title: 9094INT: Female +/+; ST6GALNAC2 WT Intestine.

last: Head

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the v4 GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with RMA Express using the default settings (Background Adjust - Yes, Normalization - Quantile, Summarization Method - Median Polish, Store Residuals - unchecked).

source_name: ST6GALNAC2 WT Intestine.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

tag: Sex

value: female

tag: genotype

value: WT

value: Intestine

tag: disease state

value: healthy


title: 9093INT: Female -/-; ST6GALNAC2 KO Intestine.

status: Public on Sep 08 2011

type: RNA

city: La Jolla

first: Steven

state: CA

country: USA

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: ST6GALNAC2 KO Intestine.

value: unknown

value: ST6GALNAC2 KO

tag: tissue


title: 9099INT: Male +/+; ST6GALNAC2 WT Intestine.

value: male


title: SK mature embryos: 13˚C vs 25˚C

city: Tsukuba

first: Shingo

last: Nakamura

state: Ibaraki

address: Kannondai 2-1-18

country: Japan

institute: National Institute of Crop Science

hyb_protocol: The hybridization and washing were performed according to the Agilent manufacturer’s instructions

scan_protocol: Scanned on an Agilent MicroarrayScanner Images were quantified using Agilent Feature Extraction Software (version 9.1).

data_processing: Agilent Feature Extraction Software (v 9.1) was used for background subtraction and LOWESS normalization.

organism: Triticum aestivum

label_protocol: TotalRNA (400 ng) was labeled with Cy3 or Cy5 using an Agilent Quick Amp Labeling kit .

growth_protocol: Wheat were grown in adjoining two rooms in a green house.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions. The yield and RNA purity were determined spectrophotometrically. Integrity was verified using an Agilent 2100 Bioanalyzer

treatment_protocol: After anthesis, the temperautures of the rooms were adjusted and maintained at 13˚C and 25˚C, repectively. The spikes were harvested at the indicated DAA.

tag: developmental stage

value: embryo

tag: cultivar

value: Shiroganekomugi

tag: temperature

tag: daa


title: 9362INT: Male +/+; ST6GALNAC2 WT Intestine.


title: 9361INT: Male -/-; ST6GALNAC2 KO Intestine.


title: N5891KO-KID: Female B4GALNT1 -/- / B4GALNT2 -/- double knockout (KO) mouse kidney.

value: Kidneys


title: Lung_Cancer_Cell_Line_NCI-H1395

status: Public on Sep 09 2011

type: genomic

city: Uppsala

first: Anders

last: Isaksson

address: Akademiska sjukhuset ing61 3tr

country: Sweden

institute: Uppsala University

description: Lung cancer cell line H-1395 and patient-matched blood cell line BL1395 were obtained from ATCC and cultured according to their recommendations. DNA extraction was performed using the DNeasy Tissue Kit (Qiagen, Hilden, Germany).

hyb_protocol: Cytogenetics Copy Number Assay User Guide (P/N 702607 Rev2)

data_processing:
Log ratio, Allele Frequency, segments produced in BioDiscovery Nexus Copy Number 3.0, European HapMap reference set, Rank Segmentation algorithm. Allele specific copy numbers produced in R with the TAPS method.
Copy number text files contain total and minor copy numbers for all segments in the cancer samples.

molecule: genomic DNA

organism: Homo sapiens

source_name: Lung cancer

extract_protocol: DNA was extracted from 2-10 frozen tissue sections (10µm) using the QIAamp DNA Mini Kit (Qiagen, Hilden, Germany). DNA concentrations were measured with a ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, U.S.A.).

tag: sample type

value: Cell line

tag: cell line


title: N5893KO-KID: Male B4GALNT1 -/- / B4GALNT2 -/- double knockout (KO) mouse kidney.


title: N61 mature embryos: 25˚C vs 13˚C color swap

description: color swap


title: N61 mature embryos: 13˚C vs 25˚C


title: N9700WT+KID: Male B4GALNT1 +/+ / B4GALNT2 +/+ wild type (WT) kidney.

source_name: Wild type (WT) kidney.


title: N3740WT+KID1: Male B4GALNT1 +/+ / B4GALNT2 +/+ wild type (WT) kidney.


title: Blood_Cell_Line_NCI-BL1395

scan_protocol: Cytogenetics Copy Number Assay User Guide (P/N 702607 Rev2)

source_name: Blood


title: N5894KO-KID: Male B4GALNT1 -/- / B4GALNT2 -/- double knockout (KO) mouse kidney.


title: Lung_Cancer_Cell_Line_NCI-H1395 and Blood_Cell_Line_NCI-BL1395

description: Lung cancer cell line H-1395 and patient-matched blood cell line BL1395 were obtained from ATCC and cultured according to their recommendations.

data_processing: CNCHP files for copy number analysis produced using Affymetrix Genotyping Console 3.1 and default settings contain Log R and Allelic Difference.

source_name: Patient-matched Lung cancer and Blood cell lines

label_protocol: Cytogenetics Copy Number Assay User Guide (P/N 702607 Rev2)

extract_protocol: DNA extraction was performed using the DNeasy Tissue Kit (Qiagen, Hilden, Germany).

tag: dna mix

value: 30% Lung Cancer

tag: cell mix


title: Lung_Cancer_Cell_Line_NCI-H1395

value: 100% Lung Cancer


title: Colorectal_Tumor_Sample_6520

description: These colon cancer samples were selected from a series of samples in a large cohort of immediately snap-frozen tumor biopsies from patients operated upon for a colorectal cancer at the hospitals in Uppsala or Västerås, Sweden. All patients had given informed consent according to the research ethical committee at Uppsala University for the storage, isolation of DNA and use of the material in research projects. The tumor cell content in the samples were at least 50% based upon an examination of a  hematoxylin-eosin stained section. All patients had stage II and III, but these samples were selected based upon microarray analysis complexity rather than any clinical characteristics. All samples were fully anonymized. Tissue was reviewed by a pathologist to contain more than 50% tumor cells on hematoxylin-eosin stained tissue section. DNA was extracted from 2-10 frozen tissue sections (10µm) using the QIAamp DNA Mini Kit (Qiagen, Hilden, Germany). DNA concentrations were measured with a ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, U.S.A.).

source_name: Colorectal cancer

value: Tumor tissue

value: colorectal cancer tumor


title: N5892KO-KID: Female B4GALNT1 -/- / B4GALNT2 -/- double knockout (KO) mouse kidney.


title: N5895KO-MG: Male B4GALNT1 -/- / B4GALNT2 -/- double knockout (KO) mammary glands.

value: Mammary Glands


title: N3738WT+KID1: Male B4GALNT1 +/+ / B4GALNT2 +/+wild type (WT) kidney.


title: N9686WT+KID: Female B4GALNT1 +/+ / B4GALNT2 +/+ wild type (WT) kidney.


title: N5892KO-MG: Female B4GALNT1 -/- / B4GALNT2 -/- double knockout (KO) mammary glands.


title: N5891KO-MG: Female B4GALNT1 -/- / B4GALNT2 -/- double knockout (KO) mammary glands.


title: N9686WT+MG: Female B4GALNT1 +/+ / B4GALNT2 +/+ wild type (WT) mammary glands.

source_name: Wild type (WT) mammary glands.


title: N5893KO-TES: Male B4GALNT1 -/- / B4GALNT2 -/- double knockout (KO) testes.

value: Testes


title: N5894KOTES: Male B4GALNT1 -/- / B4GALNT2 -/- double knockout (KO) testes.


title: N5893KO-MG: Male B4GALNT1 -/- / B4GALNT2 -/- double knockout (KO) mammary glands.


title: N5895KO-KID: Male B4GALNT1 -/- / B4GALNT2 -/- double knockout (KO) mouse kidney.


title: N3738WT+TES: Male B4GALNT1 +/+ / B4GALNT2 +/+wild type (WT) testes.

source_name: Wild type (WT) testes.


title: N9700WT+TES: Male B4GALNT1 +/+ / B4GALNT2 +/+ wild type (WT) testes.


title: N5895KO-TES: Male B4GALNT1 -/- / B4GALNT2 -/- double knockout (KO) testes.


title: N3740WT+TES: Male B4GALNT1 +/+ / B4GALNT2 +/+ wild type (WT) testes.


title: N3738WT+MG: Male B4GALNT1 +/+ / B4GALNT2 +/+wild type (WT) mammary glands.


title: Colorectal_Tumor_Sample_68


title: Colorectal_Tumor_Sample_353


title: N5892KO-THYM: Female B4GALNT1 -/- / B4GALNT2 -/- double knockout (KO) thymus.

value: female

value: Thymus


title: N5893KO-THYM: Male B4GALNT1 -/- / B4GALNT2 -/- double knockout (KO) thymus.


title: N5894KOTHYM: Male B4GALNT1 -/- / B4GALNT2 -/- double knockout (KO) thymus.


title: Colorectal_Tumor_Sample_16080


title: Colorectal_Tumor_Sample_6969


title: Colorectal_Tumor_Sample_241


title: N5891KO-THYM: Female B4GALNT1 -/- / B4GALNT2 -/- double knockout (KO) thymus.


title: Colorectal_Tumor_Sample_313


title: N5895KO-THYM: Male B4GALNT1 -/- / B4GALNT2 -/- double knockout (KO) thymus.


title: Colorectal_Tumor_Sample_16266


title: 9099 BRN1: Male +/+; ST6GALNAC2 WT Brain.

source_name: ST6GALNAC2 WT Brain

value: WT

value: Brain


title: 9094 BRN: Female +/+; ST6GALNAC2 WT Brain.

value: healthy


title: N3740WT+THYM: Male B4GALNT1 +/+ / B4GALNT2 +/+ wild type (WT) thymus.

source_name: Wild type (WT) thymus.


title: 9099 BRN2: Male +/+; ST6GALNAC2 WT Brain.


title: 9093 BRN: Female -/-; ST6GALNAC2 KO Brain.

source_name: ST6GALNAC2 KO Brain

value: ST6GALNAC2 KO


title: N3738WT+THYM: Male B4GALNT1 +/+ / B4GALNT2 +/+wild type (WT) thymus.

value: male


title: 9100 BRN: Male -/-; ST6GALNAC2 KO Brain.


title: GDWTF2SMINTES: Pure WT C57 Control, Small Intestine.

source_name: WT C57 Control, Small Intestine.

value: unknown

value: Small Intestine


title: GDWTF2BRAIN: Pure WT C57 Control, Brain.

source_name: WT C57 Control, Brain.


title: GDWTF1SMINTES: Pure WT C57 Control, Small Intestine.


title: 9362 BRN: Male +/+; ST6GALNAC2 WT Brain.


title: 9100 Lymph: Male -/-; ST6GALNAC2 KO lymph node.

source_name: ST6GALNAC2 KO lymph node

value: Lymph Node


title: 9093 Lymph: Female -/-; ST6GALNAC2 KO lymph node.


title: 9361 BRN: Male -/-; ST6GALNAC2 KO Brain.


title: 9361 Lymph: Male -/-; ST6GALNAC2 KO lymph node.


title: Colorectal_Tumor_Sample_4263


title: 9099 Lymph: Male +/+; ST6GALNAC2 WT lymph node.

source_name: ST6GALNAC2 WT lymph node


title: 9362 Lymph: Male +/+; ST6GALNAC2 WT lymph node.


title: 9093 Thyro: Female -/-; ST6GALNAC2 KO thyroid.

source_name: ST6GALNAC2 KO thyroid

value: Thyroid


title: N9700WT+THYM: Male B4GALNT1 +/+ / B4GALNT2 +/+ wild type (WT) thymus.


title: Colorectal_Tumor_Sample_5126


title: 9094 Thyro: Female +/+; ST6GALNAC2 WT thyroid.

source_name: ST6GALNAC2 WT thyroid


title: Colorectal_Tumor_Sample_201


title: GDWTF1BRAIN: Pure WT C57 Control, Brain.


title: GDWTM3SMINTES: Pure WT C57 Control, Small Intestine.


title: 9362 Thyro: Male +/+; ST6GALNAC2 WT thyroid.


title: 9100 Thyro: Male -/-; ST6GALNAC2 KO thyroid.


title: 9099 Thyro: Male +/+; ST6GALNAC2 WT thyroid.


title: 9361 Thyro: Male -/-; ST6GALNAC2 KO thyroid.


title: 3A: Treated with Bracken fern extract orogastrically, replicate #1.

source_name: Gastric mucosa treated with bracken fern extract orogastrically

tag: background strain

tag: cell type

value: gastric mucosa

tag: heliobacter pylori

value: Uninfected

tag: bracken fern (orogastrically or h2o)

value: Bracken (orogastrically)


title: GDWTM3BRAIN: Pure WT C57 Control, Brain.


title: MLE-15CTL: Mouse lung epithelial cell line MLE-15, control replicate #1.

tag: tissue/cell line

value: Lung epithelial - MLE-15

tag: pma stimulated

value: No


title: 3C: Treated with Bracken fern extract orogastrically, replicate #3.

tag: Sex


title: MLE15PMA-A: Mouse lung epithelial cell line MLE-15, PMA stimulated replicate #2.

value: Yes

tag: disease state


title: MLE15CTL-A: Mouse lung epithelial cell line MLE-15, control replicate #2.


