title: Cheng_576-4_7-days_H2O2_Rep2_ATH1

city: Hong Kong

first: Han

last: Cheng

address: Shatin

department: School of Life Science

country: China

institute: The Chinese University of Hong Kong

description: Gene expression data from 7d dark-grown Col-0 seedlings treated with 5 mM H2O2.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the Affymetrix Arabidopsis ATH1 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The chip data were normalized by the RMA method and analyzed using the affy and limma packages in R/Bioconductor.

organism: Arabidopsis thaliana

source_name: 7d dark-grown Arabidopsis Col-0 seedlings treated with 5mM H2O2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Arabidopsis Col-0 seeds were grown on half MS media for 7 d, and then the seedlings were harvested.

extract_protocol: Total RNA was extracted with the Qiagen RNeasy Plant Mini Kit under the manufacturer's instructions.

treatment_protocol: The control was grown in the dark; the hydrogen peroxide sample was grown in the dark and treated with 5mM H2O2; the light sample was grown in the light.

tag: ecotype

value: seedling

tag: treatment

value: 5 mM H2O2


title: HK_Resistant_family5459_day1

status: Public on Sep 05 2012

type: RNA

city: Santiago

first: Felipe

middle: E.

last: Reyes-López

state: Santiago

address: Av. Libertador Bernado O'Higgins 3363

country: Chile

institute: Universidad de Santiago de Chile

description: Head kidney gene expression in resistant family ID 5459 at 1 day post-infection

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 μl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 μl of 2x GEx hybridization buffer was added to the fragmentation mixture and hybridized to Atlantic salmon oligonucleotide microarrays (GPL10679) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature (RT) with GE Wash Buffer 1 (Agilent), 1 minute with 37°C GE Wash buffer 2 (Agilent), 45 seconds at RT Acetonitrile (Sigma), and 30 seconds at RT with Stabilization and drying solution (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5μm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Spot intensities and other quality control features were extracted with Feature Extraction software version 10.4.0.0 (Agilent). Nofima’s bioinformatic package STARS was used for data processing, lowess normalization, and mining.

molecule: total RNA

organism: Salmo salar

source_name: Head kidney, resistant family (5459), day 1 post-infection

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the LowInput Quick Amp Labelling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (Qiagen). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: This study was realized with 30 different families mantained each one in different freshwater tanks (146.1±14.85 fish/family) with a total of 4,457 fry. Fish were fed with commercial pellet twice a day (1% of body weight) and acclimated for 10 d at a biomass of 12 kg/m3, 10-12°C and controled conditions of pH, oxygen and ammonia levels.

extract_protocol: Total RNA was extracted from head kidney (HK) using RNeasy Lipid tissue mini kit (Qiagen), following the manufacturer’s instructions, and resuspended in free nuclease water (Invitrogen). RNA was quantified using a NanoDrop-1000 spectrophotometer (Thermo Scientific) and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies). All RNA samples employed in this work were selected with a criteria of RIN value >7.

treatment_protocol: Before the challenge the fish was starved for 24 h. Fish was challenged in the tank with 1x106 PFU/ml of Sp and He IPNV strain. Fish were kept in the bath for 2 h, after wich the water was supplied at normal level and 24 hpi the water was replaced in all tanks and were offered feed.

tag: tissue

value: Head kidney

tag: phenotype against ipnv infection

value: Resistant

tag: family id

tag: time point

value: 1 day post-infection


title: Cheng_576-6_7-days_light_Rep2_ATH1

description: Gene expression data from 7d light-grown Col-0 seedlings under 16 h light / 8 h dark photoperiod.

label: Biotin

source_name: 7d light-grown Arabidopsis Col-0 seedlings

value: light


title: Granulocytic monocytic progenitors_-7AML_15564A

city: Bronx

first: Boris

last: Bartholdy

state: NY

address: 1300 Morris Park Ave

department: Cell Biology

country: USA

institute: Albert Einstein College of Medicine

hyb_protocol: Following fragmentation, labeled cRNA of each individual sample was hybridized to Affymetrix Affymetrix Human Gene 1.0 ST microarrays (Affymetrix) and stained according to the manufacturer's instructions.

scan_protocol: Arrays were scanned according to the manufacturer's instructions.

data_processing: Data were normalized normalized with the Expression Console Software  version 1.1 from Affymetrix using Robust Multi-array Average (RMA) algorithm. MeV software was used to select differentially expressed genes by applying the following criteria: (a)Absolute value of the group mean difference greater than 1.5, and (b) p value smaller than 0.05 (Welch's t test)

label: biotin

organism: Homo sapiens

source_name: AML_granulocytic monocytic progenitors (GMP)

label_protocol: 10 ng of total RNA were used for linear amplification of cDNA using the Ovation Pico RNA Amplification Systm (Nugen), according to the manufacturer's instructions. 5 µg of cRNA were biotin-labeled using the FL-Ovation cDNA Biotin Module V2 (NuGen).

growth_protocol: primary cells

extract_protocol: human bone marrow mononuclear cells were enriched for CD34 expression using Miltenyi MACS technology. Afterwards, cells were stained with antibodies against lineage-antigens (CD2, CD3,CD4, CD7, CD8, CD10, CD11b, CD14, CD19, CD20 CD56, Glycophorin A),CD34, CD38, CD90, as well as CD123 and CD45R  in order to distinguish LT-HSC (Lin-/CD34+/CD38-/CD90+), ST-HSC (Lin-/CD34+/CD38-/CD90-), CMP (Lin-/CD34+/CD38+/CD123+/CD45R -), GMP (Lin-/CD34+/CD38+/CD123+/CD45R+) and MEP (Lin-/CD34+/CD38+/CD123-/CD45R -). Cells were subjected to 7-color 5 waysorting utilizing a high-speed cell sorter as previously described (Steidl, et al. Nature Medicine, 2006). Total RNA was extracted using a denaturing buffer containing guanidine isothiocyanate (ALLprep Kit, Qiagen) from sorted cell populations.

treatment_protocol: primary cells

tag: age

value: bone marrow

tag: karyotype


title: Cheng_576-5_7-days_light_Rep1_ATH1


title: Granulocytic monocytic progenitors_ healthy control_C0110N

source_name: Healthy control_granulocytic monocytic progenitors (GMP)

value: Healthy control


title: Cheng_576-3_7-days_H2O2%20_Rep1_ATH1


title: Granulocytic monocytic progenitors_ healthy control_C0108N


title: HK_Resistant_family5761_day1

description: Head kidney gene expression in resistant family ID 5761 at 1 day post-infection

source_name: Head kidney, resistant family (5761), day 1 post-infection


title: SCAT_240_NACL_HC_104

city: Nuthetal

first: Martin

middle: A

last: Osterhoff

address: Arthur-Scheunert-Allee 155

department: Clinical Nutrition

country: Germany

institute: German Institute of Human Nutrition

description:
sc adipose tissue, 240min, NaCl, HC, replicate3
Gene expression after NaCl administration in HC-clamp in human subcutaneous adipose tissue

hyb_protocol: According to Agilents protocol

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

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

source_name: sc adipose tissue, 240min, NaCl, HC

label_protocol: Total RNAs were processed with Agilent One Color Spike Mix Stock Solution and hybridized to a total number of 100 Agilent 60-mer Whole Human Genome (4x44K) single-color DNA microarrays according to the manufacturer’s protocol (Agilent Technologies, Germany).

extract_protocol: Total subcutaneous adipose tissue RNA was extracted from homogenates of 300mg frozen sample in Quiazol™ followed by use of Lipid Tissue RNA-Kit™ (Qiagen, Germany) according to the manufacturer’s protocol. The RNA concentration measure and quality control was performed using an ND-1000 spectrophotometer (Nanodrop, PeqLab, Erlangen, Germany) and 2100 Bioanalyser and RNA Nano Chips (Agilent Technologies, Germany).

treatment_protocol: The participants were kept in a supine position throughout the experiments. One ear lobe was made hyperaemic using topically applied Finalgon® (4 mg/g nonivamid and 25 mg/g nicoboxii) for capillary blood glucose measurement. Two cannulae were inserted into each of the forearm veins for collecting blood samples and for infusions, respectively. Insulin and glucose infusions were started at t = 0 min, following the first s.c. periumbilical adipose tissue biopsy. The venous blood samples were drawn at time points t = -70, -40, 0, 30, 60, 90, 120, 180, 210, 220, 230 and 240 min. Capillary blood glucose was measured every 5 minutes in order to adjust the glucose infusion rate to the required blood glucose level for 240 min. GIP infusion was performed in a postprandial physiological manner (2 pmol*kg-1*min-1, similar to the postprandial concentration of GIP in vivo which has been described previously between 100-120 pmol/L). Saline infusion was performed with 0.9% isotonic NaCl–solution (5 mL/h) as described previously. To avoid additional stimulation of insulin release by GIP under hyperglycemic conditions (HC with GIP infusions), diazoxide was given, 300 mg in two doses of 150 mg before start of clamps and at 120 min; to hyperpolarize the beta-cells. From each participant two adipose tissue biopsies were taken before and after infusions (t = 0, 240 min), from contralateral sites, at the level of the umbilicus. The skin was anesthetized with 1% lidocaine (10-15 mL). A small incision was made and 1 g of adipose tissue was removed under sterile conditions by using a cutting needle biopsy handy. After removal, the tissue samples were stored in an RNA protecting buffer (RNA later™, Qiagen, Germany) at 4°C until the procedure was finished, then snap-frozen in liquid nitrogen and finally stored at –80°C until total RNA isolation. Between intervention days an intermission time of at least 7 days was maintained to ensure that local irritations of the biopsied areas subsided.

value: subcutaneous adipose tissue


title: SCAT_0_NACL_HC_103

description:
sc adipose tissue, 0min, NaCl, HC, replicate2
Gene expression before NaCl administration in HC-clamp in human subcutaneous adipose tissue

source_name: sc adipose tissue, 0min, NaCl, HC


title: Granulocytic monocytic progenitors_ healthy control_C0153N


title: Granulocytic monocytic progenitors_ healthy control_C0111N


title: Cheng_576-1_7-day_dark_Rep1_ATH1

description: Gene expression data from 7d dark-grown Col-0 seedlings.

source_name: 7d dark-grown Arabidopsis Col-0 seedlings

value: control


title: long-term hematopoietic stem cell_healthy control_C0154N

source_name: healthy control_long term hematopoietic stem cell (LT_HSC)


title: Granulocytic monocytic progenitors_-7AML_16222A


title: Granulocytic monocytic progenitors_ healthy control_C0154N


title: Cheng_576-2_7-day_dark_Rep2_ATH1


title: SCAT_0_NACL_INF_101

description:
sc adipose tissue, 0min, NaCl, Inf, replicate5
Gene expression before NaCl administration in Infusion in human subcutaneous adipose tissue

source_name: sc adipose tissue, 0min, NaCl, Inf


title: Granulocytic monocytic progenitors_-7AML_10120A


title: SCAT_240_NACL_INF_102

description:
sc adipose tissue, 240min, NaCl, Inf, replicate2
Gene expression after NaCl administration in Infusion in human subcutaneous adipose tissue

source_name: sc adipose tissue, 240min, NaCl, Inf


title: Granulocytic monocytic progenitors_ healthy control_C0109N


title: SCAT_240_GIP_HC_98

description:
sc adipose tissue, 240min, GIP, HC, replicate4
Gene expression after GIP administration in HC-clamp in human subcutaneous adipose tissue

source_name: sc adipose tissue, 240min, GIP, HC


title: SCAT_0_GIP_INF_99

description:
sc adipose tissue, 0min, GIP, Inf, replicate4
Gene expression before GIP administration in Infusion in human subcutaneous adipose tissue

source_name: sc adipose tissue, 0min, GIP, Inf


title: Granulocytic monocytic progenitors_-7AML_C0118A


title: long-term hematopoietic stem cell_-7AML_16683A

source_name: AML_long- term hematopoietic stem cell (LT-HSC)


title: SCAT_240_GIP_INF_100

description:
sc adipose tissue, 240min, GIP, Inf, replicate5
Gene expression after GIP administration in Infusion in human subcutaneous adipose tissue

