title: West Nile virus NY99 (WNV)

description:
Table 3, Table 4
West Nile Virus New York 1999

source_name: WNV RNA from infected tissue culture cells

value: West Nile virus NY99 (WNV)

value: West Nile Virus New York 1999


title: Aerobic peroxynitrite chemostat culture 3. Slide 1

status: Public on May 24 2010

type: RNA

city: Sheffield

first: Robert

last: Poole

state: South Yorkshire

address: Firth Court, Western Bank

department: Molecular Biology & Biotechnology

country: United Kingdom

institute: University of Sheffield

description: no additional information

hyb_protocol: The Cy3-dCTP-labelled sample was mixed with the Cy5-dCTP-labelled sample and re-suspended in 120 ml salt-based hybridisation buffer (supplied with the microarray slides).  This was heated at 95 oC for 3 min then cooled on ice for 3 min.  The mixture was pipetted onto a microarray slide, sealed with a GeneFrame and coverslip in a hybridization chamber and incubated for 18 h at 42 °C.  Following hybridization, microarray slides (minus GeneFrame and coverslip) were washed in a series of pre-warmed (37 °C) SSC buffers for 5 min each at 37oC: 1× SSC/0.1 % SDS, 1× SSC, 0.2× SSC and 0.01× SSC.  Microarray slides were dried by centrifugation at 500 × g for 2 min before scanning.

scan_protocol: Slides were scanned on an Affymetrix 428 scanner.  The average signal intensity and local background correction were obtained using a commercially available software package from Biodiscovery, Inc (Imagene, version 4.0 and GeneSight, version 3.5).

data_processing: Spots automatically flagged as bad, negative or poor in the Imagene software were removed before the statistical analysis was carried out in GeneSight.  The mean values from each channel were log2 transformed and normalised using the Lowess method to remove intensity-dependent effects in the log2(ratios) values.  The Cy3/Cy5 fluorescent ratios were calculated from the normalized values.

molecule: total RNA

organism: Escherichia coli

source_name: Steady-state continuous cultured control aerobic samples in absence of peroxynitrite

label_protocol:
The labelling procedure uses equal quantities of RNA from adequate hydrogen peroxide and control samples
Approximately 9 µg RNA was annealed to 4.5 µg pd(N)6 random hexamers (Amersham Biosciences) by heating at 65 oC for 10 min, followed by 10 min at 22 oC and cooling on ice for 2 min. This was supplemented with 6 ml of 5× First-strand buffer (Invitrogen), 2.5 ml dNTP mixture (5 mM each dATP, dTTP, dGTP and 2 mM dCTP), 3 ml 0.1 M DTT, 2 ml 1 mM Cy5 (Perkin Elmer) and 1.5 ml Superscript III reverse transcriptase (200 U) (Invitrogen).  This was incubated at 42 oC for 3 hours.  The reaction was terminated by the addition of NaOH (7.5 ml of 1M) and HCl (7.5 ml of 1M) before the addition of TE buffer (300 ml).  Labelled cDNA was purified using a Qiaquick purification kit (Qiagen).

growth_protocol: Escherichia coli strain MG1655 was grown in a New Brunswick Scientific Bioflow III Biofermentor under continuous culture (chemostat) conditions. Cells were grown in defined media containing 2 mM glycerol as the sole and limiting source of energy and carbon. The working volume was 1 litre, and the dilution rate 0.2 h-1. For aerobic growth, the air-flow rate was 1 l/min, and the dissolved oxygen tension was maintained at 40% air saturation

extract_protocol: Samples (10 ml) were harvested directly into RNA Protect (Qiagen) to stabilize RNA, and total RNA was purified using Qiagen’s RNeasy Mini kit as recommended by the suppliers.  RNA was quantified using a BioPhotometer (Eppendorf).

treatment_protocol: At steady-state, peroxynitrite was added to the chemostat culture and to the nutrient feed at a final concentration of 300 uM. Samples were removed immediately prior to and 5 minutes after injection of peroxynitrite

tag: stress

value: control

tag: strain

value: Wild type strain MG1655

source_name: Steady-state continuous cultured control aerobic samples in presence of 300uM peroxynitrite for 5 minutes

value: 300uM peroxynitrite


title: Aerobic peroxynitrite chemostat culture 2. Slide 2

description: no additional information


title: Negative Control (Vero cell tissue culture supernatant) 01

city: New York

first: Omar

last: Jabado

state: NY

address: 722 W 168 Street 17th Fl

department: Epidemiology

country: USA

institute: Columbia University

description:
Table 3
Monkey

hyb_protocol: 65C overnight hybridization on a Agilent rotating incubator

scan_protocol: Agilent scanner 5um

data_processing: Cy3 Median Signal - Background; gMedianSignal - gBGMedianSignal (Agilent data labels).  No further processing, since non-parametric methods were used to analyze the data.

organism: Chlorocebus aethiops

source_name: RNA extracted from vero cell tissue culture

label_protocol: Total RNA conversion to cDNA with degenerate oligonucleotide primers containing a known sequence tag, then amplification using primers specific to the tag that incorporate a Genisphere 3DNA-Cy3 binding sequence

growth_protocol: infection of permissive tissue culture cell lines until cytopathic effect was observed

extract_protocol: Trizol RNA extraction followed by isopropanol precipitation

treatment_protocol: viral infection

tag: target

tag: experiment type

value: Negative Control

tag: sample type

value: Monkey


title: Negative Control (200ng Human Lung RNA) 04

description: Table 3

organism: Homo sapiens

source_name: RNA extacted from human lung tissue

value: RNA extacted from human lung tissue


title: West Nile Virus NY99 (10^4 Copies, 10ng Human Lung RNA) 04

description:
Table 1
West Nile Virus New York 1999

organism: West Nile virus

source_name: WNV RNA from infected tissue culture, quantified by TaqMan Real-Time PCR

tag: virus accession number

tag: virus taxon id

value: Known Input Virus Hybridization


title: Human herpesvirus 1 (HSV-1)

description:
Table 3, Table 4
Human herpesvirus 1

organism: Human alphaherpesvirus 1

source_name: HSV-1 RNA from infected tissue culture cells

value: Human herpesvirus 1 (HSV-1)

value: Virus Hybridization

value: Human herpesvirus 1


title: Influenza A H1N1 Texas 1991 (FLUA-H1N1)

description:
Table 3, Table 4
Influenza A H1N1 Texas 1991

organism: Influenza A virus (A/Texas/36/1991(H1N1))

source_name: FLUA-H1N1 RNA from infected tissue culture cells

value: Influenza A H1N1 Texas 1991 (FLUA-H1N1)

value: Influenza A H1N1 Texas 1991


title: Lassa virus strain Josiah (LASV)

description:
Table 3, Table 4
Lassa virus strain Josiah

organism: Lassa virus Josiah

source_name: LASV RNA from infected tissue culture cells

value: Lassa virus strain Josiah (LASV)

value: Lassa virus strain Josiah


title: Negative Control (primers alone, no Human Lung RNA)

type: other

description: Figure 1, Table 1, Table 3

molecule: other

organism: artificial sequences

source_name: water input control

value: water input control


title: Human Echovirus 18 Metcalf (EV18)

description:
Table 3, Table 4
Human Echovirus 18 strain Metcalf

organism: Echovirus E18

source_name: EV18 RNA from infected tissue culture cells

value: Human Echovirus 18 Metcalf (EV18)

value: Human Echovirus 18 strain Metcalf


title: SARS Human Coronavirus Tor2 (HCoV-SARS)

description:
Table 3, Table 4
SARS Human Coronavirus strain Tor2

organism: SARS coronavirus Tor2

source_name: HCoV-SARS RNA from infected tissue culture cells

value: SARS Human Coronavirus Tor2 (HCoV-SARS)

value: SARS Human Coronavirus strain Tor2


title: Aerobic peroxynitrite chemostat culture 2. Slide 1

description: no additional information

value: control

value: Wild type strain MG1655

value: 300uM peroxynitrite


title: Negative Control (200ng Human Lung RNA) 03

description: Table 3

value: Negative Control

value: RNA extacted from human lung tissue


title: Aerobic peroxynitrite chemostat culture 1. Slide 2

description: no additional information


title: Human adenovirus 4 (HAdV-4)

description:
Table 3, Table 4
Human adenovirus 4

organism: Human adenovirus 4

source_name: HAdV-4 RNA from infected tissue culture cells

value: Human adenovirus 4 (HAdV-4)

value: Human adenovirus 4


title: Aerobic peroxynitrite chemostat culture 1. Slide 1

description: no additional information


title: Negative Control (200ng Human Lung RNA) 01

description: Figure 1, Table 1, Table 3


title: Negative Control (200ng Human Lung RNA) 02

description: Table 3


title: dosSKO_rep2

status: Public on May 22 2010

city: Aurora

first: Ryan

middle: William

last: Honaker

state: CO

department: Microbiology

institute: University of Colorado Denver

hyb_protocol: Arrays were prehybridized in water, SSC, BSA, and SDS. Labeling reaction was concentrated to 5ul in a microcon 10 filter tube, added to tRNA, SSC, formamide, and SDS, and heated to 98 C for two minutes. Samples were hybridzed overnight at 50 C.

scan_protocol: Scanned on Molecular Device's Genepix 4000B

data_processing: see Voskuil, et al., J Exp Med. 2003 Sep 1;198(5):705-13. Significance Analysis of Microarrys (SAM) (http://www-stat.stanford.edu/~tibs/SAM/) was used to determine statistically significant induced genes in the ∆dosT experiments. See Tusher, et al., Proc Natl Acad Sci 98:5116-21

organism: Mycobacterium tuberculosis H37Rv

source_name: total RNA from aerobic cultures

label_protocol: 1.5 ug of RNA was primed with N6 primers, heated for two minutes at 98 C, then incubated 10 minutes at 25 C followed by 90 minutes at 42 C. 5mM A,G,C and 0.2mM T dNTP mix was used.

extract_protocol: Cell pellets were flash frozen on dry ice, resuspended in Trizol, and bead-beaten 3 x 40 seconds. Resulting cell lysate was added to chloroform and nucleic acids were then precipitated in isopropanol, rehydrated in 75% ethanol, then DNAse treated. Fur further purification, Quiagen RNeasy kit was used according to the manufacturer's instructions.

value: M. tuberculosis H37Rv strain ΔdosS

tag: growth

value: logarithmic phase aerobic cultures, OD600 of 0.2

source_name: total RNA from aerobic cultures with the addition of 20mM ascorbate for 1 hour


title: fat_female_High feeding level_animal 22

city: Madrid

first: Ana

middle: I

last: Fernandez

state: Madrid

address: Ctra. Coruña Km 7.5

department: Mejora Genética Animal

country: Spain

institute: INIA

description: Iberian pig breed

hyb_protocol: Standard Affymetrix protocol

scan_protocol: GCOS

data_processing: Bioconductor, GCRMA

label: biotin

organism: Sus scrofa

source_name: fat sample at 211 days, female, high

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol, MIAME recommendations

growth_protocol: Pigs were fed twice daily with the same pelleted diet until feeding restriction treatment

extract_protocol: RiboPure RNA isolation kit

treatment_protocol: Liver and fat samples were mantained at -80ºC

tag: gender

value: female

tag: breed

value: Iberian

tag: tissue

value: subcutaneous backfat


title: dosTKO_rep1

value: M. tuberculosis H37Rv strain ΔdosT


title: dosTKO_rep3


title: fat_female_Low feeding level_animal 20

description: Iberian pig breed

source_name: fat sample at 211 days, female, low


title: dosTKO_rep2


title: liver_female_Low feeding level_animal 21

description: Iberian pig breed

source_name: liver sample at 211 days, female, low

value: liver


title: liver_male_High feeding level_animal 17

description: Iberian pig breed

source_name: liver sample at 211 days, male, high

value: male


title: dosSKO_rep1


title: fat_male_High feeding level_animal 14

description: Iberian pig breed

source_name: fat sample at 211 days, male, high


title: fat_male_Low feeding level_animal 16

description: Iberian pig breed

source_name: fat sample at 211 days, male, low


title: liver_female_Low feeding level_animal 18

description: Iberian pig breed


title: liver_male_Low feeding level_animal 16

description: Iberian pig breed

source_name: liver sample at 211 days, male, low


title: fat_female_High feeding level_animal 21

description: Iberian pig breed


title: fat_female_Low feeding level_animal 23

description: Iberian pig breed


title: liver_female_High feeding level_animal 19

description: Iberian pig breed

source_name: liver sample at 211 days, female, high


title: AL1114 Biological Replicate 2

city: St Lucia

first: Jason

last: Steen

address: Carmody Road

department: IMB

country: Australia

institute: University of Queensland

description: acapasular strain, SNP in Fis results in L28S

hyb_protocol: Combimatrix chips were hybridised as per manufacturers instructions.

