title: Msx1-ER vector, plus tamoxifen, biological rep3

city: Cambridge

first: Richard

middle: A

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description: Gene expression data from C2C12 cells infected with a retrovirus expressing an Msx1-ER fusion protein, 6 hours after addition of tamoxifen  (experimental sample)

hyb_protocol: Labeled cRNA was hybridized to Affymetrix GeneChips (Mu74AV2) according to manufacturer's protocols.

scan_protocol: Microarrays were scanned and images were quantified using Affymetrix Microarray Suite 5.0 software.

data_processing: For statistical analysis, the data were preprocessed using the MAS5 algorithm (as implemented in R/Bioconductor), and differential expression was assayed using the moderated t-test from the limma package (Smyth, 2004). Probes called “absent” in all samples were excluded from further analysis, leaving 6641 of the 12488 probes on the array remaining. Genes with a p-value of less than or equal to 0.05 and a fold-change of 1.4-fold or greater between tamoxifen-treated and vehicle samples for the Msx1-ER-infected cells were considered to be differentially expressed between the two conditions. These relatively relaxed criteria were chosen because the expression data represented an early time point (i.e., 6 hours) after Msx1 induction and because the data was intended to be compared to Msx1 genomic binding data (below). We then excluded expression changes resulting from tamoxifen induction, rather than Msx1, by comparing the expression data from cells expressing the empty vector with or without tamoxifen. These analyses resulted in the identification of 101 genes that were up-regulated, and 120 genes that were down-regulated, for a total of 221 differentially regulated genes.

source_name: C2C12 cells, infected with Msx1-ER, plus tamoxifen, 6 hrs

label_protocol: cDNA was labeled using a BioArray High-Yield RNA transcript labeling kit (Enzo Life Sciences).

growth_protocol: C2C12 myoblast cells were obtained from ATCC; all studies were done using early passage cells. Cells were maintained in DMEM supplemented with 10% fetal bovine in humidified atmosphere with 5% CO2 at 37°C. For retroviral gene transfer, replication-defective pLZRS-IRES-GFP retroviruses were made in ecotropic Phoenix retroviral packaging cells (ATCC). One day prior to infection, C2C12 cells were seeded at a density of 2.5 x 105 cells/10cm plate and infected with the virus-containing supernatant supplemented with 8 μg/ml of polybrene (Sigma) for two consecutive days.

extract_protocol: RNA was extracted using Trizol reagent (Invitrogen) and purified using an RNeasy kit (Qiagen).

treatment_protocol: For expression profiling, RNA was isolated from C2C12 cells that had been infected with a retrovirus expressing the tamoxifen-regulated Msx1 protein, Msx1-ER (or with empty vector as a control), followed by induction with 0.2 nM of tamoxifen or vehicle (DMSO) for 6 hours.

tag: cultured cells

value: C2C12 cells

tag: protocol


title: Breast tumor tissue Sample68

status: Public on Aug 17 2011

type: genomic

city: Houston

first: Spiridon

last: Tsavachidis

state: TX

address: 1515 Holcombe Blvd.

department: Epidemiology

country: USA

institute: MD Anderson Cancer Center

hyb_protocol: standard affymetrix protocol

scan_protocol: standard affymetrix protocol

data_processing:
standard affymetrix protocol
Raw copy number (linear scale) is given in Sample*.txt files. The copy number data were binned in 13175 sets of consecutive Mips. CBS algorithm was applied on the 13175 bins to get segmented copy number values for each sample. Segment boundaries for each sample were combined and 1593 common segments were defined. The data matrix contains start/stop positions for each segment, and the data takes -1,0,1 values corresponding to copy number loss (copy number <1.5), neutral, copy number gain (copy number>2.5), respectively.

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: breast tumor sample 68

label_protocol: standard affymetrix protocol

extract_protocol: 5-10 (5-μm) macrodissected tumor sections containing > 80% tumor cells per protocol were pooled and treated three times with proteinase K in ATL Tissue Lysis Buffer™ (Qiagen, Valencia, CA).

treatment_protocol: retrospective collection of cases receiving standard of care

tag: Stage

value: II

tag: age at diagnosis

tag: er status

value: positive

tag: pr status

tag: tissue

value: breast cancer tumor


title: 53048_EAC

type: RNA

city: Herston

first: Derek

middle: John

last: Nancarrow

state: Queensland

address: 300 Herston Road

department: Genetics & Population Health

country: Australia

institute: Queensland Institute of Medical Research

description: esophageal adenocarcinoma biopsy taken prior to the patient undergoing treatment

data_processing: GenomeStudio software, version 2.0 (Illumina) was used to extract raw signal intensity data which was imported into GeneSpring GX version 7.3.1 (Agilent Technologies) where it was transformed (logarithm to the base 2), corrected for background (< 0.01 adjusted to 0.01) and normalized for intensity (Lowess residual to the 50th percentile) . We have chosen to include only those probes predicted to bind uniquely to the transcriptome and have a perfect match to the consensus genome (n=25049), as defined by Barbosa-Morais and co-workers [Nucleic Acids Res 38: e17, 2010.] and labelled within the appropriate supplementary file as perfect.

label: Biotin

molecule: total RNA

source_name: single whole esophageal biopsy, stored in RNAlater

label_protocol: Biotin labeled cRNA. Refer to the Illumina Gene Expression System Manual, Revision D

extract_protocol: As per QIAGEN tissue lyser protocol using ALLPREP Kit

treatment_protocol: Fresh tissue was placed directly into RNAlater solution, stored at 4°C overnight, then -20°C. Long-term storage was then at -80°C after access RNAlater was removed.

tag: tissue type

value: esophageal adenocarcinoma tumor

tag: individual id

tag: histology review type (see paper for details)

value: path info

tag: subject gender

value: male

tag: subject age (years)

tag: tumour stage

tag: matching cn sample id

tag: sample barcode


title: Msx1-ER vector, plus tamoxifen, biological rep1

state: MA

organism: Mus musculus

value: infected with Msx1-ER, plus tamoxifen, 6 hrs


title: 40334_EAC

hyb_protocol: Refer to the Illumina Gene Expression System Manual, Revision D

value: slide

value: IIA


title: Msx1-ER vector, plus tamoxifen, biological rep2


title: Msx1-ER vector, no tamoxifen, biological rep3

description: Gene expression data from C2C12 cells infected with a retrovirus expressing an Msx1-ER fusion protein, no tamoxifen added (reference sample for experiment)

source_name: C2C12 cells, infected with Msx1-ER, no tamoxifen, 6 hrs


title: Breast tumor tissue Sample67

source_name: breast tumor sample 67


title: Breast tumor tissue Sample64

source_name: breast tumor sample 64

value: I

value: negative


title: Breast tumor tissue Sample66

source_name: breast tumor sample 66


title: 40331_EAC

scan_protocol: Refer to the Illumina Gene Expression System Manual

value: III


title: Msx1-ER vector, no tamoxifen, biological rep2

value: infected with Msx1-ER, no tamoxifen, 6 hrs


title: Breast tumor tissue Sample63

source_name: breast tumor sample 63


title: Msx1-ER vector, no tamoxifen, biological rep1


title: Breast tumor tissue Sample59

source_name: breast tumor sample 59


title: Breast tumor tissue Sample58

source_name: breast tumor sample 58


title: Breast tumor tissue Sample62

source_name: breast tumor sample 62


title: Breast tumor tissue Sample60

source_name: breast tumor sample 60


title: Breast tumor tissue Sample65

source_name: breast tumor sample 65


title: Breast tumor tissue Sample61

source_name: breast tumor sample 61


title: 53114_BE-dys

description: Barrett's esophagus (without dysplasia) biopsy from the esophagus of an individual with no history of esophageal dysplasia nor esophageal adenocarcinoma

value: Barrett's esophagus (without dysplasia)

value: female


title: 53169_BE-dys


title: Breast tumor tissue Sample56

source_name: breast tumor sample 56


title: Empty vector, plus tamoxifen, biological rep2

description: Gene expression data from C2C12 cells infected with an empty vector, 6 hours after addition of tamoxifen (control sample)

source_name: C2C12 cells, infected with empty vector, plus tamoxifen, 6 hrs


title: Empty vector, plus tamoxifen, biological rep3

value: infected with empty vector, plus tamoxifen, 6 hrs


title: 53097_BE-dys


title: 53118_BE-dys


title: Breast tumor tissue Sample57

source_name: breast tumor sample 57


title: Breast tumor tissue Sample55

source_name: breast tumor sample 55


title: Empty vector, plus tamoxifen, biological rep1

value: C2C12 cells


title: 40345_EAC


title: Breast tumor tissue Sample51

source_name: breast tumor sample 51


title: Breast tumor tissue Sample52

source_name: breast tumor sample 52

value: II


title: Empty vector, no tamoxifen, biological rep3

description: Gene expression data from C2C12 cells infected with an empty vector, no tamoxifen added (control sample)

source_name: C2C12 cells, infected with empty vector, no tamoxifen, 6 hrs


title: 54014_EAC

source_name: single whole esophageal biopsy, stored in RNAlater

value: x


title: Breast tumor tissue Sample47

source_name: breast tumor sample 47

value: positive

value: breast cancer tumor


title: Empty vector, no tamoxifen, biological rep2

value: infected with empty vector, no tamoxifen, 6 hrs


title: 53038_BE-dys

value: male


title: Breast tumor tissue Sample49

source_name: breast tumor sample 49


title: Breast tumor tissue Sample53

source_name: breast tumor sample 53


title: Breast tumor tissue Sample50

source_name: breast tumor sample 50


title: Breast tumor tissue Sample54

source_name: breast tumor sample 54


title: Breast tumor tissue Sample48

source_name: breast tumor sample 48


title: 53100_BE-dys


title: Breast tumor tissue Sample44

source_name: breast tumor sample 44


title: Breast tumor tissue Sample45

source_name: breast tumor sample 45


title: 53092_BE-dys


title: Breast tumor tissue Sample46

source_name: breast tumor sample 46


title: 53059_BE-dys


title: 53052_BE-dys


title: Breast tumor tissue Sample43

source_name: breast tumor sample 43


title: Breast tumor tissue Sample42

source_name: breast tumor sample 42


title: 53032_BE-dys


title: 54025_BE-dys


title: Breast tumor tissue Sample41

source_name: breast tumor sample 41


title: Breast tumor tissue Sample36

source_name: breast tumor sample 36


title: Breast tumor tissue Sample39

source_name: breast tumor sample 39


title: Breast tumor tissue Sample35

source_name: breast tumor sample 35


title: 54077_BE-dys


title: 54045_BE-dys


title: Breast tumor tissue Sample40

source_name: breast tumor sample 40


title: Breast tumor tissue Sample38

source_name: breast tumor sample 38


title: Breast tumor tissue Sample34

source_name: breast tumor sample 34


title: 54005_BE-dys

source_name: single whole esophageal biopsy, stored in RNAlater


title: Breast tumor tissue Sample31

source_name: breast tumor sample 31


title: Breast tumor tissue Sample30

source_name: breast tumor sample 30


title: Breast tumor tissue Sample37

source_name: breast tumor sample 37


title: Breast tumor tissue Sample27

source_name: breast tumor sample 27


title: Breast tumor tissue Sample28

source_name: breast tumor sample 28


title: Breast tumor tissue Sample33

source_name: breast tumor sample 33


title: 52039_BE-dys


title: Breast tumor tissue Sample26

source_name: breast tumor sample 26


title: 53154_BE-dys


title: Breast tumor tissue Sample29

source_name: breast tumor sample 29


title: Breast tumor tissue Sample32

source_name: breast tumor sample 32


title: 52040_BE-dys


title: 54013_BE-dys


title: Breast tumor tissue Sample23

source_name: breast tumor sample 23


title: Empty vector, no tamoxifen, biological rep1

source_name: C2C12 cells, infected with empty vector, no tamoxifen, 6 hrs


title: Breast tumor tissue Sample24

source_name: breast tumor sample 24


title: Breast tumor tissue Sample20

source_name: breast tumor sample 20


title: 54080_BE-dys


title: Breast tumor tissue Sample17

source_name: breast tumor sample 17


title: 54036_BE-dys


title: Breast tumor tissue Sample21

source_name: breast tumor sample 21


title: 53015_BE-dys


title: Breast tumor tissue Sample22

source_name: breast tumor sample 22


title: Breast tumor tissue Sample15

source_name: breast tumor sample 15


title: 53164_TC

description: normal squamous biopsy from the esophagus of an individual with no history of Barrett's esophagus nor esophageal adenocarcinoma

source_name: single whole esophageal biopsy, stored in RNAlater

value: normal esophageal squamous


title: Breast tumor tissue Sample19

source_name: breast tumor sample 19


title: Breast tumor tissue Sample18

source_name: breast tumor sample 18


title: Breast tumor tissue Sample25

source_name: breast tumor sample 25


title: 52011_TC

value: slide


title: 53053_TC


title: 53029_TC


title: Breast tumor tissue Sample16

source_name: breast tumor sample 16


title: Breast tumor tissue Sample14

source_name: breast tumor sample 14


title: Breast tumor tissue Sample11

source_name: breast tumor sample 11


title: Breast tumor tissue Sample13

source_name: breast tumor sample 13


title: Breast tumor tissue Sample10

source_name: breast tumor sample 10


title: Breast tumor tissue Sample9

source_name: breast tumor sample 9


title: 53016_TC


title: Breast tumor tissue Sample7

source_name: breast tumor sample 7


title: microRNA profile of case HCC998

status: Public on Aug 16 2011

city: Guangzhou

first: Rongrong

last: Wei

address: 651 Dongfeng East Road

country: China

institute: Sun Yat-sen University

hyb_protocol: The labeled RNAs from paired HCC and NC were mixed and hybridized to the array with a 1×hybridization solution (5× Denhart’s solution, 0.5% SDS, 5× SSC) in a Hybridization Chamber (Corning Inc, Corning, NY, USA) at 46°C for 12 to 16 hours.