source_name: sc adipose tissue, 240min, GIP, Inf


title: SCAT_240_NACL_HC_96

description:
sc adipose tissue, 240min, NaCl, HC, replicate8
Gene expression after NaCl administration in HC-clamp in human subcutaneous adipose tissue


title: long-term hematopoietic stem cell_healthy control_C0109N


title: long-term hematopoietic stem cell_healthy control_C0153N


title: long-term hematopoietic stem cell_-7AML_16222A


title: long-term hematopoietic stem cell_healthy control_C0111N


title: long-term hematopoietic stem cell_-7AML_10120A


title: SCAT_0_GIP_HC_97

description:
sc adipose tissue, 0min, GIP, HC, replicate6
Gene expression before GIP administration in HC-clamp in human subcutaneous adipose tissue

source_name: sc adipose tissue, 0min, GIP, HC


title: long term hematopoietic stem cell_-7AML_10209A


title: SCAT_0_NACL_HC_95

description:
sc adipose tissue, 0min, NaCl, HC, replicate8
Gene expression before NaCl administration in HC-clamp in human subcutaneous adipose tissue


title: short term hematopoietic stem cell_healthy control_C0153N

source_name: healthy control_short term hematopoietic stem cell (ST-HSC)


title: SCAT_0_GIP_EU_89

description:
sc adipose tissue, 0min, GIP, EU, replicate8
Gene expression before GIP administration in EU-clamp in human subcutaneous adipose tissue

source_name: sc adipose tissue, 0min, GIP, EU


title: SCAT_0_NACL_EU_93

description:
sc adipose tissue, 0min, NaCl, EU, replicate9
Gene expression before NaCl administration in EU-clamp in human subcutaneous adipose tissue

source_name: sc adipose tissue, 0min, NaCl, EU


title: short term hematopoietic stem cell_healthy control_C0111N


title: SCAT_240_GIP_EU_90

description:
sc adipose tissue, 240min, GIP, EU, replicate9
Gene expression after GIP administration in EU-clamp in human subcutaneous adipose tissue

source_name: sc adipose tissue, 240min, GIP, EU


title: short term hematopoietic stem cell_-7AML_15564A

source_name: AML_short term hematopoietic stem cell (ST-HSC)


title: SCAT_240_NACL_INF_88

description:
sc adipose tissue, 240min, NaCl, Inf, replicate7
Gene expression after NaCl administration in Infusion in human subcutaneous adipose tissue


title: short term hematopoietic stem cell_healthy control_C0110N


title: SCAT_240_GIP_INF_86

description:
sc adipose tissue, 240min, GIP, Inf, replicate6
Gene expression after GIP administration in Infusion in human subcutaneous adipose tissue


title: SCAT_240_GIP_HC_92

description:
sc adipose tissue, 240min, GIP, HC, replicate7
Gene expression after GIP administration in HC-clamp in human subcutaneous adipose tissue


title: short term hematopoietic stem cell_-7AML_16222A


title: short term hematopoietic stem cell_-7AML_16683A


title: short term hematopoietic stem cell_healthy control_C0154N

description: C0154N (ST-HSC)


title: SCAT_0_GIP_HC_91

description:
sc adipose tissue, 0min, GIP, HC, replicate7
Gene expression before GIP administration in HC-clamp in human subcutaneous adipose tissue


title: SCAT_0_NACL_INF_87

description:
sc adipose tissue, 0min, NaCl, Inf, replicate8
Gene expression before NaCl administration in Infusion in human subcutaneous adipose tissue


title: SCAT_0_GIP_INF_85

description:
sc adipose tissue, 0min, GIP, Inf, replicate5
Gene expression before GIP administration in Infusion in human subcutaneous adipose tissue


title: short term hematopoietic stem cell_-7AML_10209A


title: Lymphocytes_3/28_db/db_rep2

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

description:
Mdbdb328_2
Gene expression in db/db mice after 12hr TCR mediated stimulation.

hyb_protocol: 5µg of each labelled aaRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 55µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent's Mus musculus Microarray Kit 4x44k for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), and then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing and drying on the Axon 4200AL Scanner using three color scan setting for 4x44k array slides.

data_processing: The microarray images were segmented and the median intensity of each spot was estimated by the software GenePixPro® 6.0 (Axon). The data were then imported into R software and preprocessed by the BioConductor package Limma.

label: Alexa 488

organism: Mus musculus

source_name: T lymphocytes from spleen of db/db mice, 12h TCR mediated stimulation

label_protocol: Diluted spike controls (Agilent) were added to 1µg total RNA, and labelled aaRNA was prepared using Alexa 488 dye with the Amino Allyl MessageAmp II aRNA kit (Ambion) according to the manufacturer's instructions. Dye incorporation and received aaRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the RNAqueos-4PCR kit (Ambion) following the manufacturer's recommendations. Briefly, the protocol includes different lysis solution treatments and an on-column DNase digestion. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: CD4+CD25- T lymphocytes were purified from the spleens of db/db and db/+ mice. Cells were stimulated with anti-CD3+ anti-CD28 and incubated for 12 hours at 37°C in a humidified incubator with 5% CO2.

tag: strain

tag: genotype

value: db/db

tag: phenotype

value: leptin-deficient

value: spleen

tag: cell type

value: CD4+CD25- T lymphocytes

value: stimulation with anti-CD3 and anti-CD28


title: SCAT_240_NACL_HC_84

description:
sc adipose tissue, 240min, NaCl, HC, replicate6
Gene expression after NaCl administration in HC-clamp in human subcutaneous adipose tissue

source_name: sc adipose tissue, 240min, NaCl, HC


title: SCAT_240_GIP_HC_82

description:
sc adipose tissue, 240min, GIP, HC, replicate5
Gene expression after GIP administration in HC-clamp in human subcutaneous adipose tissue


title: Lymphocytes_3/28_db/+_rep2

description:
Mdb328_2
Gene expression in db/+ mice after 12hr TCR mediated stimulation.

source_name: T lymphocytes from spleen of db/+ mice, 12h TCR mediated stimulation

value: db/+

value: wild type


title: Lymphocytes_3/28_db/db_rep1

description:
Mdbdb328_1
Gene expression in db/db mice after 12hr TCR mediated stimulation.


title: SCAT_0_NACL_HC_83

description:
sc adipose tissue, 0min, NaCl, HC, replicate7
Gene expression before NaCl administration in HC-clamp in human subcutaneous adipose tissue

source_name: sc adipose tissue, 0min, NaCl, HC


title: short term hematopoietic stem cell_healthy control_C0108N


title: LP 21_liver

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

institute: Leibniz Institute for Farm Animal Biology (FBN)

description: Gene expression data from liver sample of offspring

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 42C on Affymetrix GeneChip Porcine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning using the GeneChip scanner 3000 were performed according to Affymetrix protocols

data_processing: Data were analysed with Affymetrix GCOS 1.1.1 software using global scaling to a target signal of 500 and BioConductor.

organism: Sus scrofa

source_name: LP_liver_188 dpn

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.5 ug total RNA (Expression Analysis Technical Manual, 2009, Affymetrix).

extract_protocol: Total RNA was isolated using TRI Reagent (Sigma, Taufkirchen, Germany) according to the manufacturer’s protocol. After DNaseI treatment the RNA was cleaned up using the RNeasy Kit (Qiagen, Hilden, Germany).

tag: breed

value: offspring of German Landrace gilts

tag: ontogenetic stage

value: 188 dpn

tag: gestation diet

value: gestational low protein [LP] diet

value: liver


title: short term hematopoietic stem cell_healthy control_C0109N


title: LP 22_liver


title: SCAT_0_GIP_HC_79

description:
sc adipose tissue, 0min, GIP, HC, replicate3
Gene expression before GIP administration in HC-clamp in human subcutaneous adipose tissue


title: LP 18_liver


title: Lymphocytes_3/28_db/+_rep1

description:
Mdb328_1
Gene expression in db/+ mice after 12hr TCR mediated stimulation.


title: SCAT_240_GIP_HC_80

description:
sc adipose tissue, 240min, GIP, HC, replicate2
Gene expression after GIP administration in HC-clamp in human subcutaneous adipose tissue


title: short term hematopoietic stem cell_-7AML_10120A


title: LP 23_liver


title: LP 20_liver


title: SCAT_0_GIP_HC_81

description:
sc adipose tissue, 0min, GIP, HC, replicate4
Gene expression before GIP administration in HC-clamp in human subcutaneous adipose tissue


title: LP 19_liver


title: short-term hematopoietic stem cell_AML with normal karyotype_19595

description: 19595- ST-HSC

data_processing: Data were normalized normalized with the Expression Console Software  version 1.1 from Affymetrix using Robust Multi-array Average (RMA) algorithm. MEV software was used to select differentially expressed genes by applying the following criteria: (a) Absolute value of the group mean difference greater than 1.5, and (b) p value smaller than 0.05 (Welch's t test)

source_name: AML_short-term hematopoietic stem cells (ST-HSC)

label_protocol: 10 ng of total RNA were used for linear amplification of cDNA using the Ovation Pico RNA Amplification System (Nugen), according to the manufacturer's instructions. 5 µg of cRNA were biotin-labeled using the FL-Ovation cDNA Biotin Module V2 (NuGen).

extract_protocol: Human bone marrow mononuclear cells were enriched for CD34 expression using Miltenyi MACS technology. Afterwards, cells were stained with antibodies against lineage-antigens (CD2, CD3,CD4, CD7, CD8, CD10, CD11b, CD14, CD19, CD20 CD56, Glycophorin A), CD34, CD38, CD90, as well as CD123 and CD45R  in order to distinguish LT-HSC (Lin-/CD34+/CD38-/CD90+), ST-HSC (Lin-/CD34+/CD38-/CD90-), CMP (Lin-/CD34+/CD38+/CD123+/CD45R-), GMP (Lin-/CD34+/CD38+/CD123+/CD45R+) and MEP (Lin-/CD34+/CD38+/CD123-/CD45R-). Cells were subjected to 7-color 5 way sorting utilizing a high-speed cell sorter as previously described (Steidl et al., Nat Genet 2006). Total RNAwas extracted using a denaturing buffer containing guanidine isothiocyanate (ALLprep Kit, Qiagen) from sorted cell populations.

value: normal karyotype


title: LP 16_liver

source_name: LP_liver_28 dpn

value: 28 dpn


title: LP 15_liver


title: short-term hematopoietic stem cell_AML with normal karyotype_19179

value: bone marrow


title: LP 12_liver


title: SCAT_240_GIP_EU_78

description:
sc adipose tissue, 240min, GIP, EU, replicate4
Gene expression after GIP administration in EU-clamp in human subcutaneous adipose tissue


title: short-term hematopoietic stem cell_AML with normal karyotype_14396


title: LP 17_liver


title: LP 14_liver


title: LP 13_liver


title: SCAT_0_GIP_EU_77

description:
sc adipose tissue, 0min, GIP, EU, replicate3
Gene expression before GIP administration in EU-clamp in human subcutaneous adipose tissue


title: LP 11_liver

source_name: LP_liver_1 dpn

value: 1 dpn


title: LP 09_liver


title: LP 06_liver


title: LP 08_liver


title: SCAT_0_NACL_EU_75

description:
sc adipose tissue, 0min, NaCl, EU, replicate6
Gene expression before NaCl administration in EU-clamp in human subcutaneous adipose tissue

value: subcutaneous adipose tissue


title: Granulocytic monocytic progenitors_ AML_D3-19179

source_name: AML_granulocytic monocytic progenitors (GMP)


title: LP 05_liver

source_name: LP_liver_94 dpc

value: 94 dpc


title: Granulocytic monocytic progenitors_ AML_C8-14396


title: LP 04_liver


title: CD34+ stimulated Polybren treated LV transduced 1

type: genomic

city: Evry

first: NIZAR

last: TOULEIMAT

address: 2 rue Gaston Crémieux

country: France

institute: CEA/Institut de Génomique and Généthon

description: Sample name: 5822476029_H

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

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

data_processing:
BeadStudio software v3.2
normalized data: Average Beta
non-normalized data: Unmethylated and methylated signal intensities

