title: Normal adjacent 5

description:
N082-N
Matched adjacent biliary normal, Thailand.

source_name: matched adjacent biliary normal

value: normal biliary

value: adjacent normal tissue (N082)


title: Normal adjacent 6

status: Public on Jan 01 2013

type: genomic

city: London

first: Wei

last: Dai

address: Du Cane Road

department: Sugery and Cancer

country: United Kingdom

institute: Imperial College London

description:
W022-N
Matched adjacent biliary normal, Thailand.

hyb_protocol: Bisulphite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchips using the standard Illumina protocol.

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

data_processing: BeadStudio software methylation module 1.0.5.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Standard Illumina Protocol.

growth_protocol: Cell lines were grown in RPMI-1640 supplemented with glutamine (2mM) and 10% fetal bovine serum in humidified 5% CO2 in air incubators at 37 ̊C.

extract_protocol: DNA was extracted and purified from cell lines using the Qiagen DNeasy Tissue Kit according to standard instructions.

tag: tissue

tag: sample type

value: adjacent normal tissue (W022)


title: Normal adjacent 1

description:
R052-N
Matched adjacent biliary normal, Thailand.

value: adjacent normal tissue (R052)


title: Normal adjacent 3

description:
U064-N
Matched adjacent biliary normal, Thailand.

value: adjacent normal tissue (U064)


title: PEO1, technical rep 2

description:
PEO1_REP2
Ovarian cancer cell line isolated from patient before chemotherapy.

source_name: ovarian cancer cell line

tag: cell line


title: PEO1, technical rep 3

description:
PEO1_REP3
Ovarian cancer cell line isolated from patient before chemotherapy.


title: Primary tumor 2

description:
W111-T
Primary intrahepatic cholangiocarcinoma, Thailand, matched.

source_name: primary intrahepatic cholangiocarcinoma

value: primary intrahepatic cholangiocarcinoma

value: tumor tissue (W111)


title: PEO1, technical rep 4

description:
PEO1_REP4
Ovarian cancer cell line isolated from patient before chemotherapy.


title: Primary tumor 1

description:
R052-T
Primary intrahepatic cholangiocarcinoma, Thailand, matched.

value: tumor tissue (R052)


title: Normal adjacent 2

description:
W111-N
Matched adjacent biliary normal, Thailand.

value: adjacent normal tissue (W111)


title: Primary tumor 10

description:
R086-T
Primary intrahepatic cholangiocarcinoma, Thailand.

value: tumor tissue


title: Normal adjacent 4

description:
W027-N
Matched adjacent biliary normal, Thailand.

value: adjacent normal tissue (W027)


title: CTC_123328_20CTC

status: Public on Dec 31 2012

city: San Francisco

first: Mark

last: Magbanua

state: CA

address: 1450 3rd Street, PO Box 589001

department: HemOnc

country: USA

institute: UCSF/Helen Diller Familiy Comprehensive Cancer Center

description:
Sample name: 123328_20CTC
Matched TLDA sample name: CTC.123328.20CTC.1
Matched TLDA sample Accession Number: GSM998112

hyb_protocol: We combined and precipitated 30 uL Cy3 labeled test DNA, 30 uL Cy5 labeled reference DNA and 100 ug human Cot-1 DNA by adding 0.1 volumes of 3 M sodium acetate (pH 5.2) and 2.5 volumes of ice-cold ethanol. We collected the precipitate by centrifugation  at 14000 rpm for 45 minutes at 4C. We the final hybridization mixture containing 7ul dH20, 14uL  20% SDS, and 49 uL or Master Mix (5 mL ultra pure formamide from Invitrogen, 1g 500000MW Dextran Sulfate, 1mL 20xSSC, 1mL H20). We denatured the hybridization mixture at 73C for 15 min and then incubated the samples at 37C for 2hours to allow the Cot 1 DNA to anneal to repetitive DNA sequeces on both the sample and reference DNA. We exposed our printed arrays to 260000uJoules of UV using StrataLinker and applied a rubber cement ring around each array to form a well. After air drying the rubber cement we added our combined sample/reference hybridization solution onto the array. We placed a silicone gasket around the edge of the wells and laid a clean glass microscope slide on top of the gasket. We clamped the assembly together using binder clips to create an air tight environment. The arrays were incubated or 48-68 hours at 37C on a slowly rocking table (1rpm). After disassembling the hybridization chamber, we rinsed off the excess hybridization fluid with PN buffer (PN: 0.1 M sodium phosphate, 0.1% nonidet P40, pH 8), then washed the arrays once in a solution containing 50% formamide in 2xSSC for 15 min. at 45C and finally in PN buffer at room temperature for 15 min. We removed the ring of rubber cement, drained excess liquid from the arrays, mounted them in a solution containing 90% glycerol, 10% PBS and 1 mM DAPI, and sealed them with a cover slip.

scan_protocol: Arrays were imaged using a custom built CCD array imaging system  and analyzed using the UCSF Spot Program to calculate Cy3/Cy5 ratios.

data_processing: The aCGH data from our cohort were processed by the custom program SPROC in order to automatically filter out data points with low DAPI intensity, low correlation between Cy3 and Cy5 within each spot, and low reference/DAPI signal intensity. Clones whose ratios were derived from only one of the triplicate spots or with a triplicate log2 SD >0.2 were set as missing. The tumor data was filtered for unmapped clones and poorly performing ones identified as those missing in more than 50% of the tumor samples. A second set of triplicate spots for 38 of these clones were averaged resulting in a total of 1965 clones remaining after processing. The data were mapped to the May 2004 freeze of the human DNA sequence.

source_name: Circulating tumor cells Isolated from peripheral blood of metastatic breast cancer patient

label_protocol: BioPrime Array CGH Labeling System (Invitrogen) was used to enzymatically label approximately 600ng of test or reference DNA with Cyanine 3-dCTP or Cyanine 5-dCTP (Amersham), respectively. Briefly, DNA suspended in 11uL of water and 10uL of random prime mix was heated for 10mins at 100C and snap cooled on ice. 2.5uL of 10x-dNTP mix (8uL of 100mM dATP, 8uL of 100mM dGTP, 8uL of 100mM dTTP, 4uL of 100mM dCTP, 2uL 1M Tris, 0.4uL of 0.5M EDTA, and water), 1uL of Cy3 or Cy5 labeled dCTP( 1mM) and 0.6uL Exo-Klenow (40 U/uL) were added to the denatured DNA and incubated for 12 -20 hours at 37C. Unincorporated nucleotides were removed using a Sephadex G-50 spin-columns.

extract_protocol: Magnetic beads coated with EpCAM mAb are used to enrich for tumor cells and then subjected to FACS analysis using differentially labeled mAbs to distinguish tumor cells (EpCAM+) from leukocytes (CD45+) during sorting. Using this protocol, we isolated small pools of highly purified CTCs from breast cancer patients. DNA from Tumor cells sorted in 10uL of TE was amplified using the GenomePlex Single Cell Whole Genome Amplification Kit (Sigma-Aldrich) according to manufacturer’s protocol. The approach was evaluated using breast tumor cell model systems, BT474 and MCF7, and CTCs metastatic breast cancer (MBC) patients. Microdissection and DNA extraction of archival formalin-fixed paraffin-embedded (FFPE) primary tumor were done as previously described in Waldman FM, DeVries S, Chew KL, Moore DH, 2nd, Kerlikowske K, Ljung BM. Chromosomal alterations in ductal carcinomas in situ and their in situ recurrences. J Natl Cancer Inst 2000;92(4):313-20.

treatment_protocol: Array CGH experiments of Circulating Tumor, Primary Tumor, or cell line genomic DNA as test samples and normal human genomic DNA as reference sample.

tag: cell type

tag: assayed molecule

value: Whole genome amplified genomic DNA

source_name: Promega reference Male genomic DNA

value: Whole genome amplified reference male genomic DNA


title: CTC_123024_20CTC

description:
Sample name: 123024_20CTC
Matched TLDA sample name: CTC.123024.20CTC.1.T2
Matched TLDA sample Accession Number: GSM998106

value: Circulating tumor cells Isolated from peripheral blood of metastatic breast cancer patient


title: CTC_122030_20CTC

description:
Sample name: 122030_20CTC
Matched TLDA sample name: CTC.122030.20CTC.1
Matched TLDA sample Accession Number: GSM998093


title: CTC_120153_20CTC

description:
Sample name: 120153_20ctc
Matched TLDA sample name: CTC.120153.20CTC.1.T3
Matched TLDA sample Accession Number: GSM998062


title: PEO1, technical rep 1

description:
PEO1_REP1
Ovarian cancer cell line isolated from patient before chemotherapy.


title: CTC_117494_20CTC

description:
Sample name: 117494_20CTC
Matched TLDA sample name: CTC.117494.20CTC.1
Matched TLDA sample Accession Number: GSM998050


title: CTC_117548_20CTC

description:
Sample name: 117548_20CTC
Matched TLDA sample name: CTC.117548.20CTC.1
Matched TLDA sample Accession Number: GSM998051


title: CTC_121295_20CTC

description:
Sample name: 121295_20CTC
Matched TLDA sample name: CTC.121295.20CTC
Matched TLDA sample Accession Number: GSM998084


title: CTC_119826_20CTC

description:
Sample name: 119826_20CTC
Matched TLDA sample name: CTC.119826.20CTC.1
Matched TLDA sample Accession Number: GSM998056


title: CTC_120850_20CTC

description:
Sample name: 120850_20CTC
Matched TLDA sample name: CTC.120850.20CTC.1.T4
Matched TLDA sample Accession Number: GSM998077


title: PEO1

description:
PEO1_REP0
Ovarian cancer cell line isolated from patient before chemotherapy.


title: CTC_116285_20CTC

description:
Sample name: 116285_20CTC
Matched TLDA sample name: CTC.116285.20CTC.1
Matched TLDA sample Accession Number: GSM998045


title: CTC_122478_20CTC

description:
Sample name: 122478_20CTC
Matched TLDA sample name: CTC.122478.20CTC.1
Matched TLDA sample Accession Number: GSM998100


title: CTC_120670_20CTC

description:
Sample name: 120670_20CTC
Matched TLDA sample name: CTC.120670.20CTC.1.T3.A1
Matched TLDA sample Accession Number: GSM998072


title: CTC_121975_20CTC

description:
Sample name: 121975_20CTC
Matched TLDA sample name: CTC.121975.20CTC.1
Matched TLDA sample Accession Number: GSM998088


title: ZT26

status: Public on Dec 06 2012

type: RNA

city: Lausanne

first: Nouria

last: Hernandez

state: Vaud

address: Dorigny

department: CIG

country: Switzerland

institute: UNIL

description: gene expression data from mouse liver at ZT26

hyb_protocol: Affymetrix Mouse Gene 1.0 ST arrays were hybridized with 2.5μg of biotinylated target, at  45°C for 17 hours washed and stained according to the protocol described in Affymetrix GeneChip Expression Analysis Manual (Fluidics protocol FS450_0007).

scan_protocol: The arrays were scanned using the Affymetrix GeneChip Scanner 3000 7G and raw data was extracted from the scanned images and analyzed with the Affymetrix Power Tools software package.

data_processing: Affymerix Expression Console 1.1.2637.26569, RMA normalization

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: mouse liver at ZT26

label_protocol: For each sample, 100ng of total RNA were amplified using the WT Expression kit (Invitrogen, Carlsbad, USA; catalogue no. 4411974); the resulting sense cDNA was fragmented using UDG (uracil DNA glycosylase) and APE 1 (apurinic/apyrimidic endonuclease 1) and biotin-labelled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labelling kit (Affymetrix, Santa Clara, USA; catalogue no. 900671, Santa Clara, USA).

growth_protocol: C57/BL6 male mice (9-11 week old) were housed in a 12h Light/12h dark light regimen for 2 weeks with food and water available ad libitum during night and day.

extract_protocol: Trizol extraction of total RNA, followed by purification with the miRNeasy Mini Kit (Qiagen) following the manufacturer instructions. For each ZT, 500 ng of total RNA from each of the five mouse livers were pooled and hybridized to Mouse Gene 1.0ST arrays (Affymetrix).