scan_protocol: Hybridised arrays were scanned on a Genepix 4000b.  PMT used was max PMT with less than 20 saturated spots.

data_processing: Raw spot intensities were extracted using Microarray Imager V5.9.3 (combimatrix).  Background correction was performed using the LIMMA normexp method, and the log2 values calculated. Between-array quantile normalization was then applied to the log intensities. Spots from duplicate probes were averaged, and the averaged probe intensities analyzed using the LIMMA software package. A moderated t-test on the normalized log intensities was performed to identify significantly differing probe intensities. Probes were sorted by significance, and the False Discovery Rate used to control for multiple testing.

organism: Pasteurella multocida

source_name: Total Bacteria

label_protocol: 5ug total RNA was Reverse transcribed to cDNA with random hexamers and SuperScriptIII RT.  cDNA was NaOH treated to remove RNA contamination, and purified using Qiagen minElute columns.  2ug purified cDNA was labelled with KREAtech Cy-3-ULS.

growth_protocol: Bacteria were grown in BHI broth to OD600=~0.6

extract_protocol: Bacteria were pelleted by centrifugation, and Total RNA extracted using TRIzol.  Total RNA was DNAse treated and further purified on Rneasy mini columns

tag: capsule

value: Negative


title: fat_male_Low feeding level_animal 15

description: Iberian pig breed


title: liver_female_High feeding level_animal 20

description: Iberian pig breed


title: fat_male_High feeding level_animal 17

description: Iberian pig breed


title: liver_male_Low feeding level_animal 15

description: Iberian pig breed


title: liver_male_High feeding level_animal 14

description: Iberian pig breed


title: 12hr Cortisol +6hr LPS leukocytes 2204

status: Public on May 21 2010

city: New Brunswick

first: Stephen

middle: F

last: Lowry

state: NJ

address: 125 Paterson St

department: Surgery

institute: UMDNJ

description: 12hr Cortisol +6hr LPS

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Focus Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with GeneSpring GX11.0.1 - RMA - baseline transformation, log2 transformation

source_name: Healthy Volunteers

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

tag: id

tag: disease status

value: healthy volunteers

tag: cell type

value: Leukocytes

tag: treatment group

value: 12hr Cortisol +6hr LPS


title: 24hr post Cortisol+LPS leukocytes 2212

description: 24hr post Cortisol+LPS

value: 24hr post Cortisol+LPS


title: 12hr Cortisol +6hr LPS leukocytes 2201

description: 12hr Cortisol +6hr LPS


title: 12hr Cortisol +6hr LPS leukocytes 2203

description: 12hr Cortisol +6hr LPS


title: 24hr post Cortisol+LPS leukocytes 2204

description: 24hr post Cortisol+LPS


title: 24hr post Cortisol+LPS leukocytes 2201

description: 24hr post Cortisol+LPS


title: 6hr Cortisol leukocytes 2203

description: 6hr Cortisol

value: 6hr Cortisol


title: 12hr Cortisol +6hr LPS leukocytes 2212

description: 12hr Cortisol +6hr LPS


title: 12hr Cortisol +6hr LPS leukocytes 2205

description: 12hr Cortisol +6hr LPS


title: 12hr Cortisol +6hr LPS leukocytes 2202

description: 12hr Cortisol +6hr LPS


title: 24hr post Cortisol+LPS leukocytes 2206

description: 24hr post Cortisol+LPS


title: 24hr post saline+LPS leukocytes 2209

description: 24hr post saline+LPS

value: 24hr post saline+LPS


title: 24hr post saline+LPS leukocytes 927

description: 24hr post saline+LPS


title: 6hr Cortisol leukocytes 2212

description: 6hr Cortisol


title: 24hr post Cortisol+LPS leukocytes 2202

description: 24hr post Cortisol+LPS


title: 6hr Cortisol leukocytes 2205

description: 6hr Cortisol


title: 6hr Cortisol leukocytes 2206

description: 6hr Cortisol


title: 24hr post Cortisol+LPS leukocytes 2203

description: 24hr post Cortisol+LPS


title: 24hr post saline+LPS leukocytes 2207

description: 24hr post saline+LPS


title: 24hr post saline+LPS leukocytes 2210

description: 24hr post saline+LPS


title: 6hr Cortisol leukocytes 2202

description: 6hr Cortisol


title: 6hr Cortisol leukocytes 2204

description: 6hr Cortisol


title: 12hrs saline +6hr LPS leukocytes 2210

description: 12hrs saline +6hr LPS

value: 12hrs saline +6hr LPS


title: 12hr Cortisol +6hr LPS leukocytes 2206

description: 12hr Cortisol +6hr LPS


title: 6hrs of saline leukocytes 2207

description: 6hrs of saline

value: 6hrs of saline


title: 12hrs saline +6hr LPS leukocytes 2208

description: 12hrs saline +6hr LPS


title: 12hrs saline +6hr LPS leukocytes 921

description: 12hrs saline +6hr LPS


title: 12hrs saline +6hr LPS leukocytes 2207

description: 12hrs saline +6hr LPS


title: 6hrs of saline leukocytes 2210

description: 6hrs of saline


title: 24hr pre-treatment leukocytes 2203

description: 24hr pre-treatment

value: 24hr pre-treatment


title: 24hr pre-treatment leukocytes 2206

description: 24hr pre-treatment


title: 24hr pre-treatment leukocytes 2212

description: 24hr pre-treatment


title: 6hrs of saline leukocytes 2208

description: 6hrs of saline


title: 24hr pre-treatment leukocytes 2201

description: 24hr pre-treatment


title: 24hr pre-treatment leukocytes 2205

description: 24hr pre-treatment


title: 24hr pre-treatment leukocytes 2202

description: 24hr pre-treatment


title: 24hr pre-treatment leukocytes 927

description: 24hr pre-treatment


title: 24hr pre-treatment leukocytes 2210

description: 24hr pre-treatment


title: 24hr post Cortisol+LPS monocytes 2201

description: 24hr post Cortisol+LPS

value: Monocytes


title: 6hr Cortisol monocytes 2206

description: 6hr Cortisol


title: 24hr post Cortisol+LPS monocytes 2204

description: 24hr post Cortisol+LPS


title: 6hr Cortisol monocytes 2205

description: 6hr Cortisol


title: 24hr pre-treatment leukocytes 2207

description: 24hr pre-treatment


title: 24hr post Cortisol+LPS monocytes 2205

description: 24hr post Cortisol+LPS


title: 12hr Cortisol +6hr LPS monocytes 2206

description: 12hr Cortisol +6hr LPS


title: 24hr post Cortisol+LPS monocytes 2203

description: 24hr post Cortisol+LPS


title: 12hr Cortisol +6hr LPS monocytes 2201

description: 12hr Cortisol +6hr LPS


title: 24hr post Cortisol+LPS monocytes 2206

description: 24hr post Cortisol+LPS


title: 6hr Cortisol monocytes 2202

description: 6hr Cortisol


title: 12hr Cortisol +6hr LPS monocytes 2205

description: 12hr Cortisol +6hr LPS


title: 12hr Cortisol +6hr LPS monocytes 2212

description: 12hr Cortisol +6hr LPS


title: West Nile Virus NY99 (10^4 Copies, 200ng Human Lung RNA) 07

description:
Table 1
West Nile Virus New York 1999

source_name: WNV RNA from infected tissue culture, quantified by TaqMan Real-Time PCR

value: Known Input Virus Hybridization


title: 12hr Cortisol +6hr LPS monocytes 2204

description: 12hr Cortisol +6hr LPS


title: 6hr Cortisol monocytes 2203

description: 6hr Cortisol


title: 24hr post saline+LPS monocytes 2207

description: 24hr post saline+LPS


title: 24hr post Cortisol+LPS monocytes 2202

description: 24hr post Cortisol+LPS


title: 12hr Cortisol +6hr LPS monocytes 2202

description: 12hr Cortisol +6hr LPS


title: 12hrs saline +6hr LPS monocytes 2209

description: 12hrs saline +6hr LPS


title: 24hr post saline+LPS monocytes 2210

description: 24hr post saline+LPS


title: 12hrs saline +6hr LPS monocytes 2208

description: 12hrs saline +6hr LPS


title: 6hrs of saline monocytes 2210

description: 6hrs of saline


title: 12hrs saline +6hr LPS monocytes 2210

description: 12hrs saline +6hr LPS


title: 6hrs of saline monocytes 2207

description: 6hrs of saline


title: 24hr post saline+LPS monocytes 931

description: 24hr post saline+LPS


title: 24hr pre-treatment monocytes 2204

description: 24hr pre-treatment


title: 24hr pre-treatment monocytes 2201

description: 24hr pre-treatment


title: 24hr post saline+LPS monocytes 2209

description: 24hr post saline+LPS


title: 6hrs of saline monocytes 2209

description: 6hrs of saline


title: 12hrs saline +6hr LPS monocytes 2207

description: 12hrs saline +6hr LPS


title: 24hr pre-treatment monocytes 2207

description: 24hr pre-treatment


title: 24hr pre-treatment monocytes 2210

description: 24hr pre-treatment


title: 24hr pre-treatment monocytes 2205

description: 24hr pre-treatment


title: 24hr pre-treatment monocytes 2209

description: 24hr pre-treatment


title: 24hr pre-treatment monocytes 2208

description: 24hr pre-treatment


title: 24hr pre-treatment monocytes 2203

description: 24hr pre-treatment


title: 24hr pre-treatment monocytes 2202

description: 24hr pre-treatment


title: Negative Control (10ng Human Lung RNA)

description: Figure 1, Table 1, Table 3

source_name: RNA extacted from human lung tissue

value: Negative Control (10ng Human Lung RNA)

value: Negative Control

value: RNA extacted from human lung tissue


title: PBC_16w_2

city: Stanford

first: Keiichi

last: Kodama

state: CA

address: 269 Campus Drive, Room 2225

department: Department of Medicine, Division of Immunology & Rheumatology

institute: Stanford Univeristy School of Medicine

description: PBC_16w_2; VALUE=LOG(NOD/NOD.B10)

hyb_protocol: as described in In situ Hybridization kit-plus

scan_protocol: Agilent scanner, manufacturer's protocol

data_processing: Agilent Feature Extraction software 8.5

organism: Mus musculus

source_name: NOD

label_protocol: Agilent Low RNA Input Fluorescent Linear Amplification Kit

extract_protocol: Qiagen RNeasy

tag: tissue type

value: peripheral blood cells

tag: age

value: 16 weeks

tag: disease state

value: diabetic


title: PBC_20w_2

description: PBC_20w_2; VALUE=LOG(NOD/NOD.B10)

value: 20 weeks


title: PBC_16w_7

description: PBC_16w_7; VALUE=LOG(NOD/NOD.B10)


title: PBC_20w_4

description: PBC_20w_4; VALUE=LOG(NOD/NOD.B10)


title: PBC_16w_6

description: PBC_16w_6; VALUE=LOG(NOD/NOD.B10)


title: PBC_16w_4

description: PBC_16w_4; VALUE=LOG(NOD/NOD.B10)


title: PBC_16w_1

description: PBC_16w_1; VALUE=LOG(NOD/NOD.B10)


title: PBC_20w_1

description: PBC_20w_1; VALUE=LOG(NOD/NOD.B10)


title: PBC_20w_3

description: PBC_20w_3; VALUE=LOG(NOD/NOD.B10)


title: PBC_16w_5

description: PBC_16w_5; VALUE=LOG(NOD/NOD.B10)


title: PBC_12w_5

description: PBC_12w_5; VALUE=LOG(NOD/NOD.B10)

value: 12 weeks


title: PBC_16w_3

description: PBC_16w_3; VALUE=LOG(NOD/NOD.B10)


title: PBC_12w_6

description: PBC_12w_6; VALUE=LOG(NOD/NOD.B10)


title: PBC_12w_7

description: PBC_12w_7; VALUE=LOG(NOD/NOD.B10)


title: PBC_12w_2

description: PBC_12w_2; VALUE=LOG(NOD/NOD.B10)


title: PBC_12w_1

description: PBC_12w_1; VALUE=LOG(NOD/NOD.B10)


title: PBC_12w_4

description: PBC_12w_4; VALUE=LOG(NOD/NOD.B10)