label: Cy5 and Cy3

molecule: genomic DNA

source_name: cord blood

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions

treatment_protocol: Prior to transduction, CD34+ cells were preactivated for about 18 hours by culture in X-VIVO 20 medium (BioWhittaker Lonza, Verviers, Belgium) supplemented with penicillin/streptomycin (Gibco), 2mM glutamax (Gibco) and cytokines (Flt-3 ligand 50ng/ml, stem cell factor 25 ng/ml, thrombopoietin 25 ng/ml and interleukin-3 10ng/ml) (Peprotech, Rocky Hill, NJ) at the concentration of 5 x 105 cells per ml. Preactivated cells were then transduced by adding 5 x 107 IG/ml of LV and polybrene (4µg/ml, Sigma-Aldrich, St Louis, MO). Infection was repeated after 6h and pursued overnight. The following morning, cells were washed and used for genomic DNA extraction

value: CD34+ cell

tag: protocol

value: cytokine stimulated cells transduced with LV in the presence of polybren


title: LP 07_liver


title: SCAT_240_NACL_EU_76

description:
sc adipose tissue, 240min, NaCl, EU, replicate6
Gene expression after NaCl administration in EU-clamp in human subcutaneous adipose tissue

source_name: sc adipose tissue, 240min, NaCl, EU


title: LP 03_liver


title: SCAT_240_NACL_HC_74

description:
sc adipose tissue, 240min, NaCl, HC, replicate5
Gene expression after NaCl administration in HC-clamp in human subcutaneous adipose tissue


title: LP 10_liver


title: SCAT_0_NACL_EU_71

description:
sc adipose tissue, 0min, NaCl, EU, replicate5
Gene expression before NaCl administration in EU-clamp in human subcutaneous adipose tissue


title: Granulocytic monocytic progenitors_ AML_D2-18037


title: SCAT_240_NACL_EU_72

description:
sc adipose tissue, 240min, NaCl, EU, replicate8
Gene expression after NaCl administration in EU-clamp in human subcutaneous adipose tissue


title: LP 02_liver


title: CD34+ stimulated Polybren treated LV transduced 3

description: Sample name: 5822476029_L


title: SCAT_0_NACL_HC_73

description:
sc adipose tissue, 0min, NaCl, HC, replicate6
Gene expression before NaCl administration in HC-clamp in human subcutaneous adipose tissue


title: CD34+ stimulated Polybren treated LV transduced 2

description: Sample name: 5822476029_J


title: short-term hematopoietic stem cell_AML with normal karyotype_C1-19179


title: long-term hematopoietic stem cell_AML with normal karyotype_A5-18037

source_name: AML_long-term hematopoietic stem cells (LT-HSC)


title: SCAT_240_NACL_HC_68

description:
sc adipose tissue, 240min, NaCl, HC, replicate4
Gene expression after NaCl administration in HC-clamp in human subcutaneous adipose tissue


title: SCAT_0_GIP_EU_69

description:
sc adipose tissue, 0min, GIP, EU, replicate6
Gene expression before GIP administration in EU-clamp in human subcutaneous adipose tissue

source_name: sc adipose tissue, 0min, GIP, EU


title: Granulocytic monocytic progenitors_ healthy control_C0108N

source_name: Healthy control_granulocytic monocytic progenitors (GMP)

value: healthy control


title: HP 23_liver

source_name: HP_liver_188 dpn

value: gestational high protein [HP] diet


title: HP 21_liver


title: CD34+ stimulated and polybren treated 3

description: Sample name: 5822476029_F

value: cytokine stimulated cells cultured with polybren


title: short-term hematopoietic stem cell_AML with normal karyotype_B3-18037


title: HP 20_liver


title: SCAT_0_NACL_HC_67

description:
sc adipose tissue, 0min, NaCl, HC, replicate4
Gene expression before NaCl administration in HC-clamp in human subcutaneous adipose tissue


title: CD34+ unstimulated 3

description: Sample name: 5822476029_E

value: control untreated uncultured cells


title: Granulocytic monocytic progenitors_ healthy control_C0111N


title: Granulocytic monocytic progenitors_ AML_C4-15644


title: SCAT_240_GIP_EU_70

description:
sc adipose tissue, 240min, GIP, EU, replicate6
Gene expression after GIP administration in EU-clamp in human subcutaneous adipose tissue

source_name: sc adipose tissue, 240min, GIP, EU


title: long-term hematopoietic stem cell_AML with normal karyotype_B2-14396


title: LP 01_liver

description: Gene expression data from liver sample of offspring


title: HP 19_liver


title: long-term hematopoietic stem cell_AML with normal karyotype_B1-19179


title: HP 18_liver

source_name: HP_liver_28 dpn


title: CD34+ stimulated and polybren treated 2

description: Sample name: 5822476029_D


title: HP 24_liver


title: HP 22_liver


title: CD34+ stimulated and polybren treated 1

description: Sample name: 5822476029_B


title: Granulocytic monocytic progenitors_ healthy control_C0109N


title: SCAT_240_NACL_INF_64

description:
sc adipose tissue, 240min, NaCl, Inf, replicate6
Gene expression after NaCl administration in Infusion in human subcutaneous adipose tissue

source_name: sc adipose tissue, 240min, NaCl, Inf


title: CD34+ stimulated 2

description: Sample name: 5822476029_I

value: cytokine stimulated cells cultured for 48h


title: CD34+ unstimulated 2

description: Sample name: 5822476029_C


title: CD34+ stimulated 1

description: Sample name: 5822476029_G


title: SCAT_240_GIP_HC_66

description:
sc adipose tissue, 240min, GIP, HC, replicate6
Gene expression after GIP administration in HC-clamp in human subcutaneous adipose tissue

source_name: sc adipose tissue, 240min, GIP, HC


title: long-term hematopoietic stem cell_healthy control_C0153N

source_name: healthy control_long term hematopoietic stem cell (LT-HSC)


title: HP 16_liver

value: offspring of German Landrace gilts


title: SCAT_0_GIP_HC_65

description:
sc adipose tissue, 0min, GIP, HC, replicate2
Gene expression before GIP administration in HC-clamp in human subcutaneous adipose tissue

source_name: sc adipose tissue, 0min, GIP, HC


title: CD34+ stimulated 3

description: Sample name: 5822476029_K


title: HP 17_liver


title: brain_mouse_8

city: Worcester

first: Alexandre

last: Maucuer

state: MA

address: 364 Plantation Street

institute: INSERM

description: newborn brain

hyb_protocol: Affymetrix mouse Exon 1.0 ST arrays were hybridised according to Affymetrix's recommendations using Affymetrix labelling and hybridization kits.

scan_protocol: Washes, staining and scan of microarrays were conducted using an Affymetrix GCS3000 platform

data_processing:
Data were processed at the core probesets level using Affymetrix Expression Console Software. Probe hybridization intensity values were summarized using the probe logarithmic intensity error (PLIER) method and then quantile normalized.
probe group file: MoEx-1_0-st-v1.r2.pgf

source_name: brain newborn

label_protocol: biotin

growth_protocol: total brain dissected from newborn mice

extract_protocol: Brains were frozen in liquid N2, animal were genotyped from a piece of tail. Brains were reduced to powder using mortar and pestle with liquid nitrogen. RNA were prepared using Rneasy kit from Qiagen.

treatment_protocol: not applicable

tag: genotype/variation

value: KIS -/-

tag: litter

tag: developmental stage

value: newborn

tag: gender

value: female

value: brain


title: long-term hematopoietic stem cell_healthy control_C0109N

tag: tissue


title: Granulocytic monocytic progenitors_ healthy control_C0153N


title: short term hematopoietic stem cell_healthy control_C0110N

source_name: healthy control_short term hematopoietic stem cell (ST-HSC)


title: HP 15_liver

value: 28 dpn

value: liver


title: SCAT_240_NACL_HC_60

description:
sc adipose tissue, 240min, NaCl, HC, replicate2
Gene expression after NaCl administration in HC-clamp in human subcutaneous adipose tissue

source_name: sc adipose tissue, 240min, NaCl, HC


title: long-term hematopoietic stem cell_healthy control_C0111N

value: bone marrow


title: brain_mouse_16

description: newborn brain

value: KIS +/+


title: Granulocytic monocytic progenitors_ healthy control_C0110N


title: long-term hematopoietic stem cell_healthy control_C0154N


title: CD34+ unstimulated 1

description: Sample name: 5822476029_A


title: Granulocytic monocytic progenitors_ healthy control_C0154N


title: SCAT_0_NACL_INF_63

description:
sc adipose tissue, 0min, NaCl, Inf, replicate7
Gene expression before NaCl administration in Infusion in human subcutaneous adipose tissue

source_name: sc adipose tissue, 0min, NaCl, Inf

value: subcutaneous adipose tissue


title: SCAT_240_GIP_INF_62

description:
sc adipose tissue, 240min, GIP, Inf, replicate7
Gene expression after GIP administration in Infusion in human subcutaneous adipose tissue

source_name: sc adipose tissue, 240min, GIP, Inf


title: HP 11_liver

source_name: HP_liver_1 dpn

value: 1 dpn


title: SCAT_240_GIP_INF_56

description:
sc adipose tissue, 240min, GIP, Inf, replicate1
Gene expression after GIP administration in Infusion in human subcutaneous adipose tissue


title: SCAT_0_GIP_HC_57

description:
sc adipose tissue, 0min, GIP, HC, replicate5
Gene expression before GIP administration in HC-clamp in human subcutaneous adipose tissue


title: SCAT_0_GIP_INF_55

description:
sc adipose tissue, 0min, GIP, Inf, replicate1
Gene expression before GIP administration in Infusion in human subcutaneous adipose tissue

source_name: sc adipose tissue, 0min, GIP, Inf


title: SCAT_0_GIP_INF_61

description:
sc adipose tissue, 0min, GIP, Inf, replicate7
Gene expression before GIP administration in Infusion in human subcutaneous adipose tissue


title: brain_mouse_7

description: newborn brain


title: brain_mouse_15

description: newborn brain


title: SCAT_0_NACL_HC_59

description:
sc adipose tissue, 0min, NaCl, HC, replicate5
Gene expression before NaCl administration in HC-clamp in human subcutaneous adipose tissue

source_name: sc adipose tissue, 0min, NaCl, HC


title: SCAT_240_GIP_HC_58

description:
sc adipose tissue, 240min, GIP, HC, replicate3
Gene expression after GIP administration in HC-clamp in human subcutaneous adipose tissue


title: HP 13_liver


title: HP 14_liver


title: short term hematopoietic stem cell_healthy control_C0111N


title: HP 12_liver


title: short term hematopoietic stem cell_healthy control_C0154N

description: C0154N (ST-HSC)


title: short term hematopoietic stem cell_healthy control_C0153N


title: brain_mouse_13

description: newborn brain


title: HP 09_liver


title: HP 08_liver


title: brain_mouse_14

description: newborn brain


title: SCAT_240_GIP_EU_54

description:
sc adipose tissue, 240min, GIP, EU, replicate1
Gene expression after GIP administration in EU-clamp in human subcutaneous adipose tissue


title: brain_mouse_12

description: newborn brain


title: brain_mouse_4

description: newborn brain


title: HP 10_liver


title: brain_mouse_11

description: newborn brain


title: HP 07_liver


title: SCAT_0_GIP_EU_53

description:
sc adipose tissue, 0min, GIP, EU, replicate2
Gene expression before GIP administration in EU-clamp in human subcutaneous adipose tissue

source_name: sc adipose tissue, 0min, GIP, EU


title: short term hematopoietic stem cell_healthy control_C0108N


title: SCAT_240_NACL_INF_52

description:
sc adipose tissue, 240min, NaCl, Inf, replicate1
Gene expression after NaCl administration in Infusion in human subcutaneous adipose tissue


title: short term hematopoietic stem cell_healthy control_C0109N


title: brain_mouse_9

description: newborn brain


title: CD34pos_Donor_G

city: Hamburg

first: Christian

last: Schulze

address: Falkenried 94

institute: ZMNH

description: Gene expression hematopoietic progenitor cells

hyb_protocol: Cy3-labelled cRNA was fragmented following manufacturers instructions and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 10 rpm and 65Â°C in the Hybridization Oven (Agilent). Washing and staining of the arrays were done according to the manufacturers recommendation.