treatment_protocol: The mice were entrained with a 12h Light/12h dark light regimen with food access between ZT12 and ZT24 for 7 days (ZT0 is defined as the time when the lights are turned on and ZT12 as the time when lights are turned off). At ZT02, ZT06, ZT10, ZT14, ZT18, ZT22 and ZT26, five mice were anesthetized with isoflurane and decapitated. The livers were perfused with 5 ml of PBS through the spleen and immediately collected. Up to 100 mg of liver was snap-frozen in liquid nitrogen and kept at -80°C for RNA extraction. The rest of the livers was immediately homogenized in PBS containing 1% formaldehyde for chromatin preparation.

tag: tissue type

value: liver

tag: strain


title: ZT14

description: gene expression data from mouse liver at ZT14

source_name: mouse liver at ZT14


title: HudsonAlpha_MethylArray_PANC-1_Methyl450K

status: Public on Sep 07 2012

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

data_processing:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeHaibMethyl450

Score in the bed files is beta value x 1000

label: Cy3 or Cy5

tag: lab

value: HudsonAlpha

tag: lab description

value: Myers - Hudson Alpha Institute for Biotechnology

tag: datatype

value: MethylArray

tag: datatype description

value: DNA Methylation Array

tag: cell

tag: cell organism

value: human

tag: cell description

value: pancreatic carcinoma, (PMID:1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays.

tag: cell karyotype

value: cancer

tag: cell lineage

value: endoderm

tag: cell sex

value: M

tag: labversion

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: obtainedby

value: UW

tag: obtainedby description

value: Stamatoyannopoulous - University of Washington

tag: replicate


title: ZT02

description: gene expression data from mouse liver at ZT02

source_name: mouse liver at ZT02

tag: tissue type

tag: strain


title: HudsonAlpha_MethylArray_U87_Methyl450K

tag: lab

tag: lab description

value: ectoderm

value: F


title: ZT10

description: gene expression data from mouse liver at ZT10

source_name: mouse liver at ZT10


title: Deletion of SPBC2A9.02, biological rep 1

status: Public on Sep 11 2012

city: Shanghai

first: Wenjuan

last: Mo

address: No. 220 Handan Road

department: Life School

country: China

institute: Fudan University

description:
Pombe 8-SPBC2A9.02
Gene expression data from deletion of SPBC2A9.02.

hyb_protocol: Fragmentation of the labeled aRNA prepared the target for hybridization to GeneChip® 3' expression arrays with GeneChip® hybridization oven 640.

scan_protocol: The arrays were scanned with the GeneArray Scanner 3000 by the Command Console® (AGCC) Software.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as the normalization method. The presented gene expression intensity in each array is the mean value.

label: Biotin

organism: Schizosaccharomyces pombe

source_name: Deletion of SPBC2A9.02 during expontentially growing stage

label_protocol: Biotinylated cRNA were prepared according to the standard protocol of the GeneChip 3' IVT Express Kit supplied by Affymetrix.

growth_protocol: Cells were harvested during the expontentially growing stage (OD600 ranged from 0.5 to 1.0).

extract_protocol: Total RNA was extracted and purified using the Qiagen RNeasy Mini Kit.

treatment_protocol: No treatment was applied.

tag: genotype

value: SPBC2A9.02 deletion

tag: growth phase

value: exponential


title: Deletion of ash2, biological rep 1

description:
Pombe 7-ash2
Gene expression data from deletion of ash2.

source_name: Deletion of ash2 during expontentially growing stage

value: ash2 deletion


title: ZT22

description: gene expression data from mouse liver at ZT22

source_name: mouse liver at ZT22

value: liver


title: SM019_5.2_Tnfrsfb1_mock_d4_1

status: Public on Sep 13 2012

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for all processing steps, including hybridization and array washing.

scan_protocol: Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505B) using the XDR setting.

data_processing:
Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1-v5_95_Feb07 extraction protocol.
platform: x86_64-redhat-linux-gnu
arch: x86_64
os: linux-gnu
system: x86_64, linux-gnu
R version 2.12.2 (2011-02-25)
bioconductor packages: limma
Information on package: 'limma'
limma version: 3.6.9
limma date: 2010/12/01version
For the generation of the normalized data, the limma package was used. Background correction was performed (method=normexp, offset=1). Data was quantile normalized between arrays with the quantile normalization method and then log2 transformed.

source_name: lung, Tnfrsf1b KO, mock infected, day 4

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for all processing steps, including Cy3-cDNA probe preparation.

extract_protocol: Lung tissue was removed from RNAlater, washed in a small volume of Trizol, homogenized in 10-20 volumes (w/v) TRIzol and stored at -80°C until RNA isolation. All TRIzol lysates were processed simultaneously: they were phase-separated, and RNA was isolated from the aqueous phase (diluted 2-fold with RLT buffer) using Qiagen RNeasy Mini columns and the manufacturer's recommended protocol (Qiagen Inc., Valencia, CA). RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip format, and only intact RNA was used for microarray analyses.

treatment_protocol:
Ten-week-old mice were infected by intranasal instillation of 10^5 PFU of SARS MA15 in 50 µl of PBS or mock-infected with PBS alone. At days 4 and 7 days post-infection, lungs were harvested.
Specific lobes of the lung from each animal were harvested and briefly rinsed in cold (4ºC) PBS. Following the RNAlater (Ambion) protocol, tissue was cut into small chunks (<0.5cm in any single dimension) and placed immediately into a 10-20 volumes (w/v) (e.g. 100mg/ml) RNAlater. After a 4ºC incubation for overnight, samples were stored at -80ºC until further processing.

tag: strain/background

value: Tnfrsf1b KO

tag: gender

value: female

tag: age

value: 10 weeks

tag: tissue

value: lung

value: mock infected

tag: time of sample collection

value: day 4 post-infection


title: SM019_6.1_Tnfrsfb1_mock_d7_2

source_name: lung, Tnfrsf1b KO, mock infected, day 7

value: day 7 post-infection


title: HudsonAlpha_MethylArray_NHDF-neo_Methyl450K

source_name: NHDF-neo

value: HudsonAlpha

value: Myers - Hudson Alpha Institute for Biotechnology

tag: datatype

value: MethylArray

tag: datatype description

value: DNA Methylation Array

tag: cell

value: NHDF-neo

tag: cell organism

value: human

tag: cell description

value: neonatal dermal fibroblasts

tag: cell karyotype

value: normal

tag: cell lineage

value: mesoderm

tag: cell sex

value: U

tag: labversion


title: Wild type, biological rep 1

description:
Pombe 9-Wild type
Gene expression data from wild type.

source_name: Wild type during expontentially growing stage

tag: strain

value: SP286 diploid

value: wild type, h+ ade6-M210 ura4-D18 leu1-32

value: exponential


title: HudsonAlpha_MethylArray_ovcar-3_Methyl450K

tag: lab

tag: lab description

value: ovarian adenocarcinoma, "the NIH:OVCAR-3 line was established in 1982 by T.C. Hamilton, et al. from the malignant ascites of a patient with progressive adenocarcinoma of the ovary." - ATCC. (PMID:6604576)

value: cancer

value: F

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: obtainedby

value: UW

tag: obtainedby description

value: Stamatoyannopoulous - University of Washington

tag: replicate


title: ZT18

description: gene expression data from mouse liver at ZT18

source_name: mouse liver at ZT18

tag: tissue type

value: liver


title: SM019_4.3_Tnfrsfb1_MA15_d4_3

source_name: lung, Tnfrsf1b KO, infected with SARS MA15 virus, day 4

tag: strain/background

tag: genotype

value: Tnfrsf1b KO

tag: gender

value: female

tag: age

value: 10 weeks

tag: tissue

value: lung

value: infected with 10^5 PFU of SARS MA15 virus

tag: time of sample collection

value: day 4 post-infection


title: Deletion of SPAC27D7.08C, biological rep 1

description:
Pombe 5-SPAC27D7.08C
Gene expression data from deletion of SPAC27D7.08C.

source_name: Deletion of SPAC27D7.08C during expontentially growing stage

value: SPAC27D7.08C deletion

tag: growth phase


title: Deletion of pab1, biological rep 1

description:
Pombe 3-pab1
Gene expression data from deletion of pab1.

source_name: Deletion of pab1 during expontentially growing stage

value: pab1 deletion


title: Deletion of SPAC3F10.17, biological rep 1

description:
Pombe 6-SPAC3F10.17
Gene expression data from deletion of SPAC3F10.17.

source_name: Deletion of SPAC3F10.17 during expontentially growing stage

value: SPAC3F10.17 deletion


title: Deletion of meu29+, biological rep 1

description:
Pombe 4-meu29
Gene expression data from deletion of meu29+.

source_name: Deletion of meu29+ during expontentially growing stage

value: meu29+ deletion

value: exponential


title: SM019_5.3_Tnfrsfb1_mock_d4_2

value: mock infected


title: SM019_4.5_Tnfrsfb1_MA15_d7_2

source_name: lung, Tnfrsf1b KO, infected with SARS MA15 virus, day 7

value: day 7 post-infection


title: SM019_4.1_Tnfrsfb1_MA15_d4_1


title: SM019_6.2_Tnfrsfb1_mock_d7_3


title: SM019_5.4_Tnfrsfb1_mock_d4_3


title: ZT06

description: gene expression data from mouse liver at ZT06

source_name: mouse liver at ZT06


title: SM019_4.2_Tnfrsfb1_MA15_d4_2


title: SM019_5.1_Tnfrsfb1_MA15_d7_3


title: HudsonAlpha_MethylArray_MCF10A-Er-Src_Methyl450K_4OHTAM_1uM_36hr

value: HudsonAlpha

value: Myers - Hudson Alpha Institute for Biotechnology

tag: datatype

value: MethylArray

tag: datatype description

value: DNA Methylation Array

tag: cell

tag: cell organism

value: human

tag: cell description

value: mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER)

tag: cell lineage

value: ectoderm

tag: cell sex

value: F

tag: labversion

value: (To replace TAM_1uM_36hr) 36 h with 1 uM 4-hydroxytamoxifen (Myers)

value: Stanford

value: Snyder - Stanford University


title: Deletion of sec65+, biological rep 1

description:
Pombe 2-sec65
Gene expression data from deletion of sec65+.

source_name: Deletion of sec65+ during expontentially growing stage

value: sec65+ deletion


title: HudsonAlpha_MethylArray_SK-N-SH_RA_Methyl450K

tag: lab

tag: lab description

value: neuroblastoma cell line, treatment:differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.)

tag: cell karyotype

value: cancer

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: obtainedby

value: UW

tag: obtainedby description

value: Stamatoyannopoulous - University of Washington

tag: replicate


title: HudsonAlpha_MethylArray_HRCEpiC_Methyl450K

source_name: HRCEpiC

value: HudsonAlpha

value: HRCEpiC

value: renal cortical epithelial cells

value: normal

value: mesoderm

value: U


title: HudsonAlpha_MethylArray_HPAEpiC_Methyl450K

source_name: HPAEpiC

value: Myers - Hudson Alpha Institute for Biotechnology

value: MethylArray

value: DNA Methylation Array

value: HPAEpiC

value: human

value: pulmonary alveolar epithelial cells


title: Deletion of sgf73+, biological rep1

description:
Pombe 1-sgf73
Gene expression data from deletion of sgf73+.

source_name: Deletion of sgf73+ during expontentially growing stage

tag: genotype

value: sgf73+ deletion

tag: growth phase

value: exponential


title: HudsonAlpha_MethylArray_SK-N-SH_Methyl450K

source_name: SK-N-SH

tag: datatype

tag: datatype description

value: SK-N-SH

value: neuroblastoma, newly promoted to tier 2:not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual.

