control_FL_treated_6hpd_replicate3


title: AHR_knockdown_FL_treated_6hpd_replicate1


title: Control_FL_treated_6hpd_replicate1


title: Control_FL_treated_6hpd_replicate2


title: AHR_knockdown_BaP_treated_6hpd_replicate3


title: AHR_knockdown_BaP_treated_6hpd_replicate2

description: Raw data file received truncated at 361 rows of data


title: Control_BaP_treated_6hpd_replicate2


title: AHR_knockdown_BaP_treated_6hpd_replicate1


title: Control_BaP_treated_6hpd_replicate3


title: AHR_knockdown_DMSO_treated_6hpd_replicate3


title: Control_BaP+FL_treated_6hpd_replicate3


title: AHR_knockdown_DMSO_treated_6hpd_replicate1

description: Raw data file received truncated at 213 rows of data


title: Control_DMSO_treated_6hpd_replicate3


title: Control_DMSO_treated_6hpd_replicate2


title: 646 gfp veh::2

city: RTP

first: NIEHS

last: Microarray Core

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: gene expression in Ishikawa cells with vector vehicle

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Ishikawa cells with vector vehicle

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: None.

extract_protocol: RNA was prepared with Trizol and clean up was via the Qiagen Rneasy Kit

treatment_protocol: All Ishikawa stable ERa cell lines were starved in phenol-red free DMEM:F12 +10% stripped FBS and were treated with vehicle (0.01% DMSO) or Estradiol (E2- 10nM) for 4 or 24hrs

value: endometrial cancer cells

value: vehicle


title: 646 h2nes 24hr::2

description: gene expression in Ishikawa cells with H2NES ERa 24hr 10nM E2 treatment

tag: infected cell line

value: H2NES ERa

value: 24 hr with 10nM Estradiol


title: 646 gfp 4hr::2

description: gene expression in Ishikawa cells with vector 4hr 10 nM E2 treatment

value: 4hr with 10nM Estradiol


title: 646 gfp veh::1


title: AHR_knockdown_DMSO_treated_6hpd_replicate2


title: 646 gfp 4hr::1

source_name: Ishikawa cells with vector 4hr 10 nM E2 treatment


title: 646 h2nes 4hr::2

description: gene expression in Ishikawa cells with H2NES ERa 4hr 10nM E2 treatment


title: 646 h2nes 4hr::3

source_name: Ishikawa cells with H2NES ERa 4hr 10nM E2 treatment


title: 646 gfp veh::3


title: 646 gfp 4hr::3


title: 646 h2nes veh::1

description: gene expression in Ishikawa cells with H2NES ERa vehicle

source_name: Ishikawa cells with H2NES ERa vehicle


title: 646 h2nes 24hr::3

source_name: Ishikawa cells with H2NES ERa 24hr 10nM E2 treatment


title: 646 h2nes veh::3


title: Control_BaP_treated_6hpd_replicate1


title: 646 aa 4hr::2

description: gene expression in Ishikawa cells with AA ERa 4hr 10nM E2 treatment

value: AA ERa


title: 646 h2nes 24hr::1


title: 646 aa 24hr::1

description: gene expression in Ishikawa cells with AA ERa 24hr 10nM E2 treatment


title: 646 h2nes veh::2


title: 646 aa veh::3

description: gene expression in Ishikawa cells with AA ERa vehicle

source_name: Ishikawa cells with AA ERa vehicle


title: 646 h2nes 4hr::1


title: 646 aa 24hr::3

source_name: Ishikawa cells with AA ERa 24hr 10nM E2 treatment


title: 646 h1 24hr::2

description: gene expression in Ishikawa cells with H1 ERa 24hr 10nM E2 treatment

value: H1 ERa


title: 646 aa 4hr::3

source_name: Ishikawa cells with AA ERa 4hr 10nM E2 treatment


title: 646 h1 veh::3

description: gene expression in Ishikawa cells with H1 ERa vehicle

source_name: Ishikawa cells with H1 ERa vehicle


title: 646 wt 24hr::3

description: gene expression in Ishikawa cells with WT ERa 24hr 10nM E2 treatment

