description: Gene expression data from_sample from sample from subject 5F07, sex= Female, infection= Mock, day= 4


status: Public on Mar 18 2010

type: RNA

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

country: USA

institute: NIH

description: Gene expression data from_sample from sample from subject 5F08, sex= Female, infection= Mock, day= 2

hyb_protocol: hybridized at a constant temperature of 45◦C for approximately 16 hours

scan_protocol: GeneChips were scanned using the standard Affymetrix GeneChip Scanner

data_processing: The data were analyzed with EC using MAS5

label: biotin

molecule: total RNA

organism: Macaca fascicularis

label_protocol: All tonsil swab RNA (average 4.2 μg per swab) was used for cDNA synthesis as described (2). In vitro transcription labeling with biotinylated UTP and CTP was performed according to the manufacturer’s recommendations (Enzo Diagnostics) for 10 h at 37 °C. Amplified cRNA was purified as described above. The quality and size of cRNA was verified with an Agilent 2100 Bioanalyzer System (Agilent Technologies)

growth_protocol: GAS strain MGAS5005 (GenBank CP000017), genetically representative of contemporary serotype M1 strains, was grown as previously described (11, 12)

extract_protocol: Tonsil swabs were immediately frozen on dry ice.The swabs contained a mixture of epithelial and inflammatory cells, but microscopic examination indicated that the majority of cells were epithelial cells. Host cells were lysed using the FastPrep FP 120 system and Lysing Matrix D Tube (MP Biomedicals) with 500 μL phenol:chloroform (5:1) at pH 4.5 (Applied Biosystems), 500 μL CRSR-”GREEN” (MP Biomedicals), and 300 μL of 5 mM arunocarboxylic acid. RNA was purified in 96-well format as described (1). RNA quantity was determined with an Agilent 2100 Bioanalyzer System (Agilent Technologies)

treatment_protocol: Infection of cynomolgus macaques and sample preparation has been described extensively (11, 12). Briefly, animals were GAS-culture negative and had negligible antistreptolysin O titers, indicating no recent history of GAS exposure. Twenty animals were subjected to a mock-inoculation protocol (PBS only) for 5 weeks, rested for 4weeks, and inoculated in the upper respiratory tractwith 107 CFUsMGAS5005. Blood, saliva, and throat swabs were collected on days 0, 1, 2, 4, 7, 9, 16, 23, 32, 45, 58, 72, and 86.Only the first nine time-points were studied because specimens collected during days 0 to 32 had matching comparator specimens from the mock-infection protocol. Thirty-two clinical and laboratory parameters were measured by the same veterinarian during mock and infection periods

tag: monkey

value: cynomolgus

tag: subject id

tag: gender

value: Female

tag: infection type

value: Mock

tag: time point (day)


description: Gene expression data from_sample from sample from subject 5F03, sex= Female, infection= Mock, day= 23


description: Gene expression data from_sample from sample from subject 5E08, sex= Female, infection= GAS, day= 2

value: GAS


description: Gene expression data from_sample from sample from subject 5C08, sex= Male, infection= Mock, day= 16

value: Male


description: Gene expression data from_sample from sample from subject 5E04, sex= Female, infection= GAS, day= 16


description: Gene expression data from_sample from sample from subject 5E09, sex= Female, infection= GAS, day= 1


description: Gene expression data from_sample from sample from subject 5E06, sex= Female, infection= GAS, day= 7


description: Gene expression data from_sample from sample from subject 5E03, sex= Female, infection= GAS, day= 23


description: Gene expression data from_sample from sample from subject 5C03, sex= Male, infection= Mock, day= 1


description: Gene expression data from_sample from sample from subject 5E05, sex= Female, infection= GAS, day= 9


description: Gene expression data from_sample from sample from subject 5E10, sex= Female, infection= GAS, day= 0


description: Gene expression data from_sample from sample from subject 5B08, sex= Male, infection= GAS, day= 16


description: Gene expression data from_sample from sample from subject 5C09, sex= Male, infection= Mock, day= 23


description: Gene expression data from_sample from sample from subject 5F05, sex= Female, infection= Mock, day= 9


description: Gene expression data from_sample from sample from subject 5F02, sex= Female, infection= Mock, day= 32


description: Gene expression data from_sample from sample from subject 5C04, sex= Male, infection= Mock, day= 2


description: Gene expression data from_sample from sample from subject 5E02, sex= Female, infection= GAS, day= 32


description: Gene expression data from_sample from sample from subject 5C07, sex= Male, infection= Mock, day= 9


description: Gene expression data from_sample from sample from subject 5B10, sex= Male, infection= GAS, day= 32


description: Gene expression data from_sample from sample from subject 5C02, sex= Male, infection= Mock, day= 0


description: Gene expression data from_sample from sample from subject 5C06, sex= Male, infection= Mock, day= 7


description: Gene expression data from_sample from sample from subject 5C10, sex= Male, infection= Mock, day= 32


description: Gene expression data from_sample from sample from subject 5C05, sex= Male, infection= Mock, day= 4


description: Gene expression data from_sample from sample from subject 5B09, sex= Male, infection= GAS, day= 23


description: Gene expression data from_sample from sample from subject 5E07, sex= Female, infection= GAS, day= 4


description: Gene expression data from_sample from sample from subject 5B07, sex= Male, infection= GAS, day= 9


description: Gene expression data from_sample from sample from subject 5B06, sex= Male, infection= GAS, day= 7


description: Gene expression data from_sample from sample from subject 5B04, sex= Male, infection= GAS, day= 2


description: Gene expression data from_sample from sample from subject 5B05, sex= Male, infection= GAS, day= 4


description: Gene expression data from_sample from sample from subject 5B02, sex= Male, infection= GAS, day= 0


description: Gene expression data from_sample from sample from subject 14F06, sex= Male, infection= Mock, day= 7


description: Gene expression data from_sample from sample from subject 14F10, sex= Male, infection= Mock, day= 0


description: Gene expression data from_sample from sample from subject 14F08, sex= Male, infection= Mock, day= 2


description: Gene expression data from_sample from sample from subject 14F03, sex= Male, infection= Mock, day= 23


description: Gene expression data from_sample from sample from subject 14F05, sex= Male, infection= Mock, day= 9


description: Gene expression data from_sample from sample from subject 5B03, sex= Male, infection= GAS, day= 1


description: Gene expression data from_sample from sample from subject 14F07, sex= Male, infection= Mock, day= 4


description: Gene expression data from_sample from sample from subject 14F02, sex= Male, infection= Mock, day= 32


description: Gene expression data from_sample from sample from subject 14F04, sex= Male, infection= Mock, day= 16


description: Gene expression data from_sample from sample from subject 5F04, sex= Female, infection= Mock, day= 16


description: Gene expression data from_sample from sample from subject 14F09, sex= Male, infection= Mock, day= 1


description: Gene expression data from_sample from sample from subject 14E10, sex= Male, infection= GAS, day= 0


description: Gene expression data from_sample from sample from subject 14E07, sex= Male, infection= GAS, day= 4


description: Gene expression data from_sample from sample from subject 14E06, sex= Male, infection= GAS, day= 7


description: Gene expression data from_sample from sample from subject 14E03, sex= Male, infection= GAS, day= 23


description: Gene expression data from_sample from sample from subject 14E05, sex= Male, infection= GAS, day= 9


description: Gene expression data from_sample from sample from subject 14C10, sex= Female, infection= Mock, day= 32


description: Gene expression data from_sample from sample from subject 14E02, sex= Male, infection= GAS, day= 32


description: Gene expression data from_sample from sample from subject 14C09, sex= Female, infection= Mock, day= 23


description: Gene expression data from_sample from sample from subject 14C07, sex= Female, infection= Mock, day= 9


description: Gene expression data from_sample from sample from subject 14E04, sex= Male, infection= GAS, day= 16


description: Gene expression data from_sample from sample from subject 14E08, sex= Male, infection= GAS, day= 2


description: Gene expression data from_sample from sample from subject 14C06, sex= Female, infection= Mock, day= 7


title: Matched_Blood_19nsp

type: genomic

city: Providence

first: Graham

middle: M

last: Poage

state: RI

address: 70 Ship St

institute: Brown University

description: Hybridized to 250K_Nsp.

hyb_protocol: As per manufacturer (Affymetrix).

scan_protocol: As per manufacturer (Affymetrix).

data_processing:
Data were collected at the Harvard Partners Microarray Core Facility. Inferred copy number states of each SNP were extracted and converted from .CEL files into signal intensities using GCOS and Affymetrix Copy Number Analysis Tool (CNAT) v4.0.1. We utilized the HMM-based algorithm with defaults for tuning parameters, Gaussian smoothing, transition decay, and median scaling.

The 'GSE20939_tumor_copy_number.txt' file, which is linked to the Series GSE20939 record as a supplementary file, contains the (blood-adjusted) tumor copy number calls used in our final analyses.

molecule: genomic DNA

organism: Homo sapiens

source_name: peripheral whole blood matched_blood_19

label_protocol: As per manufacturer (Affymetrix).

extract_protocol: Qiagen Qiamp DNA extraction kit.

treatment_protocol: None.

tag: tissue

value: peripheral whole blood


title: Matched_Blood_16nsp

description: Hybridized to 250K_Nsp.

source_name: peripheral whole blood matched_blood_16


description: Gene expression data from_sample from sample from subject 14C05, sex= Female, infection= Mock, day= 4


description: Gene expression data from_sample from sample from subject 14C04, sex= Female, infection= Mock, day= 2


description: Gene expression data from_sample from sample from subject 14B10, sex= Female, infection= GAS, day= 32


title: Matched_Blood_18nsp

description: Hybridized to 250K_Nsp.

source_name: peripheral whole blood matched_blood_18


title: Matched_Blood_17nsp

description: Hybridized to 250K_Nsp.

source_name: peripheral whole blood matched_blood_17


title: Matched_Blood_9nsp

description: Hybridized to 250K_Nsp.

source_name: peripheral whole blood matched_blood_9


title: Matched_Blood_15nsp

description: Hybridized to 250K_Nsp.

source_name: peripheral whole blood matched_blood_15


title: Matched_Blood_5nsp

description: Hybridized to 250K_Nsp.

source_name: peripheral whole blood matched_blood_5


title: Matched_Blood_11nsp

description: Hybridized to 250K_Nsp.

source_name: peripheral whole blood matched_blood_11


description: Gene expression data from_sample from sample from subject 14C02, sex= Female, infection= Mock, day= 0


title: Matched_Blood_3nsp

description: Hybridized to 250K_Nsp.

source_name: peripheral whole blood matched_blood_3


description: Gene expression data from_sample from sample from subject 14B07, sex= Female, infection= GAS, day= 9


description: Gene expression data from_sample from sample from subject 13F10, sex= Male, infection= Mock, day= 0


title: Matched_Blood_2nsp

description: Hybridized to 250K_Nsp.

source_name: peripheral whole blood matched_blood_2


description: Gene expression data from_sample from sample from subject 14C03, sex= Female, infection= Mock, day= 1


title: Matched_Blood_13nsp

description: Hybridized to 250K_Nsp.

source_name: peripheral whole blood matched_blood_13


description: Gene expression data from_sample from sample from subject 14C08, sex= Female, infection= Mock, day= 16


description: Gene expression data from_sample from sample from subject 14E09, sex= Male, infection= GAS, day= 1


title: Matched_Blood_12nsp

description: Hybridized to 250K_Nsp.

source_name: peripheral whole blood matched_blood_12


description: Gene expression data from_sample from sample from subject 14B08, sex= Female, infection= GAS, day= 16


title: Matched_Blood_7nsp

description: Hybridized to 250K_Nsp.

source_name: peripheral whole blood matched_blood_7


title: Matched_Blood_14nsp

description: Hybridized to 250K_Nsp.

source_name: peripheral whole blood matched_blood_14


title: Matched_Blood_8nsp

description: Hybridized to 250K_Nsp.