value: cancer

value: ectoderm

value: F

value: No special treatment or protocol applies


title: HudsonAlpha_MethylArray_HCT-116_Methyl450K

value: HudsonAlpha

tag: cell

tag: cell organism

value: colorectal carcinoma (PMID:7214343)

value: endoderm

value: M


title: HudsonAlpha_MethylArray_HL-60_Methyl450K

value: Myers - Hudson Alpha Institute for Biotechnology

value: MethylArray

tag: cell description

value: promyelocytic leukemia cells, (PMID:276884)

tag: cell lineage

value: mesoderm

value: UW

value: Stamatoyannopoulous - University of Washington


title: HudsonAlpha_MethylArray_HMEC_Methyl450K

source_name: HMEC

value: DNA Methylation Array

value: HMEC

value: human

value: mammary epithelial cells

value: normal

tag: cell sex

value: U

tag: labversion


title: HudsonAlpha_MethylArray_T-47D_Methyl450K_DMSO_0.02pct_24hr

tag: lab

tag: lab description

value: epithelial cell line derived from a mammary ductal carcinoma.

value: cancer

value: F

value: 24 h with 0.02% Dimethyl sufloxide (DMSO) (Myers)


title: HudsonAlpha_MethylArray_HEEpiC_Methyl450K

source_name: HEEpiC

value: HudsonAlpha

value: HEEpiC

value: esophageal epithelial cells

tag: cell karyotype

value: endoderm

tag: treatment

value: No special treatment or protocol applies


title: HudsonAlpha_MethylArray_H1-hESC_Methyl450K

growth_protocol: missing

value: Myers - Hudson Alpha Institute for Biotechnology

value: MethylArray

value: embryonic stem cells

value: inner cell mass

value: M

tag: treatment description

tag: obtainedby


title: HudsonAlpha_MethylArray_HNPCEpiC_Methyl450K

source_name: HNPCEpiC

value: DNA Methylation Array

value: HNPCEpiC

value: human

value: non-pigment ciliary epithelial cells

value: UW

tag: obtainedby description

value: Stamatoyannopoulous - University of Washington

tag: replicate


title: HudsonAlpha_MethylArray_HCPEpiC_Methyl450K

source_name: HCPEpiC

value: HCPEpiC

value: choroid plexus epithelial cells

value: normal

value: ectoderm

value: U


title: HudsonAlpha_MethylArray_HCM_Methyl450K

source_name: HCM

value: HudsonAlpha

value: HCM

value: cardiac myocytes

value: mesoderm

value: No special treatment or protocol applies


title: HudsonAlpha_MethylArray_BE2_C_Methyl450K

value: Myers - Hudson Alpha Institute for Biotechnology

value: MethylArray

value: neuroblastoma, BE-C is a clone of the SK-N-BE neuroblastoma cell line (see ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from a 2-year-old individual with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy.

value: cancer

value: M


title: HudsonAlpha_MethylArray_GM12878_Methyl450K

value: DNA Methylation Array

value: human

value: B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

value: F


title: HudsonAlpha_MethylArray_GM12891_Methyl450K

value: B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment:Epstein-Barr Virus transformed


title: HudsonAlpha_MethylArray_LNCaP_Methyl450K

source_name: LNCaP

value: LNCaP

value: prostate adenocarcinoma, "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC. (Horoszewicz et al. LNCaP Model of Human Prostatic Carcinoma. Cancer Research 43, 1809-1818, April 1983.)

value: endoderm

value: UW

value: Stamatoyannopoulous - University of Washington


title: HudsonAlpha_MethylArray_PrEC_Methyl450K

source_name: PrEC

value: HudsonAlpha

value: PrEC

value: prostate epithelial cell line

value: normal

value: epithelial

value: U


title: HudsonAlpha_MethylArray_PFSK-1_Methyl450K

value: Myers - Hudson Alpha Institute for Biotechnology

value: MethylArray

value: neuroectodermal cell line derived from a cerebral brain tumor, (PMID:1316433)

value: cancer

value: ectoderm

value: M

value: No special treatment or protocol applies


title: HudsonAlpha_MethylArray_MCF-7_Methyl450K

value: DNA Methylation Array

value: human

value: mammary gland, adenocarcinoma. (PMID:4357757), newly promoted to tier 2:not in 2011 analysis

value: F

value: Duke

value: Crawford - Duke University


title: HudsonAlpha_MethylArray_NT2-D1_Methyl450K

value: HudsonAlpha

value: malignant pluripotent embryonal carcinoma (NTera-2), "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC. (PMID:6694356)

value: inner cell mass

value: Stanford

value: Snyder - Stanford University


title: HudsonAlpha_MethylArray_GM12892_Methyl450K

value: Myers - Hudson Alpha Institute for Biotechnology

value: MethylArray

value: B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment:Epstein-Barr Virus transformed

value: mesoderm


title: HudsonAlpha_MethylArray_Jurkat_Methyl450K

source_name: Jurkat

value: Jurkat

value: T lymphoblastoid derived from an acute T cell leukemia, "The Jurkat cell line was established from the peripheral blood of a 14 year old boy by Schneider et al., and was originally designated JM." - ATCC. (PMID:68013)

value: cancer

value: M

value: UW

value: Stamatoyannopoulous - University of Washington


title: HudsonAlpha_MethylArray_A549_Methyl450K_EtOH_0.02pct

value: DNA Methylation Array

value: human

value: epithelial cell line derived from a lung carcinoma tissue. (PMID:175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2:not in 2011 analysis

value: endoderm

value: 1 h with 0.02% Ethanol (Myers)


title: HudsonAlpha_MethylArray_SK-N-MC_Methyl450K

source_name: SK-N-MC

value: HudsonAlpha

value: SK-N-MC

value: neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.)

value: ectoderm

value: F

value: No special treatment or protocol applies


title: HudsonAlpha_MethylArray_HUVEC_Methyl450K

source_name: HUVEC

value: Myers - Hudson Alpha Institute for Biotechnology

value: MethylArray

value: HUVEC

value: umbilical vein endothelial cells

value: normal

value: mesoderm

value: U


title: HudsonAlpha_MethylArray_ECC-1_Methyl450K

value: DNA Methylation Array

value: human

value: epithelial cell line derived from an endometrium adenocarcinoma, fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes

value: cancer


title: HudsonAlpha_MethylArray_HEK293_Methyl450K

value: HudsonAlpha

value: embryonic kidney, cells contain Adenovirus 5 DNA (PMID:11967234)

value: Stanford

value: Snyder - Stanford University


title: HudsonAlpha_MethylArray_HCF_Methyl450K

source_name: HCF

value: HCF

value: cardiac fibroblasts

value: UW

value: Stamatoyannopoulous - University of Washington


title: HudsonAlpha_MethylArray_HRE_Methyl450K

source_name: HRE

value: Myers - Hudson Alpha Institute for Biotechnology

value: MethylArray

value: HRE

value: renal epithelial cells

value: No special treatment or protocol applies


title: HudsonAlpha_MethylArray_NHBE_Methyl450K

source_name: NHBE

value: DNA Methylation Array

value: NHBE

value: bronchial epithelial cells

value: normal

value: endoderm

value: F


title: HudsonAlpha_MethylArray_HRPEpiC_Methyl450K

source_name: HRPEpiC

value: HudsonAlpha

value: HRPEpiC

value: human

value: retinal pigment epithelial cells

value: ectoderm

value: U


title: HudsonAlpha_MethylArray_MCF10A-Er-Src_Methyl450K

value: Myers - Hudson Alpha Institute for Biotechnology

value: mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER)

value: Stanford

value: Snyder - Stanford University


title: HudsonAlpha_MethylArray_NB4_Methyl450K

value: MethylArray

value: acute promyelocytic leukemia cell line. (PMID:1995093)

value: cancer

value: mesoderm

value: No special treatment or protocol applies

value: UW

value: Stamatoyannopoulous - University of Washington


title: HudsonAlpha_MethylArray_NH-A_Methyl450K

source_name: NH-A

value: HudsonAlpha

value: DNA Methylation Array

value: NH-A

value: astrocytes (also called Astrocy)

value: normal


title: HudsonAlpha_MethylArray_AG10803_Methyl450K

value: human

value: abdominal skin fibroblasts from apparently heathly 22 year old, "8% of the cells examined showing random chromosome loss, 2% showing random chromosome gain, and 2% showing 69,XYY" -Coriell

value: M


title: HudsonAlpha_MethylArray_Caco-2_Methyl450K

value: Myers - Hudson Alpha Institute for Biotechnology

value: endoderm


title: HudsonAlpha_MethylArray_AG09319_Methyl450K

value: MethylArray

value: gum tissue fibroblasts from apparently heathly 24 year old

value: F


title: HudsonAlpha_MethylArray_GM06990_Methyl450K

value: B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah, treatment:Epstein-Barr Virus transformed

value: mesoderm


title: HudsonAlpha_MethylArray_CMK_Methyl450K

source_name: CMK

value: CMK

value: acute megakaryocytic leukemia cells, "established from the peripheral blood of a 10-month-old boy with Down's syndrome and acute megakaryocytic leukemia (AML M7) at relapse in 1985" - DSMZ. (PMID:3016165)

value: cancer

value: No special treatment or protocol applies

value: UW


title: HudsonAlpha_MethylArray_HAEpiC_Methyl450K

source_name: HAEpiC

value: HudsonAlpha

value: DNA Methylation Array

value: HAEpiC

value: amniotic epithelial cells

value: U

value: Stamatoyannopoulous - University of Washington


title: HudsonAlpha_MethylArray_GM19239_Methyl450K

value: Myers - Hudson Alpha Institute for Biotechnology

value: human

value: B-lymphocyte, lymphoblastoid, International HapMap Project, Yoruba in Ibadan, Nigera, treatment:Epstein-Barr Virus transformed

value: M

value: Duke

value: Crawford - Duke University


title: HudsonAlpha_MethylArray_SAEC_Methyl450K

source_name: SAEC

value: MethylArray

value: SAEC

value: small airway epithelial cells

value: normal

value: endoderm


title: HudsonAlpha_MethylArray_AoSMC_Methyl450K

source_name: AoSMC

value: HudsonAlpha

value: AoSMC

value: aortic smooth muscle cells

value: mesoderm

value: No special treatment or protocol applies


title: HudsonAlpha_MethylArray_AG09309_Methyl450K

value: DNA Methylation Array

value: adult toe fibroblast from apparently healthy 21 year old, "7% of the cells examined showing random chromosome loss/gain" -Coriell

value: F

value: UW

value: Stamatoyannopoulous - University of Washington


title: HudsonAlpha_MethylArray_K562_Methyl450K

value: Myers - Hudson Alpha Institute for Biotechnology

value: human

value: leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC

value: cancer


title: HudsonAlpha_MethylArray_Hepatocytes_Methyl450K

source_name: Hepatocytes

value: MethylArray

value: Hepatocytes

value: primary hepatocytes, liver perfused by enzymes to generate single cell suspension

value: B

value: Duke

value: Crawford - Duke University


title: HudsonAlpha_MethylArray_AG04450_Methyl450K

value: HudsonAlpha

value: fetal lung fibroblast

value: normal

value: endoderm

value: M


title: HudsonAlpha_MethylArray_HepG2_Methyl450K

value: DNA Methylation Array

value: hepatocellular carcinoma

value: No special treatment or protocol applies


title: HudsonAlpha_MethylArray_AG04449_Methyl450K

value: Myers - Hudson Alpha Institute for Biotechnology

value: human

value: fetal buttock/thigh fibroblast

value: UW

value: Stamatoyannopoulous - University of Washington


title: HudsonAlpha_MethylArray_ProgFib_Methyl450K

source_name: ProgFib

value: MethylArray

value: ProgFib

value: fibroblasts, Hutchinson-Gilford progeria syndrome (cell line HGPS, HGADFN167, progeria research foundation)


title: HudsonAlpha_MethylArray_SKMC_Methyl450K

source_name: SKMC

value: SKMC

value: skeletal muscle cells

value: mesoderm

value: U


title: HudsonAlpha_MethylArray_HIPEpiC_Methyl450K

source_name: HIPEpiC

value: HudsonAlpha

value: HIPEpiC

value: iris pigment epithelial cells

value: normal

value: ectoderm


title: HudsonAlpha_MethylArray_RPTEC_Methyl450K

source_name: RPTEC

value: Myers - Hudson Alpha Institute for Biotechnology

value: DNA Methylation Array

value: RPTEC

value: renal proximal tubule epithelial cells

value: No special treatment or protocol applies


title: HudsonAlpha_MethylArray_HeLa-S3_Methyl450K

value: MethylArray

value: human

value: cervical carcinoma

value: cancer

value: F

value: UW

value: Stamatoyannopoulous - University of Washington


title: HudsonAlpha_MethylArray_BJ_Methyl450K

source_name: BJ

value: HudsonAlpha

value: BJ

value: skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC.  (PMID:9916803)

value: M


title: HudsonAlpha_MethylArray_IMR90_Methyl450K

value: fetal lung fibroblasts, newly promoted to tier 2:not in 2011 analysis

value: normal

value: endoderm


title: 2 h, CCRF-CEM-C7-14, biological rep1

status: Public on Sep 01 2012

city: Manchester

first: Daphne

last: Chen

address: Oxford Road

institute: University of Manchester

description:
T2-1
Cancer Research 58: 3684-3693, 1998 (PMID 9721879).
ALL

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Affymetric GeneChip Scanner 3000 7G

data_processing: Probes were normalized using the RMA normalization method (R with Bioconductor).