value: WT ERa


title: 646 aa 24hr::2


title: 646 h1 4hr::3

description: gene expression in Ishikawa cells with H1 ERa 4hr 10nM E2 treatment


title: 646 h1 veh::2


title: 646 h1 veh::1


title: 646 h1 24hr::1

source_name: Ishikawa cells with H1 ERa 24hr 10nM E2 treatment


title: 646 aa 4hr::1


title: 646 aa veh::2


title: 646 wt 24hr::2

source_name: Ishikawa cells with WT ERa 24hr 10nM E2 treatment


title: 646 wt 4hr::3

description: gene expression in Ishikawa cells with WT ERa 4hr 10nM E2 treatment


title: 646 wt 4hr::1

source_name: Ishikawa cells with WT ERa 4hr 10nM E2 treatment


title: female sod155+/- s.c.

value: Spinal cord FACS sorted adult FCRLS+ microglia

value: B6SJL-Tg(SOD1-G93A)1Gur/J / miR-155+/-

value: female


title: 646 wt 4hr::2


title: female WT155+/- s.c.

source_name: Mouse -B6/SJL-miR-155+/- (female)


title: 646 h1 4hr::2

source_name: Ishikawa cells with H1 ERa 4hr 10nM E2 treatment


title: 646 wt veh ::1

description: gene expression in Ishikawa cells with WT ERa vehicle

source_name: Ishikawa cells with WT ERa vehicle


title: 646 wt veh ::3


title: 646 gfp 24hr::1

description: gene expression in Ishikawa cells with vector 24hr 10 nM E2 treatment

value: vector


title: 646 h1 4hr::1


title: 646 wt 24hr::1


title: female sod155-/- s.c.

value: B6SJL-Tg(SOD1-G93A)1Gur/J / miR-155-/-


title: 646 gfp 24hr::3

source_name: Ishikawa cells with vector 24hr 10 nM E2 treatment


title: 646 wt veh ::2


title: 646 gfp 24hr::2


title: male WT155+/- s.c.

source_name: Mouse -B6/SJL-miR-155+/- (male)

value: male


title: Sth1-Myc WT (replicate 2)

city: Rochester

first: Chhabi

last: Govind

state: mi

address: 333 Science and Engineering Building

department: Biological Sciences

institute: Oakland University

description: Biological replicate-2

hyb_protocol: manufacturer's recommended protocol was followed

scan_protocol: Affymetrix recommendation

data_processing:
Affymetrix GCOS software  and analyzed using Affymetrix Tiling Analysis Software (TAS).A two-sample analysis was conducted using two independently derived ChIP samples as the “treatment” group and two corresponding input samples as the “control” group for both wild type and gcn4∆ cells induced with SM.  Data were normalized using built-in quantile normalization and probe-level analysis with both perfect match and mismatch (PM/MM) probes and run with a bandwidth of 30.
Individual chromatin immunoprecipitated DNA was normalized to the corresponding input DNA are provided as .bar files

organism: Saccharomyces cerevisiae

source_name: Sth1-Myc ChIP_DNA_2

label_protocol: Labeled with biotinylated ddATP using terminal deoxynucleotidyl transferase

growth_protocol: Chromatin immunoprecipitation experiments were performed as described previously (Govind et al., 2012). Briefly, 100 ml of cells (A600 = 0.6) were cross-linked with 1% formaldehyde for 15 minutes at ambient temperature and quenched with glycine. Chromatin was isolated and fragmented by sonication (Branson450) to an average size of 300-400 base pairs. The soluble fraction of chromatin was used for ChIP using the appropriate antibodies.

