title: Control

city: Gothenburg

first: Weicheng

last: Ren

address: Guldhedsgatan 10A

country: Sweden

institute: Gothenburg University

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using Affymetrix scanner 3000 7G.

data_processing:
The array image was acquired using Affymetrix Genotyping Console Software version 4.0.
affymetrix-algorithm-name = brlmm-p

source_name: Tail and ear

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Male LxT1 mice were crossed to female BALB/c mice to generate F1 mice. Two females from the F1 litters were backcrossed to the parental male LxT1 to generate N2 mice for analysis of phenotype and genetic mapping.

extract_protocol: DNA was isolated from tails and ears using the Purgene core kit (Qiagen, Valencia, CA).

value: Control

tag: background strain(s)

value: Balb/c


title: FaDu-Bmi1

status: Public on Feb 11 2013

type: RNA

city: Taipei

first: Muh-Hwa

last: Yang

address: No.155, Sec.2, Li-Nong Street

department: Institute of Clinical Medicine

country: Taiwan

institute: National Yang-Ming University

description: miRNA expression in FaDu-Bmi1 stable clone

hyb_protocol: hybrization protocol was performed according to Agilent miRNA microarray system, and chamber type was Agilent microarray.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting. Scan speed was 25, and pixel resolution was 5 microns.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3.1 (Agilent). Data analysis by GeneSpring 7.3.1 (Agilent Technologies).

molecule: total RNA

organism: Homo sapiens

source_name: FaDu, Bmi1-overexpressing cell line

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: all cell lines were growth in RPMI1640 containg 10% FBS, and were incubated at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNAs were extracted with Trizol reagent

treatment_protocol: no treatment was performed

tag: cell type

value: Human hand and neck cancer cell

tag: cell line

value: FaDu


title: CD23low 5

status: Public on Feb 12 2013

type: genomic

label: biotin

molecule: genomic DNA

organism: Mus musculus

tag: gender

value: Male


title: Kv10.1 +/+ wildtype, mouse 3751

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

description: Kv10.1 +/+ wildtype, mouse 3751

hyb_protocol: Sense-strand DNA was hybridized on Affymetrix GeneChip Mouse Gene 1.0 ST Array.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 System.

data_processing: Microarray data were analyzed with Affymetrix GeneChip Command Console Software (Affymetrix). The advanced analysis was done with R (version 2.9) with package limma. Data preprocessing steps included RMA via usage of the R packages affy and probe summarization via the brainarray-cdf file version 10.

label_protocol: Biotinylated sense-strand DNA was generated from 100 ng of total RNA with WT Sense Target Labeling and Control Reagent (Affymetrix).

growth_protocol: No growth protocol

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

treatment_protocol: No treatment. Mice were sacrificed by CO2 inhalation followed by decapitation. Brains were removed and hippocampus were dissected.

tag: mouse age

value: 8 weeks

tag: proband sex

tag: tissue

value: hippocampus

tag: genotype/variation

value: +/+ wildtype


title: Kv10.1 +/+ wildtype, mouse 3759

description: Kv10.1 +/+ wildtype, mouse 3759


title: Kv10.1 +/+ wildtype, mouse 3750

description: Kv10.1 +/+ wildtype, mouse 3750


title: Kv10.1 +/+ wildtype, mouse 3749

description: Kv10.1 +/+ wildtype, mouse 3749


title: CD23low 6

value: Female


title: CD23low 1


title: CD23low 2


title: Kv10.1 -/- knockout, mouse 3763

description: Kv10.1 -/- knockout, mouse 3763

value: -/- knockout


title: Kv10.1 -/- knockout, mouse 3760

description: Kv10.1 -/- knockout, mouse 3760


title: Kv10.1 -/- knockout, mouse 3762

description: Kv10.1 -/- knockout, mouse 3762


title: CD23low 3


title: Kv10.1 -/- knockout, mouse 3753

description: Kv10.1 -/- knockout, mouse 3753


title: Lymphoblastoid JCVI Cy3, Agilent24M_array 3

city: Toronto

first: Andy

last: Pang

state: ON

address: MaRS Centre - East Tower, 101 College Street, Room 14-701

country: Canada

institute: The Centre for Applied Genomics

description: Competitively hybridized to Agilent 24M CGH array set.

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to the array according to the manufacturer's instructions.

scan_protocol: Scanned on an Agilent 3um-resolution scanner. Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).

data_processing: Agilent Feature Extraction Software (v 10.51.1) was used for background subtraction and Lowess normalization. The GFF file (linked to the Series record) includes the genomic coordinates and direction of calls (i.e., gain or loss).

source_name: HuRef lymphoblastoid cell line

label_protocol: As per the manufacturer's (Agilent) instructions.

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted from lymphoblastoid cell lines. DNA quality and quantity were assessed using a NanoDrop Spectrophotometer.

value: HuRef

value: lymphoblastoid

value: male

source_name: NA15510 lymphoblastoid cell line

value: female

tag: sample type

value: reference


title: Normal CD23 4

value: Normal CD23


title: Lymphoblastoid JCVI Cy3, Agilent24M_array 1


title: Normal CD23 5


title: iRUNX1_DOX+_techreplicate 4

city: Birmingham

first: Salam

middle: Adli

last: Assi

address: IBR

department: Institute for Cancer and Genomic Sciences

country: United Kingdom

institute: University of Birmingham

description:
iRUNX1_DOX+_t4_A24
with induction

hyb_protocol: Hybridisation samples were prepared for a 8-pack microarray using 600 ng cRNA each according to the hybridisation protocol from Agilent: One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling), loaded onto the 8-pack array slide and hybridised at 65 °C overnight

scan_protocol: After washing the microarray was scanned on an Agilent C Scanner using the Profile AgilentG3_GX_1Color for 8x60K microarrays (Dye channel: Green; Scan region: Scan Area (61 x 21.6 mm); Scan resolution (μm): 3; Tiff: 20 bit)

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) (protocol GE1_107_Sep09, Grid: 028005_D_F_20100614 and platform Agilent SurePrint G3 Mouse GE 8x60K). The raw data output by Feature Extraction Software was analysed using the LIMMA R package with quantile normalisation and background subtraction.

source_name: from differentiating murine hematopoietic cells

label_protocol: 25 ng RNA was labelled with Cyanine 3-CTP according to the sample preparation protocol from Agilent: One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling). Amplified labelled RNA samples were purified by using Qiagen's RNeasy mini spin columns and cRNA quantified by using a Nanodrop

growth_protocol: A single cell suspension of ES cells was transferred into IVD media (IMDM with 15 % FCS, Pen/Strep, 1 mM glutamine, 0.15 mM MTG, 0.18 mg/ml human transferrin (Roche 652202) and 50 µg/ml ascorbic acid) on 15 cm low adherence bacteriological plates (Sterilin) at a concentration of 2.5 X 104/ml. After 3.25 days embryoid bodies were collected and dissociated by digested with 1 x trypsin/EDTA. The cell suspension was re-suspended in IMDM + 20 % FCS. Flk-1+ (CD309) cells were isolated using a biotinylated Flk-1 antibody (eBioscience 13-5821) used at 5 µl per 107 cells for 10 minutes on ice, followed by 2x wash with MACS buffer (PBS + 5 % BSA and 0.5 mM EDTA). Cells bound by the antibody were then isolated using antibiotin beads and MACS LS columns (Miltenyi Biotec) according to the manufacturers instructions. Purified Flk-1+ve cells were plated in blast media (IMDM supplemented with 10% FCS, Pen/Strep, 1 mM glutamine, 0.45 mM MTG, 0.18 mg/ml human transferrin, 25 µg/ml Ascorbic acid, 20 % D4T conditioned media, 5 µg/L mVEGF (Peprotech), 10 µg/L mIL-6 (Miltenyi Biotec)) at a concentration of 8-10 X103/cm2 on gelatinized tissue culture treated dishes. D4T conditioned media was made by growing confluent D4T cells in fresh IMDM media supplemented with 10 % FCS, Pen/Strep, 1 mM glutamine, 0.15 mM MTG and 50 ng/ml acidic human FGF (R&D Sytems) for 3-4 days. After 2-2.5 days cells were trypsinised, again MACS sorted for Flk-1+ cells as described before and 2x104/ cm2 Flk-1+ cells were plated on gelatin coated tissue culture plates and cultured for 2 days. Hemogenic endothelium media – IMDM supplemented with 10 % FCS, Pen/Strep, 1 mM glutamine, 0.15 mM MTG, 0.18 mg/ml human transferrin, 25 µg/ml Ascorbic acid, Oncostatin 10 µg/ml (R&D Systems 495-MO), basic mFGF 1 µg/ml (Peprotech 450-33), mSCF 10 µg/ml (Peprotech 500-P71).

extract_protocol: RNA was extracted from cells using TRIzol® (Invitrogen) according to manufacturers instruction. First strand cDNA synthesis was carried out using M-MLV reverse transcriptase (Invitrogen) according to manufacturers instructions using 1-2 μg of RNA. Real Time PCR was carried out using ABI SYBR® green master mix with 2 μl of diluted cDNA and 0.25 μM primer per 10 μl reaction on an ABI 7500 machine.

treatment_protocol: Hemogenic endothelium (HE) cells were treated for an overnight period with 0.3 µl/ml doxycycline to induce the expression of Runx1 (Tet-on system)

tag: strain

value: hemogenic endothelium (HE) cells

value: Runx1 expression


title: Lymphoblastoid JCVI Cy3, Agilent24M_array 11


title: ESO-409

city: Boston

first: Shouyong

last: Peng

state: MA

address: 450 Brookline Avenue

department: Medical Oncology

country: USA

institute: Dana-Farber Cancer Institute

description: gene expression data from individual esophageal adenocarcinoma

hyb_protocol: Hybridization was performed at the Mount Sinai Microarray facility according to standard protocols from Affymetrix.

scan_protocol: Processed microarrays were scanned using the GeneChip Scanner 7G.

data_processing: Raw data was processed using the gene chip robust multiarray averaging approach with R/bioconductor package affydata to get normalized expression data for each probe set on the arrays. The parameters for expresso function are:  bgcorrect.method=rma, normalize.method=quantiles, pmcorrect.method=pmonly,  summary.method=medianpolish.

label: Biotin

source_name: esophageal adenocarcinoma (EAC) primary tumor

label_protocol: Total RNA (1ug) was labeled with biotin using a single-round, 3' in vitro transcription reaction (affymetrix)

extract_protocol: Stratagene RNA Isolation Kit (catalog # 200345) according to the manufacturer’s protocol. RNA quality and purity were assessed by capillary electrophoresis using an Agilent Bioanalyzer (Agilent, Santa Clara CA) and UV spectrophotometer (Nanodrop, Wilmington DE). RNA was used if the RNA integrity number was greater than 6.0 and the 260/280 ratio was greater than 1.8.

treatment_protocol: No radiation or chemotherapy

tag: tissue type

value: Tumor

tag: age

tag: ethnicity

value: Caucasian

tag: location

value: esophagus

tag: tumor grade

value: moderately

tag: barrett's associated

value: yes

tag: pathological t

tag: pathological n

tag: clinical m

tag: smoking status

value: no

tag: pack years

tag: fraction of ap*a mutations

tag: non-silent mutation rate per mb (wes)


title: Lymphoblastoid JCVI Cy3, Agilent24M_array 2

tag: cell line

tag: cell type

tag: gender


title: Normal CD23 3

tag: background strain(s)


title: Lymphoblastoid JCVI Cy3, Agilent24M_array 13

tag: sample type


title: Lymphoblastoid JCVI Cy3, Agilent24M_array 22


title: Lymphoblastoid JCVI Cy3, Agilent24M_array 6


title: Lymphoblastoid JCVI Cy3, Agilent24M_array 4


title: Lymphoblastoid JCVI Cy3, Agilent24M_array 14


title: iRUNX1_DOX+_replicate2

description:
iRUNX1_DOX+_2_A14
with induction

tag: strain

tag: genotype/variation


title: ESO-774

tag: tissue type

tag: age

tag: ethnicity

tag: location

value: poorly

value: yes-former


title: iRUNX1_DOX-_techreplicate4

description:
iRUNX1_DOX-_t4_A22
without induction

value: control


title: Lymphoblastoid JCVI Cy3, Agilent24M_array 5

value: HuRef


title: iRUNX1_DOX-_replicate3

description:
iRUNX1_DOX-_3_A21
without induction


title: Ex Vivo Blood day-14 Su44

city: Madrid

first: Juan Ángel

last: Fresno Vara

state: Madrid

address: Paseo de la castellana 261

department: INGEMM

country: Spain

institute: Hospital La Paz

description: 14-day sunitinib treated miRNA expression from white blood cells

hyb_protocol: Cy3 labeled RNA were hybridized for 20 hours at 55ºC in a hybridization oven (G2545A, Agilent) set to 20 rpm in a final concentration of 1X GE Blocking Agent and 1X Hi-RPM Hybridization Buffer, according to manufacturer's instructions (miRNA Microarray System Protocol, Agilent Technologies).