source_name: CCRF-CEM-C7-14 with dexamethasone treatment for 2 h

label_protocol: Standard Affymetrix protocol.

growth_protocol: CCRF-CEM-C7-14  cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum and 1% penicillin and streptomycin (Cambrex, NJ, USA) and were seeded into 60 mm plates for RNA extraction. Prior to the hormone treatment, the media was changed to RPMI-1640 supplemented with 10% charcoal-stripped fetal bovine serum (HyClone, UT, USA).

extract_protocol: Cells were harvested and the total RNA was extracted using the RNeasy® Plus Mini Kit and QIAshredder (Qiagen, Hilden, Germany), following the manufacturer's guidelines. RNA was quantified using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies), and RNA quality was determined by means of an RNA 6000 NanoAssay on an Agilent 2100 Bioanalyzer.

treatment_protocol: Cells were treated with 1 µM dexamethasone (Dex) (Sigma, MO, USA) at the indicated time points (0, 2 and 10 h).

tag: cell line

tag: cell type

value: leukemia

value: dexamethasone

tag: time point

value: 2 h


title: 2 h, CCRF-CEM-C7-14, biological rep2

description:
T2-2
Cancer Research 58: 3684-3693, 1998 (PMID 9721879).
ALL


title: 0 h, CCRF-CEM-C7-14, biological rep1

description:
T0-1
Cancer Research 58: 3684-3693, 1998 (PMID 9721879).
ALL

source_name: CCRF-CEM-C7-14 before dexamethasone treatment (0 h)

value: 0 h


title: 2 h, CCRF-CEM-C7-14, biological rep3

description:
T2-3
Cancer Research 58: 3684-3693, 1998 (PMID 9721879).
ALL


title: 0 h, CCRF-CEM-C7-14, biological rep3

description:
T0-3
Cancer Research 58: 3684-3693, 1998 (PMID 9721879).
ALL


title: 10 h, CCRF-CEM-C7-14, biological rep2

description:
T10-2
Cancer Research 58: 3684-3693, 1998 (PMID 9721879).
ALL

source_name: CCRF-CEM-C7-14 with dexamethasone treatment for 10 h


title: Day 17, Patient 205 (replicate) with poor risk

description:
PR_205_rep_Day 17
British Journal of Haematology 129 (6): 734-745, 2005 (PMID 15952999).

source_name: BCR-ABL patient with poor risk after treatment (day 17)

growth_protocol: Samples were obtained from 10 children with Philadelphia positive (Ph+) ALL treated uniformly. They were categorized as good risk if the marrow had <25% blasts after 8 days of therapy without imatinib and poor risk if the blast count was >25%.

extract_protocol: Cells were Ficoll separated from bone marrow aspirates. RNA was extracted using Trizol and quantified using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies). RNA quality was assessed using the RNA 6000 NanoAssay on an Agilent 2100 Bioanalyser.

treatment_protocol: The patients received 8 days of Dex and 1 dose each of anthracycline, vincristine and L-Asparaginase, according to the EsphALL protocol. Samples were analysed at day 0 (untreated) and day 17.

tag: tissue

value: bone marrow cells

tag: developmental stage

value: child

tag: disease state

value: Philadelphia positive acute lymphoblastic leukemia ((Ph+) ALL)

tag: risk

value: poor

value: dexamethasone, anthracycline, vincristine, L-Asparaginase

value: day 17

tag: patient identifier


title: Day 17, Patient 184 with good risk

description:
GR_184_Day 17
British Journal of Haematology 129 (6): 734-745, 2005 (PMID 15952999).

source_name: BCR-ABL patient with good risk after treatment (day 17)

value: good


title: Day 0, Patient 205 with poor risk

description:
PR_205_Day 0
British Journal of Haematology 129 (6): 734-745, 2005 (PMID 15952999).

source_name: BCR-ABL patient with poor risk before treatment (day 0)

value: day 0


title: Day 17, Patient 256 with good risk

description:
GR_256_Day 17
British Journal of Haematology 129 (6): 734-745, 2005 (PMID 15952999).


title: Day 0, Patient 341 with good risk

description:
GR_341_Day 0
British Journal of Haematology 129 (6): 734-745, 2005 (PMID 15952999).

source_name: BCR-ABL patient with good risk before treatment (day 0)


title: Day 0, Patient 241 with poor risk

description:
PR_241_Day 0
British Journal of Haematology 129 (6): 734-745, 2005 (PMID 15952999).


title: Day 17, Patient 205 with poor risk

description:
PR_205_Day 17
British Journal of Haematology 129 (6): 734-745, 2005 (PMID 15952999).


title: mDCs_Mock_Human6

status: Public on Jul 11 2012

city: Cleveland

first: Peter

middle: A

last: Wilkinson

state: Ohio

address: 2103 Cornell Road

department: Pathology / Systems Biology & Bioinformatics

institute: Case Western Reserve University

description:
4807240040_G
mDCs from Human6, Mock incubation.

hyb_protocol: Microarray analysis was conducted using 750ng of biotinylated cRNA hybridized to Human RefSeq-8 V3 BeadChips (Illumina) at 58°C for 20 hours, according to Illumina's direct hybridization protocol. The hybridized BeadChips were washed, blocked, stained and scanned according to Illumina's direct hybridization protocol.

scan_protocol: The arrays were scanned using an Illumina BeadStation 500GX scanner and quantified using GenomeStudio software (Illumina).

data_processing: Analysis of the GenomeStudio output data was conducted using the R statistical language and various software packages from Bioconductor. Missing values were imputed using the KNN algorithm from the impute R package. Quantile normalization was applied, followed by a log2 transformation.

source_name: FACSAria-purified mDCs population, unexposed for 24 hrs

label_protocol: Biotinylated cRNA was generated following the TotalPrep RNA labeling kit from Ambion.

extract_protocol: The cells were harvested and placed at -80C in RLT buffer. RNA was isolated using RNeasy Micro Kits (QIAgen) according to the manufacturer’s protocol. The isolated total RNA was checked for quantity and quality using a NanoDrop 2000c spectrophotometer (Thermo Fisher Scientific) and an Experion Automated Electrophoresis System.  Samples with an RQI classification ≥7.0 were selected to proceed downstream to amplification.

treatment_protocol: FACSAria-purified DC populations were incubated with rAd5, rAd28, rAd35, TLR7/8-ligand, or unexposed, for 24 hours.

tag: subject

tag: cell subset

value: myeloid dendritic cells (mDCs)

tag: stimulation

value: mock


title: Day 0, Patient 193 with good risk

description:
GR_193_Day 0
British Journal of Haematology 129 (6): 734-745, 2005 (PMID 15952999).


title: 10 h, CCRF-CEM-C7-14, biological rep1

description:
T10-1
Cancer Research 58: 3684-3693, 1998 (PMID 9721879).
ALL


title: pDCs_Mock_Human6

description:
4807240041_C
pDCs from Human6, Mock incubation.

source_name: FACSAria-purified pDCs population, unexposed for 24 hrs

value: plasmacytoid dendritic cells (pDCs)


title: control 2

status: Public on Jul 16 2012

city: Boston

middle: J

last: Park

state: MA

address: 10 Shattuck St

department: Center for Biomedical Informatics

institute: Harvard Medical School

description: replicate 2

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package (Roche NimbleGen, Inc.).

source_name: HeLa

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: HeLa cells were grown in DMEM with 10% calf serum

extract_protocol: total RNA was isolated by Trizol and sent to NimbleGen Systems Inc., Madison, WI USA for library constrcution and hybridization to the 4plex human gene expression array

treatment_protocol: Cells were transduced with a pLKO.1 lentivirus expressing a non-mammalian shRNA (SigmaAldrich SHC002V and selected with puromycin for 9 days.

value: HeLa

tag: knockdown

value: lentiviral construct shRNA SHC002

tag: expression

value: H2A.Bbd-FLAG histone


title: 0 h, CCRF-CEM-C7-14, biological rep2

description:
T0-2
Cancer Research 58: 3684-3693, 1998 (PMID 9721879).
ALL

value: leukemia

tag: treatment


title: mDCs_TLR7/8_Human6

description:
4807240040_F
mDCs from Human6, TLR78 incubation.

source_name: FACSAria-purified mDCs population, incubated with TLR7/8 for 24 hrs


title: Day 17, Patient 345with poor risk

description:
PR_345_Day 17
British Journal of Haematology 129 (6): 734-745, 2005 (PMID 15952999).


title: control 1

description: replicate 1


title: Day 17, Patient 319 with good risk

description:
GR_319_Day 17
British Journal of Haematology 129 (6): 734-745, 2005 (PMID 15952999).


title: pDCs_TLR7/8_Human6

description:
4807240041_B
pDCs from Human6, TLR78 incubation.

source_name: FACSAria-purified pDCs population, incubated with TLR7/8 for 24 hrs


title: pDCs_Ad28_Human6

description:
4807240041_A
pDCs from Human6, Ad28 incubation.

source_name: FACSAria-purified pDCs population, incubated with Ad28 for 24 hrs


title: Day 17, Patient 320 with poor risk

description:
PR_320_Day 17
British Journal of Haematology 129 (6): 734-745, 2005 (PMID 15952999).


title: Day 17, Patient 277 with good risk

description:
GR_277_Day 17
British Journal of Haematology 129 (6): 734-745, 2005 (PMID 15952999).


title: Day 0, Patient 277 with good risk

description:
GR_277_Day 0
British Journal of Haematology 129 (6): 734-745, 2005 (PMID 15952999).


title: Day 0, Patient 184 with good risk

description:
GR_184_Day 0
British Journal of Haematology 129 (6): 734-745, 2005 (PMID 15952999).


title: mDCs_Ad35_Human6

description:
4807240040_E
mDCs from Human6, Ad35 incubation.

source_name: FACSAria-purified mDCs population, incubated with Ad35 for 24 hrs


title: pDCs_Mock_Human5

description:
4807240040_A
pDCs from Human5, Mock incubation.


title: mDCs_Ad5_Human6

description:
4807240040_B
mDCs from Human6, Ad5 incubation.

source_name: FACSAria-purified mDCs population, incubated with Ad5 for 24 hrs


title: mDCs_Ad28_Human6

description:
4807240040_D
mDCs from Human6, Ad28 incubation.

source_name: FACSAria-purified mDCs population, incubated with Ad28 for 24 hrs


title: pDCs_Ad35_Human5

description:
4807240038_H
pDCs from Human5, Ad35 incubation.

source_name: FACSAria-purified pDCs population, incubated with Ad35 for 24 hrs


title: mDCs_Ad35_Human5

description:
4807240038_B
mDCs from Human5, Ad35 incubation.


title: pDCs_Ad28_Human5

description:
4807240038_G
pDCs from Human5, Ad28 incubation.


title: mDCs_Ad5_Human5

description:
4726950055_G
mDCs from Human5, Ad5 incubation.


title: pDCs_Ad5_Human4

description:
4726950055_A
pDCs from Human4, Ad5 incubation.