scan_protocol: Cy3 intensities were detected by onecolor scanning using an Agilent DNA microarray scanner (Agilent) at 5 micron resolution. Scanned image files were visually inspected for artifacts and then analyzed

data_processing: Slides were scanned using Agilent Microarray Scanner (G2565BA) followed by data extraction by Agilent Feature Extraction software version 9.5.3. with default settings for oligonucleotide expression arrays. Intensity data were processed with R and Bioconductor packages to obtain quantile-normalized and  log2-transformed intensity values. Calculated p-values for differential expression based on a moderated t-statistic were corrected for multiple testing using the Benjamini-Hochberg method. Samples were grouped according to the mobilization regimen followed (G‑CSF vs G‑CSF/CY). Comparisons were made for MS affected patients (G-CSF) vs healthy donors and G-CSF/CY vs G-CSF mobilization for MS patients only, respectively.

source_name: CD34pos, Donor G

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 700 ng RNA using the Low RNA Input linear Amplification Kit Plus, One Color protocol (Agilent Techologies, Inc. 2007; Cat. N°: 51885339) and the Agilent RNA SpikeIn Kit for One color (Agilent Techologies, Inc. 2007; Cat. N°: 51885282). Quantity and efficiency of the labeled amplified cRNA were determined using the NanoDrop ND1000 UVVIS Spectrophotometer version 3.2.1.

growth_protocol: ex vivo isolated cells

extract_protocol: White blood cells, containing the CD34+ cell fraction, were collected by leucocytapheresis from peripheral blood, frozen and stored in liquid nitrogen. All samples were thawed and processed at one center and CD34+ cells purified by magnetic bead separation using the autoMACS system (Miltenyi). Purity and viability of CD34+ cells was analyzed by Fluorescence Activated Cell Sorter (FACS). Total cellular RNA and DNA were extracted with TRIzol reagent. RNA samples were checked for quantity, purity and integrity of the 18S and 28S ribosomal bands by capillary electrophoresis using the Agilent 2100 bioanalyzer (nanoassay).

treatment_protocol: MS patients (4 donors) and age matched healthy donors (5) underwent stem cell mobilization by G-CSF (2x5μg/kg/day). An additional set of MS patients (4 donors) receiced G-CSF (5μg/kg/day) plus Cyclophosphamide (Cy, 4g/m2).

tag: mobilization

value: Cy


title: SCAT_0_NACL_INF_51

description:
sc adipose tissue, 0min, NaCl, Inf, replicate2
Gene expression before NaCl administration in Infusion in human subcutaneous adipose tissue


title: CD34pos_Donor_H

source_name: CD34pos, Donor H


title: SCAT_240_NACL_EU_50

description:
sc adipose tissue, 240min, NaCl, EU, replicate4
Gene expression after NaCl administration in EU-clamp in human subcutaneous adipose tissue

source_name: sc adipose tissue, 240min, NaCl, EU


title: HP 04_liver

description: Gene expression data from liver sample of offspring

source_name: HP_liver_94 dpc

value: 94 dpc


title: brain_mouse_2

description: newborn brain


title: CD34pos_Donor_E

source_name: CD34pos, Donor E

value: male


title: HP 06_liver

value: gestational high protein [HP] diet


title: HP 01_liver


title: CD34pos_Donor_F

source_name: CD34pos, Donor F


title: HP 05_liver


title: CD34pos_Donor_D

source_name: CD34pos, Donor D

value: no Cy


title: HP 02_liver


title: brain_mouse_1

description: newborn brain


title: SCAT_0_NACL_EU_49

description:
sc adipose tissue, 0min, NaCl, EU, replicate3
Gene expression before NaCl administration in EU-clamp in human subcutaneous adipose tissue

source_name: sc adipose tissue, 0min, NaCl, EU


title: SCAT_0_NACL_HC_47

description:
sc adipose tissue, 0min, NaCl, HC, replicate1
Gene expression before NaCl administration in HC-clamp in human subcutaneous adipose tissue


title: SCAT_240_GIP_EU_46

description:
sc adipose tissue, 240min, GIP, EU, replicate8
Gene expression after GIP administration in EU-clamp in human subcutaneous adipose tissue

source_name: sc adipose tissue, 240min, GIP, EU


title: CD34pos_Donor_B

source_name: CD34pos, Donor B


title: CD34pos_Donor_C_rep2

source_name: CD34pos, Donor C, replicate 2


title: AP 21_liver

source_name: AP_liver_188 dpn

value: 188 dpn

value: gestational adequate protein [AP] diet


title: CD34pos_Donor_C_rep1

source_name: CD34pos, Donor C, replicate 1


title: AP 18_liver

source_name: AP_liver_28 dpn

value: offspring of German Landrace gilts


title: AP 20_liver


title: SCAT_240_NACL_HC_48

description:
sc adipose tissue, 240min, NaCl, HC, replicate1
Gene expression after NaCl administration in HC-clamp in human subcutaneous adipose tissue

source_name: sc adipose tissue, 240min, NaCl, HC


title: SCAT_0_GIP_EU_45

description:
sc adipose tissue, 0min, GIP, EU, replicate1
Gene expression before GIP administration in EU-clamp in human subcutaneous adipose tissue


title: HP 03_liver


title: CD34neg_Donor_H

source_name: CD34neg, Donor H


title: AP 22_liver


title: SCAT_0_NACL_EU_43

description:
sc adipose tissue, 0min, NaCl, EU, replicate1
Gene expression before NaCl administration in EU-clamp in human subcutaneous adipose tissue


title: CD34neg_Donor_F

source_name: CD34neg, Donor F


title: AP 19_liver


title: SCAT_240_NACL_EU_44

description:
sc adipose tissue, 240min, NaCl, EU, replicate2
Gene expression after NaCl administration in EU-clamp in human subcutaneous adipose tissue


title: SCAT_0_GIP_HC_41

description:
sc adipose tissue, 0min, GIP, HC, replicate1
Gene expression before GIP administration in HC-clamp in human subcutaneous adipose tissue

source_name: sc adipose tissue, 0min, GIP, HC


title: AP 16_liver


title: SCAT_240_GIP_HC_42

description:
sc adipose tissue, 240min, GIP, HC, replicate1
Gene expression after GIP administration in HC-clamp in human subcutaneous adipose tissue

source_name: sc adipose tissue, 240min, GIP, HC


title: SCAT_0_GIP_EU_39

description:
sc adipose tissue, 0min, GIP, EU, replicate7
Gene expression before GIP administration in EU-clamp in human subcutaneous adipose tissue

source_name: sc adipose tissue, 0min, GIP, EU


title: CD34neg_Donor_D

source_name: CD34neg, Donor D


title: AP 17_liver


title: SCAT_240_GIP_EU_40

description:
sc adipose tissue, 240min, GIP, EU, replicate7
Gene expression after GIP administration in EU-clamp in human subcutaneous adipose tissue


title: AP 15_liver


title: CD34neg_Donor_E

source_name: CD34neg, Donor E


title: CD34pos_Donor_A

source_name: CD34pos, Donor A


title: H0033270

city: Bethesda

first: Hyun Min

last: Jung

state: MD

address: 6 Center Drive

department: Division of Developmental Biology

institute: National Institutes of Health

description: MicroRNA expression in oral squamous cell carcinoma tissue

hyb_protocol: Hybridization, washing, imaging, and signal extraction were performed according to Agilent-recommended procedures.

scan_protocol: Slides were scanned on Agilent DNA microarray scanner (model G2565A).

data_processing: The scanned signals were extracted using Agilent Feature Extraction (FE) software version 9.5.3.1 to perform background correction, outlier rejection for each set of replicate features, and calculation of total gene signal for each probe on the array.

label_protocol: 100 ng of total RNA per sample was dephosphorylated with calf intestine alkaline phosphatase and the pCp-Cy3 labeling molecule was ligated to the 3ʹ-ends of the RNA molecules, and then was purified using BioSpin6 (Bio-Rad, Hercules, CA).

extract_protocol: Human tissues measured approximately 60mm3 in volume were homogenized using the PowerGen 125 (Fisher Scientific, Pittsburgh, PA) in 600 µL of Lysis/Binding buffer provided in the mirVanaTM miRNA Isolation kit (Ambion/Applied Biosystems, Austin, TX) and then followed the manufacturer’s instruction to isolate total RNA.

treatment_protocol: Tissues were snap-frozen and stored at -80°C until further use.

value: cancerous tissue


title: SCAT_240_NACL_EU_38

description:
sc adipose tissue, 240min, NaCl, EU, replicate7
Gene expression after NaCl administration in EU-clamp in human subcutaneous adipose tissue

source_name: sc adipose tissue, 240min, NaCl, EU


title: H0033186

description: MicroRNA expression in normal tissue

source_name: 9449 (normal)

value: normal tissue


title: H0033269


title: CD34neg_Donor_G

description: Gene expression hematopoietic progenitor cells

source_name: CD34neg, Donor G

value: female


title: H0033185

description: MicroRNA expression in normal tissue

source_name: 9832 (normal)


title: CD34neg_Donor_C_rep2

source_name: CD34neg, Donor C, replicate 2


title: CD34neg_Donor_C_rep1

source_name: CD34neg, Donor C, replicate 1


title: H0033184

description: MicroRNA expression in normal tissue

source_name: 11104B (normal)


title: AP 14_liver

source_name: AP_liver_28 dpn

value: 28 dpn


title: AP 13_liver

value: liver


title: AP 12_liver

source_name: AP_liver_1 dpn


title: H0033183


title: SCAT_0_NACL_EU_37

description:
sc adipose tissue, 0min, NaCl, EU, replicate7
Gene expression before NaCl administration in EU-clamp in human subcutaneous adipose tissue

source_name: sc adipose tissue, 0min, NaCl, EU


title: CD34neg_Donor_B

source_name: CD34neg, Donor B


title: SCAT_0_GIP_INF_35

description:
sc adipose tissue, 0min, GIP, Inf, replicate2
Gene expression before GIP administration in Infusion in human subcutaneous adipose tissue

source_name: sc adipose tissue, 0min, GIP, Inf


title: SCAT_240_GIP_INF_36

description:
sc adipose tissue, 240min, GIP, Inf, replicate3
Gene expression after GIP administration in Infusion in human subcutaneous adipose tissue

source_name: sc adipose tissue, 240min, GIP, Inf


title: AP 10_liver

description: Gene expression data from liver sample of offspring


title: CD34neg_Donor_A

source_name: CD34neg, Donor A


title: AP 11_liver


title: CD34pos_ControlDonor_E

source_name: CD34pos, ControlDonor E


title: SCAT_240_NACL_INF_34

description:
sc adipose tissue, 240min, NaCl, Inf, replicate3
Gene expression after NaCl administration in Infusion in human subcutaneous adipose tissue

source_name: sc adipose tissue, 240min, NaCl, Inf


title: CD34pos_ControlDonor_D

source_name: CD34pos, ControlDonor D


title: SCAT_0_NACL_INF_33

description:
sc adipose tissue, 0min, NaCl, Inf, replicate3
Gene expression before NaCl administration in Infusion in human subcutaneous adipose tissue

source_name: sc adipose tissue, 0min, NaCl, Inf


title: AP 09_liver


title: H0033181


title: SCAT_240_GIP_INF_32

description:
sc adipose tissue, 240min, GIP, Inf, replicate2
Gene expression after GIP administration in Infusion in human subcutaneous adipose tissue


title: H0033180


title: AP 08_liver


title: SCAT_0_GIP_INF_31

description:
sc adipose tissue, 0min, GIP, Inf, replicate6
Gene expression before GIP administration in Infusion in human subcutaneous adipose tissue


title: CD34pos_ControlDonor_C

source_name: CD34pos, ControlDonor C


title: H0033177


title: CD34pos_ControlDonor_B

source_name: CD34pos, ControlDonor B


title: AP 07_liver


title: H0033178


title: H0033176


title: CD34neg_ControlDonor_E_rep3

source_name: CD34neg, ControlDonor E, replicate 3


title: SCAT_0_NACL_INF_29

description:
sc adipose tissue, 0min, NaCl, Inf, replicate6
Gene expression before NaCl administration in Infusion in human subcutaneous adipose tissue


title: H0033175


title: H0033174


title: SCAT_240_NACL_HC_28

description:
sc adipose tissue, 240min, NaCl, HC, replicate7
Gene expression after NaCl administration in HC-clamp in human subcutaneous adipose tissue