title: N5894KO-MG: Male B4GALNT1 -/- / B4GALNT2 -/- double knockout (KO) mammary glands.

tag: genotype

tag: tissue

value: Mammary Glands


title: MLE-15PMA: Mouse lung epithelial cell line MLE-15, PMA stimulated replicate #1.


title: 9094 Lymph: Female +/+; ST6GALNAC2 WT lymph node.

value: female


title: 3B: Treated with Bracken fern extract orogastrically, replicate #2.


title: Colorectal_Tumor_Sample_132

value: Tumor tissue

value: colorectal cancer tumor


title: 2C: Infected Helicobacter pylori, replicate #3.

source_name: Gastric mucosa infected with Helicobacter pylori

value: Infected


title: 2B: Infected Helicobacter pylori, replicate #2.


title: MLE15PMA-B: Mouse lung epithelial cell line MLE-15, PMA stimulated replicate #3.


title: MLE15CTL-B: Mouse lung epithelial cell line MLE-15, control replicate #3.


title: 2A: Infected Helicobacter pylori, replicate #1.


title: 4A: Treated with Bracken fern extract in drinking water, replicate #1.

source_name: C57B1/6 mice Treated with Bracken fern extract in drinking water

value: Bracken (H2O)


title: 1C: Control, replicate #3.

source_name: mouse gastric mucosa (control)


title: 4C: Treated with Bracken fern extract in drinking water, replicate #3.


title: 4B: Treated with Bracken fern extract in drinking water, replicate #2.


title: 1B: Control, replicate #2.


title: scott_14_frosty_Canine_2

city: Minneapolis

first: Aaron

last: Sarver

state: MN

address: 425 East River Road

department: Masonic Cancer Center

institute: University of Minnesota

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Canine 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: CEL files were normalized using the GC-RMA algorithm as implemented in the Genedata Analyst Software Package.

label: Biotin

organism: Canis lupus familiaris

source_name: primary osteosarcoma cell line

label_protocol: Biotinylated cRNA were prepared according to standard Affymetrix protocol from 2.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Primary tumor cells or cryopreserved cultured cells. Snap-frozen primary tissue used for 6 samples.

extract_protocol: RNA was prepared using the RNeasy Mini Kit and QIAshredder column (Qiagen, Valencia, CA).

value: primary osteosarcoma

tag: breed

value: German Shephard

value: MC

tag: age at diagnosis

tag: treatment

value: SOC* (died before ending chemo)

tag: survival


title: 5B: Infected Heliobacter pylori + Treated with Bracken fern extract orogastrically, replicate #2.

source_name: C57B1/6 mice Infected Heliobacter pylori + Treated with Bracken fern extract orogastrically

value: unknown


title: 1A: Control, replicate #1.

value: gastric mucosa


title: 6B: Infected Heliobacter pylori + Treated wth Bracken fern extract in drinking water, replicate#2.

source_name: Gastric mucosa infected Heliobacter pylori + Treated wth Bracken fern extract in drinking water


title: 6C: Infected Heliobacter pylori + Treated wth Bracken fern extract in drinking water, replicate#3.


title: scott_12_OSCA_73_Canine_2

source_name: primary osteosarcoma tissue

value: Golden Retriever

value: FS


title: gavin_OSCA_41_Canine_2

tag: cell line

value: Alaskan Malamute

value: ABX


title: scott_10_OSCA_71_A_Canine_2


title: gavin_OSCA_50_Canine_2

value: Rottweiler

value: M

value: PALL


title: 6A: Infected Helicobacter pylori + Treated with Bracken fern extract in drinking water, replicate#1.


title: M1-C: Retinas from RP mutant mice that were harvested from 1 month old animals, P347S+, replicate #3.

tag: tissue type

value: retina

tag: genotype/variation

value: RP Mutant

tag: sample time

value: 1 month


title: scott_5_shiloh_Canine_2

value: Belgian tervuren

value: SOC


title: scott_4_angel_Canine_2

value: primary osteosarcoma

value: Great Pyrenees

value: F


title: scott_7_rosie_Canine_2


title: 5A: Infected Heliobacter pylori + Treated with Bracken fern extract orogastrically, replicate #1.

tag: background strain

tag: cell type

value: unknown

value: Infected

value: Bracken (orogastrically)


title: 5C: Infected Heliobacter pylori + Treated with Bracken fern extract orogastrically, replicate #3.

value: gastric mucosa

tag: heliobacter pylori

tag: bracken fern (orogastrically or h2o)


title: gavin_OSCA_75_Canine_2

value: Golden Retriever

value: FS


title: scott_11_OSCA_71_B_Canine_2


title: gavin_OSCA_59_Canine_2


title: gavin_OSCA_60_Canine_2

value: Mastiff


title: scott_8_bella_Canine_2

value: Borzoi


title: gavin_OSCA_73_Canine_2


title: C1-A: Retinas from normal mice that were harvested from 1 month old animals, P347S-, replicate #1.

value: Normal


title: gavin_OSCA_57_Canine_2

value: M

value: AMP


title: C2-A: Retinas from normal mice that were harvested from 2 month old animals, P347S-, replicate #1.

value: retina

value: 2 months


title: C1-C: Retinas from normal mice that were harvested from 1 month old animals, P347S-, replicate #3.

value: 1 month


title: C2-C: Retinas from normal mice that were harvested from 2 month old animals, P347S-, replicate #3.


title: M2-C: Retinas from RP mutant mice that were harvested from 2 month old animals, P347S+, replicate #3.

value: RP Mutant


title: C1-B: Retinas from normal mice that were harvested from 1 month old animals, P347S-, replicate #2.


title: M1-A: Retinas from RP mutant mice that were harvested from 1 month old animals, P347S+, replicate #1.


title: M1-B: Retinas from RP mutant mice that were harvested from 1 month old animals, P347S+, replicate #2.


title: gavin_OSCA_56_Canine_2

value: primary osteosarcoma


title: gavin_OSCA_71_Canine_2

value: SOC


title: M2-B: Retinas from RP mutant mice that were harvested from 2 month old animals, P347S+, replicate #2.

value: unknown


title: C2-B: Retinas from normal mice that were harvested from 2 month old animals, P347S-, replicate #2.


title: M2-A: Retinas from RP mutant mice that were harvested from 2 month old animals, P347S+, replicate #1.


title: C3-A: Retinas from normal mice that were harvested from 3 month old animals, P347S-, replicate #1.

value: 3 months


title: C3-C: Retinas from normal mice that were harvested from 3 month old animals, P347S-, replicate #3.


title: gavin_OSCA_30_Canine_2

value: German Shepherd

value: MC


title: C3-B: Retinas from normal mice that were harvested from 3 month old animals, P347S-, replicate #2.


title: gavin_OSCA_8_Canine_2

value: Rottweiler


title: gavin_OSCA_11_Canine_2

source_name: metastatic osteosarcoma cell line

value: metastatic osteosarcoma

value: F


title: gavin_OSCA_23_Canine_2

value: Golden Retriever


title: gavin_OSCA_29_Canine_2

value: SOC* (died before ending chemo)


title: gavin_OSCA_32_Canine_2

value: Great Pyrenees


title: gavin_OSCA_12_Canine_2


title: M3-C: Retinas from RP mutant mice that were harvested from 3 month old animals, P347S+, replicate #3.


title: C4-A: Retinas from normal mice that were harvested from 4 month old animals, P347S-, replicate #1.

value: Normal

value: 4 months


title: M3-A: Retinas from RP mutant mice that were harvested from 3 month old animals, P347S+, replicate #1.

value: retina


title: C4-C: Retinas from normal mice that were harvested from 4 month old animals, P347S-, replicate #3.


title: gavin_OSCA_22_Canine_2

value: AMP


title: M4-A: Retinas from RP mutant mice that were harvested from 4 month old animals, P347S+, replicate #1.

value: RP Mutant


title: gavin_OSCA_17_Canine_2

value: primary osteosarcoma

value: M


title: gavin_OSCA_16_Canine_2

value: SOC


title: gavin_OSCA_19_Canine_2


title: M3-B: Retinas from RP mutant mice that were harvested from 3 month old animals, P347S+, replicate #2.

value: unknown

value: 3 months


title: gavin_OSCA_6_Canine_2

value: Rhodesian Ridgeback

value: PALL


title: gavin_OSCA_1_Canine_2

value: Rottweiler


title: VSV infected RAW264.7

city: Boston

first: Shitao

last: Li

state: MA

address: 77 Ave Louis Pasteur

department: MBIB

institute: Harvard Medical School

description: Test

data_processing: Sample data tables report normalized signal (against housekeeping genes). Fold Change worksheet, linked to the Series record, reports test/control (i.e., stimulation/unstimulation) ratios.

label: SYBR Green

source_name: RAW264.7 macrophage

label_protocol: PCR assays were performed using the RAW264.7 - Anti-viral Innate Immunity Pathway PCR assay Panel. Reverse transcription was performed from 500 ng total RNA using the RT2 First Strand Kit (SA Biosciences). Quantitative real-time PCR were performed (Light Cycler 480, Roche) with 45 cycles at 94 oC for 15 seconds and 60 oC for 60 seconds.

growth_protocol: DMEM plus 10% FBS

extract_protocol: Total RNA was extracted with RNeasy Mini Kit followed by DNase I treatment.

tag: cell tye

value: RAW264.7 macrophage

tag: activation

value: 1 M.O.I. VSV

tag: time


title: fosmire_40.2_Canine_2

value: Saint Bernard

tag: Sex

value: FS


title: Sendai infected RAW264.7

description: Test

value: 5 HA Sendai virus


title: HSV infected RAW264.7

description: Test

value: 1 M.O.I. HSV


title: LPS activated RAW264.7

description: Test

value: 10 mg/ml LPS


title: IFNb activated RAW264.7

description: Test

value: 1.5 U/ml IFNb


title: C4-B: Retinas from normal mice that were harvested from 4 month old animals, P347S-, replicate #2.

value: retina

value: Normal

value: 4 months


title: fosmire_21.3_Canine_2

value: primary osteosarcoma

value: MC

value: SOC


title: D3: Diabetic mice RNA, replicate #3.

source_name: Liver, diabetic mice

tag: tissue

value: liver

value: male

tag: disease state

value: diabetic


title: fosmire_25.2_Canine_2

tag: breed

value: Rottweiler

tag: age at diagnosis


title: RAW264.7 macrophage

description: Control

value: RAW264.7 macrophage

value: control


title: M4-C: Retinas from RP mutant mice that were harvested from 4 month old animals, P347S+, replicate #3.

value: unknown

value: RP Mutant


title: M4-B: Retinas from RP mutant mice that were harvested from 4 month old animals, P347S+, replicate #2.


title: poly(dA:dT) activated RAW264.7

description: Test

value: 1 mg/ml poly(dA:dT)


title: D1: Diabetic mice RNA, replicate #1.


title: D2: Diabetic mice RNA, replicate #2.


title: W2: Wildtype mice RNA, replicate #2.

source_name: Liver, wildtype mice

value: healthy


title: W1: Wildtype mice RNA, replicate #1.


title: fosmire_20.3_Canine_2

value: Golden Retriever

tag: treatment

value: SOC* (died before 1st chemo)

tag: survival


title: 2AN24HR

description: 2AN24HR: WildType mice injected with 100 ug (anergic condition) of influenza hemaglutinin antigen (HA), 24 hours post injection CD8 T CL4 cells were sorted by flow cytometry (FacsARIA), replicate #2.

source_name: CD8 T-cells; Anergic condition

value: CD8+ T cell

value: female


title: poly(rI:rC) activated RAW264.7

description: Test

value: 1 mg/ml poly(rI:rC)


title: W3: Wildtype mice RNA, replicate #3.


title: 1AN24HR

description: 1AN24HR: WildType mice injected with 100 ug (anergic condition) of influenza hemaglutinin antigen (HA), 24 hours post injection CD8 T CL4 cells were sorted by flow cytometry (FacsARIA), replicate #1.


title: 1DL24HR

description: 1DL24HR: Mice injected with 1 ug (deleted condition) of influenza hemaglutinin antigen (HA), 24 hours post injection CD8 T CL4 cells were sorted by flow cytometry (FacsARIA), replicate #1.

source_name: CD8 T-cells; Deletion condition


title: 3DL24HR

description: 3DL24HR: Mice injected with 1 ug (deleted condition) of influenza hemaglutinin antigen (HA), 24 hours post injection CD8 T CL4 cells were sorted by flow cytometry (FacsARIA), replicate #3.


title: 1BI96HR

description: 1BI96HR: BIM KO Clone 4 transgenic T cells were transferred into B10D2 mice then injected daily for 3 days with 1ug of KdHA peptide and sorted by flow cytometry according to their expression of CD8 and thy1.1, replicate #1.

source_name: CD8 T-cells; BIM KO Clone 4


title: 2BI96HR

description: 2BI96HR: BIM KO Clone 4 transgenic T cells were transferred into B10D2 mice then injected daily for 3 days with 1ug of KdHA peptide and sorted by flow cytometry according to their expression of CD8 and thy1.1, replicate #2.


