title: daf-16; daf-2 rsks-1-10

city: Nanjing

first: Di

last: Chen

state: Jiangsu

address: 12 Xuefu Rd, Pukou

department: Model Animal Research Center

institute: Nanjing University

description: This sample is of the daf-16; daf-2 rsks-1 mutant C. elegans. It is the tenth of ten biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Sample hybridization was done according to the manufacturers’ protocol for the 12-plex Gene Expression array platform. 4 μg of each Cy3-labeled sample was loaded onto an array on the 12-plex chip. Hybridization was done overnight on a NimbleGen hybridization system 4 unit at 42°C for 16 hours.

scan_protocol: The 12-plex chip was washed, dried and scanned on a GenePix 4200A scanner at 300PMT, 100POW.

data_processing: Arrays were quantified using the NimbleScan2 software. RMA normalization using the limma package in R (Smyth, 2005 In Bioinformatics and Computational Biology Solutions using R and Bioconductor, V.J.C. Robert Gentleman, Wolfgang Huber, Rafael A. Irizarry and Sandrine Dudoit, ed. New York: Springer.) was used to normalize the expression data.

organism: Caenorhabditis elegans

source_name: C. elegans daf-16; daf-2 rsks-1

label_protocol: 200 ng of total RNA was amplified for each experimental sample (Sigma TransPlex Complete Whole Transcriptome Amplification Kit). 1 μg of ds-cDNA was labeled with Cy3 for each experimental sample (NimbleGen One-Color DNA Labeling Kit). Total RNA extraction, amplification and labeling were randomized across experimental groups.

growth_protocol: Synchronized C. elegans animals were growing at 15C until the late L4 stage and then transferred to 25C with FUDR (10ug / ml) for 48 hours before collection.

extract_protocol: Total RNAs were extracted using the Qiagen miRneasy Mini kit. The concentration and quality of total RNA samples were assessed using a Nanodrop and Agilent’s Bioanalyzer.

tag: genetic background

tag: genotype

value: daf-16; daf-2 rsks-1

tag: phenotype

value: short-lived


title: daf-16; daf-2 rsks-1-9

status: Public on Nov 14 2013

type: RNA

country: China

description: This sample is of the daf-16; daf-2 rsks-1 mutant C. elegans. It is the nineth of ten biological replicates used in this experiment, each from separate cultures.

molecule: total RNA


title: SAMPLE 23 T8_Lilleaa

city: Aarhus

first: Michael

last: Hansen

address: Ny Munkegade 114

country: Denmark

institute: Aarhus University

hyb_protocol: As outlined in the Genisphere Array 50 Protocol Revised version 5 available at http://web.uvic.ca/cbr/grasp/microarray/array.html

scan_protocol: Scanned using a ScanArray scanner (PerkinElmer) at a resolution of 10μm and 90% laser power, manually equilibrating intensity between dyes for each slide using the photomultiplier tube settings.

data_processing: Spots were localized and quantified with the QuantArray 3.0 software (Perkin- Elmer Life Sciences), using the histogram quantification method and keeping the mean value of intensity for each spot. Local background was removed and the data from bad spots were manually excluded from the data set. For each of the two dyes on each array, spots with signal intensities lower than the mean intensity of the empty spots plus twice their standard deviation were flagged as non-expressed. Spots that had no non-expressed flag in at least one of the six studied groups (3 rivers and 2 temperatures) were kept.

organism: Salmo trutta

source_name: Temperature and river effect

label_protocol: Cy5 and Cy3 dyes of the Array50 kit (Genisphere) following the procedures at http://web.uvic.ca/cbr/grasp/microarray/array.html (Genisphere Array 50 Protocol Revised version 5), using 15microgram of RNA per reverse transcription reaction and sunbsequently OPTION 1 Ð concentration of cDNA using Millipore Microcon YM-30 concentrators.

growth_protocol: Common garden experiment in wet lab. Each full-sib family of eggs was divided into two batches, which were incubated at 5 and 8 degrees C in hatching troughs with circulated water, biological filter and temperature control. Each family was placed in separate compartments of hatching boxes, but all families and individuals experienced similar conditions.

extract_protocol: RNA was extracted from whole individuals on ice using the RNA Pure Link Minikit (Invitrogen, Paisley, UK). Each fry was homogenized individually in 0.8ml lysis buffer containing 1% 2-mercaptoethanol using a Tissuelyzer (QIAGEN, Hilden, Germany). Samples were then centrifuged at 2600 g for 5 min and 0.6 ml of the supernatant was transferred to a new 2 ml tube, 0.6 ml Trizol and 0.6 ml chloroform was added, mixed and centrifuged at 13,000 g at 4¡C for 15 min. Then, 800 µl of the upper phase was transferred to a new tube and RNA was extracted according to the manufacturer's recommendations. After RNA extraction, 1 µl of RNase inhibitor (20 units/µl, Ambion, Invitrogen, Paisley, UK) was added to prevent RNA degradation and samples were DNase treated with DNase I, amplification grade (1 unit/µl) (Invitrogen, Paisley, UK) following the manufacturer's recommendation. RNA quantity and integrity was checked on a Nanodrop instrument (ND-1000; Thermo Fisher Scientific Inc., Wilmington, Delaware, USA) and on an Experion automated electrophoresis station using RNA HighSens chips (BIORAD, Copenhagen, Denmark).

tag: tissue

value: Whole larva

tag: river

value: Lilleaa

tag: temperature


title: HCC 12

city: Kanazawa

first: Masao

last: Honda

address: Takara-Machi 13-1

department: Gastroenterology

country: Japan

institute: Kanazawa University

description: HBV moderate

hyb_protocol: according to Honda et al. Hepatology. 2006 Nov;44(5):1122-38, Honda M, et al. Gastroenterology. 2001 Mar;120(4):955-66.

scan_protocol: Quantitative assessment of the signals on the slides was carried out by scanning on a ScanArray 5000 (General Scanning, Watertown, MA, USA) followed by image analysis using GenePix Pro 4.1 (Axon Instruments, Union City, CA, USA).

data_processing: Because the levels of expression of some housekeeping genes were also changed, especially in advanced stages of liver disease, for the  normalization of data we averaged intensities of all spots obtained with  Cy3 and Cy5 in each of the 16 rectangles and adjusted intensity of each  corrected DNA spot as the average intensity ratio Cy5/Cy3 = 1.0. This  global normalization of intensity provided smaller variance of CyS/Cy3  ratio and almost equivalent results to normalization using the housekeeping genes [Honda et al. Hepatology. 2006 Nov;44(5):1122-38, Honda M, et al. Gastroenterology. 2001 Mar;120(4):955-66]. From the 9643 expression data, duplicated genes were averaged and final 8516 non redundant expression results were obtained.

organism: Homo sapiens

source_name: hepatocellular carcinoma (HCC)

label_protocol: As a reference for each microarray analysis, aRNA samples prepared from the normal liver tissue from one of the patients were used. Test RNA samples fluorescently labeled with cyanine (Cy) 5 and reference RNA labeled with Cy3 were used for microarray hybridization.

extract_protocol: Total RNA was isolated from liver biopsy or operated samples using an RNA extraction kit (Micro RNA Extraction Kit, Stratagene, La Jolla, CA, USA). Aliquots of total RNA (5 ug) were subjected to amplification with antisense RNA (aRNA) using a Message AmpTM aRNA kit (Ambion, Austin, TX, USA) as recommended by the manufacturer

treatment_protocol: HCC and non-cancerous liver specimens were obtained from 17 patients with HCV-related HCC and 17 with HBV-related HCC who underwent surgical resection of the liver. For the control normal liver, a surgically obtained tissue sample from a patient who showed no clinical signs of hepatitis was used as described previously

tag: specimen group

value: hepatitis B virus [HBV]-related

value: liver

source_name: normal liver sample from a patient

tag: sample type

value: reference


title: HCC 11

description: HBV moderate


title: HCC 13

description: HBV moderate


title: SAMPLE 28 T5_Lilleaa


title: daf-16; daf-2 rsks-1-6

description: This sample is of the daf-16; daf-2 rsks-1 mutant C. elegans. It is the sixth of ten biological replicates used in this experiment, each from separate cultures.


title: daf-16; daf-2 rsks-1-7

description: This sample is of the daf-16; daf-2 rsks-1 mutant C. elegans. It is the seventh of ten biological replicates used in this experiment, each from separate cultures.


title: HCC 10

description: HBV moderate


title: hypothalamus_1TB_repl5

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Mouse Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.22.0).

label: biotin

organism: Mus musculus

source_name: hypothalamus, tumour-bearing mice, injected with  1 million tumour cells, individual mouse, replicate 5

label_protocol: One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT expression kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands).

growth_protocol: Male CDF1 (BALB/cx DBA/2) mice aged six-to- seven weeks were obtained from Harlan Nederland (Horst, The Netherlands). Animals were individually housed one week before the start of the experiment in a climate-controlled room (12:12 dark-light cycle with a constant room temperature of 21.0±1.0 degrees centigrade). Mice were kept on a standard ad libitum diet based on AIN93M (research Diet Services, Wijk bij Duurstede, The Netherlands) and had free access to tap water.

extract_protocol: Total RNA from the hypothalamus was isolated by using RNeasy Lipid tissue kit (Qiagen, Venlo, The Netherlands). RNA concentrations were measured by absorbance at 260 nm (Nanodrop). RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0). RNA samples were either pooled or analyzed individually.

treatment_protocol: Murine C-26 adenocarcinoma cells were cultured in vitro in RPMI-1640 medium supplemented with 5% fetal calf serum and 1% penicillin–streptomycin. Tumour cells were trypsinized in a sub-confluent state and, after washing, suspended in Hanks’ balanced salt solution (HBSS) at various amounts. On day 0, under general anaesthesia (isoflurane/ N2O/O2), tumour cells in 0.2ml HBSS were inoculated subcutaneously into the right inguinal flank of the mice. Control animals received a sham injection with 0.2 ml HBSS. On day 20 mice were killed and the hypothalamus was removed.

tag: strain

tag: gender

value: male

tag: age

value: hypothalamus

tag: treatment

value: 1 million C26 adenocarcinoma cells


title: daf-16; daf-2 rsks-1-8

description: This sample is of the daf-16; daf-2 rsks-1 mutant C. elegans. It is the eighth of ten biological replicates used in this experiment, each from separate cultures.


title: SAMPLE 22 T5_Lilleaa


title: HCC 9

description: HBV moderate


title: daf-16; daf-2 rsks-1-4

description: This sample is of the daf-16; daf-2 rsks-1 mutant C. elegans. It is the fourth of ten biological replicates used in this experiment, each from separate cultures.


title: daf-16; daf-2 rsks-1-5

description: This sample is of the daf-16; daf-2 rsks-1 mutant C. elegans. It is the fifth of ten biological replicates used in this experiment, each from separate cultures.


title: SAMPLE 20 T5_Lilleaa


title: SAMPLE 19 T8_Lilleaa


title: HCC 8

description: HBV moderate


title: daf-16; daf-2 rsks-1-3

description: This sample is of the daf-16; daf-2 rsks-1 mutant C. elegans. It is the third of ten biological replicates used in this experiment, each from separate cultures.


title: HCC 6

description: HBV moderate


title: HCC 5

description: HBV moderate


title: HCC 4

description: HBV moderate


title: HCC 7

description: HBV moderate


title: SAMPLE 21 T8_Lilleaa


title: SAMPLE 16 T5_Lilleaa


title: hypothalamus_1TB_repl2

source_name: hypothalamus, tumour-bearing mice, injected with  1 million tumour cells, individual mouse, replicate 2


title: hypothalamus_1TB_repl4

source_name: hypothalamus, tumour-bearing mice, injected with  1 million tumour cells, individual mouse, replicate 4


title: hypothalamus_control_repl2

source_name: hypothalamus, control, injected with vehicle only [200ul Hank's Balanced Salt Solution (HBBS)], individual mouse, replicate 2

value: control


title: SAMPLE 17 T8_Lilleaa


title: hypothalamus_control_repl3

source_name: hypothalamus, control, injected with vehicle only [200ul Hank's Balanced Salt Solution (HBBS)], individual mouse, replicate 3


title: hypothalamus_1TB_repl1

source_name: hypothalamus, tumour-bearing mice, injected with  1 million tumour cells, individual mouse, replicate 1


title: SAMPLE 18 T5_Lilleaa


title: hypothalamus_1TB_repl3

source_name: hypothalamus, tumour-bearing mice, injected with  1 million tumour cells, individual mouse, replicate 3


title: SAMPLE 14 T5_Lilleaa


title: daf-16; daf-2 rsks-1-2

description: This sample is of the daf-16; daf-2 rsks-1 mutant C. elegans. It is the second of ten biological replicates used in this experiment, each from separate cultures.