source_name: peripheral whole blood matched_blood_8


title: Matched_Blood_10nsp

description: Hybridized to 250K_Nsp.

source_name: peripheral whole blood matched_blood_10


description: Gene expression data from_sample from sample from subject 14B09, sex= Female, infection= GAS, day= 23


title: Matched_Blood_6nsp

description: Hybridized to 250K_Nsp.

source_name: peripheral whole blood matched_blood_6


title: Matched_Blood_4nsp

description: Hybridized to 250K_Nsp.

source_name: peripheral whole blood matched_blood_4


description: Gene expression data from_sample from sample from subject 14B06, sex= Female, infection= GAS, day= 7


description: Gene expression data from_sample from sample from subject 14B02, sex= Female, infection= GAS, day= 0


title: Matched_Blood_1nsp

description: Hybridized to 250K_Nsp.

source_name: peripheral whole blood matched_blood_1


description: Gene expression data from_sample from sample from subject 14B03, sex= Female, infection= GAS, day= 1


description: Gene expression data from_sample from sample from subject 14B04, sex= Female, infection= GAS, day= 2


description: Gene expression data from_sample from sample from subject 13F09, sex= Male, infection= Mock, day= 1


title: Placenta_Spike_Pool6_Illumina

city: Austin

first: Sachin

last: Sah

state: TX

address: 2150 Woodward St, Suite 100

institute: Asuragen Inc.

hyb_protocol: Samples were hybridized to the Universal-16 Bead Chips provided by Illumina

scan_protocol: Standard Illumina scanning protocol

data_processing: The data is non-normalized raw and background corrected

source_name: Human Placenta

label_protocol: miRNAs present in the samples were labeled using manufacturer's instructions as mentioned in microRNA Expression Profiling Assay Guide 11251981-A.

extract_protocol: Total RNA was extracted from placental tissue using the miRVana Isolation Kit (Ambion). Protocol was used in such a way that small RNAs were retained.

value: Placenta


title: Placenta_Spike_Pool3_Illumina


title: Placenta_Spike_Pool7_Illumina


title: Placenta_Spike_Pool5_Illumina


description: Gene expression data from_sample from sample from subject 13F08, sex= Male, infection= Mock, day= 2


description: Gene expression data from_sample from sample from subject 14B05, sex= Female, infection= GAS, day= 4


description: Gene expression data from_sample from sample from subject 13F07, sex= Male, infection= Mock, day= 4


description: Gene expression data from_sample from sample from subject 13F02, sex= Male, infection= Mock, day= 32


description: Gene expression data from_sample from sample from subject 13F05, sex= Male, infection= Mock, day= 9


title: Placenta_Spike_Pool2_Illumina


description: Gene expression data from_sample from sample from subject 13F06, sex= Male, infection= Mock, day= 7


title: X93

city: Minneapolis

first: Aaron

last: Sarver

state: MN

address: 425 East River Road

department: Masonic Cancer Center

institute: University of Minnesota

description: colon tumor deficient MMR

hyb_protocol: The single-stranded PCR product was hybridized to the Sentrix Array Matrix, where the labeled strand bound to the bead on the array containing the complementary address sequence.

scan_protocol: The arrays were imaged using an Illumina BeadArrayTM Reader, which measures the fluorescence intensity at each addressed bead location.

data_processing:
Non-background-subtracted data obtained from BeadStudio version 3.1.1 with no background correction or normalization was log2 transformed, quantile normalized.

The non-normalized data are available in the 'GSE18392_non-normalized_data.txt' file, which is linked to the Series GSE18392 record as a supplementary file.

source_name: Colon, dMMR

label_protocol: Total RNA (200 - 400 ng) was poly-adenylated and then converted to cDNA using a biotinylated oligo-dT primer with a universal PCR sequenced at its 5’-end.  This was followed by annealing of a miRNA-specific oligonucleotide pool (MSO), which consisted of three parts: a universal PCR priming site at the 5’ end; an address sequence complementary to a capture sequence on the BeadArrayTM; and a microRNA-specific sequence at the 3’-end.  Extension of MSO was facilitated by addition of a polymerase but only if their 3’ bases were complementary to the cognate sequence in the cDNA template.  Common primers were used to amplify the cDNA templates; the primer complimentary to the BeadArrayTM was fluorescently labeled.

extract_protocol: Tissue equivalent to 7mm2 and 10-microns thick was sectioned and placed in a vial containing 400 uL of RLT buffer (QIAGEN, Chatsworth, CA) including 4 μL of beta-mercaptoethanol.  The vial was then stored at -80°C until utilized for RNA extraction using TRIzol® LSTrizol© (Invitrogen, Corp., Carlsbad, CA), according to the manufacturer’s instructions.

value: colon tumor

value: colon tumor deficient MMR


description: Gene expression data from_sample from sample from subject 13E09, sex= Male, infection= GAS, day= 1


description: Gene expression data from_sample from sample from subject 13E10, sex= Male, infection= GAS, day= 0


description: Gene expression data from_sample from sample from subject 13F04, sex= Male, infection= Mock, day= 16


description: Gene expression data from_sample from sample from subject 13F03, sex= Male, infection= Mock, day= 23


description: Gene expression data from_sample from sample from subject 13E08, sex= Male, infection= GAS, day= 2


description: Gene expression data from_sample from sample from subject 13E07, sex= Male, infection= GAS, day= 4


description: Gene expression data from_sample from sample from subject 13E06, sex= Male, infection= GAS, day= 7


description: Gene expression data from_sample from sample from subject 13E05, sex= Male, infection= GAS, day= 9


title: X924

description: colon tumor proficient MMR TNM 4

source_name: Colon, pMMR

value: colon tumor proficient MMR TNM 4


title: Placenta_Spike_Pool4_Illumina


title: X727

description: colon tumor proficient MMR TNM 4


title: X766

description: colon tumor proficient MMR TNM 4


title: X774

description: colon tumor proficient MMR TNM 3

value: colon tumor proficient MMR TNM 3


title: X766A

description: normal colon

source_name: Colon, normal

value: colon

value: normal colon


title: X98

description: colon tumor proficient MMR TNM 2

value: colon tumor proficient MMR TNM 2


description: Gene expression data from_sample from sample from subject 13E04, sex= Male, infection= GAS, day= 16


title: X79A

description: normal colon


description: Gene expression data from_sample from sample from subject 13E02, sex= Male, infection= GAS, day= 32


description: Gene expression data from_sample from sample from subject 13E03, sex= Male, infection= GAS, day= 23


description: Gene expression data from_sample from sample from subject 13C10, sex= Female, infection= Mock, day= 32


title: X663

description: colon tumor proficient MMR TNM 3


title: X660A

description: normal colon


title: X57A

description: normal colon


title: X660

description: colon tumor proficient MMR TNM 2


title: X708

description: colon tumor proficient MMR TNM 2


description: Gene expression data from_sample from sample from subject 13C06, sex= Female, infection= Mock, day= 7


description: Gene expression data from_sample from sample from subject 13C09, sex= Female, infection= Mock, day= 23


description: Gene expression data from_sample from sample from subject 13C08, sex= Female, infection= Mock, day= 16


title: X567

description: colon tumor proficient MMR TNM 2


title: X567A

description: normal colon


description: Gene expression data from_sample from sample from subject 13C07, sex= Female, infection= Mock, day= 9


description: Gene expression data from_sample from sample from subject 13C05, sex= Female, infection= Mock, day= 4


title: X61A

description: normal colon


description: Gene expression data from_sample from sample from subject 13C02, sex= Female, infection= Mock, day= 0


title: X550A

description: normal colon


title: X550

description: colon tumor proficient MMR TNM 4


title: X534A

description: normal colon


description: Gene expression data from_sample from sample from subject 13B10, sex= Female, infection= GAS, day= 32


title: X473A

description: normal colon


description: Gene expression data from_sample from sample from subject 13C03, sex= Female, infection= Mock, day= 1


title: X521

description: colon tumor proficient MMR TNM 3


description: Gene expression data from_sample from sample from subject 13B08, sex= Female, infection= GAS, day= 16


title: X460

description: colon tumor proficient MMR TNM 3


description: Gene expression data from_sample from sample from subject 13B04, sex= Female, infection= GAS, day= 2


description: Gene expression data from_sample from sample from subject 13B05, sex= Female, infection= GAS, day= 4


description: Gene expression data from_sample from sample from subject 13B06, sex= Female, infection= GAS, day= 7


description: Gene expression data from_sample from sample from subject 13B07, sex= Female, infection= GAS, day= 9


title: X42A

description: normal colon


title: X44

description: colon tumor proficient MMR TNM 3


description: Gene expression data from_sample from sample from subject 13B09, sex= Female, infection= GAS, day= 23


description: Gene expression data from_sample from sample from subject 13B03, sex= Female, infection= GAS, day= 1


description: Gene expression data from_sample from sample from subject 12F09, sex= Female, infection= Mock, day= 1


description: Gene expression data from_sample from sample from subject 12F07, sex= Female, infection= Mock, day= 4


title: X434

description: colon tumor proficient MMR TNM 3


title: X413

description: colon tumor proficient MMR TNM 3


title: Placenta_Spike_Pool1_Illumina


title: X405

description: colon tumor proficient MMR TNM 4


description: Gene expression data from_sample from sample from subject 12F10, sex= Female, infection= Mock, day= 0


title: X411

description: colon tumor proficient MMR TNM 4


title: X398A

description: normal colon


title: X418

description: colon tumor proficient MMR TNM 3


description: Gene expression data from_sample from sample from subject 12F08, sex= Female, infection= Mock, day= 2


title: X44A

description: normal colon


description: Gene expression data from_sample from sample from subject 12F04, sex= Female, infection= Mock, day= 16


title: X396A

description: normal colon


title: X390A

description: normal colon


title: X390

description: colon tumor deficient MMR


description: Gene expression data from_sample from sample from subject 12F06, sex= Female, infection= Mock, day= 7


description: Gene expression data from_sample from sample from subject 12F05, sex= Female, infection= Mock, day= 9


title: X398

description: colon tumor proficient MMR TNM 4


title: X354

description: colon tumor proficient MMR TNM 4


description: Gene expression data from_sample from sample from subject 12F03, sex= Female, infection= Mock, day= 23


title: X354A

description: normal colon


description: Gene expression data from_sample from sample from subject 13C04, sex= Female, infection= Mock, day= 2


title: X385A

description: normal colon


description: Gene expression data from_sample from sample from subject 12E09, sex= Female, infection= GAS, day= 1


description: Gene expression data from_sample from sample from subject 13B02, sex= Female, infection= GAS, day= 0


title: X40

description: colon tumor proficient MMR TNM 2


description: Gene expression data from_sample from sample from subject 12F02, sex= Female, infection= Mock, day= 32


title: X348

description: colon tumor proficient MMR TNM 4


title: X322

description: colon tumor proficient MMR TNM 4


description: Gene expression data from_sample from sample from subject 12E10, sex= Female, infection= GAS, day= 0


description: Gene expression data from_sample from sample from subject 12E06, sex= Female, infection= GAS, day= 7


description: Gene expression data from_sample from sample from subject 12E07, sex= Female, infection= GAS, day= 4


title: X301

description: colon tumor deficient MMR


description: Gene expression data from_sample from sample from subject 12E03, sex= Female, infection= GAS, day= 23


description: Gene expression data from_sample from sample from subject 12E04, sex= Female, infection= GAS, day= 16


description: Gene expression data from_sample from sample from subject 12C09, sex= Male, infection= Mock, day= 23


description: Gene expression data from_sample from sample from subject 12E05, sex= Female, infection= GAS, day= 9


description: Gene expression data from_sample from sample from subject 12C08, sex= Male, infection= Mock, day= 16


title: X299A

description: normal colon


title: X298A

description: normal colon


description: Gene expression data from_sample from sample from subject 12E02, sex= Female, infection= GAS, day= 32


description: Gene expression data from_sample from sample from subject 12E08, sex= Female, infection= GAS, day= 2