source_name: sc adipose tissue, 240min, NaCl, HC


title: SCAT_240_NACL_INF_30

description:
sc adipose tissue, 240min, NaCl, Inf, replicate5
Gene expression after NaCl administration in Infusion in human subcutaneous adipose tissue


title: AP 06_liver

source_name: AP_liver_94 dpc


title: CD34neg_ControlDonor_E_rep2

source_name: CD34neg, ControlDonor E, replicate 2


title: SCAT_240_GIP_HC_26

description:
sc adipose tissue, 240min, GIP, HC, replicate8
Gene expression after GIP administration in HC-clamp in human subcutaneous adipose tissue

source_name: sc adipose tissue, 240min, GIP, HC


title: H0033173


title: SCAT_0_NACL_HC_27

description:
sc adipose tissue, 0min, NaCl, HC, replicate3
Gene expression before NaCl administration in HC-clamp in human subcutaneous adipose tissue

source_name: sc adipose tissue, 0min, NaCl, HC


title: CD34pos_ControlDonor_A

source_name: CD34pos, ControlDonor A


title: SCAT_240_GIP_INF_24

description:
sc adipose tissue, 240min, GIP, Inf, replicate8
Gene expression after GIP administration in Infusion in human subcutaneous adipose tissue


title: CD34neg_ControlDonor_B

source_name: CD34neg, ControlDonor B, replicate 1


title: H0033172

description: MicroRNA expression in oral squamous cell carcinoma tissue


title: AP 02_liver


title: AP 05_liver


title: AP 04_liver


title: CD34neg_ControlDonor_E_rep1

source_name: CD34neg, ControlDonor E, replicate 1


title: CD34neg_ControlDonor_C

source_name: CD34neg, ControlDonor C


title: SCAT_0_GIP_INF_23

description:
sc adipose tissue, 0min, GIP, Inf, replicate8
Gene expression before GIP administration in Infusion in human subcutaneous adipose tissue

source_name: sc adipose tissue, 0min, GIP, Inf


title: CD34neg_ControlDonor_D

description: Gene expression hematopoietic progenitor cells

source_name: CD34neg, ControlDonor D


title: H0033168


title: H0033169


title: H0033171


title: H0033170


title: CD34pos_Donor_D

type: other

hyb_protocol: Cy3-labelled cRNA was hybridized to the Agilent miRNA microarray following manufacturers instructions followed by washing and staining according to the manufacturers recommendation.

data_processing: Slides were scanned using Agilent Microarray Scanner (G2565BA) followed by data extraction by Agilent Feature Extraction software version 9.5.3. with default settings for oligonucleotide expression arrays. Intensity data were processed with R and Bioconductor packages to obtain RMA-normalized and  log2-transformed intensity values.

molecule: other

source_name: CD34pos, Donor D

treatment_protocol: MS patients (4 donors) and age matched healthy donors (5) underwent stem cell mobilization by G-CSF (2x5μg/kg/day)..


title: SCAT_0_GIP_HC_25

description:
sc adipose tissue, 0min, GIP, HC, replicate8
Gene expression before GIP administration in HC-clamp in human subcutaneous adipose tissue

source_name: sc adipose tissue, 0min, GIP, HC


title: H0033167


title: CD34neg_ControlDonor_A

source_name: CD34neg, ControlDonor A, replicate 1


title: SCAT_240_GIP_EU_20

description:
sc adipose tissue, 240min, GIP, EU, replicate2
Gene expression after GIP administration in EU-clamp in human subcutaneous adipose tissue

source_name: sc adipose tissue, 240min, GIP, EU


title: SCAT_0_NACL_EU_17

description:
sc adipose tissue, 0min, NaCl, EU, replicate4
Gene expression before NaCl administration in EU-clamp in human subcutaneous adipose tissue

source_name: sc adipose tissue, 0min, NaCl, EU


title: AP 03_liver

description: Gene expression data from liver sample of offspring


title: Lymphocytes_3/28+rapa_rep3

description:
mrapa_3
Gene expression after 12hr TCR mediated stimulation and 1 h rapamycin pretreatment.

hyb_protocol: 5µg of each differentially labelled aaRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 55µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent's Homo sapiens Microarray Kit 4x44k for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), and then dried immediately by brief centrifugation.

source_name: T lymphocytes from peripheral blood, 12h TCR mediated stimulation, 1 h rapamycin pretreatment

label_protocol: Diluted spike controls (Agilent) were added to 1µg total RNA, and labelled aaRNA was prepared using cyanine 3 (Cy3), Cy5 or Alexa 488 dye with the Amino Allyl MessageAmp II aRNA kit (Ambion) according to the manufacturer's instructions. Dye incorporation and received aaRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

treatment_protocol: CD4+CD25- T lymphocytes were purified from peripheral blood of healthy donors. Cell were pretreated or not with rapamycin (100nM) for 1 hour. Then, rapamycin was removed, and the cells were stimulated with anti-CD3+ anti-CD28 and incubated for an additional 12 hours at 37°C in a humidified incubator with 5% CO2.

value: peripheral blood

value: CD4+CD25- T lymphocytes

tag: disease state

value: healthy

tag: pre-treatment

value: rapamycin

tag: treatment

value: stimulation with anti-CD3 and anti-CD28


title: SCAT_240_NACL_EU_18

description:
sc adipose tissue, 240min, NaCl, EU, replicate5
Gene expression after NaCl administration in EU-clamp in human subcutaneous adipose tissue

source_name: sc adipose tissue, 240min, NaCl, EU

value: subcutaneous adipose tissue


title: SCAT_0_NACL_INF_21

description:
sc adipose tissue, 0min, NaCl, Inf, replicate1
Gene expression before NaCl administration in Infusion in human subcutaneous adipose tissue

source_name: sc adipose tissue, 0min, NaCl, Inf


title: Lymphocytes_3/28+rapa_rep1

description:
mrapa_1
Gene expression after 12hr TCR mediated stimulation and 1 h rapamycin pretreatment.


title: Lymphocytes_3/28+rapa_rep2

description:
mrapa_2
Gene expression after 12hr TCR mediated stimulation and 1 h rapamycin pretreatment.


title: SCAT_240_NACL_INF_22

description:
sc adipose tissue, 240min, NaCl, Inf, replicate8
Gene expression after NaCl administration in Infusion in human subcutaneous adipose tissue

source_name: sc adipose tissue, 240min, NaCl, Inf


title: Lymphocytes_3/28_rep1

description:
M328_1
Gene expression after 12hr TCR mediated stimulation.

source_name: T lymphocytes from peripheral blood, 12h TCR mediated stimulation, no rapamycin pretreatment


title: CD34pos_ControlDonor_D

source_name: CD34pos, ControlDonor D


title: CD34pos_ControlDonor_C

source_name: CD34pos, ControlDonor C


title: SCAT_0_GIP_EU_19

description:
sc adipose tissue, 0min, GIP, EU, replicate5
Gene expression before GIP administration in EU-clamp in human subcutaneous adipose tissue

source_name: sc adipose tissue, 0min, GIP, EU


title: srl1-1 rep1

city: Shanghai

first: Jingjing

last: Xiang

state: Shanghai

address: 300 Fenglin Road

institute: Institute of Plant Physiol & Ecology, Chinese Academy of Sciences

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies,Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US),according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), Stabilization and Drying Solution (Cat#5185-5979, Agilent technologies, Santa Clara, CA, US)followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565BA, Agilent technologies, Santa Clara, CA, US) and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) with default settings，Scan resolution=5μm, PMT 100%，10%.

data_processing: Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

organism: Oryza sativa

source_name: cells from seedlings

label_protocol: Total RNA was amplified and labeled by Low RNA Input Linear Amplification kit.(Cat#5184-3523, Agilent technologies, Santa Clara, CA, US), 5-(3-aminoallyl)-UTP (Cat#AM8436, Ambion, Austin, TX,US), Cy3 NHS ester (Cat#PA13105,GE healthcare Biosciences, Pittsburgh, PA,US) followed the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNAs were extracted by the PicoPure RNA isolation kit (Arcturus/Molecular Devices).

value: 5 DAG (seedlings)

value: cells to be differentiated into bulliform cells


title: Lymphocytes_3/28_rep3

description:
M328_3
Gene expression after 12hr TCR mediated stimulation.


title: Lymphocytes_3/28_rep2

description:
M328_2
Gene expression after 12hr TCR mediated stimulation.


title: CD34pos_ControlDonor_B

source_name: CD34pos, ControlDonor B


title: AP 01_liver

source_name: AP_liver_94 dpc

value: 94 dpc


title: CD34pos_ControlDonor_E

source_name: CD34pos, ControlDonor E

value: male


title: Nip rep1

value: Nip

value: epidermal cells


title: CD34pos_ControlDonor_A

source_name: CD34pos, ControlDonor A


title: IR WT2

city: New York

first: Jeffrey

last: Zhao

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

description: Lin-Sca-1+c-Kit+ (LSK) cells from mice reconstituted with wild type fetal liver cells 2 following a sublethal dose of irradiation (6,5 Gy)

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

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

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. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Lin-Sca-1+c-Kit+ (LSK) cells from bone marrow

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA.

extract_protocol: Extraction of total RNA was performed by Rneasy Plus Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Mice were sublethally irradiated at 6.5 Gy

tag: strain

value: bone marrow

value: Lin-Sca-1+c-Kit+ (LSK) cells

value: wild type

value: sublethal dose of irradiation (6,5 Gy)


title: srl1-1 rep2


title: CD34pos_Donor_C

source_name: CD34pos, Donor C

value: female


title: IR WT1

description: Lin-Sca-1+c-Kit+ (LSK) cells from mice reconstituted with wild type fetal liver cells 1 following a sublethal dose of irradiation (6,5 Gy)

tag: genotype


title: SCAT_240_GIP_EU_16

description:
sc adipose tissue, 240min, GIP, EU, replicate5
Gene expression after GIP administration in EU-clamp in human subcutaneous adipose tissue

source_name: sc adipose tissue, 240min, GIP, EU


title: SCAT_0_GIP_EU_15

description:
sc adipose tissue, 0min, GIP, EU, replicate4
Gene expression before GIP administration in EU-clamp in human subcutaneous adipose tissue


title: SCAT_240_NACL_EU_14

description:
sc adipose tissue, 240min, NaCl, EU, replicate1
Gene expression after NaCl administration in EU-clamp in human subcutaneous adipose tissue


title: CD34pos_Donor_B

description: Gene expression hematopoietic progenitor cells

source_name: CD34pos, Donor B


title: SCAT_240_GIP_INF_12

description:
sc adipose tissue, 240min, GIP, Inf, replicate4
Gene expression after GIP administration in Infusion in human subcutaneous adipose tissue

source_name: sc adipose tissue, 240min, GIP, Inf


title: CD34pos_Donor_A

source_name: CD34pos, Donor A


title: IR NDN2

description: Lin-Sca-1+c-Kit+ (LSK) cells from mice reconstituted with necdin null fetal liver cells 2 following a sublethal dose of irradiation (6,5 Gy)

value: necdin null


title: CTLA-4 KO 5C.C7 T cells, biological rep2

description: in vivo gene expression data from CTLA-4 KO 5C.C7 T cells

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

data_processing: The data were analyzed with Partek and Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Mouse T cells

growth_protocol: T cells from 5C.C7 RAG2-/- CD45.1 and 5C.C7 RAG2-/- CD45.1 CTLA-4-/- were transferred into B10.A recipient mice.

