title: RA-77 PB after/before  Methotrexate

source_name: RA-77 PB after treatment

source_name: RA-77 PB before treatment


title: RA-78 PB before/after  Methotrexate

status: Public on Jan 29 2014

type: RNA

city: Ibaraki

first: Norihiro

last: Nishimoto

state: Osaka

address: 7-7-20, Saito-Asagi

country: Japan

institute: Wakayama Medical University

hyb_protocol: The labeled aRNAs (mixture of Cy3 and Cy5) was hybridized onto microarray slide for 16 hours at 42ﾟC. Slides were washed in 2xSSC+0.1% SDS, 2xSSC, 1xSSC, and 0.1xSSC before air pressure drying and scanning.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a ScanArray Lite (PerkinElmer, Boston, MA) and signal values were calculated using DNASIS Array (Hitachi Software Engineering, Tokyo, Japan).

data_processing: Log2 ratios of Cy3 to Cy5 were calculated and normalized by the method of global ratio median normalization.

molecule: total RNA

organism: Homo sapiens

source_name: RA-78 PB before treatment

label_protocol: Total RNA was amplified. 5-(3-amino allyl)-UTP was incorporated to it using Amino Allyl MessageAmp aRNA Kit (Ambion, Austin, Texas). The amino allyl aRNA was further labeled by coupling reaction with NHS ester fluorescent dye, Cy3/Cy5.

extract_protocol: Peripheral blood was collected directly into PAXGene tubes (Qiagen, Valencia, CA). Total RNA was extracted using PAXGene Blood RNA Kit with the optimal on-column DNase digestion according to the manufacturer`s instructions.

tag: gender

value: male

tag: age (y)