scan_protocol: Arrays were scanned at 5µm resolution on an Agilent DNA Microarray Scanner (G2565BA, Agilent Technologies) equipped with extended dynamic range (XDR) software.

data_processing: Data were normalized using Variance Stabilization Normalization. Only miRNAs with an average intensity over the 20th percentile of the overall intensities, a detectable signal in at least 15 out of the 76 samples hybridized and normalized mean expression over 0.9 were considered for further analysis.

source_name: Peripheral blood, day-14, sunitinib 50 mg daily, Su44

label_protocol: 100 ng of total RNA were dephosphorylated and Cyanine 3-pCp molecule was ligated to the 3´ end of each RNA molecule by using T4 RNA ligase.

extract_protocol: Leukocytes were captured using the LeukoLOCK™ System and stabilized using RNAlater (Ambion). Total RNA was extracted using the miRNeasy Mini kit (Qiagen) following the manufacturer’s protocol.

treatment_protocol: Dose reduction or dose delay as well as follow-up schedules were dictated locally. RECIST criteria were followed to assess response.

value: Leukocytes captured using LeukoLOCK

tag: mskcc

tag: psf (t)

tag: psf (s)

tag: os (t)

tag: os (s)

tag: treatment

value: sunitinib

tag: subject

tag: legend

value: MSKCC, Memorial Sloan-Kettering Cancer Center prognostic scale (0,Good, 1, intermediate, 2, Bad); PSF(T), Progression free survival (time in months); PSF(S), Progression free survival (status, 1 means relapse); OS(T), Overall Survival(time in months); OS(S), Overall Survival (status, 1 means exitus)

tag: disease state

value: renal cell carcinoma


title: ESO-682

tag: gender

value: male

tag: tumor grade

tag: barrett's associated

tag: pathological t

tag: pathological n

tag: clinical m

tag: smoking status

value: yes-current

tag: pack years

tag: fraction of ap*a mutations

tag: non-silent mutation rate per mb (wes)


title: Ex Vivo Blood day-14 Su43

source_name: Peripheral blood, day-14, sunitinib 50 mg daily, Su43

tag: cell type

tag: mskcc

tag: psf (t)

tag: psf (s)

value: MSKCC, Memorial Sloan-Kettering Cancer Center prognostic scale (0, Good, 1, intermediate, 2, Bad); PSF(T), Progression free survival (time in months); PSF(S), Progression free survival (status, 1 means relapse); OS(T), Overall Survival(time in months); OS(S), Overall Survival (status, 1 means exitus)


title: ESO-601

tag: tissue type

value: Tumor

tag: age

tag: ethnicity

tag: location


title: ESO-130

tag: gender

value: Caucasian

tag: tumor grade


title: iRUNX1_DOX-_replicate2

description:
iRUNX1_DOX-_2_A13
without induction

tag: strain

value: hemogenic endothelium (HE) cells

tag: genotype/variation


title: ESO-721

value: female

value: esophagus

value: moderately

tag: barrett's associated

tag: pathological t

tag: pathological n

tag: clinical m


title: iRUNX1_DOX+_replicate1

description:
iRUNX1_DOX+_1_A12
with induction

value: Runx1 expression


title: iRUNX1_DOX+_replicate3

description:
iRUNX1_DOX+_3_A23
with induction


title: ESO-582

value: poorly

value: no

tag: smoking status

value: yes- current

tag: pack years

tag: fraction of ap*a mutations

tag: non-silent mutation rate per mb (wes)


title: ESO-913


title: Lymphoblastoid JCVI Cy3, Agilent24M_array 12

tag: cell line

value: HuRef

tag: cell type

value: lymphoblastoid

tag: sample type

value: reference


title: iRUNX1_DOX-_replicate1

description:
iRUNX1_DOX-_1_A11
without induction

value: control


title: CD23low 4

tag: background strain(s)

value: Male


title: Normal CD23 2

value: Normal CD23

value: Female


title: Lymphoblastoid JCVI Cy3, Agilent24M_array 17

value: male


title: Ex Vivo Blood day-14 Su41

source_name: Peripheral blood, day-14, sunitinib 50 mg daily, Su41

value: Leukocytes captured using LeukoLOCK

tag: mskcc

tag: psf (t)

tag: psf (s)

tag: os (t)

tag: os (s)

tag: treatment

value: sunitinib

tag: subject

tag: legend

value: MSKCC, Memorial Sloan-Kettering Cancer Center prognostic scale (0,Good, 1, intermediate, 2, Bad); PSF(T), Progression free survival (time in months); PSF(S), Progression free survival (status, 1 means relapse); OS(T), Overall Survival(time in months); OS(S), Overall Survival (status, 1 means exitus)

tag: disease state

value: renal cell carcinoma


title: Ex Vivo Blood day-14 Su40

source_name: Peripheral blood, day-14, sunitinib 50 mg daily, Su40


title: Normal CD23 1

tag: gender


title: Ex Vivo Blood day-14 Su39

source_name: Peripheral blood, day-14, sunitinib 50 mg daily, Su39


title: ESO-327

tag: tissue type

value: Tumor

tag: age

tag: ethnicity

value: Caucasian

tag: location

value: esophagus

tag: tumor grade

tag: barrett's associated

tag: pathological t

tag: pathological n

tag: clinical m

tag: smoking status

tag: pack years


title: Ex Vivo Blood day-14 Su37

source_name: Peripheral blood, day-14, sunitinib 50 mg daily, Su37

tag: cell type

tag: mskcc

tag: psf (t)

tag: psf (s)

tag: os (t)

tag: os (s)


title: Ex Vivo Blood day-14 Su34

source_name: Peripheral blood, day-14, sunitinib 50 mg daily, Su34

tag: treatment

tag: subject

tag: legend

tag: disease state


title: Ex Vivo Blood day-14 Su36

source_name: Peripheral blood, day-14, sunitinib 50 mg daily, Su36


title: Ex Vivo Blood day-14 Su32

source_name: Peripheral blood, day-14, sunitinib 50 mg daily, Su32


title: Ex Vivo Blood day-14 Su33

source_name: Peripheral blood, day-14, sunitinib 50 mg daily, Su33


title: ESO-837

tag: tissue type

tag: gender

tag: age

tag: ethnicity

tag: location

tag: tumor grade

value: moderately

value: yes

value: no

tag: fraction of ap*a mutations

tag: non-silent mutation rate per mb (wes)


title: Ex Vivo Blood day-14 Su31

source_name: Peripheral blood, day-14, sunitinib 50 mg daily, Su31

tag: cell type

tag: mskcc


title: Ex Vivo Blood day-14 Su29

source_name: Peripheral blood, day-14, sunitinib 50 mg daily, Su29

tag: psf (t)

tag: psf (s)


title: ESO-874

value: poorly

tag: barrett's associated

tag: pathological t

tag: pathological n

tag: clinical m

tag: smoking status

tag: pack years


title: ESO-1060

tag: tissue type

tag: gender


title: ESO-838

tag: age

tag: ethnicity


title: Lymphoblastoid JCVI Cy3, Agilent24M_array 18

tag: cell line

value: HuRef

value: lymphoblastoid

value: female

tag: sample type

value: reference


title: Ex Vivo Blood day-14 Su28

source_name: Peripheral blood, day-14, sunitinib 50 mg daily, Su28

tag: os (t)

tag: os (s)

tag: treatment

tag: subject

tag: legend

tag: disease state


title: OECM1-let7i

hyb_protocol: Hybridization was performed according to the standard Affymetrix protocol (see complete protocol descriptions: http://www.affymetrix.com/support/technical/manual/expression_manual.affx

scan_protocol: Arrays were scanned with the Affymetrix GeneChip® Scanner 3000 7G and the data was extracted using Microarray Analysis Suite 5.0 (Affymetrix).

data_processing: We used the Affymetrix GeneChip Suite 5.0 software (MAS 5.0) to calculate raw expression values for each probe sets on the U133 2.0 oligonucleotide arrays.

source_name: Head and neck cancer cell line OECM1 transfected with pmCherry-let7i

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol (see complete protocol descriptions: http://www.affymetrix.com/support/technical/manual/expression_manual.affx)

growth_protocol: cultivated in RPMI + 10% fetal bovine serum

extract_protocol: Cells were lysed by adding 2 ml of trizol reagent (Invitrogen) and homogenized by passing through a syringe with a needle (26G). RNA was picked up in the aqueous phase following phase separation by chloroform. The RNA was then precipitate with isopropanol, washed with ethanol (75%), dissolved in DEPC-treated RNAse/DNAse free water and quantified by spectrophotometry.

tag: transfection


title: iPS CTRL-1 c26

city: Bethesda

first: Yanqin

state: Maryland

address: 10 Center Dr.

institute: NIH

hyb_protocol: Labeled and Fragmented ST cDNA was hybridized to Human Exon 1.0 ST arrays for 16 hours at 45C in an hybridization oven.

scan_protocol: Stained chips were scanned in Affymetrix GCS 3000G scanner

data_processing:
Affymetrix Expression Console RMA normalization, the probesets were summarized at ‘extended’ (mRNA evidence) level
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.extended.mps

source_name: iPSC derived from Fib CTRL1

label_protocol: Target labeling of RNA for Human exon arrays was done using the Affymetrix/Ambion WT cDNA synthesis and labeling protocol.

growth_protocol: Fibroblast were cultured in Dulbecco's Modified Eagle Medium (DMEM, Gibco), 10% fetal bovine serum (FBS) Sigma-Aldrich, 1% Penicillin-Streptomycin–Glutamine (PSG, Gibco), iPSC and H1 were grown on MEF (GlobalStem) in DMEM/F12, supplemented with 20% knockout serum replacement (KSR), 0.1mM nonessential amino acids, 1mM L-glutamine (all Gibco), 10ng/mL recombinant human fibroblast like growth factor-basic (Peprotech, Rocky Hill, NJ), 0.1mM 2-mercaptoethanol (Sigma-Aldrich)

extract_protocol: Cell lysates were homogenized using the QIAshredder Kit (Qiagen) and total RNA was extracted using the RNeasy Mini Kit (Qiagen).

tag: cell type

value: iPS CTRL-1 c26


title: ES-H1, p32

source_name: human ES line

value: ES

tag: passage


title: OECM1-mCherry

source_name: Head and neck cancer cell line OECM1 transfected with pmR-mCherry empty vector

value: pmR-mCherry  empty vector


title: Ex Vivo Blood day-14 Su27

source_name: Peripheral blood, day-14, sunitinib 50 mg daily, Su27

value: Leukocytes captured using LeukoLOCK

tag: mskcc

tag: psf (t)

tag: psf (s)

value: sunitinib


title: iPS CTRL-1 c3

value: iPS CTRL-1 c3


title: Ex Vivo Blood day-14 Su25

source_name: Peripheral blood, day-14, sunitinib 50 mg daily, Su25

value: MSKCC, Memorial Sloan-Kettering Cancer Center prognostic scale (0,Good, 1, intermediate, 2, Bad); PSF(T), Progression free survival (time in months); PSF(S), Progression free survival (status, 1 means relapse); OS(T), Overall Survival(time in months); OS(S), Overall Survival (status, 1 means exitus)

value: renal cell carcinoma


title: ES-H1, p39


title: Ex Vivo Blood day-14 Su26

source_name: Peripheral blood, day-14, sunitinib 50 mg daily, Su26


title: iPS TERT[R1084P]c13

source_name: iPSC derived from Fib TERT[R1084P]

value: iPS TERT[R1084P]c13


title: Ex Vivo Blood day-14 Su24

source_name: Peripheral blood, day-14, sunitinib 50 mg daily, Su24


title: ESO-718

source_name: esophageal adenocarcinoma (EAC) primary tumor

tag: tissue type

value: Tumor

tag: gender

value: male

value: Caucasian

tag: location

value: esophagus

tag: tumor grade

value: moderately

tag: barrett's associated

tag: pathological t

tag: pathological n

tag: clinical m

tag: smoking status

value: yes-former

tag: pack years

tag: fraction of ap*a mutations

tag: non-silent mutation rate per mb (wes)