scan_protocol: scanned in a LuxScanTM -10K Scanner (capitalBio Inc.,Beijing, China).

data_processing: quantile normalization across multiple arrays, log 2 transformation of expression levels,BRB ArrayTools v.3.7.1 was used.

source_name: Hepatocellular carcinoma

label_protocol: 2.5 μg of total RNA was employed with 100 nmol/L of pCp-DY647 or pCp-DY547 (Dharmacon, Lafayette, CO, USA) and 15 Units of T4 RNA ligase (USB, Cleveland, Oh, USA) in a total reaction volume of 20 µL at 16°C overnight

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

source_name: Matched noncancerous liver tissue of hepatocellular carcinoma


title: microRNA profile of case HCC997


title: microRNA profile of case HCC996


title: 52036_TC


title: WT_Hras_SV40LT

city: Fukuoka

first: Satoru

last: Koyanagi

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku

department: Pharmaceutics

country: Japan

institute: Kyushu University

hyb_protocol: 1.5 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

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

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: vector-transfected, wild-type, MEFs

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

growth_protocol: Cells were maintained in Dulbecco’s modified Eagle’s medium supplemented with 10% FBS, 20 microM beta-mercaptoethanol, and 1x nonessential amino acid mix

extract_protocol: Total RNA was extracted using the TRIzol.

tag: genotype/variation

value: wild-type

tag: cell type

value: MEFs


title: Breast tumor tissue Sample5

source_name: breast tumor sample 5

value: negative


title: 53005_BE-dys


title: Breast tumor tissue Sample6

source_name: breast tumor sample 6


title: Breast tumor tissue Sample12

source_name: breast tumor sample 12

value: I


title: MEF Nelf-b KO rep2

city: Boston

first: Jianlong

last: Sun

address: 1 Blackfan Street

department: Hematology/Oncology

institute: Boston Children's Hospital

description: replicate 2

hyb_protocol: Standard Ilumina procotol as described in previous publication (Genome Research 14: 2347).

scan_protocol: BeadChips were scanned on a BeadArray Reader (illumina) using BeadScan software (v3.2, Illumina).

data_processing: Scanned data were uploaded into GenomeStudio software ( v1.1, Illumina) via the gene expression module (Direct Hyb).

source_name: mouse embryonic fibroblast derived from a Nelf-bfl/- embryo

label_protocol: RNAs were labeled using the Illumina TotalPrep RNA Amplification Kit (Ambion, #AMIL1791).

growth_protocol: MEFs were maintained in Dulbecco's modification of Eagle's medium supplemented with 10% fetal bovine serum.

extract_protocol: Total RNA was extracted form the virus-infected cells with miRNeasy mini kit (Qiagen) according to manufacturer's instruction.

treatment_protocol: MEFs were infected with Cre-expressing retrovirus and selected with 2mg/ml puromycin for 7 days.

value: embryonic fibroblasts

tag: treatment

value: MEF infected with Cre-expressing virus

tag: strain

value: mixed background of 129/SvJ, C57BL/6, and FVB


title: 54011_TC

source_name: single whole esophageal biopsy, stored in RNAlater

value: female


title: 53072_TC


title: 53073_TC


title: MEF control rep2

description: replicate 2

treatment_protocol: MEFs were infected with a control virus and selected with 2mg/ml puromycin for 7 days.

value: MEF infected with control virus


title: MEF Nelf-b KO rep1

description: replicate 1


title: MEF control rep1

description: replicate 1


title: Breast tumor tissue Sample3

source_name: breast tumor sample 3

tag: Stage

value: II


title: microRNA profile of case HCC992


title: microRNA profile of case HCC991


title: microRNA profile of case HCC993


title: Breast tumor tissue Sample4

source_name: breast tumor sample 4

tag: age at diagnosis


title: microRNA profile of case HCC990


title: microRNA profile of case HCC989


title: Breast tumor tissue Sample1

source_name: breast tumor sample 1

tag: er status


title: Breast tumor tissue Sample2

source_name: breast tumor sample 2

tag: pr status


title: microRNA profile of case HCC98


title: microRNA profile of case HCC995


title: microRNA profile of case HCC97


title: microRNA profile of case HCC88


title: microRNA profile of case HCC91


title: microRNA profile of case HCC94


title: microRNA profile of case HCC86


title: microRNA profile of case HCC668


title: microRNA profile of case HCC663


title: microRNA profile of case HCC669


title: microRNA profile of case HCC76


title: microRNA profile of case HCC678


title: microRNA profile of case HCC677


title: microRNA profile of case HCC8


title: microRNA profile of case HCC674


title: microRNA profile of case HCC654


title: microRNA profile of case HCC657


title: microRNA profile of case HCC652


title: microRNA profile of case HCC85


title: microRNA profile of case HCC641


title: microRNA profile of case HCC648


title: microRNA profile of case HCC636


title: microRNA profile of case HCC612


title: microRNA profile of case HCC625


title: microRNA profile of case HCC607


title: microRNA profile of case HCC611


title: microRNA profile of case HCC602


title: Breast tumor tissue Sample8

source_name: breast tumor sample 8

tag: tissue


title: microRNA profile of case HCC597


title: ATF4_Hras_SV40LT

source_name: vector-transfected, Atf4-null, MEFs


title: microRNA profile of case HCC605


title: microRNA profile of case HCC646


title: microRNA profile of case HCC591


title: microRNA profile of case HCC593


title: microRNA profile of case HCC594


title: microRNA profile of case HCC590


title: microRNA profile of case HCC635


title: microRNA profile of case HCC583


title: microRNA profile of case HCC571


title: microRNA profile of case HCC581


title: microRNA profile of case HCC569


title: microRNA profile of case HCC560


title: microRNA profile of case HCC554


title: microRNA profile of case HCC555


title: microRNA profile of case HCC559


title: 436 VCaP xenograft biopsy at relapse

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

description:
436 VCaP xenograft biopsy at relapse
436_VCaP_Cx_relapse
Raw data file: US45102975_251616210187_S01_GE2-v5_10_Apr08_1_4.txt

hyb_protocol: Hybridizations to Agilent 44K whole human genome expression oligonucleotide microarray slides (Agilent Technologies, Inc., Santa Clara, CA) following the manufacturer’s suggested protocols.

scan_protocol: Fluorescence array images were collected for Cy3 and Cy5 using the Agilent DNA microarray scanner G2505B (Agilent Technologies, Inc., Santa Clara, CA).

data_processing: Agilent Feature Extraction software was used to grid, extract, and normalize the Agilent array data using Agilent's default protocol (essentially LOWESS dye normalization on background subtracted signal values) Spots of poor quality or average intensity levels <300 were removed from further analysis.

label_protocol: Amplified amino-allyl cDNA from each experimental sample was labeled with Cy3 fluorescent dye (reference amino-allyl cDNA was labeled with Cy5) following the manufacturer’s suggested protocols.

extract_protocol: To provide a reference standard RNA for use on two-color oligo microarrays, we pooled equal amounts of total RNA isolated from LNCaP, DU145, PC3, and CWR22 cell lines (American Type Culture Collection, Manassas, VA) growing at log phase in dye-free RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) (Invitrogen, Carlsbad, CA).  Reference RNA was purified using TRIzol (Invitrogen, Carlsbad, CA) following the manufacturer’s protocol. Reference RNA was then further purified by RNeasy maxi kit and treated with DNAse using the RNase-Free DNase Set (Qiagen Inc, Valencia, CA) followed by two rounds of mRNA amplification with amino-allyl incorporation in the second round using the Ambion MessageAmp aRNA Kit (Ambion Inc, Austin, TX), according to the manufacturer’s specifications.  Second round aRNA labeled with Cy5.

tag: gender

tag: cell line

value: reference pool of LNCaP, DU145, PC3, and CWR22 cell lines

extract_protocol: Total RNA was isolated from VCaP biopsy samples by liquid nitrogen homogenization followed by purification using the RNeasy maxi kit (Qiagen Inc, Valencia, CA) which included on-column DNAse digestion using the RNase-Free DNase Set (Qiagen Inc, Valencia, CA) followed by one round of mRNA amplification with amino-allyl incorporation using the Ambion MessageAmp aRNA Kit (Ambion Inc, Austin, TX), according to the manufacturer’s specifications. One round aRNA labeled with Cy3.

value: VCaP xenograft

tag: xenograft details

value: VCaP xenografts were established in the flanks of male scid mice by injecting ~2 million cells in 50% Matrigel. When the tumors reached ~1 cm, biopsies were obtained and then the mice were castrated. Additional biopsies were obtained 4 days after castration, and the tumors were harvested at relapse. Frozen sections were examined to confirm that the samples used for RNA and protein extraction contained predominantly non-necrotic tumor.


title: microRNA profile of case HCC586


title: microRNA profile of case HCC582


title: microRNA profile of case HCC550


title: microRNA profile of case HCC563


title: microRNA profile of case HCC551


title: microRNA profile of case HCC548


title: microRNA profile of case HCC546


title: microRNA profile of case HCC545


title: microRNA profile of case HCC541


title: microRNA profile of case HCC542


title: microRNA profile of case HCC536


title: microRNA profile of case HCC534


title: microRNA profile of case HCC533


description:
434 VCaP xenograft biopsy four days after castration
434_VCaP_Cx_d4
Raw data file: US45102975_251616210187_S01_GE2-v5_10_Apr08_1_3.txt


title: microRNA profile of case HCC532


description:
436 VCaP xenograft biopsy before castration
436_VCaP_Cx_d0
Raw data file: US45102975_251616210186_S01_GE2-v5_10_Apr08_1_3.txt


description:
434 VCaP xenograft biopsy before castration
434_VCaP_Cx_d0
Raw data file: US45102975_251616210187_S01_GE2-v5_10_Apr08_1_2.txt


title: microRNA profile of case HCC528


description:
436 VCaP xenograft biopsy four days after castration
436_VCaP_Cx_d4
Raw data file: US45102975_251616210185_S01_GE2-v5_10_Apr08_1_4.txt


title: 434 VCaP xenograft biopsy at relapse

description:
434 VCaP xenograft biopsy at relapse
434_VCaP_Cx_relapse
Raw data file: US45102975_251616210185_S01_GE2-v5_10_Apr08_1_2.txt


description:
433 VCaP xenograft biopsy four days after castration
433_VCaP_Cx_d4
Raw data file: US45102975_251616210185_S01_GE2-v5_10_Apr08_1_1.txt


title: 433 VCaP xenograft biopsy at relapse

description:
433 VCaP xenograft biopsy at relapse
433_VCaP_Cx_relapse
Raw data file: US45102975_251616210187_S01_GE2-v5_10_Apr08_1_1.txt


title: microRNA profile of case HCC531


description:
433 VCaP xenograft biopsy before castration
433_VCaP_Cx_d0
Raw data file: US45102975_251616210186_S01_GE2-v5_10_Apr08_1_1.txt


title: microRNA profile of case HCC526


title: P17_D1_NK

city: Ljubljana

first: Kristina

last: Gruden

address: Vecna pot 111

department: Department of Biotechnology and Systems Biology

country: Slovenia

institute: National Institute of Biology

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were log2 transformed and normalised using robust spline normalisation with lumi package in R

source_name: NK lymphocytes isolated from peripheral blood mononuclear cells

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

growth_protocol: Cells were not grown.

extract_protocol: Peripheral blood samples were obtained from healthy individuals with informed consent that were age- and gender equilibrated. . Fasting morning (between 7 and 9 am) samples were collected from each donor on three separate days within one month period. Each time peripheral blood was withdrawn. Samples were immediately processed for isolation of mononuclear cells and further lymphocyte subset isolation using positive selection of CD4 cells and positive selection of of NK cells (magnetic nanoparticle based kits from StemCell Inc., Canada. Cell pellets were frozen at -80°C until total RNA extraction. Total RNA was extracted using QIAGEN RNeasy mini kit, treated with DNase I (Invitrogen), concentrated and purified with QIAGEN RNeasy miniElute Cleanup Kit in accordance with the prescribed protocols provided with kits. Quality control and quantification of RNA was performed with NanoDrop ND-1000 spectrophotometer and Agilent Bioanalyser.