title: X299

description: colon tumor deficient MMR


title: X334A

description: normal colon


title: X27A

description: normal colon


title: X24A

description: normal colon


title: X27

description: colon tumor proficient MMR TNM 4


description: Gene expression data from_sample from sample from subject 12C10, sex= Male, infection= Mock, day= 32


description: Gene expression data from_sample from sample from subject 12C05, sex= Male, infection= Mock, day= 4


description: Gene expression data from_sample from sample from subject 12C06, sex= Male, infection= Mock, day= 7


description: Gene expression data from_sample from sample from subject 12C07, sex= Male, infection= Mock, day= 9


title: X243A

description: normal colon


title: X237

description: colon tumor proficient MMR TNM 3


title: X201

description: colon tumor proficient MMR TNM 4


title: X199A

description: normal colon


title: X185A

description: normal colon


description: Gene expression data from_sample from sample from subject 12C03, sex= Male, infection= Mock, day= 1


title: X178

description: colon tumor proficient MMR TNM 3


description: Gene expression data from_sample from sample from subject 12C02, sex= Male, infection= Mock, day= 0


description: Gene expression data from_sample from sample from subject 12B08, sex= Male, infection= GAS, day= 16


description: Gene expression data from_sample from sample from subject 12B07, sex= Male, infection= GAS, day= 9


description: Gene expression data from_sample from sample from subject 12B10, sex= Male, infection= GAS, day= 32


title: X173

description: colon tumor deficient MMR


description: Gene expression data from_sample from sample from subject 12B09, sex= Male, infection= GAS, day= 23


title: X170

description: colon tumor proficient MMR TNM 2


description: Gene expression data from_sample from sample from subject 12C04, sex= Male, infection= Mock, day= 2


title: X171A

description: normal colon


title: X171

description: colon tumor proficient MMR TNM 4


description: Gene expression data from_sample from sample from subject 12B06, sex= Male, infection= GAS, day= 7


title: X167

description: colon tumor proficient MMR TNM 2


title: X163

description: colon tumor proficient MMR TNM 2


description: Gene expression data from_sample from sample from subject 12B05, sex= Male, infection= GAS, day= 4


title: X18

description: colon tumor proficient MMR TNM 2


description: Gene expression data from_sample from sample from subject 12B03, sex= Male, infection= GAS, day= 1


title: X132A

description: normal colon


description: Gene expression data from_sample from sample from subject 12B04, sex= Male, infection= GAS, day= 2


description: Gene expression data from_sample from sample from subject 11F08, sex= Male, infection= Mock, day= 2


description: Gene expression data from_sample from sample from subject 11F09, sex= Male, infection= Mock, day= 1


description: Gene expression data from_sample from sample from subject 11F07, sex= Male, infection= Mock, day= 4


description: Gene expression data from_sample from sample from subject 11F10, sex= Male, infection= Mock, day= 0


title: X132

description: colon tumor proficient MMR TNM 4


description: Gene expression data from_sample from sample from subject 11F05, sex= Male, infection= Mock, day= 9


title: X120A

description: normal colon


description: Gene expression data from_sample from sample from subject 11F06, sex= Male, infection= Mock, day= 7


title: X110

description: colon tumor proficient MMR TNM 4


title: X109

description: colon tumor proficient MMR TNM 2


title: T400.anon3

description: colon tumor proficient MMR TNM 2


title: T400.anon14

description: colon tumor proficient MMR TNM 2


title: T400.anon2

description: colon tumor proficient MMR TNM 3


title: T400.anon11

description: colon tumor proficient MMR TNM 3


description: Gene expression data from_sample from sample from subject 11F03, sex= Male, infection= Mock, day= 23


title: T400.anon1

description: colon tumor proficient MMR TNM 3


title: T400.85

description: colon tumor proficient MMR TNM 2


description: Gene expression data from_sample from sample from subject 12B02, sex= Male, infection= GAS, day= 0


description: Gene expression data from_sample from sample from subject 11F02, sex= Male, infection= Mock, day= 32


description: Gene expression data from_sample from sample from subject 11E05, sex= Male, infection= GAS, day= 9


description: Gene expression data from_sample from sample from subject 11E06, sex= Male, infection= GAS, day= 7


description: Gene expression data from_sample from sample from subject 11E09, sex= Male, infection= GAS, day= 1


description: Gene expression data from_sample from sample from subject 11F04, sex= Male, infection= Mock, day= 16


title: T400.79

description: colon tumor proficient MMR TNM 2


description: Gene expression data from_sample from sample from subject 11E07, sex= Male, infection= GAS, day= 4


title: T400.8

description: colon tumor proficient MMR TNM 3


title: T400.534

description: colon tumor proficient MMR TNM 2


description: Gene expression data from_sample from sample from subject 11E10, sex= Male, infection= GAS, day= 0


title: T400.754

description: colon tumor proficient MMR TNM 2


description: Gene expression data from_sample from sample from subject 11E04, sex= Male, infection= GAS, day= 16


title: T400.505

description: colon tumor proficient MMR TNM 2


title: T400.501

description: colon tumor proficient MMR TNM 2


title: T400.478

description: colon tumor deficient MMR


title: T400.462

description: colon tumor proficient MMR TNM 2


description: Gene expression data from_sample from sample from subject 11E03, sex= Male, infection= GAS, day= 23


title: T400.449

description: colon tumor proficient MMR TNM 3


description: Gene expression data from_sample from sample from subject 11C10, sex= Female, infection= Mock, day= 32


title: T400.42

description: colon tumor proficient MMR TNM 2


title: T400.415

description: colon tumor proficient MMR TNM 2


description: Gene expression data from_sample from sample from subject 11E02, sex= Male, infection= GAS, day= 32


description: Gene expression data from_sample from sample from subject 11E08, sex= Male, infection= GAS, day= 2


description: Gene expression data from_sample from sample from subject 11C08, sex= Female, infection= Mock, day= 16


description: Gene expression data from_sample from sample from subject 11C06, sex= Female, infection= Mock, day= 7


description: Gene expression data from_sample from sample from subject 11C09, sex= Female, infection= Mock, day= 23


description: Gene expression data from_sample from sample from subject 11C07, sex= Female, infection= Mock, day= 9


description: Gene expression data from_sample from sample from subject 11C04, sex= Female, infection= Mock, day= 2


title: T400.404

description: colon tumor proficient MMR TNM 2


title: T400.409

description: colon tumor proficient MMR TNM 3


title: T400.403A

description: normal colon


title: T400.334

description: colon tumor deficient MMR


title: T400.396

description: colon tumor proficient MMR TNM 3


title: T400.302

description: colon tumor deficient MMR


description: Gene expression data from_sample from sample from subject 11C05, sex= Female, infection= Mock, day= 4


title: T400.259

description: colon tumor proficient MMR TNM 3


title: T400.248

description: colon tumor proficient MMR TNM 2


title: T400.402

description: colon tumor deficient MMR


description: Gene expression data from_sample from sample from subject 11C02, sex= Female, infection= Mock, day= 0


description: Gene expression data from_sample from sample from subject 11C03, sex= Female, infection= Mock, day= 1


description: Gene expression data from_sample from sample from subject 11B08, sex= Female, infection= GAS, day= 16


title: T400.164

description: colon tumor deficient MMR


title: T400.227

description: colon tumor proficient MMR TNM 2


title: T400.24

description: colon tumor proficient MMR TNM 3


description: Gene expression data from_sample from sample from subject 11B07, sex= Female, infection= GAS, day= 9


title: T400.16

description: colon tumor proficient MMR TNM 3


description: Gene expression data from_sample from sample from subject 11B06, sex= Female, infection= GAS, day= 7


title: T400.101

description: colon tumor proficient MMR TNM 3


description: Gene expression data from_sample from sample from subject 11B05, sex= Female, infection= GAS, day= 4


description: Gene expression data from_sample from sample from subject 11B10, sex= Female, infection= GAS, day= 32


title: T400.166

description: colon tumor deficient MMR


description: Gene expression data from_sample from sample from subject 11B09, sex= Female, infection= GAS, day= 23


title: T400.2

description: colon tumor deficient MMR


title: T200.anon3

description: colon tumor proficient MMR TNM 2


description: Gene expression data from_sample from sample from subject 11B03, sex= Female, infection= GAS, day= 1


description: Gene expression data from_sample from sample from subject 11B02, sex= Female, infection= GAS, day= 0


title: T200.anon2

description: colon tumor proficient MMR TNM 3


title: T200.anon14

description: colon tumor proficient MMR TNM 2


description: Gene expression data from_sample from sample from subject 11B04, sex= Female, infection= GAS, day= 2


title: T200.anon11

description: colon tumor proficient MMR TNM 3


description: Gene expression data from_sample from sample from subject 10F06, sex= Female, infection= Mock, day= 7


description: Gene expression data from_sample from sample from subject 10F05, sex= Female, infection= Mock, day= 9


description: Gene expression data from_sample from sample from subject 10F10, sex= Female, infection= Mock, day= 0


description: Gene expression data from_sample from sample from subject 10F04, sex= Female, infection= Mock, day= 16


description: Gene expression data from_sample from sample from subject 10F09, sex= Female, infection= Mock, day= 1


description: Gene expression data from_sample from sample from subject 10F03, sex= Female, infection= Mock, day= 23


description: Gene expression data from_sample from sample from subject 10F07, sex= Female, infection= Mock, day= 4


description: Gene expression data from_sample from sample from subject 10F02, sex= Female, infection= Mock, day= 32


description: Gene expression data from_sample from sample from subject 10F08, sex= Female, infection= Mock, day= 2


title: T200.anon1

description: colon tumor proficient MMR TNM 3


title: T200.919.2a

description: colon tumor proficient MMR TNM 2


title: T200.79

description: colon tumor proficient MMR TNM 2


title: T200.85

description: colon tumor proficient MMR TNM 2


title: T200.8

description: colon tumor proficient MMR TNM 3


title: T200.919.1a

description: colon tumor proficient MMR TNM 2


title: T200.754

description: colon tumor proficient MMR TNM 2


title: T200.565.2a

description: colon tumor proficient MMR TNM 3


description: Gene expression data from_sample from sample from subject 10E08, sex= Female, infection= GAS, day= 2


description: Gene expression data from_sample from sample from subject 10E10, sex= Female, infection= GAS, day= 0


description: Gene expression data from_sample from sample from subject 10E07, sex= Female, infection= GAS, day= 4


title: T200.534

description: colon tumor proficient MMR TNM 2


description: Gene expression data from_sample from sample from subject 10E06, sex= Female, infection= GAS, day= 7


title: T200.565.1a

description: colon tumor proficient MMR TNM 3


title: T200.478

description: colon tumor deficient MMR


title: T200.505

description: colon tumor proficient MMR TNM 2


description: Gene expression data from_sample from sample from subject 10E05, sex= Female, infection= GAS, day= 9


title: T200.462

description: colon tumor proficient MMR TNM 2


title: T200.45.2a

description: colon tumor proficient MMR TNM 2


title: T200.45.1a

description: colon tumor proficient MMR TNM 2


description: Gene expression data from_sample from sample from subject 10E03, sex= Female, infection= GAS, day= 23


description: Gene expression data from_sample from sample from subject 10E09, sex= Female, infection= GAS, day= 1


description: Gene expression data from_sample from sample from subject 10E04, sex= Female, infection= GAS, day= 16


title: T200.449

description: colon tumor proficient MMR TNM 3


title: T200.501

description: colon tumor proficient MMR TNM 2


description: Gene expression data from_sample from sample from subject 10E02, sex= Female, infection= GAS, day= 32


description: Gene expression data from_sample from sample from subject 10C10, sex= Male, infection= Mock, day= 32


title: T200.415

description: colon tumor proficient MMR TNM 2


description: Gene expression data from_sample from sample from subject 10C05, sex= Male, infection= Mock, day= 4


description: Gene expression data from_sample from sample from subject 10C08, sex= Male, infection= Mock, day= 16