title: HCC 3

description: HBV moderate


title: HCC 2

description: HBV well


title: hypothalamus_control_repl1

source_name: hypothalamus, control, injected with vehicle only [200ul Hank's Balanced Salt Solution (HBBS)], individual mouse, replicate 1


title: daf-2 rsks-1-10

description: This sample is of the daf-2 rsks-1 mutant C. elegans. It is the tenth of ten biological replicates used in this experiment, each from separate cultures.

source_name: C. elegans daf-2 rsks-1

value: daf-2 rsks-1

value: long-lived


title: SAMPLE 15 T8_Lilleaa


title: daf-16; daf-2 rsks-1-1

description: This sample is of the daf-16; daf-2 rsks-1 mutant C. elegans. It is the first of ten biological replicates used in this experiment, each from separate cultures.


title: daf-2 rsks-1-8

description: This sample is of the daf-2 rsks-1 mutant C. elegans. It is the eighth of ten biological replicates used in this experiment, each from separate cultures.


title: SAMPLE 13 T8_Lilleaa


title: hypothalamus_1TB_pooled

source_name: hypothalamus, tumour-bearing mice, injected with  1 million tumour cells, pooled RNA from 5 animals


title: hypothalamus_control_pooled

source_name: hypothalamus, control, injected with vehicle only [200ul Hank's Balanced Salt Solution (HBBS)], pooled RNA from 4 animals


title: daf-2 rsks-1-9

description: This sample is of the daf-2 rsks-1 mutant C. elegans. It is the nineth of ten biological replicates used in this experiment, each from separate cultures.


title: daf-2 rsks-1-7

description: This sample is of the daf-2 rsks-1 mutant C. elegans. It is the seventh of ten biological replicates used in this experiment, each from separate cultures.


title: HCC 1

description: HBV well


title: daf-2 rsks-1-6

description: This sample is of the daf-2 rsks-1 mutant C. elegans. It is the sixth of ten biological replicates used in this experiment, each from separate cultures.


title: SAMPLE 12 T5_Lilleaa


title: SAMPLE 11 T8_Lilleaa


title: SAMPLE 8 T5_Lilleaa


title: SAMPLE 10 T5_Lilleaa


title: SALK_033618C_3h_NaCl_rep2

city: Harbin

first: Yujia

last: Liu

address: 26 Hexing Road

institute: Northeast Forestry University

description: Gene expression after 3h in NaCl-treatmented Arabidopsis seedlings of SALK_033618C

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), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit. Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

data_processing: The scanned images were analyzed with R-software (The R Project for Statistical Computing, http:// www. r-project.org/) of SAS system statistics to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Arabidopsis thaliana

source_name: SALK_033618C, 3h, NaCl, replicate 2

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: AtbHLH112-overexpression plants and mutant (SALK_033618C) plants seedlings grown in freshwater-irrigated pots filled with the artificial soil (Vermiculite: perlite: soil = 3:1:1, v/v) in a relative humidity of 55% under long-day conditions (16-h light/8-h dark)at 22°C (±2°C).

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Four-week-old seedlings of T3 homozygous lines of the AtbHLH112-overexpression plants and mutant (SALK_033618C) plants with or without 150 mM NaCl treatment for 3 hours. The whole seedlings including root and shoot were harvested and pooled for each treatment before freezing in liquid nitrogen and storage at -80ºC for RNA isolation.

value: whole seedling

value: Four-week-old

tag: genotype/variation


title: daf-2 rsks-1-5

description: This sample is of the daf-2 rsks-1 mutant C. elegans. It is the fifth of ten biological replicates used in this experiment, each from separate cultures.


title: SAMPLE 7 T8_Lilleaa


title: WT Treg

city: Madison

first: Eui Ho

last: Kim

state: Wisconsin

address: 2015 Linden Dr.

department: Pathobiological Sciences

country: USA

institute: University of Wisconsin-Madison

description:
Gene expression
male, WT B6, 6 week old

hyb_protocol: hybridization and wash were done according to the Illumina's manual. (Hyb:Incubation at 58c for at least 14 hours)

scan_protocol: by Illumina iScan

data_processing: GeneSpring

source_name: WT B6 spleen

label_protocol: Labeling procedures were carred out according to the standard protocol from Illumina.

extract_protocol: Rneasy RNA extraction kit (Qiagen) was used.

value: WT

tag: cell type

value: CD4+ CD25+ GITR+ (Treg) cells


title: AtbHLH112_3h_NaCl_rep2

description: Gene expression after 3h in NaCl-treatmented Arabidopsis seedlings of AtbHLH112

source_name: AtbHLH112, 3h, NaCl, replicate 2


title: SALK_033618C_3h_NaCl_rep1

source_name: SALK_033618C, 3h, NaCl, replicate 1


title: mtf1-4, biological rep 1

city: West Lafayette

first: Nagesh

last: Sardesai

state: IN

address: 201 W. State St.

department: Biological Sciences

institute: Purdue University

description: Gene expression data from roots

hyb_protocol: Hybridization was carried out according to the Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).

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

data_processing: The data were analyzed employing the software packages "Biobase" and "affy" in Bioconductor.

source_name: mtf1-4 roots

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: 14-day old Arabidopsis seedlings were transferred to B5 liquid medium and grown at 23C with shaking at 100 rpm for 12 days.

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

treatment_protocol: Roots were harvested from wild-type Col0 and mutant mtf1-1 and mtf1-4 plants and stored at -80C till RNA extraction.

value: root

tag: ecotype


title: Bach2 KO Treg

description:
Gene expression
male, Bach2 KO, 7 week old

source_name: Bach2 KO spleen

value: Bach2 KO


title: SALK_033618C_3h_NaCl_rep3

source_name: SALK_033618C, 3h, NaCl, replicate 3


title: SAMPLE 5 T8_Lilleaa

source_name: Temperature and river effect

value: Whole larva


title: mtf1-1, biological rep 3

description: Gene expression data from roots

source_name: mtf1-1 roots


title: AtbHLH112_3h_NaCl_rep3

source_name: AtbHLH112, 3h, NaCl, replicate 3


title: SAMPLE 6 T5_Lilleaa

value: Lilleaa


title: daf-2 rsks-1-4

description: This sample is of the daf-2 rsks-1 mutant C. elegans. It is the fourth of ten biological replicates used in this experiment, each from separate cultures.


title: daf-2 rsks-1-2

description: This sample is of the daf-2 rsks-1 mutant C. elegans. It is the second of ten biological replicates used in this experiment, each from separate cultures.


title: daf-2 rsks-1-3

description: This sample is of the daf-2 rsks-1 mutant C. elegans. It is the third of ten biological replicates used in this experiment, each from separate cultures.


title: AtbHLH112_3h_NaCl_rep1

source_name: AtbHLH112, 3h, NaCl, replicate 1


title: mtf1-4, biological rep 3

description: Gene expression data from roots


title: SAMPLE 9 T8_Lilleaa


title: daf-2-9

description: This sample is of the daf-2 mutant C. elegans. It is the eighth of nine biological replicates used in this experiment, each from separate cultures.

source_name: C. elegans daf-2


title: daf-2-10

description: This sample is of the daf-2 mutant C. elegans. It is the nineth of nine biological replicates used in this experiment, each from separate cultures.


title: mtf1-1, biological rep 2

description: Gene expression data from roots


title: mtf1-4, biological rep 2

description: Gene expression data from roots


title: SAMPLE 4 T5_Lilleaa


title: SALK_033618C_3h_H2O_rep3

description: Gene expression after 3h in H2O-treatmented Arabidopsis seedlings of SALK_033618C

source_name: SALK_033618C, 3h, H2O, replicate 3


title: daf-2-8

description: This sample is of the daf-2 mutant C. elegans. It is the seventh of nine biological replicates used in this experiment, each from separate cultures.


title: SAMPLE 3 T8_Lilleaa


title: daf-2-7

description: This sample is of the daf-2 mutant C. elegans. It is the sixth of nine biological replicates used in this experiment, each from separate cultures.


title: mtf1-1, biological rep 1

description: Gene expression data from roots


title: daf-2 rsks-1-1

description: This sample is of the daf-2 rsks-1 mutant C. elegans. It is the first of ten biological replicates used in this experiment, each from separate cultures.


title: Col0, biological rep 3

description: Gene expression data from roots

source_name: Col0 roots

value: wild type


title: SAMPLE 2 T5_Lilleaa


title: SALK_033618C_3h_H2O_rep1

source_name: SALK_033618C, 3h, H2O, replicate 1


title: Col0, biological rep 2

description: Gene expression data from roots


title: AtbHLH112_3h_H2O_rep2

description: Gene expression after 3h in H2O-irrigated Arabidopsis seedlings of AtbHLH112

source_name: AtbHLH112, 3h, H2O, replicate 2


title: AtbHLH112_3h_H2O_rep3

source_name: AtbHLH112, 3h, H2O, replicate 3


title: SALK_033618C_3h_H2O_rep2

source_name: SALK_033618C, 3h, H2O, replicate 2


title: AtbHLH112_3h_H2O_rep1

source_name: AtbHLH112, 3h, H2O, replicate 1


title: daf-2-6

description: This sample is of the daf-2 mutant C. elegans. It is the fifth of nine biological replicates used in this experiment, each from separate cultures.


title: WT, TDM, 3

city: Bunkyo-ku

first: Chikara

last: Komiya

state: Tokyo

address: 1-5-45 Yushima

department: Molecular Endocrinology and Metabolism

institute: Tokyo Medical and Dental University

hyb_protocol: Following fragmentation, aRNA were hybridized on Mouse Genome 430 2.0 using Hybridization oven 640.   Gene Chips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Gene Chip Scanner 3000.

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 500.

source_name: WT macrophages stimulated with TDM

label_protocol: Biotinylated aRNA were prepared according to Gene Chip 3' IVT Express Kit aRNA amplification procedure and Gene Chip 3' IVT Express KitUse Manual p/N 702646 Rev.1

extract_protocol: Extraction of total RNA was performed using RNeasy Plus Universal Mini Kit.

treatment_protocol: Peritoneal macrophages from WT and Mincle KO mice were stimulated  by TDM (10 μg/well) or  vehicle (isopropanol) for 24 h.

value: Peritoneal macrophages

value: female

value: 12 weeks


title: KO, TDM, 2

source_name: KO macrophages stimulated with TDM

value: Mincle KO


title: Pooled kidney_wild type_biological replicate 2

city: Scarborough

first: Jennifer

last: Fetting

state: ME

address: 81 Research Dr.

institute: Maine Medical Center Research Institute

description: gene expression data from pooled E14.5 wild type mouse kidneys

hyb_protocol: Samples were injected into arrays and placed in the Affymetrix Genechip® Hybridization Oven 640 at 45° C and 60 RPM for 17 hours overnight.  Arrays were stained using the Affymetrix Genechip® Fluidics Station 450

scan_protocol: Arrays were scanned with the Affymetrix Genechip® Scanner 3000.

data_processing: Microarray data was analyzed with XRAY software (Biotique Systems Inc). Genes with at least 4 probes and a P-value of less than 0.01 were selected for all analyses.

source_name: E14.5 wild type kidneys

label_protocol: An RNA input of 50ng was used to generate cDNA through the First Strand and Second Strand synthesis reactions of the Ovation® Pico WTA System from NuGEN.  The cDNA samples were then purified using an Agencourt® RNAClean® XP magnetic bead protocol.  Following purification, samples were amplified using SPIA reagents from the Ovation® Pico WTA System from NuGEN.  A second cDNA purification is performed using an Agencourt® RNAClean® XP magnetic bead protocol.  Sample concentrations were determined using a 33ug/mL/A260 constant on a Nanodrop 1000 Spectrophotometer.      Approximately 3.5ug of SPIA amplified cDNA was used to generate sense-target cDNA with the WT-Ovation™ Exon Module kit from NuGEN.  Sense-target cDNA samples were then purified using Zymo Research DNA Clean spin columns.  Sample concentrations were determined using a 33ug/mL/A260 constant on a Nanodrop 1000 Spectrophotometer.  Approximately 5ug of cDNA generated using the Ovation® Pico WTA System V2 was fragmented and labeled using the Encore® Biotin Module from NuGEN.  Efficiency of the biotin labeling reaction was verified using NeutrAvidin (10mg/mL) with a gel-shift assay.