treatment_protocol: Cells were not treated in any way.

tag: person

value: person 17

tag: day

value: day 1

tag: Sex

tag: age

tag: body mass index (kg/m2)

value: NK lymphocytes


title: P17_D3_NK

value: day 3


title: P16_D2_NK

value: person 16

value: day 2


title: P14_D3_NK

value: person 14

value: male


title: microRNA profile of case HCC525


title: microRNA profile of case HCC520


title: microRNA profile of case HCC510


title: microRNA profile of case HCC506


title: microRNA profile of case HCC505


title: microRNA profile of case HCC502


title: microRNA profile of case HCC499


title: microRNA profile of case HCC484


title: microRNA profile of case HCC501


title: microRNA profile of case HCC493


title: P13_D1_NK

value: person 13


title: P14_D1_NK


title: P13_D3_NK


title: P16_D1_NK


title: microRNA profile of case HCC488


title: microRNA profile of case HCC487


title: P8_D3_NK

value: person 8


title: P10_D5_NK

value: person 10

value: day 5


title: P14_D2_NK


title: P12_D3_NK

value: person 12


title: microRNA profile of case HCC482


title: P9_D6_NK

value: person 9

value: day 6

value: female


title: microRNA profile of case HCC503


title: microRNA profile of case HCC496


title: P8_D2_NK


title: P6_D3_NK

value: person 6


title: microRNA profile of case HCC994


title: microRNA profile of case HCC480


title: P7_D3_NK

value: person 7


title: P4_D3_NK

value: person 4


title: P5_D2_NK

value: person 5

value: NK lymphocytes


title: microRNA profile of case HCC453


title: microRNA profile of case HCC462


title: microRNA profile of case HCC466


title: microRNA profile of case HCC456


title: microRNA profile of case HCC469


title: P7_D2_NK


title: microRNA profile of case HCC450


title: P6_D1_NK

value: day 1


title: microRNA profile of case HCC449


title: microRNA profile of case HCC443


title: microRNA profile of case HCC446


title: P3_D3_NK

value: person 3

value: day 3


title: microRNA profile of case HCC448


title: P4_D2_NK

value: day 2

value: male


title: P5_D1_NK


title: P3_D2_NK


title: P1_D4_NK

value: person 1

value: day 4


title: microRNA profile of case HCC439


title: P1_D3_NK


title: microRNA profile of case HCC437


title: P3_D1_NK


title: P2_D2_NK

value: person 2


title: P17_D2_CD4

source_name: CD4+ lymphocytes isolated from peripheral blood mononuclear cells

value: person 17

value: CD4+ lymphocytes


title: microRNA profile of case HCC431


title: microRNA profile of case HCC348


title: microRNA profile of case HCC422


title: microRNA profile of case HCC339


title: P16_D3_CD4

value: person 16


title: P17_D3_CD4

value: female


title: microRNA profile of case HCC341


title: microRNA profile of case HCC440


title: P2_D3_NK


title: microRNA profile of case HCC424


title: microRNA profile of case HCC331


title: P17_D1_CD4


title: microRNA profile of case HCC338


title: microRNA profile of case HCC335


title: microRNA profile of case HCC325


title: microRNA profile of case HCC321


title: microRNA profile of case HCC428


title: microRNA profile of case HCC317


title: microRNA profile of case HCC309


title: microRNA profile of case HCC314


title: microRNA profile of case HCC303


title: microRNA profile of case HCC308


title: microRNA profile of case HCC301


title: P15_D1_CD4

value: person 15


title: microRNA profile of case HCC299


title: microRNA profile of case HCC287


title: microRNA profile of case HCC268


title: microRNA profile of case HCC235


title: microRNA profile of case HCC230


title: microRNA profile of case HCC246


title: microRNA profile of case HCC250


title: P16_D2_CD4


title: P15_D3_CD4


title: microRNA profile of case HCC222


title: microRNA profile of case HCC225


title: microRNA profile of case HCC224


title: microRNA profile of case HCC208


title: microRNA profile of case HCC212


title: microRNA profile of case HCC204


title: microRNA profile of case HCC277


title: P16_D1_CD4


title: P13_D3_CD4

value: person 13


title: P13_D1_CD4


title: P14_D2_CD4

value: person 14


title: P12_D4_CD4

value: person 12


title: P15_D2_CD4


title: P14_D1_CD4


title: P13_D2_CD4


title: P14_D3_CD4


title: P12_D3_CD4


title: P12_D5_CD4

value: day 5


title: P10_D4_CD4

value: person 10


title: microRNA profile of case HCC219


title: microRNA profile of case HCC201


title: microRNA profile of case HCC195


title: microRNA profile of case HCC189


title: microRNA profile of case HCC172


title: microRNA profile of case HCC183


title: microRNA profile of case HCC181


title: microRNA profile of case HCC196


title: microRNA profile of case HCC164


title: microRNA profile of case HCC166


title: microRNA profile of case HCC162


title: Starvation at T120, Biological replicate 2

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

country: Netherlands

institute: Delft University of Technology

description: Starvation phase. Sample taken 120 minutes after switching off the feed pump

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

scan_protocol: Scanning of the Affymetrix Genechip® microarrays was performed with The Affymetrix scanner 3000 following Affymetrix instructions.

data_processing: Data were processed with the GeneChip® Operating Software version 1.2 (GCOS 1.2) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 300.

organism: Saccharomyces cerevisiae

source_name: Starvation 120 minutes after switching off the feed pump of the retentostat culture, replicate #2

label_protocol: The double-stranded cDNA was purified (Genechip Sample cleanup Module, Qiagen) before in vitro transcription and labeling (GeneChip IVT Labeling Kit, Affymetrix). Probe preparation were performed following Affymetrix instructions. The quality of total RNA, cDNA, cRNA and fragmented cRNA were checked using the Agilent Bioanalyzer 2100

growth_protocol: The prototrophic laboratory strain Saccharomyces cerevisiae CEN.PK113-7D (MATa MAL2-8c SUC2, obtained from Dr P. Kötter, Frankfurt, Germany) was used in the present study. Stock cultures were prepared from a shake flask culture on YPD medium (Sherman, 1991, Meth.Enzymol., 194: 3-21.) grown to stationary phase, by addition of glycerol (20 % v.v-1) and storage of 2 ml aliquots in sterile vials at -80 °C. Pre-cultures for retentostat cultivation were made by inoculating a frozen stock culture in 500 ml shake-flasks with 100 ml synthetic medium (Verduyn et al., 1992, Yeast, 8: 501-517.) at pH 6 with 2 % glucose. Anaerobic glucose-limited retentostats with a dilution rate of 0.025 h-1 and a working volume of 1.4 litre were operated as described previously (Boender et al., 2009, Appl.Environ.Microbiol., 75: 5607-5614.). Duplicate retentostat cultures were started from independent anaerobic, glucose-limited chemostat cultures grown at the same dilution rate. Retentostat cultivation was started when macroscopic measurements (culture dry weight and specific carbon-dioxide production rate) changed by less than 2% during two consecutive volume changes, by redirecting the effluent through an AppliSense Sample Filter assembly (0.22 µm pore size, Applikon, Schiedam, The Netherlands) instead of through the standard effluent tube. The synthetic medium was supplemented with 50 g.l-1 of glucose and 1.5 ml.l-1 of a 20 % (wt.wt-1) solution of the antifoaming agent Struktol J673 (Schill and Seilacher AG, Hamburg, Germany). After 14 d of retentostat cultivation, when the estimated specific growth rate had decreased to 0.0016 h-1, the supply of fresh medium was terminated. This caused immediate starvation since the residual glucose level in the glucose-limited retentostat was already extremely low (Boender et al., 2009, Appl.Environ.Microbiol., 75: 5607-5614.). All other parameters were kept the same; cultures were sparged with ultra-pure nitrogen at 0.7 l.min-1, pH at was kept at 5.0 – 5.1 by dual titration with 2 M KOH and 2 M H2SO4, and temperature was controlled at 30 °C.

extract_protocol: The concentration of biomass for total RNA isolation, using hot-phenol chloroform extraction, was increased to 50 mg for the retentostat sample (T0) and for the starvation samples 100 mg was used. For each array, total RNA was extracted using the hot-phenol method (Schmitt et al., 1990, Nucleic Acids Res., 18: 3091–3092) and checked for quality (Total RNA chip, Agilent). Poly(A)+ RNA was enriched from total RNA using an oligotex kit (Qiagen Benelux B.V, Venlo, Netherlands). Double-stranded cDNA synthesis was carried out using 15 µg poly(A)+ RNA and the components of the One cycle cDNA Synthesis kit (Affymetrix).

treatment_protocol: 50 to 100 ml of culture broth was sampled directly from the chemostat into a beaker containing 200 ml of liquid nitrogen.  With vigorous stirring, the sample froze instantly.  The frozen sample was then broken into small fragments and transferred to 50 ml centrifuge tubes.  These were thawed at room temperature, returned regularly to ice to ensure the temperature was maintained as close to zero as possible.  The volume corresponding to 120 mg of cells were spun down (5000 rpm at 0°C for 4 min), resuspended in 2 ml ice-cold AE buffer (50 mM sodium acetate, 10 mM EDTA, pH 5.0) and aliquotted into 5 eppendorfs. The tubes were immediately placed in a waterbath for 5 min at 65°C, vortexed then stored at -80°C.

value: CEN.PK113-7D (MATa MAL2-8c SUC2

tag: starvation duration (minutes)


title: microRNA profile of case HCC15

source_name: Hepatocellular carcinoma


title: microRNA profile of case HCC119

source_name: Matched noncancerous liver tissue of hepatocellular carcinoma


title: Starvation at T30, Biological replicate 2

description: Starvation phase. Sample taken 30 minutes after switching off the feed pump

source_name: Starvation 30 minutes after switching off the feed pump of the retentostat culture, replicate #2


title: Starvation at T60, Biological replicate 1

description: Starvation phase. Sample taken 60 minutes after switching off the feed pump

source_name: Starvation 60 minutes after switching off the feed pump of the retentostat culture, replicate #1


title: Starvation at T120, Biological replicate 1

source_name: Starvation 120 minutes after switching off the feed pump of the retentostat culture, replicate #1


title: Starvation at T60, Biological replicate 2

source_name: Starvation 60 minutes after switching off the feed pump of the retentostat culture, replicate #2


title: Starvation at T10, Biological replicate 2

description: Starvation phase. Sample taken 10 minutes after switching off the feed pump

source_name: Starvation 10 minutes after switching off the feed pump of the retentostat culture, replicate #2


title: microRNA profile of case HCC157


title: microRNA profile of case HCC110


title: P8_D3_CD4

value: person 8

value: day 3

tag: cell type


title: P7_D2_CD4

value: person 7

value: day 2

value: male


title: P7_D3_CD4


title: P9_D6_CD4

value: person 9

value: day 6


title: microRNA profile of case HCC11


title: P10_D1_CD4

value: day 1

value: CD4+ lymphocytes


title: P5_D2_CD4

value: person 5


title: P8_D1_CD4

value: female


title: P6_D1_CD4

value: person 6


title: Calorie restriction T0, Biological replicate 2

description: Glucose-limited anaerobic retentostat, 14 days of age. Sample taken before switching off the feed pump. Used as T0

source_name: Retentostat culture used as time point 0, replicate #2


title: P7_D1_CD4


title: Starvation at T10, Biological replicate 1

source_name: Starvation 10 minutes after switching off the feed pump of the retentostat culture, replicate #1


title: P8_D2_CD4


title: P6_D2_CD4


title: microRNA profile of case HCC108


title: microRNA profile of case HCC1031


title: microRNA profile of case HCC1032


title: Starvation at T30, Biological replicate 1

source_name: Starvation 30 minutes after switching off the feed pump of the retentostat culture, replicate #1


title: Calorie restriction T0, Biological replicate 1

source_name: Retentostat culture used as time point 0, replicate #1


title: P5_D1_CD4


title: microRNA profile of case HCC1029


title: microRNA profile of case HCC1027


title: P4_D3_CD4

value: person 4


title: microRNA profile of case HCC1024


title: P3_D3_CD4

value: person 3


title: microRNA profile of case HCC1021


title: P3_D2_CD4


title: P2_D3_CD4

value: person 2


title: Cerebellum-WT-1

city: Louisville

first: Scott

middle: Carl

last: Smith

state: KY

address: 511 S. Floyd St.