title: Lymphoblastoid JCVI Cy3, Agilent24M_array 19

source_name: HuRef lymphoblastoid cell line

tag: cell line

value: HuRef

tag: cell type

value: lymphoblastoid

source_name: NA15510 lymphoblastoid cell line

value: female

tag: sample type


title: iPS CTRL-1 c2

value: iPS CTRL-1 c2


title: Ex Vivo Blood day-14 Su19

source_name: Peripheral blood, day-14, sunitinib 50 mg daily, Su19

tag: mskcc

tag: psf (t)

tag: os (t)

tag: os (s)

tag: treatment

tag: subject

tag: legend

tag: disease state


title: Ex Vivo Blood day-14 Su20

source_name: Peripheral blood, day-14, sunitinib 50 mg daily, Su20

tag: psf (s)


title: Ex Vivo Blood day-14 Su22

source_name: Peripheral blood, day-14, sunitinib 50 mg daily, Su22


title: iPS TERT[R1084P]c5.1

value: iPS TERT[R1084P]c5.1


title: iPS TERT[R1084P]c 7

value: iPS TERT[R1084P]c 7


title: iPS TERT[R889X]m c20

source_name: iPSC derived from Fib TERT[R889X]m

value: iPS TERT[R889X]m c20


title: Ex Vivo Blood day-14 Su18

source_name: Peripheral blood, day-14, sunitinib 50 mg daily, Su18

value: Leukocytes captured using LeukoLOCK

value: sunitinib


title: Ex Vivo Blood day-14 Su21

source_name: Peripheral blood, day-14, sunitinib 50 mg daily, Su21

value: MSKCC, Memorial Sloan-Kettering Cancer Center prognostic scale (0,Good, 1, intermediate, 2, Bad); PSF(T), Progression free survival (time in months); PSF(S), Progression free survival (status, 1 means relapse); OS(T), Overall Survival(time in months); OS(S), Overall Survival (status, 1 means exitus)

value: renal cell carcinoma


title: Ex Vivo Blood day-14 Su17

source_name: Peripheral blood, day-14, sunitinib 50 mg daily, Su17


title: Ex Vivo Blood day-14 Su14

source_name: Peripheral blood, day-14, sunitinib 50 mg daily, Su14


title: iPS TERT[R889X]f c20

source_name: iPSC derived from Fib TERT[R889X]f

value: iPS TERT[R889X]f c20


title: iPS TERC[-58>G] c18

source_name: iPSC derived from Fib TERC[-58>G]

value: iPS TERC[-58>G] c18


title: iPS TERT[R889X]f c4.1

value: iPS TERT[R889X]f c4.1


title: iPS TERC[-58>G] c13

value: iPS TERC[-58>G] c13


title: iPS TERT[R889X]f c2

value: iPS TERT[R889X]f c2


title: Fib TERT[R889X]m

source_name: fibroblast

value: Fib TERT[R889X]m


title: Fib CTRL1

value: Fib CTRL1


title: Ex Vivo Blood day-14 Su13

source_name: Peripheral blood, day-14, sunitinib 50 mg daily, Su13


title: Fib TERC[-58>G]

value: Fib TERC[-58>G]


title: Ex Vivo Blood day-14 Su11

source_name: Peripheral blood, day-14, sunitinib 50 mg daily, Su11


title: Ex Vivo Blood day-14 Su16

source_name: Peripheral blood, day-14, sunitinib 50 mg daily, Su16


title: Ex Vivo Blood day-14 Su12

source_name: Peripheral blood, day-14, sunitinib 50 mg daily, Su12


title: Ex Vivo Blood day-14 Su04

source_name: Peripheral blood, day-14, sunitinib 50 mg daily, Su04


title: Ex Vivo Blood day-14 Su05

source_name: Peripheral blood, day-14, sunitinib 50 mg daily, Su05


title: Ex Vivo Blood day-14 Su07

source_name: Peripheral blood, day-14, sunitinib 50 mg daily, Su07


title: Lymphoblastoid JCVI Cy3, Agilent24M_array 24

source_name: HuRef lymphoblastoid cell line

value: HuRef

value: lymphoblastoid

tag: gender

value: male

source_name: NA15510 lymphoblastoid cell line

value: female

value: reference


title: Ex Vivo Blood day-14 Su42

source_name: Peripheral blood, day-14, sunitinib 50 mg daily, Su42

value: Leukocytes captured using LeukoLOCK

value: MSKCC, Memorial Sloan-Kettering Cancer Center prognostic scale (0, Good, 1, intermediate, 2, Bad); PSF(T), Progression free survival (time in months); PSF(S), Progression free survival (status, 1 means relapse); OS(T), Overall Survival(time in months); OS(S), Overall Survival (status, 1 means exitus)


title: Fib TERT[R1084P]

value: Fib TERT[R1084P]


title: Ex Vivo Blood day-14 Su10

source_name: Peripheral blood, day-14, sunitinib 50 mg daily, Su10

value: sunitinib

value: MSKCC, Memorial Sloan-Kettering Cancer Center prognostic scale (0,Good, 1, intermediate, 2, Bad); PSF(T), Progression free survival (time in months); PSF(S), Progression free survival (status, 1 means relapse); OS(T), Overall Survival(time in months); OS(S), Overall Survival (status, 1 means exitus)

value: renal cell carcinoma


title: Ex Vivo Blood day-14 Su08

source_name: Peripheral blood, day-14, sunitinib 50 mg daily, Su08


title: Ex Vivo Blood day-14 Su06

source_name: Peripheral blood, day-14, sunitinib 50 mg daily, Su06


title: Ex Vivo Blood day-14 Su03

source_name: Peripheral blood, day-14, sunitinib 50 mg daily, Su03


title: Ex Vivo Blood Basal Su44

source_name: Peripheral blood, basal, Su44

value: basal


title: Ex Vivo Blood day-14 Su02

source_name: Peripheral blood, day-14, sunitinib 50 mg daily, Su02


title: Prostate_Cancer [G275]

city: Rotterdam

first: Guido

last: Jenster

department: Urology

country: Netherlands

institute: Erasmus MC

hyb_protocol: Standard hybridization protocol for Affymetrix human exon 1.0 ST

scan_protocol: Standard scanner for Affymetrix human exon 1.0 ST

data_processing:
Cel files were processed using Partek RMA core probeset level
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core

source_name: radical prostatectomy prostate tumor

label_protocol: Standard whole transcript labeling protocol from Affymetrix human exon 1.0 ST

growth_protocol: Samples are radical prostatectomy tissues directly taken from the patient

extract_protocol: The standard protocol from RNA-Bee (Campro Scientific) was used to extract total RNA

treatment_protocol: Samples were taken from the surgically removed prostate and fresh frozen in liq N2-cooled iso-pentane

tag: psa progression

value: no

tag: development of metastasis

tag: initial psa (ug/l)

tag: gleason score

tag: pt-stage


title: iPS TERC[-58>G] c14

source_name: iPSC derived from Fib TERC[-58>G]

tag: cell type

value: iPS TERC[-58>G] c14


title: Prostate_Cancer [G289]


title: Prostate_Cancer [G288]

value: yes


title: Prostate_Cancer [G268]


title: Prostate_Cancer [G270]


title: Prostate_Cancer [G230]


title: Prostate_Cancer [G226]


title: Prostate_Cancer [G201]


title: Ex Vivo Blood Basal Su42

description: Basal miRNA expression from white blood cells

source_name: Peripheral blood, basal, Su42


title: Ex Vivo Blood Basal Su41

source_name: Peripheral blood, basal, Su41


title: Ex Vivo Blood Basal Su40

source_name: Peripheral blood, basal, Su40


title: Ex Vivo Blood day-14 Su01

source_name: Peripheral blood, day-14, sunitinib 50 mg daily, Su01


title: Prostate_Cancer [G262]


title: Prostate_Cancer [G192]


title: Prostate_Cancer [G197]


title: Fib TERT[R889X]f

source_name: fibroblast

value: Fib TERT[R889X]f


title: Ex Vivo Blood Basal Su36

source_name: Peripheral blood, basal, Su36


title: Ex Vivo Blood Basal Su43

source_name: Peripheral blood, basal, Su43


title: Prostate_Cancer [G195]


title: Prostate_Cancer [G271]


title: Ex Vivo Blood Basal Su34

source_name: Peripheral blood, basal, Su34


title: Ex Vivo Blood Basal Su39

source_name: Peripheral blood, basal, Su39


title: Prostate_Cancer [G188]


title: Prostate_Cancer [G190]


title: Prostate_Cancer [G182]


title: Ex Vivo Blood Basal Su33

source_name: Peripheral blood, basal, Su33


title: Ex Vivo Blood Basal Su37

source_name: Peripheral blood, basal, Su37


title: Ex Vivo Blood Basal Su31

source_name: Peripheral blood, basal, Su31


title: Ex Vivo Blood Basal Su32

source_name: Peripheral blood, basal, Su32


title: Prostate_Cancer [G177]


title: Prostate_Cancer [G176]


title: Ex Vivo Blood Basal Su28

source_name: Peripheral blood, basal, Su28


title: Prostate_Cancer [G165]


title: Ex Vivo Blood Basal Su25

source_name: Peripheral blood, basal, Su25


title: Ex Vivo Blood Basal Su26

source_name: Peripheral blood, basal, Su26


title: Prostate_Cancer [G173]

source_name: radical prostatectomy prostate tumor


title: Ex Vivo Blood Basal Su27

source_name: Peripheral blood, basal, Su27


title: Ex Vivo Blood Basal Su24

source_name: Peripheral blood, basal, Su24


title: Prostate_Cancer [G187]


title: Ex Vivo Blood Basal Su29

source_name: Peripheral blood, basal, Su29


title: Prostate_Cancer [G154]


title: Prostate_Cancer [G178]


title: Prostate_Cancer [G150]


title: Prostate_Cancer [G146]


title: Ex Vivo Blood Basal Su21

source_name: Peripheral blood, basal, Su21


title: Ex Vivo Blood Basal Su20

source_name: Peripheral blood, basal, Su20


title: Ex Vivo Blood Basal Su19

source_name: Peripheral blood, basal, Su19


title: Ex Vivo Blood Basal Su18

source_name: Peripheral blood, basal, Su18


title: Ex Vivo Blood Basal Su17

source_name: Peripheral blood, basal, Su17


title: Prostate_Cancer [G157]


title: Prostate_Cancer [G160]


title: Prostate_Cancer [G124]


title: Ex Vivo Blood Basal Su16

source_name: Peripheral blood, basal, Su16


title: Ex Vivo Blood Basal Su14

source_name: Peripheral blood, basal, Su14


title: Prostate_Cancer [G108]


title: Prostate_Cancer [G110]


title: Prostate_Cancer [G082]


title: Prostate_Cancer [G085]


title: Prostate_Cancer [G079]


title: Prostate_Cancer [G072]


title: Ex Vivo Blood Basal Su12

source_name: Peripheral blood, basal, Su12


title: Ex Vivo Blood Basal Su11

source_name: Peripheral blood, basal, Su11


title: Ex Vivo Blood Basal Su10

source_name: Peripheral blood, basal, Su10


title: Ex Vivo Blood Basal Su22

source_name: Peripheral blood, basal, Su22


title: Ex Vivo Blood Basal Su08

source_name: Peripheral blood, basal, Su08


title: Ex Vivo Blood Basal Su07

source_name: Peripheral blood, basal, Su07


title: Ex Vivo Blood Basal Su06

source_name: Peripheral blood, basal, Su06


title: Ex Vivo Blood Basal Su13

source_name: Peripheral blood, basal, Su13


title: Prostate_Cancer [G102]

source_name: radical prostatectomy prostate tumor


title: Prostate_Cancer [G089]


title: Ex Vivo Blood Basal Su05

source_name: Peripheral blood, basal, Su05


title: Prostate_Cancer [G106]


title: Ex Vivo Blood Basal Su02

source_name: Peripheral blood, basal, Su02


title: Prostate_Cancer [G056]


title: Ex Vivo Blood Basal Su03

source_name: Peripheral blood, basal, Su03


title: Prostate_Cancer [G014]


title: Prostate_Cancer [G008]


title: Prostate_Cancer [G053]


title: Prostate_Cancer [G032]


title: Ex Vivo Blood Basal Su01

source_name: Peripheral blood, basal, Su01


title: Prostate_Cancer [G037]

value: unknown


title: Prostate_Cancer [G042]


title: Prostate_Cancer [G004]


title: Prostate_Cancer [G007]