title: 3AN24HR

description: 3AN24HR: WildType mice injected with 100 ug (anergic condition) of influenza hemaglutinin antigen (HA), 24 hours post injection CD8 T CL4 cells were sorted by flow cytometry (FacsARIA), replicate #3.


title: cortex_knockout_replicate 2 B Chip

first: Gerald

middle: M

last: Pao

address: 10010 North Torrey Pines

department: Laboratory of Genetics

institute: Salk Institute

description: Standard Affymetrix Protocol

hyb_protocol: Standard Affymetrix Protocol

scan_protocol: Standard Affymetrix Protocol

data_processing: Only intensity values called Present were considered and values were processed using default MAS 5.0 parameters.

label: Standard Affymetrix Protocol

source_name: mouse P7 cortex

label_protocol: Standard Affymetrix Protocol

extract_protocol: TRIZOL

tag: BRCA1 conditional knockout or wildtype cortex


title: cortex_knockout_replicate 3 B Chip

description: Standard Affymetrix Protocol


title: cortex_wildtype_replicate 1 B Chip

description: Standard Affymetrix Protocol


title: cortex_wildtype_replicate 2 B Chip

description: Standard Affymetrix Protocol


title: 1hrKCl_S421A_RepC_sc16

city: Brookline

first: Harrison

middle: Wren

last: Gabel

address: 7 Linden St Apt 3

department: Neurobiology

description: E16+7DIV cortical culture neurons

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Expression Set 430 2.0 microarray. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Genechip Scanner 3000.

data_processing: Data were processed using Affymetrix Expression Console Version 1.1 RMA workflow with quantile normalization and general background correction. Differential expression analysis was performed using GeneSpring GX (Agilent technologies) and custom statistical analysis see methods of Cohen et al. neuron 2011 for details.

source_name: cultured cortical neurons E16+7DIV

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA.

growth_protocol: Dissociated cortical cultures (E16+7DIV) grown in neurobasal media supplemented with B27, glutamine, and pen/strep.

extract_protocol: RNA was isolated by extraction using Trizol (invitrogen) according to the manufactures instructions, and then further purfied using qiagen minelute columns.

treatment_protocol: Neuronal cultures were pre-treated with 1 µM tetrodotoxin (TTX) and 100 µM D-APV (Tocris Bioscience) overnight to reduce endogenous neuronal activity prior to stimulation and then left unstimulated or membrane depolarized with 55 mM extracellular KCl by addition of 0.5 volumes of prewarmed depolarization buffer (170 mM KCl, 2 mM CaCl2, 1 mM MgCl2, 10 mM HEPES pH7.5) for 1 hour or 6 hours.

tag: condition

value: 1 hr KCl depolarized

tag: litter

value: C

tag: genotype/variation

value: MeCP2 S421A

tag: strain/background

value: ES cells derived from a 129 background and injected into C57BL6 mice to generate chimeras. The resulting strain was extensively backcrossed into C57BL6(>10 generations) before cortical cultures were derived.


title: VisCortex_S421A_rep2_scG

description: P17  visual cortex RNA

hyb_protocol: 2 ug of Fragmented and Biotinylated  cDNA were hybridized for 16 hr at 45C on Mouse Gene 1.0 ST microarray. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix Genechip Scanner 3000

data_processing: Data were processed using Affymetrix Expression Console Version 1.1 RMA workflow, quantile normalization and general background correction. Differential expression analysis was performed using GeneSpring GX (Agilent technologies) and custom statistical analysis see methods of Cohen et al. neuron 2011 for details.

source_name: P17 visual cortex

label_protocol: Biotinylated  cDNA were prepared according to the standard Affymetrix protocol from 100ng total RNA

growth_protocol: P17 mice (WT and MeCP2 S421A littermates) were grown under standard housing conditions.

treatment_protocol: Mice were sacrificed and visual cortex dissected. All mice were male littermates from one of two litters.

tag: strain


title: 1VH96HR

description: 1VH96HR: Wild Type mice were injected injected only once with a strain of vaccinia virus that express hemagglutinin from influenza, replicate #1.

source_name: CD8 T-cells; mouse injected with strain of vaccinia virus that express hemagglutinin from influenza

tag: cell type


title: 6hrKCl_S421A_RepC_sc18

description: E16+7DIV cortical culture neurons

value: 6 hr KCl depolarized


title: VisCortex_WT_rep2_scE

description: P17  visual cortex RNA

value: WT


title: VisCortex_WT_rep2_scH

description: P17  visual cortex RNA


title: VisCortex_S421A_rep1_scC

description: P17  visual cortex RNA


title: cortex_knockout_replicate 1 B Chip

description: Standard Affymetrix Protocol


title: 1hrKCl_WT_RepC_sc15

description: E16+7DIV cortical culture neurons


title: 3BI96HR

description: 3BI96HR: BIM KO Clone 4 transgenic T cells were transferred into B10D2 mice then injected daily for 3 days with 1ug of KdHA peptide and sorted by flow cytometry according to their expression of CD8 and thy1.1, replicate #3.


title: VisCortex_WT_rep1_scB

description: P17  visual cortex RNA


title: VisCortex_WT_rep1_scD

description: P17  visual cortex RNA


title: 2DL24HR

description: 2DL24HR: Mice injected with 1 ug (deleted condition) of influenza hemaglutinin antigen (HA), 24 hours post injection CD8 T CL4 cells were sorted by flow cytometry (FacsARIA), replicate #2.


title: cortex_wildtype_replicate 3 B Chip

description: Standard Affymetrix Protocol


title: 6hrKCl_WT_RepC_sc17

description: E16+7DIV cortical culture neurons


title: VisCortex_S421A_rep2_scF

description: P17  visual cortex RNA


title: E.albidus_ Cu-NP 600mg/Kg_rep3

city: Aveiro

first: Susana

middle: Isabel Lopes

last: Gomes

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

department: Biology

country: Portugal

institute: CESAM & University of Aveiro

description: The hybridization performed here was the control sample vs the 600 mg/Kg Cu-NP exposure sample.

hyb_protocol: Prior to hybridization, arrays were incubated for 30-45 min at 42°C in a prehybridization solution (50% formamide, 5x saline sodium citrate (SSC), 0.1% sodium dodecyl sulphate (SDS), 0.1mg/mL BSA). The vacuum dried targets (both reference and treatment target) were resuspended in a hybridization solution (50% formamide, 5x SSC, 0.1% SDS, 0.1mg/mL BSA and 0.1mg/mL sheared salmon sperm) and denaturated at 95°C. The cooled targets were subsequently applied onto the prehybridized slides and incubated overnight at 42°C. After hybridization, arrays were washed in solutions with increasing stringency (decreasing concentrations of SSC and SDS) and dried with N2.

scan_protocol: Scanning was performed using an Agilent Microarray Scanner (Agilent Technologies) at 532 and 635 nm for Cy3 and Cy5 respectively. The images acquired were assessed using QuantArray (Packard Biochip Technologies) for spot identification and quantification of fluorescent signal intensities.

data_processing: The limmaGUI package (based on limma (Smyth 2005)) in the R (2.8.0) software environment (http://www.R-project.org) was used for background subtraction, normalization and succeeding statistical analysis of the microarray datasets. The Log2 transformed Cy3/Cy5 ratio data were normalized using the global loess (Yang et al., 2002), which is an intensity-based method.

organism: Enchytraeus albidus

source_name: E.albidus exposed to 600 mg/Kg of Cu-NP for 48h

label_protocol: The production of cDNA and subsequent amino-allyl labelling were performed according to the protocol described in detail by Van der Ven et al. (2005) and Soetaert et al. (2006). In brief, 7µg of total RNA was mixed with Lucidea control mRNA spike mix (Amersham, UK) to be reverse-transcribed using the Superscript II, Random hexamer primers (both Invitrogen) in the presence of dNTPs with 2/3 aa-dTTP/dTTP (Sigma-Aldrich, Belgium). After an overnight incubation period (42°C) the amino-allyl-incorporated cDNA was purified using a modified Qiagen PCR spin colomn protocol (Van der Ven et al., 2005). In a next step, Cy3/Cy5 esters (Amersham) were used for covalent coupling to the amino-allyl labelled cDNA. The vacuum dried cDNA samples (dissolved in a 0,1M carbonate buffer (pH 9.0)) were mixed with the Cy3/Cy5 esters (dissolved in 100% DMSO) and incubated for an hour in the dark at room temperature. Hereafter, a second cleanup reaction was performed to establish the removal of the remaining uncoupled dyes (QIAquick PCR purification kit, Qiagen, USA). The quality of eluted and labelled cDNA was analysed using the Nanodrop® spectrophotometer. Samples with an FOI (frequence of incorporated dye) between 20 and 50 were selected for hybridization and an amount of 150 pmol labelled target was vacuum dried.

extract_protocol: 15 worms per replicate were collected. Samples were shock-frozen in liquid nitrogen and stored in RNAlater (Ambion, USA) at -80°C. All RNA extractions were performed using the TRIzol® method (Invitrogen, Belgium) followed by a DNAse treatment using 1,5U RNAse-free DNAse and 1U RNAse inhibitor (Fermentas, Germany) per 50µl sample and subsequent phenol/chloroform extractions. The purity of the RNA samples was checked using the ND-1000 spectrophotometer (Nanodrop®, USA) through measurement of the 260nm/280nm and 260nm/230nm absorbance. For all used samples these ratios were approximately 2. To verify the intactness of the RNA samples, a denaturating formaldehyde agarose gel electrophoresis was performed.

value: Whole body extracts (15 organisms)

tag: stage of development

value: Adult organisms with well developed clitellum

tag: exposure

value: 600 mg Cu-NP/Kg soil

source_name: E.albidus maintained for the same 48h in clean soil - Control RNA sample


title: unstim_WT_RepC_sc13

description: E16+7DIV cortical culture neurons

value: unstimulated


title: AN3

description: AN3: Purified TCR transgenic CD8 T cells stimulated in vivo using a strong antigenic signal (anergy conditions) with cognate antigen, replicate #3.

source_name: CD8+ T cells; Anergy Conditions


title: 2VH96HR

description: 2VH96HR: Wild Type mice were injected injected only once with a strain of vaccinia virus that express hemagglutinin from influenza, replicate #2.


title: 1hrKCl_S421A_RepB_sc10

description: E16+7DIV cortical culture neurons

value: B


title: E.albidus_ Cu-NP 1000mg/Kg_rep3

description: The hybridization performed here was the control sample vs the 1000 mg/Kg Cu-NP exposure sample.

source_name: E.albidus exposed to 1000 mg/Kg of Cu-NP for 48h

value: 1000 mg Cu-NP/Kg soil


title: unstim_S421A_RepC_sc14

description: E16+7DIV cortical culture neurons


title: AN1

description: AN1: Purified TCR transgenic CD8 T cells stimulated in vivo using a strong antigenic signal (anergy conditions) with cognate antigen, replicate #1.


title: E.albidus_ Cu-NP 800mg/Kg_rep3

description: The hybridization performed here was the control sample vs the 800 mg/Kg Cu-NP exposure sample.

source_name: E.albidus exposed to 800 mg/Kg of copper-nanoparticles (Cu-NP) for 48h

value: 800 mg Cu-NP/Kg soil


title: E.albidus_ Cu-NP 1000mg/Kg_rep2

source_name: E.albidus exposed to 1000 mg/Kg of copper-nanoparticles (Cu-NP) for 48h


title: 6hrKCl_S421A_RepA_sc12

description: E16+7DIV cortical culture neurons


title: E.albidus_ Cu-NP 600mg/Kg_rep2

source_name: E.albidus exposed to 600 mg/Kg of copper-nanoparticles (Cu-NP) for 48h


title: E.albidus_ Cu-NP 800mg/Kg_rep2


title: DL1

description: DL1:purified TCR transgenic CD8 T cells stimulated in vivo using a weak antigenic signal (deletion conditions) with cognate antigen, replicate #1.

source_name: CD8+ T cells; Deletion conditions


title: AN2

description: AN2: purified TCR transgenic CD8 T cells stimulated in vivo using a strong antigenic signal (anergy conditions) with cognate antigen, triplicate #2.

source_name: CD8+ T cells; Anergy conditions


title: DL2

description: DL2:purified TCR transgenic CD8 T cells stimulated in vivo using a weak antigenic signal (deletion conditions) with cognate antigen, replicate #2.


title: 6hrKCl_WT_RepB_sc11

description: E16+7DIV cortical culture neurons


title: VisCortex_S421A_rep1_scA

description: P17  visual cortex RNA


title: E.albidus_ Cu-NP 1000mg/Kg_rep1


title: E.albidus_ Cu-NP 800mg/Kg_rep1


title: E.albidus_ Cu-NP 400mg/Kg_rep1

description: The hybridization performed here was the control sample vs the 400 mg/Kg Cu-NP exposure sample.

source_name: E.albidus exposed to 400 mg/Kg of copper-nanoparticles (Cu-NP) for 48h

value: 400 mg Cu-NP/Kg soil


title: E.albidus_ CuCl2 1000mg/Kg_rep3

description: The hybridization performed here was the control sample vs the 1000 mg/Kg CuCl2 exposure sample.