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

treatment_protocol: T cells from 5C.C7 RAG2-/- CD45.1 and 5C.C7 RAG2-/- CD45.1 CTLA-4-/- mice were activated by immunization with MCC peptide and LPS and after 4 days sorted for RNA extraction.

value: T cells

value: CTLA-4 KO 5C.C7

tag: background mouse strain


title: SCAT_0_NACL_INF_9

description:
sc adipose tissue, 0min, NaCl, Inf, replicate4
Gene expression before NaCl administration in Infusion in human subcutaneous adipose tissue

source_name: sc adipose tissue, 0min, NaCl, Inf


title: SCAT_0_NACL_EU_13

description:
sc adipose tissue, 0min, NaCl, EU, replicate8
Gene expression before NaCl administration in EU-clamp in human subcutaneous adipose tissue

source_name: sc adipose tissue, 0min, NaCl, EU


title: SCAT_240_NACL_EU_4

description:
sc adipose tissue, 240min, NaCl, EU, replicate3
Gene expression after NaCl administration in EU-clamp in human subcutaneous adipose tissue

source_name: sc adipose tissue, 240min, NaCl, EU


title: IR NDN1

description: Lin-Sca-1+c-Kit+ (LSK) cells from mice reconstituted with necdin null fetal liver cells 1 following a sublethal dose of irradiation (6,5 Gy)

tag: cell type


title: wild type 5C.C7 T cells, biological rep3

description: in vivo gene expression data from wild type 5C.C7 T cells

value: wild type 5C.C7


title: CTLA-4 KO 5C.C7 T cells, biological rep1


title: SCAT_240_GIP_EU_3

description:
sc adipose tissue, 240min, GIP, EU, replicate3
Gene expression after GIP administration in EU-clamp in human subcutaneous adipose tissue


title: CTLA-4 KO 5C.C7 T cells, biological rep3


title: SCAT_0_NACL_EU_2

description:
sc adipose tissue, 0min, NaCl, EU, replicate2
Gene expression before NaCl administration in EU-clamp in human subcutaneous adipose tissue


title: wild type 5C.C7 T cells, biological rep2


title: wild type 5C.C7 T cells, biological rep1


title: Head of stage 41 embryo-xMLTK-MO injected-rep1

status: Public on Sep 04 2012

city: Kyoto

first: Eisuke

last: Nishida

address: Kitashirakawa, Sakyo-ku

department: Department of Cell and Developmental Biology

country: Japan

institute: Graduate School of Biostudies, Kyoto University

description: xMLTK-MO was injected into the animal pole of all blastomeres at the four-cell stage. The heads of embryos were cut out and harvested at 72 hours after fertilization (corresponding to about stage 41).

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Xenopus laevis Genome 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Styation 450.

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner.

data_processing: The raw data were normalized with RMA algorithm.

organism: Xenopus laevis

source_name: Heads of stage 41 embryos_xMLTK-depleted

label_protocol: Biotinylated cRNA were prepared from 150 ng total RNA using the GeneChip 3’ IVT Express Kit (Affymetrix) according to the manufacturer’s instruction.

growth_protocol: Xenopus embryos were obtained by in vitro fertilization and cultured in 0.1× MBS at 22°C

extract_protocol: Total RNA was extracted using TRIsol reagent, treated with DNase (TURBO DNase, Ambion), and then purified using RNeasy Mini Kit (QIAGEN) according to the manufacturer’s instruction.

treatment_protocol: Morpholino (MO) was injected into the animal pole of all blastomeres (10 ng/cell) at the four-cell stage. The heads of embryos were cut out and harvested at 72 hours after fertilization (corresponding to about stage 41).

value: Head of stage 41 embryo

value: xMLTK-MO


title: Kidney B Lgr5 neg

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

country: Netherlands

institute: msterdam UMC and University of Amsterdam

description:
ext391
Lgr5ki_GFP-negative 1.

hyb_protocol: Biotin terminal labeled sense strand DNA was generated from 100 ng total RNA using the Ambion WT Expression Kit (Applied Biosytems, 4425209 Rev. C), followed by end labeling using the Affymetrix GeneChip WT Terminal Labeling Kit conforming to the manufacturer's instructions (P/N 702808 Rev. 4). Final yields were measured using a Nanodrop 1000 (v.3.8.0, Thermo Scientific). The labeled samples were hybridized on Affymetrix Mouse Gene 1.1 ST arrays using a GeneChip Hybridisation Oven 640. Chips were labeled and washed using  the GeneChip Hybridisation, Wash, and Stain Kit (Affymetrix) in a GeneChip Fluidics Station 450 (P/N 08-0092).

scan_protocol: Scanning was performed using a GeneChip Scanner 3000 7G conforming to the manufacturer's instructions (P/N 702731).

data_processing: AffyPowerTools-rma-sketch.

source_name: FACS-sorted cells from cultured embryonic kidneys from Lgr5-EGFP-Ires-CreERT2 mice, Lgr5 negative

label_protocol: WT labeling kit (www.affymetrix.com).

growth_protocol: Murine embryonic kidneys were isolated and cultured as previously described (Giuliani, Journal of Urology 2008 (PMID 18006007)).

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen) following the manufacturer's instructions.

treatment_protocol: Embryonic kidneys were identified by fluorescence microscopy and enzymatically digested to a single cell solution using TrypLE (Sigma Aldrich) and DNase.

value: embryonic kidney

tag: lgr5 expression level

value: negative


title: Head of stage 41 embryo-xSox6-MO injected-rep1

description: xSox6-MO was injected into the animal pole of all blastomeres at the four-cell stage. The heads of embryos were cut out and harvested at 72 hours after fertilization (corresponding to about stage 41).

source_name: Heads of stage 41 embryos_xSox6-depleted


title: Kidney D Lgr5 neg

description:
ext394
Lgr5ki_GFP-negative 2.


title: Kidney A Lgr5 pos

description:
ext390
Lgr5ki_GFP-positive 1.

source_name: FACS-sorted cells from cultured embryonic kidneys from Lgr5-EGFP-Ires-CreERT2 mice, Lgr5 positive

value: positive


title: Head of stage 41 embryo-CoMO injected-rep1

description: CoMO was injected into the animal pole of all blastomeres at the four-cell stage. The heads of embryos were cut out and harvested at 72 hours after fertilization (corresponding to about stage 41).

source_name: Heads of stage 41 embryos injected with CoMO

value: CoMO


title: Patient 4_ day35

city: Houston

first: Mahmoud

middle: Ali

last: Mohammad

state: Texas

address: 1100 Bates St.

department: Pediatrics-Nutrition

institute: Baylor College of Medicine

description: Patient 4_ day35 post delivery

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using  Cubic Spline normalisation and substracted for background with  GenomeStudio version 1.9.0, Illumina Inc.

label: Biotin-labeled & Cy3 stained

source_name: Milk Fat Globule

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

extract_protocol: Total RNA was extracted with Trizol reagent according to manufacturer specifications. Total RNA concentration was measured using NanoDrop spectrophotometer. Quality control was performed using the Experion RNA StdSens Analysis Kit, Bio-Rad Laboratories.concentration was measured using NanoDrop spectrophotometer (NanoDrop Technologies,   Wilmington, DE). RNA quality was assessed using the ExperionTMRNA StdSens Analysis Kit (Bio-Rad Laboratories, Hercules, CA).

tag: sample

value: breast milk fat globule

value: Female

tag: bmi

value: Lean

tag: sample time

value: day 35 post delivery


title: Patient 4_ day42

description: Patient 4_ day42 post delivery

value: day 42 post delivery


title: Patient 5_ day42

description: Patient 5_ day42 post delivery


title: Patient 6_ day42

description: Patient 6_ day42 post delivery


title: Patient 2_ day42

description: Patient 2_ day42 post delivery


title: Patient 7_ day35

description: Patient 7_ day35 post delivery


title: Patient 1_ day42

description: Patient 1_ day42 post delivery


title: Patient 7_ day42

description: Patient 7_ day42 post delivery


title: Kidney B Lgr5 pos

description:
ext392
Lgr5ki_GFP-positive 2.


title: Nip rep2

source_name: cells from seedlings

tag: genotype/variation

value: Nip

value: 5 DAG (seedlings)

value: epidermal cells


title: Patient 3_ day42

description: Patient 3_ day42 post delivery


title: Patient 2_ day35

description: Patient 2_ day35 post delivery


title: Patient 3_ day35

description: Patient 3_ day35 post delivery


title: Patient 1_ day35

description: Patient 1_ day35 post delivery


title: Patient 6_ day28

description: Patient 6_ day28 post delivery

value: day 28 post delivery


title: Patient 5_ day35

description: Patient 5_ day35 post delivery


title: Patient 1_ day28

description: Patient 1_ day28 post delivery


title: Patient 4_ day28

description: Patient 4_ day28 post delivery


title: Patient 6_ day35

description: Patient 6_ day35 post delivery


title: Patient 5_ day28

description: Patient 5_ day28 post delivery


title: Patient 7_ day21

description: Patient 7_ day21 post delivery

value: day 21 post delivery


title: Patient 7_ day28

description: Patient 7_ day28 post delivery


title: Patient 6_ day21

description: Patient 6_ day21 post delivery


title: Patient 4_ day21

description: Patient 4_ day21 post delivery


title: Patient 2_ day28

description: Patient 2_ day28 post delivery


title: Patient 1_ day21

description: Patient 1_ day21 post delivery


title: Patient 3_ day28

description: Patient 3_ day28 post delivery


title: Patient 5_ day21

description: Patient 5_ day21 post delivery


title: Patient 3_ day21

description: Patient 3_ day21 post delivery


title: Patient 2_ day21

description: Patient 2_ day21 post delivery


title: Patient 7_ day14

description: Patient 7_ day14 post delivery

value: day 14 post delivery


title: Patient 7_ day7

description: Patient 7_ day7 post delivery

value: day 7 post delivery


title: Patient 2_ day14

description: Patient 2_ day14 post delivery


title: Patient 3_ day14

description: Patient 3_ day14 post delivery


title: Patient 6_ day7

description: Patient 6_ day7 post delivery


title: Patient 7_ 96h

description: Patient 7_ 96h post delivery

value: 96h post delivery


title: Patient 3_ day7

description: Patient 3_ day7 post delivery


title: Patient 1_ day14

description: Patient 1_ day14 post delivery


title: Patient 4_ day7

description: Patient 4_ day7 post delivery


title: Patient 4_ day14

description: Patient 4_ day14 post delivery


title: Patient 3_ 96h

description: Patient 3_ 96h post delivery


title: Patient 5_ 96h

description: Patient 5_ 96h post delivery


title: Patient 5_ day7

description: Patient 5_ day7 post delivery


title: Patient 5_ day14

description: Patient 5_ day14 post delivery


title: Patient 2_ 96h

description: Patient 2_ 96h post delivery


title: Patient 2_ day7

description: Patient 2_ day7 post delivery


title: Patient 4_ 96h

description: Patient 4_ 96h post delivery


title: Patient 1_ 96h

description: Patient 1_ 96h post delivery


title: Patient 1_ day7

description: Patient 1_ day7 post delivery


title: Patient 4_ 84h

description: Patient 4_ 84h post delivery

value: 84h post delivery


title: Patient 7_ 84h

description: Patient 7_ 84h post delivery


title: Patient 6_ 84h

description: Patient 6_ 84h post delivery


title: Patient 5_ 84h

description: Patient 5_ 84h post delivery


title: Patient 3_ 84h

description: Patient 3_ 84h post delivery


title: Patient 1_ 84h

description: Patient 1_ 84h post delivery


title: Patient 7_ 72h

description: Patient 7_ 72h post delivery

value: 72h post delivery


title: Patient 2_ 84h

description: Patient 2_ 84h post delivery


title: Digestive gland_pool4_2

city: Legnaro

first: Massimo

last: Milan

state: PD

address: Viale dell'Università 16

department: Dept. of Department of Public Health, Comparative Pathology,and Veterinary Hygiene

country: Italy

institute: University of Padova

description: Pool consisting of 5 digestive glands

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: Array was scanned according to standard Agilent protocol at a resolution of 5 microns modifying default setting to scan the slide twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%)

data_processing: Data processed with FeatureExtraction v9.5 and quantile normalized using R2.6.1 statistical software

organism: Ruditapes philippinarum

source_name: Pool of Ruditapes philippinarum digestive glands sampled in Venice Lagoon

label_protocol: Amplified and labeled according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

extract_protocol: Extracted according to QiAgen RNeasy MiniKit protocol for tissue samples