department: Neurosurgery

institute: Kentucky Spinal Cord Injury Research Center

description: postnatal day 21

hyb_protocol: Arrays were washed and stained using the GeneChip® Hybridization Wash and Stain Kit (Part# 900720, Affymetrix, Santa Clara, CA)  in GeneChip®  Fluidics Stations 450 (Affymetrix, Santa Clara, CA)

scan_protocol: The arrays were scanned in a GeneChip® Scanner 3000 7G (Affymetrix, Santa Clara)according to the manufacturer's instruction.

data_processing: The dChip DNA-Chip analyzer software was downloaded from www.dchip.org. Default settings were used with the following exceptions: model-based model method and mismatch probe background subtraction options were employed, fold change of controls was set to ±1.2,  the log fold change was set to 50, with a p-value of 0.05 and false discovery rate (FDR)-correction.

label_protocol: Single-stranded cDNA was generated from the amplified cRNA using the WT cDNA Synthesis Kit (Affymetrix). Samples were labeled and hybridized following the Affymetrix standard protocol for their GeneChip® Expression 3' Amplification One-Cycle Target Labeling kit (Part# 900493, Affymetrix, Santa Clara, CA). Samples were then hybridized to Affymetrix MOE 430_2.0 arrays.

growth_protocol: Mice were generated as described elsewhere (Niedernhofer LJ, et al., Nature 2006, 444(21):1038-1043). At postnatal day 21 animals were euthanized and the hippocampus and cerebellum were removed and immediately frozen on dry ice.

extract_protocol: RNeasy kit (Qiagen, Valencia, CA) per manufacturer's instructions

tag: back ground strain

value: FVB  C57BL/6 crosses

tag: genotype/variation

tag: brain region

value: Cerebellum


title: Hippocampus-WT-3

description: postnatal day 21

value: Hippocampus


title: Cerebellum-WT-2

description: postnatal day 21


title: Cerebellum-KO-3

description: postnatal day 21


title: Hippocampus-WT-2

description: postnatal day 21


title: microRNA profile of case HCC1020


title: Cerebellum-WT-3

description: postnatal day 21


title: Cerebellum-KO-2

description: postnatal day 21


title: microRNA profile of case HCC102


title: Hippocampus-KO-2

description: postnatal day 21


title: P1_D4_CD4

value: person 1

value: day 4


title: microRNA profile of case HCC1019


title: P1_D1_CD4


title: Cerebellum-KO-1

description: postnatal day 21


title: Hippocampus-WT-1

description: postnatal day 21


title: microRNA profile of case HCC1016


title: P4_D2_CD4

value: day 2


title: microRNA profile of case HCC1011


title: P2_D1_CD4


title: microRNA profile of case HCC1009


title: microRNA profile of case HCC1023


title: Hippocampus-KO-1

description: postnatal day 21


title: microRNA profile of case HCC1007


title: microRNA profile of case HCC1004


title: microRNA profile of case HCC1003


title: microRNA profile of case HCC1000


title: microRNA profile of case HCC1014


title: R783_CD34+LAF

city: Milan

first: Giuliana

last: Gregato

address: Via ripamonti 435

department: Anatomy pathology

country: Italy

institute: IEO

hyb_protocol: Hybridization mix for target dilution (100 mM MES, 1 M [Na+], 20 mM EDTA, 0.01% Tween 20) was prepared as indicated by Affymetrix, including DMSO at a final concentration of 7% and pre-mixed biotin-labelled control oligo B2 and bioB, bioC, bioD and cre controls (Affymetrix cat #900299) at a final concentration of 50 pM, 1.5 pM, 5 pM, 25 pM and 100 pM, respectively. Targets were diluted in hybridization buffer at a concentration of 25 ng/ul and denatured at 99 °C for 5 minutes and centrifuged at maximum speed for 1 minute prior to introduction into the GeneChip cartridge. A single GeneChip Human Gene 1.0 ST was then hybridized with each biotin-labelled sense target. Hybridizations were performed for 16 h at 45 °C in a rotisserie oven. GeneChip cartridges were washed and stained with GeneChip Hybridization, Wash and Stain Kit in the Affymetrix fluidics station following the FS450_0007 standard protocol, including the following steps: (1) (wash) 10 cycles of 2 mixes/cycle with Wash Buffer A at 30 °C; (2) (wash) 6 cycles of 15 mixes/cycle with Wash Buffer B at 50 °C; (3) stain of the probe array for 5 min in SAPE solution at 35 °C; (4) (wash) 10 cycles of 4 mixes/cycle with Wash Buffer A at 30 °C; (5) stain of the probe array for 5 min in antibody solution at 35 °C; (6) stain of the probe array for 5 min in SAPE solution at 35 °C; (7) (final wash) 15 cycles of 4 mixes/cycle with Wash Buffer A at 35 °C; (8) fill the probe array with Array Holding buffer.

scan_protocol: Images were scanned using an Affymetrix GeneChip Scanner3000 7G, using default parameters. The resulting images were analysed using GeneChip Operating Software v1.2 (GCOS1.2).

data_processing:
The data were preprocessed with RMA using Partek GS software from Partek Inc., St.Louis, Missouri, USA using default settings. All analysis were performed considering only 28829 probesets belonging to the category main
probe group file: HuGene-1_0-st-v1.r4.pgf
meta-probeset file: HuGene-1_0-st-v1.na30.1.hg19.probeset.csv

source_name: CD34+ cells from Leucapheresis

label_protocol: Biotin-labelled cDNA targets were synthesized starting from 200 ng of total RNA. Double stranded cDNA synthesis and related cRNA was performed with GeneChip WT cDNA Synthesis and Amplification Kit . With the same kit was synthesized the sense strand cDNA before to be fragmented and labelled with GeneChip WT Teminal Labeling Kit.. All steps of the labelling protocol were performed as suggested by Affymetrix (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).

extract_protocol: Total RNA extraction  with QiaAmp RNA blood mini kit with DnaseI Rnase-free treatment.

treatment_protocol: digestion with collagenase and purification with CD34+ beads for Lipotransfer aspirates; mobilization of bone marrow cells with growth factors and purification with CD34+ cells for Leucapheresis


title: R783_CD34+FAT

source_name: CD34+ cells from Lipotransfer aspirate


title: Hippocampus-KO-3

description: postnatal day 21


title: R765_FAT_CD34+

description: R765_FAT_CD34+_24-06-2010_pz12_(HuGene-1_0-st-v1).CEL


title: fresh-frozen tissue_MDT_EP89

status: Public on Aug 15 2011

city: Heidelberg

first: Hendrik

last: Witt

state: BW

address: INF 580

department: Molecular Genetics

country: Germany

institute: German Cancer Research Center

hyb_protocol: Hybridization was carried out in a GeneTAC Hybridization Station (Genomic Solutions, Oberhaching, Germany) for 36 hr at 378C.

scan_protocol: We scanned hybridized microarrays at a 5-mm resolution and variable PMT voltage to obtain maximal signal intensities with <0.1% probe saturation,a count ratio of 0.8–1.2 (Cy3/Cy5), and maximal congruence of histogram curves, using a Gene-Pix 4000B microarray scanner (Axon Instruments)

data_processing: Data were filtered according to signal/background ratio (>3.0), mean/median spot intensity (<0.3), and replicate standard deviation (<0.25) and normalized by print-tip loess. To identify regions of similar genomic status within the array-CGH data, we applied the segmentation software GLAD. Imbalances with log2 ratios of less than -1.0 were scored as putative homozygous deletions, because this threshold corresponds to an average copy number of less than 1, suggesting the presence of at least one subpopulation of cells with homozygous deletions. Gains with log2 ratios higher than 1.0 were scored as amplifications. Chromosomal mapping information was based on Ensembl (v49) and position of candidate genes was verified using Ensembl v52.

source_name: brain/ependymoma

label_protocol: Cell-line DNA and reference DNA from healthy donors were differentially labeled with Cy3-/ Cy5-conjugated dCTP by use of a BioPrime DNA Labeling Kit (Invitrogen, Karlsruhe, Germany).

extract_protocol: Extraction of high molecular weight DNA from frozen tumor samples of DKFZ cohort was carried out as previously described (Pfister et al., 2009). Briefly, genomic DNA from peripheral blood mononuclear cells of healthy donors (pool of ten male and female donors, respectively, age 25-40 years) used as a control was isolated by use of the Qiagen DNA Blood Midi-Kit (Hilden, Germany).

value: F

tag: localization

value: supratentorial

source_name: reference DNA from healthy donors

tag: reference

value: DNA from healthy donors

value: peripheral blood


title: R765_LAF_CD34+


title: fresh-frozen tissue_MDT_EP93

value: M

value: posterior fossa


title: fresh-frozen tissue_MDT_EP87


title: degU stat rep3

city: Braunschweig

first: Rebekka

last: Biedendieck

address: Rebenring 56

department: Institute of Microbiology

institute: Technische Universtität Braunschweig

hyb_protocol: 300 ng of Cy3-labeled RNA and 300 ng of Cy5-labeled RNA were mixed and fragmented, and hybridized to the microarray at 65 °C for 17 hours using the Agilent Hybridization Chamber according to the manufacturer’s instructions.

scan_protocol: The microarrays were scanned with the help of the Agilent C Scanner (Agilent Technologies, USA) using the software Agilent Scan Controll 8.4.1

data_processing: For feature extraction the software Feature Extraction 10.7.3.1 (Agilent Technologies, USA) was used, data processing was carried out using the Bioconducter – Linear Models for Microarray analysis (LIMMA) package of the R language (http://www.r-project.org).

organism: Priestia megaterium

source_name: pMMdegU stationary

label_protocol: RNA samples were labelled with Cy3 (pMMdegU, sample) and Cy5 (pMM1520, control) using the ULS fluorescent labelling kit (Kreatech, Germany).

growth_protocol: cells were grown in LB medium (baffled flasks) at 37 °C with vigorous shaking (170 rpm, innova 44, New Brunswick Scientific)

extract_protocol: after treatment of the cells with sodium azide, cells were disrupted using a Mikro Dismembrator S (Sartorius AG, Göttingen, Germany) at 2700 rpm with cooling for 4 min, RNA was subsequently isolated from the supernatant using the High Pure RNA Isolation Kit (Roche Diagnostics GmbH, Mannheim, Germany)

treatment_protocol: induction of expression was done at an OD(546 nm) of 0.5 by adding xylose to a final concentration of 0.25 %