title: Prostate_Cancer_xenograft [PC346B]

description: xenograft on NMRI nu/nu male mice

data_processing:
Cel files were processed using Partek RMA extended probeset level
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.extended

source_name: prostate tumor

growth_protocol: Cell lines were cultured in their standard culture medium; Xenografts were grown on NMRI nu/nu male mice

treatment_protocol: Samples were directly used for RNA isolation or fresh frozen in liq N2-cooled iso-pentane

tag: prostate cancer xenograft


title: Prostate_Cancer_xenograft [PCEW]

description: xenograft on NMRI nu/nu male mice

value: PCEW


title: Ex Vivo Blood Basal Su04

source_name: Peripheral blood, basal, Su04

tag: mskcc


title: Prostate_Cancer [G018]


title: Prostate_Cancer_xenograft [PC310]

description: xenograft on NMRI nu/nu male mice


title: Prostate_Cancer_xenograft [PC329]

description: xenograft on NMRI nu/nu male mice


title: Prostate_Cancer_xenograft [PC339]

description: xenograft on NMRI nu/nu male mice


title: Prostate_Cancer_xenograft [PC324]

description: xenograft on NMRI nu/nu male mice


title: Prostate_Cancer_xenograft [PC374]

description: xenograft on NMRI nu/nu male mice


title: Prostate_Cancer [G006]


title: Prostate_Cancer_xenograft [PC135]

description: xenograft on NMRI nu/nu male mice


title: Prostate_Cancer_xenograft [PC133]

description: xenograft on NMRI nu/nu male mice


title: OECM1-sh-Bmi1

description: miRNA expression in knockdown of Bmi1 OECM1  stable clone

source_name: OECM1, knockdown expression of Bmi1 cell line

value: Human hand and neck cancer cell

tag: cell line


title: Prostate_Cancer_cell_line [VCaP]

value: VCaP


title: WT_6h

first: Lukas

last: Baitsch

department: Cancer Biology

institute: Dana Farber Cancer Institute

description: gene expression at 6h post stimulation

hyb_protocol: Hybridization was performed according to manufacturer recommendations to Agilent Whole Human Genome Oligo Microarrays (4x44k).

scan_protocol: Agilend microarray scanner system (Agilent).

data_processing: data was obtained using the Feature Extraction Software version v.9.1. Background correction, Normalization, and Filtering were done using  the Agi4x44PreProcess software package for Bioconductor. The preinstalled thresholds for probe filtering were applied, which filter probes that do not fulfull the following criteria in at least 75% of the samples: (i) above detection limit, (ii) are found, (iii) above negative controls and (iv) are not saturated. After filtering, 33114 probes remaind in the dataset. The limma package was used to calculate differentially expressed genes.

label_protocol: 1ug RNA was amplified using a T7-based amplification protocol and labeled with Cyanine 3 (Cy3).

growth_protocol: primary CD8 T cells were transduced with sequence-optimized NY-ESO-1 specific TCR variants and cultivated in RPMI + 8% HS + 10U/ml rhIL-2 for 24h

extract_protocol: After incubation, cells were washed with ice-cold PBS and then quick frozen in liquid nitrogen. RNA extraction was isolated using NucleoSpin RNA II extraction protocol (MN).

treatment_protocol: cells were either left untreated (baseline, 0h) or were stimulated with 0.002ug/ml unlabeled NY-ESO-1(57-165)-specific multimer for 6h at 37 degrees celsius

value: primary CD8 T cells

tag: transduced with

value: sequence-optimized NY-ESO-1 specific TCR variant, WT

tag: affinity

tag: stimulated with


title: Prostate_Cancer_xenograft [PC82]

description: xenograft on NMRI nu/nu male mice


title: TMa_6h

description: gene expression at 6h post stimulation

value: sequence-optimized NY-ESO-1 specific TCR variant, TMa

value: 0.002ug/ml unlabeled NY-ESO-1(57-165)-specific multimer for 6h


title: Prostate_Cancer_xenograft [PC295]

description: xenograft on NMRI nu/nu male mice


title: TMb_6h

description: gene expression at 6h post stimulation

value: sequence-optimized NY-ESO-1 specific TCR variant, TMb


title: G50A_6h

description: gene expression at 6h post stimulation

value: sequence-optimized NY-ESO-1 specific TCR variant, G50A


title: V49I_6h

description: gene expression at 6h post stimulation

value: sequence-optimized NY-ESO-1 specific TCR variant, V49I


title: A97L_0h

description: baseline gene expression

value: sequence-optimized NY-ESO-1 specific TCR variant, A97L

value: none (untreated baseline; 0h)


title: Prostate_Cancer_cell_line [LAPC4]


title: Prostate_Cancer_cell_line [22RV1]


title: DM_0h

description: baseline gene expression

value: sequence-optimized NY-ESO-1 specific TCR variant, DM


title: V49I_0h

description: baseline gene expression


title: OECM1-sh-SC

description: miRNA expression in OECM1-scramble control stable clone

source_name: OECM1, scramble expresing cell line


title: wtc51_0h

description: baseline gene expression

value: sequence-optimized NY-ESO-1 specific TCR variant, wtc51


title: DM_6h

description: gene expression at 6h post stimulation


title: A97L_6h

description: gene expression at 6h post stimulation


title: TMb_0h

description: baseline gene expression


title: TMa_0h

description: baseline gene expression


title: G50A_0h

description: baseline gene expression


title: Bmi1 knockdown

description: microRNA expression profile of Bmi1 knockdown cell

hyb_protocol: 2X hybridization buffer (Agilent Technologies, USA) was added to the labeled mixture to a final volume of 45 ul. The mixture was heated for 5 min at 100°C and immediately cooled to 0°C. Each 45 ul sample was hybridized onto an Agilent human miRNA Microarray R14 V2 (Agilent Technologies, USA) at 55°C for 20 h.

scan_protocol: After hybridization, slides were washed for 5 min in Gene Expression Wash Buffer 1 at room temperature, then for 5 min in Gene Expression Wash Buffer 2 at 37°C. Slides were scanned on an Agilent microarray scanner (Agilent Technologies, model G2505C) at 100% and 5% sensitivity settings.

data_processing: Feature Extraction (Agilent Technologies) software version 10.7.3.1 was used for image analysis.

source_name: Bmi1 knockdown

label_protocol: 0.1 ug of total RNAs were dephosphorylated and labeled with pCp-Cy3 by Agilent miRNA Complete Labeling and Hyb Kit (Agilent Technologies, USA, microRNA Spike- In Apply).

growth_protocol: Cells were cultivated in RPMI + 10% fetal bovine serum

treatment_protocol: Cells were transfected with scramble vector or knockdown shRNA for stable cell establishment.

tag: knockdown


title: Twist1 konckdown

description: microRNA expression profile of Twist1 knockdown cell

source_name: Twist1 konckdown


title: Prostate_Cancer_cell_line [MDAPCa2B]


title: Prostate_Cancer_cell_line [LNCaP]

value: LNCaP


title: Prostate_Cancer_cell_line [PC346C]


title: scramble control

description: microRNA expression profile of control cells

source_name: scramble control

value: scramble control


title: H295R_5*10-5 M 9-cisRA_replicate 3

status: Public on Feb 10 2013

city: Budapest

first: Diana

middle: Rita

last: Szabo

address: Szentkirályi u. 46

country: Hungary

institute: Semmelweis University

description: Gene expression after 24hr in 5*10-5 M 9cisRA treated cells

hyb_protocol: Labeled RNA was purified and hybridized to Agilent Whole Human Genome Microarray slides, according to the manufacturer’s protocol.

scan_protocol: After washing, array scanning and feature extraction was performed with default scenario by Agilent DNA Microarray Scanner and Feature Extraction Software 9.5.3.

data_processing: Total gene signal normalization at the 75th percentile of raw signal values and baseline transformation at the median of all samples was performed by GeneSpring software 10.1 following Agilent's recommendation. Genes were filtered by flag values (100% of samples are present or marginal in at least one group) and raw data (expression is higher than 20 percentile in the 100% of samples in at least one group). Fold change filter was set to 2-fold between 9-cisRA-treated groups versus control cells.

source_name: H295R cell line, 24h, 5*10-5 M 9-cisRA treated, replicate 3

label_protocol: Total RNA (200 ng) was labeled with Cy3 and amplified using Low Input Quick Amp Labeling Kit according to the instructions of the manufacturer.

growth_protocol: For the gene expression H295R expreiment 2*10^6 cells were grown in a 12,5cm2 cell sulture flask / samples

extract_protocol: Total RNA was isolated from 2*10^6 9cisRA treated and control cells with Qiagen miRNeasy Mini Kit and Rnase-Free Dnase Set according to the manufacture's protocol (Qiagen GmbH, Hilden, Germany). RNA concentration was measured by NanoDrop 1000 Spectrophotometer (Thermo Fisher Scientific Inc., Waltham, MA, USA) and RNA integrity was determined by an Agilent 2100 Bioanalyzer System (Agilent Technologies Inc., Santa Clara, CA, USA). Samples with an RNA integrity number (RIN) above 8.0 were used for further analysis.

treatment_protocol: Cells were treated for 24h with 9cisRA at a final concentration of 2.5*10-5, 5*10-5 and 7.5*10-5 M dissolved in absolute ethanol. The control groups were treated with the same amount of ethanol.

tag: treatment


title: 4

city: Shanghai

first: zhigang

last: zhang

address: No. 800, Dong Chuan Road

department: Shanghai cancer Institute

country: China

institute: Shanghai Jiaotong University

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Illumina GenomeStudio Software

source_name: SMMC-7721 cell

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

growth_protocol: Cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% (v/v) fetal bovine serum (FBS) and 1% antibiotics at 37°C in a humidified incubator under 5% CO2 condition.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Cells were treated with 100nM Norepinephrine for 24h.

value: Lenti-MAOA plus Norepinephrine


title: WT_0h

description: baseline gene expression


title: mouse 512 left kidney ligature

city: VILLEJUIF

first: christophe

last: desterke

address: 14-16 avenue Paul Vaillant Couturier

department: UFR medecine institute Andre Lwoff

country: France

institute: university Paris Sud11

description: SAMPLE 6

hyb_protocol: hybridization overnight (17hours, 65°C), washing: Agilent gene expression wash buffer 1 for 1 min at room temperature followed by a second wash with preheated Agilent gene expression wash buffer 2 (37°C) for 1 min, last acetonitrile.

scan_protocol: Agilent's microarray scanner system (Agilent Technologies)

data_processing: The Agilent G2567AA Feature Extraction Software (v.9.1) was used to process the microarray files. The software determines feature intensities (including background subtraction), rejects outliers and calculates statistical confidences. Raw data were normalized by dividing the intensity values by their mediane

source_name: mouse kidney ligatured

label_protocol: Cy3-labeled fragmented cRNA

growth_protocol: Primary cells from mouse kidney ligatured or not

extract_protocol: Agilent Gene Expression Hybridization Kit (Agilent Technologies)

treatment_protocol: Kidney Ligature in vivo in mouse (mus musculus CD-1)

tag: strain

tag: tissue

value: ligatured left kidney

value: Primary cells


title: MeWo parental cells + over-expression of miR-1908

city: New York

first: Nora

last: Pencheva

state: NY

address: 1230 York Avenue, Box 194

institute: Nora Pencheva

description: biological source: 78-year old while male with malignant melanoma' , 'origin: lymph metastases', 'cell type: skin, melanoma

hyb_protocol: Biotin-labeled probes were hybridized to Illumina human HT-12 v3 BeadChips using manufacturer's standard conditions

scan_protocol: After hybridization,Illumina human HT-12 v3 BeadChips were scanned on BeadArray Reader system, in accordance with manufacturer's standard protocol

data_processing: Raw signal intensity was median-normalized using the median of the population containing all probe intensities for a given sample

source_name: human melanoma cell lines

label_protocol: Total RNA was biotin labeled by converting RNA to cDNA using biotinylated oligo (dT) and random nonamer primers

extract_protocol: Total RNA from various cell lines was extracted using the miRvana kit (AM1560, Applied Biosystems)