value: digestive glands


title: Patient 5_ 72h

description: Patient 5_ 72h post delivery


title: Patient 3_ 72h

description: Patient 3_ 72h post delivery


title: Digestive gland_pool3_2

description: Pool consisting of 5 digestive glands


title: Gills_pool2

description: Pool consisting of 5 gills

source_name: Pool of Ruditapes philippinarum gills sampled in Venice Lagoon

value: gills


title: Gills_pool3

description: Pool consisting of 5 gills


title: Patient 1_ 60h

description: Patient 1_ 60h post delivery

value: breast milk fat globule

value: 60h post delivery


title: Patient 2_ 60h

description: Patient 2_ 60h post delivery

value: Female

value: Lean


title: Patient 6_ 72h

description: Patient 6_ 72h post delivery


title: Digestive gland_pool1_2

description: Pool consisting of 5 digestive glands


title: Patient 6_ 48h

description: Patient 6_ 48h post delivery

value: 48h post delivery


title: Digestive gland_pool3

description: Pool 3 consisting of 5 digestive glands

data_processing: Data processed with FeatureExtraction v9.5 and normalized using R2.6.1 statistical software

label: Cyanine 3

source_name: digestive glands sampled in Venice Lagoon


title: Patient 4_ 48h

description: Patient 4_ 48h post delivery


title: Digestive gland_pool2

description: Pool 2 consisting of 5 digestive glands


title: Patient 3_ 60h

description: Patient 3_ 60h post delivery


title: Patient 4_ 72h

description: Patient 4_ 72h post delivery


title: Gills_pool1

description: Pool consisting of 5 gills


title: Patient 2_ 72h

description: Patient 2_ 72h post delivery


title: Patient 7_ 60h

description: Patient 7_ 60h post delivery


title: Patient 5_ 48h

description: Patient 5_ 48h post delivery


title: Patient 1_ 72h

description: Patient 1_ 72h post delivery


title: Patient 6_ 60h

description: Patient 6_ 60h post delivery


title: Digestive gland_pool4

description: Pool 4 consisting of 5 digestive glands


title: Digestive gland_pool1

description: Pool 1 consisting of 5 digestive glands


title: Patient 5_ 60h

description: Patient 5_ 60h post delivery


title: Patient 4_ 60h

description: Patient 4_ 60h post delivery


title: Patient 7_ 48h

description: Patient 7_ 48h post delivery


title: Patient 6_ day14

description: Patient 6_ day14 post delivery


title: Patient 3_ 48h

description: Patient 3_ 48h post delivery


title: Patient 2_ 48h

description: Patient 2_ 48h post delivery


title: Patient 5_ 36h

description: Patient 5_ 36h post delivery

value: 36h post delivery


title: Patient 7_ 36h

description: Patient 7_ 36h post delivery


title: Patient 4_ 12h

description: Patient 4_ 12h post delivery

value: 12h post delivery


title: Patient 3_ 36h

description: Patient 3_ 36h post delivery


title: Patient 6_ 24h

description: Patient 6_ 24h post delivery

value: 24h post delivery


title: Patient 4_ 24h

description: Patient 4_ 24h post delivery


title: Patient 2_ 36h

description: Patient 2_ 36h post delivery


title: Patient 1_ 24h

description: Patient 1_ 24h post delivery


title: Patient 3_ 12h

description: Patient 3_ 12h post delivery


title: Patient 1_ 36h

description: Patient 1_ 36h post delivery


title: Patient 7_ 12h

description: Patient 7_ 12h post delivery


title: Patient 5_ 12h

description: Patient 5_ 12h post delivery


title: Patient 6_ 6h

description: Patient 6_ 6h post delivery

value: 6h post delivery


title: Patient 5_ 24h

description: Patient 5_ 24h post delivery


title: Patient 1_ 48h

description: Patient 1_ 48h post delivery


title: Patient 4_ 6h

description: Patient 4_ 6h post delivery


title: Patient 4_ 36h

description: Patient 4_ 36h post delivery


title: Patient 1_ 12h

description: Patient 1_ 12h post delivery


title: Patient 2_ 12h

description: Patient 2_ 12h post delivery


title: Patient 7_ 24h

description: Patient 7_ 24h post delivery


title: Patient 3_ 24h

description: Patient 3_ 24h post delivery


title: Patient 7_ 6h

description: Patient 7_ 6h post delivery


title: Patient 6_ 36h

description: Patient 6_ 36h post delivery


title: Patient 6_ 12h

description: Patient 6_ 12h post delivery


title: Patient 3_ 6h

description: Patient 3_ 6h post delivery


title: Patient 6_ 96h

description: Patient 6_ 96h post delivery


title: Patient 2_ 24h

description: Patient 2_ 24h post delivery


title: Patient 5_ 6h

description: Patient 5_ 6h post delivery


title: Patient 2_ 6h

description: Patient 2_ 6h post delivery


title: Patient 1_ 6h

description: Patient 1_ 6h post delivery


title: 08B019053_IDC

city: East Melbourne

first: Kylie

middle: L

last: Gorringe

state: Victoria

address: St Andrew's Pl

department: Research Division

country: Australia

institute: Peter MacCallum Cancer Centre

hyb_protocol: standard affymetrix protocol

scan_protocol: standard affymetrix protocol

data_processing:
standard affymetrix protocol
Copy number values were obtained against a baseline of normal DNA samples. The matrix file provides a normalised copy number ratio for each probe and sampls where 2=normal, <1.7 = loss, >2.3 = gain

source_name: IDC FFPE tissue

label_protocol: standard affymetrix protocol

extract_protocol: up to 20x 10 micron FFPE sections were needle microdissected for epithelial cells. Total genomic DNA was isolated using the DNeasy Blood and Tissue Kit (Qiagen) using a modified protocol: Wu L, Patten N, Yamashiro CT, Chui B (2002) Extraction and amplification of DNA from formalin-fixed, paraffin-embedded tissues. Appl Immunohistochem Mol Morphol 10 (3):269-274

treatment_protocol: retrospective cases received standard care

tag: grade

value: Low

tag: er status

value: Positive


title: 08B019650_DCIS

source_name: DCIS FFPE tissue


title: 08B019650_IDC

value: High


title: 09B000695_DCIS

value: Negative


title: 06B028776_DCIS

value: Intermediate


title: 07B010780_DCIS


title: 06B023950_IDC


title: 06B023950_DCIS


title: 08B014029_IDC


title: 08B024416_DCIS


title: 09B000695_IDC


title: 06B023705_IDC


title: 06B026518_IDC


title: 06B028776_IDC


title: 08B019053_DCIS


title: 07B013730_DCIS


title: 07B010780_IDC


title: 08B014029_DCIS


title: 06B026518_DCIS


title: 07B013730_IDC


title: 08B024416_IDC


title: 06B023705_DCIS


title: 06B023202_IDC


title: 06B019681_DCIS


title: H3Cit26 ChIP-chip E2 (replicate A)

city: Ithaca

first: Xuesen

last: Zhang

address: Hungerford Hill RD

institute: Cornell Univ.

hyb_protocol: see NimbleGen website

scan_protocol: see NimbleGen website

data_processing: Genomic data analysis was performed using the statistical programming language R (R Development Core Team). All data processing scripts are available upon request.

source_name: MCF-7 Input DNA from E2

label_protocol: See nimblegen website. Input DNA was labelled with cy3 and ChIP DNA was labelled with cy5.

extract_protocol: MCF-7 breast cancer cells were charcoal-stripped for 3 days, stimulated with 100 nM E2 for 45 min at 37 °C, cross-linked with 1% paraformaldehyde for 10 min at 37°C, and quenched in 125 mM glycine for 5 min at 4°C. The cells were collected by centrifugation and sonicated in lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris•HCl, pH 7.9, 1x protease inhibitor cocktail) to generate chromatin fragments of ~500 bp in length. The material was clarified by centrifugation, diluted 10-fold in dilution buffer (0.5% Triton X-100, 2 mM EDTA, 150 mM NaCl, 20 mM Tris•HCl, pH 7.9, 1x protease inhibitor cocktail), and pre-cleared with protein A-agarose beads. The pre-cleared, chromatin-containing supernatant was used in immunoprecipitation reactions with an antibody against H3Cit26. The immunoprecipitated genomic DNA and a sample of input material were cleared of protein and residual RNA by digestion with proteinase K and RNase H, respectively. The DNA was then extracted with phenol:chloroform:isoamyl alcohol and precipitated with ethanol. The material was then amplified with LM-PCR.

treatment_protocol: 100 nM E2 for 45 min

tag: cell line

tag: chip antibody

source_name: MCF-7 ChIP DNA from E2

tag: vendor

value: Abcam

tag: catalog

tag: lot#


title: 06B023202_DCIS


title: H3Cit26 ChIP-chip E2 (replicate B)

growth_protocol: MCF-7 breast cancer cells were charcoal-stripped for 3 days


title: 06B016411_IDC


title: 06B012714_IDC


title: 06B007268_DCIS


title: 06B019681_IDC


title: 06B012784_DCIS


title: Yeast_MSS11_Deletion_LowN Sample 2

city: Ann Arbor

first: Anuj

last: Kumar

state: Michigan

address: 4063 Kraus Natural Sciences Building 830 N. University Avenue

department: Molecular, Cellular, and Developmental Biology (MCDB)

institute: University of Michigan

hyb_protocol: Microarray hybridization was performed with the Yeast Genome S98 Array (Affymetrix, Inc, Santa Clara, CA). The sample was hybridized to the standard array for 16 hours at 45 degrees Celsius. The standard array was then washed and stained using a fluidics station and then scanned.

scan_protocol: Arrays were scanned using the GeneArray Scanner.

data_processing: The MATLAB Bioinformatics toolbox was used. Specifically, the affygcrma routine was used to perform GC Robust Multi-array Average (GCRMA) on the Affymetrix microarray probe-level data.

organism: Saccharomyces cerevisiae

source_name: Yeast strains in a filamentous genetic background deleted for FLO8 and MSS11 under nitrogen stress

label_protocol: Biotin-labled cRNA was generated from total RNA. Single stranded cDNA was synthesized by reverse transcription using poly (A) RNA present in the starting total RNA sample. Single stranded cDNA was then converted into double stranded cDNA which was extracted with phenol/chloroform and then precipitated with ethanol. An in vitro transcription (IVT) reaction was then carried out in the presence of biotinylated UTP and CTP to produce biotin-labeled cRNA from the double stranded cDNA. cRNA is then fragmented in the presence of heat and Mg++, before hybridization to the arrays.

extract_protocol: PHG was induced in homozygous diploid strains deleted for MSS11 and FLO8, respectively, by standard protocols using low-nitrogen growth media. Briefly, a 50 ml yeast culture was grown at 30 degrees Celsius to an OD600 of 0.6 (cell density of approximately 4.3 x 10^6) in YPD medium (1% yeast extract, 2% peptone, 2% glucose). Cells were harvested by centrifugation and washed twice before being transferred to SLAD medium (2% glucose, 50 micro-m ammonium sulfate, 0.17% yeast nitrogen base without amino acid and ammonium sulfate, supplemented with essential amino acids for nutritional auxotrophies). RNA was prepared according to standard protocols using the Poly(A) Purist kit (Ambion, Austin, TX). RNA concentration and purity were determined spectrophotometrically and by gel electrophoresis.

value: S. cerevisiae Y825/6 (sigma 1278b genetic background)


title: SVTneg1 CAs: 762TuD cell line sample

city: Wildau

first: Christoph

last: Standfuß

address: Bahnhofstraße

department: Bioinformatics

institute: Technical University of Applied Sciences

description:
Cell line SVTneg1 CAs
Klein A, Li N, Nicholson JM, McCormack AA, Graessmann A, Duesberg P. Transgenic oncogenes induce oncogene-independent cancers with individual karyotypes and phenotypes. Cancer Genet Cytogenet. 2010 Jul 15;200(2):79-99.

hyb_protocol: Hybridization conditions: 50C, 60 rpm, 16-18 h; in an hybridization oven (Hybridization Oven 640, Affymetrix). Washing and staining was performed with a fluidics station (GeneChip Fluidics Station 450, Affymetrix), which is controlled by Affymetrix software GeneChip Command Console v2.0.

scan_protocol: Scanning was performed with the GeneChip Scanner 3000 7G (Affymetrix), which is controlled by Affymetrix software GeneChip Command Console v2.0.

data_processing: CEL files were generated with the Affymetrix GeneChip Command Console. Normalization and allele summarization were performed with the Affymetrix Power Tools Software Package. Copy number alteration (CNA) for each SNP was computed by log2 ratios between each sample and a reference dataset.