extract_protocol: Kidneys were dissected from 3 Foxd1+/- intercross litters. 2 pairs of kidneys from different litters were pooled to generate each biological replicate.

value: kidneys


title: daf-2-3

description: This sample is of the daf-2 mutant C. elegans. It is the third of nine biological replicates used in this experiment, each from separate cultures.


title: Pooled kidney_wild type_biological replicate 3


title: KO, TDM, 1


title: SAMPLE 1 T8_Lilleaa


title: WT, TDM, 2


title: Col0, biological rep 1

description: Gene expression data from roots


title: daf-2-1

description: This sample is of the daf-2 mutant C. elegans. It is the first of nine biological replicates used in this experiment, each from separate cultures.


title: WT, TDM, 1


title: Pooled kidney_wild type_biological replicate 1


title: rsks-1-8

description: This sample is of the rsks-1 mutant C. elegans. It is the seventh of nine biological replicates used in this experiment, each from separate cultures.

source_name: C. elegans rsks-1


title: Pooled kidney_foxd1null_biological replicate 3

description: gene expression data from pooled E14.5 Foxd1 null mouse kidneys

source_name: E14.5 Foxd1 null kidneys

value: Foxd1 null


title: daf-2-2

description: This sample is of the daf-2 mutant C. elegans. It is the second of nine biological replicates used in this experiment, each from separate cultures.


title: KO, vehicle, 2

source_name: KO macrophages stimulated with vehicle


title: Pooled kidney_foxd1null_biological replicate 2


title: KO, vehicle, 1


title: Pooled kidney_foxd1null_biological replicate 1


title: rsks-1-6

description: This sample is of the rsks-1 mutant C. elegans. It is the fifth of nine biological replicates used in this experiment, each from separate cultures.


title: rsks-1-2

description: This sample is of the rsks-1 mutant C. elegans. It is the second of nine biological replicates used in this experiment, each from separate cultures.


title: WT, vehicle, 3

source_name: WT macrophages stimulated with vehicle


title: KO, vehicle, 3


title: rsks-1-4

description: This sample is of the rsks-1 mutant C. elegans. It is the fourth of nine biological replicates used in this experiment, each from separate cultures.


title: rsks-1-3

description: This sample is of the rsks-1 mutant C. elegans. It is the third of nine biological replicates used in this experiment, each from separate cultures.


title: rsks-1-10

description: This sample is of the rsks-1 mutant C. elegans. It is the nineth of nine biological replicates used in this experiment, each from separate cultures.


title: rsks-1-7

description: This sample is of the rsks-1 mutant C. elegans. It is the sixth of nine biological replicates used in this experiment, each from separate cultures.


title: hypothalamus_control

hyb_protocol: Hybridization of 5.5μg labelled cDNA was done overnight for 17 hours, at 60 rpm, at 45ºC in a Hybridization Oven 640 (Affymetrix). The protocol was conducted as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5). Washing and staining of the arrays were done on an Affymetrix 450 fluidics station using the protocol FS450_0001, as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5).

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).

source_name: hypothalamus, control, injected with vehicle only [200ul Hank's Balanced Salt Solution (HBBS)], pooled RNA from 4 animals

extract_protocol: Total RNA from the hypothalamus was isolated by using RNeasy Lipid tissue kit (Qiagen, Venlo, The Netherlands). RNA concentrations were measured by absorbance at 260 nm (Nanodrop). RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0). Equal amounts of RNA were pooled and analysed by microarray.

value: male

value: hypothalamus

value: control


title: WT, vehicle, 2


title: N2-10

description: This sample is of wild-type C. elegans. It is the nineth of nine biological replicates used in this experiment, each from separate cultures.

source_name: C. elegans N2

value: normal lifespan


title: hypothalamus_0.5TB_pooled

source_name: hypothalamus, tumour-bearing mice, injected with  0.5 million tumour cells, pooled RNA from 4 animals

value: 0.5 million C26 adenocarcinoma cells


title: rsks-1-9

description: This sample is of the rsks-1 mutant C. elegans. It is the eighth of nine biological replicates used in this experiment, each from separate cultures.

value: long-lived


title: hypothalamus_1TB_pooled

source_name: hypothalamus, tumour-bearing mice, injected with  1 million tumour cells, pooled RNA from 3 animals

value: 1 million C26 adenocarcinoma cells


title: rsks-1-1

description: This sample is of the rsks-1 mutant C. elegans. It is the first of nine biological replicates used in this experiment, each from separate cultures.


title: hypothalamus_2TB_pooled

source_name: hypothalamus, tumour-bearing mice, injected with  2 million tumour cells,  RNA from 1 animal

value: 2 million C26 adenocarcinoma cells


title: Wild type rep5

city: Madrid

first: Daniel

last: Muñoz

state: Madrid

address: Calle Melchor Fernandez Almagro 3

department: Molecular Oncology

country: Spain

institute: CNIO

hyb_protocol: Labeled samples were hybridized to Mouse Gene Expression G3 8x60K (Agilent microarray design ID 028005, P/N G4852A)

scan_protocol: Processed Microarrays were scanned on a G2565C DNA microarray scanner (Agilent) and images were analyzed with Agilent Feature Extraction Software (version 10.1.1), which performed feature quantification and additive detrend correction.

data_processing: Microarray background subtraction was carried out using normexp method. Normalization was performed using quantiles. Differentially expressed genes were obtained by applying linear models with R limma package {Smyth GK, Michaud J and Scott HS. (2005). Use of within-array replicate spots for assessing differential expression in microarray experiments. Bioinformatics 21: 2067-2075.} (Bioconductor project, http://www.bioconductor.org). To account for multiple hypotheses testing, the estimated significance level (p value) was adjusted using Benjamini & Hochberg False Discovery Rate (FDR) correction.

source_name: mesonephric tubules

label_protocol: Hybridization chamber type: SureHyb hybridization chamber (Agilent). Quantity of labeled extract used: 600 ng. Volume: 50 µL. Temperature (ºC): 65. Duration: 17 hours.

extract_protocol: Total RNA from mycrodissections was extracted using the Arcturus Pico Pure RNA isolation Kit (Life Technologies) following the manufacturer’s instructions.

treatment_protocol: Frozen cryosections from WT and p21-/- embryos were obtained and stained with 0.5% toluidine blue (Sigma-Aldrich) for 10 seconds and then where washed in pure ethanol and water 20 seconds each

value: Wild type


title: p21KO -/- rep3

value: p21 knockout


title: N2-7

description: This sample is of wild-type C. elegans. It is the eighth of nine biological replicates used in this experiment, each from separate cultures.

value: wild type


title: control chondrocytes, biological rep 2

city: Los Angeles

first: Lick Pui

last: Lai

state: CA

address: 1425 San Pablo St, 3rd fl

institute: University of Southern California

description: Gene expression data from postnatal day 30 control mouse growth plate chondrocytes

hyb_protocol: 5.5 mg of single-strand DNA was fragmented and labbeled before hybridization for 17 hr at 45C on Mouse 1.0 Gene ST array. Arrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned with the GeneChip Scanner 3000 7G.

data_processing: Data were analyzed with dChip with default analysis setting.

source_name: postnatal day 30 control mice

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 300ng total RNA (Ambion WT expression kit protocol)

extract_protocol: Total RNA was isolated with Rneasy mini kit from Qiagen

tag: organ

value: hindlimb growth plate

tag: background strain

value: mixed FVB, 129S6 and C57CL/6


title: WT, vehicle, 1

value: Peritoneal macrophages

value: WT

value: female

value: 12 weeks


title: p21KO -/- rep2


title: mutant chondrocytes, biological rep 1

description: Gene expression data from postnatal day 30 mutant mouse growth plate chondrocytes

source_name: postnatal day 30 Lkb1 mutant mice


title: mutant chondrocytes, biological rep 3


title: control chondrocytes, biological rep 3


title: N2-6

description: This sample is of wild-type C. elegans. It is the seventh of nine biological replicates used in this experiment, each from separate cultures.

tag: genetic background


title: N2-3

description: This sample is of wild-type C. elegans. It is the fourth of nine biological replicates used in this experiment, each from separate cultures.

tag: genotype


title: Wild type rep4

tag: phenotype


title: N2-8

description: This sample is of wild-type C. elegans. It is the third of nine biological replicates used in this experiment, each from separate cultures.


title: N2-5

description: This sample is of wild-type C. elegans. It is the sixth of nine biological replicates used in this experiment, each from separate cultures.


title: N2-4

description: This sample is of wild-type C. elegans. It is the fifth of nine biological replicates used in this experiment, each from separate cultures.


title: p21KO -/- rep1


title: mutant chondrocytes, biological rep 2


title: Wild type rep3


title: N2-2

description: This sample is of wild-type C. elegans. It is the second of nine biological replicates used in this experiment, each from separate cultures.


title: Wild type rep2


title: N2-1

description: This sample is of wild-type C. elegans. It is the first of nine biological replicates used in this experiment, each from separate cultures.


title: Wild type rep1


title: Vehicle treatment, 7 hours (replication 2)

status: Public on Nov 13 2013

first: Kaoru

last: Mogushi

address: 2-1-1 Hongo

department: Intractable Disease Research Center

institute: Juntendo University

description: Gene expression profile of lung tissue

hyb_protocol: Hybridization and signal detection of  Mouse Gene 1.0 ST Arrays (Affymetrix) was performed following the manufacturer's instruction using the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: The data was normalized by robust multichip analysis (RMA) using R/Bioconductor.

source_name: Lung tissue

label_protocol: The cDNA was prepared using GeneChip WT Terminal Labeling Kit (Affymetrix).

extract_protocol: Total RNA was extracted from tissue specimens using RNeasy kit (Qiagen, Hilden, Germany). Integrity of obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: For the intratracheal administration of mepenzolate, mice were maintained under anesthesia with chloral hydrate (500 mg/kg) and mepenzolate in PBS was administered via micropipette.

value: Vehicle

tag: time


title: H3-hpr1∆ asyn

type: genomic

city: Seville

first: Andrés

last: Aguilera

address: Av. Américo Vespucio 24

department: Genome BIology

institute: CABIMER, Universidad de Sevilla

hyb_protocol: Approximately 10 μg of DNA was hybridzed per array using the Affymetrix hybridization kit. The arrays were hybridized for 16 hours at 45° at 60 rpm using an Affymetrix hybridization oven. The probe was removed from these arrays and reused to hybridize the remaining three arrays.

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000 7G.

data_processing:
Primary data analyses were carried out using the Affymetrix TAS 1.1.02 software to obtain hybridization intensity, signal log2 ratio value and change P-value for each locus. For the discrimination of positive and negative signals for the binding, we compared the chromatin-immunoprecipitated fraction with the supernatant fraction by using three criteria. First, the reliability of strength of signal was judged by detection of signal log2 ratio of each locus (log2 ratio ≥ 0.75). Second, the reliability of binding ratio was judged by change P-value (P ≤ 0.01). Third, clusters consisting of at least seven contiguous probe-sets (max. gap 250bp, min run. 30bp) that filled the above two criteria were selected.