value: MeWo

value: over-expression of miR-1908


title: mouse 512 right no kidney ligature

description: SAMPLE 5

source_name: mouse kidney not ligatured

value: control lateral right kidney


title: mouse 495 left kidney ligature

description: SAMPLE 2


title: H295R_7.5*10-5 M 9-cisRA_replicate 2

description: Gene expression after 24hr in 7.5*10-5 M 9cisRA treated cells

source_name: H295R cell line, 24h, 7.5*10-5 M 9-cisRA treated, replicate 2


title: H295R_7.5*10-5 M 9-cisRA_replicate 1

source_name: H295R cell line, 24h, 7.5*10-5 M 9-cisRA treated, replicate 1


title: H295R_7.5*10-5 M 9-cisRA_replicate 3

source_name: H295R cell line, 24h, 7.5*10-5 M 9-cisRA treated, replicate 3


title: H295R_5*10-5 M 9-cisRA_replicate 2

source_name: H295R cell line, 24h, 5*10-5 M 9-cisRA treated, replicate 2


title: LM2 cells + miR-199a-5p knock-down

description: biological source: 78-year old while male with malignant melanoma' , 'origin: lymph metastases', 'cell type: skin, melanoma', 'in vivo selected lung metastatic derivatives

value: LM2 metastatic derivative of MeWo

value: miR-199a-5p KD


title: mouse 485 right no kidney ligature

description: SAMPLE 3


title: LM2 cells + miR-1908 knock-down

description: biological source: 78-year old while male with malignant melanoma' , 'origin: lymph metastases', 'cell type: skin, melanoma', ' in vivo selected lung metastatic derivatives

value: miR-1908 KD


title: mouse 485 left kidney ligature

description: SAMPLE 4


title: H295R_control_replicate 3

description: Gene expression after 24hr in control H295R cells

source_name: H295R cell line, 24h, control, replicate 3


title: 3

description: replicate 1

value: Lenti-vector plus Norepinephrine


title: LM2 cells + short hairpin control

description: biological source: 78-year old while male with malignant melanoma' , 'origin: lymph metastases', 'cell type: skin, melanoma', 'in vivo selected metastatic derivatives

value: short hairpin control


title: LM2 cells + miR-199a-3p knock-down

value: miR-199a-3p KD


title: Genes expression in dNK

city: He fei

first: yan

middle: fu

last: Wang

address: 443 huangshan road

institute: University of Science and Technology of China

description: Gene expression in dNK

hyb_protocol: 875 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent 44K Human Whole Genome microarays for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel Greenis set to Green)

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

source_name: Decidua NK cells

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

extract_protocol: Total RNA was extracted from each sample using Trizol (Qiagen) according to the manufacturer's protocol. RNA was then further purified using RNeasy mini spin columns (Qiagen).

treatment_protocol: CD56+CD3- NK cells from normal decidua, cord blood, and peripheral blood have been sorted by FACS Aria.

value: decidua

value: CD56+CD3- NK cells


title: Genes expression in cNK

description: Gene expression in cNK

source_name: Cord blood NK cells

value: cord blood


title: Genes expression in pNK

description: Gene expression in pNK

source_name: Peripheral blood NK cells

value: peripheral blood


title: H295R_2.5*10-5 M 9-cisRA_replicate 2

description: Gene expression after 24hr in 2.5*10-5 M 9cisRA treated cells

source_name: H295R cell line, 24h, 2.5*10-5 M 9-cisRA treated, replicate 2


title: 1

description: replicate 1

value: Lenti-vector


title: H295R_2.5*10-5 M 9-cisRA_replicate 3

source_name: H295R cell line, 24h, 2.5*10-5 M 9-cisRA treated, replicate 3


title: wtc51_6h

description: gene expression at 6h post stimulation

value: primary CD8 T cells

value: sequence-optimized NY-ESO-1 specific TCR variant, wtc51

value: 0.002ug/ml unlabeled NY-ESO-1(57-165)-specific multimer for 6h


title: H295R_5*10-5 M 9-cisRA_replicate 1

source_name: H295R cell line, 24h, 5*10-5 M 9-cisRA treated, replicate 1


title: MeWo parental cells + control hairpin

value: MeWo

value: control hairpin


title: CD133+ and CD133- cells sorted from FU-MMT-1 cell line

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: ScanArray Express (PerkinElmer Japan Co., Ltd.) was used for scanning. Images were quantified using GenePix Pro version 6.0(Axon Instruments).

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal.

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: After cell sorting by FacsArea, CD133+ and CD133- populations were cultured to recover the cells in Ham's DMEM-12 with 10% FBS and maintained at 37ºC (humidified, 5% CO2) for 12 hours, then cells were trypsinezed and collected.

extract_protocol: The total mRNA of CD133+ and CD133- cells were extracted and purified by the RiboPureTM kit (Applied Biosystems, Van Allen Way, Carlsbad, CA).

treatment_protocol: No treatment was applied prior to biological material after cell sorting process.

value: Human uterine carcinosarcoma-derived FU-MMT-1

value: CD133+ population

value: CD133- population


title: H295R_2.5*10-5 M 9-cisRA_replicate 1

source_name: H295R cell line, 24h, 2.5*10-5 M 9-cisRA treated, replicate 1


title: H295R_control_replicate 2

source_name: H295R cell line, 24h, control, replicate 2


title: H295R_control_replicate 1

source_name: H295R cell line, 24h, control, replicate 1


title: heart MHC-Plin5 1

status: Public on Feb 09 2013

city: Baltimore

first: carole

last: sztalryd

address: 650 West Redwwod Street

department: Medicine

institute: University of Maryland

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Raw data were normalized by RMA method at gene level using Affymetrix Expression Console.

source_name: heart fasted

label_protocol: Ambio WT expression kit and geneChip WT terminal labeling and control kit ( Affimetrix, Ca)

extract_protocol: qiagen Rnease kit (Qiagen CA)

tag: genetic background

tag: gender

value: male

value: heart

tag: genotype


title: Neuron,  Hmgn1-/-, biological rep1

first: Iris

last: Zhu

address: 9000 Rockville Pike

institute: National Institute of Health

description: Gene expression data from Neuron

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: Scanning was performed with the Affymetrix GeneChip scanner using default settings.

data_processing: All analysis was performed using R and BioConductor. Expression levels were derived using the Robust Multichip Average (RMA) protocol with default setting and differentially expressed genes were identified using an empirical Bayes method implemented in the R package “Limma”

source_name: Neuron,  Hmgn1-/-

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA.

growth_protocol: The ES cells were co-cultured with mitomycin-c treated mouse primary embryonic fibroblast feeders or cultured under feeder-free conditions, they were maintained in Knock-out Dulbecco’s modified Eagle’s medium, with 20% serum replacement, 0.055 mM β-mercaptoethanol, 2mM L-glutamine, 0.1mM MEM non-essential amino acid, 5000 U/ml penicillin/streptomycin, and 1000 U/ml LIF. In vitro differentiation of ES cells along neural lineage was performed using the Mouse Dopaminergic Neuron Differentiation Kit (R&D System) according to the manufacturer’s instruction.

extract_protocol: Total RNA was isolated by RNeasy Mini Kit (Qiagen) followed by “on-column” DNase I treatment according to the manufacturer's instructions.

value: Neuron


title: Neuron,  Hmgn1-/-, biological rep2

description: Gene expression data from Neuron


title: heart MHC-Plin5 4


title: Neuron,  Hmgn1+/+, biological rep2

description: Gene expression data from Neuron

source_name: Neuron,  Hmgn1+/+


title: heart control 3

value: control


title: Embyonic stem cell,  Hmgn1-/-, biological rep3

description: Gene expression data from embyonic stem cells

source_name: Embyonic stem cell,  Hmgn1-/-

value: Embyonic stem cell


title: Embyonic stem cell,  Hmgn1-/-, biological rep2


title: mouse 495 right no kidney ligature

description: SAMPLE 1

source_name: mouse kidney not ligatured

value: control lateral right kidney

value: Primary cells


title: MeWo parental cells + over-expression of miR-199a

hyb_protocol: Biotin-labeled probes were hybridized to Illumina human HT-12 v3 BeadChip using manufacturer's standard conditions

scan_protocol: After hybridization,Illumina human HT-12 v3 BeadChips were scanned on BeadArray Reader system, in accordance with manufacturer's standard protocol.

source_name: human melanoma cell lines

value: over-expression of miR-199a


title: Neural progenitor,  Hmgn1-/-, biological rep1

description: Gene expression data from neural progenitor

source_name: Neural progenitor,  Hmgn1-/-

value: Neural progenitor


title: Neural progenitor,  Hmgn1-/-, biological rep3


title: heart MHC-Plin5 3


title: heart MHC-Plin5 2


title: Neuron,  Hmgn1-/-, biological rep3

description: Gene expression data from Neuron


title: heart control 1


title: heart control 2


title: Neural progenitor,  Hmgn1+/+, biological rep2

source_name: Neural progenitor,  Hmgn1+/+


title: Neuron,  Hmgn1+/+, biological rep3

description: Gene expression data from Neuron


title: Neuron,  Hmgn1+/+, biological rep1

description: Gene expression data from Neuron


title: heart control 4


title: Neural progenitor,  Hmgn1+/+, biological rep3


title: Neural progenitor,  Hmgn1+/+, biological rep1


title: Embyonic stem cell,  Hmgn1-/-, biological rep1


title: Neural progenitor,  Hmgn1-/-, biological rep2


title: Embyonic stem cell,  Hmgn1+/+, biological rep3

source_name: Embyonic stem cell,  Hmgn1+/+


title: Embyonic stem cell,  Hmgn1+/+, biological rep2


title: Ldb1+/+, biological rep2

city: Oxford

first: Supat

last: Thongjuea

address: Headington

department: MRC Molecular Haematology Unit

institute: The Weatherall Institute of Molecular Medicine

description: Gene expression data from hemangioblast in vitro equivalent cells with Ldb1 +/+.

hyb_protocol: Hybridization was performed by the affymetrix standard protocol on the Mouse Genome 430 2.0 Array

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip® Scanner 3000 according to the manufacturer protocol.

data_processing: Affymetrix GeneChip® Expression Arrays were normalized with the standard RMA protocol by the Affy Bioconductor package

label: biotin-labelled cRNA

source_name: hemangioblast  equivalent cells

label_protocol: RNA was converted to biotin-labelled cRNA, hybridised on the Mouse Genome 430 2.0 Array

growth_protocol: Ldb1+/+ and Ldb1-/- ES cells were grown in suspension at 10.000 cells/ml on nonadherent dishes in IMDM medium (without Leukemia Inhibitory Factor (LIF)) with 15% FCS, 1% P/S, 1% L-glutamine (Gibco, Cat.25030-08), 0.05μg/ml transferrin (Roche, Cat.652-202), 0.05μg/ml ascorbic acid (Sigma, Cat.A-4544), 3μl/ml monothioglycerol (Sigma, Cat.M-6145) for day 4 EBs and 1.8μl/ml for day 6 and day 8 EBs. 5% protein free hybridoma medium II (Gibco, Cat.12040-077) was added for day 6 and day 8 EBs

extract_protocol: RNA was isolated from Ldb1+/+ and Ldb1-/- Flk1+ cells with the QIAGEN RNeasy Mini Kit and integrity was checked on the Agilent 2100 Bioanalyzer.

tag: cell-type

value: Ldb1+/+ from Flk1+ cells

tag: age

value: Flk1+ BL-CFCs isolated from day 4 embryoid bodies


title: Ldb1+/+, biological rep3


title: Ldb1-/-, biological rep1

description: Gene expression data from hemangioblast in vitro equivalent cells without Ldb1.

value: Ldb1-/- from Flk1+ cells


title: Ldb1-/-, biological rep2


title: blood-rebound (189 d.p.i.)-Animal RWf7

status: Public on Feb 08 2013

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

hyb_protocol: Following fragmentation, 20 micrograms of cRNA were diluted into 300 microlitres of hybridization cocktail, with 200 microlitres hybridized for 16 hr at 45 C on GeneChip Rhesus Macaque Genome Array in Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Data from .CEL files were analyzed using Partek Genomics Suite.

organism: Macaca mulatta

source_name: Animal RWf7 blood-rebound (189 d.p.i.)

label_protocol: Biotinylated cRNAs were prepared using a modified version of the 2-cycle Affymetrix protocol from 0.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix). 5 peptide-nucleic acid (PNA) blocking oligonucleotides directed against consensus sequences in the macaque and mangabey hemoglobin I and II genes were added into the initial reverse-transcription reaction.

growth_protocol: All animals used in this study were housed at the Yerkes National Primate Research Center (Atlanta, GA) in accordance with the regulations of the American Association of Accreditation of Laboratory Animal Care standards. This study was approved by the Institutional Animal Care and Usage Committees (IACUC) of Emory University and the University of Pennsylvania.

extract_protocol: RNA was extracted using the PAXgene RNA Isolation Kit according to manufacturer's instructions.