source_name: FACSAria-purified pDCs population, incubated with Ad5 for 24 hrs


title: mDCs_TLR7/8_Human4

description:
4690176027_G
mDCs from Human4, TLR78 incubation.


title: pDCs_Mock_Human3

description:
4690176027_B
pDCs from Human3, Mock incubation.


title: pDCs_Ad28_Human3

description:
4690176024_G
pDCs from Human3, Ad28 incubation.


title: mDCs_Mock_Human4

description:
4690176027_H
mDCs from Human4, Mock incubation.


title: mDCs_TLR7/8_Human3

description:
4690176024_C
mDCs from Human3, TLR78 incubation.


title: mDCs_Ad35_Human4

description:
4690176027_F
mDCs from Human4, Ad35 incubation.


title: mDCs_Ad28_Human3

description:
4690176024_A
mDCs from Human3, Ad28 incubation.


title: pDCs_Ad35_Human4

description:
4726950055_D
pDCs from Human4, Ad35 incubation.


title: mDCs_Ad5_Human4

description:
4690176027_C
mDCs from Human4, Ad5 incubation.


title: pDCs_TLR7/8_Human4

description:
4726950055_E
pDCs from Human4, TLR78 incubation.


title: pDCs_Mock_Human4

description:
4726950055_F
pDCs from Human4, Mock incubation.


title: mDCs_Ad28_Human5

description:
4807240038_A
mDCs from Human5, Ad28 incubation.


title: mDCs_Mock_Human5

description:
4807240038_D
mDCs from Human5, Mock incubation.


title: pDCs_TLR7/8_Human3

description:
4690176027_A
pDCs from Human3, TLR78 incubation.


title: pDCs_Ad35_Human3

description:
4690176024_H
pDCs from Human3, Ad35 incubation.


title: pDCs_Ad28_Human4

description:
4726950055_C
pDCs from Human4, Ad28 incubation.


title: pDCs_Ad5_Human3

description:
4690176024_E
pDCs from Human3, Ad5 incubation.


title: mDCs_Ad28_Human4

description:
4690176027_E
mDCs from Human4, Ad28 incubation.


title: mDCs_Ad5_Human3

description:
4690176014_G
mDCs from Human3, Ad5 incubation.


title: mDCs_Mock_Human3

description:
4690176024_D
mDCs from Human3, Mock incubation.


title: mDCs_Ad35_Human3

description:
4690176024_B
mDCs from Human3, Ad35 incubation.


title: pDCs_Ad28_Human1

description:
4690176013_G
pDCs from Human1, Ad28 incubation.


title: HepG2 gambogic acid 0.75μM

status: Public on Jun 15 2012

city: Guangzhou

first: Jinbao

last: Liu

address: Dongfeng xi road 195#

institute: Guangzhou medical college

hyb_protocol: Hybridization was performed in KangChen Bio-tech Inc. (http://www.kangchen.com.cn) following standard Nimblegen protocol.

scan_protocol: Scanning was performed in KangChen Bio-tech Inc. (http://www.kangchen.com.cn) following standard Nimblegen protocol.

data_processing: Raw signal intensities were normalized in RMA method by NimbleScan v2.5, and low intensity genes were filtered (Genes that Intensity >= 50.0 in 5 out of 5 samples were chosen for further analysis).

source_name: HepG2, 0.75μM gambogic acid

label_protocol: Labeling was performed in KangChen Bio-tech Inc. (http://www.kangchen.com.cn) following standard Nimblegen protocol.

growth_protocol: The hepatocellular carcinoma cells were cultured in complete DMEM medium and supplied with 10% FBS.

extract_protocol: Total RNA was isolated using the RNeasy RNA isolation kit (Qiagen) following the supplier's protocol.

treatment_protocol: Human HepG2 heptoma cells were treated with vehicle, gambogic acid (0.25, 0.5, 0.75 uM) or bortezomib (50 nM) for 9 h, and then total RNA were extracted for DNA microarray analysis.

value: hepatoma cell line

value: 0.75μM gambogic acid


title: mDCs_Mock_Human1

description:
4690176013_F
mDCs from Human1, Mock incubation.


title: Glt25d2 cells, cortex, TRAP RNA, FLX treated, biological rep2

status: Public on Jun 01 2012

city: New York

first: Eric

middle: F

last: Schmidt

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

hyb_protocol: Standard Affymetrix protocol for the mouse 430 2.0 platform.

data_processing: GCRMA normalization within biological replicate groups was performed in GeneSpring GX 7.3.1.

label_protocol: Affymetrix two cycle amplification kit, starting with 15 ng of total RNA.

extract_protocol: TRAP affinity purification of ribosomes from BAC transgenic mice (see accompanying manuscript), followed by Trizol-LS extraction, DNase treatment, and RNeasy Minelute Cleanup.

treatment_protocol: Glt25d2 bacTRAP mice were administered either a fluoxetine (0.167 mg/ml)/1% saccharine solution (FLX) or 1% saccharine alone (VEH) for 15-18 days and then sacrificed for TRAP profiling.

tag: strain

value: backcrossed 3-5 generations on C57BL/6 from FVB

tag: rna

value: TRAP

tag: driver

tag: line

value: cortex

value: fluoxetine


title: WT_CIS, rep3

status: Public on Jun 30 2012

city: Seoul

first: Sang Geon

last: Kim

state: Seoul

address: San56-1, Sillim-dong, Kwanak-gu

department: College of Pharmacy

country: South Korea

institute: Seoul National University

description: C57BL/6 mice (9 weeks old) were intraperitoneally injected with a single dose of cisplatin (15 mg/kg body weight).

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Illumina BeadScan 500 System.

data_processing: The data were quantile normalized using R (version 2.9.1) with BeadArray (version 1.12.1).

source_name: mouse kidney, cisplatin

label_protocol: According to the Illumina Gene Expression System Manual.

growth_protocol: Animals were cared for under the guidelines of the Institutional Animal Use and Care Committee at Seoul National University. Male C57BL/6 mice (9 weeks old) were purchased from Samtako Company (Osan, Korea), and housed at 20±2°C with 12-h light/dark cycles and a relative humidity of 50±5% (Tecniplast, Varese, Italy) under filtered, pathogen-free air, with food (Purina, Korea) and water available ad libitum.

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

treatment_protocol: C57BL/6 mice (9 weeks old) were intraperitoneally injected with a single dose of cisplatin (15 mg/kg body weight) or vehicle (saline).

tag: genotype

value: WT

tag: gender

value: male

tag: age

value: 9 weeks

value: kidney

value: cisplatin


title: WT, rep2

description: C57BL/6 mice (9 weeks old) were intraperitoneally injected with a single dose of vehicle (saline).

source_name: mouse kidney, control

tag: tissue

value: saline control


title: mDCs_Ad5_Human1

description:
4690176013_A
mDCs from Human1, Ad5 incubation.

value: myeloid dendritic cells (mDCs)


title: mDCs_TLR7/8_Human1

description:
4690176013_E
mDCs from Human1, TLR78 incubation.


title: HepG2 gambogic acid 0.5μM

source_name: HepG2, 0.5μM gambogic acid

tag: cell line

tag: cell type

value: 0.5μM gambogic acid


title: mDCs_Ad35_Human1

description:
4690176013_D
mDCs from Human1, Ad35 incubation.


title: WT, rep3


title: HepG2 Control

source_name: HepG2, control

value: vehicle control


title: WT_CIS, rep2


title: Glt25d2 cells, cortex, TRAP RNA, VEH treated, biological rep3

scan_protocol: Standard Affymetrix protocol for the mouse 430 2.0 platform.

value: vehicle


title: WT_CIS, rep1


title: S100a10 cells, p11 KO, cortex, TRAP RNA, VEH treated, biological rep2

treatment_protocol: S100a10 bacTRAP/p11 KO mice were administered either a fluoxetine (0.167 mg/ml)/1% saccharine solution (FLX) or 1% saccharine alone (VEH) for 15-18 days and then sacrificed for TRAP profiling.


title: Glt25d2 cells, cortex, TRAP RNA, FLX treated, biological rep3


title: S100a10 cells, p11 KO, cortex, TRAP RNA, FLX treated, biological rep1


title: S100a10 cells, p11 KO, cortex, TRAP RNA, FLX treated, biological rep2


title: WT, rep1


title: HepG2 gambogic acid 0.25μM

source_name: HepG2, 0.25μM gambogic acid

value: 0.25μM gambogic acid


title: Glt25d2 cells, cortex, TRAP RNA, VEH treated, biological rep1


title: Glt25d2 cells, cortex, TRAP RNA, VEH treated, biological rep2


title: S100a10 cells, p11 KO, cortex, TRAP RNA, VEH treated, biological rep3


title: HepG2 bortezomib 50nM

source_name: HepG2, 50nM bortezomib

value: hepatoma cell line

value: 50nM bortezomib


title: S100a10 cells, cortex, TRAP RNA, VEH treated, biological rep3

treatment_protocol: S100a10 bacTRAP mice were administered either a fluoxetine (0.167 mg/ml)/1% saccharine solution (FLX) or 1% saccharine alone (VEH) for 15-18 days and then sacrificed for TRAP profiling.

value: backcrossed 3-5 generations on C57BL/6 from FVB


title: Glt25d2 cells, cortex, TRAP RNA, FLX treated, biological rep1

value: TRAP


title: S100a10 cells, p11 KO, cortex, TRAP RNA, FLX treated, biological rep3

value: cortex


title: S100a10 cells, p11 KO, cortex, TRAP RNA, VEH treated, biological rep1


title: S100a10 cells, cortex, TRAP RNA, VEH treated, biological rep2


title: S100a10 cells, cortex, TRAP RNA, FLX treated, biological rep2

value: fluoxetine


title: S100a10 cells, cortex, TRAP RNA, FLX treated, biological rep3


title: S100a10 cells, cortex, TRAP RNA, biological rep3b

source_name: S100a10 cells, cortex, TRAP RNA


title: S100a10 cells, cortex, TRAP RNA, biological rep2b


title: S100a10 cells, cortex, TRAP RNA, VEH treated, biological rep1


title: S100a10 cells, cortex, TRAP RNA, biological rep1b


title: Glt25d2 cells, cortex, TRAP RNA, biological rep3

source_name: Glt25d2 cells, cortex, TRAP RNA


title: S100a10 cells, cortex, TRAP RNA, FLX treated, biological rep1


title: Glt25d2 cells, cortex, TRAP RNA, biological rep2


title: Glt25d2 cells, cortex, TRAP RNA, biological rep1


title: Whole cortex, input RNA, biological rep3

status: Public on May 25 2012

source_name: Whole cortex, input RNA

value: input


title: S100a10 cells, cortex, TRAP RNA, biological rep3


title: Whole cortex, input RNA, biological rep2


title: S100a10 cells, cortex, TRAP RNA, biological rep2


title: S100a10 cells, cortex, TRAP RNA, biological rep1


title: Whole cortex, input RNA, biological rep1


title: ES25

city: chicago

first: chunjiang

last: he

state: il

address: 900 east 57th st

institute: university of chicago

description: RMA expression value derived from Expression Console software; extended-exon analysis

hyb_protocol: Samples were hybridized with GeneChip Mouse Exon 1.0 ST Arrays (Affymetrix) and scanned at NIH.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Raw data were processed with the Expression console (Affymetrix) for background correction and normalization log2 transformation. Data analysis and statistical evaluations were performed with customized R codes (version 2.10.1, http://www.r-project.org/).

source_name: mouse ES EB

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

extract_protocol: RNA was isolated with the miRNeasy Mini Kit (Qiagen), according to the manufacturers instructions. Inclusion of 10 mL/L of the RNase inhibitor NucleoGuard (AmpTec) in the lysis buffer improved RNA yield and recoveries of long transcripts. All samples were treated with TURBO DNA-free (Ambion) to remove trace amounts of genomic DNA. A 2-round amplification was performed with the ExpressArt TRinucleotide mRNA Amplification Kit (AmpTec) according to the manufacturers instructions.