Results file description: Locus identification, raw signal intensity, detection signal log ratio, and change p-value was obtained using the Affymetrix TAS 1.1.02 software.

label: Biotin

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: H3 ChIP DNA from HPBAR-1D, asynchronous culture

label_protocol: Chromatin-immunoprecipitated DNA was purified and amplified by random priming as described (Katou et al. 2003): A total of 10 μg of amplified DNA was digested with DNaseI to a mean size of 100 bp and purified, and the fragments were end-labeled with Biotin-N6-ddATP.

growth_protocol: Yeast cells were grown in YPD to mid-log phase at 25°C.

extract_protocol: ChIP was carried out as previously described (Katou et al. 2003, 2006): We disrupted 1.5 × 10^7 cells by Multi-beads shocker (MB400U, Yasui Kikai) using glass beads. Anti-Histone H3 polyclonal antibody ab1791 (Abcam, Serotec) and anti-phospho-Histone H3 (Ser10) polyclonal 06-570 (Millipore) were used for ChIP.

value: MATa ade2-1 ura3 leu2-3,112 his3-11,15 can1-100, bar1∆::HYG, hpr1∆::HIS3

tag: cell cycle stage

value: asynchronous

tag: chip antibody

source_name: Input DNA from HPBAR-1D, asynchronous culture


title: KO, TDM, 3

source_name: KO macrophages stimulated with TDM

tag: tissue

value: Mincle KO


title: control chondrocytes, biological rep 1


title: Vehicle treatment, 7 hours (replication 1)

description: Gene expression profile of lung tissue


title: Vehicle treatment, 25 hours (replication 2)

description: Gene expression profile of lung tissue


title: H3-WT asyn

source_name: H3 ChIP DNA from WBAR1, asynchronous culture

source_name: Input DNA from WBAR1, asynchronous culture


title: daf-2-5

description: This sample is of the daf-2 mutant C. elegans. It is the fourth of nine biological replicates used in this experiment, each from separate cultures.

source_name: C. elegans daf-2


title: H3S10P-hpr1∆ S-rep1

description: This Sample represents 2 replicates.

source_name: H3S10P ChIP DNA from HPBAR-1D, S-phase culture

treatment_protocol: Cells were released from G1 into 0.2 M HU. Samples were collected after 1hr and processed for ChIP.

value: S

source_name: Input DNA from HPBAR-1D, S-phase culture


title: NK-DC, 0 hr

city: Brescia

first: Pascal

last: Seeger

address: Viale Europa 11

department: Department of Molecular and Translational Medicine

country: Italy

institute: University of Brescia

description: Control

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://sabiosciences.com/pcrarraydataanalysis.php.
For the normalization uses the housekeeping gene HPRT1 was used.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Fold Change worksheet reports test/control (i.e., NK-DC(2 hrs)/NK-DC(0 hr)) ratios.

label: SYBR Green

source_name: Monocyte-derived immature dendritic cell and IL-15-activated natural killer cells

label_protocol: PCR assays were performed using the Human Common Cytokines RT² Profiler™ PCR Array (Qiagen) following the Manufacturer’s instructions. Reverse transcription was performed from 1000 ng total RNA using the RT2 First Strand Kit (SA Biosciences). Quantitative real-time PCR were performed (iCycler™; Bio-Rad) with 40 cycles at 95 oC for 15 seconds and 60 oC for 60 seconds.

extract_protocol: Total RNA was extracted with the RNeasy Mini Kit (Qiagen).

tag: cell types

value: immature dendritic cell and activated natural killer cells

tag: cell

value: cell ratio:NK:DC ratio = 1:1

value: 0 hr


title: NK-DC, 2 hrs

description: Test

value: 2 hrs


title: Vehicle treatment, 25 hours (replication 1)

description: Gene expression profile of lung tissue


title: Mepenzolate treatment, 7 hours (replication 2)

description: Gene expression profile of lung tissue

value: Mepenzolate


title: NK-DC, 6 hrs

description: Test

value: 6 hrs


title: StromaLTbR-KO_fresh_rep2

city: Moscow

first: Marina

middle: Alekseevna

last: Afanasyeva

address: Vavilova 32

country: Russia

institute: Engelhardt Institute of Molecular Biology, RAS

description: H

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: After background substitution the data were normalized using cubic spline normalization with Genome Studio

source_name: Mouse spleen

label_protocol: Biotinylated cRNA was prepared with Illumina® TotalPrep™ RNA Amplification Kit  (Ambion®)

extract_protocol: Total RNA was extracted with TRIzol. RNA was quantified using Nanodrop and its quality was assessed by Agilent Total RNA 6000 chip.

value: splenic stroma

tag: strain

value: LTbR-/-


title: StromaWT_cultured_rep2

description:
Adherent cells from total spleen grinded with scissors were cultured in full DMEM (10%FBS) and used for RNA isolation at week 3-4 of culture (passage 2-3).
B

value: LTbR+/+


title: H3S10P-hpr1∆ G1-rep1

description: This Sample represents 2 replicates.

source_name: H3S10P ChIP DNA from HPBAR-1D, G1 arrested culture

treatment_protocol: Cell synchronization in G1 was accomplished by treatment of exponentially growing cells with 3µg/ml alpha-factor pheromone for 2.5 h.

source_name: Input DNA from HPBAR-1D, G1 arrested culture


title: Mepenzolate treatment, 7 hours (replication 1)

description: Gene expression profile of lung tissue


title: Mepenzolate treatment, 25 hours (replication 1)

description: Gene expression profile of lung tissue


title: SplenocytesWT_rep1

description: E

value: splenocyte


title: StromaLTbR-KO_fresh_rep1

description: G


title: StromaWT_cultured_rep1

description:
Adherent cells from total spleen grinded with scissors were cultured in full DMEM (10%FBS) and used for RNA isolation at week 3-4 of culture (passage 2-3).
A


title: StromaWT_fresh_rep1

description: C


title: H3S10P-WT S-rep1

description: This Sample represents 2 replicates.

source_name: H3S10P ChIP DNA from WBAR1, S-phase culture

source_name: Input DNA from WBAR1, S-phase culture


title: H3S10P-WT G1-rep1

description: This Sample represents 2 replicates.

source_name: H3S10P ChIP DNA from WBAR1, G1 arrested culture

source_name: Input DNA from WBAR1, G1 arrested culture


title: non CD24-CD44+, ALDH+ flow sorted cells from SUM159 cell line, biological rep 2

city: Houston

first: yang

last: CONG

state: TX

address: 6565 Fannin St.,

department: Department of Systems Medicine and Bioengineering

institute: Houston Methodist Research Institution

description: cells from SUM159 cell line were flow sorted to select for CD24-CD44+ cells and compared with non-CD24-CD44+ cells; cells from SUM159 cell line were flow sorted to select for ALDH+ cells and compared with ALDH- cells

hyb_protocol: Gene expression analyses used Affymetrix U133 Plus 2.0 human oligonucleotide microarrays. Preparation of cRNA, hybridizations, washes and detection were done as recommended by the supplier.

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner (Agilent).

data_processing: Expression data were analyzed by the Robust Multi-array Average method (RMA) in R using Bioconductor and associated packages.

source_name: SUM159, non-CD24-CD44+, ALDH+

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

extract_protocol: Total RNA was isolated using RNeasy Micro Kit (Qiagen, Valencia, CA), and total RNA with enriched miRNA was isolated using miRNeasy mini Kit, according to the manufacturer’s instructions.

tag: cell line

tag: aldh+

value: ALDH+


title: non CD24-CD44+, ALDH+ flow sorted cells from SUM149 cell line, biological rep 2

description: cells from SUM149 cell line were flow sorted to select for CD24-CD44+ cells and compared with non-CD24-CD44+ cells; cells from SUM149 cell line were flow sorted to select for ALDH+ cells and compared with ALDH- cells

source_name: SUM149, non-CD24-CD44+, ALDH+


title: StromaWT_fresh_rep2

description: D


title: Mepenzolate treatment, 25 hours (replication 2)

description: Gene expression profile of lung tissue

source_name: Lung tissue

tag: treatment


title: CD24-CD44+, ALDH+ flow sorted cells from SUM159 cell line, biological rep 2


title: non CD24-CD44+, ALDH+ flow sorted cells from MCF7 cell line

description: cells from MCF7 cell line were flow sorted to select for CD24-CD44+ cells and compared with non-CD24-CD44+ cells; cells from MCF7 cell line were flow sorted to select for ALDH+ cells and compared with ALDH- cells

source_name: MC7, non-CD24-CD44+, ALDH+


title: non-CD24-CD44+, ALDH- flow sorted cells from SUM149 cell line, biological rep 1

source_name: SUM149, non-CD24-CD44+, ALDH-

value: ALDH-


title: CD24-CD44+, ALDH- flow sorted cells from SUM149 cell line, biological rep 1


title: CD24-CD44+, ALDH- flow sorted cells from SUM159 cell line, biological rep 1


title: CD24-CD44+, ALDH+ flow sorted cells from SUM149 cell line, biological rep 2


title: non-CD24-CD44+, ALDH- flow sorted cells from SUM159 cell line, biological rep 1

source_name: SUM159, non-CD24-CD44+, ALDH-


title: non-CD24-CD44+, ALDH- flow sorted cells from normal breast cells of patient

description: cells from normal breast cells of patient were flow sorted to select for CD24-CD44+ cells and compared with non-CD24-CD44+ cells; cells from normal breast cells of patient were flow sorted to select for ALDH+ cells and compared with ALDH- cells

source_name: human normal breast, non-CD24-CD44+, ALDH-


title: SSC rep 1

city: Seoul

first: LIM

last: JUNG JIN

address: 606-5 Yeoksam-dong, Gangnam-gu

department: Fertility Center of CHA Gangnam Medical Center

country: South Korea

institute: CHA University

description: Gene expression after 14 days cultured SSCs set 1

hyb_protocol: After the labeled RNAs were placed in an Agilent SurePrint G3 Human Gene Expression 8x60K Microarray (Agilent Technologies) and covered with a Gasket 8-plex slide (Agilent Technologies), the slides were hybridized for 17 hr at 65°C.

scan_protocol: The arrays were analyzed on an Agilent scanner using the associated software.

data_processing: The gene expression levels were calculated using Feature Extraction v10.7.3.1 (Agilent Technologies).

source_name: Spermatogonial Stem Cells from testis replicate 1

label_protocol: The Cy3-labeled RNAs were resuspended in 50 μl of hybridization solution (Agilent Technologies).

extract_protocol: Each total RNA sample (200 ng) obtained from the ESC-derived PGC-like cells and testis-derived SSCs were labeled and amplified using the Low Input Quick Amp Labeling kit (Agilent Technologies, Palo Alto, CA).

treatment_protocol: hESCs cultured in EB medium for 3 days and re-cultured for 4 additional days in EB medium with BMP4 and RA to specify PGC-like cells. The resultant cells were cultured in germ cell (GC)-proliferation medium for 7 days.

tag: sample type

value: cultured cells

tag: gender

value: male (XY)

tag: cell type

value: Spermatogonial Stem Cells from testis


title: non CD24-CD44+, ALDH+ flow sorted cells from normal breast cells of patient, biological rep 2

source_name: human normal breast, non-CD24-CD44+, ALDH+


title: non CD24-CD44+, ALDH+ flow sorted cells from xenograft of MC1 cell line

description: cells from MC1 cell line were flow sorted to select for CD24-CD44+ cells and compared with non-CD24-CD44+ cells; cells from MC1 cell line were flow sorted to select for ALDH+ cells and compared with ALDH- cells

source_name: MC1, non-CD24-CD44+, ALDH+


title: CD24-CD44+, ALDH- flow sorted cells from MCF7 cell line

source_name: MC7, CD24-CD44+, ALDH-


title: CD24-CD44+, ALDH+ flow sorted cells from MCF7 cell line

source_name: MC7, CD24-CD44+, ALDH+


title: PGC-like cell rep 2

description: Gene expression after 14 days treatment protocol set 2

source_name: PGC-like cells from undifferentiated hESC replicate 2


title: non-CD24-CD44+, ALDH- flow sorted cells from MCF7 cell line

source_name: MC7, non-CD24-CD44+, ALDH-


title: non-CD24-CD44+, ALDH- flow sorted cells from xenograft of MC1 cell line

source_name: MC1, non-CD24-CD44+, ALDH-


title: SSC rep 2


title: CD24-CD44+, ALDH- flow sorted cells from normal breast cells of patient

source_name: human normal breast, CD24-CD44+, ALDH-


title: CD24-CD44+, ALDH- flow sorted cells from MCF10A cell line

description: cells from MCF10A cell line were flow sorted to select for CD24-CD44+ cells and compared with non-CD24-CD44+ cells; cells from MCF10A cell line were flow sorted to select for ALDH+ cells and compared with ALDH- cells

source_name: MCF10A, CD24-CD44+, ALDH-


title: non-CD24-CD44+, ALDH- flow sorted cells from MCF10A cell line

source_name: MCF10A, non-CD24-CD44+, ALDH-


title: CD24-CD44+, ALDH+ flow sorted cells from MCF10A cell line

source_name: MCF10A, CD24-CD44+, ALDH+


title: non CD24-CD44+, ALDH+ flow sorted cells from MCF10A cell line

source_name: MCF10A, non-CD24-CD44+, ALDH+


title: PGC-like cell rep 1

description: Gene expression after 14 days treatment protocol set 1

source_name: PGC-like cells from undifferentiated hESC replicate 1


title: hESC rep 2

description: Gene expression after 0hr treatment protocol set 2

source_name: undifferentiated hESC replicate 2

value: undifferentiated hESC


title: CD24-CD44+, ALDH+ flow sorted cells from xenograft of MC1 cell line

source_name: MC1, CD24-CD44+, ALDH+


title: CD24-CD44+, ALDH- flow sorted cells from xenograft of MC1 cell line

source_name: MC1, CD24-CD44+, ALDH-


title: hESC rep 1

description: Gene expression after 0hr treatment protocol set 1

source_name: undifferentiated hESC replicate 1


title: brain-microglia-S6-1114545 (Expression Console)

city: St Louis

first: Winnie

middle: W

last: Pong

state: MO

address: 660 S. Euclid Avenue

department: Department of Neurology

institute: Washington University School of Medicine

description:
brain microglia biological replicate 1
S6

hyb_protocol: Following fragmentation with NuGen Encore Biotin Module,5.0 ug of cDNA were hybridized into the GeneChip Hybridization Oven 640 for 18 hr at 45C on Exon 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing:
The data was analyzed with the Affymetrix GeneChip Command Console. Microarray expression data was processed using Command Console (Affymetrix, Inc) and the raw (.CEL) files generated were QC’d using Expression Console software with Affymetrix default RMA Gene analysis settings.(Affymetrix, Inc).  Probe summarization (Robust Multichip Analysis, RMA), quality control analysis, and probe annotations were performed according to recommended guidelines (Expression Console Software, Affymetrix, Inc.).
We used the Partek workflow as well as Aroma to analyze the Affymetrix Mouse Exon 1.0ST array to generate the DE gene list.
probe group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm9.full.mps

source_name: brain-microglia

label_protocol: Biotinylated cDNA were prepared according to the standard NuGen WT-Ovation Pico RNA Amplification system from 500pg-50 ng total RNA

growth_protocol: not applicable

extract_protocol: Total RNA was isolated from snap-frozen sorted cell pellets using TRIzol-chloroform extraction, resuspended in 10µl Ambion Nuclease-free water (Life Technologies).