source_name: E.albidus exposed to 1000 mg/Kg of CuCl2 for 48h

value: 1000 mg CuCl2/Kg soil


title: unstim_S421A_RepB_sc8

description: E16+7DIV cortical culture neurons


title: E.albidus_ CuCl2 1000mg/Kg_rep1


title: E.albidus_ CuCl2 1000mg/Kg_rep2


title: DL3

description: DL3:purified TCR transgenic CD8 T cells stimulated in vivo using a weak antigenic signal (deletion conditions) with cognate antigen, replicate #3.

value: CD8+ T cell

value: female


title: E.albidus_ Cu-NP 400mg/Kg_rep2


title: E.albidus_ Cu-NP 400mg/Kg_rep3


title: 6hrKCl_WT_RepA_sc5

description: E16+7DIV cortical culture neurons

value: A


title: 1hrKCl_WT_RepB_sc9

description: E16+7DIV cortical culture neurons

value: 1 hr KCl depolarized


title: 6hrKCl_S421A_RepA_sc6

description: E16+7DIV cortical culture neurons

value: MeCP2 S421A


title: unstim_WT_RepB_sc7

description: E16+7DIV cortical culture neurons


title: NV1

description: NV1: Control, naive transgenic CD8 cells, replicate #1.

source_name: CD8+ T cells; Naive control


title: E.albidus_ Cu-NP 600mg/Kg_rep1


title: E.albidus_ CuCl2 800mg/Kg_rep3

description: The hybridization performed here was the control sample vs the 800 mg/Kg CuCl2 exposure sample.

source_name: E.albidus exposed to 800 mg/Kg of CuCl2 for 48h

value: 800 mg CuCl2/Kg soil


title: E.albidus_ CuCl2 600mg/Kg_rep3

description: The hybridization performed here was the control sample vs the 600 mg/Kg CuCl2 exposure sample.

source_name: E.albidus exposed to 600 mg/Kg of CuCl2 for 48h

value: 600 mg CuCl2/Kg soil


title: E.albidus_ CuCl2 800mg/Kg_rep1


title: NV2

description: NV2: Control, naive transgenic CD8 cells, replicate #2.


title: NV3

description: NV3: Control, naive transgenic CD8 cells, replicate #3.


title: E.albidus_ CuCl2 800mg/Kg_rep2


title: 1hrKCl_S421A_RepA_sc4

description: E16+7DIV cortical culture neurons

source_name: cultured cortical neurons E16+7DIV

value: ES cells derived from a 129 background and injected into C57BL6 mice to generate chimeras. The resulting strain was extensively backcrossed into C57BL6(>10 generations) before cortical cultures were derived.


title: E.albidus_ CuCl2 600mg/Kg_rep4

value: Whole body extracts (15 organisms)


title: E.albidus_ CuCl2 400mg/Kg_rep2

description: The hybridization performed here was the control sample vs the 400 mg/Kg CuCl2 exposure sample.

source_name: E.albidus exposed to 400 mg/Kg of CuCl2 for 48h

value: Adult organisms with well developed clitellum

value: 400 mg CuCl2/Kg soil


title: E.albidus_ CuCl2 400mg/Kg_rep3


title: E.albidus_ CuCl2 600mg/Kg_rep2


title: 1hrKCl_WT_RepA_sc3

description: E16+7DIV cortical culture neurons

value: WT


title: unstim_S421A_RepA_sc2

description: E16+7DIV cortical culture neurons

value: unstimulated


title: rest_wildtype_replicate 3

description: Standard Affymetrix Protocol

source_name: mouse P7 brain

tag: BRCA1 conditional knockout or wildtype brain, minus the cortex


title: cortex_wildtype_replicate 2 A Chip

description: Standard Affymetrix Protocol

source_name: mouse P7 cortex


title: cortex_wildtype_replicate 3 A Chip

description: Standard Affymetrix Protocol


title: cortex_knockout_replicate 1 A Chip

description: Standard Affymetrix Protocol


title: E.albidus_ CuCl2 400mg/Kg_rep1

source_name: E.albidus maintained for the same 48h in clean soil - Control RNA sample


title: cortex_knockout_replicate 3 A Chip

description: Standard Affymetrix Protocol


title: rest_wildtype_replicate 2

description: Standard Affymetrix Protocol


title: St 2 days_rep1

status: Public on Sep 07 2011

description: The hybridization performed here was the reference sample vs the OECD-St soil exposure sample.

data_processing: BRB Array Tools version 3.8.1 Stable Release (http://linus.nci.nih.gov/BRB-ArrayTools.html) was used for background subtraction, normalization and succeeding statistical analysis of the microarray datasets. The Log2 transformed Cy3/Cy5 ratio data were normalized using the loess method (Smith and Speed, 2003), which is an intensity-based method.

source_name: Reference sample: E. albidus exposed in OECD standard soil (pool from 2, 4 and 8 days of exposure)

extract_protocol: 10 worms per replicate were collected. Samples were shock-frozen in liquid nitrogen and stored in RNAlater (Ambion, USA) at -80°C. All RNA extractions were performed using the TRIzol® method (Invitrogen, Belgium) followed by a DNAse treatment using 1,5U RNAse-free DNAse and 1U RNAse inhibitor (Fermentas, Germany) per 50µl sample and subsequent phenol/chloroform extractions. The purity of the RNA samples was checked using the ND-1000 spectrophotometer (Nanodrop®, USA) through measurement of the 260nm/280nm and 260nm/230nm absorbance. For all used samples these ratios were approximately 2. To verify the intactness of the RNA samples, a denaturating formaldehyde agarose gel electrophoresis was performed.

value: Whole body extracts (10 organisms)

value: OECD standard soil (pool from exposure during 2, 4 and 8 days)

source_name: Test sample: E.albidus exposed in OECD-St (standard) soil for 2 days

value: OECD-St soil

tag: time

value: 2 days


title: St 8 days_rep1

tag: tissue

source_name: Test sample: E.albidus exposed in OECD-St (standard) soil for 8 days

value: 8 days


title: St 8 days_rep2


title: St 8 days_rep3


title: unstim_WT_RepA_sc1

description: E16+7DIV cortical culture neurons


title: St 4 days_rep3

source_name: Test sample: E.albidus exposed in OECD-St (standard) soil for 4 days

value: 4 days


title: rest_knockout_replicate 2

description: Standard Affymetrix Protocol


title: OregonR^TOW Stage 11/12 MCM2-7 ChIP

city: Cambridge

first: Terry

middle: L.

last: Orr-Weaver

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

hyb_protocol: Slides were hybridized to custom Agilent tiling arrays and washed as per Agilent recommendations

scan_protocol: Arrays were scanned on an Agilent scanner per manufacturer's protocol

data_processing: Raw data was median normalized using the Ringo package in R in order to generate .wig files containing smoothed log ratios.

organism: Drosophila melanogaster

source_name: MCM2-7 ChIP DNA from OregonR^TOW pooled stage 11 and 12 egg chambers

label_protocol: DNA was labeled using Invitrogen's BioPrime Total for Agilent aCGH labeling kit

growth_protocol: Drosophila were grown on standard cornmeal, molasses agar media

extract_protocol: Staged egg chambers were fixed with 2% formaldehyde in Grace's medium for 15 min at room temperature followed by quenching with 0.125 M glycine for 5 min (4 samples of 300 egg chambers each). The cells were washed twice with TBS and placed in 0.5 mL of ChIP lysis buffer (50 mM HEPES/KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-Deoxycholate). The crosslinked chromatin was sheared to an average size of 300-1000 bp by three 12-second pulses using a Branson 250 sonicator. The lysate was then centrifuged to remove cell debris. 50 uL was saved for the input DNA from each sample. The chromatin supernatant was then incubated overnight with 5 uL of MCM2-7 antibody (Steve Bell, MIT) at 4C. After incubation with 30 uL protein G Dynabeads beads (Invitrogen) for 2h at 4C, the immune complexes were collected using the Dynal magnetic strip and washed with the following buffers at room temperature for 5 minutes each: 2X ChIP lysis buffer, 2X high salt (500mM NaCl) ChIP lysis buffer, 1X ChIP lysis buffer, 1X TE. The protein-DNA complexes were eluted from the beads in 100 uL ChIP elution buffer (50 mM Tris/HCl pH 8.0, 10 mM EDTA/1% SDS) at 65C for 15 min followed by another wash with 150 uL TE/0.67% SDS. Eluates were pooled and incubated at 65C for at least 6 hours. Input DNAs were similarly subject to reversal of crosslinks with 200 µL TE/1% SDS. DNAs from four samples were pooled together. Samples were treated with 100 ug proteinase K at 37C for 2 hours. DNA samples were phenol chloroform extracted twice and ethanol precipitated.

treatment_protocol: Stage 11 and 12 egg chambers were hand sorted from 2-3 day fattened female flies

value: egg chambers

value: OregonR^TOW

tag: chip antibody

source_name: Input DNA from OregonR^TOW Stage 11 and 12 egg chambers

value: none; input DNA


title: pH 8 days_rep3

description: The hybridization performed here was the reference sample vs the OECD-pH modified soil exposure sample.

source_name: Test sample: E.albidus exposed in OECD-pH modified soil for 8 daysE.albidus exposed in OECD-pH modified soil for 8 days

value: OECD-pH modified soil


title: rest_knockout_replicate 3

description: Standard Affymetrix Protocol


title: pH 8 days_rep2


title: St 2 days_rep3


title: St 4 days_rep2


title: cortex_knockout_replicate 2 A Chip

description: Standard Affymetrix Protocol


title: St 2 days_rep2


title: rest_knockout_replicate 1

description: Standard Affymetrix Protocol


title: rest_wildtype_replicate 1

description: Standard Affymetrix Protocol


title: cortex_wildtype_replicate 1 A Chip

description: Standard Affymetrix Protocol


title: St 4 days_rep1


title: pH 4 days_rep2

source_name: Test sample: E.albidus exposed in OECD-pH modified soil for 4 days


title: pH 8 days_rep1

source_name: Test sample: E.albidus exposed in OECD-pH modified soil for 8 days


title: pH 4 days_rep1


title: pH 2 days_rep3

source_name: Test sample: E.albidus exposed in OECD-pH modified soil for 2 days


title: pH 4 days_rep3


title: OM 8 days_rep3

description: The hybridization performed here was the reference sample vs the OECD-OM modified soil exposure sample.

source_name: Test sample: E.albidus exposed in OECD-OM (organic matter) modified soil for 8 days

value: OECD-OM modified soil


title: pH 2 days_rep2


title: OM 4 days_rep1

source_name: Test sample: E.albidus exposed in OECD-OM (organic matter) modified soil for 4 days


title: OM 8 days_rep1


title: OM 8 days_rep2


title: pH 2 days_rep1


title: clay 2 days_rep2

description: The hybridization performed here was the reference sample vs the OECD-clay modified soil exposure sample.

source_name: Test sample: E.albidus exposed in OECD-clay modified soil for 2 days

value: OECD-clay modified soil


title: OM 4 days_rep2


title: clay 8 days_rep3

source_name: Test sample: E.albidus exposed in OECD-clay modified soil for 8 days


title: clay 2 days_rep1


title: clay 8 days_rep2


title: OM 2 days_rep1

source_name: Test sample: E.albidus exposed in OECD-OM (organic matter) modified soil for 2 days


title: OM 4 days_rep3


title: clay 4 days_rep1

source_name: Test sample: E.albidus exposed in OECD-clay modified soil for 4 days


title: clay 4 days_rep2


title: clay 8 days_rep1


title: clay 4 days_rep3


title: OM 2 days_rep3


title: OM 2 days_rep2


title: clay 2 days_rep3


title: Bleomycin treated IL-13Ra2(C57BL/6) KO Replicate 4

city: Princeton

first: Sudhir

last: Varma

state: NJ

address: 1215 Wessex Pl

institute: HiThru Analytics

description: Biological Replicate 4

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

scan_protocol: Scanned on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).

data_processing: Agilent Feature Extraction Software (v 10.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: Fibrosis model: Bleomycin treated total lung RNA

label_protocol: 20 µg of total RNA were primed with 2 µl of 100 µM oligo dT primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3 or Cy5-label