title: PBC_12w_8

description: PBC_12w_8; VALUE=LOG(NOD/NOD.B10)


title: PBC_10d_8

description: PBC_10d_8; VALUE=LOG(NOD/NOD.B10)

value: 10 days


title: PBC_12w_3

description: PBC_12w_3; VALUE=LOG(NOD/NOD.B10)


title: PBC_8w_5

description: PBC_8w_5; VALUE=LOG(NOD/NOD.B10)

value: 8 weeks


title: PBC_4w_3

description: PBC_4w_3; VALUE=LOG(NOD/NOD.B10)

value: 4 weeks


title: PBC_8w_4

description: PBC_8w_4; VALUE=LOG(NOD/NOD.B10)


title: PBC_8w_3

description: PBC_8w_3; VALUE=LOG(NOD/NOD.B10)


title: PBC_8w_2

description: PBC_8w_2; VALUE=LOG(NOD/NOD.B10)


title: PBC_8w_1

description: PBC_8w_1; VALUE=LOG(NOD/NOD.B10)


title: PBC_8w_7

description: PBC_8w_7; VALUE=LOG(NOD/NOD.B10)


title: PBC_10d_7

description: PBC_10d_7; VALUE=LOG(NOD/NOD.B10)


title: PBC_4w_2

description: PBC_4w_2; VALUE=LOG(NOD/NOD.B10)


title: PBC_10d_3

description: PBC_10d_3; VALUE=LOG10(NOD/NOD.B10)


title: PBC_4w_1

description: PBC_4w_1; VALUE=LOG(NOD/NOD.B10)


title: PBC_10d_6

description: PBC_10d_6; VALUE=LOG(NOD/NOD.B10)


title: PBC_10d_2

description: PBC_10d_2; VALUE=LOG10(NOD/NOD.B10)


title: PBC_10d_1

description: PBC_10d_1; VALUE=LOG10(NOD/NOD.B10)


title: Periodontal Plaque 17 (HOMIM-v.03)

type: genomic

city: Boston

first: Bruce

middle: J

last: Paster

state: MA

address: 140 Fenway

institute: The Forsyth Institute

description: 16S rRNA genes are PCR amplified from DNA extracts using 16S rRNA universal forward and reverse primers and labeled via incorporation of Cy3-dCTP in a second nested PCR.

hyb_protocol: Prior to hybridization, slides were blocked with sodium borohydride (NaBH4, 1X PBS, 99% ethanol) in order to reduce unreactive aldehyde groups, thus minimizing the fluorescent background.  Fourteen microliter of each labeled and purified PCR sample were mixed with 6 µl of hybridization buffer containing 2X SSC, 0.2 µg/µl yeast tRNA, 0.1% SDS, and heated for 5 minutes at 100oC. After that, 10 µl of each solution were loaded slowly at one corner and under the cover slip, allowing capillary action to pull the solution over the array. Slides were then placed on incubation racks in a humidified chamber, and hybridization was then performed at 55oC for 16 h in a microarray incubator. Slides were removed from the hybridization chamber and sunk into a water bath containing a washing solution (2X SSC, 10%SDS, at 55oC) to remove the cover slips. The slides were washed using an automated microarray robotic instrument. A washing program was set up as follow: one washing in buffer (2X SSC, 10%SDS) at 55oC for 2 minutes, a second washing in 2X SSC buffer at room temperature for 2 minutes, and a final washing in 0.1X SSC buffer at room temperature for 2 minutes. Once the slides are finished spinning in the centrifuge, they were removed and placed in a light-proof container until scanning.

scan_protocol: The microarray slides are scanned using an Axon 4000B scanner and crude data is extracted using GenePix Pro software. Data are normalized by comparing individual signal intensities to the average of signals from universal probes.

data_processing: Individual probe spot net intensity was calculated by subtracting the foreground intensity (F532) with background intensity (B532); intensity was set to 1 if net intensity is <1 or signal to noise ratio (F532/B532) < 2; between-the-array signal normalization was done based on mean universal 16S sequence probe intensities; signals were also scaled to be within the same minimal and maximal intensities range across arrays; normalized and scaled intensities of the same probe sequence were then averaged. The averaged unique probe intensities were then raised to the power of 0.3 and then converted to ordinal numbers on a 0-5 scale, with 0=not detected and 1 to 5 reflect increasing signal strength. For detail analysis procedure see: http://bioinformatics.forsyth.org/homim

molecule: genomic DNA

source_name: Periodontal Plaque

label_protocol: Two separate PCR reactions were set up with, respectively, forward primer 5´-CCA GAG TTT GAT YMT GGC-3´ with reverse primer  5´-GAA GGA GGT GWT CCA RCC GCA -3´, and forward primer 5´-GAC TAG AGT TTG ATY MTG GC-3´ with reverse primer 5´-GYT ACC TTG TTA CGA CTT-3´.  Two µl of genomic DNA template were added to the reaction mixture (final volume 25 µl) containing 20 pmol of each primer, 40 nmol  of deoxytriphosphates, 1.5 mM Mg2+ and 1 U of Platinum  High Fidelity Taq polymerase (Invitrogen, San Diego, CA). The samples were preheated at 94°C for 2 min, followed by 32 cycles of amplification under the following conditions: 94°C for 30 s, 55°C for 30 s, and 68°C for 1.5 min, with an additional 1 s for each cycle. A final 10 min elongation step at 68°C was added. The results of the PCR amplification were examined by electrophoresis in a 1% agarose gel. The two parallel PCR reactions were combined and the products purified with QIAquick PCR Purification Kit (Qiagen).Purified PCR products were labeled via the incorporation of Cy3-dCTP during a second reaction. Briefly, 7 μL of each product were added into a 25 μL reaction mixture containing 15 pmol of the forward primer 9F (5`-GAGTTTGATYMTGGCTCAG-3`) , 5 pmol of the 1492R primer , 2.5 μL 10•X high fidelity PCR buffer, 2 mM MgSO4, 2.5 μL of deoxynucleotide triphosphate mixture without deoxycytidine triphosphate (10 mM, 0.2 mM final concentration of each deoxynucleotide), 2.5 μL of deoxycytidine triphosphate mixture (1 μL of 1 mM Cy3-dCTP + 4 μL of 2 mM dCTP, 0.2 mM final concentration), 0.25 μL 10% Triton X, and 1.25 U Taq polymerase. The PCR program included an initial denaturation step at 94oC for 2 minutes, followed by 40 cycles of denaturation at 94oC for 30s, annealing at 55oC for 30s, elongation at 68C for 1.5 minute with an additional 1 s for each cycle, and a final elongation step at 68oC for 10 minutes.

extract_protocol: Bacterial DNA was eluted from PerioPaper strips (GCF) and from paper points (subgingival sample), respectively, per patient using 400 ml buffer (1 × 388 PBS or TE). Genomic DNA was then extracted using the QiaAmp DNA isolation kit 389 (QiaGen)

value: periodontitis

value: Subgingival paper point


title: PBC_8w_6

description: PBC_8w_6; VALUE=LOG(NOD/NOD.B10)


title: Periodontal Plaque 11 (HOMIM-v.03)


title: Periodontal Plaque 14 (HOMIM-v.03)


title: Periodontal Plaque 10 (HOMIM-v.03)


title: Periodontal Plaque 13 (HOMIM-v.03)


title: Periodontal Plaque 8 (HOMIM-v.03)


title: Periodontal Plaque 16 (HOMIM-v.03)


title: Periodontal Plaque 12 (HOMIM-v.03)


title: PBC_10d_4

description: PBC_10d_4; VALUE=LOG10(NOD/NOD.B10)


title: Periodontal Plaque 7 (HOMIM-v.03)


title: PBC_10d_5

description: PBC_10d_5; VALUE=LOG10(NOD/NOD.B10)


title: Periodontal Plaque 15 (HOMIM-v.03)


title: Periodontal Plaque 6 (HOMIM-v.03)


title: Gingival Crevicular Fluid 6 (HOMIM-v.03)

source_name: Gingival Crevicular Fluid

value: gingival crevicular fluid


title: Periodontal Plaque 4 (HOMIM-v.03)


title: Periodontal Plaque 9 (HOMIM-v.03)


title: Periodontal Plaque 1 (HOMIM-v.03)


title: Periodontal Plaque 2 (HOMIM-v.03)


title: Gingival Crevicular Fluid 5 (HOMIM-v.03)


title: Gingival Crevicular Fluid 4 (HOMIM-v.03)


title: Gingival Crevicular Fluid 3 (HOMIM-v.03)


title: Gingival Crevicular Fluid 1 (HOMIM-v.03)


title: Periodontal Plaque 5 (HOMIM-v.03)


title: Gingival Crevicular Fluid 2 (HOMIM-v.03)


title: Periodontal Plaque 3 (HOMIM-v.03)


title: Gingival Crevicular Fluid 11 (HOMIM-v.02)


title: Gingival Crevicular Fluid 10 (HOMIM-v.02)


title: yeast treated with DMSO, biological rep1

city: Beijing

first: Chenghua

last: Li

address: Qinghuayuan

department: Biological Sciences and Technology

country: China

institute: Tsinghua University

hyb_protocol: Hybridization was performed according to standard Affymetrix procedures. Briefly, 10ug cRNA was hybridized for 16hr at 45℃ on Affymetrix GeneChip® Yeast Genome 2.0 Arrays in an Affymetrix ® Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix ® GeneChip® Scanner 3000.

data_processing: Normalization and expression analysis was performed using DNA-chip analyzer (dChip). Invariant Set Normalization was used to normalize arrays at the probe level, and the model-based method was used to calculate expression values.

organism: Saccharomyces cerevisiae

source_name: yeast treated with 1% DMSO for 5 hours

label_protocol: Biotinylated cRNA was prepared according to standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Wild type BY4742 yeast strain grown in YPD to mid-log phase were inoculated 1:1 into fresh YPD supplemented with either DMSO (D) or CQ (Q) and grown at 30℃ at 175 rpm in a shaking incubator.

extract_protocol: Total RNA was extracted using the hot phenol method (Collart, M. A., and Oliviero, S. (2001) Curr Protoc Mol Biol Chapter 13, Unit13 12).

treatment_protocol: One percent (v/v) DMSO (D) or 80 µM CQ (Q) was supplemented into the yeast culture medium.

tag: strain

tag: media supplement

value: 1% DMSO


title: Gingival Crevicular Fluid 9 (HOMIM-v.02)


title: yeast treated with CQ, biological rep3

source_name: yeast treated with 80 µM CQ for 5 hours

value: 80 µM CQ


title: yeast treated with DMSO, biological rep3


title: Gingival Crevicular Fluid 8 (HOMIM-v.02)


title: yeast treated with CQ, biological rep2


title: Gingival Crevicular Fluid 6 (HOMIM-v.02)


title: Gingival Crevicular Fluid 5 (HOMIM-v.02)


title: yeast treated with DMSO, biological rep2


title: Gingival Crevicular Fluid 3 (HOMIM-v.02)


title: yeast treated with CQ, biological rep1


title: Gingival Crevicular Fluid 7 (HOMIM-v.02)


title: C57B/L6 biological rep 2

city: Richmond

first: Amanda

last: Waterstrat

state: KY

address: 521 Lancaster Ave

department: Biological Sciences

institute: Eastern Kentucky University

description: gene expression data from young C57B/L6 lineage negative bone marrow cells selected by FACS to enrich for hematopoietic stem and progenitor cells

hyb_protocol: standard hybridization protocol for MG 430 v2.0 Affymetrix Microarray Chip

scan_protocol: Affymetrix GeneArray scanner

data_processing: MAS 5.0

source_name: Lineage negative bone marrow cells

label_protocol: biotin-conjugated probes

growth_protocol: primary bone marrow from adult female mice, enriched for hematopoietic stem and progenitor cells by negative selection of hematopoietic lineage markers

extract_protocol: Total RNA extracted with Quiagen Rneasy Mini Kit

treatment_protocol: strain comparison; C57B/L6 vs B.D(Chr5)

value: young adult (6-16 weeks)

value: Lineage negative bone marrow cells

tag: genetic background


title: C57B/L6 biological rep 1


title: Gingival Crevicular Fluid 2 (HOMIM-v.02)


title: C57B/L6 biological rep 3


title: B.D(Chr5) biological rep 2

description: gene expression data from young B.D(Chr5) lineage negative bone marrow cells selected by FACS to enrich for hematopoietic stem and progenitor cells


title: B.D(Chr5) biological rep 1


title: B.D(Chr5) biological rep 3


title: Gingival Crevicular Fluid 4 (HOMIM-v.02)


title: Gingival Crevicular Fluid 1 (HOMIM-v.02)


title: BCG wild type vs BCG with empty pMV361 at OD 0.2 rep 1

city: Guadalajara

first: Mario

middle: A

last: Flores Valdez

state: Jalisco

address: Av. Normalistas No. 800

department: Col. Colinas de la Normal

country: Mexico

institute: Centro de Investigación y Asistencia en Tecnología y diseño del Estado de Jalisco, A.C.