title: T200.404

description: colon tumor proficient MMR TNM 2


title: T200.409

description: colon tumor proficient MMR TNM 3


description: Gene expression data from_sample from sample from subject 10B10, sex= Male, infection= GAS, day= 32


description: Gene expression data from_sample from sample from subject 10C07, sex= Male, infection= Mock, day= 9


description: Gene expression data from_sample from sample from subject 10C04, sex= Male, infection= Mock, day= 2


title: T200.403A

description: normal colon


description: Gene expression data from_sample from sample from subject 10C03, sex= Male, infection= Mock, day= 1


title: T200.402

description: colon tumor deficient MMR


title: T200.396

description: colon tumor proficient MMR TNM 3


description: Gene expression data from_sample from sample from subject 10C02, sex= Male, infection= Mock, day= 0


description: Gene expression data from_sample from sample from subject 10B09, sex= Male, infection= GAS, day= 23


title: T200.334

description: colon tumor deficient MMR


title: T200.42

description: colon tumor proficient MMR TNM 2


title: T200.259

description: colon tumor proficient MMR TNM 3


title: T200.248

description: colon tumor proficient MMR TNM 2


title: T200.24

description: colon tumor proficient MMR TNM 3


title: T200.227

description: colon tumor proficient MMR TNM 2


description: Gene expression data from_sample from sample from subject 10B04, sex= Male, infection= GAS, day= 2


title: T200.166

description: colon tumor deficient MMR


title: T200.2

description: colon tumor deficient MMR


title: T200.165.1a

description: colon tumor proficient MMR TNM 3


title: T200.165.2a

description: colon tumor proficient MMR TNM 3


description: Gene expression data from_sample from sample from subject 10B08, sex= Male, infection= GAS, day= 16


title: T200.101

description: colon tumor proficient MMR TNM 3


title: T200.133.1a

description: colon tumor proficient MMR TNM 3


title: T200.133.2a

description: colon tumor proficient MMR TNM 3


title: T200.164

description: colon tumor deficient MMR


title: T200.302

description: colon tumor deficient MMR


description: Gene expression data from_sample from sample from subject 10B07, sex= Male, infection= GAS, day= 9


description: Gene expression data from_sample from sample from subject 10C09, sex= Male, infection= Mock, day= 23


title: anon.8H

description: colon tumor proficient MMR TNM 2


description: Gene expression data from_sample from sample from subject 10B05, sex= Male, infection= GAS, day= 4


description: Gene expression data from_sample from sample from subject 10B02, sex= Male, infection= GAS, day= 0


title: T200.16

description: colon tumor proficient MMR TNM 3


description: Gene expression data from_sample from sample from subject 10B06, sex= Male, infection= GAS, day= 7


description: Gene expression data from_sample from sample from subject 10B03, sex= Male, infection= GAS, day= 1


title: Placenta_Spike_Pool5_Agilent

hyb_protocol: As per Agilents recommendations.

scan_protocol: Slides were scanned immediately after washing on the Axon 4000B scanner using one color scan setting (Scan resolution was 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3.1 (Agilent) using default parameters (protocol miRNA-v1_95_May07 and Grid: 016436_D_20070426) to obtain background subtracted Processed Signal intensities.

source_name: Human Placenta_Spike_Pool5

label_protocol: Cyanine-3 (Cy3) labeled miRNA was prepared from 100ng Total RNA using the Agilents labeling protocol and Asuragen's internal standard operating procedures.


title: Placenta_Spike_Pool6_Agilent

source_name: Human Placenta_Spike_Pool6


title: Placenta_Spike_Pool7_Agilent

source_name: Human Placenta_Spike_Pool7


title: anon.12

description: colon tumor proficient MMR TNM 2


title: Placenta_Spike_Pool4_Agilent

source_name: Human Placenta_Spike_Pool4


title: Placenta_Spike_Pool3_Agilent

source_name: Human Placenta_Spike_Pool3


title: Placenta_Spike_Pool2_Agilent

source_name: Human Placenta_Spike_Pool2


title: Placenta_Spike_Pool1_Agilent

source_name: Human Placenta_Spike_Pool1


title: Placenta_Spike_Pool7_Ambion/Affy

hyb_protocol: Hybridization, washing, staining, imaging, and signal extraction were performed according to Affymetrix-recommended procedures, except that the 20X GeneChip Eukaryotic Hybridization Control cocktail was omitted from the hybridization.

scan_protocol: Scanned as per Asuragen's standard operating procedures.

data_processing:
Two overlapping probes were designed for each mature miRNA candidate. The staggered probe design provides the flexibility required for probes to capture slight variations in the ends of the processed mature miRNA. For computationally predicted miRNA, this probe design strategy accounts for the uncertainty associated with predicting the precise cleavage site of the processed mature miRNA.  The signal processing implemented for the Ambion miRChip is a multi-step process involving probe specific signal detection calls, background estimate and correction, constant variance stabilization and either array scaling or global normalization. For each probe, an estimated background value is subtracted that is derived from the median signal of a set of G-C-matched anti-genomic controls. Arrays within a specific analysis experiment were normalized together according to the variance stabilization method described by Huber et al. (Huber et al., 2002).
Based on historical performance of the probes on a training data set, each of the two probes is assigned to either A or B bin. Variance Stabilization Normalization (VSN) technique is used to normalize the data. A probes are used for data interpretation.

label: Biotin

label_protocol: Samples were processed by Asuragen Services (Austin,TX), according to the company’s standard operating procedures. Briefly, samples were biotinylated and purified using BioSpin6 (Bio-Rad, Hercules CA).


title: normal plasma cellS - CPNORM4

city: Salamanca

first: Norma

middle: Carmen

last: Gutierrez

department: Hematology

country: Spain

institute: University Hospital

description: normal plasma cellS - CPNORM4

hyb_protocol: Labeled RNA was hybridized to Human Gene 1.0 ST Array

scan_protocol: Washing and scanning were performed using GeneChip System of Affymetrix (GeneChip Hybridization Oven 640, GeneChip Fluidics Station 450 and GeneChip Scanner 7G).

data_processing: Expression value for each probe set was calculated using RMAExpress program that uses RMA (Robust Multi-Array Average) algorithm.

source_name: Bone marrow, healthy

label_protocol: Labelling and hybridizations were performed according to protocols from Affymetrix. Briefly, 100-300 ng of total RNA were amplified and labeled using the WT Sense Target labelling and control reagents kit (Affymetrix Inc., Santa Clara, CA, USA)

extract_protocol: Total RNA was extracted from normal and tumor plasma cells using miRNEasy Mini Kit (Qiagen, Valencia, USA) following manufacturer's protocol. The RNA integrity was assessed using Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).

value: bone marrow

tag: cell type

value: CD138-positive plasma cell

tag: disease

value: healthy


title: normal plasma cellS - CPNORM3

description: normal plasma cellS - CPNORM3


title: MM - RB deletion - p1204

description: MM - RB deletion - p1204

source_name: Bone marrow, MM

value: multiple myeloma


title: normal plasma cellS - CPNORM5

description: normal plasma cellS - CPNORM5


title: MM - RB deletion - p1237

description: MM - RB deletion - p1237


title: MM - RB deletion - p1019

description: MM - RB deletion - p1019


title: Placenta_Spike_Pool6_Ambion/Affy

value: Female


title: Placenta_Spike_Pool5_Ambion/Affy


title: normal plasma cellS - CPNORM2

description: normal plasma cellS - CPNORM2


title: MM - RB deletion - p1279

description: MM - RB deletion - p1279


title: MM - RB deletion - p891

description: MM - RB deletion - p891


title: normal plasma cellS - CPNORM1

description: normal plasma cellS - CPNORM1


title: MM - RB deletion - p1292

description: MM - RB deletion - p1292


title: Placenta_Spike_Pool3_Ambion/Affy


title: MM - RB deletion - p1021

description: MM - RB deletion - p1021


title: MM - RB deletion - p1371

description: MM - RB deletion - p1371


title: MM - RB deletion - p846

description: MM - RB deletion - p846


title: MM - RB deletion - p1005

description: MM - RB deletion - p1005


title: Placenta_Spike_Pool2_Ambion/Affy


title: Placenta_Spike_Pool4_Ambion/Affy


title: Placenta_Spike_Pool1_Ambion/Affy


title: miR - normal plasma cell - CPNORM4

description: miR - normal plasma cell - CPNORM4

data_processing:
The SDS files are the raw files for real-time PCR data and are readable by Applied Biosystems SDS Software v2.3. SDS Software is available for download from the Applied Biosystems website.
Normalization was performed with the mean of RNU44 and RNU48.
CT = threshold cycle value
dCT = CT_(miRNA) - CT_(control miRNA) for comparisons between MM samples and normal PC.
ddCT = dCT_(MM) - dCT_(average normal PC) for comparisons between MM samples.
The dCT and ddCT data are presented as log10 of the relative quantity of each miRNA.

label: FAM

label_protocol: Standard Taqman Assay


title: miR - normal plasma cell - CPNORM3

description: miR - normal plasma cell - CPNORM3


description: Gene expression data from_sample from sample from subject 10C06, sex= Male, infection= Mock, day= 7