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

value: IL13RA2 Knockout

tag: model

value: Fibrosis

value: Lung

source_name: Saline treated total lung RNA

tag: reference

value: Saline treated total lung RNA

tag: age

value: 4-6 week


title: Bleomycin treated IL-13Ra2(C57BL/6) KO Replicate 2

description: Biological Replicate 2


title: Bleomycin treated IL-13Ra2(C57BL/6) KO Replicate 3

description: Biological Replicate 3


title: Bleomycin treated wild type (C57BL/6) Replicate 4

description: Biological Replicate 4

value: WT


title: Bleomycin treated IL-13Ra2(C57BL/6) KO Replicate 1

description: Biological Replicate 1


title: Bleomycin treated wild type (C57BL/6) Replicate 3

description: Biological Replicate 3


title: Bleomycin treated IL-13Ra1(C57BL/6) KO Replicate 2

description: Biological Replicate 2

value: IL13RA1 Knockout


title: Bleomycin treated wild type (C57BL/6) Replicate 1

description: Biological Replicate 1


title: Bleomycin treated IL-13Ra1(C57BL/6) KO Replicate 1

description: Biological Replicate 1


title: Bleomycin treated IL-13Ra1(C57BL/6) KO Replicate 3

description: Biological Replicate 3


title: SEA treated IL-13Ra2(C57BL/6) KO Replicate 5

description: Biological Replicate 5

source_name: Allergy model: SEA treated total lung RNA

value: Allergy

source_name: PBS treated total lung RNA

value: PBS treated total lung RNA


title: SEA treated IL-13Ra1(C57BL/6) KO Replicate 4

description: Biological Replicate 4


title: SEA treated IL-13Ra2(C57BL/6) KO Replicate 4

description: Biological Replicate 4


title: Bleomycin treated IL-13Ra1(C57BL/6) KO Replicate 4

description: Biological Replicate 4


title: SEA treated IL-13Ra2(C57BL/6) KO Replicate 2

description: Biological Replicate 2


title: SEA treated IL-13Ra1(C57BL/6) KO Replicate 3

description: Biological Replicate 3


title: Bleomycin treated wild type (C57BL/6) Replicate 2

description: Biological Replicate 2


title: SEA treated wild type (C57BL/6) Replicate 5

description: Biological Replicate 5


title: SEA treated IL-13Ra1(C57BL/6) KO Replicate 2

description: Biological Replicate 2


title: SEA treated IL-13Ra2(C57BL/6) KO Replicate 3

description: Biological Replicate 3


title: SEA treated IL-13Ra1(C57BL/6) KO Replicate 5

description: Biological Replicate 5


title: SEA treated wild type (C57BL/6) Replicate 3

description: Biological Replicate 3


title: SEA treated wild type (C57BL/6) Replicate 4

description: Biological Replicate 4


title: SEA treated IL-13Ra2(C57BL/6) KO Replicate 1

description: Biological Replicate 1


title: SEA treated wild type (C57BL/6) Replicate 1

description: Biological Replicate 1


title: lung_C57Bl/6_12hr/mutant-toxin_rep4

city: Oklahoma City

first: Bart

last: Frank

state: OK

institute: OMRF

description: 12 hr E687C mutant toxin

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using Matlab quantile normalization

source_name: lung

label_protocol: Total RNA was labeled using Ambion Illunina Total Prep RNA kit following the manufacturer's directions

extract_protocol: Lung tissues were homogenized in 1mL of TRIZOL using a Tissue-Tearer (BioSpec Products, SS30F-ER30-MR30).  The RNA was then isolated using the RNeasy Mini Kit from QIAGEN following the kit protocol.

treatment_protocol: Preparations of mixed protective antigen (PA) plus LeTx or mixed PA plus E687C mutant toxin diluted with PBS pH 8.0 were administered to groups (4 mice per group) of mice. The dosage per mouse was 120 mg PA + 50 mg LeTx, or 120 mg PA + 50 mg E687C mutant toxin for E687C mutant toxin delivered in a volume of 0.25 mL per mouse.  The mice were euthanized 12 hours later and lung tissue collected.

tag: gender

value: female

value: 6 wk old

tag: agent

value: E687C mutant-toxin


title: SEA treated IL-13Ra1(C57BL/6) KO Replicate 1

description: Biological Replicate 1


title: lung_C57Bl/6_12hr/WT-toxin_rep3

description: 12 hr WT toxin

value: WT-toxin


title: SEA treated wild type (C57BL/6) Replicate 2

description: Biological Replicate 2


title: lung_C57Bl/6_12hr/mutant-toxin_rep2

description: 12 hr E687C mutant toxin


title: lung_C57Bl/6_12hr/mutant-toxin_rep3

description: 12 hr E687C mutant toxin


title: lung_C57Bl/6_12hr/WT-toxin_rep4

description: 12 hr WT toxin


title: lung_A/J_12hr/mutant-toxin_rep3

description: 12 hr E687C mutant toxin

value: A/J


title: lung_C57Bl/6_12hr/WT-toxin_rep1

description: 12 hr WT toxin


title: lung_A/J_12hr/mutant-toxin_rep1

description: 12 hr E687C mutant toxin


title: lung_C57Bl/6_12hr/mutant-toxin_rep1

description: 12 hr E687C mutant toxin


title: lung_A/J_12hr/mutant-toxin_rep4

description: 12 hr E687C mutant toxin


title: lung_C57Bl/6_12hr/WT-toxin_rep2

description: 12 hr WT toxin


title: lung_A/J_12hr/WT-toxin_rep3

description: 12 hr WT toxin


title: lung_C57Bl/6_6hr/mutant-toxin_rep3

description: 6 hr E687C mutant toxin

treatment_protocol: Preparations of mixed protective antigen (PA) plus LeTx or mixed PA plus E687C mutant toxin diluted with PBS pH 8.0 were administered to groups (4 mice per group) of mice. The dosage per mouse was 120 mg PA + 50 mg LeTx, or 120 mg PA + 50 mg E687C mutant toxin for E687C mutant toxin delivered in a volume of 0.25 mL per mouse.  The mice were euthanized 6 hours later and lung tissue collected.


title: lung_C57Bl/6_6hr/WT-toxin_rep3

description: 6 hr WT toxin


title: lung_A/J_12hr/WT-toxin_rep4

description: 12 hr WT toxin


title: lung_C57Bl/6_6hr/mutant-toxin_rep1

description: 6 hr E687C mutant toxin


title: lung_C57Bl/6_6hr/WT-toxin_rep1

description: 6 hr WT toxin


title: lung_A/J_12hr/mutant-toxin_rep2

description: 12 hr E687C mutant toxin


title: lung_C57Bl/6_6hr/mutant-toxin_rep2

description: 6 hr E687C mutant toxin


title: lung_A/J_12hr/WT-toxin_rep2

description: 12 hr WT toxin


title: lung_A/J_6hr/mutant-toxin_rep1

description: 6 hr E687C mutant toxin


title: lung_A/J_12hr/WT-toxin_rep1

description: 12 hr WT toxin


title: lung_C57Bl/6_6hr/mutant-toxin_rep4

description: 6 hr E687C mutant toxin


title: lung_A/J_6hr/WT-toxin_rep1

description: 6 hr WT toxin


title: lung_C57Bl/6_6hr/WT-toxin_rep4

description: 6 hr WT toxin


title: lung_A/J_6hr/mutant-toxin_rep4

description: 6 hr E687C mutant toxin


title: lung_A/J_6hr/WT-toxin_rep4

description: 6 hr WT toxin


title: lung_A/J_6hr/mutant-toxin_rep3

description: 6 hr E687C mutant toxin


title: HB00G4X_3/18/08_1:45_PM

city: Oslo

first: Trude

middle: Holmeide

last: Ågesen

address: Ullernch. 70

department: Department of Cancer Prevention

country: Norway

institute: Oslo University Hospital

hyb_protocol: Chemilunimescent Detection Kit from Applied Biosystems

scan_protocol: Scanned using AB1700 Chemilunimescent Microarray Analyzer

data_processing: Image preparation, signal intensity quantification and initial analysis were performed utsing the accompanying software from Applied biosystems (version 1.1.1). Only probes with normalized signals more than three standard deviations greater than the local background levels in at least half of the samples were included. Values with low quality scores were noted as missing and probes affected by array batch variation were identified and removed. The resulting dataset included 17 085 probes.

label: digoxigenein (DIG)-labeled

source_name: colorectal cancer tissue

label_protocol: NanoAmp RT-IVT Labeling Kit from Applied Biosystems and DIG-UTP from Roche

extract_protocol: Primary tumor: AllPrep DNA/RNA Mini Kit (Qiagen); normal colonic mucosa: Ambion RiboPure Kit (Applied Biosystems)

tag: age at diagnosis

tag: tumor stage

value: IV

tag: localization

value: colon

tag: microsatellite instability (msi) status

value: MSS

tag: tissue type

value: primary tumor


title: HB00IWJ_12/10/08_11:37_AM

source_name: normal colonic mucosa

value: male

value: normal colonic mucosa


title: HB00G5F_3/18/08_2:00_PM

value: II


title: lung_A/J_6hr/WT-toxin_rep3

description: 6 hr WT toxin

tag: strain


title: HB00G56_3/18/08_12:26_PM

value: III


title: HB00IWM_12/10/08_11:52_AM


title: HB00G50_3/18/08_12:41_PM

value: I


title: HB00G4Y_3/18/08_11:42_AM

value: MSI-H


title: HB00IWZ_12/10/08_12:09_PM


title: lung_C57Bl/6_6hr/WT-toxin_rep2

description: 6 hr WT toxin


title: HB008AC_2/27/08_11:59_AM


title: HB006Z8_9/19/07_10:26_AM


title: HB006YW_1/30/08_11:39_AM


title: lung_A/J_6hr/mutant-toxin_rep2

description: 6 hr E687C mutant toxin


title: HB00G57_3/18/08_11:57_AM


title: HB00IWF_12/10/08_11:22_AM


title: HB00G5G_3/18/08_12:55_PM


title: HB00G54_3/18/08_1:29_PM


title: HB008FI_2/27/08_12:13_PM


title: HB008FQ_2/27/08_10:38_AM

value: rectum


title: lung_A/J_6hr/WT-toxin_rep2

description: 6 hr WT toxin


title: HB008AG_2/22/08_12:26_PM


title: HB008AP_2/27/08_11:07_AM


title: HB008AN_2/27/08_11:22_AM


title: HB008FV_2/27/08_10:52_AM


title: HB00G5D_3/18/08_11:13_AM


title: HB008AQ_2/27/08_12:28_PM


title: HB008FS_2/12/08_1:59_PM


title: HB008FK_2/12/08_1:45_PM


title: HB008FF_2/27/08_11:42_AM


title: HB008FJ_2/12/08_2:29_PM


title: HB008AE_2/12/08_1:30_PM


title: HB008AK_2/22/08_11:54_AM

value: MSI-L


title: HB008FR_2/22/08_11:05_AM

value: female


title: HB008FE_2/12/08_3:01_PM


title: HB008FU_2/12/08_1:14_PM


title: HB008FN_2/7/08_3:25_PM


title: HB008FL_2/12/08_2:44_PM


title: HB008AR_2/7/08_3:10_PM


title: HB008FP_2/7/08_2:55_PM


title: HB006YV_2/7/08_1:54_PM


title: HB008AF_2/22/08_10:34_AM


title: HB00CVW_1/30/08_1:26_PM


title: hsfb1_hsfb2b_over_wt_5d_seedlings-heat32_30min-rep4

first: Nobutaka

last: Mitsuda

address: Central 6 Higashi 1-1-1

department: Bioproduction Research Institute

institute: National Institute of Advanced Industrial Science and Technology

description: Biological replicate 4 of 4. harvested after heat treatment. Many mutant and wild-type plants were grown in a same plate.

hyb_protocol: Hybridized using Gene Expression Hybridization kit (Agilent) and washed by Gene Expression wash pack (Agilent).

scan_protocol: Scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction Software (version 9.1.3.1).

data_processing: Agilent Feature Extraction Software (v 9.1.3.1) was used for background subtraction and LOWESS normalization. After that, signal of each probe was divided by median value of filter-passed probes.

organism: Arabidopsis thaliana

source_name: Wild-type (Col-0) _32°C_30min

label_protocol: 1 µg of total RNA was used for labeling procedure using QickAmp Labeling kit (Two-color) (Agilent).

growth_protocol: All plants were grown in Gamborg B5 (2% sucrose) agar media in 16hr light / 8hr dark cycle in 23 Celsius degree. Many plants of the mutant and wild type were grown in same one plate for each replicate.

extract_protocol: Plant RNeasy Mini kit (QIAGEN) was used to isolate total RNA.

treatment_protocol: Plates were submerged into water of 32 Celsius degree for 30 minutes.

tag: ecotype

tag: genotype

value: wild type

value: seedling

tag: treatment

value: heat (32 Celsius degree) for 30 min.

source_name: hsfb1 hsfb2b double mutant_32°C_30 min

value: hsfb1 hsfb2b double mutant

value: heat (32°C) for 30 min.


title: HB006ZE_2/7/08_2:08_PM

value: colon


title: HB006YT_2/7/08_2:25_PM

value: MSS


title: HB006YQ_1/30/08_12:48_PM

value: primary tumor


title: hsfb1_hsfb2b_over_wt_5d_seedlings-heat32_30min-rep1

description: Biological replicate 1 of 4. harvested after heat treatment. Many mutant and wild-type plants were grown in a same plate.


title: HB006YR_1/30/08_12:28_PM

value: male


title: HB00CVS_1/30/08_12:13_PM


title: hsfb1_hsfb2b_over_wt_5d_seedlings-heat32_30min-rep2

description: Biological replicate 2 of 4. harvested after heat treatment. Many mutant and wild-type plants were grown in a same plate.


title: HEK293 cells was overexpressed the alternative spliced form of lactoferrin gene (ΔLF)

city: seoul

first: Ju Hee

last: Kim

address: pil-dong 3-ga

department: Life Science

country: South Korea

institute: Dongguk University

hyb_protocol: See http://www.phalanxbiotech.com/ for updated protocols

source_name: Alternatively spliced form (ΔLF) was overexpressed in HEK293 cells

growth_protocol: The Flp-In T-Rex human HEK293 cell cultured in DMEM medium with 10% fetal calf serum and penicillin-streptomycin.