treatment_protocol: Tissue was dissociated, enriched by Percoll gradient, and cells were flow sorted.

value: brain

value: microglia

tag: age

value: 6 weeks

value: Female


title: SplenocytesWT_rep2

description: F

source_name: Mouse spleen


title: bonemarrow-monocyte-S3-1114542 (Expression Console)

description:
bone marrow monocyte biological replicate 1
S3

source_name: bonemarrow-monocyte

value: bone marrow

value: monocyte


title: non CD24-CD44+, ALDH+ flow sorted cells from HCC1954 cell line

description: cells from HCC1954 cell line were flow sorted to select for CD24-CD44+ cells and compared with non-CD24-CD44+ cells; cells from HCC1954 cell line were flow sorted to select for ALDH+ cells and compared with ALDH- cells

source_name: HCC1954, non-CD24-CD44+, ALDH+


title: brain-microglia-S10-1119010 (Aroma)

description:
brain microglia biological replicate 3
S10

data_processing:
Data processed with RMA and quantile normalized using BioC aroma.affymetrix.
We used the Partek workflow as well as Aroma to analyze the Affymetrix Mouse Exon 1.0ST array to generate the DE gene list.
probe group file: MoEx-1_0-st-v1.r2.pgf

value: Male


title: bonemarrow-monocyte-S8-1119011 (Aroma)

description:
bone marrow monocyte biological replicate 2
S8


title: bonemarrow-monocyte-S3-1114542 (Aroma)


title: CD24-CD44+, ALDH+ flow sorted cells from HCC1954 cell line


title: non-CD24-CD44+, ALDH- flow sorted cells from HCC1954 cell line

source_name: HCC1954, non-CD24-CD44+, ALDH-


title: 5N-H3K27me3-ChIP

city: Xiamen

first: Shubin

last: Gao

address: Chengzhi building 110,Xiang'an South Road

department: Basic Medical Sciences

institute: Medical College,Xiamen University

description: H3K27me3 ChIP in HCC specimens 5N

hyb_protocol: The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction.

source_name: H3K27me3 ChIP DNA from HCC specimens X5N

label_protocol: 1 µg ChIP DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers (ChIP DNA isolated from normal rabbit IgG-immunoprecipitated cells) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: Fresh HCC specimens were at -80°C.

extract_protocol: Grind the tissue(50-100mg) into a fine powder by Biopulverizer. Add 10ml of culture medium and tissue to the dish. Crosslink by adding 270ul of 37% formaldehyde to a final concentration of 1% to the dish in the hood. Incubate for 10 minutes at  room temperature(RT) on orbital shaker. Followed by quenching with 0.125 M glycine for 5 min. The tissue were washed twice with ice-cold PBS and lysed in 1 ml of lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris pH8.0) for at least 30 min on ice. The crosslinked chromatin was sheared to an average size of 500 bp by ten 30-second pulses using a BiorupterTM sonicator (Diagenode). The lysate was then centrifuged to remove cell debris, and the chromatin was quantified in a UV spectrophotometer. The chromatin (400 µg) was diluted 10-fold in dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA 16.7 mM Tris pH8.10, 167 mM NaCl) and pre-cleared with 25 µl protein A sepharose beads (pre-absorbed with salmon sperm DNA and BSA) for 2 h at 4C. The chromatin supernatant was then incubated overnight with 5 µg of purified antibody at 4C. After incubation with protein A sepharose beads (50 µl) for 2h at 4C, the immune complexes were collected by centrifugation and washed with the following buffers each for 10 min at 4C; RIPA buffer (150 mM NaCl, 50 mM Tris pH8.0, 0.1% SDS), high-salt buffer (500 mM NaCl, 50 mM Tris pH8.0, 0.1% SDS, 1% NP40) LiCl buffer (250 mM LiCl, 50 mM Tris pH8.0, 0.5% Na deoxycholate, 1% NP40) and 2x TE (20 mM Tris pH8.0, 2 mM EDTA). The protein-DNA complexes were eluted from the beads in 450 µl elution buffer (1% SDS, 100 mM NaHCO3) at 55C for 2 h followed by the addition of proteinaseK to 500 µg/ml and overnight incubaton at 65C. Genomic DNA was isolated from the precipitated material as well as from the sheared chromatin input (1/100 of the material used for ChIP) by phenol extraction and ethanol precipitation.

treatment_protocol: HCC specimens were transported by dry ice.

value: HCC specimens and their adjacent tissues

source_name: Input DNA from HCC specimens X4N


title: CD24-CD44+, ALDH- flow sorted cells from HCC1954 cell line


title: 60 hours larval samples

city: Dunedin

first: Peter

middle: Kenneth

last: Dearden

address: 710 Cumberland St

department: Department of Biochemistry

country: New Zealand

institute: University of Otago

hyb_protocol: Labelled samples were hybridised to the slides in Ambion Slide hybe buffer.  The microarrays were then incubated in a 42 degree waterbath overnight.  The following day the arrays were washed in 2xSSC(+0.1%SDS), 1xSSC(+0.1%SDS), 0.5xSSC and 0.1xSSC and dried prior to scanning.

scan_protocol: Microarrays were scanned with the GenePix 40000B Microarray scanner (Molecular devices) and analysed with the GenePix Pro 4.0 software to produce the gpr files

data_processing: Data analysis was performed using GeneSpring GX10 to analyse the gpr files.  The data was normalised using the LOWESS algorithm and no baseline transformation was performed.  The probes were filtered by expression with those showing expression below 1000 removed.  The normalised values  Cy3/Cy5 fluorescence ratios were calcualted based on the expression values from all four biological replicate microarrays at each time-point taking into account the dye swaps.  An un-paired t-test with a P-value cut of 0.05 was used to determine genes that showed a signficant difference in expression between the samples.  No multiple testing correction was used.

organism: Apis mellifera

source_name: Workers

label_protocol: RNA was amplified and labelled using the Ambion Amino Allyl MessageAmp™ II aRNA Amplification kit.  Samples were labelled with Alexa Fluor dyes 647 or 555.

growth_protocol: Queen larvae were produced by grafting (moving with a small paintbrush) newly hatched larvae into artificial queen cells which were then placed in a queen-less hive where they were fed royal jelly by adult nurse bees. Worker larvae were left in their original cells and placed in another hive where they were fed worker jelly.

extract_protocol: Total RNA was extracted using TRIZOL (Invitogen) and purified with RNeasy columns (Qiagen)

treatment_protocol: Upon collection in the field larvae were stored in liquid nitrogen then later transferred to -80˚C untill RNA was extracted

tag: developmental stage and caste

value: 60 hour old larvae raised as workers

source_name: Queens

value: 60 hour old larvae raised as queens


title: 108 hours larval samples

value: 108 hour old larvae raised as workers

value: 108 hour old larvae raised as queens


title: bonemarrow-monocyte-S8-1119011 (Expression Console)


title: 84 hours larval samples

value: 84 hour old larvae raised as workers

value: 84 hour old larvae raised as queens


title: 12 hours larval samples

value: 12 hour old larvae raised as workers

value: 12 hour old larvae raised as queens


title: 36 hours larval samples

value: 36 hour old larvae raised as workers

value: 36 hour old larvae raised as queens


title: 132 hours larval samples

description: This time point has three replicates instead of four

value: 132 hour old larvae raised as workers

value: 132 hour old larvae raised as queens


title: brain-microglia-S6-1114545 (Aroma)

value: brain

value: microglia

value: 6 weeks

value: Female


title: brain-microglia-S10-1119010 (Expression Console)

value: Male


title: 6 hours larval samples

value: 6 hour old larvae raised as workers

value: 6 hour old larvae raised as queens


title: bonemarrow-monocyte-S7-1119009 (Expression Console)

description:
bone marrow monocyte biological replicate 3
S7

value: bone marrow

value: monocyte


title: 5C-H3K27me3-ChIP

description: H3K27me3 ChIP in HCC specimens 5C

source_name: H3K27me3 ChIP DNA from HCC specimens X5C

value: HCC specimens and their adjacent tissues

source_name: Input DNA from HCC specimens X4C


title: bonemarrow-monocyte-S7-1119009 (Aroma)


title: 4N-H3K27me3-ChIP

description: H3K27me3 ChIP in HCC specimens 4N

source_name: H3K27me3 ChIP DNA from HCC specimens X4N

source_name: Input DNA from HCC specimens X2N


title: Zebrafish_self_to_self_rep1

status: Public on Nov 12 2013

city: Barcelona

first: Eva

middle: Lima

last: Oliveira

state: Barcelona

address: Carrer Jordi Girona 18-26

department: Environmental Chemistry

institute: IDAEA CSIC

description: G3 control embryo vs G3 control embryo at 2 dpf. Self to self 1

hyb_protocol: These following components were added in this order: 825ng of Cy3 labeled cRNA, 825 of Cy5 labeled cRNA, 11ul of 10x blocking Reagent, a volume of nuclease free water up to 52.8ul and 2.2ul of 25x fragmentation buffer. Incubate at 60ºC for exactly 30 minutes. Immediately cool on ice. Stop reaction by adding 55ul of 2x GEx Hybridization Buffer.  100ml of hybridization cocktail was used to each array. Set the Agilent hybridization oven at 65ºC and rotation speed to 10rpm, during 17hours. After hybridization, slides were washed. One last Acetonitrile wash was perform, followed by a stabilization and dry solution wash.

scan_protocol: Microarrays were scanned using an Agilent DNA Microarray Scanner G2505C, and data were acquired using Agilent's Feature Extraction Software version 10.5.1.1

data_processing: The scanned images were analyzed with Feature Extraction Software v 10.5.1.1 (Agilent) using default parameters (protocol GE2_105_jan09 and Grid: 026437_D_F_20110614) to obtain background subtracted and spatially detrended Processed Signal intensities

organism: Danio rerio

source_name: pooled embryos control G3

label_protocol: Cyanine 3-CTP samples and Cyanine 5-CTP samples were prepare from 200ng of total RNA using the Two-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling kit (Agilent), followed by the purification of the labelled/amplified RNA using Qiagen RNeasy mini kit.

growth_protocol: Zebrafish (D. rerio) embryos and eleutheroembryos were obtained by natural mating and raised at 28.5 ◦C (Kimmel et al., 1995) with a 12L:12D photoperiod in embryo water [90  g/mL of Instant Ocean (Aquarium Systems, Sarrebourg, France; http://zfin.org/), 0.58 mM CaSO4·2H2O, dissolved in reverse osmosis purified water]. Animal stages were recorded as days or hours postfertilization (dpf or hpf).

extract_protocol: Total RNA was isolated from 50 embryos per replicate using Trizol reagent protocol (Invitrogen). RNA concentration was measured by spectrophotometric absorption at 260nm in Nanodrop ND-800 (nanodrop technologies, Wilmington, DE) and their integrity checked by Agilent 2100 bioanalyzer (agilent technologies, Santa Clara CA).