value: embyonic Body cell 25


title: ES22

value: embyonic Body cell 22


title: ES23

value: embyonic Body cell 23


title: ES16

value: embyonic Body cell 16


title: ES24

value: embyonic Body cell 24


title: 1000PPF BL

status: Public on May 02 2012

city: Yokohama

first: Miyako

last: Kusano

state: Kanagawa

address: 1-7-22, Suehiro, Tsurumi

country: Japan

institute: RIKEN CSRS

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16 hr on GeneChip Tomato Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip scanner 3000 integrated with Affymetrix® Microarray Suite software.

data_processing: The microarray data normalization and background correction was performed using robust multi-array average (RMA) with Bioconductor package 'simpleaffy'.

organism: Solanum lycopersicum

source_name: leaf, high light for 2 weeks

label_protocol: Biotinylated cRNA was labeled using a biotinylated nucleotide analog/ribonucleotide mix using GeneChip IVT Labeling Kit (Affymetrix, Inc., Santa Clara, CA, USA).

growth_protocol: Seeds from tomatoes (Solanum lycopersicum, cv. Reiyo) were sown in pots (volume: 2 l) with rockwool (Nittobo, Japan) and grown in a hydroponics system with a nutrient solution containing N, P, and K at 122, 21, and 156.6 mg/l, respectively (one-fourth concentration of Otsuka Hydroponic Composition, Otsuka Chemical, Japan), in a growth chamber at 25 °C/20 °C (light/dark) and 900 ppm CO2 concentration with a light/dark cycle of 16 h/8 h at Chiba University, Matsudo, Japan. Photosynthetic photon flux (PPF) level in the growth chamber was adjusted to 450-500 pmol m-2 s-1 when we measured at the meristem of each tomato plant (light source: Ceramic metal halide lamps).

extract_protocol: Total RNA isolation was performed using RNeasy Plant Mini Kit (QIAGEN, Valencia, CA, USA) according to the manufacturer's instruction.

treatment_protocol: After flowering in Summer 2010, we removed leaves and trusses from each plant except for the second truss, a leaf below the second truss and the meristem. LED irrigation was directly applied to the leaf using the plant irradiation system. Plant material was harvested after 0, 1 and 2 weeks.

tag: cultivar

value: Reiyo

value: leaf

tag: light intensity

tag: sampling point

value: 2 weeks


title: ES26

value: embyonic Body cell 26


title: ES12

value: embyonic Body cell 12


title: 1000PPF CL


title: ES14

value: embyonic Body cell 14


title: ES20

value: embyonic Body cell 20


title: ES8

value: embyonic Body cell 8


title: ES3

value: embyonic Body cell 3


title: ES17

value: embyonic Body cell 17


title: ES7

value: embyonic Body cell 7


title: ES9

value: embyonic Body cell 9


title: ES15

value: embyonic Body cell 15


title: ES13

value: embyonic Body cell 13


title: ES6

value: embyonic Body cell 6


title: ES4

value: embyonic Body cell 4


title: ES2

value: embyonic Body cell 2


title: ES11

value: embyonic Body cell 11


title: ES10

value: embyonic Body cell 10


title: RNA Polymerase II phosphorylated on serine 2 (ePol), rep2

status: Public on May 08 2012

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

country: Germany

institute: LMU Munich

description: S2 cells, ePol ChIP-chip.

hyb_protocol: Performed by imaGenes (www.imagenes-bio.de).

data_processing: Raw signals of all channels in all replicate arrays were log2 transformed and quantile normalized in R/Bioconductor.

organism: Drosophila melanogaster

source_name: ePol IP DNA

growth_protocol: Cells were grown in Schneider's Medium supplemented with 10% FCS, penicillin and streptomycin.

extract_protocol: ChIP DNA: Cells were crosslinked in growth medium using 1% formaldehyde for 60 minutes in icewater. Fixation was quenched by addition of glycine to a final concentration of 125 mM. After washing, cells were resuspended in RIPA buffer and sonciated using the Bioruptor (Diagenode, Belgium) 8 times 30 seconds using the 'high' setting. Fragment size of the obtained chromatin was checked to be between 300 bp and 700 bp. Chromatin was precleared using a protein A/protein G-sepharose mixture for 1 hr at 4°C. 200 µl chromatin was incubated with appropriate amounts of antibodies in a total volume of 500 µl RIPA buffer at 4°C overnight. After washing and crosslink reversal, immunoprecipitated nucleic acids were purified on GFX columns (GE Healthcare). IP DNA was amplified using the WGA kit (Sigma).

treatment_protocol: No treatment.

tag: chip antibody

value: RNA polymerase II H5 monoclonal

tag: chip antibody catalog#

tag: antibody vendor

value: Covance

source_name: Input DNA

extract_protocol: Input DNA: Cells were crosslinked in growth medium using 1% formaldehyde for 60 minutes in icewater. Fixation was quenched by addition of glycine to a final concentration of 125 mM. After washing, cells were resuspended in RIPA buffer and sonciated using the Bioruptor (Diagenode, Belgium) 8 times 30 seconds using the 'high' setting. Fragment size of the obtained chromatin was checked to be between 300 bp and 700 bp. After crosslink reversal, nucleic acids were purified on GFX columns (GE Healthcare). Input DNA was amplified using the WGA kit (Sigma).


title: 1000PPF BP

source_name: fruit, high light for 2 weeks

value: Reiyo

value: pericarp

value: 2 weeks


title: ES21

value: embyonic Body cell 21


title: ES5

value: embyonic Body cell 5


title: ES18

value: embyonic Body cell 18


title: 200PPF BP

source_name: fruit, low light for 2 weeks

value: 200 PPF


title: 1000PPF B

source_name: leaf, high light for 1 week

value: leaf

value: 1 week


title: 1000PPF AP


title: 200PPF B

source_name: leaf, low light for 1 week


title: 200PPF AP


title: 1000PPF A


title: 1000PPF AL


title: 0 week C

source_name: leaf, before light irradiation

value: 0 PPF

value: 0 weeks


title: 200PPF CP


title: 0 week B


title: 200PPF BL

source_name: leaf, low light for 2 weeks


title: 0 week A


title: 1000PPF C


title: 200PPF C


title: 200PPF CL


title: 200PPF AL


title: ES19

value: embyonic Body cell 19


title: ExM_KO_5_r3

status: Public on May 01 2012

first: Santiago

last: Zelenay

address: 44 Lincoln's Inn Fields

institute: Cancer Research UK London Research Institute

description:
polyA RNA
CD8α+-like DCs differentiated with Flt3L for 10 days.

hyb_protocol: Hybridization was performed for 16 hours using the FS450_0001 fluidics protocol.

scan_protocol: GeneChip scanner 3000 7G.

data_processing:
Quantile normalised probe level and core level signal estimates were generated using Plier implemented in APT (apt-1.10.0, Affymetrix). Antigenomic probes were used for background.

Probe group file: MoEx-1_0-st-v1.r2.pgf
Meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm8.core.mps
Exons used in analysis: core
Genome build: mm8

source_name: CD8α+-like dendritic cells, Clec9a gfp/gfp, cultured with dead cells

label_protocol: Whole transcript (WT) sense target labeling protocol V1.0 from Affymetrix. The GeneChip® Poly-A RNA Control Kit, and the human RiboMinus transcriptome isolation kit from Invitrogen, were used in the protocol.

growth_protocol: Bone marrow cells were cultured in the presence of 100 ng/ml FLT3L for 10 days.

extract_protocol: RNA was extracted using the RNeasy Mini kit (Qiagen). Total RNAs were DNase-treated on the column.

treatment_protocol: Co-cultured with UV-treated dead cells treated with UVC (240mJ/cm2) and let in culture for 24h.

value: Clec9a gfp/gfp

value: CD8α+-like dendritic cells

tag: treatment

value: cultured with dead cells

tag: treatment duration

value: 5 h


title: ExM_KO_5_r1

tag: strain


title: ExM_WT_0_r1

source_name: CD8α+-like dendritic cells, wild type, untreated

value: wild type

value: 0 h


title: ExM_KO_5_r2


title: 1000PPF CP

value: Reiyo

value: pericarp


title: ExM_WT_0_r3


title: ExM_KO_0_r2

source_name: CD8α+-like dendritic cells, Clec9a gfp/gfp, untreated


title: ExM_KO_0_r1


title: ES1

value: embyonic Body cell 1


title: RNA Polymerase II phosphorylated on serine 2 (ePol), rep3

description: S2 cells, ePol ChIP-chip.

scan_protocol: Performed by imaGenes (www.imagenes-bio.de).

value: RNA polymerase II H5 monoclonal

value: Covance


title: ExM_KO_0_r3


title: ExM_WT_5_r3

source_name: CD8α+-like dendritic cells, wild type, cultured with dead cells


title: ExM_WT_0_r2


title: embryo under C3, biological rep2

status: Public on Apr 09 2012

first: Ting

last: Xu

address: No. 1239 Road Siping

institute: Tongji University

description:
Zebrafish_C3-2
Gene expression data from embryos exposed to deionized water at 8hpf.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Zebrafish Genome Arrays. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArrayTM scanner 3000.

data_processing: The data were analyzed with GeneChip Operating Software (GCOS) Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The target signal was set to 500.

organism: Danio rerio

source_name: Zebrafish embryos exposed to deionized water

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 ug total RNA (GeneChip Expression Analysis Technical Manual, Affymetrix).

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

treatment_protocol: 30 min. egg collections at 25C were exposed in pentachlorophenol solution according to the different concentrations C1-C3. Embryos of the appropriate stage were manually selected under the dissecting scope. Selected embryos were rinsed with PBS and then transferred to a microtube filled with Trizol solution (Invitrogen).

value: Tuebingen

tag: genotype/variation

value: whole body

tag: developmental stage

value: embryos at about 8hpf (gastrula)

value: deionized water


title: embryo under C3, biological rep1

description:
Zebrafish_C3-1
Gene expression data from embryos exposed to deionized water at 8hpf.


title: UGM_UNT_24h_rep1

status: Public on Apr 27 2012

city: Madison

first: William

last: Ricke

state: Wisconsin

address: 1111 Highland Ave

department: Urology

institute: University of Wisconsin

description:
UGM untreated
Male day 16 urogenital sinus mesenchyme from C57BL/6 mice. Cells were grown to confluency and treated for 72h in media containing charcoal-stripped serum before RNA was collected.

hyb_protocol: Hybridization, washes, and staining with phycoerythrin-streptavidin (including antibody enhancement step) were carried out as recommended by Affymetrix for eukaryotic expression arrays, using a hybridization oven and fluidics station purchased from Affymetrix.

scan_protocol: Scans were done with an Affymetrix scanner exactly as recommended by Affymetrix.

data_processing: Background subtraction and normalization were done with the Bioconductor GCRMA method.

source_name: mouse urogenital sinus mesenchyme, untreated (UNT)

label_protocol: Biotinylated cDNA was prepared with kits from NuGEN as recommended by the supplier.

growth_protocol: Cells were grown to 80% confluency in RPMI 1640, 5% FBS, and 5ug/ml Plasmocin.

extract_protocol: Extraction of total RNA was performed using the Omega Bio-Tek RNA Extraction Kit, according to the manufacturer's instructions.

treatment_protocol: Media containing FBS was removed from flasks. Cells were rinsed with PBS before treatments were added. Cells were treated for 72 hours in RPMI 1640, 5% dextran charcoal-stripped serum, and 5ug/ml Plasmocin (Untreated). Testosterone (12nM)- and estrogen (120pM)-treated cells were also cultured for 72 hours prior to collection.

value: male

value: day 16

value: urogenital sinus mesenchyme (UGM) cells

value: 72 hrs


title: embryo under C2, biological rep1

description:
Zebrafish_C2-1
Gene expression data from embryos exposed to 50 ug/L pentachlorophenol at 8hpf.

source_name: Zebrafish embryos exposed to 50 ug/L pentachlorophenol

value: 50 ug/L pentachlorophenol


title: embryo under C3, biological rep3

description:
Zebrafish_C3-3
Gene expression data from embryos exposed to deionized water at 8hpf.