source_name: 762TuD cell line sample cytosine arabinoside sensitive

label_protocol: Labeling, hybridization and scanning were carried out at Atlas Biolabs GmbH (Berlin, Germany). Genomic DNA was labeled according to the Affymetrix Genome-Wide Human SNP Nsp/Sty 6.0 User Guide (P/N 702504, Rev 3). 500 nanograms of genomic DNA were used as starting material.

extract_protocol: DNA was extracted using Purelink Genomic DNA Kit (K1820, Invitrogen) in accordance with the manufacturers protocol.

tag: phenotype

value: cytosine arabinoside sensitive


title: 06B013071_DCIS


title: 06B016411_DCIS


title: 06B012784_IDC


title: 06B007268_IDC


title: 06B003597_DCIS


title: 06B014753_IDC


title: Yeast_FLO8_Deletion_LowN Sample 2

data_processing: The MATLAB Bioinformatics toolbox was used. Specifically, the affygcrma routine was used to perform GC Robust Multi-array Average (GCRMA) on the Affymetrix microarray probe-level data across six CEL files.

label_protocol: Biotin-labled cRNA was generated from total RNA.  Single stranded cDNA was synthesized by reverse transcription using poly (A) RNA present in the starting total RNA sample. Single stranded cDNA was then converted into double stranded cDNA which was extracted with phenol/chloroform and then precipitated with ethanol.  An in vitro transcription (IVT) reaction was then carried out in the presence of biotinylated UTP and CTP to produce biotin-labeled cRNA from the double stranded cDNA.  cRNA is then fragmented in the presence of heat and Mg++, before hybridization to the arrays.

extract_protocol: PHG was induced in homozygous diploid strains deleted for MSS11 and FLO8, respectively, by standard protocols using low-nitrogen growth media.  Briefly, a 50 ml yeast culture was grown at 30 degrees Celsius to an OD600 of 0.6 (cell density of approximately 4.3 x 10^6) in YPD medium (1% yeast extract, 2% peptone, 2% glucose).  Cells were harvested by centrifugation and washed twice before being transferred to SLAD medium (2% glucose, 50 micro-m ammonium sulfate, 0.17% yeast nitrogen base without amino acid and ammonium sulfate, supplemented with essential amino acids for nutritional auxotrophies).  RNA was prepared according to standard protocols using the Poly(A) Purist kit (Ambion, Austin, TX).  RNA concentration and purity were determined spectrophotometrically and by gel electrophoresis.

tag: strain


title: Yeast_FLO8_Deletion_LowN Sample 3


title: 06B014753_DCIS


title: Yeast_MSS11_Deletion_LowN Sample 1


title: Yeast_FLO8_Deletion_LowN Sample 1


title: 06B012714_DCIS


title: Yeast_FLO8_Deletion_LowN Sample 4


title: 06B000341_IDC


title: NORLAKII: normal NMRI mouse sample

description:
normal
Klein A, Guhl E, Zollinger R, Tzeng YJ, Wessel R, Hummel M, Graessmann M and Graessmann A. Gene expression profiling: cell cycle deregulation and aneuploidy do not cause breast cancer formation in WAP-SVT/t transgenic animals. J Mol Med. 2005 May;83(5):362-76. Klein A, Wessel R, Graessmann M, Jürgens M, Petersen I, Schmutzler R, Niederacher R, Arnold N, Meindl A, Scherneck S, Seitz S and Graessmann A. Comparison of gene expression data from human and mouse breast cancers: Identification of a conserved breast tumor gene set. Int J Cancer. 2007 Aug 1;121(3):683-8.

source_name: normal mammary gland tissue, first day of lacation

tag: genetic background

value: NMRI

tag: tissue

value: normal mammary gland


title: WAP-SVT-t mouse sample LAK IV

description:
transgenic, no tumor
Klein A, Guhl E, Zollinger R, Tzeng YJ, Wessel R, Hummel M, Graessmann M and Graessmann A. Gene expression profiling: cell cycle deregulation and aneuploidy do not cause breast cancer formation in WAP-SVT/t transgenic animals. J Mol Med. 2005 May;83(5):362-76. Klein A, Wessel R, Graessmann M, Jürgens M, Petersen I, Schmutzler R, Niederacher R, Arnold N, Meindl A, Scherneck S, Seitz S and Graessmann A. Comparison of gene expression data from human and mouse breast cancers: Identification of a conserved breast tumor gene set. Int J Cancer. 2007 Aug 1;121(3):683-8.

source_name: WAP-SVT/T mammary gland tissue, first day of lactation

tag: transgene

value: WAP-SVT-t

value: non-malignant hyperplastic mammary glands


title: 583 tumor 1: WAP-SVT/t breast cancer sample

description:
tumor
Klein A, Guhl E, Zollinger R, Tzeng YJ, Wessel R, Hummel M, Graessmann M and Graessmann A. Gene expression profiling: cell cycle deregulation and aneuploidy do not cause breast cancer formation in WAP-SVT/t transgenic animals. J Mol Med. 2005 May;83(5):362-76. Klein A, Wessel R, Graessmann M, Jürgens M, Petersen I, Schmutzler R, Niederacher R, Arnold N, Meindl A, Scherneck S, Seitz S and Graessmann A. Comparison of gene expression data from human and mouse breast cancers: Identification of a conserved breast tumor gene set. Int J Cancer. 2007 Aug 1;121(3):683-8.

source_name: WAP-SVT/T mammary gland tissue, tumor

value: breast cancer tumor


title: 06B013071_IDC


title: WAP-SVT-t mouse sample LAK I


title: 597pos9 tumor: WAP-SVT/t breast cancer sample


title: 06B003597_IDC


title: SWR biological rep2

city: London

first: Sarah

last: Lloyd

address: Queen Square

department: Neurodegenerative Disease

country: United Kingdom

institute: MRC Prion Unit, UCL Institute of Neurology

hyb_protocol: 10 ug of fragmented cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 v2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChip Scanner 3000 (Affymetrix)

data_processing: Data were scaled and normalised using R package Affy from Bioconductor.

source_name: SWR biological rep2

label_protocol: One cycle Target Labeling Assay kit (Affymetrix) according to manufacturer's instructions

extract_protocol: RNA extracted with a Maxi Rneasy kit (Qiagen) followed by an additional DNAase I digest (Qiagen) and clean up step using Mini Rneasey kit (Qiagen) all according to manufacturer's instructions.

value: Brain

value: SWR/OlaHsd


title: SWR biological rep1

source_name: SWR biological rep1


title: SWR biological rep5

source_name: SWR biological rep5


title: SJL biological rep4

source_name: SJL biological rep4

value: SJL/OlaHsd


title: NORLAKIII: normal NMRI mouse sample


title: NZW biological rep4

source_name: NZW biological rep4

value: NZW/OlaHsd


title: SWR biological rep4

source_name: SWR biological rep4


title: SJL biological rep5

source_name: SJL biological rep5


title: H3Cit26 ChIP-chip EtOH (replicate A)

source_name: MCF-7 Input DNA from EtOH

treatment_protocol: EtOH for 45 min

source_name: MCF-7 ChIP DNA from EtOH


title: Pt_hipp_5

city: Dallas

first: Genevieve

last: Konopka

state: TX

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: UT Southwestern Medical Center

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing:
R (expresso), quantile normalization:
bgcorrect.method=mas
normalize.method=quantiles
pmcorrect.method=mas

organism: Pan troglodytes

label_protocol: Affymetrix

extract_protocol: Qiagen Rneasy kit

tag: brain region

value: hipp

tag: sample identifier


title: SVTneg1 CAr: 762TuD cell line sample

description:
Cell line SVTneg1 CAr
Klein A, Li N, Nicholson JM, McCormack AA, Graessmann A, Duesberg P. Transgenic oncogenes induce oncogene-independent cancers with individual karyotypes and phenotypes. Cancer Genet Cytogenet. 2010 Jul 15;200(2):79-99.

source_name: 762TuD cell line sample cytosine arabinoside resistant

value: cytosine arabinoside resistant


title: H3Cit26 ChIP-chip EtOH (replicate B)


title: Pt_FP_6

value: FP


title: SWR biological rep3

source_name: SWR biological rep3


title: NZW biological rep5

source_name: NZW biological rep5


title: SJL biological rep3

source_name: SJL biological rep3


title: Pt_hipp_6


title: SJL biological rep2

source_name: SJL biological rep2


title: Pt_caud_6

value: caud


title: Pt_hipp_4


title: NZW biological rep2

source_name: NZW biological rep2


title: FVB biological rep5

source_name: FVB biological rep5

value: FVB/NHsd


title: NZW biological rep3

source_name: NZW biological rep3


title: 06B000341_DCIS

source_name: DCIS FFPE tissue

value: High

value: Negative


title: FVB biological rep4

source_name: FVB biological rep4


title: Pt_FP_5


title: FVB biological rep2

source_name: FVB biological rep2


title: C57 biological rep5

source_name: C57 biological rep5


title: FVB biological rep3

source_name: FVB biological rep3


title: Pt_FP_3


title: SJL biological rep1

source_name: SJL biological rep1


title: NZW biological rep1

source_name: NZW biological rep1


title: Pt_caud_5


title: Pt_FP_4


title: Pt_hipp_3


title: strain rpoA14, biological rep1

city: Cambridge

first: Christine

last: Santos

address: 77 Massachusetts Ave, 56-422

institute: Massachusetts Institute of Technology

description: Gene expression data from strain rpoA14 in mid-exponential phase

hyb_protocol: Standard Affymetrix protocols were used for hybridization.

scan_protocol: Standard Affymetrix protocols were used for scanning.

data_processing: The data was analyzed using the Affymetrix Gene Chip Operating Software v1.4 using default settings.

organism: Escherichia coli

source_name: Escherichia coli rpoA14

label_protocol: Standard Affymetrix protocols were used for labeling.

growth_protocol: Strains were grown in 50 ml MOPS minimal medium (Teknova) at 37°C with 225 rpm orbital shaking.

extract_protocol: Cultures were harvested at an OD600 of approximately 0.4, and total RNA was extracted using the QIAGEN RNeasy Mini Kit according to the manufacturer’s protocol.

tag: genotype

value: E. coli K12 ΔpheA ΔtyrR lacZ::PLtetO-1-tyrAfbraroGfbr tyrR::PLtetO-1-tyrAfbraroGfbr pHACM-rpoA14


title: Pt_caud_4


title: strain rpoA14, biological rep3


title: C57 biological rep4

source_name: C57 biological rep4


title: strain rpoD3, biological rep3

description: Gene expression data from strain rpoD3 in mid-exponential phase

source_name: Escherichia coli rpoD3

value: E. coli K12 ΔpheA ΔtyrR lacZ::PLtetO-1-tyrAfbraroGfbr tyrR::PLtetO-1-tyrAfbraroGfbr pHACM-rpoD3


title: FVB biological rep1

source_name: FVB biological rep1


title: strain rpoA27, biological rep1

description: Gene expression data from strain rpoA27 in mid-exponential phase

source_name: Escherichia coli rpoA27

value: E. coli K12 ΔpheA ΔtyrR lacZ::PLtetO-1-tyrAfbraroGfbr tyrR::PLtetO-1-tyrAfbraroGfbr pHACM-rpoA27


title: strain rpoA27, biological rep3


title: strain rpoA27, biological rep2


title: Pt_FP_2


title: strain rpoA14, biological rep2


title: strain rpoD3, biological rep2


title: strain rpoD3, biological rep1


title: Pt_hipp_2


title: Pt_hipp_1


title: strain P2, biological rep1

description: Gene expression data from strain P2 in mid-exponential phase

source_name: Escherichia coli P2

value: E. coli K12 ΔpheA ΔtyrR lacZ::PLtetO-1-tyrAfbraroGfbr tyrR::PLtetO-1-tyrAfbraroGfbr


title: Pt_caud_3


title: Hu_hipp_7


title: C57 biological rep3

source_name: C57 biological rep3


title: strain P2, biological rep2


title: strain P2, biological rep3


title: C57 biological rep1

source_name: C57 biological rep1


title: Pt_caud_1


title: Pt_FP_1


title: Hu_caud_7


title: C57 biological rep2

source_name: C57 biological rep2