treatment_protocol: Three treated embryo replicates and three control replicates with 50 fertilized eggs from the 4-cell stage to the 128-cell stage were exposed for 48h in a 100ml glass. Treated solutions were prepared with 0.05uM of PAMAM dendrimer Generation 3 dissolved in water for fish and the control solutions treatments were prepared and directly prepared in embryo water. All the solutions were prepared on the same day of the experiment and renewal each day.   Three treated embryo replicates and three control replicates with 50 fertilized eggs from the 4-cell stage to the 128-cell stage were exposed for 48h in a 100ml glass. Treated solutions were prepared with 0.5uM of PAMAM dendrimer Generation 4 dissolved in water for fish and the control solutions treatments were prepared and directly prepared in embryo water. All the solutions were prepared on the same day of the experiment and renewal each day.

tag: developmental stage

value: 2 dpf embryo

tag: agent

value: water control

value: Water control


title: Zebrafish_self_to_self_rep2

description: G4 control embryo vs G4 control embryo at 2 dpf. Self to self 2

source_name: pooled embryos control G4


title: Zebrafish_self_to_self_rep3

description: G3 control embryo vs G3 control embryo at 2 dpf. Self to self 3


title: brain-microglia-S9-1119008 (Expression Console)

description:
brain microglia biological replicate 2
S9


title: 4C-H3K27me3-ChIP

description: H3K27me3 ChIP in HCC specimens 4C

source_name: H3K27me3 ChIP DNA from HCC specimens X4C

source_name: Input DNA from HCC specimens X2C


title: heart tissue of control

city: Beijing

first: Qinghua

last: Cui

address: 38 Xueyuan Road

institute: Peking University

hyb_protocol: The labeled cRNAs were hybridized onto the Mouse LncRNA Array v2.0 (8 x 60K, Arraystar).

scan_protocol: After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v12.0 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 1 out of 6 samples have flags in Present or Marginal (All Targets Value) were chosen for further data analysis.

source_name: mouse heart of control

label_protocol: The sample preparation and microarray hybridization were performed based on the manufacturer’s standard protocols with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method.

extract_protocol: Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

value: Heart

tag: Sex


title: plasma of control

source_name: mouse plasma of control

value: Plasma


title: brain-microglia-S9-1119008 (Aroma)

source_name: brain-microglia


title: Zebrafish_G4_rep3

description: Biological replicate 3 of 3. G4 embryo treated vs water control embryo treated at 2 dpf

source_name: embryos treated with G4

treatment_protocol: Three treated embryo replicates and three control replicates with 50 fertilized eggs from the 4-cell stage to the 128-cell stage were exposed for 48h in a 100ml glass. Treated solutions were prepared with 1.5mg/L PAMAM dendrimer Generation 3 dissolved in water for fish and the control solutions treatments were prepared and directly prepared in embryo water. All the solutions were prepared on the same day of the experiment and renewal each day.   Three treated embryo replicates and three control replicates with 50 fertilized eggs from the 4-cell stage to the 128-cell stage were exposed for 48h in a 100ml glass. Treated solutions were prepared with 1.5mg/L PAMAM dendrimer Generation 4 dissolved in water for fish and the control solutions treatments were prepared and directly prepared in embryo water. All the solutions were prepared on the same day of the experiment and renewal each day.

value: 1.5mg/L of G4


title: Zebrafish_G4_rep2

description: Biological replicate 2 of 3. G4 embryo treated vs water control embryo treated at 2 dpf


title: Zebrafish_G4_rep1

description: Biological replicate 1 of 3. G4 embryo treated vs water control embryo treated at 2 dpf


title: Zebrafish_G3_rep2

description: Biological replicate 2 of 3. G3 embryo treated vs water control embryo treated at 2 dpf

source_name: embryos treated with G3

value: 1.5mg/L of G3


title: Zebrafish_G3_rep3

description: Biological replicate 3 of 3. G3 embryo treated vs water control embryo treated at 2 dpf


title: Zebrafish_G3_rep1

description: Biological replicate 1 of 3. G3 embryo treated vs water control embryo treated at 2 dpf


title: whole blood of HF mouse

source_name: mosue whole blood of HF

value: Whole blood


title: Zebrafish_self_to_self_rep5

description: G4 control embryo vs G4 control embryo at 2 dpf. Self to self 5

value: 3 dpf embryo


title: Zebrafish_self_to_self_rep4

description: G3 control embryo vs dmso control 0.1%. Self to self 4

source_name: pooled embryos control dmso

value: dmso control 0.1%


title: heart tissue of HF mouse

source_name: mosue heart of HF


title: whole blood of control

source_name: mouse whole blood of control


title: HepG2 SUZ12-ChIP

description: SUZ12 ChIP in HepG2 cells

source_name: SUZ12 ChIP DNA from HepG2 cells

growth_protocol: HepG2 cell were obtained from the Type Culture Collection of the Chinese Academy of Sciences (Shanghai, China). Which were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Gibco) supplemented with 10% fetal bovine serum (FBS, Hyclone) and 1% penicillin–streptomycin.

extract_protocol: 5x10E6 cells were fixed with 1% formaldehyde in culture medium for 10 min at room temperature followed by quenching with 0.125 M glycine for 5 min. The cells were washed twice with ice-cold PBS and lysed in 1 ml of lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris pH8.0) for at least 30 min on ice. The crosslinked chromatin was sheared to an average size of 500 bp by ten 30-second pulses using a BiorupterTM sonicator (Diagenode). The lysate was then centrifuged to remove cell debris, and the chromatin was quantified in a UV spectrophotometer. The chromatin (400 µg) was diluted 10-fold in dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA 16.7 mM Tris pH8.10, 167 mM NaCl) and pre-cleared with 25 µl protein A sepharose beads (pre-absorbed with salmon sperm DNA and BSA) for 2 h at 4C. The chromatin supernatant was then incubated overnight with 5 µg of purified antibody at 4C. After incubation with protein A sepharose beads (50 µl) for 2h at 4C, the immune complexes were collected by centrifugation and washed with the following buffers each for 10 min at 4C; RIPA buffer (150 mM NaCl, 50 mM Tris pH8.0, 0.1% SDS), high-salt buffer (500 mM NaCl, 50 mM Tris pH8.0, 0.1% SDS, 1% NP40) LiCl buffer (250 mM LiCl, 50 mM Tris pH8.0, 0.5% Na deoxycholate, 1% NP40) and 2x TE (20 mM Tris pH8.0, 2 mM EDTA). The protein-DNA complexes were eluted from the beads in 450 µl elution buffer (1% SDS, 100 mM NaHCO3) at 55C for 2 h followed by the addition of proteinaseK to 500 µg/ml and overnight incubaton at 65C. Genomic DNA was isolated from the precipitated material as well as from the sheared chromatin input (1/100 of the material used for ChIP) by phenol extraction and ethanol precipitation.

treatment_protocol: HepG2 cells were passaged to a new dish and cultured 2 days

value: Hepatocellular carcinoma

source_name: Input DNA from HepG2 cells


title: 3N-H3K27me3-ChIP

description: H3K27me3 ChIP in HCC specimens 3N

source_name: H3K27me3 ChIP DNA from HCC specimens X3N

source_name: Input DNA from HCC specimens X1N


title: HepG2 H3K27me3-ChIP

description: H3K27me3 ChIP in HepG2 cells

source_name: H3K27me3 ChIP DNA from HepG2 cells


title: HepG2 EZH2-ChIP

description: EZH2 ChIP in HepG2 cells

source_name: EZH2 ChIP DNA from HepG2 cells


title: 3C-H3K27me3-ChIP

description: H3K27me3 ChIP in HCC specimens 3C

source_name: H3K27me3 ChIP DNA from HCC specimens X3C

source_name: Input DNA from HCC specimens X1C


title: ROTT_BI_541.2

city: Cambridge

first: Elinor

last: Karlsson

state: MA

address: 7 Cambridge Center

institute: Broad Institute

description: Genomic DNA extracted from blood was genotyped using the Illumina CanineHD Genotyping BeadChip

hyb_protocol: Standard Illumina protocol for Infinium HD Beadchip

scan_protocol: Illumina iScan with Dual-Scanner Autoloader

data_processing: Illumina GenomeStudio Version 2011.1 with Genotyping Module 1.9.4

organism: Canis lupus familiaris

source_name: blood

extract_protocol: Genomic DNA was isolated from whole blood (QIAamp DNA Midi kit).