treatment_protocol: 8 rhesus macaques were inoculated i.v. with 3000 TCID50 of SIVmac239. At days 58 or 177 animals in reciprocal groups were adminstered depleting antibody OKT8F or sham. At days 63 and 182 animals were adminsteredreverse transcriptase inhibitors 9-R-(2-phosphonomethoxypropyl)adenine (PMPA; tenofovir) and beta-2,3-dideoxy-3-thia-5-fluorocytidine (FTC; emtricitabine) i.m. (30mg/kg/animal/day). Blood was drawn into PaxGene RNA tubes prior to SIV infection and at post-infection times indicated. Full description of animal treatment in  As previously published in Klatt NR, Shudo E, Ortiz AM, Engram JC, Paiardini M, et al. (2010) CD8+ Lymphocytes Control Viral Replication in SIVmac239-Infected Rhesus Macaques without Decreasing the Lifespan of Productively Infected Cells. PLoS Pathog 6(1): e1000747. doi:10.1371/journal.ppat.1000747.

tag: rna sample id

tag: array facility id

tag: animal id

tag: age at infection (yrs)

tag: m/f

value: F

tag: starting wt (kg)

tag: expt day actual

tag: expt day

tag: depletion status

value: rebound (189 d.p.i.)

tag: siv infection status

value: Chronic

tag: infection

value: SIV+

tag: infection group

value: B

tag: bleed date

tag: rna purification date

tag: rna purification batch

tag: hybridization batch

tag: chamber batch

tag: acquisition date

tag: scan date


title: blood-rebound (189 d.p.i.)-Animal RUe7

source_name: Animal RUe7 blood-rebound (189 d.p.i.)

tag: rna sample id

tag: array facility id

tag: animal id


title: Embyonic stem cell,  Hmgn1+/+, biological rep1

tag: strain

tag: tissue

tag: genotype


title: Ldb1+/+, biological rep1

tag: cell-type

tag: age


title: Ldb1-/-, biological rep3


title: blood-post-ART (70 d.p.i.)-Animal RUe7

source_name: Animal RUe7 blood-post-ART (70 d.p.i.)

tag: age at infection (yrs)

tag: m/f

tag: starting wt (kg)

tag: expt day actual

tag: expt day

tag: depletion status

value: post-ART (70 d.p.i.)

tag: siv infection status

tag: infection


title: blood-5-day-post-depletion (182 d.p.i.)-Animal RUe7

source_name: Animal RUe7 blood-5-day-post-depletion (182 d.p.i.)

value: 5-day-post-depletion (182 d.p.i.)

tag: infection group

tag: bleed date

tag: rna purification date

tag: rna purification batch

tag: hybridization batch

tag: chamber batch

tag: acquisition date

tag: scan date


title: blood-pre-depletion (31 d.p.i.)-Animal RSq8

source_name: Animal RSq8 blood-pre-depletion (31 d.p.i.)

tag: rna sample id

tag: array facility id

tag: animal id

value: pre-depletion (31 d.p.i.)


title: blood-171 d.p.i.-Animal RUe7

source_name: Animal RUe7 blood-171 d.p.i.

tag: age at infection (yrs)

tag: m/f

tag: starting wt (kg)


title: blood-post-ART (70 d.p.i.)-Animal RWf7

source_name: Animal RWf7 blood-post-ART (70 d.p.i.)

tag: expt day actual

tag: expt day

tag: depletion status


title: blood-5-day-post-depletion (182 d.p.i.)-Animal RWf7

source_name: Animal RWf7 blood-5-day-post-depletion (182 d.p.i.)

tag: siv infection status

tag: infection

tag: infection group


title: blood-Chronic (>180 d.p.i)-Animal RWf7

source_name: Animal RWf7 blood-Chronic (>180 d.p.i)

value: Chronic (>180 d.p.i)

tag: bleed date

tag: rna purification date

tag: rna purification batch


title: blood-pre-depletion (31 d.p.i.)-Animal RWf7

source_name: Animal RWf7 blood-pre-depletion (31 d.p.i.)

value: Acute

tag: hybridization batch

tag: chamber batch

tag: acquisition date


title: blood-Uninfected-Animal RWf7

source_name: Animal RWf7 blood-Uninfected

tag: rna sample id

tag: array facility id

value: Uninfected

value: SIV-

tag: scan date


title: blood-10 d.p.i.-Animal RWf7

source_name: Animal RWf7 blood-10 d.p.i.

tag: animal id

tag: age at infection (yrs)

tag: m/f


title: blood-5-day-post-depletion (182 d.p.i.)-Animal RSq8

source_name: Animal RSq8 blood-5-day-post-depletion (182 d.p.i.)

tag: starting wt (kg)

tag: expt day actual

tag: expt day


title: blood-post-ART (70 d.p.i.)-Animal XHB

source_name: Animal XHB blood-post-ART (70 d.p.i.)

value: XHB

tag: depletion status

tag: siv infection status

tag: infection


title: blood-14 d.p.i.-Animal RWf7

source_name: Animal RWf7 blood-14 d.p.i.

tag: infection group

tag: bleed date

tag: rna purification date


title: blood-171 d.p.i.-Animal XHB

source_name: Animal XHB blood-171 d.p.i.

tag: rna purification batch

tag: hybridization batch

tag: chamber batch


title: blood-rebound (189 d.p.i.)-Animal RSq8

source_name: Animal RSq8 blood-rebound (189 d.p.i.)

tag: rna sample id

tag: array facility id

tag: acquisition date


title: Spdef -/- mice, biological rep1

first: Ilene

last: Gipson

address: 20 Staniford ST

institute: Schepens Eye Research Institute

description:
Gene expression data from conjunctival epithelium of Spdef -/- mice
MCSP-1

source_name: Spdef -/- mouse conjunctival epithelium

growth_protocol: Eyes with intact eyelids were excised from 8 week-old Spdef +/+ and Spdef -/- mice and embedded into OCT and frozen on dry ice.

extract_protocol: Total RNA was isolated from laser captured sections of conjunctival epithelium of Spdef +/+ and Spdef -/- mice using an Arcturus PicoPure Isolation Kit.

treatment_protocol: Conjunctival tissue from Spdef +/+ and Spdef -/- mice was cryostat-sectioned at -20C. Sections (6 µm were collected on Artcurus PEN Membrane glass slided and staied with H&E prior to laser capture microdissection. Forty percent of the conjunctival epithelium, as measured from the deepest part of the fornix cul-de-sac, was captured using a Laser Microdissection Microscope. One eye from 1 male and 1 female animal were pooled into a single sample.

tag: strain

tag: tissue

value: conjunctival epithelium

tag: gender

value: Male and female

tag: age

value: 8 week-old


title: Spdef +/+ mice, biological rep3

description:
Gene expression data from conjunctival epithelium of Spdef +/+ mice
MCWT3

source_name: Spdef +/+ mouse conjunctival epithelium


title: blood-rebound (70 d.p.i.)-Animal RPp6

source_name: Animal RPp6 blood-rebound (70 d.p.i.)

tag: animal id

tag: age at infection (yrs)

tag: m/f

tag: starting wt (kg)

tag: expt day actual

tag: expt day

value: rebound (70 d.p.i.)

value: A

tag: scan date


title: k4_wt_rep3

city: Heidelberg

first: James

middle: P

last: Reddington

address: Meyerhofstrasse 1

institute: EMBL

description: comparison of Dnmt1+/+ vs Dnmt1-/- mouse embryonic fibroblasts

hyb_protocol: Hybridisation was perfromed according to Nimblegen instructions by a Nimblegen service centre

scan_protocol: Scanning was perfromed according to Nimblegen instructions by a Nimblegen service centre

data_processing: Raw signals were normalised using the loess and scale methods of the limma R package. ChIP signals were normalised to input by calculating the log2 ratio of ChIP/Input signals.

source_name: input DNA for Dnmt1+/+ MEFs for H3K4me3 rep3

label_protocol: Labelling was perfromed according to Nimblegen instructions by a Nimblegen service centre

growth_protocol: MEFs were cultured under standard conditions

extract_protocol: Native ChIP was performed as described previously (Eskeland et al, 2010, Mol Cell, 38: 452-464) with the following adaptations. Protein-A coated Dynabeads (Invitrogen) were used throughout. Chromatin was digested with 25U of Mnase (micrococcal nuclease)(Worthington) for exactly 10min at room temperature. Following immunoprecipitation beads were washed three times for 10 min at 4°C in N-ChIP wash buffer (150mM NaCl; 10mM Tris pH8; 2mM EDTA; 1% NP40; 1% sodium deoxycholate w/v). Controls for N-ChIP experiments included a species matched IgG to control for background, negative and positive genomic regions to show specificity, and the use of input DNA to control for technical variations between cell lines or treatments. Antibodies were tested by western blot for recognition of histone-sized proteins only and by specific enrichment at positive control regions by N-ChIP. Enrichments were measured by qPCR.

treatment_protocol: Not applicable

tag: background strain

value: unknown [Lande-Diner et al 2007 (PMID:17311920)]

tag: cell type

value: Mouse embryonic fibroblasts

tag: genotype

tag: chip antibody

value: None, input DNA

source_name: ChIP DNA for Dnmt1+/+ MEFs for H3K4me3 rep3

tag: antibody vendor

value: Upstate

tag: antibody catalog number


title: blood-post-ART (70 d.p.i.)-Animal RSq8

source_name: Animal RSq8 blood-post-ART (70 d.p.i.)

tag: rna sample id

tag: array facility id

value: F

tag: depletion status

value: post-ART (70 d.p.i.)

tag: siv infection status

value: Chronic

tag: infection

value: SIV+

tag: infection group

value: B

tag: bleed date

tag: rna purification date

tag: rna purification batch

tag: hybridization batch

tag: chamber batch

tag: acquisition date


title: blood-5-day-post-depletion (182 d.p.i.)-Animal XHB

source_name: Animal XHB blood-5-day-post-depletion (182 d.p.i.)

tag: animal id

tag: age at infection (yrs)

tag: m/f

tag: starting wt (kg)

tag: expt day actual

tag: expt day

value: 5-day-post-depletion (182 d.p.i.)

tag: scan date


title: k4_ko_rep3

source_name: input DNA for Dnmt1-/- MEFs for H3K4me3 rep3

tag: background strain

tag: cell type

tag: genotype

tag: chip antibody

source_name: ChIP DNA for Dnmt1-/- MEFs for H3K4me3 rep3

tag: antibody vendor

tag: antibody catalog number


title: blood-171 d.p.i.-Animal RSq8

source_name: Animal RSq8 blood-171 d.p.i.

tag: rna sample id

tag: array facility id

tag: depletion status

tag: siv infection status

tag: infection

tag: infection group

tag: bleed date

tag: rna purification date

tag: rna purification batch


title: Spdef -/- mice, biological rep2

description:
Gene expression data from conjunctival epithelium of Spdef -/- mice
MCSP-2

tag: strain

tag: tissue

tag: gender

tag: age


title: blood-171 d.p.i.-Animal RWf7

source_name: Animal RWf7 blood-171 d.p.i.

tag: animal id

tag: age at infection (yrs)

tag: m/f

tag: starting wt (kg)

tag: expt day actual

tag: expt day

tag: hybridization batch

tag: chamber batch

tag: acquisition date

tag: scan date


title: k4_ko_rep1

source_name: input DNA for Dnmt1-/- MEFs for H3K4me3 rep1

tag: background strain

tag: cell type

tag: genotype

tag: chip antibody

source_name: ChIP DNA for Dnmt1-/- MEFs for H3K4me3 rep1

tag: antibody vendor

tag: antibody catalog number


title: blood-5-day-post-depletion (63 d.p.i.)-Animal RRf6

source_name: Animal RRf6 blood-5-day-post-depletion (63 d.p.i.)

tag: rna sample id

tag: array facility id

tag: depletion status

value: 5-day-post-depletion (63 d.p.i.)

tag: siv infection status

value: Acute

tag: infection

tag: infection group

tag: bleed date

tag: rna purification date

tag: rna purification batch


title: blood-5-day-post-depletion (63 d.p.i.)-Animal RPp6

source_name: Animal RPp6 blood-5-day-post-depletion (63 d.p.i.)