value: cynomolgus

value: Mock


title: miR - normal plasma cell - CPNORM5

description: miR - normal plasma cell - CPNORM5


title: miR - normal plasma cell - CPNORM1

description: miR - normal plasma cell - CPNORM1


title: miR - normal plasma cell - CPNORM2

description: miR - normal plasma cell - CPNORM2


title: miR - MM - t(14;16) - p1357

description: miR - MM - t(14;16) - p1357


title: miR - MM - t(14;16) - p1375

description: miR - MM - t(14;16) - p1375


title: miR - MM - t(4;14) - p585

description: miR - MM - t(4;14) - p585


title: MM - t(14;16) - p1375

description: MM - t(14;16) - p1375


title: MM - t(4;14) - p1437

description: MM - t(4;14) - p1437


title: MM - t(4;14) - p774

description: MM - t(4;14) - p774


title: MM - RB deletion - p831

description: MM - RB deletion - p831


title: MM - t(14;16) - p1297

description: MM - t(14;16) - p1297


title: MM - RB deletion - p709

description: MM - RB deletion - p709


title: MM - t(4;14) - p614

description: MM - t(4;14) - p614


title: MM - t(14;16) - p1489

description: MM - t(14;16) - p1489


title: MM - t(4;14) - p1212

description: MM - t(4;14) - p1212


title: MM - t(4;14) - p1133

description: MM - t(4;14) - p1133


title: MM - t(4;14) - p685

description: MM - t(4;14) - p685


title: MM - RB deletion - p790

description: MM - RB deletion - p790


title: MM - t(14;16) - p1357

description: MM - t(14;16) - p1357


title: MM - RB deletion - p841

description: MM - RB deletion - p841


title: MM - t(4;14) - p744

description: MM - t(4;14) - p744


title: MM - t(4;14) - p585

description: MM - t(4;14) - p585


title: MM - t(4;14) - p726

description: MM - t(4;14) - p726


title: MM - t(4;14) - p697

description: MM - t(4;14) - p697


title: MM - t(4;14) - p898

description: MM - t(4;14) - p898


title: MM - t(4;14) - p1252

description: MM - t(4;14) - p1252


title: mir - MM - t(14;16) - p1297

description: mir - MM - t(14;16) - p1297


title: miR - MM - t(14;16) - p1489

description: miR - MM - t(14;16) - p1489


title: miR - MM - RB deletion - p1371

description: miR - MM - RB deletion - p1371


title: miR - MM - t(4;14) - p774

description: miR - MM - t(4;14) - p774


title: miR - MM - RB deletion - p1292

description: miR - MM - RB deletion - p1292


title: MM - t(4;14) - p579

description: MM - t(4;14) - p579


title: MM - t(4;14) - p1464

description: MM - t(4;14) - p1464


title: miR - MM - RB deletion - p1237

description: miR - MM - RB deletion - p1237


title: miR - MM - RB deletion - p1279

description: miR - MM - RB deletion - p1279


title: miR - MM - RB deletion - p1021

description: miR - MM - RB deletion - p1021


title: MM - t(4;14) - p446

description: MM - t(4;14) - p446


title: miR - MM - RB deletion - p1204

description: miR - MM - RB deletion - p1204


title: miR - MM - RB deletion - p1019

description: miR - MM - RB deletion - p1019


title: MM - t(4;14) - p843

description: MM - t(4;14) - p843


title: MM - t(4;14) - p664

description: MM - t(4;14) - p664


title: MM - t(11;14) - p1562

description: MM - t(11;14) - p1562


title: MM - t(11;14) - p1390

description: MM - t(11;14) - p1390


title: miR - MM - RB deletion - p891

description: miR - MM - RB deletion - p891


title: miR - MM - RB deletion - p1005

description: miR - MM - RB deletion - p1005


title: MM - t(11;14) - p1077

description: MM - t(11;14) - p1077


title: MM - t(11;14) - p623

description: MM - t(11;14) - p623


title: MM - t(11;14) - p1411

description: MM - t(11;14) - p1411


title: MM - t(11;14) - p753

description: MM - t(11;14) - p753


title: MM - Normal FISH - p1616

description: MM - Normal FISH - p1616


title: MM - RB deletion and P53 deletion - p895


title: MM - t(11;14)  - p591

description: MM - t(11;14)  - p591


title: MM - Normal FISH - p1605

description: MM - Normal FISH - p1605


title: miR - MM - RB deletion - p841

description: miR - MM - RB deletion - p841


title: MM - t(11;14) - p1249

description: MM - t(11;14) - p1249


title: MM - Normal FISH - p1553

description: MM - Normal FISH - p1553


title: MM - Normal FISH - p1542

description: MM - Normal FISH - p1542


title: MM - t(11;14) - p1202

description: MM - t(11;14) - p1202


title: miR - MM - RB deletion - p790

description: miR - MM - RB deletion - p790


title: miR - MM - RB deletion - p846

description: miR - MM - RB deletion - p846


title: MM - Normal FISH - p1538

description: MM - Normal FISH - p1538


title: MM - Normal FISH - p1453

description: MM - Normal FISH - p1453


title: MM - t(11;14) - p613

description: MM - t(11;14) - p613


title: seedlings at T2, biological rep1

city: Boston

first: Jen

last: Sheen

state: MA

address: 185 Cambridge st. CPZN7620

department: Molecular Biology

institute: Massachusetts General Hospital

description: Gene expression data from Arabidopsis seedlings treated with 2 nM flg22 for 60 min

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized on the Arabidopsis ATH1 GeneChips using the Affymetrix 640 Hybridization Oven. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using GeneChip Scanner 7G with AutoLoader.

data_processing: The data were analyzed in FlexArray with RMA including background correction and normalization.

organism: Arabidopsis thaliana

source_name: Arabidopsis seedlings

label_protocol: Total RNA (9.0 µg) were amplified, biotinylated and fragmented using the BioArrayTM HighYieldTM RNA transcript labelling kit (Enzo) according to the manufacturer’s instructions.

growth_protocol: Seedlings were grown in walk-in room on the top shelf for 8 days in MS liquid medium

extract_protocol: Total RNA was extracted using RNeasy plant mini kit (Qiagen) according to the manufacturer’s protocol

treatment_protocol: Treated with 2nM flg22 for 30 and 60 min.

value: seedlings

tag: genotype

tag: age

value: 8 days, seedlings

tag: agent

tag: time


title: miR - MM - Normal FISH - p1605

description: miR - MM - Normal FISH - p1605


title: miR - MM - Normal FISH - p1616

description: miR - MM - Normal FISH - p1616


title: miR - MM - Normal FISH - p1553

description: miR - MM - Normal FISH - p1553


title: MM - Normal FISH - p1367

description: MM - Normal FISH - p1367


title: MM - Normal FISH - p1326

description: MM - Normal FISH - p1326


title: MM - Normal FISH - p1314

description: MM - Normal FISH - p1314


title: MM - Normal FISH - p1327

description: MM - Normal FISH - p1327


title: miR - MM - Normal FISH - p1542

description: miR - MM - Normal FISH - p1542


title: MM - Normal FISH - p1320

description: MM - Normal FISH - p1320


title: miR - MM - Normal FISH - p1453

description: miR - MM - Normal FISH - p1453


title: miR - MM - Normal FISH - p1367

description: miR - MM - Normal FISH - p1367


title: MM - Normal FISH - p694

description: MM - Normal FISH - p694


title: seedlings at T0, biological rep1

description: Gene expression data from Arabidopsis seedlings

value: control


title: seedlings at T1, biological rep1

description: Gene expression data from Arabidopsis seedlings treated with 2 nM flg22 for 30 min


title: MM - t(11;14) - p708

description: MM - t(11;14) - p708


title: miR - MM - Normal FISH - p1327

description: miR - MM - Normal FISH - p1327


title: MM - Normal FISH - p1274

description: MM - Normal FISH - p1274


title: miR - MM - Normal FISH - p1538

description: miR - MM - Normal FISH - p1538


title: miR - MM - Normal FISH - p1326

description: miR - MM - Normal FISH - p1326


title: miR - MM - Normal FISH - p1314

description: miR - MM - Normal FISH - p1314


title: miR - MM - Normal FISH - p1320

description: miR - MM - Normal FISH - p1320


title: protoplasts at T2, biological rep2 [CPK]

description: Gene expression data from Arabidopsis mesophyll protoplasts transfected with CPK11ac DNA for 6 hr

source_name: Arabidopsis leaves

label_protocol: Total RNA (10 µg) were amplified, biotinylated and fragmented using the BioArrayTM HighYieldTM RNA transcript labelling kit (Enzo) according to the manufacturer’s instructions.

growth_protocol: Arabidopsis plants (Col-0) were grown in a controlled room for 28 days at 22oC, 60% relative humidity, 75 uE light and 12 hr photoperiod.

treatment_protocol: Protoplasts (0.8 - 2 million) were transfected with 1 mg DNA/ml protoplasts using PEG-calcium and incubated in 10 ml 0.5 M mannitol, 4 mM MES pH 5.7 and 20 mM KCl for 6 hr at 25oC.

value: mesophyll protoplasts

value: 28 days, leaf 5-7

tag: protocol

value: expression of constitutively active CPK11ac


title: miR - MM - Normal FISH - p1274

description: miR - MM - Normal FISH - p1274


title: miR - MM - Normal FISH - p694

description: miR - MM - Normal FISH - p694


title: Dros-Sal-25.01.08

city: Kiel

first: Ahmed

middle: Abdelsadik Mohammed

last: Kahlil

state: SH

address: Olshausenstraße 40

department: Zoophysiology

country: Germany

institute: Christian-Albrechts-Universität

description: First biological replicate

hyb_protocol: The hybridization solution for all arrays used has the following recipe:     Per 54 µl DIG Easy Hyb adds:                                          2.88 µl 10 mg/ml yeast tRNA                                          2.88 µl 10 mg/ml salmon sperm DNA  Adjust the probes  to 200 pmol of each, mix with the buffer and take 40 µl of the previous mixture into a 500 µl tube; incubate at 65 °C for 10 minutes to denature the probe. Set the coverslip on a raised surface over the microarray slide and pipette the denatured probe between them avoiding any bubbles introducing. Close the hybridization chamber, enclosed with Aluminum foil, and incubate in a 42 °C hybridization oven for 12-18 hours. Wash1X SSC insert the slide, stir for 90 minutes. Wash 15 minutes 2 times with 1X SSC, 0.1 % Triton x-100 at 60°C, and with 0.1 X SSC, Triton x-100 (L3) at 37 °C for 10 minutes 2 times. Immerse the slide in a Coplin jar filled with 0.1 XSSC for 30 seconds and in ddH2O for 10 seconds

scan_protocol: Scanned on an Genepix  4000B scanner (Axon Instruments, Molecular Devices, München, Germany). Images were quantified using Genpix pro Feature Extraction Software (version A.7.5).

data_processing: SUB-GRID normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Online GENETRAFFIC tool was used.

organism: Drosophila melanogaster

source_name: Larval salivary glands

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM Odt7I and Capfinder DNA primer at 65°C for 5 min, then reversed transcribed at 45°C for 1 h in the presence of 400 U SuperScript II RTase (Takara), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-labe

growth_protocol: Animals growing up on standard cornmeal media at 25 centigrade

extract_protocol: RNAmagic according to the manufacturer's protocol

treatment_protocol: Ectopic activation  in the salivary gland line(SGS3-gal4) under the control of UAS-PGRPLCx

tag: sample type

source_name: Salivary Glands

value: IMD Pathway activated


title: miR - MM - t(4;14) - p1212

description: miR - MM - t(4;14) - p1212


title: NSCB_CGH_385K_315_WA01

city: Madison

first: Melodee

last: Patterson

state: WI

address: 510 Charmany Dr Ste 58 & 59

institute: WiCell

description: This CGH experiment is designed to detect deletion, insertation, amplication, etc. in the sample relative to the reference.

hyb_protocol: 7.9.1. Set the Roche NimbleGen Hybridization System 12 to 48°C. With the cover closed, allow at least 3 hours for the temperature to stabilize. 7.9.2. Hybridization Solution Master Mix per Chip 7.9.2.1. Thaw Alignment Oligo on ice, protected from light. 7.9.2.2. Add 11.8µl 2X Hybridization Buffer to 0.2ml PCR tube. 7.9.2.3. Add 4.7µl Hybridization Component A. 7.9.2.4. Add 0.5µl Alignment Oligo. Total amount of solution is 17.0µl. 7.9.2.5. Vortex to mix. 7.9.2.6. Briefly centrifuge samples using a tabletop centrifuge and keep on ice, protected from light. 7.9.3. Combine Test and Reference DNA Samples 7.9.3.1. Quantify each sample using the NanoDrop as described in SOP-SS-001 7.9.3.2. Combine 6µg each of test and reference labeled DNA in a PCR tube and bring to total volume of 5µl with VWR water. The combined volume of the test and reference samples must not exceed 5.0µl. Each of the labeled samples must fall within the concentration range of 2400-3400/ml. 7.9.3.2.1. If the concentration of the labeled sample is low, dehydrate the labeled sample in the SpeedVac at high heat for 3 minutes with tube lids open. Monitor the volume of sample to prevent complete dehydration. 7.9.3.2.2. If the concentration is still too low, reprecipitate starting from the second DNA precipitation (do NOT add 11.5ul of 5M NaCl) and rehydrate the pellet in a smaller volume of VWR water. 7.9.3.2.3. If the concentration of either sample is greater than 3400 µg/ml, dilute with VWR water to achieve the acceptable concentration range. 7.9.3.3. Add 13µl Hybridization Solution Master Mix to combined labeled DNA. 7.9.3.4. Vortex the samples for 20 seconds and quickly centrifuge in tabletop centrifuge. Keep samples protected from light. 7.9.3.5. Place samples in 95ºC thermocycler for 5 minutes. 7.9.3.6. Briefly vortex and centrifuge samples. 7.9.3.7. Quickly transfer the 0.2ml PCR tubes to the Roche NimbleGen Hybridization System 12 sample block (pre-heated to 48°C) for at least 5 minutes before sample loading. 7.9.4. Prepare X1 Mixer 7.9.4.1. Prepare X1 mixer according to NimbleGen™ Arrays User Guide (CGH Analysis v5.0). 7.9.5. Load Sample 7.9.5.1. Quickly transfer labeled DNA sample from PCR tube in 48ºC sample block to a 2.0 ml tube. 7.9.5.2. Dispense 18µl of sample into the bottom X1 mixer hole using a Gilson Microman M100 pipette. 7.9.5.3. Dry any excess sample from X1 mixer holes using a Kimwipe. 7.9.5.4. Seal top and bottom X1 mixer holes with mixer port seals. 7.9.5.5. Close the bay clamp. 7.9.5.6. Dampen humid cover with Millipore water and place over bays. Humid covers must be kept damp throughout hybridization. 7.9.5.7. Close the Roche NimbleGen Hybridization System 12 lid. 7.9.5.8. Turn on the Mixing Panel on the Hybridization System, set the mix mode to B, and press the mix button to start mixing. 7.9.5.9. Confirm that the Hybridization System recognizes the slide in each occupied bay by indicator light turning green. 7.9.5.10. Hybridize the sample to the array(s) for 40-42 hours at 48°C. 7.10. Sample Storage 7.10.1. Label the remaining labeled DNA according to the following format: 7.10.2. Store labeled DNA samples at -20C in “CGH Labeled Samples” box for up to two weeks. 7.11. Array Washing 7.11.1. Turn on GenePix 4000B to warm up lasers prior to beginning wash procedure. 7.11.2. Disassemble and wash arrays according to NimbleGen™ Arrays User Guide (CGH Analysis v5.0) with the following exceptions: 7.11.2.1. Heat both Wash Buffer I solutions to 42ºC. 7.11.2.2. Agitate array in Wash Buffer I for 3 minutes. 7.11.2.3. Follow 1 minute agitation in Wash Buffer 2 with a 2 minute incubation. 7.11.3. Perform washes protecting arrays from light and ozone. 7.11.4. Place array in corresponding case and wrap case in aluminum foil. 7.11.4.1. Label with CGH number. 7.11.5. Scan arrays immediately after washing (ref: SOP-CH-309). 7.12. Array Storage 7.12.1. Store scanned arrays in the dessicator.