extract_protocol: Total RNA from the MCF-7 cell was isolated using the Trizol (Qiagen, Valencia, CA) according to the supplier’s protocols.

tag: cell line

source_name: Isolated total RNA from HEK293 cells


title: Wild_type_Col0-9d_seedlings-rep3

description:
Col4
Total RNA from wild-type 9d whole seedlings of set3.

hyb_protocol: Following fragmentation, 15 micro g of cRNA were hybridized for 16 hrs at 45 Celsius degrees on the GeneChip. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. All signals were divided by the median value of all probe sets.

source_name: Wild type Col-0, 9d whole seedlings

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 micro g of total RNA.

growth_protocol: Seedlings were grown in half-strength MS agar medium with 2% sucrose in continuous light at 22 Celsius degrees.

extract_protocol: Total RNA was extracted using the Plant RNeasy kit (QIAGEN) following the manufacturer's instructions.

treatment_protocol: None.

tag: cultivar

value: wt

tag: tissue

value: whole seedlings

value: 9 days

tag: experimental set


title: hsfb1_hsfb2b_over_wt_5d_seedlings-heat32_30min-rep3

description: Biological replicate 3 of 4. harvested after heat treatment. Many mutant and wild-type plants were grown in a same plate.


title: myb3r1_myb3r4-9d_seedlings-rep3

description:
IH4
Total RNA from myb3r1 myb3r4 9d whole seedlings of set3.

source_name: myb3r1 myb3r4 double mutant, 9d whole seedlings

value: myb3r1 myb3r4 double mutation


title: CN-AML [4954590055_H]

city: Stockholm

first: Stefan

last: Deneberg

department: Internal medicine/Huddinge

institute: Karolinska Institutet

data_processing: Quantile Normalization using Bead Studio

source_name: Bone marrow

label_protocol: TotalPrep RNA Labeling Kit, Ambion

extract_protocol: Rneasy (Qiagen), Quality control with Agilent Bioanalyzer

treatment_protocol: Ficoll separated, snap frozen -80 pelleted cells

value: M

tag: tertile of methylation of pcg targets (0=low,1=intermediate, 2= high)

tag: os 2 year

value: n

tag: pfs 2 year

tag: cr

value: y


title: myb3r1_myb3r4-9d_seedlings-rep2

description:
IH3
Total RNA from myb3r1 myb3r4 9d whole seedlings of set2.

tag: age


title: CN-AML [4954590057_C]

tag: gender


title: CN-AML [4954590055_I]

value: F


title: HEK293 cells was overexpressed the secreted form of lactoferrin gene (sLF)

scan_protocol: See http://www.phalanxbiotech.com/ for updated protocols

source_name: Secreted form (sLF) was overexpressed in HEK293 cells


title: CN-AML [4954590057_H]


title: CN-AML [4954590057_I]


title: OregonR^TOW Stage 11/12 ORC2 ChIP

source_name: ORC2 ChIP DNA from OregonR^TOW pooled stage 11 and 12 egg chambers

extract_protocol: Staged egg chambers were fixed with 2% formaldehyde in Grace's medium for 15 min at room temperature followed by quenching with 0.125 M glycine for 5 min (4 samples of 300 egg chambers each). The cells were washed twice with TBS and placed in 0.5 mL of ChIP lysis buffer (50 mM HEPES/KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-Deoxycholate). The crosslinked chromatin was sheared to an average size of 300-1000 bp by three 12-second pulses using a Branson 250 sonicator. The lysate was then centrifuged to remove cell debris. 50 uL was saved for the input DNA from each sample. The chromatin supernatant was then incubated overnight with 2 uL of ORC2 antibody (Steve Bell, MIT) at 4C. After incubation with 30 uL protein G Dynabeads beads (Invitrogen) for 2h at 4C, the immune complexes were collected using the Dynal magnetic strip and washed with the following buffers at room temperature for 5 minutes each: 2X ChIP lysis buffer, 2X high salt (500mM NaCl) ChIP lysis buffer, 1X ChIP lysis buffer, 1X TE. The protein-DNA complexes were eluted from the beads in 100 uL ChIP elution buffer (50 mM Tris/HCl pH 8.0, 10 mM EDTA/1% SDS) at 65C for 15 min followed by another wash with 150 uL TE/0.67% SDS. Eluates were pooled and incubated at 65C for at least 6 hours. Input DNAs were similarly subject to reversal of crosslinks with 200 µL TE/1% SDS. DNAs from four samples were pooled together. Samples were treated with 100 ug proteinase K at 37C for 2 hours. DNA samples were phenol chloroform extracted twice and ethanol precipitated.

tag: cell type

value: egg chambers

value: OregonR^TOW

tag: chip antibody

source_name: Input DNA from OregonR^TOW Stage 11 and 12 egg chambers

value: none; input DNA


title: OregonR^TOW Stage 10 MCM2-7 ChIP

source_name: MCM2-7 ChIP DNA from OregonR^TOW stage 10 egg chambers

treatment_protocol: Stage 10 egg chambers were hand sorted from 2-3 day fattened female flies

source_name: Input DNA from OregonR^TOW Stage 10 egg chambers


title: HB00CVX_1/23/08_12:19_PM

tag: age at diagnosis

value: female

tag: tumor stage

value: I

tag: localization

tag: microsatellite instability (msi) status

tag: tissue type


title: ECH_ISE6_Inf1

city: Galveston

first: Jeeba

middle: A

last: Kuriakose

state: TX

address: 301 University Blvd

department: Pathology

institute: University of Texas Medical Branch

description:
Ehrlichia chaffeensis Arkansas: NC_007799
Infected host cell lines: RNA from Ehrlichia chaffeensis infected ISE6 cells. Three biological replicates from this infected cell line used, each from separate cultures.
Negative control: RNA from uninfected ISE6 cells. Single sample was used for background signal substraction.

hyb_protocol: Hybridization was performed at MD Anderson Cancer Center, Genomics Facility (Houston, TX) according to the NimbleGen Arrays User’s Guide (Gene Expression Analysis v3.2). Briefly,Hybridized to the microarray for 16 hours at 42°C.

scan_protocol: Arrays were scanned using GenePix 400B microarray scanner (Molecular Devices, Sunnyvale, CA) according to the NimbleGen Arrays User’s Guide (Gene Expression Analysis v3.2).

data_processing:
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization and background correction as implemented in the NimbleScan software package and for each cell line, values from uninfected sample (.calls file provided) was substracted from the infected sample values  to generate gene expression values.
ArrayStar4 software was used to generated (DNASTAR Inc., Madison, WI),  mean log2 expression values.

organism: Ehrlichia chaffeensis str. Arkansas

source_name: Ehrlichia chaffeensis Arkansas_ISE6

label_protocol: Labeling was performed at MD Anderson Cancer Center, Genomics Facility (Houston, TX) according to the NimbleGen Arrays User's Guide (Gene Expression Analysis v3.2). Briefly, double-stranded cDNA was random-prime labeled with Cy3-nonamers and hybridized to the microarray for 16 hrs at 42°C.

growth_protocol: E. chaffeensis (Arkansas strain) was cultivated in a human monocyte leukemia cells (THP-1) and tick cells (AAE2 and ISE6).  THP-1 cells were cultured in Dulbecco’s modified Eagle’s medium (Invitrogen, Carlsbad, CA) supplemented with 10% fetal bovine serum (HyClone, Logan, UT), 1% HEPES buffer (Sigma, St. Louis, MO), 1% sodium pyruvate (Sigma) at 37°C in a humidified 5% CO2 atmosphere.  AAE2 and ISE6  cells were cultured in L15B300 medium supplemented with 10% fetal bovine serum (Harlan, Indianapolis, IN), 10% tryptose phosphate broth (BD, Sparks, MD) and 1% bovine lipoprotein cholesterol concentrate (MP Biomedicals, Irvine, CA) at 34°C .

extract_protocol: Total RNA was purified from uninfected and E. chaffeensis-infected (90% infected) THP-1, AAE2 and ISE6 cells using Tri reagent (Ambion, Austin, TX).  Genomic DNA was eliminated by treatment with Turbo DNA-free (Ambion) according to the manufacturer’s protocol.  Polyadenylated host mRNA was removed using oligo (dT) columns (Oligotex, Qiagen, Valencia, CA), and bacterial RNA was enriched using Terminator (Epicenter Biotechnologies, Madison, WI) that selectively digests RNAs with 5’-monophosphates; 5’-monophosphates that are present only on ribosomal RNA.  RNA concentration was determined by NanoDrop  (Thermo Scientific, Wilmington, DE) and quality confirmed by Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) at the UTMB Genomics Core Facility.  The RNA quality requirements were established as: A260/A280 ≥ 1.8, A260/A230 ≥ 1.8 and concentrations ≥ 1µg/ul.

tag: host

value: Ixodes

tag: cell line

value: ISE6 tick cells


title: ECH_THP-1_Inf1

description:
Ehrlichia chaffeensis Arkansas: NC_007799
Infected host cell lines: RNA from Ehrlichia chaffeensis infected THP-1 cells. Three biological replicates from this infected cell line used, each from separate cultures.
Negative control: RNA from uninfected THP-1 cells. Single sample was used for background signal substraction.

source_name: Ehrlichia chaffeensis Arkansas_THP-1

value: Homo sapiens

value: THP-1 human monocyte leukemia cells


title: HB006YU_1/30/08_11:22_AM

value: III

value: rectum

value: MSS

value: primary tumor


title: CN-AML [4954590057_F]


title: CN-AML [4954590055_A]


title: Caco2Ntx3

status: Public on Sep 06 2011

description: Caco2Ntx3: RNA from Human Caco-2 colon epithelial cells (cells were used at passage 37, grown in 6 well plates and were 90% confluent when RNA was Harvested), replicate #3.

data_processing: The data were analyzed with RMA Express using the default settings (Background Adjust - Yes, Normalization - Quantile, Summarization Method - Median Polish, Store Residuals - unchecked).

source_name: Human Caco-2 colon epithelial cells (cells were used at passage 37, grown in 6 well plates and were 90% confluent when RNA was Harvested).

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

value: Colon epithelial


title: Caco2Ntx1

description: Caco2Ntx1: RNA from Human Caco-2 colon epithelial cells (cells were used at passage 37, grown in 6 well plates and were 90% confluent when RNA was Harvested), replicate #1.


title: Caco2Ntx2

description: Caco2Ntx2: RNA from Human Caco-2 colon epithelial cells (cells were used at passage 37, grown in 6 well plates and were 90% confluent when RNA was Harvested), replicate #2.


title: HB006ZB_1/30/08_11:54_AM

source_name: colorectal cancer tissue


title: CN-AML [4954590057_K]

value: M


title: CN-AML [4954590055_B]

value: y


title: T84Ntx1

description: T84Ntx1: RNA from Human T84 intestinal epithelial cells (cells were used at passage 68, grown in 6 well tissue culture plates and were about 90% confluent when RNA was harvested), replicate #1.

source_name: Human T84 intestinal epithelial cells (cells were used at passage 68, grown in 6 well tissue culture plates and were about 90% confluent when RNA was harvested).

value: Intestinal epithelial


title: T84Ntx2

description: T84Ntx2: RNA from Human T84 intestinal epithelial cells (cells were used at passage 68, grown in 6 well tissue culture plates and were about 90% confluent when RNA was harvested), replicate #2.


title: Wild_type_Col0-9d_seedlings-rep1

description:
Col2
Total RNA from wild-type 9d whole seedlings of set1.

tag: cultivar

tag: genotype

value: wt

tag: tissue

value: whole seedlings

value: 9 days


title: Wild_type_Col0-9d_seedlings-rep2

description:
Col3
Total RNA from wild-type 9d whole seedlings of set2.

tag: experimental set


title: CN-AML [4954590055_C]

tag: tertile of methylation of pcg targets (0=low,1=intermediate, 2= high)

tag: os 2 year

value: n

tag: pfs 2 year


title: HB006Z1_10/19/07_10:02_AM

tag: gender

value: male

value: II

value: colon


title: ECH_AAE2_Inf1

description:
Ehrlichia chaffeensis Arkansas: NC_007799
Infected host cell lines: RNA from Ehrlichia chaffeensis infected AAE2 cells. Three biological replicates from this infected cell line used, each from separate cultures.
Negative control: RNA from uninfected AAE2 cells. Single sample was used for background signal substraction.

source_name: Ehrlichia chaffeensis Arkansas_AAE2

value: Amblyomma

value: AAE2 tick cells


title: T84IFN2

description: T84IFN2: RNA from T84 cells which had been treated with 100U/ml Interferon gamma for 24 hours, replicate #2.

tag: cell type


title: HB006YX_1/23/08_11:42_AM

value: female

value: IV


title: T84IFN3

description: T84IFN3: RNA from T84 cells which had been treated with 100U/ml Interferon gamma for 24 hours, replicate #3.


title: HB006YP_9/19/07_10:42_AM

value: rectum

value: MSS


title: T84Ntx3

description: T84Ntx3: RNA from Human T84 intestinal epithelial cells (cells were used at passage 68, grown in 6 well tissue culture plates and were about 90% confluent when RNA was harvested), replicate #3.


title: S: Patu-S cells low/no metastatic potential and high transglutamase activity to induce grade 1 tumors, replicate #1.