extract_protocol: The ChIP and Input DNA was extracted by Phenol:Chloform method after reverse-crosslinking at 65 degree C, and after proteinase K treatment. DNA was fragmented with DNase prior to labeling

treatment_protocol: The cells were treated with 0.65 µM of sulfometuron methyl (SM; Chemservice, cat# N-13254) for 20 minutes and processed for ChIP analysis

value: Sulfometuron Methyl

tag: strain

value: BY4741 wild type yeast

tag: myc-tagged

tag: sample type

value: ChIP DNA

tag: antibodies

value: anti-Myc

value: input


title: Sth1-Myc WT (replicate 1)

description: Biological replicate-1

source_name: Sth1-Myc ChIP_DNA_1


title: Sth1-Myc gcn4Δ  (replicate 2)

description: Biological replicate-2

source_name: Sth1-Myc_gcn4Δ ChIP_DNA_2

value: BY4741 gcn4Δ yeast


title: Sth1-Myc gcn4Δ  (replicate 1)

description: Biological replicate-1

source_name: Sth1-Myc_gcn4Δ ChIP_DNA_1


title: male sod155+/- s.c.


title: male sod155-/- s.c.


title: STH1-TET_Rpb3_SC_DOX_2

description: Biological Replicate-2

hyb_protocol: The samples were lableled using BioPrime Array CGH Genomic Labeling Module kit and hybridized according to the Manufacturer's recommended protocol

scan_protocol: Agilent Technologies Scanner G2505B US45102973

data_processing: Data processed on R. Median normalization carried out.

label_protocol: manufacturer's recommended protocol was followed

treatment_protocol: The cells were either grown in SC or YPD. For inducing Gcn4, the cells were grown in SC and then treated with 0.65 µM of sulfometuron methyl (SM; Chemservice, cat# N-13254) for 20 minutes and processed for ChIP analysis. The kin28as/bur2Δ were treated with 1NA-PP1 and bur1as/ctk1Δ strains were treated with 3MB-PP1 before processing for cross-linking and chromatin preparation

value: Doxycycline

tag: promoter

tag: antibody

value: Rpb3 (Neoclone:W0012)

tag: parent strain


title: STH1-TET_Rpb3_SC_DOX_1

description: Bological Replicate-1

tag: treatment


title: STH1-TET_H3_SC_DOX_2

description: Biological Replicate-2


title: STH1-TET_Rpb3_SC_ND_2

description: Biological Replicate-2


title: STH1-TET_Rpb3_SM_ND_2

description: Biological Replicate-2

value: Sulfometuron methyl


title: STH1-TET_H3_SM_ND_2

description: Biological Replicate-2


title: STH1-TET_H3_SC_ND_2

description: Biological Replicate-2


title: STH1-TET_H3_SC_DOX_1

description: Bological Replicate-1


title: STH1-TET_Rpb3_SC_ND_1

description: Bological Replicate-1


title: STH1-TET_H3_SM_ND_1

description: Bological Replicate-1


title: kina28as/bur2Δ_Rpb3_SM_1

description: Bological Replicate-1

value: Sulfometuron methyl + 1NA-PP1


title: STH1-TET_H3_SC_ND_1

description: Bological Replicate-1


title: STH1-TET_Rpb3_SM_DOX_2

description: Biological Replicate-2

value: Sulfometuron methyl +Doxycycline


title: kina28as/bur2Δ_Rpb3_SC_2

description: Biological Replicate-2


title: STH1-TET_Rpb3_SM_ND_1

description: Bological Replicate-1


title: STH1-TET_Rpb3_SM_DOX_1

description: Bological Replicate-1


title: kina28as/bur2Δ_Rpb3_SC_1

description: Bological Replicate-1


title: kina28as/bur2Δ_Sth1_Myc_SM_2

description: Biological Replicate-2


title: kina28as/bur2Δ_Sth1_Myc_SC_1

description: Bological Replicate-1


title: kina28as/bur2Δ_Rpb3_SM_2

description: Biological Replicate-2


title: bur1as/ctk1Δ_Rpb3_SC_2

description: Biological Replicate-2


title: kina28as/bur2Δ_Sth1_Myc_SC_2

description: Biological Replicate-2


title: bur1as/ctk1Δ_Rpb3_SC_1

description: Bological Replicate-1


title: kina28as/bur2Δ_Sth1_Myc_SM_1

description: Bological Replicate-1


title: bur1as/ctk1Δ_Sth1_Myc_SM_2

description: Biological Replicate-2

value: Sulfometuron methyl + 3MB-PP1


title: bur1as/ctk1Δ_Sth1_Myc_SC_2

description: Biological Replicate-2