tag: animal id

tag: age at infection (yrs)

tag: m/f

tag: starting wt (kg)

tag: expt day actual

tag: expt day

tag: hybridization batch

tag: chamber batch

tag: acquisition date


title: Spdef +/+ mice, biological rep1

description:
Gene expression data from conjunctival epithelium of Spdef +/+ mice
MCWT1

tag: strain

tag: tissue

value: conjunctival epithelium

tag: gender

tag: age


title: Spdef +/+ mice, biological rep2

description:
Gene expression data from conjunctival epithelium of Spdef +/+ mice
MCWT2

value: Male and female


title: blood-5-day-post-depletion (63 d.p.i.)-Animal RZl5

source_name: Animal RZl5 blood-5-day-post-depletion (63 d.p.i.)

tag: rna sample id

tag: array facility id

tag: depletion status

tag: siv infection status

tag: infection

tag: infection group

tag: scan date


title: Spdef -/- mice, biological rep3

description:
Gene expression data from conjunctival epithelium of Spdef -/- mice
MCSP-3

value: 8 week-old


title: blood-rebound (70 d.p.i.)-Animal RZl5

source_name: Animal RZl5 blood-rebound (70 d.p.i.)

tag: animal id

tag: age at infection (yrs)

tag: m/f

tag: starting wt (kg)

value: rebound (70 d.p.i.)

tag: bleed date

tag: rna purification date

tag: rna purification batch


title: k4_wt_rep1

source_name: input DNA for Dnmt1+/+ MEFs for H3K4me3 rep1

tag: background strain

tag: cell type

tag: genotype

tag: chip antibody

source_name: ChIP DNA for Dnmt1+/+ MEFs for H3K4me3 rep1

tag: antibody vendor

tag: antibody catalog number


title: k4_wt_rep2

source_name: input DNA for Dnmt1+/+ MEFs for H3K4me3 rep2

source_name: ChIP DNA for Dnmt1+/+ MEFs for H3K4me3 rep2


title: blood-rebound (189 d.p.i.)-Animal XHB

source_name: Animal XHB blood-rebound (189 d.p.i.)

tag: rna sample id

tag: array facility id

value: XHB

tag: expt day actual

tag: expt day

tag: depletion status

value: rebound (189 d.p.i.)

tag: siv infection status

tag: hybridization batch

tag: chamber batch

tag: acquisition date


title: RR_Rap_rep-3

city: NY

first: Hana

last: Totary-Jain

address: 150, St. NICHOLAS AVE

institute: Columbia University

description: Gene expression data from RR cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on mouse Genome Array 430 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000

data_processing: The data were analyzed with genechip operation software version 1.4 (GCOS 1.4), using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 250.

source_name: rapamycin > 6 months

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (one cycle cDNA Synthesis kit P/N 900431)

growth_protocol: rapamycin sensitive (RS) cells (BC3H1, ATCC)  cultured in Dulbecco’s modified essential medium (DMEM) media supplemented with 20% fetal bovine serum (FBS), penicillin (100 U/ml) and streptomycin (100 mg/ml). Rapamycin resistant cells (RR1) were developed by culturing BC3H1 cells in the presence of 1 uM rapamycin for 6 months.

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

treatment_protocol: RS cells were treated with 100 nM rapamycin, or DMSO for 24h. RR cells were constantly treated with 1uM rapamycin

value: rapamycin resistant brain tumors


title: RR_Rap_rep-1

description: Gene expression data from RR cells


title: blood-5-day-post-depletion (63 d.p.i.)-Animal RLi6

source_name: Animal RLi6 blood-5-day-post-depletion (63 d.p.i.)

tag: animal id

tag: age at infection (yrs)

tag: m/f

tag: starting wt (kg)

tag: infection

tag: infection group

value: A

tag: bleed date

tag: rna purification date

tag: scan date


title: RR_Rap_rep-2

description: Gene expression data from RR cells

tag: cell type


title: blood-10 d.p.i.-Animal XHB

source_name: Animal XHB blood-10 d.p.i.

tag: rna sample id

tag: array facility id

tag: expt day actual

tag: rna purification batch


title: RS_Rap_rep2

description: Gene expression data from rapamycin treated Rapamycin sensitive cells

source_name: Rapamycin sensitive 100nM rapamycin, 24h

tag: cell line


title: k27_ko_rep2

source_name: input DNA for Dnmt1-/- MEFs for H3K27me3 rep2

tag: background strain

value: unknown [Lande-Diner et al 2007 (PMID:17311920)]

value: Mouse embryonic fibroblasts

tag: genotype

tag: chip antibody

value: None, input DNA

source_name: ChIP DNA for Dnmt1-/- MEFs for H3K27me3 rep2

tag: antibody vendor

value: Upstate

tag: antibody catalog number


title: RS_DMSO_rep3

description: Gene expression data from untreated Rapamycin sensitive cells

source_name: Rapamycin sensitive cells DMSO, 24 h


title: RS_DMSO_rep1


title: blood-rebound (70 d.p.i.)-Animal RLi6

source_name: Animal RLi6 blood-rebound (70 d.p.i.)

tag: animal id

tag: age at infection (yrs)

tag: m/f

value: F

tag: starting wt (kg)

tag: expt day

tag: depletion status

tag: siv infection status

value: SIV+

tag: hybridization batch

tag: chamber batch

tag: acquisition date


title: k27_wt_rep2

source_name: input DNA for Dnmt1+/+ MEFs for H3K27me3 rep2

tag: cell type

source_name: ChIP DNA for Dnmt1+/+ MEFs for H3K27me3 rep2


title: RS_Rap_rep1

tag: cell line


title: blood-pre-depletion (31 d.p.i.)-Animal XHB

source_name: Animal XHB blood-pre-depletion (31 d.p.i.)

tag: rna sample id

tag: array facility id

tag: expt day actual

value: pre-depletion (31 d.p.i.)

tag: infection

tag: infection group

value: B

tag: bleed date

tag: rna purification date

tag: rna purification batch

tag: scan date


title: blood-14 d.p.i.-Animal XHB

source_name: Animal XHB blood-14 d.p.i.

tag: animal id

tag: age at infection (yrs)

tag: m/f

tag: starting wt (kg)

tag: expt day

value: Acute


title: RS_DMSO_rep2


title: blood-rebound (70 d.p.i.)-Animal RRf6

source_name: Animal RRf6 blood-rebound (70 d.p.i.)

tag: depletion status

tag: siv infection status

tag: hybridization batch

tag: chamber batch

tag: acquisition date


title: RS_Rap_rep3

tag: cell line


title: k27_ko_rep3

source_name: input DNA for Dnmt1-/- MEFs for H3K27me3 rep3

tag: background strain

tag: cell type

tag: genotype

tag: chip antibody

source_name: ChIP DNA for Dnmt1-/- MEFs for H3K27me3 rep3

tag: antibody vendor

tag: antibody catalog number


title: k27_wt_rep3

source_name: input DNA for Dnmt1+/+ MEFs for H3K27me3 rep3

source_name: ChIP DNA for Dnmt1+/+ MEFs for H3K27me3 rep3


title: blood-Uninfected-Animal XHB

source_name: Animal XHB blood-Uninfected

tag: rna sample id

tag: array facility id

tag: animal id

tag: expt day actual

value: Uninfected

tag: infection

value: SIV-

tag: infection group

tag: bleed date

tag: rna purification date

tag: rna purification batch

tag: scan date


title: k27_ko_rep1

source_name: input DNA for Dnmt1-/- MEFs for H3K27me3 rep1

source_name: ChIP DNA for Dnmt1-/- MEFs for H3K27me3 rep1


title: [C. albicans-efg1-cph1-]-[from Ileum]-[Rep6]

first: Carol

last: Kumamoto

address: 136 Harrison Ave

department: Molecular Biology and Microbiology

institute: Tufts University

description: efg1- cph1- ileum 6

hyb_protocol: Overnight 42oC Slide Booster chamber

scan_protocol: Scan Array GX

data_processing: Quantarray GeneSpring GX 7.3 Expression used for analysis.  Normalization was Intensity dependent (Lowess) per spot and per microarray with a signal cut-off value of 800.  Genes with statistical significance were selected with a t-test p-value <0.05.

organism: Candida albicans

source_name: efg1- cph1- C. albicans cells from murine ileum

label_protocol: amno allyl messageAmp II aRNA amplication

extract_protocol: PureLink Trizol extraction

tag: genotype/variation

value: efg1- cph1-

tag: inoculated into

value: antibiotic-treated BALB/c mice by oral gavage

source_name: Reference

value: wild type

tag: cultured

value: YPD medium at 37C to exponential phase


title: [C. albicans-efg1-cph1-]-[from Ileum]-[Rep1]

description: efg1- cph1- ileum 1


title: [C. albicans-efg1-cph1-]-[from Ileum]-[Rep4]

description: efg1- cph1- ileum 4


title: [C. albicans-efg1-cph1-]-[from Ileum]-[Rep5]

description: efg1- cph1- ileum 5


title: [C. albicans-efg1-cph1-]-[from Ileum]-[Rep2]

description: efg1- cph1- ileum 2


title: [C. albicans-efg1-cph1-]-[from Ileum]-[Rep3]

description: efg1- cph1- ileum 3


title: blood-pre-depletion (31 d.p.i.)-Animal RPp6

source_name: Animal RPp6 blood-pre-depletion (31 d.p.i.)

tag: age at infection (yrs)

tag: m/f

tag: starting wt (kg)

tag: expt day

tag: depletion status

tag: siv infection status

tag: hybridization batch

tag: chamber batch

tag: acquisition date


title: k27_wt_rep1

source_name: input DNA for Dnmt1+/+ MEFs for H3K27me3 rep1

tag: background strain

tag: cell type

tag: genotype

tag: chip antibody

source_name: ChIP DNA for Dnmt1+/+ MEFs for H3K27me3 rep1

tag: antibody vendor

tag: antibody catalog number


title: k4_ko_rep2

source_name: input DNA for Dnmt1-/- MEFs for H3K4me3 rep2

source_name: ChIP DNA for Dnmt1-/- MEFs for H3K4me3 rep2


title: [C. albicans-efg1-efh1-]-[from Ileum]-[Rep5]

description: efg1- efh1- ileum 5

source_name: efg1- efh1- C. albicans cells from murine ileum

tag: genotype/variation

value: efg1- efh1-

tag: inoculated into


title: [C. albicans-efg1-efh1-]-[from Ileum]-[Rep6]

description: efg1- efh1- ileum 6

tag: cultured


title: [C. albicans-efg1-efh1-]-[from Ileum]-[Rep2]

description: efg1- efh1- ileum 2


title: [C. albicans-efg1-efh1-]-[from Ileum]-[Rep3]

description: efg1- efh1- ileum 3


title: blood-10 d.p.i.-Animal RPp6

source_name: Animal RPp6 blood-10 d.p.i.

tag: rna sample id

tag: array facility id

tag: animal id

tag: age at infection (yrs)

tag: m/f

tag: expt day actual

tag: infection

tag: infection group

value: A

tag: bleed date

tag: rna purification date

tag: rna purification batch

tag: scan date


title: [C. albicans-efg1-efh1-]-[from Ileum]-[Rep1]

description: efg1- efh1- ileum 1


title: [C. albicans-efg1-efh1-]-[from Ileum]-[Rep4]

description: efg1- efh1- ileum 4


title: [C. albicans-efg1-]-[from Ileum]-[Rep6]

description: efg1- ileum 6

source_name: efg1- C. albicans cells from murine ileum


title: blood-Chronic (>180 d.p.i)-Animal RUe7

source_name: Animal RUe7 blood-Chronic (>180 d.p.i)

tag: starting wt (kg)

tag: expt day

tag: depletion status

value: Chronic (>180 d.p.i)

tag: siv infection status

value: Chronic

tag: hybridization batch

tag: chamber batch

tag: acquisition date


title: blood-Uninfected-Animal RPp6

source_name: Animal RPp6 blood-Uninfected

tag: rna sample id

tag: array facility id

tag: animal id


title: blood-pre-depletion (31 d.p.i.)-Animal RUe7

source_name: Animal RUe7 blood-pre-depletion (31 d.p.i.)

tag: age at infection (yrs)

tag: m/f

tag: expt day actual


title: blood-pre-depletion (31 d.p.i.)-Animal RZl5

source_name: Animal RZl5 blood-pre-depletion (31 d.p.i.)

tag: infection

tag: infection group

tag: bleed date


title: blood-14 d.p.i.-Animal RUe7

source_name: Animal RUe7 blood-14 d.p.i.

tag: rna purification date

tag: rna purification batch

tag: scan date


title: blood-10 d.p.i.-Animal RUe7

source_name: Animal RUe7 blood-10 d.p.i.