source_name: Patu-S cells low/no metastatic potential and high transglutamase activity to induce grade 1 tumors.

value: Patu-S

tag: disease state

value: Pancreatic Cancer


title: T84IFN1

description: T84IFN1: RNA from T84 cells which had been treated with 100U/ml Interferon gamma for 24 hours, replicate #1.


title: S1: Patu-S cells low/no metastatic potential and high transglutamase activity to induce grade 1 tumors, replicate #2.


title: CD34+ tumor epithelial cells from VEGF gain of function mouse

city: Brussels

first: Benjamin

last: Beck

address: Route de Lennik 808

department: IRIBHM

country: Belgium

institute: ULB

hyb_protocol: A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix MOE 430 2.0 arrays followed by staining and washing in a GeneChip® fluidics station 450 (Affymetrix) according to the manufacturer’s procedures.

scan_protocol: To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).

data_processing: Data processing was done in the R programming environment, in conjunction with the packages developed within the Bioconductor project (http://www.bioconductor.org; Gentleman et al., 2004). Cel-files were processed according to the MAS5.0 algorithm as implemented in the 'simpleaffy' package.

source_name: CD34+ VEGF

label_protocol: RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturers protocol (Affymetrix).

extract_protocol: Microprep kit, RNeasy, Stratagene

treatment_protocol: wild type or K14CreER:Rosa-VEGF-164 mice were treated with DMBA at postnatal day 23, 25 and 27 with DMBA (9,10-dimethyl-1,2-benzanthracene) and then treated twice, weekly for several weeks with TPA (12-O-tetradecanoyl phorbol-13-acetate). 7 weeks old mice were treated again twice with DMBA.


title: S2: Patu-S cells low/no metastatic potential and high transglutamase activity to induce grade 1 tumors, replicate #3.

first: Steven

last: Head

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the v4 GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.


title: 0.15% Bile Salt Mix Stress, 90 minutes, static, 5% CO2 (EHEC strain: 86-24)

city: Toronto

first: Debora

last: Foster

state: Ontario

address: 350 Victoria Street

department: Chemistry and Biology

country: Canada

institute: Ryerson University

description: Before normalization, each individual array spot was pruned to exclude bad or empty spots flagged by GenePix Pro 3.0. Normalization was preformed using the LOWESS algorithm.  For each point, three biological and two technical replicates were measured, resulting in a maximum of 6 gene expression values per gene per treatment.

hyb_protocol: Eighty-one micro-litres of prewarmed AdvaHybC™ hybridisation solution (Advalytix, Germany) was added to each sample. The samples were then denatured at 95oC for 3 minutes then cooled to 42oC. The samples were loaded onto the microarrays and incubated in the SlideBooster™ (Advalytix, Germany) at 42oC overnight. After hybridisation, the microarray was washed 3 times for 10 to 15 minutes in 1× SSC, 0.1% sodium dodecyl sulfate solution at 50°C after removal of the coverslip in room-temperature 1× SSC. The slide was rinsed in room temperature 1× SSC, then 0.1× SSC. The slide was dried at 25×g for 5 minutes.

scan_protocol: Microarrays were scanned using the Agilent G2565BA scanner; this yielded two 16-bit TIFF images per array, one corresponding to the Cy3 channel and one corresponding to the Cy5 channel. These images were then quantified using GenePix Pro 3.0 (Molecular Devices, USA).

data_processing: Signal intensities were averaged among the technical replicates.  Two types of data analysis were performed: to indentify density-dependent changes in gene expression, single averaged normalized signal intensities for each treatment point were compared to the average of corresponding unstressed control signal intensities.  Genes which showed a relative signal log2ratio (SLR) value above 1.0 or below -1.0 were selected for further analysis.

organism: Escherichia coli

source_name: Cy5 labeled EHEC bile salt-stressed in DMEM, 90 minutes

label_protocol: 20 micrograms total RNA was reverse-transcribed with the use of SuperScript II RNase H- Reverse Transcriptase and random primers (Invitrogen, USA, 150 ng/µl final concentration) in the presence of 0.5 mM dCTP, 0.5 mM dGTP, 0.5 mM dATP, 0.15 mM dTTP (GE Healthcare, USA), and 0.15 mM of aminoallyl-dUTP (Sigma, USA). The reaction was allowed to proceed for two hours at 42°C. To stop the reaction and hydrolyse the remaining RNA sodium hydroxide was added to a final concentration of 160 mM and the samples were heated at 65 oC for 15 minutes. The samples were neutralised and the cDNA was purified using the CyScribe™ GFX purification kit (GE Healthcare, USA). Aminoallyl labelled cDNA then underwent a chemical reaction with Cy3 or Cy5 monofunctional NHS-Esters (GE Healthcare, USA). This reaction was stopped by the addition of hydroxylamine to a final concentration of 1.24 M. Labelled samples were then purified using the CyScribe™ GFX purification kit (GE Healthcare, USA). Purified labelled cDNA was dried in a speed vac, just until dry, and then resuspended to a final volume of 9 µl including 45 µg of calf thymus DNA (Sigma, USA) and 45 µg of yeast tRNA (Invitrogen, USA).

growth_protocol: Bacteria were grown in LB broth overnight and subcultured in DMEM to OD600 of 0.4. Bacteria were then spun down, media removed and repalced with DMEM plus 0.15% bile salt mix.

extract_protocol: RNA was extracted using Trizol (Invitrogen)

treatment_protocol: Bile salt stress was done in DMEM at pH 7.4 (unbuffered) at 37C, 5% CO2, static incubation for 90 minutes

tag: ehec strain

source_name: Cy3 labeled EHEC grown in DMEM pH 7.4, 90 minutes

growth_protocol: Bacteria were grown in LB broth overnight and subcultured in DMEM to OD600 of 0.4. Bacteria were then spun down, media removed and repalced with DMEM.

treatment_protocol: Control treatment. Bacteria were grown in DMEM pH 7.4, 90 minutes, 37C, 5% CO2, static (unstressed)


title: WT ISW1 Flag-IP Replicate 2

city: Kansas City

first: Michaela

last: Smolle

state: Missouri

address: 1000 E 50th Street

institute: Stowers Institute for Medical Research

description: Biological Replicate 2 of 3. ChIP enrichment of FLAG-IP over Input in the YMS078 ISW1-3xFLAG strain.

hyb_protocol: The hybridization mixture (Oligo CGH/Chip-on-chip hybridization kit, Agilent) was prepared according to manufacturer’s instructions with the addition of 20 ug of T7 blocking oligo (ttt ttt ttt ttt tt cac gcg tct ccc) , and hybridized overnight at 65°C. Microarrays were washed using the Oligo aCCH/Chip-on-chip Wash buffers (Agilent) according to  manufacturer’s instructions.

scan_protocol: Scanned on Agilent Technologies Scanner G2505C US45102919 Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).

data_processing: Data processed in R (version 2.12.1) using MEDIAN normalization, MA<-normalizeWithinArrays(RG,method=median).

organism: Saccharomyces cerevisiae

source_name: IP DNA FLAG antibody

label_protocol: Briefly, 50 ng of IP or input DNA were treated with 2.5 U CIP enzyme (NEB) for 1 hour at 37°C, followed by phenol:chloroform extraction and ethanol precipitation. The CIP-treated template was incubated with 20 U TdT (NEB) for 20 minutes at 37°C for T-tailing the ends, and the product isolated with the MinElute Reaction Cleanup Kit (Qiagen). An anchored T7 promoter-(dA)18 oligo was added by annealing and filling with 5 U Exo- Klenow (NEB) for 4 hours at 37°C, followed by phenol:chloroform extraction and ethanol precipitation. In vitro transcription was performed at 37°C overnight using the Ampliscribe T7 transcription kit (Epicentre Biotechnologies). RNAs purified using the RNeasy Mini Kit (Qiagen) and quantified on a Nanodrop 2000 Spectrophotometer (Thermo Scientific). For the second round amplification, 100 ng of RNA was reverse transcribed using Superscript III reverse transcriptase (Invitrogen) and purified with the MinElute Reaction Cleanup Kit (Qiagen). The T7 promoter primer was added to the product through a Klenow filling reaction as described above, followed by in vitro transcription with amino allyl-UTP (Ambion) instead of UTP. Final reaction cleanup was performed with the RNeasy Mini Kit (Qiagen). For the labeling reactions, 8 ug of amino allyl-incorporated RNA in a 5 uL volume of 0.1 M Carbonate Buffer, pH 8.7, was mixed with 5 uL (0.01 nmol) Cy3 or Cy5 dye (GE Healthcare) in DMSO (Sigma) and incubated at room temperature for 2 hours. Reactions were quenched with 5 uL 4 M hydroxylamine at room temperature for 15 minutes, purified by RNeasy MinElute Cleanup Kit (Qiagen), and the dye incorporation measured using the Nanodrop 2000 (Thermo Scientific). 4ug of input and IP were combined and fragmented (Fragmentation Reagent Kit, Ambion) according to manufacturer’s instructions.

growth_protocol: These strains were grown in YPD to an OD of 1.0. Cells were cross-linked and processed for the ChIP assay. The cell lysates were used to immunoprecipitate Isw1-3xFlag (2 ul αFLAG per IP).

extract_protocol: Lysates were prepared by bead beating in FA lysis buffer (50mM HEPES pH7.5, 1mM EDTA, 1% Triton X-100, 0.1%sodium deoxycholate and 150mM NaCl). The ChIP lysates were used to immunoprecipitate FLAG-tagged Isw1. The immune complexes were pulled down with 50 ml of Protein G Dynabeads (Invitrogen) per IP and washed with FA lysis buffer, FA lysis buffer with 1M NaCl, FA lysis buffer with 0.5M NaCl, TEL buffer (0.25M LiCl, 1%NP-40, 1% sodium deoxycholate, 1mM EDTA, 10mM TrisHCL, pH8.1), and twice with TE. The Immune complexes were eluted with Elution buffer (1%SDS in TE with250mM NaCl). The eluates were RNase A treated and Proteinase K was added to remove the bound proteins. Crosslinkss were reversed by incubating at 65 C overnight. Samples were phenol:chloroform treated and ethanol precipitated. Input samples were treated the same way from the RNase A step.

tag: strain

tag: chip antibody

value: anti-FLAG (M2 mouse monoclonal)

tag: chip antibody manufacturer

value: Sigma

tag: chip antibody catalog #

tag: sample type

value: 3xFLAG tagged Isw1

source_name: Input DNA


title: T2: Patu-T cells high metastatic and low transglutamase activity to cause grade 2/3 tumors, replicate #3.

city: La Jolla

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

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

source_name: Patu-T cells high metastatic and low transglutamase activity to cause grade 2/3 tumors.

tag: cell line

value: Patu-T


title: T1: Patu-T cells high metastatic and low transglutamase activity to cause grade 2/3 tumors, replicate #2.


title: PST-2: Sulf-2 expressing non-small cell lung cancer (NSCLC) line P-ST, replicate #2.

value: P-ST

tag: sulf-2 expressing

value: Yes

value: Non-small lung cancer


title: WT ISW1 Flag-IP Replicate 3

description: Biological Replicate 3 of 3. ChIP enrichment of FLAG-IP over Input in the YMS078 ISW1-3xFLAG strain.


title: H460-3: Sulf-2 expressing non-small cell lung cancer (NSCLC) line H460, replicate #3.


title: PST-1: Sulf-2 expressing non-small cell lung cancer (NSCLC) line P-ST, replicate #1.


title: Pc-1: Normal bronchial epithelial cell population P-C, replicate #1.

value: P-C


title: CD34+ tumor epithelial cells from wild-type mouse

source_name: CD34+ wild type

tag: genotype

value: wild-type


title: H460-1: Sulf-2 expressing non-small cell lung cancer (NSCLC) line H460, replicate #1.


title: H292-2: Sulf-2 expressing non-small cell lung cancer (NSCLC) line H292, replicate #2.


title: H292-3: Sulf-2 expressing non-small cell lung cancer (NSCLC) line H292, replicate #3.


title: T: Patu-T cells high metastatic and low transglutamase activity to cause grade 2/3 tumors, replicate #1.


title: H1975-2: Sulf-2 negative non-small cell lung cancer (NSCLC) line H1975, replicate #2.

value: No


title: H1975-1: Sulf-2 negative non-small cell lung cancer (NSCLC) line H1975, replicate #1.


title: H1975-3: Sulf-2 negative non-small cell lung cancer (NSCLC) line H1975, replicate #3.


title: H292-1: Sulf-2 expressing non-small cell lung cancer (NSCLC) line H292, replicate #1.


title: H1703-2: Sulf-2 negative non-small cell lung cancer (NSCLC) line H1703, replicate #2.


title: H1703-3: Sulf-2 negative non-small cell lung cancer (NSCLC) line H1703, replicate #3.


title: CALU6-2: Sulf-2 expressing non-small cell lung cancer (NSCLC) line Calu-6, replicate #2.


title: CALU6-1: Sulf-2 expressing non-small cell lung cancer (NSCLC) line Calu-6, replicate #1.


title: BST-2: Sulf-2 expressing non-small cell lung cancer (NSCLC) line B-ST, replicate #2.

value: B-ST


title: BST-3: Sulf-2 expressing non-small cell lung cancer (NSCLC) line B-ST, replicate #3.