scan_protocol: NimbleGen scan protocol

data_processing:
1. Image extraction:
NimbleScan provided by NimbleGen is used to extract signal data from image files
(*.TFF). Signals from the scan for Cy3 (green channel) are saved in a file named as chipID_532.pair while signals from the scan for Cy5 (red channel) are saved in a file named as chipID_635.pair.
2. Normalization:
Signals from Cy3/Cy5 channels are transformed by logarithms to base 2 and normalized with loess or qspline (Workman et al., 2002) algorithms by R to resolve the systematic errors and bias introduced by the microarray experimental platform. The log ratios of the signals are obtained by subtracting the log transformed signals from one channel by the corresponding ones from another channel.
3. Data smoothing and break-points identification:
Ratios of the normalized data are plotted by the corresponding genome locations. The data are smoothed by an adaptive weights smoothing algorithm (GLAD R-package, Wang et al., 2005), break-points are identified by a binary segmentation algorithm (DNAcopy R-package, Olshen et al., 2004) or by the segmentation algorithm available within Nimbelgen’s Nimblescan software.
4. Data visualization:
CGH results can be saved as SignalMap GFF files and can be visualized by SignalMap provided by NimbleGen. CGH results can also be visualized by other software, such as aCGHViewer (Shankar et al., 2006), CHARMView (Myers et al., 2005), etc. However, different software requires different input format.

label_protocol:
7.7.1. Cy3/Cy5 Labeling
7.7.1.1. Verify that the DNA concentration is between 25 and 30ng/ul for all test and reference samples.
7.7.1.2. Thaw the Cy3/Cy5 random nonamers on ice, protected from light.
7.7.1.3. Add 1µg of sonicated test DNA to 40 µl Cy3 dye. Bring to volume in 80 µl VWR water. Repeat for all test samples to be labeled.
7.7.1.4. Add 1 µg of sonicated reference DNA to 40 µl Cy5 dye. Bring to volume in 80 µl VWR water. Repeat for all reference samples to be labeled.
7.7.1.5. Vortex and quickly centrifuge test and reference DNA samples.
7.7.1.6. Incubate samples for 10 minutes at 98ºC protecting from light.
7.7.1.7. Rapidly transfer samples to an ice-water bath for 5 minutes protecting from light.
7.7.1.8. Prepare 20µl of the following aha-dNTP/Klenow Master Mix for each test and reference sample.
7.7.1.8.1. aha-dNTP/Klenow Master Mix per Sample
7.7.1.8.1.1. Thaw all reagents and aha-dNTP/Klenow master mix on ice.
7.7.1.8.1.2. Add 9µl VWR water to 0.2ml PCR tube.
7.7.1.8.1.3. Add 10µl 50X aha-dNTP Mix.
7.7.1.8.1.4. Add 1µl Klenow (50U/µl). DO NOT vortex. Total amount of solution is 20µl.
7.7.1.9. Add 20μl of the aha-dNTP/Klenow Master Mix to each of the cooled samples. Keep on ice.
7.7.1.10. Pipette to mix (15 times). DO NOT vortex.
7.7.1.11. Briefly centrifuge samples using a tabletop centrifuge.
7.7.1.12. Incubate the samples for 2 hours 15 minutes at 37°C in thermocycler protected from light.
7.7.1.13. Remove samples from thermocycler, keep at room temperature. Heat thermocycler to 98ºC. Place samples back into thermocycler and incubate for 10 minutes at 98ºC.
7.7.1.14. Rapidly transfer samples to an ice-water bath for 5 minutes protecting samples from light.
7.7.1.15. Add 1 µl of Klenow (50U/µl) to each sample.
7.7.1.16. Pipette to mix (15 times). DO NOT vortex.
7.7.1.17. Briefly centrifuge samples using a tabletop centrifuge.
7.7.1.18. Place samples in thermocycler at 37ºC for overnight amplification.
7.7.2. First DNA Precipitation
7.7.2.1. Set Roche Nimblegen Hybridization System 12 to 48ºC if proceeding to hybridization in the same day to allow for at least 3 hours of stabilization.
7.7.2.2. Cool centrifuge to 4ºC.
7.7.2.3. Add 10µl of 0.5M EDTA to each sample to stop the overnight amplification reaction.
7.7.2.4. Add 11.5 µl of 5M NaCl to each sample, then vortex for 10 seconds.
7.7.2.5. Briefly centrifuge samples using a tabletop centrifuge.
7.7.2.6. Transfer each sample into a 1.5ml tube containing 200 µl of isopropanol.
7.7.2.7. Vortex samples for 20 seconds.
7.7.2.8. Incubate at room temperature for 10 minutes, protected from light.
7.7.2.9. Centrifuge at 13,000 rpm 4ºC for 10 minutes.
7.7.2.10. Aspirate supernatant.
7.7.2.11. Rinse pellet with 500µl of 80% ice-cold ethanol. As you rinse, gently wash pellet from tube wall.
7.7.2.12. Centrifuge at 13,000 rpm 4ºC for 2 minutes.
7.7.2.13. Aspirate supernatant.
7.7.2.14. Dry contents in a SpeedVac with tube lids open on ‘low’ heat until dry (5-15 minutes), protected from light. Close lids when dried.
7.7.2.15. Proceed to Alexa Fluor Labeling or store labeled samples at -20°C, protected from light.
7.7.2.15.1. Frozen samples are stable for up to 2 weeks at -20ºC.
7.7.3. Alexa Fluor Labeling
7.7.3.1. Thaw one vial of Alexa Fluor 555 dye per Cy3-labeled test DNA sample on ice. Keep protected from light.
7.7.3.2. Thaw one vial of Alexa Fluor 647 dye per Cy5-labeled reference DNA sample on ice. Keep protected from light.
7.7.3.3. Thaw Alexa Fluor Labeling Buffer on ice.
7.7.3.4. Add 5 µl VWR water to each DNA sample.
7.7.3.5. Place samples in thermocycler at 42ºC for 5 minutes.
7.7.3.6. Add 3 µl Labeling Buffer to each DNA sample.
7.7.3.7. Vortex and quickly centrifuge DNA samples.
7.7.3.8. Add 2 µl DMSO to one of the vials of Alexa Fluor dye (either 555 or 647).
7.7.3.9. Vortex for 10 seconds to dissolve Alexa Fluor dye.
7.7.3.10. Immediately add 8 µl of corresponding DNA to the dissolved dye.
7.7.3.11. Pipette up and down to further dissolve dye pellet, replace lid and vortex briefly to mix.
7.7.3.12. Incubate at room temperature, protected from light for 1 hour.
7.7.3.13. Repeat steps 7.7.3.8.-7.7.3.12 for each Cy-labeled DNA to be labeled with Alexa Fluor dyes.
7.7.4. Second DNA Precipitation
7.7.4.1. Add 100 µl VWR water to each labeled DNA sample.
7.7.4.2. Add 11.5 µl of 5M NaCl to each sample.
7.7.4.3. Vortex for 10 seconds.
7.7.4.4. Briefly centrifuge samples using a tabletop centrifuge.
7.7.4.5. Transfer each sample into 1.5ml tubes containing 200 µl each of isopropanol.
7.7.4.6. Vortex samples for 20 seconds.
7.7.4.7. Incubate at room temperature for 10 minutes, protected from light.
7.7.4.8. Centrifuge at 13,000 rpm 4ºC for 10 minutes.
7.7.4.9. Aspirate supernatant.
7.7.4.10. Add 500µl of 80% ice-cold ethanol to the pellet and gently wash pellet from tube wall by pipetting.
7.7.4.11. Centrifuge at 13,000 rpm 4ºC for 2 minutes.
7.7.4.12. Aspirate supernatant.
7.7.4.13. Dry contents in a SpeedVac with tube lids open on ‘low’ heat until dry (5-15 minutes), protected from light. Close lids when dried.
7.7.4.14. Proceed to ‘Specific Activity Calculation’ or store labeled samples at -20°C, protected from light. Frozen samples are stable for up to 2 weeks at -20ºC.

extract_protocol:
1. Determine When to Harvest hES cells for DNA Extraction
A) At least 1x10^6 hES cells should be harvested for DNA extraction, depending on the quantity
required.
B) Yields of genomic DNA will vary from sample to sample depending on the amount and type of cells processed. In addition, the quality of starting material will affect DNA yield.
C) Estimated yield for hES cells: 5pg of DNA per cell (5μg DNA per 10^6 cells). One well of a 6-well plate will normally have between 1-4x106 hES cells by day 5 after passage.
2. Trypsinize the Cells
A) The following steps should be performed in a sterile biosafety cabinet while wearing personal protective equipment.
B) Add 1.5ml of 1X trypsin-EDTA working solution (pre-warmed to 37oC) to each well of a 6- well plate.
C) Return the plate to the 37C incubator for 2-3 minutes.
D) Remove the plate from the incubator and observe cell detachment with an inverted phase contrast microscope. Proceed to next step when colony edges begin to lift off the plate.
E) Using a sterile glass serological pipet, gently pipet up and down to detach the cells and break up the cell clumps.
F) Pool the detached cells in a 15ml centrifuge tube containing 5ml of trypsin stop solution within 5-7 minutes of adding the trypsin-EDTA solution.
G) Gently pipet the solution up and down to mix thoroughly.
H) Centrifuge the tube for 5 minutes at 1000 RPM.
3. RNA Digestion
A) Aspirate the supernatant and gently flick the tube until the pellet is resuspended.
B) Slowly add 200μl PBS to the cells while tapping gently on the tube to ensure good mixing.
C) Add 4μl RNase A (100mg/ml) and incubate at room temperature (RT) for 2 minutes.
4. Protein Digestion
A) Add 20μl Proteinase K and 200μl Buffer AL to the sample, mixing thoroughly by
vortexing. It is important that the solution is immediately and thoroughly mixed by
vortexing and pipetting to yield a homogenous solution.
NOTE: Do not add proteinase K directly to buffer AL.
B) Incubate the cell solution in a 70°C waterbath for 10 minutes.
5. DNA Precipitation and Separation of Cellular Components
A) Add 200μl ethanol (96-100%) to the sample, and mix thoroughly by vortexing.
B) A white precipitate may form on addition of ethanol. This precipitate does not interfere with the DNeasy procedure.
C) Pipet the mixture (including all of the precipitate) into the DNeasy Mini spin column placed in a 2ml collection tube. Centrifuge at ≥6000 x g (8000 rpm) for 1 minute. Discard flowthrough and collection tube.
NOTE: In order to obtain optimum DNA yield and quality, it is important not to overload
the spin column. The maximum number of hES cells that should be used in a DNA
extraction is 5x106 (normally, 2 wells of a 6-well plate). For larger amounts of starting material use multiple spin columns.
6. Wash the DNA
A) Place the DNeasy spin column in a new collection tube and add 500μl of Buffer AW1.
B) Centrifuge at ≥6000 x g (8000rpm) for 1 minute. Discard flow-through and collection tube.
C)Place the DNeasy spin column in a new collection tube and add 500μl of buffer AW2.
D) Centrifuge at 20,000 x g (14,000 rpm) for 3 minutes to dry the DNeasy membrane. Discard flow-through and collection tube.
NOTE: It is important to dry the membrane of the DNeasy Mini spin column, since
residual ethanol may interfere with subsequent reactions. This centrifugation step ensures that no residual ethanol will be carried over during the following elution.
E) Following the centrifugation step, remove the DNeasy Mini spin column carefully so the column does not come into contact with the flow-through, since this will result in carryover of ethanol. If carryover of ethanol occurs, place the spin column in a new collection tube and centrifuge again for 1 minute at 20,000 x g (14,000 rpm). Again discard the flow-through and collection tube.
7. Elution
A) Place the DNeasy Mini spin column in a clean 1.5ml or 2ml microcentrifuge tube and pipet 50-200μl Buffer AE directly onto the DNeasy membrane. Incubate the column at room temperature for 1 minute and then centrifuge for 1 minute at ≥6000 x g (8000rpm) to elute.
NOTE: Elution with less than 200μl of Buffer AE increases the final DNA concentration in the elute, but also decreases the overall DNA yield.
B) Repeat elution step as described in 7 A).
NOTE: A new microcentrifuge tube can be used for the second elution step to prevent dilution of the first elute. Alternatively, to combine the two elutes, the microcentrifuge tube from step 4.7.1 can be reused for the second elution step.
NOTE: More than 200μl should not be eluted into a 1.5 ml microcentrifuge tube because the DNeasy spin column will come into contact with the elute.