tag: starting wt (kg)

tag: expt day

tag: depletion status


title: expres_MBD3_3

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

institute: Justus-Liebig-University Giessen

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials. Heat cocktails at 99C for 5 minutes, then 42C for 5 minutes centrifuge at max speed for 1 minute, Transfer 200ul of hyb solution to each array, then tape holes, Hybridize 17 hours at 45C at 60rpm. Fluidics washing is FS450_0001.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using Aroma.Affymetrix package within R software. RMA background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities and then quantile normalized.
probe_group_file: HuGene-1_0_st-v1,r3.cdf

source_name: HeLa

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

growth_protocol: HeLa cells were cultured at 37°C with 5% CO2 in DMEM media

extract_protocol: Total RNA was extracted using TRIZOL following the manufacturer's protocol.

treatment_protocol: HeLa cells were treated with MBD2- and MBD3- specific siRNA as well as scrambled siRNA as control. For transfection Lipofectamine RNAiMax reagent (Invitrogen) was used.    For each of the 3 conditions we prepared 3 independent RNA samples using TRIZOL. RNA was purified 6 days after transfection following the manufacturer’s protocol.

tag: cell line

value: HeLa

tag: transfection

value: siRNA MBD3


title: blood-Uninfected-Animal RZl5

source_name: Animal RZl5 blood-Uninfected

tag: rna sample id

value: F

tag: siv infection status

tag: hybridization batch

tag: chamber batch

tag: acquisition date


title: [C. albicans-efg1-]-[from Ileum]-[Rep5]

description: efg1- ileum 5

tag: genotype/variation

tag: inoculated into

source_name: Reference

tag: cultured


title: [C. albicans-efg1-]-[from Ileum]-[Rep4]

description: efg1- ileum 4


title: blood-10 d.p.i.-Animal RZl5

source_name: Animal RZl5 blood-10 d.p.i.

tag: array facility id

tag: animal id

tag: age at infection (yrs)

tag: m/f

tag: expt day actual

tag: infection

value: SIV+

tag: infection group

tag: bleed date


title: blood-Uninfected-Animal RUe7

source_name: Animal RUe7 blood-Uninfected

tag: starting wt (kg)

tag: expt day

tag: depletion status

tag: rna purification date

tag: rna purification batch

tag: scan date


title: [C. albicans-efg1-]-[from Ileum]-[Rep3]

description: efg1- ileum 3

tag: genotype/variation


title: blood-14 d.p.i.-Animal RZl5

source_name: Animal RZl5 blood-14 d.p.i.

tag: rna sample id

tag: siv infection status

tag: hybridization batch

tag: chamber batch

tag: acquisition date


title: expres_MBD2_2

tag: cell line

tag: transfection

value: siRNA MBD2


title: expres_MBD2_3


title: expres_MBD3_2


title: [C. albicans-efg1-]-[from Ileum]-[Rep1]

description: efg1- ileum 1

tag: inoculated into

tag: cultured


title: expres_control_3

value: siRNA scrambled


title: expres_control_1


title: blood-14 d.p.i.-Animal RRf6

source_name: Animal RRf6 blood-14 d.p.i.

tag: array facility id

tag: animal id

tag: age at infection (yrs)

tag: m/f

tag: expt day actual

value: Acute

tag: infection

tag: infection group

tag: bleed date


title: blood-Chronic (>180 d.p.i)-Animal RRf6

source_name: Animal RRf6 blood-Chronic (>180 d.p.i)

tag: rna sample id

tag: starting wt (kg)

tag: expt day

tag: depletion status

tag: rna purification date

tag: rna purification batch

tag: scan date


title: expres_control_2

tag: cell line

tag: transfection


title: expres_MBD3_1


title: blood-pre-depletion (31 d.p.i.)-Animal RRf6

source_name: Animal RRf6 blood-pre-depletion (31 d.p.i.)

tag: array facility id

value: pre-depletion (31 d.p.i.)

tag: siv infection status

tag: hybridization batch

tag: chamber batch

tag: acquisition date


title: blood-10 d.p.i.-Animal RRf6

source_name: Animal RRf6 blood-10 d.p.i.

tag: animal id

tag: age at infection (yrs)

tag: m/f

tag: expt day actual

tag: infection


title: expres_MBD2_1


title: [C. albicans-WT]-[from Ileum]-[Rep7]

description: WT ileum 7

source_name: WT C. albicans cells from murine ileum

tag: genotype/variation

value: WT

tag: inoculated into

tag: cultured


title: [C. albicans-efg1-]-[from Ileum]-[Rep2]

description: efg1- ileum 2

source_name: efg1- C. albicans cells from murine ileum


title: [C. albicans-WT]-[from Ileum]-[Rep6]

description: WT ileum 6


title: [C. albicans-WT]-[from Ileum]-[Rep5]

description: WT ileum 5


title: par8-1

city: Edinburgh

first: Sally

last: Lowell

address: 5 Little France Drive

department: MRC Centre for Regenerative Medicine

institute: University of Edinburgh

data_processing: Raw data was processed in R using the beadarray (Dunning et al., 2007) and limma (Smyth, 2005) packages from the Bioconductor suite (Gentleman et al., 2004). Briefly, we removed low-quality probes from the input data. The data was subsequently quantile-normalized and log2-transformed before assessing differential expression with the limma algorithms. We considered genes differentially expressed which had an FDR-adjusted p-value of at most 0.05 and a fold change of 1.5 or more for at least one time point in comparison to the 0-hour baseline.

source_name: Parental control ES cells 8 hr dox treatment replicate 1

label_protocol: 100 ng of RNA were reverse transcribed into ds cDNA and transcribed/amplified into biotin labeled cRNA using an Illumina TotalPrep RNA Amplification Kit (AMIL1791, Ambion)

growth_protocol: GMEM + LIF + FCS

extract_protocol: RNA was prepared using Absolutely RNA Purification Kits (Agilent).

treatment_protocol: Addition of 1μg/mL dox

tag: strain

tag: cell type

value: Parental control mouse ES cells


title: blood-Chronic (>180 d.p.i)-Animal RSq8

source_name: Animal RSq8 blood-Chronic (>180 d.p.i)

tag: rna sample id

tag: starting wt (kg)

tag: expt day

tag: depletion status

tag: infection group

value: B

tag: bleed date

tag: rna purification date

tag: rna purification batch

tag: scan date


title: tte24-2

source_name: dox-inducible Tcf15-E47 ES cells 24 hr dox treatment- replicate 2

value: dox-inducible Tcf15-E47 mouse ES cells


title: par8-2

source_name: Parental control ES cells 8 hr dox treatment replicate 2


title: [C. albicans-WT]-[from Ileum]-[Rep4]

city: Boston

description: WT ileum 4

value: antibiotic-treated BALB/c mice by oral gavage

value: wild type

value: YPD medium at 37C to exponential phase


title: par0-1

description: Used as baseline to calclute fold-change for par samples

source_name: Parental control ES cells 0 hr dox treatment replicate 1


title: blood-14 d.p.i.-Animal RPp6

source_name: Animal RPp6 blood-14 d.p.i.

tag: array facility id

tag: animal id

tag: age at infection (yrs)

tag: m/f

tag: siv infection status

value: A

tag: hybridization batch

tag: chamber batch

tag: acquisition date


title: blood-Uninfected-Animal RRf6

source_name: Animal RRf6 blood-Uninfected

tag: rna sample id

tag: expt day actual

value: Uninfected

tag: infection

value: SIV-


title: [C. albicans-WT]-[from Ileum]-[Rep3]

description: WT ileum 3

tag: genotype/variation

tag: inoculated into

source_name: Reference

tag: cultured


title: tte12-2

source_name: dox-inducible Tcf15-E47 ES cells 12 hr dox treatment- replicate 2

tag: strain

tag: cell type


title: blood-10 d.p.i.-Animal RSq8

source_name: Animal RSq8 blood-10 d.p.i.

tag: starting wt (kg)

tag: expt day

tag: depletion status

tag: infection group

tag: bleed date

tag: rna purification date

tag: rna purification batch

tag: scan date


title: tte8-1

source_name: dox-inducible Tcf15-E47 ES cells 8 hr dox treatment- replicate 1


title: tte12-1

source_name: dox-inducible Tcf15-E47 ES cells 12 hr dox treatment- replicate 1


title: tte24-1

source_name: dox-inducible Tcf15-E47 ES cells 24 hr dox treatment- replicate 1


title: [C. albicans-WT]-[from Ileum]-[Rep1]

description: WT ileum 1


title: blood-Chronic (>180 d.p.i)-Animal RLi6

source_name: Animal RLi6 blood-Chronic (>180 d.p.i)

tag: array facility id

tag: animal id

tag: age at infection (yrs)

tag: m/f

value: Chronic (>180 d.p.i)

tag: siv infection status

value: Chronic

tag: hybridization batch

tag: chamber batch

tag: acquisition date


title: par0-2

source_name: Parental control ES cells 0 hr dox treatment replicate 2

tag: strain

tag: cell type


title: [C. albicans-WT]-[from Ileum]-[Rep2]

description: WT ileum 2

source_name: WT C. albicans cells from murine ileum

tag: genotype/variation

tag: inoculated into

tag: cultured


title: tte0-2

description: Used as baseline to calclute fold-change for tte samples

source_name: dox-inducible Tcf15-E47 ES cells 0 hr dox treatment- replicate 2


title: tte8-2

source_name: dox-inducible Tcf15-E47 ES cells 8 hr dox treatment- replicate 2


title: tte0-1

source_name: dox-inducible Tcf15-E47 ES cells 0 hr dox treatment replicate 1


title: blood-Uninfected-Animal RSq8

source_name: Animal RSq8 blood-Uninfected

tag: rna sample id

value: F

tag: starting wt (kg)

tag: expt day actual

tag: expt day

tag: depletion status

tag: infection

tag: infection group

tag: bleed date


title: blood-14 d.p.i.-Animal RSq8

source_name: Animal RSq8 blood-14 d.p.i.

tag: array facility id

tag: animal id

tag: age at infection (yrs)

tag: m/f

tag: siv infection status

value: SIV+

tag: rna purification date

tag: rna purification batch

tag: scan date


title: [C. albicans-efg1-cph1-]-[from Cecum]-[Rep4]

description: efg1- cph1- cecum 4

source_name: efg1- cph1- C. albicans cells from murine cecum

tag: genotype/variation

value: efg1- cph1-

tag: inoculated into

tag: cultured


title: Overexpressor, Dam 3

city: Urbana

first: Thomas

middle: Xavier

last: Garcia

state: IL

address: 2001 S. Lincoln Ave

department: Department of Comparative Biosciences

institute: University of Illinois at Urbana-Champaign

description: Overexpressor, replicate 3

data_processing: The data were normalized using average normalization from using Illumina Genome Studio GUI (Genome studio 2010.3 and Gene Expression Module 1.8.0).

label_protocol: Epicentre TargetAmp Nano Labeling Kit for Illumina Expression BeadChip

growth_protocol: Heterozygous Tg(AMH-cre)1Flor (Amh-cre) (Lecureuil et al., 2002) female mice were mated to homozygous floxed Gt(Rosa)26Sortm1(Notch1)Dam/J (RosaNICD) (Murtaugh et al., 2003) male mice to generate F1 Amh-cre;RosaNICD/+ overexpressors and RosaNICD/+ controls.

extract_protocol: QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Mice were housed at 25 degrees Celsius with a 12L:12D photoperiod and given standard rodent chow and water ad libitum.

tag: strain

value: mixed B6/CD1 background

value: Amh-cre;RosaNICD/+ overexpressors

tag: developmental stage

value: embryonic day 14.5

tag: tissue

value: testis


title: blood-pre-depletion (31 d.p.i.)-Animal RLi6

source_name: Animal RLi6 blood-pre-depletion (31 d.p.i.)

tag: rna sample id

tag: starting wt (kg)

tag: expt day actual

tag: expt day

tag: depletion status

value: pre-depletion (31 d.p.i.)

value: Acute

tag: infection

tag: hybridization batch

tag: chamber batch

tag: acquisition date


title: Control, Dam 3

description: Control, replicate 3

value: RosaNICD/+ control


title: [C. albicans-efg1-cph1-]-[from Cecum]-[Rep2]

description: efg1- cph1- cecum 2

value: antibiotic-treated BALB/c mice by oral gavage

value: wild type


title: [C. albicans-efg1-cph1-]-[from Cecum]-[Rep1]

description: efg1- cph1- cecum 1

value: YPD medium at 37C to exponential phase


title: [C. albicans-efg1-cph1-]-[from Cecum]-[Rep3]

description: efg1- cph1- cecum 3


title: Control, Dam 2

description: Control, replicate 2