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67684.gif

hyb_protocol: not provided

scan_protocol: GenePix 4000A

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

organism: Mycobacterium tuberculosis

source_name: BCG WT

label_protocol: not provided

extract_protocol: Amount of extract labeled: 2-3 ug of total RNA

value: BCG SSI 1331 wild type

growth_protocol: OD at Harvest = 0.2; Growth Temperature = 37oC; Static or Shaking = Shaking; Shaking Speed = 100 rpm; Media = Middlebrook 7H9 supplemented with albumin-dextrose complex (ADC) and 0.05% Tween 80

value: BCG SSI 1331 with empty pMV361


title: H37Rv dosR KO vs BCG with pMFdosR at OD 0.4 rep 1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-08/69524.gif

source_name: MTB H37Rv Rv3132c-Rv3134c KO (dosR KO)

value: H37Rv DosR KO

source_name: BCG SSI 1331::pMFdosR

growth_protocol: OD at Harvest = 0.4; Growth Temperature = 37oC; Static or Shaking = Shaking; Shaking Speed = 100 rpm; Media = Middlebrook 7H9 supplemented with albumin-dextrose complex (ADC) and 0.05% Tween 80

value: BCG SSI 1331 with pMFdosR


title: H37Rv dosR KO vs BCG with pMFdosR at OD 0.4 rep 4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-08/69527.gif


title: BCG wild type vs BCG with pMFdosR at OD 0.2 rep 3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67689.gif


title: BCG wild type vs BCG with pMFdosR at OD 0.2 rep 4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67723.gif


title: BCG wild type vs BCG with empty pMV361 at OD 0.4 rep 5

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67732.gif


title: BCG wild type vs BCG with pMFdosR at OD 0.2 rep 5

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67725.gif


title: BCG wild type vs BCG with pMFdosR at OD 0.2 rep 2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67688.gif


title: H37Rv dosR KO vs BCG with pMFdosR at OD 0.4 rep 3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-08/69526.gif


title: BCG wild type vs BCG with empty pMV361 at OD 0.4 rep 4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67731.gif


title: BCG wild type vs BCG with empty pMV361 at OD 0.2 rep 4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67722.gif


title: BCG wild type vs BCG with empty pMV361 at OD 0.2 rep 2

description: Image: http://smd.stanford.edu/MicroArray/gifs//67685.gif


title: BCG wild type vs BCG with empty pMV361 at OD 0.4 rep 3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67729.gif


title: BCG wild type vs BCG with pMFdosR at OD 0.4 rep 3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67737.gif


title: BCG wild type vs BCG with empty pMV361 at OD 0.4 rep 2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67728.gif


title: BCG wild type vs BCG with empty pMV361 at OD 0.4 rep 1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67726.gif


title: H37Rv dosR KO vs BCG with pMFdosR at OD 0.4 rep 2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-08/69525.gif


title: BCG wild type vs BCG with pMFdosR at OD 0.2 rep 1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67687.gif


title: BCG wild type vs BCG with pMFdosR at OD 0.4 rep 2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67735.gif


title: BCG wild type vs BCG with pMFdosR at OD 0.4 rep 4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67738.gif


title: BCG wild type vs BCG with pMFdosR at OD 0.4 rep 1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67734.gif


title: BCG wild type vs BCG with empty pMV361 at OD 0.2 rep 3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67686.gif


title: DBA/2J biological rep 1

description: gene expression data from LSK cells isolated from young C57B/L6, DBA/2J and Chr5 congenic strains.  LSK cells were selected from bone marrow by FACS to enrich for hematopoietic stem and progenitor cells.

hyb_protocol: standard hybridization protocol for  for Sentrix-Mouse 6 Whole Genome Expression Beadchip

scan_protocol: Signal intensities captured by Illumina Bead Array Reader and analyzed using Illumina BeadStudio v1.5.0.34

data_processing: Average expression values were obtained for each of the four strains and normalized by the Rank Invariant normalization method.  *Note, due to quality control analysis, one of the DBA/2J samples was excluded from further analysis.  Differential gene expression between C57B/L6 vs B.D(Chr5) and DBA/2J vs D.B.(Chr5).

label: biotinylated; standard Illumina protocol for Sentrix Mouse-6 Expression bead chip

source_name: Lineage negative, Sca-1+, c-kit+ bone marrow cells

label_protocol: biotinylated according to standard Illumina protocol for Sentrix-Mouse 6 Whole Genome Expression Beadchip

growth_protocol: primary bone marrow from adult female mice, enriched for hematopoietic stem and progenitor cells by negative selection of hematopoietic lineage markers, and positive selection for Sca-1 and c-Kit.

treatment_protocol: strain comparison; C57B/L6 vs B.D(Chr5) and DBA/2J vs D.B.(Chr5)


title: D.B(Chr5) biological rep 2

value: Lineage negative, Sca-1+, c-kit+ bone marrow cells


title: DBA/2J biological rep 2


title: B.D(Chr5) biological rep 1


title: C57B/L6 biological rep 3


title: D.B(Chr5) biological rep 1


title: B.D(Chr5) biological rep 3


title: B.D(Chr5) biological rep 2


title: D.B(Chr5) biological rep 3


title: C57B/L6 biological rep 2


title: CD44-hi/CD62L-lo/CD8+ effector memory T cells, biol rep 3

city: Ann Arbor

first: Rork

last: Kuick

state: MI

address: University of Michigan, SPH II, 1415 Washington Heights, Room M2533

institute: University of Michigan

description: donor CD44-lo/CD62L-hi/CD8+ T cells from normal C3H.SW mice were transplanted together with T cell-depleted bone marrow into 4 lethally irradiated (10Gy) B6/SJL recipient mice to induce GVHD.  After 14 days CD44-hi/CD62L-lo/CD8+ T cells were purified from pooled T cells from the recipients.

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Ann Arbor quantile-normalized trimmed-mean method (PMID: 15705192).

source_name: CD44-hi/CD62L-lo/CD8+ effector memory T cells, biological replicate 3

label_protocol: Biotinylated cRNA for each sample was prepared from 600ng total RNA using two rounds of RT and T7 promoter-based in-vitro transcription.

extract_protocol: Total RNA was isolated from the harvested cells using Trizol (Invitrogen) and cleanup performed with an RNeasy kit (Qiagen)

tag: Sex of donor mice

value: female

tag: Sex of recipient mice

value: male


title: CD44-hi/CD62L-lo/CD8+ effector memory T cells, biol rep 2

source_name: CD44-hi/CD62L-lo/CD8+ effector memory T cells, biological replicate 2


title: CD44-lo/CD62L-hi/CD8+ postmitotic T cells, biol rep 3

description: donor CD44-lo/CD62L-hi/CD8+ T cells from normal C3H.SW mice were transplanted together with T cell-depleted bone marrow into 4 lethally irradiated (10Gy) B6/SJL recipient mice to induce GVHD.  After 14 days CD44-lo/CD62L-hi/CD8+ postmitotic T cells were purified from pooled T cells from the recipients.

source_name: CD44-lo/CD62L-hi/CD8+ postmitotic T cells, biological replicate 3


title: C57B/L6 biological rep 1


title: Naïve CD44-lo/CD62L-hi/CD8+ T cells, biol rep 1

description: Naïve CD44-lo/CD62L-hi/CD8+ T cells purified from pooled CD8+ T cells from 2 normal C3H.SW mice.

source_name: Naïve CD44-lo/CD62L-hi/CD8+ T cells, biological replicate 1

tag: Sex


title: Danio rerio-Gill-Zn-supplemented-14d-Rep5

status: Public on May 20 2010

city: Cardiff

first: Peter

last: Kille

address: Park Place

department: Cardiff School of Biosciences

institute: Cardiff University

description: Danio rerio Gill from Zn-supplemented group harvested at 14d biologival replicant 5

hyb_protocol: The arrayed slides were pre-hybridised in a buffer containing 25% formamide, 5x SSC, 0.1% SDS and 1 mg/ml BSA at 42C for 45 min, followed by washing in double-distilled H2O three times and then air-dried. Equal amounts of Cy3 and Cy5-labelled cDNA were combined and hybridised in 1x hybridisation buffer, containing 25% formamide, 5x SSC, 0.5x Denhardt’s, 0.1 µg/µl yeast tRNA and 0.1% SDS, at 42C for 16–20 h in a sealed humid hybridisation chamber (Camlab). The slide was washed for 5 min sequentially in 2x SSC/0.1% SDS buffer (at 42C), 0.1x SSC/0.1% SDS buffer and 0.1x SSC buffer and air-dried.

scan_protocol: Scanning was performed with a ScanArrayTM Express HT Microarray Scanner (Perkin Elmer, MA, USA) at the appropriate wavelength for each channel, i.e. at 550nm for Cy3 and at 650nm for Cy5.

data_processing: Spot intensities from each scanned image were quantified using Bluefuse software (BlueGnome) which is based on Bayesian statistical method. Lowess normalisation was applied to the quantified data set. The probe intensities with low confidence (P<0.05) were filtered out and the normalised data were then uploaded onto GeneSpring 7.3X software (Agilent Technologies). Within GeneSpring the data was expressed by dividing the test channel (Cy5) by the value of the control channel (Cy3) and normalised within each chip using the 50th percentile and for each gene to its median value.

organism: Danio rerio

label_protocol: The amino-allyl indirect labelling method (CYSCRIBE™ First Strand cDNA Labeling Kit, GE Healthcare) was used to obtain Cy3 (reference) or Cy5 (samples)-labelled cDNA. The Cy3- or Cy5- cDNA sample was individually purified using QIAquick PCR purification columns (Qiagen).

growth_protocol: Juvenile zebrafish, Danio rerio (0.44 ± 0.06g), were obtained from Neil Hardy Aquatica Ltd. (Surrey, UK). The fish were divided into three experimental groups with each group held in four identical tanks (40 fish per tank), and supplied with a continuous flow of aerated reconstituted reverse osmosis water at 26-28ºC. The reconstituted water was composed of 0.6 mM NaCl, 41 µM Na2SO4, 13.6 µM KCl, 150 µM CaCl2, 3.4 µM NaHCO3, 78 µM MgCl2. In addition, each tank was equipped with a dosing system, which added Zn, as ZnSO4.7H2O (BDH Chemicals), to provide a nominal zinc concentration in the tanks of 0.25 µM (16.3 µg L-1). The fish were fed a purified mash diet (Fish Nutrition Unit, University of Plymouth, UK) containing an analysed zinc concentration of 233 mg kg-1 (3.56 mmol kg-1) at a rate of 4% of their body mass per day.

extract_protocol: Total RNA was extracted from dissected gill samples using TRIzol Reagent (Invitrogen) according to the manufacture’s protocol. Two gills from one fish were pooled and extracted together. The RNA samples were further subject to DNase I digestion using DNA-free kit (Ambion). The quality of the RNA samples was assessed using the Agilent 2100 Bioanalyser (Agilent Technologies). The reference RNA was purified from whole bodies of fish under control condition.

treatment_protocol: After one-week acclimation to laboratory conditions, a nominal zinc concentration of 5 µM (330 µg L-1) was introduced for a group of four tanks through a dosing system (zinc supplemented group). The feed for this fish group was replaced with that containing an analysed zinc concentration of 2023 mg kg-1 (30.9 mmol kg-1 (). A group of fish in four separate tanks was kept at the same levels of zinc in water and feed as before (water: 0.25 µM, feed: 233 mg kg-1). The two water and feed compositions were otherwise identical. Feed ratio was kept at 4% of body mass per day for both groups. The zinc concentrations in water from all tanks were monitored daily using Inductively Coupled Plasma Mass Spectroscopy (PerkinElmer Elan DRC ICP-MS) on HNO3 acidified samples. The measured water zinc concentrations in control and excess groups were 0.25±0.09 μM and 4.02±1.2μM (mean±SD, N=14), respectively. The experiment continued for 14 days and no mortalities or necropsies were observed.