title: embryo under C1, biological rep2

description:
Zebrafish_C1-2
Gene expression data from embryos exposed to 20 ug/L pentachlorophenol at 8hpf.

source_name: Zebrafish embryos exposed to 20 ug/L pentachlorophenol

value: 20 ug/L pentachlorophenol


title: embryo under C2, biological rep2

description:
Zebrafish_C2-2
Gene expression data from embryos exposed to 50 ug/L pentachlorophenol at 8hpf.

value: wild type


title: ExM_WT_5_r1

tag: genotype

value: CD8α+-like dendritic cells

value: cultured with dead cells

value: 5 h


title: CB1190_glycolate_rep3

status: Public on Feb 21 2012

city: Berkeley

first: Ariel

last: Grostern

address: 209 O'Brien Hall

department: Civil & Environmental Engineering

institute: UC Berkeley

hyb_protocol: Hybridization followed the procedure of the Affymetrix protocol for Modified FlexMidi_euk2v3 for P. aeruginosa Array.

scan_protocol: Chips were scanned using an Affymetrix GeneChip Scanner 3000 scanner.

data_processing: Primary data was generated with RMAExpress 1.05. Quantile normalization with background adjustment was performed across all arrays, and the PLM summarization method was used.

organism: Pseudonocardia dioxanivorans CB1190

source_name: Pseudonocardia dioxanivorans strain CB1190 cells, glycolate-grown

label_protocol: cDNA was obtained from 5 ug of RNA following the Affymetrix protocol for RT. RNA template was degraded with NaOH treatment. cDNA was fragmented with DNaseI, and fragmented cDNA while terminally labeled with biotin.

growth_protocol: Cells were grown in AMS medium amended with pyruvate (45 mM) or 1,4-dioxane (4.7 mM) or glycolate (2 mM)

extract_protocol: Nucleic acids were obtained following cell lysis with heating and bead-beating in the presence of SDS and phenol. Phenol/chloroform extraction, followed by column-based purification, was performed. Nucleic acids were treated with DNaseI and RNA was finally purified by RNeasy purification.

treatment_protocol: Cells were harvested by filtration and scraped from the filter into vials that were frozen at -80C.

value: glycolate (2 mM)


title: embryo under C1, biological rep3

description:
Zebrafish_C1-3
Gene expression data from embryos exposed to 20 ug/L pentachlorophenol at 8hpf.


title: CB1190_glycolate_rep2


title: ExM_WT_5_r2

city: London


title: embryo under C2, biological rep3

description:
Zebrafish_C2-3
Gene expression data from embryos exposed to 50 ug/L pentachlorophenol at 8hpf.


title: RNA Polymerase II phosphorylated on serine 2 (ePol), rep1

description: S2 cells, ePol ChIP-chip.

label_protocol: Performed by imaGenes (www.imagenes-bio.de).

source_name: ePol IP DNA

value: RNA polymerase II H5 monoclonal


title: CB1190_glycolate_rep1


title: embryo under C1, biological rep1

description:
Zebrafish_C1-1
Gene expression data from embryos exposed to 20 ug/L pentachlorophenol at 8hpf.


title: UGM_TE2_24h_rep1

description:
UGM T+E treated
Male day 16 urogenital sinus mesenchyme from C57BL/6 mice. Cells were grown to near confluency and T+E2 treated for 72h before RNA was collected.

source_name: mouse urogenital sinus mesenchyme, T+E2 treated

tag: gender

value: testosterone + estradiol-17 beta


title: CB1190_dioxane_rep3

source_name: Pseudonocardia dioxanivorans strain CB1190 cells, dioxane-grown

value: 1,4-dioxane (4.7 mM)


title: CB1190_dioxane_rep2


title: CB1190_dioxane_rep1


title: CB1190_pyruvate_rep2

source_name: Pseudonocardia dioxanivorans strain CB1190 cells, pyruvate-grown

value: pyruvate (45 mM)


title: CB1190_pyruvate_rep3


title: CB1190_pyruvate_rep1


title: AG24 DAC2-rep2

status: Public on Feb 16 2012

city: Milwaukee

first: Sheng

last: Yang

state: WI

address: 8701 Watertown Plank Road

department: Human and Molecular Genetics Center

institute: Medical College of Wisconsin

description:
DAC2 ES cells, 5 days after passage.
Gene expression interrogating 31099 transcripts.

hyb_protocol: RNA from each culture was independently analyzed. Labeled RNA was hybridized to the Affymetrix GeneChip rat genome RG230 plus 2.0 array in accordance to the Affymetrix GeneChip expression analysis technical manual. After hybridization, arrays were washed and then stained with PE-conjugated streptavidin (Molecular Probes).

scan_protocol: Arrays were scanned using the GeneChip Scanner 3000.  Image data were quantified with Affymetrix Expression Console Software.

data_processing: The quantified raw signal intensities were normalized with Robust Multichip Analysis (RMA; www.bioconductor.org/).  Analysis of variation (ANOVA) was conducted and false discovery rates (FDR) were determined using Partek Genomics Suite 6.2 (Partek Incorporated).  Differentially expressed probe sets were defined as those possessing ANOVA p<0.01, FDR<0.10 and a log2 ratio >1.5 between the compared groups.  Ontological pathway analysis was performed with the Database for Annotation, Visualization, and Integrated Discovery (DAVID; http://david.abcc.ncifcrf.gov/).  Hierarchical clustering was conducted with Genesis software.

organism: Rattus norvegicus

source_name: rat DAC2 embryonic stem cells

label_protocol: Purified RNA (~100 ng) was amplified/labeled using an Affymetrix Express Kit.

growth_protocol: Rat and mouse embryonic fibroblast (EF) cells were prepared from e14.5 embryos (statement of protocol approval from IACUC), and cultured in Dulbecco's Modified Eagle's Medium (DMEM) containing 10% (fetal calf serum) FBS (HyClone), 2 mM L-glutamine, 1% non-essential amino acid, and 0.1 mM 2-mercaptoethanol. Rat IPS cell lines were cultured on Mitomycin C-treated mouse EF cells in knock-out (KO) medium, which contains DMEM with 20% knock out serum (Invitrogen), 2 mM L-glutamine, 1% non-essential amino acid, 0.1 mM 2-mercaptoethanol and 1000U/ml (Leukemia inhibitory factor) LIF (Chemicon).

extract_protocol: About 1,000,000 rat IPS, ES and EF cells were collected and treated by TRIZ reagent for RNA extracting.

treatment_protocol: Rat ES and IPS cells were cultured in 2i medium. Rat EF cells were cultured in MEF medium.

value: embryonic stem (ES) cells

value: positive

tag: nanog


title: AG18 FHH-REF2-rep2

description:
FHH rat embryonic fibroblast cells, 6 days after passage.
Gene expression interrogating 31099 transcripts.

source_name: FHH rat embryonic fibroblast cell 2

tag: background strain

value: FHH

tag: age

value: embryonic fibroblast (EF) cells

tag: morphology

value: same as mouse embryonic fibroblast cells


title: AG16 FHH-REF1-rep2

source_name: FHH rat embryonic fibroblast cell 1

tag: cell type


title: AG14 DAC8-rep2

description:
DAC8 ES cells, 5 days after passage.
Gene expression interrogating 31099 transcripts.

source_name: rat DAC8 embryonic stem cells

tag: cell line


title: AG17 FHH-REF2-rep1


title: AG9 FHH-IPS-A1-rep1

description:
FHH IPS cells, 5 days after passage.
Gene expression interrogating 31099 transcripts.

source_name: FHH rat induced pluripotent stem cells A1

value: induced pluripotent stem (IPS) cells


title: AG15 FHH-REF1-rep1


title: AG12 FHH-IPS-A2-rep2

source_name: FHH rat induced pluripotent stem cells A2


title: AG13 DAC8-rep1


title: DAC Treated Primary Leukemia 1307 - Day14

status: Public on Mar 21 2012

city: Ghent

first: Leander

last: Van Neste

address: Coupure Links 653

department: Molecular Biotechnology

country: Belgium

institute: Ghent University

description:
Bisulfite treated genomic DNA
DAC treated primary leukemia, 14 days post treatment
X1307_DAC_d14

hyb_protocol: Bisulphite converted (EZ DNA methylation kit) DNA was amplified, fragmented and hybridised to Illumina HumanMethylation450 Beadchip using standard Illumina protocol

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

data_processing: Raw methylated and unmethylated signals are used to recalculate beta values without background subtraction. Probes with a detection p-value equal to or greater than .05 are set to NA. Data handling and processing done in R.

source_name: Primary Leukemia

label_protocol: Standard Illumina Protocol

extract_protocol: Phenol-chloroform extraction

tag: disease state

value: Primary Cancer

value: leukemia cells

tag: treatement

value: DAC

tag: time

value: day 14


title: AG23 DAC2-rep1


title: Primary Leukemia 1307 - Day 14

description:
Bisulfite treated genomic DNA
Untreated primary leukemia
X1307_Mock_d14

value: Untreated


title: DAC Treated Primary Leukemia 1107 - Day 7

description:
Bisulfite treated genomic DNA
DAC treated primary leukemia, 7 days post treatment
X1107_DAC_d7

value: day 7


title: Primary Leukemia 1307 - Day 3

description:
Bisulfite treated genomic DNA
Untreated primary leukemia
X1307_Mock_d3

value: day 3


title: DAC Treated Normal Bone Marrow BM1

description:
Bisulfite treated genomic DNA
DAC treated normal bone marrow
BM1_DAC

source_name: Normal Bone Marrow

value: Normal

tag: tissue

value: bone marrow


title: DAC Treated Primary Leukemia 1307 - Day 3

description:
Bisulfite treated genomic DNA
DAC treated primary leukemia, 3 days post treatment
X1307_DAC_d3


title: AG11 FHH-IPS-A2-rep1


title: Normal Bone Marrow BM1

description:
Bisulfite treated genomic DNA
Untreated normal bone marrow
BM1_Mock


title: Normal Bone Marrow BM2

description:
Bisulfite treated genomic DNA
Untreated normal bone marrow
BM2


title: AG10 FHH-IPS-A1-rep2


title: Primary Leukemia 1107 - Day 7

description:
Bisulfite treated genomic DNA
Untreated primary leukemia
X1107_Mock_d7


title: human leukemia 50

status: Public on Jan 13 2012

description: RMA expression value derived from Expression Console software; extended-exon analysis

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) and scanned at the UC Microarray Core Facility.

source_name: human leukemia

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix)

value: leukemia

value: human leukemia cell line


title: human leukemia 48


title: human leukemia 58


title: human leukemia 51


title: human leukemia 40


title: human leukemia 47


title: human leukemia 52


title: human leukemia 45


title: human leukemia 41


title: human leukemia 39


title: human leukemia 44


title: human leukemia 43


title: human leukemia 29


title: human leukemia 30


title: human leukemia 37


title: human leukemia 57


title: human leukemia 34


title: human leukemia 42


title: human leukemia 35


title: human leukemia 38


title: human leukemia 33


title: human leukemia 36


title: human leukemia 28


title: human leukemia 56


title: human leukemia 32


title: human leukemia 49


title: human leukemia 81


title: human leukemia 31


title: human leukemia 46


title: human leukemia 79


title: human leukemia 3


title: human leukemia 78


title: human leukemia 27


title: human leukemia 24


title: human leukemia 80


title: human leukemia 76


title: human leukemia 73


title: human leukemia 26


title: human leukemia 25


title: human leukemia 75


title: human leukemia 72


title: human leukemia 74


title: human leukemia 23


title: human leukemia 71


title: human leukemia 68


title: human leukemia 66


title: human leukemia 2


title: human leukemia 22


title: human leukemia 18


title: human leukemia 19


title: human leukemia 20


title: human leukemia 70


title: human leukemia 69


title: human leukemia 17


title: human leukemia 15


title: human leukemia 21


title: human leukemia 14


title: human leukemia 65


title: Mo17

status: Public on Nov 21 2011

city: St. Paul

first: Steve

middle: R

last: Eichten

state: MN

address: 1445 Gortner Ave

department: Plant Biology

institute: University of Minnesota

hyb_protocol: 24-34ug of labeled DNAs (input DNA, IP DNA) were hybridized to the 2.1M feature arrays according to the array manufacturer protocol (42°C, 16-20hrs).  The arrays were washed according to the array manufacturer's protocol.

scan_protocol: Arrays were scanned according to the NimbleScan CGH User Guide protocol, which specifies parameters for the GenePix4000B Scanner (Axon/Molecular Devices) used to collect data.

data_processing:
Images were aligned and quantified using NimbleScan software (Roche NimbleGen), which produced .pair reports of raw data.