title: H460-2: Sulf-2 expressing non-small cell lung cancer (NSCLC) line H460, replicate #2.


title: BEAS2B-1: Normal bronchial epithelial cell population BEAS2B, replicate #1.

source_name: Normal bronchial epithelial cell population BEAS-2B


title: BEAS2B-3: Normal bronchial epithelial cell population BEAS2B, replicate #3.


title: BST-1: Sulf-2 expressing non-small cell lung cancer (NSCLC) line B-ST, replicate #1.


title: BEAS2B-2: Normal bronchial epithelial cell population BEAS2B, replicate #2.


title: CALU6-3: Sulf-2 expressing non-small cell lung cancer (NSCLC) line Calu-6, replicate #3.


title: A549-5: Sulf-2 expressing non-small cell lung cancer (NSCLC) line A549, replicate #3.


title: A549-4: Sulf-2 expressing non-small cell lung cancer (NSCLC) line A549, replicate #2.


title: A549-3: Sulf-2 expressing non-small cell lung cancer (NSCLC) line A549, replicate #1.


title: CON3: Human control lungs, replicate #3.

source_name: Human healthy control lungs

tag: tissue

value: lung

value: healthy


title: CON2: Human control lungs, replicate #2.


title: CON1: Human control lungs, replicate #1.


title: C2B: Untreated with 5-aza-2'-deoxycytidine (control); replicate #2.

source_name: Human colon cancer cells (HCT-15) untreated with 5-aza-2'-deoxycytidine (control)

tag: treated w/ 5-aza-2'-deoxycytidine

value: Untreated

value: Colon Cancer


title: IPF3: Human idiopathic pulmonary fibrosis (IPF) lungs, replicate #3.

value: idiopathic pulmonary fibrosis


title: T2B: Treated with 5-aza-2'-deoxycytidine (control); replicate #2.

source_name: Human colon cancer cells (HCT-15) treated with 5-aza-2'-deoxycytidine

value: Treated


title: T1B: Treated with 5-aza-2'-deoxycytidine (control); replicate #1.


title: T3B: Treated with 5-aza-2'-deoxycytidine (control); replicate #3.


title: C3B: Treated with 5-aza-2'-deoxycytidine (control); replicate #3.


title: IPF1: Human idiopathic pulmonary fibrosis (IPF) lungs, replicate #1.


title: IPF2: Human idiopathic pulmonary fibrosis (IPF) lungs, replicate #2.


title: C1B: Untreated with 5-aza-2'-deoxycytidine (control); replicate #1.


title: ACT: Activated (stimulated) human B cells, replicate #1.

source_name: Activated (stimulated) human B cells.

value: B cells

tag: activated


title: DON2ACT: Activated (stimulated) human B cells, replicate #3.


title: DON3REST: Resting (unactivated) human B cells, replicate #4.

source_name: Resting (unactivated) human B cells.


title: DON2REST: Resting (unactivated) human B cells, replicate #3.


title: DON1ACT: Activated (stimulated) human B cells, replicate #2.


title: DON3ACT: Activated (stimulated) human B cells, replicate #4.


title: DON1REST: Resting (unactivated) human B cells, replicate #2.


title: 11TNF: Human Corneal Epithelial cells (HCE-T), INFG/TNF replicate #1.

source_name: Human Corneal Epithelial cells (HCE-T) treated with INFG/TNF

value: Human Corneal Epithelial cells (HCE-T)

tag: Sex

value: female

tag: treated w/

value: Not Treated


title: REST: Resting (unactivated) human B cells, replicate #1.


title: 12TNF: Human Corneal Epithelial cells (HCE-T), INFG/TNF replicate #2.


title: 13TNF: Human Corneal Epithelial cells (HCE-T), INFG/TNF replicate #3.


title: 21TNFLAC: Human Corneal Epithelial cells (HCE-T), INFG/TNF+lacritin replicate #1.

source_name: Human Corneal Epithelial cells (HCE-T) treated with INFG/TNF+lacritin

value: Lacritin


title: 33TNFC25: Human Corneal Epithelial cells (HCE-T), INFG/TNF+C-25 replicate #3.

source_name: Human Corneal Epithelial cells (HCE-T), INFG/TNF+C-25 (negative control deletion construct)


title: 31TNFC25: Human Corneal Epithelial cells (HCE-T), INFG/TNF+C-25  replicate #1.


title: 23TNFLAC: Human Corneal Epithelial cells (HCE-T), INFG/TNF+lacritin  replicate #3.


title: 22TNFLAC: Human Corneal Epithelial cells (HCE-T), INFG/TNF+lacritin  replicate #2.


title: 21LAC: Human Corneal Epithelial cells (HCE-T), lacritin replicate #1.

source_name: Human Corneal Epithelial cells (HCE-T), lacritin stimulation


title: 13SER: Human Corneal Epithelial cells (HCE-T), serum replicate #3.

source_name: Human Corneal Epithelial cells (HCE-T), serum stimulation


title: 23LAC: Human Corneal Epithelial cells (HCE-T), lacritin replicate #3.


title: 11SER: Human Corneal Epithelial cells (HCE-T), serum replicate #1.


title: 12SER: Human Corneal Epithelial cells (HCE-T), serum replicate #2.


title: 31C25: Human Corneal Epithelial cells (HCE-T), C-25 replicate #1.

source_name: Human Corneal Epithelial cells (HCE-T) treated with C-25 (negative control deletion construct)


title: 32C25: Human Corneal Epithelial cells (HCE-T), C-25 replicate #2.


title: F3-2_5-30: Clonal population derived (by FACS sorting for low u-PAR) from RKO C2 (designated RKO C2 F3), replicate #2.

source_name: Clonal population derived (by FACS sorting for low u-PAR) from RKO C2 (designated RKO C2 F3).

value: RKO


title: F3-3_6-2: Clonal population derived (by FACS sorting for low u-PAR) from RKO C2 (designated RKO C2 F3), replicate #3.


title: 33C25: Human Corneal Epithelial cells (HCE-T), C-25 replicate #3.


title: 32TNFC25: Human Corneal Epithelial cells (HCE-T), INFG/TNF+C-25  replicate #2.


title: 22LAC: Human Corneal Epithelial cells (HCE-T), lacritin replicate #2.


title: WTA-3w-CON: WTA sample control, replicate #2.

source_name: wild-type VSMC differentiated into bone-like cells with osteogenic media control.

value: vascular smooth muscle cells (VSMC)

tag: treated w/ stz

value: Wild Type


title: C2-3_6-2: Clonal population of the RKO of the colon cancer cell line (designated RKO C2), replicate #3.

source_name: Clonal population of the RKO colon cancer cell line (designated RKO C2).


title: Cult. IP-Ast P7 Withdraw biological replicate 1

city: Stanford

first: Lynette

last: Foo

address: 299 Campus Drive

institute: Stanford University

description: astrocytes isolated by immunopanning with ITGB5 and cultured in serum for 7 days, washed 3x dPBS and cultured in HBEGF for another 7d before isolation, Foo et al

hyb_protocol: 3' IVT Express Kit from Affymetrix

scan_protocol: Affymetrix GeneChip Scanner 3000 7G

data_processing: DNASTAR ArrayStar Software with RMA normalization

organism: Rattus norvegicus

source_name: rat forebrain p7

label_protocol: 3' IVT Express Kit from Affymetrix

extract_protocol: QIAGEN RNeasy minikit

value: forebrain

tag: cell type

value: astrocytes

tag: acute/cultured

value: cultured p7 in 10% foetal calf serum 7 days, HBEGF 7 more days


title: Cult. IP-Ast P7 Withdraw biological replicate 3


title: Cult. IP-Ast P7 Withdraw biological replicate 2


title: WT2-3w-CON: WT2 sample control, replicate #1.

value: No

tag: disease state


title: WT2-3w-0.4mM: WT2 sample treated with 0.4mM stroptozotocin, replicate #1.

source_name: wild-type VSMC differentiated into bone-like cells with osteogenic media treated with 0.4mM stroptozotocin.

value: Yes


title: C2-1_5-27: Clonal population of the RKO of the colon cancer cell line (designated RKO C2), replicate #1.


title: F3-1_5-27: Clonal population derived (by FACS sorting for low u-PAR) from RKO C2 (designated RKO C2 F3), replicate #1.


title: B6-30MINWD-2: 30 minutes wounded dendritic epidermal T-cells (DETC), replicate #2.

value: dendritic epidermal T-cells (DETC)

tag: wounded

value: Wounded

tag: time measured post wounding

value: 30 min


title: PST-3: Sulf-2 expressing non-small cell lung cancer (NSCLC) line P-ST, replicate #3.

value: P-ST

value: Non-small lung cancer


title: C2-2_5-30: Clonal population of the RKO of the colon cancer cell line (designated RKO C2), replicate #2.

value: Colon Cancer


title: WTA-3w-0.4mM: WTA sample treated with 0.4mM stroptozotocin, replicate #2.


title: DOXnegACTplus-1: ACVR2 WT -DOX/+Activin A, replicate #1.

source_name: Colorectal cancer cell line HCT116 with doxycycline inducible expression of TGFBR2, ACVR2 and AIM2 (ACVR2 WT -DOX/+Activin A)

value: Colorectal Cancer


title: B6-2HRWD: Two hours wounded dendritic epidermal T-cells (DETC), replicate #1.

value: Two hours


title: B6-0HRWD: Zero hour wounded dendritic epidermal T-cells (DETC), replicate #1.

value: Zero hour


title: B6-30MINWD: 30 minutes wounded dendritic epidermal T-cells (DETC), replicate #1.


title: DOXnegACTplus-2: ACVR2 WT -DOX/+Activin A, replicate #2.


title: B6-2HRWD-2: Two hours wounded dendritic epidermal T-cells (DETC), replicate #2.


title: B6-2HRWD-4: Two hours wounded dendritic epidermal T-cells (DETC), replicate #4.


title: DOXnegACTplus-3: ACVR2 WT -DOX/+Activin A, replicate #3.


title: Cult. IP-Astrocytes P7 Serum biological replicate 2

description: astrocytes isolated by immunopanning with ITGB5 and cultured for 7 days in serum before isolation, Foo et al

value: cultured P7 in 10% foetal calf serum 7 days


title: B6-4HRWD: Four hours wounded dendritic epidermal T-cells (DETC), replicate #1.

value: Four hours


title: Cult. IP-Astrocytes P7 Serum biological replicate 1


title: B6NW-3: Non-wounded dendritic epidermal T-cells (DETC), replicate #3.

value: Non-wounded


title: B6NW-2: None-wounded dendritic epidermal T-cells (DETC), replicate #2.

source_name: Non-wounded dendritic epidermal T-cells (DETC)


title: myb3r1_myb3r4-9d_seedlings-rep1

city: Tsukuba

description:
IH2
Total RNA from myb3r1 myb3r4 9d whole seedlings of set1.

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

source_name: myb3r1 myb3r4 double mutant, 9d whole seedlings

tag: cultivar

value: myb3r1 myb3r4 double mutation

value: whole seedlings

tag: age

value: 9 days

tag: experimental set


title: B6-2HRWD-3: Two hours wounded dendritic epidermal T-cells (DETC), replicate #3.


title: DOXplusACTplus-1: ACVR2 WT +DOX/+Activin A, replicate #1.

source_name: Colorectal cancer cell line HCT116 with doxycycline inducible expression of TGFBR2, ACVR2 and AIM2 (ACVR2 WT +DOX/+Activin A)

tag: cell line


title: WT ISW1 Flag-IP Replicate 1

description: Biological Replicate 1 of 3. ChIP enrichment of FLAG-IP over Input in the YMS078 ISW1-3xFLAG strain.

source_name: IP DNA FLAG antibody

tag: strain

tag: chip antibody

value: anti-FLAG (M2 mouse monoclonal)

tag: chip antibody manufacturer

value: Sigma

tag: chip antibody catalog #

tag: sample type

value: 3xFLAG tagged Isw1

source_name: Input DNA


title: Cult. IP-Ast. P7 biological replicate 3

description: astrocytes isolated by immunopanning with ITGB5 and cultured for 7 days before isolation, Foo et al

tag: tissue

value: forebrain

value: astrocytes

value: cultured p1 in HBEGF 5ng/ml


title: B6NW: B6NW: Non-wounded dendritic epidermal T-cells (DETC), replicate #1.

value: dendritic epidermal T-cells (DETC)


title: C57-WT1-6HR: C57 wild type mice 6 hours post infection with parasites, Leishmania Major, replicate #1.

source_name: Lymph node C57 wildtype 6 hours post infection with parasites, Leishmania Major.

tag: background strain

tag: genotype

value: WT

value: leukocyte

tag: time after infection

value: 6 hours

value: Leishmania major


title: DOXplusACTplus-2: ACVR2 WT +DOX/+Activin A, replicate #2.

value: Yes

value: Colorectal Cancer


title: C57-WT4-6HR: C57 wildtype 6 hours post infection with parasites, Leishmania Major, replicate #2.

tag: cell type


title: DOXplusACTplus-3: ACVR2 WT +DOX/+Activin A, replicate #3.

tag: disease state


title: Cult. IP-Ast. P7 biological replicate 1

tag: acute/cultured