value: Gill

tag: treatment

value: Zn-supplemented

tag: time

tag: replicate number

source_name: Common reference from whole body Danio rerio

value: Control

value: Whole Body


title: CD44-lo/CD62L-hi/CD8+ postmitotic T cells, biol rep 1

source_name: CD44-lo/CD62L-hi/CD8+ postmitotic T cells, biological replicate 1


title: Naïve CD44-lo/CD62L-hi/CD8+ T cells, biol rep 2

source_name: Naïve CD44-lo/CD62L-hi/CD8+ T cells, biological replicate 2


title: Naïve CD44-lo/CD62L-hi/CD8+ T cells, biol rep 3

source_name: Naïve CD44-lo/CD62L-hi/CD8+ T cells, biological replicate 3


title: CD44-hi/CD62L-lo/CD8+ effector memory T cells, biol rep 1

source_name: CD44-hi/CD62L-lo/CD8+ effector memory T cells, biological replicate 1


title: CD44-lo/CD62L-hi/CD8+ postmitotic T cells, biol rep 2

source_name: CD44-lo/CD62L-hi/CD8+ postmitotic T cells, biological replicate 2


title: Danio rerio-Gill-Zn-supplemented-7d-Rep3

description: Danio rerio Gill from Zn-supplemented group harvested at 7d biologival replicant 3

tag: tissue


title: Danio rerio-Gill-Zn-supplemented-14d-Rep4

description: Danio rerio Gill from Zn-supplemented group harvested at 14d biologival replicant 4


title: Danio rerio-Gill-Zn-supplemented-14d-Rep3

description: Danio rerio Gill from Zn-supplemented group harvested at 14d biologival replicant 3


title: Danio rerio-Gill-Zn-supplemented-14d-Rep2

description: Danio rerio Gill from Zn-supplemented group harvested at 14d biologival replicant 2


title: Danio rerio-Gill-Zn-supplemented-4d-Rep4

description: Danio rerio Gill from Zn-supplemented group harvested at 4d biologival replicant 4


title: Danio rerio-Gill-Zn-supplemented-7d-Rep1

description: Danio rerio Gill from Zn-supplemented group harvested at 7d biologival replicant 1


title: Danio rerio-Gill-Zn-supplemented-7d-Rep2

description: Danio rerio Gill from Zn-supplemented group harvested at 7d biologival replicant 2


title: Danio rerio-Gill-Zn-supplemented-7d-Rep5

description: Danio rerio Gill from Zn-supplemented group harvested at 7d biologival replicant 5


title: Danio rerio-Gill-Zn-supplemented-4d-Rep3

description: Danio rerio Gill from Zn-supplemented group harvested at 4d biologival replicant 3


title: Danio rerio-Gill-Zn-supplemented-4d-Rep5

description: Danio rerio Gill from Zn-supplemented group harvested at 4d biologival replicant 5


title: Danio rerio-Gill-Zn-supplemented-14d-Rep1

description: Danio rerio Gill from Zn-supplemented group harvested at 14d biologival replicant 1


title: Danio rerio-Gill-Zn-supplemented-24h-Rep4

description: Danio rerio Gill from Zn-supplemented group harvested at 24h biologival replicant 4


title: Danio rerio-Gill-Zn-supplemented-24h-Rep3

description: Danio rerio Gill from Zn-supplemented group harvested at 24h biologival replicant 3


title: Danio rerio-Gill-Zn-supplemented-4d-Rep2

description: Danio rerio Gill from Zn-supplemented group harvested at 4d biologival replicant 2


title: Danio rerio-Gill-Zn-supplemented-4d-Rep1

description: Danio rerio Gill from Zn-supplemented group harvested at 4d biologival replicant 1


title: Danio rerio-Gill-Zn-supplemented-24h-Rep2

description: Danio rerio Gill from Zn-supplemented group harvested at 24h biologival replicant 2


title: Danio rerio-Gill-Zn-supplemented-8h-Rep2

description: Danio rerio Gill from Zn-supplemented group harvested at 8h biologival replicant 2


title: Danio rerio-Gill-Zn-supplemented-8h-Rep3

description: Danio rerio Gill from Zn-supplemented group harvested at 8h biologival replicant 3


title: Danio rerio-Gill-Zn-supplemented-8h-Rep4

description: Danio rerio Gill from Zn-supplemented group harvested at 8h biologival replicant 4


title: Danio rerio-Gill-control-sup-14d-Rep1

description: Danio rerio Gill from control group harvested at 14d biologival replicant 1

value: control


title: Danio rerio-Gill-Zn-supplemented-24h-Rep5

description: Danio rerio Gill from Zn-supplemented group harvested at 24h biologival replicant 5


title: Danio rerio-Gill-Zn-supplemented-24h-Rep1

description: Danio rerio Gill from Zn-supplemented group harvested at 24h biologival replicant 1


title: Danio rerio-Gill-control-sup-14d-Rep4

description: Danio rerio Gill from control group harvested at 14d biologival replicant 4


title: Danio rerio-Gill-Zn-supplemented-8h-Rep1

description: Danio rerio Gill from Zn-supplemented group harvested at 8h biologival replicant 1


title: Danio rerio-Gill-control-sup-14d-Rep5

description: Danio rerio Gill from control group harvested at 14d biologival replicant 5


title: Danio rerio-Gill-control-sup-7d-Rep5

description: Danio rerio Gill from control group harvested at 7d biologival replicant 5


title: Danio rerio-Gill-control-sup-14d-Rep3

description: Danio rerio Gill from control group harvested at 14d biologival replicant 3


title: Danio rerio-Gill-control-sup-14d-Rep2

description: Danio rerio Gill from control group harvested at 14d biologival replicant 2


title: Danio rerio-Gill-control-sup-7d-Rep6

description: Danio rerio Gill from control group harvested at 7d biologival replicant 6


title: Danio rerio-Gill-Zn-supplemented-7d-Rep4

description: Danio rerio Gill from Zn-supplemented group harvested at 7d biologival replicant 4


title: Danio rerio-Gill-Zn-supplemented-8h-Rep5

description: Danio rerio Gill from Zn-supplemented group harvested at 8h biologival replicant 5


title: Danio rerio-Gill-control-sup-7d-Rep4

description: Danio rerio Gill from control group harvested at 7d biologival replicant 4


title: Danio rerio-Gill-control-sup-24h-Rep2

description: Danio rerio Gill from control group harvested at 24h biologival replicant 2


title: Danio rerio-Gill-control-sup-24h-Rep3

description: Danio rerio Gill from control group harvested at 24h biologival replicant 3


title: Danio rerio-Gill-control-sup-7d-Rep3

description: Danio rerio Gill from control group harvested at 7d biologival replicant 3


title: Danio rerio-Gill-control-sup-24h-Rep1

description: Danio rerio Gill from control group harvested at 24h biologival replicant 1


title: Danio rerio-Gill-control-sup-4d-Rep3

description: Danio rerio Gill from control group harvested at 4d biologival replicant 3


title: Danio rerio-Gill-control-sup-4d-Rep2

description: Danio rerio Gill from control group harvested at 4d biologival replicant 2


title: Danio rerio-Gill-control-sup-8h-Rep1

description: Danio rerio Gill from control group harvested at 8h biologival replicant 1


title: Danio rerio-Gill-control-sup-8h-Rep5

description: Danio rerio Gill from control group harvested at 8h biologival replicant 5


title: Danio rerio-Gill-control-sup-24h-Rep4

description: Danio rerio Gill from control group harvested at 24h biologival replicant 4


title: Danio rerio-Gill-control-sup-7d-Rep2

description: Danio rerio Gill from control group harvested at 7d biologival replicant 2


title: Danio rerio-Gill-control-sup-4d-Rep4

description: Danio rerio Gill from control group harvested at 4d biologival replicant 4


title: Danio rerio-Gill-control-sup-8h-Rep2

description: Danio rerio Gill from control group harvested at 8h biologival replicant 2


title: Danio rerio-Gill-Zn-deficient-14d-Rep2

description: Danio rerio Gill from Zn-deficient group harvested at 14d biologival replicant 2

hyb_protocol: The arrayed slides were pre-hybridised in a buffer containing 25% formamide, 5x SSC, 0.1% SDS and 1 mg/ml BSA at 42oC for 45 min, followed by washing in double-distilled H2O three times and then air-dried. Equal amounts of Cy3 and Cy5-labelled cDNA were combined and hybridised in 1x hybridisation buffer, containing 25% formamide, 5x SSC, 0.5x Denhardt’s, 0.1 µg/µl yeast tRNA and 0.1% SDS, at 42oC for 16–20 h in a sealed humid hybridisation chamber (Camlab). The slide was washed for 5 min sequentially in 2x SSC/0.1% SDS buffer (at 42oC), 0.1x SSC/0.1% SDS buffer and 0.1x SSC buffer and air-dried.

treatment_protocol: After one-week acclimation, zinc deficiency was induced to a group of fish spread over four tanks by changing to reconstituted water without additional zinc supplementation and providing a low zinc (26 mg kg-1) diet. The zinc concentrations in the water were monitored daily using Inductively Coupled Plasma Mass Spectroscopy (PerkinElmer Elan DRC ICP-MS). The measured zinc concentrations for zinc deficiency and control groups were 0.04±0.05 μM (2.61 μg L-1) and 0.25±0.09 μM (16.3 μg L-1), respectively. The experiment continued for 14 days and no mortalities or necropsies were observed.

value: Zn-deficient


title: Danio rerio-Gill-Zn-deficient-14d-Rep5

description: Danio rerio Gill from Zn-deficient group harvested at 14d biologival replicant 5


title: Danio rerio-Gill-Zn-deficient-14d-Rep4

description: Danio rerio Gill from Zn-deficient group harvested at 14d biologival replicant 4


title: Danio rerio-Gill-control-sup-24h-Rep5

description: Danio rerio Gill from control group harvested at 24h biologival replicant 5


title: Danio rerio-Gill-control-sup-8h-Rep3

description: Danio rerio Gill from control group harvested at 8h biologival replicant 3


title: Danio rerio-Gill-Zn-deficient-14d-Rep3

description: Danio rerio Gill from Zn-deficient group harvested at 14d biologival replicant 3


title: Danio rerio-Gill-control-sup-4d-Rep1

description: Danio rerio Gill from control group harvested at 4d biologival replicant 1


title: Danio rerio-Gill-Zn-deficient-7d-Rep4

description: Danio rerio Gill from Zn-deficient group harvested at 7d biologival replicant 4


title: Danio rerio-Gill-Zn-deficient-14d-Rep1

description: Danio rerio Gill from Zn-deficient group harvested at 14d biologival replicant 1


title: Danio rerio-Gill-Zn-deficient-7d-Rep5

description: Danio rerio Gill from Zn-deficient group harvested at 7d biologival replicant 5


title: Danio rerio-Gill-Zn-deficient-7d-Rep3

description: Danio rerio Gill from Zn-deficient group harvested at 7d biologival replicant 3


title: Danio rerio-Gill-Zn-deficient-7d-Rep1

description: Danio rerio Gill from Zn-deficient group harvested at 7d biologival replicant 1


title: Danio rerio-Gill-Zn-deficient-4d-Rep5

description: Danio rerio Gill from Zn-deficient group harvested at 4d biologival replicant 5


title: Danio rerio-Gill-Zn-deficient-4d-Rep3

description: Danio rerio Gill from Zn-deficient group harvested at 4d biologival replicant 3


title: Danio rerio-Gill-Zn-deficient-4d-Rep2

description: Danio rerio Gill from Zn-deficient group harvested at 4d biologival replicant 2


title: Single cell comparison of R2 Old vs R2 Young, rep 3, AAA

city: St Augustine

first: Andrea

middle: B

last: Kohn

state: FL

address: 9505 Ocean Shore Blvd

department: Whitney lab

institute: University of Florida

description:
R2Old R2Young-3
Biological replicate 3 of 3.