value: human embryonic stem (hES)

tag: cell line


title: Dros-Sal-05.03.08

description: Second Technical replicate


title: NSCB_CGH_385K_302_WA01


title: miR - MM - t(4;14) - p1133

description: miR - MM - t(4;14) - p1133


title: protoplasts at T0, biological rep1 [CPK]

description: Gene expression data from Arabidopsis mesophyll protoplasts transfected with control DNA for 6 hr


title: miR - MM - t(4;14) - p1252

description: miR - MM - t(4;14) - p1252


title: miR - MM - t(4;14) - p898

description: miR - MM - t(4;14) - p898


title: Dros-Sal-25.02.08

description: First Technical replicate


title: Matched_Blood_19sty

description: Hybridized to 250K_Sty.

source_name: peripheral whole blood matched_blood_19

value: peripheral whole blood


title: 14028_Lung_2D_IV_Nude_mouse2

city: San Diego

first: nabil

last: arrach

state: CA

address: 10905 Road to the cure

department: Viori

institute: Burnham Institute for Medical Research

description: biological replicate

hyb_protocol: overnight hyb on Corning UltraGAPS slides at 42°C in 25% formamide / 5xSSC / 0.1% BSA

scan_protocol: Perkin Elmer ScanArray 5000 scanner, image acquisition with ScanArray Express 3.0.1 software, spot quantification using Quantarray 3.0 software, adaptive quantification, protocol STv7S_01_051201

data_processing: normalized based on total signal for each channel, background subtracted VALUE data obtained from log of normalized background subtracted ch1/ch2 signal.

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

source_name: Lung 2D IV Nude

label_protocol: incorporation of Cy3-dCTP with Superscript RT and random hexamers

extract_protocol: RNeasy kit (QIAGEN)

tag: test

value: Lung 2 days after IV injection into nude mice

label_protocol: incorporation of Cy5-dCTP with Superscript RT and random hexamers

tag: reference

value: Salmonella typhimurium 14028 grown O/N in LB at 37C with aeration


title: Matched_Blood_16sty

description: Hybridized to 250K_Sty.

source_name: peripheral whole blood matched_blood_16


title: The abomasal mucosa of calf#967 reinfected with Ostertagia ostertagi for 14 days

city: Beltsville

first: Robert

middle: W

last: Li

state: MD

address: Barc East

department: Animal & Natural Resources Institute

institute: USDA

description: see Li et al., 2006

hyb_protocol: single dye

scan_protocol: Axon GenePix 4000B at 5 uM resolution

data_processing: The data presented here are normalized fluorescent intensities from either 4 or 8 spots of perfect match oligos. The raw data are log-transformed and then subject to quantitle normalization using R package

organism: Bos taurus

source_name: Drug-attenuated 5th reinfection

label_protocol: Cy3-labeled nonamer priming

growth_protocol: Indoor fed with standard ration

extract_protocol: Trizol followed with DNase digestion and Qiagen RNeasy purification

treatment_protocol: drug-attenuated 5th reinfection

tag: breed

value: Holstein

value: bull calf

value: 8-9 months


title: The abomasal mucosa of calf#966 reinfected with Ostertagia ostertagi for 14 days

description: see Li et al., 2006


title: 14028_Lung_2D_IV_Nude_mouse3

description: biological replicate


title: Matched_Blood_18sty

description: Hybridized to 250K_Sty.

source_name: peripheral whole blood matched_blood_18


title: miR - MM - t(4;14) - p1437

description: miR - MM - t(4;14) - p1437

value: bone marrow

value: CD138-positive plasma cell

value: multiple myeloma


title: miR - MM - t(4;14) - p726

description: miR - MM - t(4;14) - p726


title: protoplasts at T1, biological rep2 [CPK]

description: Gene expression data from Arabidopsis mesophyll protoplasts transfected with CPK5ac DNA for 6hr

value: expression of constitutively active CPK5ac


title: miR - MM - t(4;14) - p697

description: miR - MM - t(4;14) - p697


title: miR - MM - t(4;14) - p744

description: miR - MM - t(4;14) - p744


title: Dros-Sal-26.02.08

description: Second biological replicate


title: miR - MM - t(4;14) - p685

description: miR - MM - t(4;14) - p685


title: 14028_Lung_2D_IV_Nude_mouse1

description: biological replicate


title: miR - MM - t(4;14) - p614

description: miR - MM - t(4;14) - p614


title: Matched_Blood_13sty

description: Hybridized to 250K_Sty.

source_name: peripheral whole blood matched_blood_13


title: The abomasal mucosa of calf#964 drug-attenuated control, uninfected

description: see Li et al., 2006

source_name: Drug-attenuated control, uninfected

treatment_protocol: drug-attenuated control


title: Matched_Blood_10sty

description: Hybridized to 250K_Sty.

source_name: peripheral whole blood matched_blood_10


title: Matched_Blood_17sty

description: Hybridized to 250K_Sty.

source_name: peripheral whole blood matched_blood_17


title: Matched_Blood_12sty

description: Hybridized to 250K_Sty.

source_name: peripheral whole blood matched_blood_12


title: Matched_Blood_15sty

description: Hybridized to 250K_Sty.

source_name: peripheral whole blood matched_blood_15


title: Matched_Blood_9sty

description: Hybridized to 250K_Sty.

source_name: peripheral whole blood matched_blood_9


title: Matched_Blood_11sty

description: Hybridized to 250K_Sty.

source_name: peripheral whole blood matched_blood_11


title: Matched_Blood_8sty

description: Hybridized to 250K_Sty.

source_name: peripheral whole blood matched_blood_8


title: The abomasal mucosa of calf#963 drug-attenuated control, uninfected

description: see Li et al., 2006


title: miR - MM - t(4;14) - p579

description: miR - MM - t(4;14) - p579

source_name: Bone marrow, MM


title: 14028_PC3_tumor_2D_IT_Nude_mouse1

description: biological replicate

source_name: PC3 2D IT Nude

value: PC3 2 days after IT injection into nude mice


title: miR - MM - t(4;14) - p446

description: miR - MM - t(4;14) - p446


title: 14028_PC3_tumor_2D_IT_Nude_mouse4

description: biological replicate


title: The abomasal mucosa of calf#965 drug-attenuated control, uninfected

description: see Li et al., 2006


title: Matched_Blood_5sty

description: Hybridized to 250K_Sty.

source_name: peripheral whole blood matched_blood_5


title: The abomasal mucosa of calf#962 reinfected with Ostertagia ostertagi for 14 days

description: see Li et al., 2006


title: The abomasal mucosa of calf#961 uninfected

description: see Li et al., 2006

source_name: naive control

treatment_protocol: no treatment

value: 3-4 months


title: Matched_Blood_4sty

description: Hybridized to 250K_Sty.

source_name: peripheral whole blood matched_blood_4


title: 14028_liver_2D_IV_Nude_mouse1

description: biological replicate

source_name: Liver 2D IV Nude

value: Liver 2 days after IV injection into nude mice


title: Matched_Blood_14sty

description: Hybridized to 250K_Sty.

source_name: peripheral whole blood matched_blood_14


title: The abomasal mucosa of calf#960 uninfected

description: see Li et al., 2006


title: Matched_Blood_7sty

description: Hybridized to 250K_Sty.

source_name: peripheral whole blood matched_blood_7


title: miR - MM - t(4;14) - p664

description: miR - MM - t(4;14) - p664


title: 14028_MDA_tumor_2D_IT_Nude_mouse5

description: biological replicate

source_name: MDA 2D IT Nude

value: MDA 2 days after IT injection into nude mice


title: 14028_Spleen_2D_IV_Nude_mouse2

description: biological replicate

source_name: Spleen 2D IV Nude

value: Spleen 2 days after IV injection into nude mice


title: The abomasal mucosa of claf#958 drug-attenuated control, uninfected

description: see Li et al., 2006

source_name: Drug-attenuated control, uninfected


title: miR - MM - t(4;14) - p1464

description: miR - MM - t(4;14) - p1464


title: mir - MM - RB deletion and P53 deletion - p895


title: 14028_liver_2D_IV_Nude_mouse3

description: biological replicate


title: miR - MM - t(11;14) - p1562

description: miR - MM - t(11;14) - p1562


title: The abomasal mucosa of calf#957 infected with Ostertagia ostertagi for 14 days

description: see Li et al., 2006

source_name: Primary infection

treatment_protocol: parasite infection


title: miR - MM - t(4;14) - p843

description: miR - MM - t(4;14) - p843


title: 14028_Spleen_2D_IV_Nude_mouse3

description: biological replicate


title: miR - MM - t(11;14) - p1411

description: miR - MM - t(11;14) - p1411


title: 14028_MDA_tumor_2D_IT_Nude_mouse4

description: biological replicate


title: miR - MM - t(11;14) - p1249

description: miR - MM - t(11;14) - p1249


title: The abomasal mucosa of calf#956 infected with Ostertagia ostertagi for 14 days

description: see Li et al., 2006


title: Matched_Blood_2sty

description: Hybridized to 250K_Sty.

source_name: peripheral whole blood matched_blood_2


title: miR - MM - t(11;14) - p1202

description: miR - MM - t(11;14) - p1202


title: The abomasal mucosa of calf#955 uninfected

description: see Li et al., 2006


title: miR - MM - t(11;14) - p1077

description: miR - MM - t(11;14) - p1077


title: Matched_Blood_1sty

description: Hybridized to 250K_Sty.

source_name: peripheral whole blood matched_blood_1


title: Matched_Blood_3sty

description: Hybridized to 250K_Sty.

source_name: peripheral whole blood matched_blood_3


title: Matched_Blood_6sty

description: Hybridized to 250K_Sty.