tag: breed

value: rottweiler

value: female

value: blood

tag: disease state

value: osteosarcoma


title: ROTT_BI_541

label_protocol: Standard Illumina protocol for Infinium HD Beadchip

tag: tissue


title: plasma of HF mouse

source_name: mosue plasma of HF

value: Male


title: ROTT_BI_557

value: male

value: osteosarcoma-free


title: ROTT_BI_469


title: ROTT_BI_514


title: ROTT_BI_478


title: ROTT_BI_440


title: ROTT_BI_3923


title: ROTT_BI_46993


title: ROTT_BI_4924


title: ROTT_BI_394


title: ROTT_BI_467


title: ROTT_BI_543


title: ROTT_BI_34730


title: ROTT_BI_3477


title: ROTT_BI_3676


title: ROTT_BI_3826


title: ROTT_BI_389


title: ROTT_BI_542


title: ROTT_BI_424


title: ROTT_BI_14572


title: ROTT_BI_3921


title: ROTT_BI_14571


title: ROTT_BI_453


title: ROTT_BI_3478


title: ROTT_BI_34727


title: ROTT_BI_433


title: ROTT_BI_530


title: ROTT_BI_538


title: ROTT_BI_14565


title: ROTT_BI_339


title: ROTT_BI_3348


title: ROTT_BI_338


title: ROTT_BI_334


title: ROTT_BI_333


title: ROTT_BI_342


title: ROTT_BI_330


title: ROTT_BI_328


title: ROTT_BI_331


title: ROTT_BI_30643


title: ROTT_BI_340


title: ROTT_BI_33278


title: ROTT_BI_3254


title: ROTT_BI_33189


title: ROTT_BI_332


title: ROTT_BI_26312


title: ROTT_BI_29967


title: ROTT_BI_3253


title: ROTT_BI_26305


title: ROTT_BI_327


title: ROTT_BI_26307


title: ROTT_BI_26313


title: ROTT_BI_33276


title: ROTT_BI_2989


title: ROTT_BI_26311


title: ROTT_BI_26306


title: ROTT_BI_26304


title: ROTT_BI_14563


title: ROTT_BI_26301


title: ROTT_BI_14555


title: ROTT_BI_26310


title: ROTT_BI_26299


title: ROTT_BI_26296


title: ROTT_BI_26302


title: ROTT_BI_26303


title: ROTT_BI_12433


title: ROTT_BI_26295


title: ROTT_BI_26286


title: ROTT_BI_26300


title: ROTT_BI_26298


title: ROTT_BI_26275


title: ROTT_BI_26293


title: ROTT_BI_26297


title: ROTT_BI_26282


title: ROTT_BI_26164


title: ROTT_BI_24846


title: ROTT_BI_26288


title: ROTT_BI_26294


title: ROTT_BI_26285


title: ROTT_BI_24845


title: ROTT_BI_11267


title: ROTT_BI_26280


title: ROTT_BI_26278


title: ROTT_BI_26284


title: ROTT_BI_25858


title: ROTT_BI_24713


title: ROTT_BI_262


title: ROTT_BI_24126


title: ROTT_BI_11268


title: ROTT_BI_26279


title: ROTT_BI_21845


title: ROTT_BI_l459


title: ROTT_BI_ucd13


title: ROTT_BI_26274


title: ROTT_BI_793


title: ROTT_BI_11267.2


title: ROTT_BI_21187


title: ROTT_BI_l1077


title: ROTT_BI_767


title: ROTT_BI_737


title: ROTT_BI_740


title: ROTT_BI_756


title: ROTT_BI_9740


title: ROTT_BI_737.2


title: ROTT_BI_751


title: ROTT_BI_14581


title: ROTT_BI_7368


title: ROTT_BI_25314


title: ROTT_BI_767.2


title: ROTT_BI_770.2


title: ROTT_BI_7263


title: ROTT_BI_723


title: ROTT_BI_755


title: ROTT_BI_770


title: ROTT_BI_715


title: ROTT_BI_726


title: ROTT_BI_14585


title: ROTT_BI_722.2


title: ROTT_BI_24125


title: ROTT_BI_6654


title: ROTT_BI_l-457


title: ROTT_BI_6634


title: ROTT_BI_722


title: ROTT_BI_633


title: ROTT_BI_723.2


title: ROTT_BI_616


title: ROTT_BI_724


title: ROTT_BI_611.2


title: ROTT_BI_613


title: ROTT_BI_613.2


title: ROTT_BI_605


title: ROTT_BI_599


title: ROTT_BI_9454


title: ROTT_BI_597


title: ROTT_BI_611


title: ROTT_BI_612.2


title: ROTT_BI_599.2


title: ROTT_BI_604


title: ROTT_BI_612


title: ROTT_BI_604.2


title: ROTT_BI_614


title: ROTT_BI_596


title: ROTT_BI_14575


title: ROTT_BI_14574


title: IWH_IW-OS-03|121

value: Irish Wolfhound


title: IWH_IW-OS-04|169


title: IWH_IW-NC-45|134


title: IWH_IW-NC-97|123


title: IWH_IW-NC-29|150


title: IWH_IW-NC-49|157


title: ROTT_BI_59353


title: IWH_IW-NC-88|136


title: IWH_IW-NC-85|131


title: ROTT_BI_10510


title: IWH_IW-NC-253|173


title: IWH_IW-OS-01|67


title: IWH_IW-NC-73|107


title: IWH_IW-NC-62|175


title: IWH_IW-NC-251|170


title: IWH_IW-NC-258|161


title: ROTT_BI_615


title: IWH_IW-NC-223|137


title: IWH_IW-NC-215|155


title: IWH_10/7/11|31


title: IWH_10/7/11|31.2


title: IWH_IW-NC-228|142


title: IWH_IW-NC-24|105


title: IWH_10/7/16|61


title: IWH_IW-NC-218|158


title: IWH_IW-NC-207|115


title: IWH_IW-NC-229|98


title: IWH_IW-NC-148|109


title: IWH_IW-NC-20|112


title: IWH_IW-NC-195|127


title: IWH_IW-NC-180|156


title: IWH_IW-NC-122|24


title: IWH_IW-NC-41|164


title: IWH_IW-NC-15|145


title: IWH_IW-NC-138|52


title: IWH_IW-NC-117|19


title: IWH_IW-NC-123|91


title: IWH_10/7/10|66


title: IWH_IW-NC-106|103


title: IWH_7388|78


title: IWH_IW-NC-209|138


title: IWH_IW-NC-101|167


title: IWH_7386|1


title: IWH_IW-NC-115|99


title: IWH_IW-NC-103|140


title: IWH_IW-NC-192|160


title: IWH_7271|23


title: IWH_6354|38


title: IWH_3555|54


title: IWH_38288|3


title: IWH_10/7/7|63


title: IWH_10/7/9|26


title: IWH_7367|29


title: IWH_6612|32


title: IWH_5964|73


title: IWH_46941|45


title: IWH_46501|58


title: IWH_3553|25


title: IWH_34516|21


title: IWH_23536|95


title: IWH_23535|6


title: IWH_23534|49


title: IWH_25672|80


title: IWH_23537|14


title: IWH_3545|77


title: IWH_IW-NC-259|190


title: IWH_3543|62


title: IWH_23533|93


title: IWH_10/7/6|88


title: IWH_7270|8


title: IWH_10/7/96|37


title: IWH_14495|53


title: IWH_10/7/98|83


title: IWH_10/7/3|41.2


title: IWH_23532|27


title: IWH_23531|30


title: IWH_10/7/74|22


title: IWH_10/7/80|16


title: IWH_10/7/65|57


title: IWH_10/7/66|84


title: IWH_10/7/3|41


title: IWH_10/7/77|36


title: IWH_10/7/6|88.2


title: IWH_10/7/36|64


title: IWH_10/7/50|17


title: IWH_10/7/88|2


title: IWH_10/7/84|11


title: IWH_IW-OS-57|133


title: IWH_10/7/59|33


title: IWH_10/7/45|13


title: IWH_10/7/63|42


title: IWH_10/7/61|82


title: IWH_10/7/29|90.2


title: IWH_IW-OS-56|130


title: IWH_10/7/29|90


title: IWH_10/7/56|60


title: IWH_10/7/2|86


title: IWH_10/7/34|59


title: IWH_10/7/31|50


title: IWH_IW-OS-53|159


title: IWH_IW-OS-49|177


title: IWH_IW-OS-48|183


title: IWH_IW-OS-47|184


title: IWH_10/7/62|70


title: IWH_IW-OS-50|188


title: IWH_10/7/87|55


title: IWH_10/7/33|7


title: IWH_IW-OS-44|154


title: IWH_IW-OS-46|108


title: IWH_IW-OS-41|149


title: IWH_IW-OS-55|151


title: IWH_IW-OS-40|118


title: IWH_10/7/27|92


title: IWH_IW-OS-42|111


title: IWH_IW-OS-43|48


title: IWH_IW-OS-54|181


title: IWH_IW-OS-39|132


title: IWH_IW-OS-45|129


title: IWH_IW-OS-28|110


title: IWH_IW-OS-31|180


title: IWH_IW-OS-30|100


title: IWH_10/7/23|74


title: IWH_IW-OS-33|153


title: IWH_IW-OS-36|191


title: IWH_IW-OS-32|162


title: IWH_IW-OS-34|178


title: IWH_IW-OS-20|43


title: IWH_IW-OS-27|96


title: IWH_IW-OS-19|128


title: IWH_IW-OS-26|101


title: IWH_IW-OS-24|152


title: IWH_IW-OS-18|76


title: IWH_IW-OS-22|176


title: IWH_IW-OS-35|146


title: IWH_IW-OS-13|4


title: IWH_10/7/95|44


title: IWH_IW-OS-16|141


title: IWH_IW-OS-12|174


title: IWH_IW-OS-15|28


title: IWH_IW-OS-11|117


title: IWH_IW-OS-07|104


title: IWH_IW-OS-09|72


title: IWH_IW-OS-06|171


title: IWH_10/7/17|12


title: IWH_IW-OS-29|135


title: IWH_IW-OS-10|89


title: GREY_BI_0442_COMSTOCK_442

value: greyhound


title: IWH_10/7/0|68


title: IWH_10/7/18|85


title: GREY_BI_29672_BROAD_29672


title: GREYHOUND_BI_89973_ALVAREZ_AKC4

value: unknown


title: GREYHOUND_BI_89975_ALVAREZ_AKC9


title: GREY_BI_0460_COMSTOCK_460


title: GREY_BI_33210_COMSTOCK_393


title: GREY_BI_33058_COMSTOCK_80


title: GREYHOUND_BI_89974_ALVAREZ_AKC5


title: GREYHOUND_BI_89976_ALVAREZ_AKC11


title: GREY_BI_0513_COMSTOCK_513


title: GREY_BI_0482_COMSTOCK_482


title: GREY_BI_33199_COMSTOCK_356


title: GREY_BI_33216_COMSTOCK_419


title: GREY_BI_6583_COMSTOCK_276


title: GREY_BI_26436_BROAD_26436


title: GREYHOUND_BI_89972_ALVAREZ_AKC1


title: GREYHOUND_BI_89977_ALVAREZ_AKC12


title: GREY_BI_33196_COMSTOCK_351


title: GREY_BI_6997_COMSTOCK_418


title: GREY_BI_0459_COMSTOCK_459


title: GREY_BI_33180_COMSTOCK_326


title: GREY_BI_0417_COMSTOCK_417


title: GREY_BI_33205_COMSTOCK_386


title: GREY_BI_0391_COMSTOCK_391


title: GREY_BI_0438_COMSTOCK_438


title: GREY_BI_33215_COMSTOCK_411


title: GREY_BI_0490_COMSTOCK_490


title: GREY_BI_0445_COMSTOCK_445


title: GREY_BI_0485_COMSTOCK_485


title: GREY_BI_3594_BROAD_3594


title: GREY_BI_33178_COMSTOCK_323


title: GREY_BI_0522_COMSTOCK_522


title: GREY_BI_0470_COMSTOCK_470


title: GREY_BI_33214_COMSTOCK_407


title: GREY_BI_0376_COMSTOCK_376


title: GREY_BI_0520_COMSTOCK_520


title: GREY_BI_33204_COMSTOCK_373


title: GREY_BI_33177_COMSTOCK_313


title: GREY_BI_33203_COMSTOCK_370


title: GREY_BI_0449_COMSTOCK_449


title: GREY_BI_0521_COMSTOCK_521


title: GREY_BI_0317_COMSTOCK_317


title: GREY_BI_33211_COMSTOCK_398


title: GREY_BI_0515_COMSTOCK_515


title: GREY_BI_33212_COMSTOCK_400


title: GREY_BI_33168_COMSTOCK_280


title: GREY_BI_0601_COMSTOCK_601


title: GREY_BI_33219_COMSTOCK_426


title: GREY_BI_0461_COMSTOCK_461


title: GREY_BI_0422_COMSTOCK_422


title: GREY_BI_0397_COMSTOCK_397


title: GREY_BI_15216_COMSTOCK_589


title: GREY_BI_15206_COMSTOCK_590


title: GREY_BI_15020_COMSTOCK_555


title: GREY_BI_33174_COMSTOCK_303


title: GREY_BI_7006_COMSTOCK_86


title: GREY_BI_0430_COMSTOCK_430


title: GREY_BI_0431_COMSTOCK_431


title: GREY_BI_33073_COMSTOCK_132


title: GREY_BI_33175_COMSTOCK_306


title: GREY_BI_6593_COMSTOCK_233


title: GREY_BI_0359_COMSTOCK_359


title: GREY_BI_15079_COMSTOCK_364


title: GREY_BI_32897_COMSTOCK_42


title: GREY_BI_6594_COMSTOCK_250


title: GREY_BI_14993_COMSTOCK_600


title: GREY_BI_031_COMSTOCK_31


title: GREY_BI_15005_COMSTOCK_591


title: GREY_BI_0525_COMSTOCK_525


title: GREY_BI_0299_COMSTOCK_299


title: GREY_BI_032_COMSTOCK_32


title: GREY_BI_0544_COMSTOCK_544


title: GREY_BI_15207_COMSTOCK_552


title: GREY_BI_33172_COMSTOCK_292


title: GREY_BI_030_COMSTOCK_30


title: GREY_BI_14998_COMSTOCK_598


title: GREY_BI_029_COMSTOCK_29


title: GREY_BI_7004_COMSTOCK_300


title: GREY_BI_7031_COMSTOCK_118


title: GREY_BI_6534_COMSTOCK_74


title: GREY_BI_15217_COMSTOCK_587


title: GREY_BI_33082_COMSTOCK_151


title: GREY_BI_33171_COMSTOCK_291


title: GREY_BI_32901_COMSTOCK_48


title: GREY_BI_0534_COMSTOCK_534


title: GREY_BI_32902_COMSTOCK_49


title: GREY_BI_15212_COMSTOCK_588


title: GREY_BI_0554_COMSTOCK_554


title: GREY_BI_0575_COMSTOCK_575


title: GREY_BI_15062_COMSTOCK_137


title: GREY_BI_028_COMSTOCK_28


title: GREY_BI_6590_COMSTOCK_194


title: GREY_BI_15202_COMSTOCK_593


title: GREY_BI_32900_COMSTOCK_47


title: GREY_Comst_500_BI_44017


title: GREY_BI_0533_COMSTOCK_533


title: GREY_BI_9460_BROAD_9460


title: GREY_BI_027_COMSTOCK_27


title: GREY_BI_16282_BROAD_16282


title: GREY_BI_0532_COMSTOCK_532


title: GREY_BI_20721_BROAD_20721


title: GREY_BI_7389_BROAD_7389


title: GREY_Comst_648_BI_44024


title: GREY_Comst_509_BI_14568


title: GREY_BI_26711_BROAD_26711


title: GREY_BI_11392_BROAD_11392


title: GREY_BI_27441_BROAD_27441


title: GREY_Comst_491_BI_44016


title: GREY_BI_11103_BROAD_11103


title: GREY_BI_9643_BROAD_9643


title: GREY_Comst_654_BI_44027


title: GREY_BI_7011_BROAD_7011


title: GREY_Comst_602_BI_14994


title: GREY_Comst_651_BI_44025


title: GREY_BI_11111_BROAD_11111


title: GREY_BI_33169_COMSTOCK_281


title: GREY_Comst_584_BI_44022


title: GREY_BI_11105_BROAD_11105


title: GREY_BI_7010_BROAD_7010


title: GREY_Comst_607_BI_14995


title: GREY_Comst_508_BI_44020


title: GREY_BI_26458_BROAD_26458


title: GREY_BI_25857_BROAD_25857


title: GREY_Comst_504_BI_44019


title: GREY_Comst_660_BI_44029


title: GREY_Comst_696_BI_6994


title: GREY_BI_25031_BROAD_25031


title: GREY_BI_7007_BROAD_7007


title: GREY_Comst_121_BI_6513


title: GREY_Comst_88_BI_6511


title: GREY_Comst_658_BI_44028


title: GREY_BI_9644_BROAD_9644


title: GREY_BI_5935_BROAD_5935


title: GREY_BI_7002_BROAD_7002


title: GREY_BI_6222_BROAD_6222


title: GREY_BI_6992_BROAD_6992


title: GREY_BI_6998_BROAD_6998


title: GREY_BI_6993_BROAD_6993


title: GREY_BI_6205_BROAD_6205


title: GREY_BI_3747_BROAD_3747


title: GREY_BI_6512_BROAD_6512


title: GREY_BI_6556_BROAD_6556


title: GREY_BI_3598_BROAD_3598


title: GREY_BI_6645_BROAD_6645


title: GREY_BI_6221_BROAD_6221


title: GREY_BI_5422_BROAD_5422


title: GREY_BI_6203_BROAD_6203


title: GREY_BI_24085_BROAD_24085


title: PVD2 morphant Animal caps, stage 9, Replicate 2

city: Copenhagen

first: Joshua

last: Brickman

address: Blegdamsvej 3B

department: The Danish Stem Cell Centre (DanStem)

institute: University of Copenhagen

description: embryos injected at two-cells stage with PVD2  morpholino oligos and dissected at stage 8

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. Hybridization and washed were performed according to manufacturer's instructions.