tag: expression

value: degU, stationary phase

source_name: pMM1522 stationary

value: control vector, stationary phase


title: degU stat rep5


title: fresh-frozen tissue_MDT_EP85

tag: tissue


title: fresh-frozen tissue_MDT_EP92

tag: gender


title: degU stat rep2


title: degU exp rep2

source_name: pMMdegU exponential

value: degU, exponential phase

source_name: pMM1522 exponential

value: control vector, exponential phase


title: fresh-frozen tissue_MDT_EP84


title: fresh-frozen tissue_MDT_EP86


title: fresh-frozen tissue_MDT_EP95


title: degU stat rep4


title: fresh-frozen tissue_MDT_EP80


title: fresh-frozen tissue_MDT_EP9


title: fresh-frozen tissue_MDT_EP8


title: fresh-frozen tissue_MDT_EP94


title: degU exp rep1


title: degU exp rep3


title: fresh-frozen tissue_MDT_EP96


title: fresh-frozen tissue_MDT_EP79


title: fresh-frozen tissue_MDT_EP76


title: degU stat rep1


title: fresh-frozen tissue_MDT_EP60


title: fresh-frozen tissue_MDT_EP58


title: fresh-frozen tissue_MDT_EP67


title: fresh-frozen tissue_MDT_EP77


title: fresh-frozen tissue_MDT_EP69


title: fresh-frozen tissue_MDT_EP57


title: fresh-frozen tissue_MDT_EP29

value: spinal


title: fresh-frozen tissue_MDT_EP43


title: fresh-frozen tissue_MDT_EP47


title: fresh-frozen tissue_MDT_EP41


title: fresh-frozen tissue_MDT_EP4


title: fresh-frozen tissue_MDT_EP56


title: fresh-frozen tissue_MDT_EP32


title: fresh-frozen tissue_MDT_EP30


title: fresh-frozen tissue_MDT_EP50


title: fresh-frozen tissue_MDT_EP5


title: fresh-frozen tissue_MDT_EP27


title: fresh-frozen tissue_MDT_EP22


title: fresh-frozen tissue_MDT_EP33


title: fresh-frozen tissue_MDT_EP153


title: fresh-frozen tissue_MDT_EP54


title: fresh-frozen tissue_MDT_EP152


title: fresh-frozen tissue_MDT_EP154


title: fresh-frozen tissue_MDT_EP149


title: fresh-frozen tissue_MDT_EP31


title: fresh-frozen tissue_MDT_EP25


title: fresh-frozen tissue_MDT_EP16


title: fresh-frozen tissue_MDT_EP148


title: fresh-frozen tissue_MDT_EP42


title: fresh-frozen tissue_MDT_EP147


title: fresh-frozen tissue_MDT_EP135


title: fresh-frozen tissue_MDT_EP140


title: fresh-frozen tissue_MDT_EP132


title: fresh-frozen tissue_MDT_EP133


title: microRNA profile of case HCC103

source_name: Hepatocellular carcinoma

source_name: Matched noncancerous liver tissue of hepatocellular carcinoma


title: fresh-frozen tissue_MDT_EP130


title: fresh-frozen tissue_MDT_EP124


title: fresh-frozen tissue_MDT_EP120


title: fresh-frozen tissue_MDT_EP117


title: fresh-frozen tissue_MDT_EP126


title: fresh-frozen tissue_MDT_EP119


title: fresh-frozen tissue_MDT_EP118


title: fresh-frozen tissue_MDT_EP146


title: fresh-frozen tissue_MDT_EP125


title: fresh-frozen tissue_MDT_EP122


title: fresh-frozen tissue_MDT_EP115


title: fresh-frozen tissue_MDT_EP123


title: fresh-frozen tissue_MDT_EP134


title: fresh-frozen tissue_MDT_EP116


title: fresh-frozen tissue_MDT_EP144


title: fresh-frozen tissue_MDT_EP113


title: fresh-frozen tissue_MDT_EP114


title: fresh-frozen tissue_MDT_EP128


title: fresh-frozen tissue_MDT_EP111


title: fresh-frozen tissue_MDT_EP105


title: fresh-frozen tissue_MDT_EP112


title: fresh-frozen tissue_MDT_EP108


title: fresh-frozen tissue_MDT_EP106


title: PtfbE-tfbX/Δura3ΔtfbD_temp-37C_od-0.506_1

first: Serdar

last: Turkarslan

address: 401 Terry Ave

institute: Institute for Systems Biology

description: Halobacterium salinarum NRC-1 Δura3ΔtfbD knockout harboring synthetic tfbX with tfbE promoter grown in CM at 37C until OD600= 0.506 vs NRC-1

hyb_protocol: see http://www.chem.agilent.com/Scripts/PDS.asp?lPage=34519 for details

scan_protocol: ScanArray 5000, using Packard BioChip ScanArray software. See http://www.systemsbiology.org/Scientists_and_Research/Technology/ISB_Facilities/Microarray for microarray scanning details

data_processing: Agilent FeatureExtraction for spotfinding/quantitation. See http://www.systemsbiology.org/Scientists_and_Research/Technology/Data_Management/Microarray_Pipeline for more details

organism: Halobacterium salinarum NRC-1

source_name: PtfbE-tfbX in Δura3ΔtfbD knockout at 37C OD600= 0.506

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-35

growth_protocol: Halobacterium salinarum NRC-1 strains were batch cultured in rich media (CM) in flasks at either 25°C or 37°C with constant shaking (125 rpm)

extract_protocol: Total RNA was prepared from the cell pellets using the mirVANA RNA isolation kit

treatment_protocol: Culture aliquots (~4 ml) were collected over early (OD600: ~0.2), mid (OD600: ~0.4) and late (OD600: ~0.8) phases of growth, centrifuged (16 000 g, 90 s), and flash frozen.

tag: strain

tag: temperature

tag: od

source_name: Halobacterium NRC-1 Reference sample

value: wild type


title: PtfbE-tfbX/Δura3ΔtfbD_temp-25C_od-0.412_1

description: Halobacterium salinarum NRC-1 Δura3ΔtfbD knockout harboring synthetic tfbX with tfbE promoter grown in CM at 25C until OD600= 0.412 vs NRC-1

source_name: PtfbE-tfbX in Δura3ΔtfbD knockout at 25C OD600= 0.412


title: fresh-frozen tissue_MDT_EP102


title: PtfbD-tfbX/Δura3ΔtfbD_temp-25C_od-0.801_1

description: Halobacterium salinarum NRC-1 Δura3ΔtfbD knockout harboring synthetic tfbX with tfbD promoter grown in CM at 25C until OD600= 0.801 vs NRC-1

source_name: PtfbD-tfbX in Δura3ΔtfbD knockout at 25C OD600= 0.801


title: PtfbD-tfbX/Δura3ΔtfbD_temp-25C_od-0.227_1

description: Halobacterium salinarum NRC-1 Δura3ΔtfbD knockout harboring synthetic tfbX with tfbD promoter grown in CM at 25C until OD600= 0.227 vs NRC-1

source_name: PtfbD-tfbX in Δura3ΔtfbD knockout at 25C OD600= 0.227


title: fresh-frozen tissue_MDT_EP1


title: PtfbD-tfbX/Δura3ΔtfbD_temp-37C_od-0.233_1

description: Halobacterium salinarum NRC-1 Δura3ΔtfbD knockout harboring synthetic tfbX with tfbD promoter grown in CM at 37C until OD600= 0.233 vs NRC-1

source_name: PtfbD-tfbX in Δura3ΔtfbD knockout at 37C OD600= 0.233


title: PtfbD-tfbX/Δura3ΔtfbD_temp-25C_od-0.419_1

description: Halobacterium salinarum NRC-1 Δura3ΔtfbD knockout harboring synthetic tfbX with tfbD promoter grown in CM at 25C until OD600= 0.419 vs NRC-1

source_name: PtfbD-tfbX in Δura3ΔtfbD knockout at 25C OD600= 0.419


title: PtfbD-tfbX/Δura3ΔtfbD_temp-37C_od-0.471_1

description: Halobacterium salinarum NRC-1 Δura3ΔtfbD knockout harboring synthetic tfbX with tfbD promoter grown in CM at 37C until OD600= 0.471 vs NRC-1

source_name: PtfbD-tfbX in Δura3ΔtfbD knockout at 37C OD600= 0.471


title: PtfbE-tfbX/Δura3ΔtfbD_temp-37C_od-0.828_1

description: Halobacterium salinarum NRC-1 Δura3ΔtfbD knockout harboring synthetic tfbX with tfbE promoter grown in CM at 37C until OD600= 0.828 vs NRC-1

source_name: PtfbE-tfbX in Δura3ΔtfbD knockout at 37C OD600= 0.828


title: PtfbD-tfbX/Δura3ΔtfbD_temp-37C_od-0.828_1

description: Halobacterium salinarum NRC-1 Δura3ΔtfbD knockout harboring synthetic tfbX with tfbD promoter grown in CM at 37C until OD600= 0.828 vs NRC-1

source_name: PtfbD-tfbX in Δura3ΔtfbD knockout at 37C OD600= 0.828


title: vector/Δura3ΔtfbD_temp-25C_od-0.212_1

description: Halobacterium salinarum NRC-1 Δura3ΔtfbD knockout harboring control plasmid grown in CM at 25C until OD600= 0.212 vs NRC-1

source_name: vector in Δura3ΔtfbD knockout at 25C OD600= 0.212


title: vector/Δura3ΔtfbD_temp-25C_od-0.437_1

description: Halobacterium salinarum NRC-1 Δura3ΔtfbD knockout harboring control plasmid grown in CM at 25C until OD600= 0.437 vs NRC-1

source_name: vector in Δura3ΔtfbD knockout at 25C OD600= 0.437


title: PtfbE-tfbX/Δura3ΔtfbD_temp-25C_od-0.205_1

description: Halobacterium salinarum NRC-1 Δura3ΔtfbD knockout harboring synthetic tfbX with tfbE promoter grown in CM at 25C until OD600= 0.205 vs NRC-1

source_name: PtfbE-tfbX in Δura3ΔtfbD knockout at 25C OD600= 0.205


title: PtfbE-tfbX/Δura3ΔtfbD_temp-25C_od-0.239_1

description: Halobacterium salinarum NRC-1 Δura3ΔtfbD knockout harboring synthetic tfbX with tfbE promoter grown in CM at 25C until OD600= 0.239 vs NRC-1

source_name: PtfbE-tfbX in Δura3ΔtfbD knockout at 25C OD600= 0.239


title: vector/Δura3ΔtfbD_temp-25C_od-0.874_1

description: Halobacterium salinarum NRC-1 Δura3ΔtfbD knockout harboring control plasmid grown in CM at 25C until OD600= 0.874 vs NRC-1

source_name: vector in Δura3ΔtfbD knockout at 25C OD600= 0.874


title: fresh-frozen tissue_MDT_EP100

source_name: brain/ependymoma

source_name: reference DNA from healthy donors


title: PtfbE-tfbX/Δura3ΔtfbD_temp-37C_od-0.245_1

description: Halobacterium salinarum NRC-1 Δura3ΔtfbD knockout harboring synthetic tfbX with tfbE promoter grown in CM at 37C until OD600= 0.245 vs NRC-1

source_name: PtfbE-tfbX in Δura3ΔtfbD knockout at 37C OD600= 0.245


title: vector/Δura3ΔtfbD_temp-37C_od-0.236_1

description: Halobacterium salinarum NRC-1 Δura3ΔtfbD knockout harboring control plasmid grown in CM at 37C until OD600= 0.236 vs NRC-1

source_name: vector in Δura3ΔtfbD knockout at 37C OD600= 0.236

source_name: Halobacterium NRC-1 Reference sample


title: vector/Δura3ΔtfbD_temp-37C_od-0.834_1

description: Halobacterium salinarum NRC-1 Δura3ΔtfbD knockout harboring control plasmid grown in CM at 37C until OD600= 0.834 vs NRC-1

source_name: vector in Δura3ΔtfbD knockout at 37C OD600= 0.834


title: PtfbE-tfbX/Δura3ΔtfbD_temp-25C_od-0.819_1

description: Halobacterium salinarum NRC-1 Δura3ΔtfbD knockout harboring synthetic tfbX with tfbE promoter grown in CM at 25C until OD600= 0.819 vs NRC-1

source_name: PtfbE-tfbX in Δura3ΔtfbD knockout at 25C OD600= 0.819


title: fresh-frozen tissue_MDT_EP110


title: LAP-tTA-3_7weeks

first: Chunsheng

last: Zhang

address: 33 Avenue Louis Pasteur

institute: Merck

hyb_protocol: GeneChip microarrays are loaded with the fragmented target sample/hybridization buffer mix using standard manual techniques.  Arrays are hybridized for 18 hours at 45C with vigorous mixing.   Unbound sample is removed and staining is accomplished through the binding of streptavidin conjugated phycoerythrin to the hybridized target. Excess label is removed.  Washing and staining steps are performed by the Affymetrix FS450 fluidics station using standard protocols.

scan_protocol: Arrays are scanned using a GeneChip Scanner 3000 7G with a 48 array autoloader. The scanner maintains the optimal temperature for the arrays prior to and during scanning.

data_processing: Data were loaded into the Rosetta Resolver system (Rosetta Biosoftware, Seattle, WA) and processed using the RMA algorithm (http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=12582260).  Intensities were calculated based on RMA, a Rosetta-developed error, and a MAS-5 p-value.  The Rosetta-developed error is used in the calculation of xdev for the ratio p-values as described in section 2.2 (http://bioinformatics.oxfordjournals.org/cgi/content/full/22/9/1111).

label_protocol: The final in vitro transcription incorporates biotin moieties that are later labeled with phycoerythrin.  After amplification, samples are put through a controlled fragmentation to improve hybridization sensitivity and consistency.  The labeled molecules are biotinylated-cRNA.

extract_protocol: Samples are processed in parallel in 96-well plates to minimize potential variation.  Reaction purification is achieved using magnetic binding beads for cDNA and Qiagen RNeasy kits for cRNA purification.