source_name: peripheral whole blood matched_blood_6


title: miR - MM - t(11;14) - p753

description: miR - MM - t(11;14) - p753


title: miR - MM - t(11;14) - p708

description: miR - MM - t(11;14) - p708


title: 14028_Spleen_2D_IV_Nude_mouse1

description: biological replicate


title: 14028_PC3_tumor_2D_IT_Nude_mouse5

description: biological replicate


title: Placenta_Spike_Pool4_Exiqon

description:
Hy5 raw data file: 0_Exiqon_13764700_S01_Cropped.txt
Hy3 raw data file: 1_Exiqon_13764700_S01_Cropped.txt

hyb_protocol: The samples were hybridized on the miRCURY™ LNA Array (v.9.2) as per Exiqons protocols.

scan_protocol: Arrays were scanned as per Exiqons protocols.

data_processing: Log ratios between the Hy3/Hy5 have been provided along with the normalized independent Hy3 and Hy5 signals. The quantified signals (background correction) were normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm.

source_name: Human Placenta_Spike_Pool4

label_protocol: The samples were labeled using the miRCURY™ Hy3™/Hy5™ power labeling kit

value: Placenta

value: Female

source_name: Human Placenta Pools_1-7


title: Placenta_Spike_Pool5_Exiqon

description:
Hy5 raw data file: 0_Exiqon_13764701_S01_Cropped.txt
Hy3 raw data file: 1_Exiqon_13764701_S01_Cropped.txt

source_name: Human Placenta_Spike_Pool5


title: The abomasal mucosa of calf#954 infected with Ostertagia ostertagi for 14 days

description: see Li et al., 2006


title: 14028_PC3_tumor_2D_IT_Nude_mouse6

description: biological replicate

source_name: PC3 2D IT Nude


title: miR - MM - t(11;14) - p591

description: miR - MM - t(11;14) - p591

source_name: Bone marrow, MM


title: miR - MM - t(11;14) - p613

description: miR - MM - t(11;14) - p613


title: The abomasal mucosa of calf#953 uninfected

description: see Li et al., 2006

source_name: naive control


title: Placenta_Spike_Pool1_Exiqon

description:
Hy5 raw data file: 0_Exiqon_13764697_S01_Cropped.txt
Hy3 raw data file: 1_Exiqon_13764697_S01_Cropped.txt

source_name: Human Placenta_Spike_Pool1


title: Placenta_Spike_Pool7_Exiqon

description:
Hy5 raw data file: 0_Exiqon_13764703_S01_Cropped.txt
Hy3 raw data file: 1_Exiqon_13764703_S01_Cropped.txt

source_name: Human Placenta_Spike_Pool7


title: Placenta_Spike_Pool2_Exiqon

description:
Hy5 raw data file: 0_Exiqon_13764698_S01_Cropped.txt
Hy3 raw data file: 1_Exiqon_13764698_S01_Cropped.txt

source_name: Human Placenta_Spike_Pool2


title: Placenta_Spike_Pool3_Exiqon

description:
Hy5 raw data file: 0_Exiqon_13764753_S01_Cropped.txt
Hy3 raw data file: 1_Exiqon_13764753_S01_Cropped.txt

source_name: Human Placenta_Spike_Pool3


title: 14028_MDA_tumor_2D_IT_Nude_mouse3

description: biological replicate

source_name: MDA 2D IT Nude


title: 14028_liver_2D_IV_Nude_mouse2

description: biological replicate

source_name: Liver 2D IV Nude


title: 14028_MDA_tumor_2D_IT_Nude_mouse6

description: biological replicate


title: The abomasal mucosa of calf#952 infected with Ostertagia ostertagi for 14 days

description: see Li et al., 2006

source_name: Primary infection


title: 2wk ctrl 2

status: Public on Mar 17 2010

city: Syracuse

first: Frank

middle: A

last: Middleton

state: NY

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

description: propriospinal neuron gene expression data at different time points following spinal cord transection or sham. Additional details in published paper.

hyb_protocol: Following fragmentation, 5.75 micrograms of cDNA were hybridized for 16 hr at 45C on Rat ST Gene Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix 7G/4C scanner.

data_processing: The data were imported into GeneSpring GX (Agilent) and RMA normalized.

organism: Rattus norvegicus

source_name: thoracic non-injured spinal cord, 2 week control

label_protocol: Biotinylated cDNA were prepared according to the standard Nugen WT Ovation Pico Kit protocol with Exon Module Kit, from 50 nanograms total RNA

extract_protocol: RNeasy Mini (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Thoracic proporiospinal neurons that project to the lumbar enlargement were retrogradely labeled by fluorescent tracer injection prior to transection of the spinal cord and subsequently laser-dissected following different post-lesion or control survival times

value: laser-dissected neurons from spinal cord

tag: strain

value: Long Evans

tag: injury

value: thoracic non-injured spinal cord

value: 2 week control


title: 4d ctrl 1

source_name: thoracic non-injured spinal cord, 4 days control

tag: gender

value: 4 days control


title: 3d post 2

source_name: thoracic transected spinal cord, 3 days post lesion

value: thoracic transected spinal cord

value: 3 days post lesion


title: 4d ctrl 4


title: CD44(+), 2

city: Tokyo

first: Osamu

last: Nagano

state: DDS PhD

address: ３５　Shinanomachi

department: Institute for Advanced Medical Research

country: Japan

institute: Keio University School of Medicine

description: Gene expression data from glandular stomach of K19-Wnt1/C2mE mouse.

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55ul containing 25x fragmentation buffer and 10x blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55ul of 2xGE hybridization buffer(HI-RPM) was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR Lo 10% ).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_10_Apr08 and Grid: 014868_D_F_20070820) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Mus musculus

source_name: K19-Wnt1/C2mE, gastric tumor, CD44+

label_protocol: 25ng total RNA was amplified by MessageAmp™ II aRNA Amplification Kit#1751(Ambion), and 0.2 ug aRNA labeled Cyanine-3 (Cy3)  using the One-Color Quick Amp Labering 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.

extract_protocol: RNA was prepared using the NucleoSpin RNA XS (MACHEREY-NAGEL GmbH & Co. KG,Düren) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Gastric tumors from 30-week-old K19-Wnt1/C2mE mice were digested for 3 h at 37°C in Ham’s F-12 medium supplemented with 5% fetal bovine serum, penicillin (100 U/ml), streptomycin (100 mg/ml), bovine insulin (5 mg/ml), collagenase (300 U/ml), and hyaluronidase (100 U/ml). Red blood cells were then lysed by the addition of NH4Cl to a final concentration of 100 mM at room temperature, and tissue fragments were dissociated by gentle pipetting first in the presence of 0.25% trypsin for 1 to 2 min and then in the additional presence of dispase (5 mg/ml) and DNase I (0.1 mg/ml) for 2 min. The mixture was then filtered through a 40-mm nylon mesh to yield a single-cell suspension.

tag: transgenic background

value: glandular stomach tumor

value: Lin- CD44+

value: 30 weeks


title: 4d ctrl 2


title: 3d post 3


title: 2wk post 4

source_name: thoracic transected spinal cord, 2 week post lesion

value: 2 week post lesion


title: CD44(+), 1

tag: tissue


title: 2wk post 3

tag: cell type


title: 2wk ctrl 4


title: CD44(-), 2

source_name: K19-Wnt1/C2mE, gastric tumor, CD44-

value: Lin- CD44-


title: 3d post 4


title: CD44(-), 1


title: 3d post 1


title: 4d ctrl 3


title: 2wk ctrl 3


title: 2wk ctrl 1


title: 14028_PC3_tumor_2D_IT_Nude_mouse2

description: biological replicate

value: PC3 2 days after IT injection into nude mice

value: Salmonella typhimurium 14028 grown O/N in LB at 37C with aeration


title: 14028_MDA_tumor_2D_IT_Nude_mouse1

description: biological replicate

value: MDA 2 days after IT injection into nude mice


title: 1wk post 5

source_name: thoracic transected spinal cord, 1 week post lesion

value: 1 week post lesion


title: 14028_MDA_tumor_2D_IT_Nude_mouse2

description: biological replicate


title: The abomasal mucosa of calf#959 reinfected with Ostertagia ostertagi for 14 days

description: see Li et al., 2006

source_name: Drug-attenuated 5th reinfection

value: Holstein

value: bull calf

value: 8-9 months


title: 1wk post 4

value: laser-dissected neurons from spinal cord

value: Long Evans

value: Female


title: 1wk post 2

value: thoracic transected spinal cord


title: 1m post 2

source_name: thoracic transected spinal cord, 1 month post lesion

value: 1 month post lesion


title: air1delta, biological replicate 2

city: Basel

first: Katrina

last: Woolcock

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

description: mb20081112yspt1fr_04_air1delta_28.10.2008_494p53_258_(Sp20b_M_v04).CEL

hyb_protocol: hybridization was performed according to standard Affymetrix procedure

scan_protocol: Scanning was performed with Affymetrix GCC Scan Control v. 3.0.0.1214

data_processing: An R-based script, available on request, was used for the analysis. Values were normalized with justRMA() function from R/Bioconductor package affy using standard parameters.

organism: Schizosaccharomyces pombe

label_protocol: RNA was processed according to the GeneChip Whole Transcript (WT) Double-Stranded Target Assay Manual from Affymetrix

growth_protocol: Strains were grown at 30°C in YES (Yeast Extract with Supplements)

extract_protocol: RNA was isolated from cells collected at OD600=0.5 using the hot phenol method

tag: genome/variation


title: 1wk post 1


title: cid14delta, biological replicate 2

description: mb20080624yspt1fr_04_cid14delta_SPB101_2wk_16.6.2008_267p60_228_(Sp20b_M_v04).CEL


title: 1m post 1


title: miR - MM - t(11;14) - p1390

description: miR - MM - t(11;14) - p1390

source_name: Bone marrow, MM

value: bone marrow

value: CD138-positive plasma cell

tag: disease

value: multiple myeloma


title: air1delta, biological replicate 1

description: mb20081112yspt1fr_03_air1delta_24.10.2008_494p48_258_(Sp20b_M_v04).CEL


title: 1m ctrl 3

source_name: thoracic non-injured spinal cord, 1 month control

tag: age

value: thoracic non-injured spinal cord

value: 1 month control


title: 1m ctrl 4


title: tip.rep5

city: South San Francisco

first: Josh

last: Kaminker

address: 1 DNA Way

department: Bioinformatics and Computational Biology

institute: Genentech

hyb_protocol: Agilent's In situ Hybridization kit

scan_protocol: Agilent DNA microarray scanner

data_processing: Rosetta Resolver Feature Extraction Version 8.5.1.1 Linear & LOWESS normalized

label_protocol: Agilent's Low input RNA Linear Amp kit

extract_protocol: RNA was extracted using the Arcturus PicoPure kit (MDS Analytical Technologies, #KIT0204) according to manufacturers instructions.  RNA quality was assessed using an Agilent 2100 Bioanalyzer.

value: tip

tag: replicate

source_name: Universal Mouse Reference RNA: Stratagene Catalog #740100

value: Universal Mouse Reference RNA (Stratagene Catalog #740100)


title: tip.rep3


title: stalk.rep3

value: stalk


title: tip.rep2


title: cid14delta, biological replicate 1

description: mb20080624yspt1fr_03_cid14delta_SPB101_1wk_11.6.2008_267p60_228_(Sp20b_M_v04).CEL


title: non_vasculature_retina_control.rep3

source_name: 8814_NVR control

value: non vasculature retina control


title: stalk.rep4


title: tip.rep6


title: tip.rep4


title: stalk.rep1


title: miR - MM - t(11;14) - p623

description: miR - MM - t(11;14) - p623


title: tip.rep1


title: stalk.rep2


title: 1m ctrl 1

tag: time


title: wt, biological replicate 1

description: mb20080624yspt1fr_01_wildtype_SPB76_1wk_11.6.2008_267p60_228_(Sp20b_M_v04).CEL

source_name: wild type

value: wild type


title: 1m ctrl 2


title: non_vasculature_retina_control.rep1


title: 14028_PC3_tumor_2D_IT_Nude_mouse3

description: biological replicate

source_name: PC3 2D IT Nude

value: PC3 2 days after IT injection into nude mice

value: Salmonella typhimurium 14028 grown O/N in LB at 37C with aeration