Detailed protocols are available in the 'GSE18783_Materials_and_Methods.txt' file, which is linked to the Series GSE18783 record as a supplementary file.

hyb_protocol: The recommended amount of 750 ng of labeled cRNA was fragmented and hybridized to the arrays using recommended procedures described in the In situ Hybridization Kit PlusTM (Agilent Technologies). Controls provided in the In situ Hybridization Kit were spiked in at the time of hybridization. The arrays were washed according to the manufacturer's recommended protocol.

scan_protocol: The arrays were scanned on an Agilent Technologies G2565AA Microarray ScannerTM. Data were extracted after scanning using Agilent’s Feature Extraction 5.1.1TM software.

data_processing: The balancing between the Cy3 and Cy5 signals within each array was performed by the RANK order method using LOWESS smoothing procedure as implemented in the Agilent feature extraction software version 7.0 (http://chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=30997). The background on all arrays analyzed for the Cy3 and Cy5 channels was observed to be nearly identical (41.8 +/- 1.1) over all 44,000 features. No local background subtraction was performed; instead the data was filtered by P-values obtained from fitting the signal and background values and spatial detrending algorithm. Only data that had P-values of less than or equal to 0.01 (meaning feature signal is significantly and positively higher than background signal) on both Cy3 and Cy5 channels from each array was used for further analysis (“floor”). A suite of algorithms are also included in the processing of the final TIFF image involving an error-model proprietary to Agilent that has been pre-determined to give the best corrected data for downstream analysis. All experiments were performed in triplicate from three independent samples from 3 different animals.

organism: Aplysia californica

source_name: R2 old neuron

label_protocol: cRNA production was preformed using Agilent’s Low RNA Input Linear Amplification kitTM (Agilent Technologies). All amplification reactions involved only one round of amplification. Concentration of the cRNA was determined by GeneSpec IIITM and the 2100 Bioanalyzer both described above. The cRNA was labeled either using the direct method in Agilent’s Low RNA Input Linear Amplification kit or with an indirect technique using the MicroMax ASAP RNA labeling kitTM (PerkinElmer).

growth_protocol: Aplysia californica were obtained from the NIH/University of Miami National Resource for Aplysia and held in 40-400 liter aquaria with circulating fresh seawater at 15-17º C.

extract_protocol: Total RNA was extracted using RNAqueousTM or RNAqueous-MicroTM (Ambion, Austin, TX) kits depending on sample size. Before further processing of the RNA, quality was checked using a 2100 BioanalyzerTM (Agilent Technologies). Small aliquots of extracted RNA were loaded on a 6000 Nano Lab chip that produces an electropherogram image along with a gel-like image of the sample representing peak ratios of the 28s/18s RNA contained in the sample. Moreover, it provides information about potential DNA contamination and the approximate RNA concentration. Additionally, RNA concentration was measured spectrophotometrically by using the GeneSpec III systemTM (Mirai Bio).

treatment_protocol: Aplysia californica of appropriate age and weight were used. Animals were anesthetized by injection of 60% (volume/body weight) isotonic MgCl2 (337mM) prior to removal of the CNS. Ganglia were mechanically removed with fine forceps and scissors and cell were isolated as described above. Neurons were then fixed in 75% ethanol for several minutes and RNA isolated immediately.

value: cholinergic neuron

tag: neuron

value: old

source_name: R2 young neuron

value: young


title: Danio rerio-Gill-Zn-deficient-7d-Rep2

description: Danio rerio Gill from Zn-deficient group harvested at 7d biologival replicant 2


title: Danio rerio-Gill-Zn-deficient-4d-Rep4

description: Danio rerio Gill from Zn-deficient group harvested at 4d biologival replicant 4


title: Abdominal Ganglion Young vs Abdominal Ganglion Old, rep 1

description:
AbdGang Young AbdGang Old 1
Biological replicate 1 of 3.

Detailed protocols are available in the 'GSE18783_Materials_and_Methods.txt' file, which is linked to the Series GSE18783 record as a supplementary file.

source_name: Abdominal ganglion, young

label_protocol: cRNA production was performed using Agilent’s Low RNA Input Linear Amplification kitTM (Agilent Technologies). All amplification reactions involved only one round of amplification. Concentration of the cRNA was determined by GeneSpec IIITM and the 2100 Bioanalyzer both described above. The cRNA was labeled either using the direct method in Agilent’s Low RNA Input Linear Amplification kit or with an indirect technique using the MicroMax ASAP RNA labeling kitTM (PerkinElmer).

extract_protocol: Total RNA was extracted using RNAqueousTM or RNAqueous-MicroTM (Ambion, Austin, TX) kits depending on sample size. Before further processing of the RNA, quality was checked using a 2100 BioanalyzerTM (Agilent Technologies). Small aliquots of extracted RNA were loaded on a 6000 Nano Lab chip that produces an electropherogram image along with a gel-like image of the sample representing peak ratios of the 28s/18s RNA contained in the sample. Moreover it provides information about potential DNA contamination and the approximate RNA concentration. Additionally RNA concentration was measured spectrophotometrically by using the GeneSpec III systemTM (Mirai Bio).

treatment_protocol: Aplysia californica weighing 25-30g for the young subgroup and 1000-14000g for the old subgroup were used (see GSE18783_Table1.txt, which is linked to the Series GSE18783 record as a supplementary file). Animals were anesthetized by injection of 60% (volume/body weight) isotonic MgCl2 (337mM) prior to removal of the CNS. Ganglia were mechanical removed with fine forceps and scissors and cell were isolated as described above. Neurons were then fixed in 75% ethanol for several minutes and RNA isolated immediately.

value: abdominal ganglion

source_name: Abdominal ganglion, old


title: Danio rerio-Gill-Zn-deficient-24h-Rep5

description: Danio rerio Gill from Zn-deficient group harvested at 24h biologival replicant 5


title: R2 old vs CNS, biol rep 2, AAA

description:
Biological replicate 2

Detailed protocols are available in the 'GSE18783_Materials_and_Methods.txt' file, which is linked to the Series GSE18783 record as a supplementary file.

data_processing: The balancing between the Cy3 and Cy5 signals within each array was performed by the RANK order method using LOWESS smoothing procedure as implemented in the Agilent feature extraction software version 7.0 (http://chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=30997). The background on all arrays analyzed for the Cy3 and Cy5 channels was observed to be nearly identical (41.8 +/- 1.1) over all 44,000 features. No local background subtraction was performed; instead the data was filtered by P-values obtained from fitting the signal and background values and spatial detrending algorithm. Only data that had P-values of less than or equal to 0.01 (meaning feature signal is significantly and positively higher than background signal) on both Cy3 and Cy5 channels from each array was used for further analysis (“floor”). A suite of algorithms are also included in the processing of the final TIFF image involving an error-model proprietary to Agilent that has been pre-determined to give the best corrected data for downstream analysis. All experiments were performed in triplicates from three independent samples from 3 different animals.

source_name: CNS

value: central nervous system (CNS)


title: LPL1 old vs CNS, biol rep 3, AAA

description:
Biological replicate 3

Detailed protocols are available in the 'GSE18783_Materials_and_Methods.txt' file, which is linked to the Series GSE18783 record as a supplementary file.

source_name: LPL1 old neuron


title: R2 old vs CNS, biol rep 3, AAA


title: Abdominal Ganglion Young vs Abdominal Ganglion Old, rep 2

description:
AbdGang Young AbdGang Old 2
Biological replicate 2 of 3.

Detailed protocols are available in the 'GSE18783_Materials_and_Methods.txt' file, which is linked to the Series GSE18783 record as a supplementary file.


title: R2 young vs CNS, biol rep 1, AAA

description:
Biological replicate 1

Detailed protocols are available in the 'GSE18783_Materials_and_Methods.txt' file, which is linked to the Series GSE18783 record as a supplementary file.


title: Single cell comparison of R2 Old vs R2 Young, rep 1, AAA

description:
R2Old R2Young-1
Biological replicate 1 of 3.

Detailed protocols are available in the 'GSE18783_Materials_and_Methods.txt' file, which is linked to the Series GSE18783 record as a supplementary file.


title: R2 young vs CNS, biol rep 3, AAA


title: Danio rerio-Gill-Zn-deficient-4d-Rep1

description: Danio rerio Gill from Zn-deficient group harvested at 4d biologival replicant 1


title: LPL1 old vs CNS, biol rep 1, AAA


title: LPL1 old vs CNS, biol rep 2, AAA


title: R2 old vs CNS, biol rep 1, AAA


title: R2 young vs CNS, biol rep 2, AAA


title: Danio rerio-Gill-Zn-deficient-24h-Rep3

description: Danio rerio Gill from Zn-deficient group harvested at 24h biologival replicant 3


title: Danio rerio-Gill-Zn-deficient-24h-Rep4

description: Danio rerio Gill from Zn-deficient group harvested at 24h biologival replicant 4


title: Single cell comparison of R2 Old vs R2 Young, rep 2, AAA

description:
R2Old R2Young-2
Biological replicate 2 of 3.

Detailed protocols are available in the 'GSE18783_Materials_and_Methods.txt' file, which is linked to the Series GSE18783 record as a supplementary file.


title: LPL1 young vs CNS, biol rep 3, AAA

source_name: LPL1 young neuron


title: Abdominal Ganglion Young vs Abdominal Ganglion Old, rep 3

description:
AbdGang Young AbdGang Old 3
Biological replicate 3 of 3.

Detailed protocols are available in the 'GSE18783_Materials_and_Methods.txt' file, which is linked to the Series GSE18783 record as a supplementary file.


title: Danio rerio-Gill-Zn-deficient-24h-Rep1

description: Danio rerio Gill from Zn-deficient group harvested at 24h biologival replicant 1


title: LPL1 young vs CNS, biol rep 2, AAA


title: Danio rerio-Gill-Zn-deficient-24h-Rep2

description: Danio rerio Gill from Zn-deficient group harvested at 24h biologival replicant 2


title: Danio rerio-Gill-Zn-deficient-8h-Rep4

description: Danio rerio Gill from Zn-deficient group harvested at 8h biologival replicant 4


title: Danio rerio-Gill-control-14d-Rep3

description: Danio rerio Gill from control group harvested at 14d biologival replicant 3


title: Danio rerio-Gill-control-14d-Rep1

description: Danio rerio Gill from control group harvested at 14d biologival replicant 1


title: Danio rerio-Gill-Zn-deficient-8h-Rep5

description: Danio rerio Gill from Zn-deficient group harvested at 8h biologival replicant 5


title: Danio rerio-Gill-Zn-deficient-8h-Rep1

description: Danio rerio Gill from Zn-deficient group harvested at 8h biologival replicant 1


title: Danio rerio-Gill-control-14d-Rep4

description: Danio rerio Gill from control group harvested at 14d biologival replicant 4


title: Danio rerio-Gill-control-14d-Rep5

description: Danio rerio Gill from control group harvested at 14d biologival replicant 5


title: Danio rerio-Gill-control-14d-Rep2

description: Danio rerio Gill from control group harvested at 14d biologival replicant 2


title: LPL1 young vs CNS, biol rep 1, AAA

description:
Biological replicate 1

Detailed protocols are available in the 'GSE18783_Materials_and_Methods.txt' file, which is linked to the Series GSE18783 record as a supplementary file.


title: Danio rerio-Gill-control-7d-Rep6

description: Danio rerio Gill from control group harvested at 7d biologival replicant 6


title: Danio rerio-Gill-Zn-deficient-8h-Rep2

description: Danio rerio Gill from Zn-deficient group harvested at 8h biologival replicant 2


title: Danio rerio-Gill-control-7d-Rep4

description: Danio rerio Gill from control group harvested at 7d biologival replicant 4


title: Danio rerio-Gill-control-4d-Rep2

description: Danio rerio Gill from control group harvested at 4d biologival replicant 2


title: Danio rerio-Gill-control-24h-Rep4

description: Danio rerio Gill from control group harvested at 24h biologival replicant 4


title: Danio rerio-Gill-control-7d-Rep2

description: Danio rerio Gill from control group harvested at 7d biologival replicant 2


title: Danio rerio-Gill-Zn-deficient-8h-Rep3

description: Danio rerio Gill from Zn-deficient group harvested at 8h biologival replicant 3


title: Danio rerio-Gill-control-4d-Rep1

description: Danio rerio Gill from control group harvested at 4d biologival replicant 1


title: Danio rerio-Gill-control-4d-Rep3

description: Danio rerio Gill from control group harvested at 4d biologival replicant 3


title: Danio rerio-Gill-control-24h-Rep2

description: Danio rerio Gill from control group harvested at 24h biologival replicant 2


title: Danio rerio-Gill-control-4d-Rep4

description: Danio rerio Gill from control group harvested at 4d biologival replicant 4


title: Danio rerio-Gill-control-24h-Rep1

description: Danio rerio Gill from control group harvested at 24h biologival replicant 1


title: 14839--BloodWhole

city: Rehovot

first: Einat

last: Sitbon

address: 10 Plaut St

country: Israel

institute: Rosetta Genomics

hyb_protocol: Slides were incubated with the labeled RNA for 12-16 h at 55°C and then washed according to Agilent GE washes.