value: liver

value: FVB

value: LAP-tTA

tag: disease state

value: normal


title: Δura3DtfbE_temp-25C_od-0.867_1

description: Halobacterium salinarum NRC-1 Δura3DtfbE knockout grown in CM at 25C OD600= 0.867 vs NRC-1

source_name: Δura3DtfbE knockout at 25C OD600= 0.867


title: LAP-tTA-Tre-met-dis-Liv-6_14weeks

value: LAP-tTA-Tre-c-Met


title: Δura3DtfbE_temp-25C_od-0.196_1

description: Halobacterium salinarum NRC-1 Δura3DtfbE knockout grown in CM at 25C OD600= 0.196 vs NRC-1

source_name: Δura3DtfbE knockout at 25C OD600= 0.196


title: Δura3DtfbE_temp-25C_od-0.418_1

description: Halobacterium salinarum NRC-1 Δura3DtfbE knockout grown in CM at 25C OD600= 0.418 vs NRC-1

source_name: Δura3DtfbE knockout at 25C OD600= 0.418


title: Δura3ΔtfbD_temp-25C_od-0.798_1

description: Halobacterium salinarum NRC-1 Δura3ΔtfbD knockout grown in CM at 25C OD600= 0.798 vs NRC-1

source_name: Δura3ΔtfbD knockout at 25C OD600= 0.798


title: LAP-tTA-5_7weeks


title: TRE-met-3_6weeks

value: Tre-c-Met


title: LAP-tTA-Tre-met-ad-Liv-1_14weeks


title: TRE-met-2_6weeks


title: Δura3ΔtfbD_temp-25C_od-0.465_1

description: Halobacterium salinarum NRC-1 Δura3ΔtfbD knockout grown in CM at 25C OD600= 0.465 vs NRC-1

source_name: Δura3ΔtfbD knockout at 25C OD600= 0.465


title: LAP-tTA-2_7weeks


title: TRE-met-5_6weeks


title: LAP-tTA-Tre-met-ad-Liv-2_14weeks


title: LAP-tTA-Tre-met-dis-Liv-2_14weeks


title: LAP-tTA-Tre-met-Tum-3b_14weeks

value: tumor


title: Δura3_temp-25C_od-0.807_1

description: Halobacterium salinarum NRC-1 Δura3 knockout grown in CM at 25C OD600= 0.807 vs NRC-1

source_name: Δura3 knockout at 25C OD600= 0.807


title: Δura3ΔtfbD_temp-25C_od-0.207_1

description: Halobacterium salinarum NRC-1 Δura3ΔtfbD knockout grown in CM at 25C OD600= 0.207 vs NRC-1

source_name: Δura3ΔtfbD knockout at 25C OD600= 0.207


title: TRE-met-6_6weeks


title: LAP-tTA-Tre-met-ad-Liv-3_14weeks


title: LAP-tTA-Tre-met-Tum-4a_14weeks


title: LAP-tTA-Tre-met-Tum-6a_14weeks


title: FVB-WT-6_14weeks

value: WT


title: LAP-tTA-Tre-met-ad-Liv-6_14weeks


title: Δura3_temp-25C_od-0.519_1

description: Halobacterium salinarum NRC-1 Δura3 knockout grown in CM at 25C OD600= 0.519 vs NRC-1

source_name: Δura3 knockout at 25C OD600= 0.519


title: LAP-tTA-Tre-met-Tum-6b_14weeks


title: MB231_siRelB_TNF_4h

city: Singapore

first: Peiyong

last: Guan

address: 60 Biopolis Street, Genome, #02-01

country: Singapore

institute: Genome Institute of Singapore

description: siRelB TNF4h

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: Illumina Inc. BeadStudio version 3.2.7; Shift to 75 percentile

source_name: Breast cancer cell line (MDA-MB-231)

label_protocol: standard Illumina protocol

growth_protocol: MDA-MB-231 was cultured in were grown in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum and 5000U/mL penicillin/streptomycin (Invitrogen) and maintained at 37 °C with 5% CO2.

extract_protocol: Total RNA was isolated using Trizol (Invitrogen) and purified with the RNeasy Mini Kit (Qiagen).

treatment_protocol: MDA-MB-231 was transfected with siRNA of negative control, EZH2, RelA, and RelB respectively followed by treatment of 10ng/ml TNFalpha for 4 hours.

tag: cell line

tag: treatment group


title: Δura3_temp-25C_od-0.240_1

description: Halobacterium salinarum NRC-1 Δura3 knockout grown in CM at 25C OD600= 0.240 vs NRC-1

source_name: Δura3 knockout at 25C OD600= 0.240


title: MB231_siRelA_TNF_4h

description: siRelA TNF4h


title: H3 ChIP in pch2 cells replicate 2

city: New York

first: Andreas

last: Hochwagen

state: NY

address: 1009 Silver Center 100 Washington Square East

institute: New York University

description: biological replicate 2 of 2 of Histone 3 ChIP in pch2 cells

hyb_protocol: Samples were co-hybridized to custom Agilent arrays in 1X Agilent hybridization buffer at 65 degrees for 16 hours. Samples were washed according to manufacturer's instructions.

scan_protocol: Agilent scanner using the AgilentHD_CGH protocol (5μM resolution, 100% PMT for each laser). Images were quantified using Agilent Feature Extraction Software (version 10.1.1.1).

data_processing:
Cy3 and Cy5 levels and background were calculated using Agilent Feature Extractor software. Background normalization, log2 ratios for each experiment and scale normalizations across each set of duplicated experiments were calculated using the sma package in R (Yang, et al., 2001), a computer language and environment for statistical computing (v2.1.0, http://www.r-project.org).
Replicate datesets are the normalized log2 ratio (immunoprecipitated DNA signal / input DNA signal). The final values are average of the individual replicate log2 ratios.

source_name: meiotic budding yeast cells, 3 hours in SPO-medium

label_protocol: Half of the immunoprecipitated DNA or one tenth of the input DNA was labeled with Cy3- or Cy5-dUTP (GE Healthcare) by random priming using 4 µg random nonamer oligo (Integrated DNA Technologies) and 10 units of Klenow (New England Biolabs). Unincorporated dye was removed using microcon columns (30-kDa MW cutoff, Millipore).

growth_protocol: Cells were pre-grown in presporulation medium (BYTA) and transferred into sporulation medium (SPO) at 0 hours.

extract_protocol: 25 ml of cells were harvested after 3 hours in sporulation media. Chromatin immunoprecipitation was performed as described (Aparicio et al., 1997). One tenth of the lysate was removed as an input sample. Proteins were immunoprecipitated with the indicated antibodies in combination with 20 µl GammaBind-Sepharose (GE Healthcare) for 16 hours at 4°C.

tag: ip or input

value: IP

tag: chip antibody

value: 2 µg Histone H3 antibody (Ab1791, Abcam)

source_name: meiotic budding yeast cells

value: input


title: MB231_siEZH2_TNF_4h

description: siEZH2 TNF4h


title: MB231_siRelB_CTRL

description: siRelB CTRL


title: LAP-tTA-Tre-met-Tum-1a_14weeks

tag: age


title: LAP-tTA-6_7weeks


title: LAP-tTA-Tre-met-Tum-5a_14weeks


title: H3K4me3 ChIP in wild type cells replicate 2

description: biological replicate 2 of 2 of Histone 3K4me3 ChIP in wild type cells

value: 2 µg Histone H3K4me3 antibody (Ab8580, Abcam)


title: LAP-tTA-Tre-met-ad-Liv-5_14weeks


title: H3 ChIP in wild type cells replicate 2

description: biological replicate 2 of 2 of Histone 3 ChIP in wild type cells


title: MB231_siNC_TNF_4h

description: siNC TNF4h


title: H3K4me3 ChIP in pch2 cells replicate 2

description: biological replicate 2 of 2 of Histone 3K4me3 ChIP in pch2 cells


title: FVB-WT-4_14weeks


title: TRE-met-1_6weeks


title: H3 ChIP in wild type cells replicate 1

description: biological replicate 1 of 2 of Histone 3 ChIP in wild type cells


title: LAP-tTA-Tre-met-Tum-2b_14weeks


title: H3 ChIP in pch2 cells replicate 1

description: biological replicate 1 of 2 of Histone 3 ChIP in pch2 cells


title: FVB-WT-5_14weeks


title: MB231_siNC_CTRL_rep3

description: siNC CTRL_3


title: LAP-tTA-Tre-met-Tum-1b_14weeks


title: LAP-tTA-Tre-met-Tum-7b_14weeks


title: H3K4me3 ChIP in pch2 cells replicate 1

description: biological replicate 1 of 2 of Histone 3K4me3 ChIP in pch2 cells


title: FVB-WT-3_14weeks


title: FVB-WT-2_14weeks


title: LAP-tTA-Tre-met-dis-Liv-7_14weeks


title: MB231_siRelA_CTRL

description: siRelA CTRL


title: MB231_siEZH2_CTRL_rep3

description: siEZH2 CTRL_3


title: LAP-tTA-Tre-met-Tum-4b_14weeks


title: MB231_siEZH2_CTRL_rep1

description: siEZH2 CTRL_1


title: H3K4me3 ChIP in wild type cells replicate 1

description: biological replicate 1 of 2 of Histone 3K4me3 ChIP in wild type cells


title: Mre11 ChIP in pch2 cells replicate 2

description: biological replicate 2 of 2 of Mre11 ChIP in pch2 cells

value: 2 µg Myc antibody (9E11, Abcam)


title: LAP-tTA-Tre-met-dis-Liv-3_14weeks


title: FVB-WT-7_14weeks


title: MB231_siEZH2_CTRL_rep2

description: siEZH2 CTRL_2


title: LAP-tTA-Tre-met-dis-Liv-4_14weeks


title: Mre11 ChIP in wild-type cells replicate 1

description: biological replicate 1 of 2 of Mre11 ChIP in wild-type cells


title: TRE-met-7_6weeks


title: TRE-met-4_6weeks


title: LAP-tTA-1_7weeks


title: LAP-tTA-Tre-met-Tum-2a_14weeks


title: MB231_siNC_CTRL_rep1

description: siNC CTRL_1


title: LAP-tTA-Tre-met-Tum-5b_14weeks


title: FVB-WT-1_14weeks


title: LAP-tTA-Tre-met-ad-Liv-4_14weeks


title: Mer2 ChIP in pch2 cells replicate 1

description: biological replicate 1 of 2 of Mer2 ChIP in pch2 cells


title: Mre11 ChIP in pch2 cells replicate 1

description: biological replicate 1 of 2 of Mre11 ChIP in pch2 cells


title: LAP-tTA-Tre-met-dis-Liv-1_14weeks


title: LAP-tTA-Tre-met-Tum-3a_14weeks


title: Mer2 ChIP in pch2 cells replicate 2

description: biological replicate 2 of 2 of Mer2 ChIP in pch2 cells


title: vector/Δura3ΔtfbD_temp-37C_od-0.485_1

description: Halobacterium salinarum NRC-1 Δura3ΔtfbD knockout harboring control plasmid grown in CM at 37C until OD600= 0.485 vs NRC-1

source_name: vector in Δura3ΔtfbD knockout at 37C OD600= 0.485


title: Mre11 ChIP in wild-type cells replicate 2

description: biological replicate 2 of 2 of Mre11 ChIP in wild-type cells


title: MB231_siNC_CTRL_rep2

description: siNC CTRL_2


title: Mer2 ChIP in wild type cells replicate 1

description: biological replicate 1 of 2 of Mer2 ChIP in wild type cells


title: LAP-tTA-Tre-met-dis-Liv-5_14weeks


title: LAP-tTA-Tre-met-Tum-7a_14weeks


title: Mer2 ChIP in wild type cells replicate 2

description: biological replicate 2 of 2 of Mer2 ChIP in wild type cells


title: Microbiota depleted mice rep5

city: Oslo

first: Leonardo

middle: A.

last: Meza-Zepeda

address: Ullernchausseen 70

department: Dept. of Tumor Biology

country: Norway

institute: The Norwegian Radium Hospital

description: Mice 5

data_processing: The data were normalised using quantile normalisation in R using Bioconductor packages

source_name: Colon intestinal epithelial cells

extract_protocol: The IECs were resuspended in TRI Reagent® (Ambion Applied Biosystems, Foster City, CA), and stored at -70oC until RNA isolation according to manufacturer’s intructions

treatment_protocol: After 17 days of antibiotic treatment(microbiota depleted mice) or water (control mice)  mice were anaesthetized with 150 µl Hypnorm® (fentanyl citrate 0.315 mg/ml and fluanison 10 mg/ml, VetaPharma Ltd) and midazolam (5 mg/ml, B. Braun Meslungen AG) subcutaneously and bled to death by cardiac puncture. Colon was swiftly excised and flushed with 2x 10 ml ice cold PBS (w/o Mg2+ and Ca2+) and kept moist. Mesenteric and adipose tissue was removed from the colon which was subsequently opened longitudinally, then cut transversally in 5 cm long pieces and incubated 25 min in 25 ml 20 mM EDTA (Sigma-Aldrich, St. Louis, MO) at room temperature on a shaker before being vigorously hand shaken for 5 minutes. The IECs were harvested in a fresh tube, washed twice in ice cold PBS, resuspended in TRI Reagent® (Ambion Applied Biosystems, Foster City, CA).

tag: condition

value: Microbiota depleted

value: BALB/c

value: Male

value: 8-9 weeks

tag: cell type

value: Colon intestinal epithelial cells


title: LAP-tTA-Tre-met-ad-Liv-7_14weeks

value: liver

value: FVB

tag: genotype/variation


title: Rec114 ChIP in pch2 cells replicate 2

description: biological replicate 2 of 2 of Rec114 ChIP in pch2 cells


title: Microbiota depleted mice rep3

description: Mice 3


title: Sendai infected_S1376

city: München

first: Olivia

last: Prazeres da Costa

state: Bavaria

address: Trogerstr. 30

department: Medical Microbiology, Immunology and Hygiene

institute: Technische Universität München

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: RMA Normalization of Expression Console.