Pair files exported from NimbleScan were imported into the Bioconductor statistical environment (http://bioconductor.org/). Sample-dependent MeDIP enrichments were estimated for each probe by fitting a fixed linear model accounting for array, dye, and sample effects to the data using the limma package (Smyth, 2004). The following contrasts were then fit: B73 IP vs. B73 input; Mo17 input vs. B73 input; Mo17 IP vs. (Mo17 input vs. B73 input); B73 IP vs. (Mo17 IP vs. (Mo17 input vs. B73 input)). Moderated t-statistics and the log-odds score for differential MeDIP enrichment was computed by empirical Bayes shrinkage of the standard errors with the False Discovery Rate controlled to 0.05. Results were loaded into relational databases and a Generic Genome Browser for downstream analyses.

organism: Zea mays

source_name: Mo17 input

label_protocol: Amplified input and immunoprecipitated methylated DNA (IP) samples were labeled (3 x 1ug per reaction) using Cy3 and Cy5, respectively.

extract_protocol: Genomic DNAs were extracted using CTAB and purified using phenol:chloroform/Na-Acetate purification and EtOH precipitation.  15-30ug of genomic DNA were sonicated (5 reps x 10 seconds with >1 minute on ice between reps).  Methylated DNAs were isolated from 400ng of sonicated DNA using the Zymo Research Methylated DNA IP kit (Cat # D5101), which contains the anti-5-methylcytosine monoclonal antibody.  50-100ng of methylated DNA and 50-100ng of sonicated (input control) DNAs were amplified using the Sigma Whole Genome Amplification kit (Cat # WGA2-10RXN).

treatment_protocol: Genomic DNAs were sonicated, amplified, and fluorophore-labeled.

value: seedling leaf (L3)

tag: chip antibody

tag: biological replicates

source_name: Mo17 IP

treatment_protocol: Genomic DNAs were sonicated, and methylated DNAs were isolated, amplified, and fluorophore-labeled.

tag: antibody vendor

value: Zymo Research

tag: antibody lot


title: human leukemia 11


title: human leukemia 54


title: human leukemia 61


title: human leukemia 63


title: B73

source_name: B73 input

source_name: B73 IP


title: mRNA_LA_3

status: Public on Sep 10 2011

type: SRA

first: Jeff

last: Hsu

state: OH

address: 9500 Euclid Ave

department: Cellular and Molecular Medicine

institute: Cleveland Clinic Lerner Research Institute

description: mRNA seq of Left atrial tissue

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version 1.3
For the poly-A enriched mRNA samples, reads were aligned to hg19 using tophat with the following parameters -r 0 --solexa1.3-quals -G hg19gene.gtf
For the miRNA-seq data, reads were aligned to miRBase Release 17 hairpins using bowtie with the -best option and allowing for 1 mismatch.  Aligned reads were then collapsed down to mature sequences.
genome build: hg19
processed data files format and content: Counts were obtained from the BAM files using custom scripts.

source_name: Left Atrial Tissue

extract_protocol: Total RNA was extracted using QIAGEN miRNeasy Mini Kits from 20 mg of atrial tissue samples.  Sequencing libraries were made following Illumina's mRNA protocol.  Briefly, RNA was purified by poly-A selection using oligo(dT) beads and chemically fragmented.  First and second strand cDNA synthesis was followed by end-repair and 3' adenylation.  5' and 3' Illumina adapters were ligated and size-selected using gel-purification and PCR amplification.   Using the same total RNA preparations, a smallRNA-sequencing library was constructed following Illumina's Alternative v1.5 smallRNA-seq protocol (Part # 15002615).  Briefly, 5' and 3' adapters were ligated onto the small RNAs and amplified.  The cDNA with adapters was size selected between 93-100 bp and 36 bp single-end sequencing was performed.

value: Left Atrial Heart


title: mRNA_RA_4

description: mRNA seq of Right atrial tissue

source_name: Right Atrial Tissue

value: Right Atrial Heart


title: human leukemia 12


title: human leukemia 62


title: mRNA_LA_1

description: mRNA seq of Left atrial tissue


title: mRNA_RA_1

description: mRNA seq of Right atrial tissue


title: mRNA_LA_4

description: mRNA seq of Left atrial tissue


title: mRNA_RA_3

description: mRNA seq of Right atrial tissue


title: human leukemia 9


title: human leukemia 13


title: human leukemia 6


title: Patient 13

status: Public on Aug 30 2011

hyb_protocol: Array hybridization, washing, blocking, and Cy3 staining was performed according to the Illumina protocol.

scan_protocol: Arrays were scanned with an Illumina Bead Array Reader.

data_processing: Quantile normalization after Log2 transformation using BeadStudio V3.0.14 by Illumina

source_name: Sarcoma, pre-treatment biopsy

label_protocol: Amplification and labeling was done using the Illumina TotalPrep RNA Amplification Kit.

extract_protocol: RNA was isolated from tumor tissue using Qiagen RNeasy kit.

tag: histology

value: fibroblastic osteosarcoma

tag: response

value: Good-responder


title: B73 Control

description: The Cy5 sample (B73 no antibody control) serves as a control for noise signal on the array.

source_name: B73 gDNA control

treatment_protocol: Genomic DNA was fluorophore-labeled.

tag: genotype

source_name: B73 negative control IP

treatment_protocol: Genomic DNAs were sonicated, and DNAs were isolated with water substituted for the monoclonal antibody.  The resulting material was amplified and fluorophore-labeled.


title: Patient 15

value: leiomyosarcoma

value: Poor-responder


title: human leukemia 64


title: Patient 17

value: fibroblastic sarcoma


title: Patient 14

value: well-diff/de-diff liposarcoma


title: human leukemia 60


title: Patient 12

value: pleomorphic liposarcoma


title: human leukemia 10


title: human leukemia 4


title: Patient 11


title: human leukemia 7


title: Patient 10

value: myxoid liposarcoma


title: mRNA_LA_2

description: mRNA seq of Left atrial tissue


title: Patient 8

value: sarcoma not otherwise specified


title: Patient 9


title: Patient 7


title: lateral_E

status: Public on Aug 24 2011

city: Oxford

first: T

middle: Grant

last: Belgard

address: Le Gros Clark Building, South Parks Road

department: Department of Physiology, Anatomy and Genetics

institute: University of Oxford

data_processing: Bam: Reads were processed with versions 1.4 and 1.6 of the Illumina pipeline.  The internal insert size and standard deviation was estimated for each library by empirically calculating the full width at half max (FWHM) for an internal insert size distribution constructed using uniquely mapping reads on the same chromosome from Illumina's Gerald pipeline.  The insert size was estimated to be the midpoint of the minimum and maximum insert sizes at half (or greater) the frequency of the most common insert size, and the standard deviation was calculated under a Gaussian assumption StdDev=FWHM/(2*sqrt(2ln2)).  Using this insert size and standard deviation, lanes were separately mapped with TopHat v1.0.13 to the mouse reference genome (mm9, downloaded from UCSC) plus all splice junctions from the UCSC Table Browser (cite) tables all_mrna (mouse mRNAs), intronEst (mouse spliced ESTs), and xenoMrna (mRNAs mapped from other species to mouse) with the following options: butterfly search, closure search, fill gaps, microexon search, min anchor length = 5, min isoform fraction = 0.0, max intron length = 500 kb.  In a second round of TopHat mapping (default options except min isoform fraction = 0.0), all novel junctions identified from any sample in the previous step were given to TopHat again (as raw junctions), so splice junctions could be measured across all samples in an unbiased manner.  Laminar samples were dissected from dorsal cortex (overlapping S1 and some motor cortex) and, separately, lateral cortex (partially overlapping S2 and insular cortex) from mice matched in number, strain, sex, litter distribution, and age to the original set of mice.  These additional eight adult male mice (56 days old; C57BL/6J strain) were also killed by cervical dislocation according to approved schedule one UK Home Office guidelines (Scientific Procedures Act, 1986).  These were treated exactly as described above, with the following exceptions: sample B was not split and RNA underwent two rounds of poly(A) selection.  Lanes with aberrant GC content were discarded and all reads were trimmed to correspond to two ends of 50 base pairs each.  A read fragment was discarded if any of the following conditions was met: either read failed Illuminaâs chastity filter, either read had eight or more bases (corresponding to tophatâs default minimum anchor length) with a Phred-scaled quality score less than three, either read mapped (bowtie v0.12.7 allowing up to two mismatches) to spliced or unspliced rRNAs, tRNAs or mitochondrial rRNAs as defined by Ensembl (release 62).  Fragment internal insert size and standard deviation were estimated with the FWHM technique.  Fragments were subsequently mapped on a lane-by-lane basis with tophat v1.2.0 (Trapnell et al., 2009) enabling microexon search, coverage search, butterfly search, and providing gene models corresponding to Ensembl (release 62).  All splice sites found in any lane (from original or replicate dorsal cortex samples, or lateral cortex samples) then combined for a final round of tophat mapping in which new splice site detection was disabled but all previously detected splice sites were provided.

molecule: polyA RNA

source_name: lateral cortex

extract_protocol: Total RNA >200 nt was extracted using the RNeasy Lipid Tissue Mini kit (QIAGEN), following the manufacturer's instructions and using the on-column DNase digest.  RNA quantity was assessed using a NanoDrop 1000 spectrophotometer (ThermoScientific), and RNA quality and integrity assessed using a BioAnalyzer (Agilent Laboratories).  Total RNA was prepared for paired-end deep sequencing on Illumina's Genome Analyzer II following the manufacturer's protocol.  Briefly, poly(A) RNA was enriched using Dynal oligo(dT) beads (Invitrogen) [enriched twice for the dorsal and lateral cortex samples; see publication for full details].  This was fragmented using the RNA fragmentation kit (Ambion).  First- and second-strand cDNA was synthesized with random hexamer primers (Invitrogen) and SuperScript II (Invitrogen).  Ends were repaired using T4 DNA polymerase and Klenow DNA polymerase.  A single adenosine and Illumina adapters were ligated using Klenow 3'-to-5' exo-nuclease.  Following gel purification of cDNA templates, the library was enriched with 15 rounds of PCR before being added to the flow cell for paired-end sequencing (51 nt from either end, of which 50 nt was used in mapping; except for two libraries in sample F where 76 nt were sequenced from either end, using 75 in mapping).  Paired-end library average internal insert sizes (standard deviations) were as follows: A 164 (27); B1 239 (29); B2 193 (28); C 184 (21); D 208 (22); E 172 (24); F 184 (28); DC2 A 287 (31); DC2 B 290 (28); DC2 C 291 (28); DC2 D 269 (30); DC2 E 284 (31); DC2 F 279 (21); LC A 281 (40); LC B 275 (32); LC C 282 (41); LC D 267 (29); LC E 268 (38); LC F 272 (34).

value: lateral cortex

tag: number of pooled mice

tag: strain

tag: Sex

value: male

tag: laminar sample (see publication)

value: E


title: lateral_C

tag: age

value: C


title: Patient 6

value: MFH


title: human leukemia 59

value: leukemia

tag: cell line

value: human leukemia cell line


title: Patient 2


title: Patient 1


title: human leukemia 53

tag: disease state


title: lateral_B

value: B


title: lateral_A

value: A


title: dorsal_F

source_name: dorsal cortex

value: dorsal cortex

value: F


title: dorsal_E


title: human leukemia 5


title: Patient 20

value: Good-responder


title: dorsal_D

value: D


title: Patient 19

value: fibroblastic sarcoma


title: human leukemia 8


title: dorsal_B


title: dorsal_A


title: lateral_F


title: dorsal_C