scan_protocol: Arrays were scanned using Agilent DNA Microarray Scanner Bundle (Agilent Technologies, Santa Clara, CA) at a resolution of 5 micrometer, dual pass at 100% and 10% PMT power. Array images were analyzed using Agilent Feature Extraction software.

data_processing: Array images were analyzed using the Feature Extraction software (FE) 9.5.1 (Agilent, Santa Clara, CA). Triplicate spots were combined to produce one signal for each probe by taking the logarithmic mean of reliable spots. All data were log-transformed (base two) and the analysis was performed in log-space. A reference data vector for normalization R was calculated by taking the median expression level of a subset of all probes (all miRNAs in miRBase 10) across samples. For each sample data vector S, a 2nd degree polynomial F was found so as to provide the best fit between the sample data and the reference data, such that R≈F(S). For each probe in the sample (element Si in the vector S), the normalized value (in log-space) Mi was calculated from the initial value Si by transforming it with the polynomial function F, so that Mi=F(Si).

organism: Homo sapiens

source_name: BloodWhole--BloodWhole

label_protocol: A total of 2-2.5 µg of total RNA was labeled by ligation of an RNA-linker, p-rCrU-Cy/dye (Eurogentec S.A.; Cy3 or Cy5), to the 3' end. Synthetic small RNA was spiked into the RNA before labeling to verify the labeling efficiency.

extract_protocol: Total RNA was extracted twice from each sample of 23 human formalin-fixed paraffin-embedded (FFPE) samples derived from cancerous tissue. RNA was isolated using ten 10-µm-thick tissue sections using the miRdicatorTM extraction protocol developed at Rosetta Genomics. Briefly, the sample was incubated repeatedly in xylene at 57oC to remove excess paraffin, followed by washing in ethanol. Proteins were degraded by incubation in proteinase K solution at 45oC for a few hours. The RNA was extracted with acid phenol:chloroform followed by ethanol precipitation and DNAse digestion. Total RNA quantity and quality were checked by spectrophotometry (Nanodrop ND-1000).

tag: preservation

value: Blood, Whole

tag: organ

tag: barcode


title: Danio rerio-Gill-control-24h-Rep5

description: Danio rerio Gill from control group harvested at 24h biologival replicant 5


title: 14838--BloodCells

source_name: BloodCells--BloodCells

value: Blood Cells


title: Danio rerio-Gill-control-7d-Rep3

description: Danio rerio Gill from control group harvested at 7d biologival replicant 3


title: 14837-Normal-Liver

source_name: Fresh-Normal-Liver

value: Fresh

tag: indication

value: Normal

value: Liver


title: Danio rerio-Gill-control-24h-Rep3

description: Danio rerio Gill from control group harvested at 24h biologival replicant 3


title: 14836-Normal-Heart

source_name: Fresh-Normal-Heart

value: Heart


title: 14835-Normal-Brain

source_name: Fresh-Normal-Brain

value: Brain


title: 14455-Normal-Bladder

source_name: Fresh-Normal-Bladder

value: Bladder


title: Danio rerio-Gill-control-sup-8h-Rep4

description: Danio rerio Gill from control group harvested at 8h biologival replicant 4

value: Gill

source_name: Common reference from whole body Danio rerio

value: Control


title: 14448-Tumor-Breast

source_name: Paraffin-Tumor-Breast

value: Paraffin

value: Tumor

value: Breast


title: Danio rerio-Gill-control-8h-Rep5

description: Danio rerio Gill from control group harvested at 8h biologival replicant 5

value: control

value: Whole Body


title: Danio rerio-Gill-control-8h-Rep4

source_name: Danio rerio Gill from control group harvested at 8h biologival replicant 4


title: Danio rerio-Gill-control-8h-Rep2

description: Danio rerio Gill from control group harvested at 8h biologival replicant 2


title: 14447-Tumor-Lung

source_name: Paraffin-Tumor-Lung-including the histological types: Non-small; adenocarcinoma Neuroendocrine; Small Non-small; Large Non-small; squamous Non-small;  squamous Non-small

value: Lung

tag: histological type

value: including the histological types:Non-small; adenocarcinoma Neuroendocrine; Small Non-small; Large Non-small; squamous Non-small;  squamous Non-small


title: Danio rerio-Gill-control-8h-Rep3

description: Danio rerio Gill from control group harvested at 8h biologival replicant 3


title: Danio rerio-Gill-control-7d-Rep5

description: Danio rerio Gill from control group harvested at 7d biologival replicant 5


title: 14446-Tumor-Cervix

source_name: Paraffin-Tumor-Cervix-adenocarcinoma

value: Cervix

value: adenocarcinoma


title: Control and IAA-overproducing cells, replicate 5

city: Napoli

first: Carmen

last: Bianco

address: Via p. Castellino 111

country: Italy

institute: IGB-CNR

hyb_protocol: Microarrays were prehybridized for 30 min at 42°C. Following prehybridization, microarrays were washed and hybridization was performed at 42°C for 16 h in hybridization solution (25% formamide, 5× SSC, 0.1% SDS) supplemented with 50 μg ml−1 sonicated salmon sperm DNA. Before applying the hybridization sample to the microarray, it was denatured for 5 min at 65°C. Microarrays were then washed, dried by centrifugation and scanned.

scan_protocol: Scanned on ScanArrayPro scanner (PerkinElmer).

data_processing: LOWESS normalization with Analyzer 3.0 Software.

organism: Sinorhizobium meliloti

source_name: RD64 cells

label_protocol: Fluorescent-labeled cDNA was prepared according to an amino–allyl dye coupling protocol as adapted by Becker and Ruberg (2003), starting from 10 μg of total RNA with only one modification: after RNA hydrolysis, the cleanup of amino–allyl-labeled first-strand cDNA was performed by using QiaQuick PCR Purification columns.

growth_protocol: Exponentially growing and IAA-overproducing RD64 cells.

extract_protocol: For RNA isolation, cell pellets were resuspended and incubated for 10 min at 65°C in 1 ml pre-warmed lysis solution (1.4% SDS, 4 mM EDTA, 75 μg proteinase K). Proteins were precipitated by adding 0.5 ml of 5 M NaCl at 4°C. The samples were then centrifuged, the nucleic acid precipitated from the supernatant by adding isopropanol, and the pellet resuspended in diethylpirocarbonate (DEPC)-treated water. Residual DNA present in the RNA preparations was removed by incubation at 37°C with 5 U of DNase I (Epicentre Technologies) and 40 U of RNAse Block ribonuclease inhibitor (Stratagene) for 30 min. The isolated RNA was further extracted with phenol–chloroform–isoamylalcohol and chloroform–isoamylalcohol, precipitated with 2.5 vol of ethanol and then dissolved in diethylpyrocarbonate-treated water.

value: untreated

source_name: Control cells

growth_protocol: Exponentially growing 1021 control cells.


title: 14445-Tumor-Esophagus

value: Esophagus

value: Squamous cell carcinoma


title: Danio rerio-Gill-control-8h-Rep1

description: Danio rerio Gill from control group harvested at 8h biologival replicant 1


title: 14444-Tumor-Bladder

value: Transitional cell carcinoma


title: 14443-Normal-Lung

source_name: Fresh-Normal-Lung

value: Fresh

value: Normal


title: Control and IAA-overproducing cells, replicate 6


title: Control and IAA-overproducing cells, replicate 2

description: PROBE.II


title: Control and IAA-overproducing cells, replicate 3

description: PROBE.III


title: Control and Trp treated cells, replicate 6

source_name: Trp treated cells

growth_protocol: Exponentially growing cells treated with 0.5 mM Trp for 3 hours.

value: Trp

growth_protocol: Exponentially growing cells.


title: Control and Trp treated cells, replicate 5


title: Control and IAA-overproducing cells, replicate 1

description: PROBE.I


title: 13063-Tumor-Pancreas

source_name: Paraffin-Tumor-Pancreas-adenocarcinoma

tag: disease

value: Pancreas neoplasia

value: Pancreas


title: 14329-Tumor-Kidney

source_name: Paraffin-Tumor-Kidney-Renal cell carcinoma; Clear cell carcinoma

value: Kidney neoplasia

value: Paraffin

value: Tumor

value: Kidney


title: Control and Trp treated cells, replicate 1

tag: strain


title: Control and IND treated cells, replicate 4

source_name: IND treated cells

growth_protocol: Exponentially growing cells treated with 0.5 mM IND for 3 hours.

value: IND


title: Control and IND treated cells, replicate 5


title: Control and Trp treated cells, replicate 4


title: Control and IND treated cells, replicate 6


title: Control and IAA-overproducing cells, replicate 4


title: Control and Trp treated cells, replicate 2


title: 11072-Tumor adjacent-Lung

value: Lung neoplasia

value: Tumor adjacent

value: Lung


title: Control and Trp treated cells, replicate 3

value: untreated


title: 7151-Tumor-Ovary

source_name: Paraffin-Tumor-Ovary-Surface; Serous; Malignant; adenocarcinoma

value: Ovary neoplasia

value: Ovary


title: Control and IND treated cells, replicate 3


title: Control and IND treated cells, replicate 2


title: 7141-Metastasis-Lung

value: Melanoma

value: Metastasis

value: Melanocytes

value: malignant melanoma


title: 7136-Metastasis-Lung

value: Endometrial neoplasia

value: Endometrium

value: Endometrial adenocarcinoma


title: Control and ICA treated cells, replicate 5

description: PROBE.VIII

source_name: ICA treated cells

growth_protocol: Exponentially growing cells treated with 0.5 mM ICA for 3 hours.

value: ICA


title: Control and IND treated cells, replicate 1


title: Control and ICA treated cells, replicate 6

description: PROBE.IX


title: 7140-Metastasis-Lung

source_name: Paraffin-Metastasis-Kidney-Renal cell carcinoma; Clear cell carcinoma

value: Kidney neoplasia

value: Paraffin


title: Control and ICA treated cells, replicate 4

description: PROBE.VII


title: 7126-Metastasis-Lung

value: Laryngeal neoplasia

value: Larynx

value: Non-small; squamous


title: Control and ICA treated cells, replicate 2


title: 7112-Metastasis-Lung

value: Lung neoplasia

value: Lung

value: salivary gland

value: carcinoma


title: 7119-Tumor-Bile duct

value: Bile duct neoplasia

value: Tumor

value: Bile duct

value: cholangiocarcinoma


title: Control and ICA treated cells, replicate 1

value: untreated


title: 7093-Metastasis-Lymph Node

value: Tongue neoplasia

value: Metastasis

value: Lymph Node

value: Tongue

value: Squamous cell carcinoma


title: Control and IAA treated cells, replicate 4

description: PROBE.IV

source_name: IAA treated cells

growth_protocol: Exponentially growing cells treated with 0.5 mM IAA for 3 hours.

value: IAA


title: 7096-Metastasis-Lymph Node

value: Breast neoplasia

value: Paraffin

value: Breast

value: adenocarcinoma


title: Control and IAA treated cells, replicate 6

description: PROBE.VI


title: 7097-Metastasis-Lymph Node

value: Lung neoplasia

value: Lung

value: Non-small; adenocarcinoma


title: Transgenic 3

first: Sang Hyun

last: Lee

address: 44 Binney Street, SM970

department: Cancer Biology

institute: Dana-Farber Cancer Institute

description: Gene expression data of mPIN of mouse (20 weeks old)

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

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

source_name: ventral prostate

label_protocol: standard Affymetrix protocol

extract_protocol: Total RNA was purified with Trizol and additional purification with Rneasy column.

tag: disease state

value: mPIN (mouse prostatic intraepithelial neoplasia)

tag: age

value: 20 weeks

value: ventral prostate

value: FVB


title: Wild type 1

description: Gene expression data of normal prostate of mouse (20 weeks old)

value: normal


title: 3930-Tumor adjacent-Bladder

value: Bladder neoplasia

value: Tumor adjacent

value: Bladder


title: 4143-Tumor-Colon

source_name: Paraffin-Tumor-Colon-adenocarcinoma

value: Colon neoplasia

value: Tumor

value: Colon


title: Control and IAA treated cells, replicate 5

description: PROBE.V

value: untreated

value: IAA


title: Wild type 3


title: Wild type 4


title: Control and IAA treated cells, replicate 3


title: Transgenic 1


title: 3393-Tumor-Breast

source_name: Paraffin-Tumor-Breast

value: Breast neoplasia

value: Paraffin

value: Breast


title: Control and 2,4-D treated cells, replicate 6

description: PROBE.XII

source_name: 2,4-D treated cells

growth_protocol: Exponentially growing cells treated with 0.5 mM 2,4-D for 3 hours.