source_name: Sendai infected

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

growth_protocol: not applicable

extract_protocol: RNA trizol extraction, DNA digestion

treatment_protocol: not applicable

value: spleen

value: wildtype

tag: infection

value: Sendai


title: Microbiota depleted mice rep2

description: Mice 2


title: Microbiota depleted mice rep4

description: Mice 4


title: Rec114 ChIP in pch2 cells replicate 1

description: biological replicate 1 of 2 of Rec114 ChIP in pch2 cells


title: Control mice rep3

description: Mice 3

value: Control


title: Hop1 ChIP in pch2 cells replicate 2

description: biological replicate 2 of 2 of Hop1 ChIP in pch2 cells

value: 2 µg Hop1 antibody (gift of Nancy Hollingsworth)


title: Control mice rep4

description: Mice 4


title: Microbiota depleted mice rep1

description: Mice 1


title: Sendai infected_S1375


title: Rec114 ChIP in wild type cells replicate 3

description: biological replicate 3 of 3 of Rec114 ChIP in wild type cells

value: wild type

value: IP


title: Rec114 ChIP in wild type cells replicate 1

description: biological replicate 1 of 3 of Rec114 ChIP in wild type cells

value: input


title: Hop1 ChIP in pch2 cells replicate 1

description: biological replicate 1 of 2 of Hop1 ChIP in pch2 cells


title: Control mice rep1

description: Mice 1


title: Rec114 ChIP in wild type cells replicate 2

description: biological replicate 2 of 3 of Rec114 ChIP in wild type cells


title: Hop1 ChIP in wild type cells replicate 2

description: biological replicate 2 of 2 of Hop1 ChIP in wild type cells


title: Sendai infected_S1377


title: Control mice rep5

description: Mice 5


title: Control mice rep6

description: Mice 6


title: LAP-tTA-7_7weeks

value: LAP-tTA

value: normal


title: Control mice rep2

description: Mice 2


title: Baki-1MuLV infected_S1374

source_name: Baki-1MuLV infected


title: wildtype PBS_S1370

source_name: wildtype


title: Hop1 ChIP in wild type cells replicate 1

description: biological replicate 1 of 2 of Hop1 ChIP in wild type cells


title: Baki-1MuLV infected_S1373


title: ssDNA in dmc1 cells with a Chr2:12 reciprocal translocation replicate 2

description: biological replicate 2 of 2 of ssDNA in dmc1 cells with a Chr2:12 reciprocal translocation

data_processing:
Cy3 and Cy5 levels and background were calculated using Agilent Feature Extractor software. Background normalization, log2 ratios for each experiment and scale normalizations across each set of duplicated experiments were calculated using the sma package in R (Yang, et al., 2001), a computer language and environment for statistical computing (v2.1.0, http://www.r-project.org).
Replicate datesets are the normalized log2 ratio (experimental ssDNA signal (5 hours timepoint) / control ssDNA (0 hour timepoint)). The final values are average of the individual replicate log2 ratios.

source_name: meiotic budding yeast cells, 0 or 5 hours in SPO-medium

label_protocol: 1.5 μg of ssDNA was labeled with Cy3-dUTP or Cy5-dUTP (GE Healthcare) by random priming without denaturation using 4 µg random nonamer oligo (Integrated DNA Technologies) and 10 units of Klenow (New England Biolabs). Unincorporated dye was removed using microcon columns (30-kDa MW cutoff, Millipore).

growth_protocol: Cells were pre-grown in presporulation medium (BYTA) and transferred into sporulation medium (SPO) at 0 hours. Samples were isolated at the indicated timepoints.

extract_protocol: To isolate ssDNA, ~10^9 cells were fixed in 70% ethanol at –20°C. Cells were spheroplasted in sorbitol buffer (1M sorbitol, 1% beta-mercaptoethanol, 0.2 mg/ml zymolyase 100T, 0.1M EDTA, pH 7.4), lysed in NDS (0.6% SDS, 300mM EDTA, 10mM Tris.HCl, pH 9.5). DNA was deproteinated with proteinase K (0.25mg/ml; Roche) at 50°C, twice phenol extracted, treated with RNase A, and stored in TE (1mM EDTA, 10mM Tris.HCl, pH 7.5) at 4°C. 25 μg DNA were digested to completion with EcoRI (New England Biolabs). ssDNA was enriched by batch absorption to BND cellulose (Sigma). Briefly, a 50% slurry of BND-cellulose was equilibrated in NET (1M NaCl, 10mM Tris, pH 7.6, 1mM EDTA). Digested DNA was adjusted to 1M NaCl and ssDNA was incubated with a 500 μl bed volume of BND-cellulose for 5 minutes. Resin was washed with five bed volumes of NET. ssDNA was eluted five times with 600 μl NET + 1.8% caffeine. DNA was precipitated and concentrated for microarray analysis.

tag: time in spo (hours)


title: wildtype PBS_S1371


title: Baki-1MuLV infected_S1372


title: wildtype PBS_S1369


title: Secondary ET infection-4dpi

city: Beltsville

first: Duk Kyung

last: Kim

state: MD

address: Bldg. 1043, BARC-East

institute: USDA, ARS

description: Secondary ET infected IEL, 4dpi, Biological replicate 1 of 2

hyb_protocol: Hybridizations were performed overnight at 50°C using HybIt hybridization buffer (TeleChem, Sunnyvale, CA) in ArrayIt reaction cassettes.  Following hybridization, the slides were rinsed in 0.5 X SSC, 0.01% SDS and washed once for 15 min at room temperature in 0.2 X SSC, 0.2% SDS at 50°C, 3 times for 1 min at room temperature in 0.2 X SSC, and 3 times for 1 min at room temperature in distilled water.

scan_protocol: Images were scanned on a ScanArray Lite microarray analysis system (Perkin-Elmer, Boston, MA) at a resolution of 10 µm.  The scanned images for each channel were quantified using ScanArray Express version 3.0 software (Perkin-Elmer).

data_processing: The MIDAS 2.19 of the TM4 package (http://www.tigr.org) was used to qualify and normalize the array data.  Two-step normalization, total intensity, and global LOWESS plot methods were applied followed by standard deviation (SD) regularization between blocks and slides.

organism: Gallus gallus

source_name: IEL from non-infected control

label_protocol: Aminoallyl-labeled RNA from IELs was prepared using the Amino Allyl Message Amp II aRNA Amplification Kit (Ambion, Austin, TX).  Two of 20 μg aliquots of each aminoallyl-RNA sample were fluorescently labeled with AlexaFluor 555 or AlexaFluor 647 (Invitrogen).  RNA concentrations and labeling efficiencies were determined spectrophotometrically.

growth_protocol: One week-old chickens were uninfected (negative control) or were orally inoculated with sporulated oocysts of EA, EM, or ET.  One week later, the infected chickens were challenged with an identical inoculum of the homologous parasite.  Intestinal samples were collected daily from 5 birds in a treatment group at from 1 to 6 dpi following primary and secondary infections.  Cecum, duodenum, and jejunum were collected from the birds challenged with EA, EM, and ET, respectively.

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

treatment_protocol: Intestines were cut longitudinally and washed three times with ice-cold Hanks’ balanced salt solution (HBSS) containing 100 U/ml of penicillin and 100 mg/ml of streptomycin (Sigma, St. Louis, MO).  The mucosal layer of intestine was carefully scraped using a cell scraper and IELs were isolated by Percoll density gradient centrifugation.

value: Duodena, Jejuna, Ceca

value: Intestinal Intraepithelial lymphocytes (IEL)

source_name: IEL from secondary ET infection at 4dpi

value: Ceca

tag: parasite

value: ET

value: secondary

tag: time

value: 4 dpi


title: C57BL/6, young_S1169

description: C57BL/6, young

tag: tissue


title: Secondary ET infection-6dpi

description: Secondary ET infected IEL, 6dpi, Biological replicate 1 of 2

source_name: IEL from secondary ET infection at 6dpi

value: 6 dpi


title: Secondary ET infection-5dpi-dye swap

description: Secondary ET infected IEL, 5dpi, Biological replicate 2 of 2 (Dye-exchange of Replicate 1)

source_name: IEL from secondary ET infection at 5dpi

value: 5 dpi


title: Secondary ET infection-3dpi-dye swap

description: Secondary ET infected IEL, 3dpi, Biological replicate 2 of 2 (Dye-exchange of Replicate 1)

source_name: IEL from secondary ET infection at 3dpi

value: 3 dpi


title: Secondary ET infection-4dpi-dye swap

description: Secondary ET infected IEL, 4dpi, Biological replicate 2 of 2 (Dye-exchange of Replicate 1)


title: Secondary ET infection-6dpi-dye swap

description: Secondary ET infected IEL, 6dpi, Biological replicate 2 of 2 (Dye-exchange of Replicate 1)


title: Secondary ET infection-5dpi

description: Secondary ET infected IEL, 5dpi, Biological replicate 1 of 2


title: ssDNA in pch2 dmc1 cells replicate 1

description: biological replicate 1 of 2 of ssDNA in pch2 dmc1 cells

tag: strain

value: pch2 dmc1


title: ssDNA in pch2 dmc1 cells replicate 2


title: C57BL/6, old_S1170

description: C57BL/6, old

value: spleen

value: wildtype


title: ssDNA in sir2 dmc1 cells replicate 2

description: biological replicate 2 of 2 of ssDNA in sir2 dmc1 cells

value: sir2 dmc1


title: Secondary ET infection-2dpi

description: Secondary ET infected IEL, 2dpi, Biological replicate 1 of 2

source_name: IEL from secondary ET infection at 2dpi

value: 2 dpi


title: ssDNA in dmc1 rDNA delete cells replicate 2

description: biological replicate 1 of 2 of ssDNA in dmc1 rDNA delete cells

value: dmc1 rDNA delete


title: ssDNA in dmc1 cells with a Chr2:12 reciprocal translocation replicate 1

description: biological replicate 1 of 2 of ssDNA in dmc1 cells with a Chr2:12 reciprocal translocation


title: ssDNA in sir2 dmc1 cells replicate 1

description: biological replicate 1 of 2 of ssDNA in sir2 dmc1 cells


title: ssDNA in orc1-161 dmc1 cells replicate 2

description: biological replicate 1 of 2 of ssDNA in orc1-161 dmc1 cells

value: orc1-161 dmc1


title: ssDNA in orc1-161 dmc1 cells replicate 1


title: TLR379-/-, old_S1168

description: TLR379-/-, old

value: TLR379-/- knockout


title: ssDNA in dmc1 rDNA delete cells replicate 1


title: Secondary ET infection-3dpi

description: Secondary ET infected IEL, 3dpi, Biological replicate 1 of 2

value: Duodena, Jejuna, Ceca


title: TLR379-/-, young_S1167

description: TLR379-/-, young


title: Secondary ET infection-1dpi

description: Secondary ET infected IEL, 1dpi, Biological replicate 1 of 2

value: Intestinal Intraepithelial lymphocytes (IEL)

source_name: IEL from secondary ET infection at 1dpi

value: 1 dpi


title: Secondary ET infection-2dpi-dye swap

description: Secondary ET infected IEL, 2dpi, Biological replicate 2 of 2 (Dye-exchange of Replicate 1)

value: Ceca

value: ET


title: Secondary ET infection-1dpi-dye swap

description: Secondary ET infected IEL, 1dpi, Biological replicate 2 of 2 (Dye-exchange of Replicate 1)

value: secondary


title: Primary ET infection-6dpi

description: Primary ET infected IEL, 6dpi, Biological replicate 1 of 2

source_name: IEL from primary ET infection at 6dpi

value: primary

value: 6 dpi


title: Primary ET infection-5dpi

description: Primary ET infected IEL, 5dpi, Biological replicate 1 of 2

source_name: IEL from primary ET infection at 5dpi

value: 5 dpi


title: Primary ET infection-5dpi-dye swap

description: Primary ET infected IEL, 5dpi, Biological replicate 2 of 2 (Dye-exchange of Replicate 1)


title: Primary ET infection-2dpi

description: Primary ET infected IEL, 2dpi, Biological replicate 1 of 2

source_name: IEL from primary ET infection at 2dpi


title: Primary ET infection-4dpi-dye swap

description: Primary ET infected IEL, 4dpi, Biological replicate 2 of 2 (Dye-exchange of Replicate 1)

source_name: IEL from primary ET infection at 4dpi

value: 4 dpi


title: Primary ET infection-3dpi

description: Primary ET infected IEL, 3dpi, Biological replicate 1 of 2

source_name: IEL from primary ET infection at 3dpi

value: 3 dpi


title: Primary ET infection-4dpi

description: Primary ET infected IEL, 4dpi, Biological replicate 1 of 2


title: E16.5 Testes (SF-1 2KR homozygous vs WT)

city: San Francisco

first: Holly

last: Ingraham

state: CA

address: 1550 4th street, Rock Hall Rm 281

institute: UCSF

hyb_protocol: Cy3 or Cy5 labeled cDNA probes are hybridized on arrays in 3X SSC, 0.25 mg/ml PolyA RNA, 0.25 mg/ml Yeast tRNA, 25 mM Hepes pH 7.4, and 0.25% SDS at 65 degrees Celcius overnight using the Maui Mixer AO hybridization chamber mixers and the Maui Hybridization chamber (Biomicro Systems)

scan_protocol: Arrays are scanned using the GenePix4000B Scanner at channels 635 and 532

data_processing: Raw data (.gpr) files were uploaded to NOMAD 2.0 and normalized using "75 Percent Correlation NF" normalization factor.  VALUE column is the log2 ratio of test (635) SIG minus BKD over control (532) SIG minus BKD.