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner (model G2505-64120) at 100% PMT for Cy3 channel and 10% PMT for Cy5 channel with a scan resolution of 5µm

data_processing: Data are extracted with Agilent Feature Extraction Software.The data were further processed with NIA ANOVA tool utilities.See http://lgsun.grc.nia.nih.gov/ANOVA for details.The data is normalized with the following method:(1) Take values from the columns gDyeNormSignal,rDyeNormSignal in the raw files and log-transform them using: log10(max(x,1)). These values will be referenced below as Xgi and Xri where i is array number. (2) Take average of Xri's for the oligo among 48 arrays in the series: AverXr = average(Xri). (3) For each array estimate Yi = Xgi-Xri+AverXr (4) Round Yi to 4 decimal digits. This is used as the normalized VALUE for each spot.

organism: Xenopus laevis

source_name: Embryos injected with PVD2 morpholino

label_protocol: 2.5µg of total RNA were processed using Agilent’s Quick Amp Labelling Kit. Labelled cRNA were purified using Rneasy Mini kit (Qiagen)

growth_protocol: Whole embryos were injected at two cells stage and cultured in 1/10 normal amphibian medium until stage 9 and 10.  Animal caps were dissected from injected embryos at stage 8,  cultured in 3/4 normal amphibian medium and collected at stage 9 and 10.

extract_protocol: Total RNA was prepared from 3 whole embryos or 25 animal caps using Qiagen Rneasy Kit according to manufacturer's instructions.

treatment_protocol: Embryos were injected using 60ng of morpholino in each blastomere using either Control morpholino or PVD2 morpholino mixture.

tag: Stage

value: Late blastula (9)

value: Animal caps

source_name: pooled whole embryo

tag: stages

value: Whole embryo


title: PVD2 morphant Animal caps, stage10, Replicate 1

value: Early gastrula (10)


title: GREY_BI_5234_BROAD_5234


title: PVD2 morphant Animal caps, stage 9, Replicate 1


title: PVD2 morphant Whole embryo, stage 10, Replicate 2

description: embryos injected at two-cells stage with PVD2  morpholino oligos


title: PVD2 morphant Whole embryo, stage10, Replicate 1


title: GREY_BI_6201_BROAD_6201


title: GREY_BI_3491_BROAD_3491


title: GREY_BI_6202_BROAD_6202


title: GREY_BI_6587_BROAD_6587


title: PVD2 morphant Whole embryo, stage 9, Replicate 2


title: GREY_BI_6219_Comstock_212


title: PVD2 morphant Whole embryo, stage 9, Replicate 1


title: GREY_BI_6214_BROAD_6214


title: GREY_BI_6595_BROAD_6595


title: GREY_BI_6554_BROAD_6554


title: Control Animal caps, stage10, Replicate 1

description: embryos injected at two-cells stage with control morpholino oligos and dissected at stage 8

source_name: Embryos injected with control morpholino


title: GREY_BI_3986_BROAD_3986


title: PVD2 morphant Animal caps, stage 10, Replicate 2


title: GREY_Comst_517_BI_44021


title: Control Animal caps, stage 9, Replicate 1


title: Control Whole embryo, stage 10, Replicate 2

description: embryos injected at two-cells stage with control morpholino oligos


title: GREY_BI_6553_BROAD_6553


title: Control Whole embryo, stage10, Replicate 1


title: Control Animal caps, stage 10, Replicate 2


title: GREY_BI_6209_BROAD_6209


title: GREY_Comst_503_BI_44018


title: Control Whole embryo, stage 9, Replicate 2


title: GREY_BI_6563_BROAD_6563


title: GREY_BI_3489_BROAD_3489


title: Control Whole embryo, stage 9, Replicate 1


title: GREY_BI_6561_BROAD_6561


title: GREY_BI_6584_BROAD_6584


title: GREY_BI_3984_UMINN_35


title: GREY_BI_6208_BROAD_6208


title: GREY_BI_6585_BROAD_6585


title: GREY_BI_6533_BROAD_6533


title: GREY_BI_3761_BROAD_3761


title: GREY_BI_3198_BROAD_3198


title: GREY_BI_6564_BROAD_6564


title: GREY_BI_44026_Comst_652


title: GREY_BI_3488_BROAD_3488


title: GREY_BI_6207_BROAD_6207


title: GREY_BI_6166_BROAD_6166


title: GREY_BI_3749_BROAD_3749


title: GREY_BI_48527_Comst_594


title: GREY_BI_10973_BROAD_10973


title: GREY_BI_2871_BROAD_2871


title: GREY_BI_3496_BROAD_3496


title: GREY_BI_4973_BROAD_4973


title: Control Animal caps, stage 9, Replicate 2


title: GREY_BI_10813_TUFTS_157732


title: GREY_BI_39023_OSA


title: GREY_BI_0789_COMSTOCK_789


title: FreshBs_untreated_S_442

city: Riverside

first: Eugene

middle: L

last: Bolotin

address: 900 university ave

department: Cell Biology and Neuroscience

institute: UC Riverside

hyb_protocol: cRNA was randomized and hybridized in a single batch to Illumina HumanHT-12_V4 expression beadchips (Illumina, San Diego, CA) at Channing Laboratory (Division of Network Medicine, Brigham and Women's Hospital, Boston MA) according to the manufacturer’s protocols.

scan_protocol: Manufacturer standard.

data_processing: R lumi package was used for analysis,  log2 values were quantile normalized

label_protocol: All RNAs were converted to biotin-labeled cRNA using the Illumina TotalPrep-96 RNA amplification kit (Applied Biosystems, Foster City, CA) in a single batch.

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from 10ml of blood using IsoPrep (Matrix Technologies) and transformed by EBV. Viable cells remaining after six weeks were considered to be LCLs. PBMCs were isolated from the remaining 50ml of blood using Lymphoprep (VWR), and B-lymphocytes were specifically isolated from PBMCs using the B-cell Negative Isolation kit (Invitrogen) according to the manufacturer's protocol. Aliquots of B-cells were incubated with FITC-conjugated CD19 fluorescent antibodies and the proportion of CD19 positive cells (B-cells only) was determined by FACS analysis (BD FACS Calibur) of 10,000 gated events. Only preparations with >90% B-lymphocyte purity were used for further analysis.

extract_protocol: RNA was isolated from all samples and stored at -80°C.

treatment_protocol: B-cells and LCLs were incubated with either 2 µM activated simvastatin or a sham buffer for 24 hours in RPMI media supplemented with 500 U/ml penicillin/streptomycin, 10% FBS and 2 nmol/L GlutaMAX, and all cultures were maintained at 37°C with 5% CO2.  The B-cells were statin or sham exposed at the time of isolation  while LCLs were frozen, thawed and exposed as a single batch. Simvastatin, obtained as a gift from Merck, was activated.

tag: tissue source

value: Peripheral blood mononuclear cells

tag: cell subtype

value: native B cells

tag: treated with

value: sham buffer for 24 h


title: GREY_BI_6198_BROAD_6198


title: CellLine_untreated_S_402

value: lymphoblastoid cell lines (LCLs)


title: CellLine_untreated_S_457


title: GREY_BI_32771_OSA


title: CellLine_untreated_S_442


title: CellLine_Simvastatin_S_402

value: 2 µM activated simvastatin for 24 h


title: GREY_BI_34710_BROAD_34710

value: female

value: blood


title: CellLine_Simvastatin_S_442


title: GREY_BI_14996_COMSTOCK_608


title: CellLine_Simvastatin_S_453


title: GREY_BI_3593_BROAD_3593


title: GREY_BI_0774_COMSTOCK_774

value: osteosarcoma


title: GREY_BI_6513_BROAD_6513

value: male


title: CellLine_untreated_S_453


title: GREY_BI_6555_BROAD_6555


title: GREY_BI_6197_BROAD_6197

value: osteosarcoma-free


title: FreshBs_Simvastatin_S_442


title: CellLine_Simvastatin_S_457


title: GREY_BI_3967_BROAD_3967


title: GREY_BI_Label_736_LABEL_736


title: GREY_BI_Label_879_LABEL_879


title: GREY_BI_0662_COMSTOCK_662


title: GREY_BI_3602_BROAD_3602


title: CellLine_untreated_SCRNA_4


title: GREY_BI_15192_COMSTOCK_506


title: CellLine_Simvastatin_S_493_B


title: CellLine_Simvastatin_S_462


title: GREY_BI_6510_COMSTOCK_75


title: CellLine_untreated_SCRNA_3


title: GREY_BI_30126_BROAD_30126


title: GREY_BI_14981_COMSTOCK_674


title: GREY_BI_6522_COMSTOCK_502


title: CellLine_untreated_S_493_B


title: CellLine_Simvastatin_S_454


title: FreshBs_Simvastatin_S_454


title: GREY_BI_15191_COMSTOCK_505


title: FreshBs_untreated_S_493_B


title: GREY_BI_15210_COMSTOCK_568


title: GREY_BI_15215_COMSTOCK_573


title: FreshBs_untreated_S_454


title: GREY_BI_Label_725_LABEL_725


title: GREY_BI_0498_COMSTOCK_498


title: FreshBs_Simvastatin_S_462


title: GREY_BI_27090_BROAD_27090


title: GREY_BI_Label_724_LABEL_724


title: FreshBs_untreated_S_462


title: GREY_BI_3490_BROAD_3490


title: GREY_BI_14992_COMSTOCK_619


title: CellLine_untreated_S_462


title: CellLine_Simvastatin_S_401


title: CellLine_untreated_S_454


title: CellLine_untreated_S_401


title: FreshBs_Simvastatin_S_341_B


title: GREY_BI_34515_BROAD_34515


title: GREY_BI_0566_COMSTOCK_566


title: GREY_BI_15001_COMSTOCK_618


title: CellLine_untreated_S_341_B


title: FreshBs_Simvastatin_S_401


title: CellLine_Simvastatin_S_342


title: FreshBs_Simvastatin_S_493_B


title: GREY_BI_0762_COMSTOCK_762


title: GREY_BI_15000_COMSTOCK_617


title: FreshBs_untreated_S_341_B


title: FreshBs_untreated_S_401


title: CellLine_Simvastatin_S_341_B


title: GREY_BI_35065_BROAD_35065


title: CellLine_untreated_S_342


title: CellLine_untreated_SCRNA_2


title: GREY_BI_33639_BROAD_33639


title: GREY_BI_15016_COMSTOCK_562


title: GREY_BI_15013_COMSTOCK_569


title: FreshBs_untreated_S_068


title: GREY_BI_15012_COMSTOCK_570


title: FreshBs_Simvastatin_S_342


title: FreshBs_Simvastatin_S_068


title: GREY_BI_38287_BROAD_38287


title: GREY_BI_39581_BROAD_39581


title: GREY_BI_0511_COMSTOCK_511


title: FreshBs_untreated_S_289


title: GREY_BI_0759_COMSTOCK_759


title: CellLine_untreated_S_068


title: GREY_BI_6527_COMSTOCK_531


title: CellLine_untreated_S_289


title: GREY_BI_15014_COMSTOCK_567