title: Wild type 2


title: 1945-Tumor adjacent-Colon


title: Transgenic 4


title: Control and IAA treated cells, replicate 2


title: Transgenic 2


title: Control and IAA treated cells, replicate 1


title: Control and 2,4-D treated cells, replicate 5

description: PROBE.XI


title: Control and 2,4-D treated cells, replicate 4

description: PROBE.X


title: 1634-Normal-Endometrium

source_name: Fresh-Normal-Endometrium

value: Fresh

value: Normal

value: Endometrium


title: Control and ICA treated cells, replicate 3

value: ICA


title: Control and 2,4-D treated cells, replicate 1


title: 1936-Tumor-Bladder

value: Transitional cell carcinoma


title: 1633-Normal-Kidney

source_name: Fresh-Normal-Kidney

value: Kidney


title: 1458-Tumor adjacent-Liver

value: Liver neoplasia

value: Liver

value: Nodular hyperplasia


title: 1619-Normal-Lymph Node

source_name: Fresh-Normal-Lymph Node

value: Lymph Node


title: Control and 2,4-D treated cells, replicate 2

source_name: Control cells


title: 1456-Tumor-Liver

value: Tumor

value: Hepatocellular carcinoma


title: 782-Tumor-Lung

source_name: Paraffin-Tumor-Lung-Non-small; squamous

value: Lung neoplasia

value: Lung

value: Non-small; squamous


title: 983-Tumor-Prostate

source_name: Paraffin-Tumor-Prostate

value: Prostate neoplasia

value: Paraffin

value: Prostate


title: 872-Tumor adjacent-Breast

value: Breast neoplasia

value: Tumor adjacent

value: Breast


title: Control and 2,4-D treated cells, replicate 3

value: untreated


title: Yy1het rep2

city: Parkville

first: Matthew

last: Ritchie

state: Victoria

address: 1G Royal Parade

department: Epigenetics and Development Division

institute: The Walter and Eliza Hall Institute of Medical Research

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization after being log2 transformed using the beadarray package in R

source_name: Fetal liver LSK cells

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

extract_protocol: RNA was extracted using QIAGEN RNeasy micro kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: genotype

tag: cell type

value: fetal liver LSK cell


title: Yy1het rep4

description: replciate 4


title: Wt rep4

description: replicate 4


title: Plt88 rep4

description: replicate 4


title: Bmi1ko rep2

description: replicate 2


title: Wt rep5

description: replicate 5


title: Yy1het rep3

description: replicate 3


title: Bmi1ko rep3

description: replicate 3


title: Wt rep7

description: replicate 7


title: Plt88 rep3

description: replicate 3


title: Wt rep2

description: replicate 2


title: Wt rep1

description: replicate 1


title: Bmi1ko rep1

description: replicate 1


title: Wt rep6

description: replicate 6


title: Plt88 rep2

description: replicate 2


title: Wt rep3

description: replicate 3


title: Yy1het rep1

description: replicate 1


title: Plt88 rep1

description: replicate 1


title: TypeIIIGD_3

city: Bethesda

first: Kory

middle: R

last: Johnson

state: MD

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

description: Cultured Skin Fibroblasts, Gaucher Disease Type III, biological replicate 3

hyb_protocol: Labeled cRNA were hybridized to Affymetrix Human U133A_2 GeneChips (Affymetrix, Inc) in blinded interleaved fashion.

scan_protocol: Affymetrix scanner 3000 was used in conjunction with Affymetrix GeneChip Operation Software to generate ~580,000 probe measurements/hybridized cRNA.

data_processing: The “rma” function in bioconductor (http://www.bioconductor.org/) was used to summarize probe measurements and generate normalized gene fragment expression values for each hybridized cRNA.  Quality of data was assured via sample-level inspection by Tukey box plot, covariance-based PCA scatter plot, and correlation-based Heat Map.  Gene fragments not having at least one expression value greater then system noise were deemed non-informative and discarded.  System noise was defined as the lowest expression value at which the LOWESS fit of observed CV for each gene fragment by mean expression value for each gene fragment changes from non-linear to linear.  For gene fragments not discarded, expression values were floored to equal system noise if less than system noise then subject to significance testing.  The one-factor ANOVA under BH FDR MCC condition (alpha criteria<0.05) was used to identify gene fragments having expression values significantly associated with differences in gender.  Spearman correlation under BH FDR MCC condition (alpha criteria<0.05) was used to identify gene fragments having expression values significantly associated with differences in age.  Gene fragments found to have expression values significantly associated with differences in age and/or gender were discarded before testing gene fragment expression for significant association with Type I and/or Type III GD.  Testing gene fragment expression for significant association with Type I and/or Type III GD was done using the one-factor ANOVA under BH FDR MCC condition (alpha criteria<0.05).  For gene fragments found to have expression significantly associated with Type I and/or Type III GD, the Tukey HSD test was used to code gene fragments having a post-hoc p-value < 0.05 between Type I GD vs. control, Type III GD vs. control, and/or Type III GD vs. Type I GD.  These codes were used classify gene fragments having expression significantly association with Type I and/or Type III GD as significantly dysregulated in Type I GD only, significantly dysregulated in Type III GD only, significantly and concordantly dysregulated in both Type I GD and Type III GD, or significantly and disconcordantly dysregulated in both Type I GD and Type III GD.  Gene fragment annotations and associated gene functions were obtained using IPA (Ingenuity, Inc.).

label_protocol: Labeling was performed on a sample-by-sample basis according to manufacturer’s guidelines for use with the Affymetrix Human Genome U133A_2 GeneChip (Affymetrix, Inc).  DNase treatment was included as part of isolation to remove possible contaminating DNA.  Bioanalyzer nanochip (Agilent, Inc) and NanoDrop (ThermoFisher, Inc) were used to validate and quantitate the RNA prior to cRNA synthesis and labeling.  For cRNA synthesis and labeling, 5ug of total RNA was used per sample in conjunction with the Affymetrix 3’ one-cycle Target labeling Kit (Affymetrix, Inc).

growth_protocol: Cells were grown on DMEM medium  (InVitrogen, Carlsbad, CA) supplemented with 20% heat-inactivated fetal bovine serum (Hyclone, Logan, UT) and 2 mM L-glutamine, and were used before passage 10.   All cultures were initiated at 7.5 x 105 cells per 75 cm2 flask.  The culture medium was changed every 3-4 days.

extract_protocol: On day 16, approximately 10 days post-confluence, cells were harvested following trypsinization.   Cells from triplicate flasks were pooled, washed twice with phosphate buffered saline and re-suspended in PBS.  Cell numbers were determined using a Coulter Counter Model Z.   The total cell suspension was divided into aliquots for RNA extraction, lipid analysis, and determination of residual glucocerebrosidase activity.  The cell suspensions were centrifuged at 1000 x g for 5 min and dry cell pellets were stored at -80 C until used.

tag: gender

value: male

value: 4 yrs


title: TypeIIIGD_4

description: Cultured Skin Fibroblasts, Gaucher Disease Type III, biological replicate 4

value: female

value: 25 yrs


title: TypeIIIGD_1

description: Cultured Skin Fibroblasts, Gaucher Disease Type III, biological replicate 1


title: TypeIIIGD_2

description: Cultured Skin Fibroblasts, Gaucher Disease Type III, biological replicate 2

value: 2 yrs


title: TypeIGD_3

description: Cultured Skin Fibroblasts, Gaucher Disease Type I, biological replicate 3

value: 47 yrs


title: TypeIGD_2

description: Cultured Skin Fibroblasts, Gaucher Disease Type I, biological replicate 2

value: 71 yrs


title: TypeIIIGD_5

description: Cultured Skin Fibroblasts, Gaucher Disease Type III, biological replicate 5


title: TypeIGD_1

description: Cultured Skin Fibroblasts, Gaucher Disease Type I, biological replicate 1

value: 68 yrs


title: TypeIGD_4

description: Cultured Skin Fibroblasts, Gaucher Disease Type I, biological replicate 4

value: 42 yrs


title: Control_3

description: Cultured Skin Fibroblasts, Wild-Type Control, biological replicate 3

value: 32 yrs


title: Control_4

description: Cultured Skin Fibroblasts, Wild-Type Control, biological replicate 4

value: 22 yrs


title: Control_2

description: Cultured Skin Fibroblasts, Wild-Type Control, biological replicate 2


title: camptothecin_6 hours_rep3

city: ORSAY

first: Martin

last: Dutertre

address: Rue Henri Becquerel

country: France

institute: INSERM

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Exon-level analyses were obtained using the Affymetrix Power Tools software, the RMA-sketch algorithm, core probesets, and antigenomic probes for background correction.

source_name: MCF7 cells

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: MCF7 cells were maintained in DMEM with 10% fetal bovine serum in a CO2 humidified chamber at 37 °C

extract_protocol: Total RNA was isolated using Trizol total RNA isolation reagent (Invitrogen) according to the manufacturer's protocol.

treatment_protocol: Cells were treated with camptothecin (1 µM) or 0.1% DMSO as a control.

value: ER+ breast cancer

tag: cell line

tag: agent

value: camptothecin

tag: replicate


title: camptothecin_6 hours_rep2


title: control_6 hours_rep3

value: control


title: Control_1

description: Cultured Skin Fibroblasts, Wild-Type Control, biological replicate 1

value: 29 yrs


title: liver_3x_amplified_rep3

city: Leipzig

first: Thomas

last: Giger

address: Deutscher Platz 6

department: Evolutionary Genetics

country: Germany

institute: Max-Planck-Institute of Evolutionary Anthropology

hyb_protocol: Hybridization, washing and staining to Affymetrix® GeneChip® Mouse Genome arrays was carried out following standard Affymetrix® protocols.

scan_protocol: GeneChips® were scanned using the GeneChip Scanner 3000.

data_processing: Affymetrix® microarray image data were collected with Affymetrix® GeneChip® Operating Software version 1.1 using default parameters. Probe set expression values were calculated using the Robust Multichip Average for small RNA quantities (sRMA) algorithm (Cope et al. 2006). As probe weights for signal summary statistic calculation, we used the inverse of the probe specific coefficient of variation calculated across chips.   Probe sets were defined as expressed if the P-value determined by a signed rank test of perfect match versus mismatch signal distributions was lower or equal 0.05 in at least three chip experiments in a tissue.

source_name: liver, 3X amplified

label_protocol: The 1X Samples were processed according to the Affymetrix standard protocol which involved one linear amplification. The 3X Samples were amplified through two rounds using the RiboAmp HS kit (Arcturus). Amplified RNA was converted to cDNA using Round 2 components of the RiboAmp HS kit, labelled by in vitro transcription in the presence of biotinylated UTP. The quality of the amplified RNA was assessed with a Bioanalyzer Nanochip (Agilent). Amplified cRNA samples were chemically fragmented according to instructions in the Affymetrix sample preparation protocol.

extract_protocol: Total RNA was isolated using TRIzol® reagent from the frozen mouse tissue according to manufacturer’s instructions. After isolation, the RNA was column purified with the Qiagen® RNeasy® kit.

tag: developmental stage

value: adult

tag: tissue

value: liver

tag: linear amplification


title: cerebellum_3x_amplified_rep2

source_name: cerebellum, 3X amplified

value: cerebellum


title: camptothecin_6 hours_rep1


title: cortex_3x_amplified_rep3

source_name: cortex, 3X amplified

value: cortex


title: cerebellum_3x_amplified_rep3


title: control_6 hours_rep2


title: cortex_3x_amplified_rep2


title: Single cell comparison of R2 Old vs R2 Young, rep 2, DAA

description:
DR2Old R2Young-2
Biological replicate 2 of 3.

Detailed protocols are available in the 'GSE18783_Materials_and_Methods.txt' file, which is linked to the Series GSE18783 record as a supplementary file.

source_name: R2 old neuron

value: cholinergic neuron

tag: neuron

value: old

source_name: R2 young neuron

value: young


title: Single cell comparison of R2 Old vs R2 Young, rep 3, DAA

description:
DR2Old R2Young-3
Biological replicate 3 of 3.

Detailed protocols are available in the 'GSE18783_Materials_and_Methods.txt' file, which is linked to the Series GSE18783 record as a supplementary file.


title: liver_3x_amplified_rep2


title: control_6 hours_rep1


title: liver_3x_amplified_rep1


title: TypeIGD_5

description: Cultured Skin Fibroblasts, Gaucher Disease Type I, biological replicate 5

value: male

value: 31 yrs