source_name: SF-1 wild type whole testis RNA

label_protocol: Follows the Amersham CyDye (Cy3/Cy5) Reactive Dye Protocols for Post Labelling Aminoallyl-cDNA and Aminoallyl-aRNA (GE Healthcare)

extract_protocol: Purelink RNA Mini Kit (Life Technologies)

value: Mixed 129 X C57BL/6 X FVB

tag: genotype

value: Wild Type

tag: gender

value: Male

value: Embryonic Day 16.5

value: Testis

source_name: SF-1 2KR homozygous whole testis RNA

value: SF-1 2KR Homozygous


title: Primary ET infection-3dpi-dye swap

description: Primary ET infected IEL, 3dpi, Biological replicate 2 of 2 (Dye-exchange of Replicate 1)

value: Duodena, Jejuna, Ceca


title: Primary ET infection-6dpi-dye swap

description: Primary ET infected IEL, 6dpi, Biological replicate 2 of 2 (Dye-exchange of Replicate 1)

value: Intestinal Intraepithelial lymphocytes (IEL)


title: LAP-tTA-4_7weeks

value: liver

value: FVB

value: LAP-tTA

tag: disease state

value: normal


title: Primary ET infection-2dpi-dye swap

description: Primary ET infected IEL, 2dpi, Biological replicate 2 of 2 (Dye-exchange of Replicate 1)

value: Ceca

value: ET

value: primary

value: 2 dpi


title: Primary ET infection-1dpi

description: Primary ET infected IEL, 1dpi, Biological replicate 1 of 2

source_name: IEL from primary ET infection at 1dpi

value: 1 dpi


title: Secondary EM infection-6dpi

description: Secondary EM infected IEL, 6dpi, Biological replicate 1 of 2

source_name: IEL from secondary EM infection at 6dpi

value: Jejuna

value: EM

value: secondary

value: 6 dpi


title: Secondary EM infection-4dpi

description: Secondary EM infected IEL, 4dpi, Biological replicate 1 of 2

source_name: IEL from secondary EM infection at 4dpi

value: 4 dpi


title: 4 week Adrenals (SF-1 2KR homozygous vs WT)

source_name: SF-1 wild type whole adrenal RNA

value: Mixed 129 X C57BL/6 X FVB

value: Wild Type

value: Male

value: 28 days

value: Adrenal

source_name: SF-1 2KR homozygous whole adrenal RNA

value: SF-1 2KR homozygous


title: 5 week Testes (SF-1 2KR Homozygous vs WT)

value: 35 days

value: Testis


title: Secondary EM infection-4dpi-dye swap

description: Secondary EM infected IEL, 4dpi, Biological replicate 2 of 2 (Dye-exchange of Replicate 1)

source_name: IEL from non-infected control

value: Duodena, Jejuna, Ceca

value: Intestinal Intraepithelial lymphocytes (IEL)


title: Secondary EM infection-5dpi-dye swap

description: Secondary EM infected IEL, 5dpi, Biological replicate 2 of 2 (Dye-exchange of Replicate 1)

source_name: IEL from secondary EM infection at 5dpi

value: 5 dpi


title: 10_II

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

institute: Institut fuer Zellbiologie

description: Gene expression data from PCPEC infected with S. suis strain 10

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

scan_protocol: The scanning of the microarray was done with the GeneChip Scanner 3000 (Affymetrix, St. Clara, CA) at 1.56 micron resolution.

data_processing: The data were analyzed with GCOS 1.4 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1000.

organism: Sus scrofa

source_name: PCPEC, infected with S. suis strain 10

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual v2, 2004, Affymetrix).

growth_protocol: PCPEC were grown in DMEM/HAM’s F12 1:1 supplemented with 4 mM L-glutamine, 10% heat inactivated fetal calf serum (FCS), 5 µg/ml insulin and penicillin (100 U/ml)/streptomycin (100 µg/ml). In order to suppress the growth of contaminating fibroblast-like cells, 20 µM of cytosine-arabinoside were added. Upon confluence, PCPEC were cultivated in serum-free medium and used for the experiments 2-5 days later.

extract_protocol: Following incubation cells were washed 3 times with PBS and harvested by trypsination. Afterwards cells were washed with PBS and RNA isolation was performed with Trizol (Invitrogen, Karlsruhe, Germany). RNA was further purified using the Qiagen RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturers instructions.

treatment_protocol: PCPEC were exposed to viable bacteria with a MOI of 10 in culture medium for 2 hrs. After the 2 hrs incubation bacteria were inactivated by addition of penicillin/streptomycin to a final concentration of 125 U/ml penicillin and 125 µg/ml streptomycin. Subsequently, cells were incubated for further 4 hrs.

value: Primary epithelial cells derived from porcine choriod plexus


title: Primary ET infection-1dpi-dye swap

description: Primary ET infected IEL, 1dpi, Biological replicate 2 of 2 (Dye-exchange of Replicate 1)

value: Ceca

value: ET

value: primary

value: 1 dpi


title: 10_I


title: E16.5 Adrenals (SF-1 2KR homozygous vs WT)

value: Embryonic Day 16.5

value: SF-1 2KR Homozygous


title: Secondary EM infection-3dpi

description: Secondary EM infected IEL, 3dpi, Biological replicate 1 of 2

source_name: IEL from secondary EM infection at 3dpi

value: Jejuna

value: EM

value: secondary

value: 3 dpi


title: Secondary EM infection-5dpi

description: Secondary EM infected IEL, 5dpi, Biological replicate 1 of 2


title: Secondary EM infection-6dpi-dye swap

description: Secondary EM infected IEL, 6dpi, Biological replicate 2 of 2 (Dye-exchange of Replicate 1)

value: 6 dpi


title: 10_cps_delta_EF_I

description: Gene expression data from PCPEC infected with S. suis strain 10cpsDEF

source_name: PCPEC, infected with S. suis strain 10cpsDEF


title: Secondary EM infection-3dpi-dye swap

description: Secondary EM infected IEL, 3dpi, Biological replicate 2 of 2 (Dye-exchange of Replicate 1)


title: Secondary EM infection-2dpi

description: Secondary EM infected IEL, 2dpi, Biological replicate 1 of 2

source_name: IEL from secondary EM infection at 2dpi

value: 2 dpi


title: Secondary EM infection-1dpi-dye swap

description: Secondary EM infected IEL, 1dpi, Biological replicate 2 of 2 (Dye-exchange of Replicate 1)

source_name: IEL from secondary EM infection at 1dpi


title: 10_cps_delta_EF_II


title: Secondary EM infection-2dpi-dye swap

description: Secondary EM infected IEL, 2dpi, Biological replicate 2 of 2 (Dye-exchange of Replicate 1)


title: Secondary EM infection-1dpi

description: Secondary EM infected IEL, 1dpi, Biological replicate 1 of 2


title: con_II

description: Gene expression data from un-treated PCPEC

source_name: PCPEC, un-treated


title: Primary EM infection-5dpi

description: Primary EM infected IEL, 5dpi, Biological replicate 1 of 2

source_name: IEL from primary EM infection at 5dpi


title: Primary EM infection-4dpi

description: Primary EM infected IEL, 4dpi, Biological replicate 1 of 2

source_name: IEL from primary EM infection at 4dpi

value: 4 dpi


title: Primary EM infection-6dpi-dye swap

description: Primary EM infected IEL, 6dpi, Biological replicate 2 of 2 (Dye-exchange of Replicate 1)

value: Duodena, Jejuna, Ceca

source_name: IEL from primary EM infection at 6dpi


title: con_I


title: Primary EM infection-5dpi-dye swap

description: Primary EM infected IEL, 5dpi, Biological replicate 2 of 2 (Dye-exchange of Replicate 1)

value: Intestinal Intraepithelial lymphocytes (IEL)


title: Primary EM infection-4dpi-dye swap

description: Primary EM infected IEL, 4dpi, Biological replicate 2 of 2 (Dye-exchange of Replicate 1)


title: Primary EM infection-3dpi

description: Primary EM infected IEL, 3dpi, Biological replicate 1 of 2

source_name: IEL from primary EM infection at 3dpi


title: Primary EM infection-2dpi

description: Primary EM infected IEL, 2dpi, Biological replicate 1 of 2

source_name: IEL from primary EM infection at 2dpi


title: Primary EM infection-6dpi

description: Primary EM infected IEL, 6dpi, Biological replicate 1 of 2


title: Primary EM infection-3dpi-dye swap

description: Primary EM infected IEL, 3dpi, Biological replicate 2 of 2 (Dye-exchange of Replicate 1)


title: Primary EM infection-2dpi-dye swap

description: Primary EM infected IEL, 2dpi, Biological replicate 2 of 2 (Dye-exchange of Replicate 1)


title: Secondary EA infection-6dpi-dye swap

description: Secondary EA infected IEL, 6dpi, Biological replicate 2 of 2 (Dye-exchange of Replicate 1)

source_name: IEL from secondary EA infection at 6dpi

value: Duodena

value: EA


title: Secondary EA infection-5dpi-dye swap

description: Secondary EA infected IEL, 5dpi, Biological replicate 2 of 2 (Dye-exchange of Replicate 1)

source_name: IEL from secondary EA infection at 5dpi

value: 5 dpi


title: Secondary EA infection-6dpi

description: Secondary EA infected IEL, 6dpi, Biological replicate 1 of 2


title: Secondary EA infection-5dpi

description: Secondary EA infected IEL, 5dpi, Biological replicate 1 of 2


title: Secondary EA infection-4dpi

description: Secondary EA infected IEL, 4dpi, Biological replicate 1 of 2

source_name: IEL from secondary EA infection at 4dpi


title: Primary EM infection-1dpi-dye swap

description: Primary EM infected IEL, 1dpi, Biological replicate 2 of 2 (Dye-exchange of Replicate 1)

source_name: IEL from primary EM infection at 1dpi


title: Primary EM infection-1dpi

description: Primary EM infected IEL, 1dpi, Biological replicate 1 of 2

source_name: IEL from non-infected control


title: Secondary EA infection-4dpi-dye swap

description: Secondary EA infected IEL, 4dpi, Biological replicate 2 of 2 (Dye-exchange of Replicate 1)


title: Gastrointestinal stromal sarcoma 04-326H fresh-frozen sample with WGA (Sigma platform), SNP

city: Taipei

first: Cher-wei

last: Liang

address: 7 Chung-Shan S. Rd.

department: Pathology

country: Taiwan

institute: National Taiwan University Hospital

description:
9N_04-326HFreshWGASigma
Hybridized to 250K_Nsp.

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

scan_protocol: The arrays were washed using Affymetrix fluidics stations, and scanned using the GeneChip Scanner 3000.

data_processing: CEL files and TXT files (generated by Affymetrix GTYPE using the DM algorithm) were processed by dChip and model-based expression performed using the PM/MM model. Normalization was performed using the reference normalization algorithm developed at St. Jude and described in Mullighan et al. Nature 2007;446:758.

source_name: GISS 04-326H fresh-frozen sample with WGA (Sigma platform)

label_protocol: As per the manufacturer (Affymetrix).

growth_protocol: Genomic DNAs were obtained from fresh-frozen and formalin-fixed paraffin-embedded (FFPE) tumor samples.

extract_protocol: Genomic DNA was extracted from fresh-frozen and FFPE mesenchymal tumor samples using the QIAamp DNA Mini Kit and QIAamp DNA FFPE Tissue Kit, respectively. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.

treatment_protocol: WGA was performed using the REPLI-g® FFPE kit (Qiagen, Valencia, CA, USA) and GenomePlex® Tissue Whole Genome Amplification WGA5 kit (Sigma, Saint Louis, MO, USA) in parallel in accordance with the manufacturers’ protocols.

value: gastrointestinal stromal sarcoma (GISS)

tag: tumor identifier

tag: tissue preparation

value: fresh-frozen

tag: wga platform_id

value: Sigma thermocycling protocol


title: Secondary EA infection-3dpi

description: Secondary EA infected IEL, 3dpi, Biological replicate 1 of 2

source_name: IEL from secondary EA infection at 3dpi


title: Secondary EA infection-3dpi-dye swap

description: Secondary EA infected IEL, 3dpi, Biological replicate 2 of 2 (Dye-exchange of Replicate 1)