tag: disease state

value: rheumatoid arthritis

tag: tissue

value: peripheral blood

tag: patient

tag: treatment

value: before methotrexate/MTX

source_name: RA-78 PB after treatment

value: after methotrexate/MTX


title: RA-79 PB after/before  Methotrexate

source_name: RA-79 PB after treatment

value: female

source_name: RA-79 PB before treatment


title: RA-74 PB before/after  Methotrexate

source_name: RA-74 PB before treatment

source_name: RA-74 PB after treatment


title: RA-76 PB after/before  Methotrexate

source_name: RA-76 PB after treatment

source_name: RA-76 PB before treatment


title: RA-81 PB after/before  Methotrexate

source_name: RA-81 PB after treatment

source_name: RA-81 PB before treatment


title: RA-79 PB before/after  Methotrexate


title: RA-74 PB after/before  Methotrexate


title: RA-75 PB before/after  Methotrexate

source_name: RA-75 PB before treatment

source_name: RA-75 PB after treatment


title: RA-76 PB before/after  Methotrexate


title: RA-77 PB before/after  Methotrexate


title: RA-73 PB after/before  Methotrexate

source_name: RA-73 PB after treatment

source_name: RA-73 PB before treatment


title: RA-75 PB after/before  Methotrexate


title: RA-72 PB after/before  Methotrexate

source_name: RA-72 PB after treatment

source_name: RA-72 PB before treatment


title: RA-67 PB after/before  Methotrexate

source_name: RA-67 PB after treatment

source_name: RA-67 PB before treatment


title: RA-68 PB after/before  Methotrexate

source_name: RA-68 PB after treatment

source_name: RA-68 PB before treatment


title: RA-70 PB before/after  Methotrexate

source_name: RA-70 PB before treatment

source_name: RA-70 PB after treatment


title: RA-70 PB after/before  Methotrexate


title: RA-69 PB before/after  Methotrexate

source_name: RA-69 PB before treatment

source_name: RA-69 PB after treatment


title: RA-71 PB before/after  Methotrexate

source_name: RA-71 PB before treatment

source_name: RA-71 PB after treatment


title: RA-69 PB after/before  Methotrexate


title: RA-72 PB before/after  Methotrexate


title: RA-65 PB after/before  Methotrexate

source_name: RA-65 PB after treatment

source_name: RA-65 PB before treatment


title: RA-63 PB after/before  Methotrexate

source_name: RA-63 PB after treatment

source_name: RA-63 PB before treatment


title: RA-64 PB after/before  Methotrexate

source_name: RA-64 PB after treatment

source_name: RA-64 PB before treatment


title: RA-73 PB before/after  Methotrexate

source_name: RA-73 PB before treatment

source_name: RA-73 PB after treatment


title: RA-67 PB before/after  Methotrexate

source_name: RA-67 PB before treatment

source_name: RA-67 PB after treatment


title: RA-71 PB after/before  Methotrexate


title: RA-62 PB after/before  Methotrexate

source_name: RA-62 PB after treatment

source_name: RA-62 PB before treatment


title: RA-59 PB after/before  Methotrexate

source_name: RA-59 PB after treatment

source_name: RA-59 PB before treatment


title: RA-66 PB before/after  Methotrexate

source_name: RA-66 PB before treatment

source_name: RA-66 PB after treatment


title: RA-64 PB before/after  Methotrexate


title: RA-63 PB before/after  Methotrexate


title: RA-68 PB before/after  Methotrexate

source_name: RA-68 PB before treatment

source_name: RA-68 PB after treatment


title: RA-61 PB before/after  Methotrexate

source_name: RA-61 PB before treatment

source_name: RA-61 PB after treatment


title: RA-65 PB before/after  Methotrexate

source_name: RA-65 PB before treatment

source_name: RA-65 PB after treatment


title: RA-66 PB after/before  Methotrexate


title: RA-60 PB before/after  Methotrexate

source_name: RA-60 PB before treatment

source_name: RA-60 PB after treatment


title: RA-78 PB after/before  Methotrexate

source_name: RA-78 PB after treatment

source_name: RA-78 PB before treatment


title: RA-58 PB after/before  Methotrexate

source_name: RA-58 PB after treatment

source_name: RA-58 PB before treatment


title: RA-62 PB before/after  Methotrexate

source_name: RA-62 PB before treatment

source_name: RA-62 PB after treatment


title: RA-61 PB after/before  Methotrexate


title: RA-60 PB after/before  Methotrexate


title: RA-59 PB before/after  Methotrexate

source_name: RA-59 PB before treatment

source_name: RA-59 PB after treatment


title: RA-57 PB after/before  Methotrexate

source_name: RA-57 PB after treatment

source_name: RA-57 PB before treatment


title: RA-58 PB before/after  Methotrexate


title: RA-55 PB before/after  Methotrexate

source_name: RA-55 PB before treatment

source_name: RA-55 PB after treatment


title: RA-56 PB after/before  Methotrexate

source_name: RA-56 PB after treatment

source_name: RA-56 PB before treatment


title: RA-57 PB before/after  Methotrexate


title: RA-54 PB after/before Tocilizumab

source_name: RA-54 PB after treatment

value: after Tocilizumab/MRA

source_name: RA-54 PB before treatment

value: before Tocilizumab/MRA


title: RA-55 PB after/before  Methotrexate


title: RA-51 PB after/before Tocilizumab

source_name: RA-51 PB after treatment

source_name: RA-51 PB before treatment


title: RA-52 PB before/after Tocilizumab

source_name: RA-52 PB before treatment

source_name: RA-52 PB after treatment


title: RA-52 PB after/before Tocilizumab


title: RA-53 PB before/after Tocilizumab

source_name: RA-53 PB before treatment

source_name: RA-53 PB after treatment


title: RA-53 PB after/before Tocilizumab


title: RA-50 PB before/after Tocilizumab

source_name: RA-50 PB before treatment

source_name: RA-50 PB after treatment


title: RA-48 PB before/after Tocilizumab

source_name: RA-48 PB before treatment

source_name: RA-48 PB after treatment


title: RA-47 PB after/before Tocilizumab

source_name: RA-47 PB after treatment

source_name: RA-47 PB before treatment


title: RA-44 PB after/before Tocilizumab

source_name: RA-44 PB after treatment

source_name: RA-44 PB before treatment


title: RA-43 PB after/before Tocilizumab

source_name: RA-43 PB after treatment

source_name: RA-43 PB before treatment


title: RA-56 PB before/after  Methotrexate

source_name: RA-56 PB before treatment

source_name: RA-56 PB after treatment


title: RA-46 PB before/after Tocilizumab

source_name: RA-46 PB before treatment

source_name: RA-46 PB after treatment


title: RA-45 PB after/before Tocilizumab

source_name: RA-45 PB after treatment

source_name: RA-45 PB before treatment


title: RA-44 PB before/after Tocilizumab


title: RA-51 PB before/after Tocilizumab

source_name: RA-51 PB before treatment

source_name: RA-51 PB after treatment


title: RA-50 PB after/before Tocilizumab

source_name: RA-50 PB after treatment

source_name: RA-50 PB before treatment


title: RA-49 PB after/before Tocilizumab

source_name: RA-49 PB after treatment

source_name: RA-49 PB before treatment


title: RA-54 PB before/after Tocilizumab

source_name: RA-54 PB before treatment

source_name: RA-54 PB after treatment


title: RA-45 PB before/after Tocilizumab


title: RA-46 PB after/before Tocilizumab


title: RA-47 PB before/after Tocilizumab

source_name: RA-47 PB before treatment

source_name: RA-47 PB after treatment


title: RA-49 PB before/after Tocilizumab


title: RA-48 PB after/before Tocilizumab

source_name: RA-48 PB after treatment

source_name: RA-48 PB before treatment


title: RA-43 PB before/after Tocilizumab

source_name: RA-43 PB before treatment

source_name: RA-43 PB after treatment


title: RA-42 PB before/after Tocilizumab

source_name: RA-42 PB before treatment

source_name: RA-42 PB after treatment


title: RA-42 PB after/before Tocilizumab


title: RA-40 PB before/after Tocilizumab

source_name: RA-40 PB before treatment

source_name: RA-40 PB after treatment


title: RA-38 PB after/before Tocilizumab

source_name: RA-38 PB after treatment

source_name: RA-38 PB before treatment


title: RA-41 PB after/before Tocilizumab

source_name: RA-41 PB after treatment

source_name: RA-41 PB before treatment


title: RA-40 PB after/before Tocilizumab


title: RA-39 PB before/after Tocilizumab

source_name: RA-39 PB before treatment

source_name: RA-39 PB after treatment


title: RA-39 PB after/before Tocilizumab


title: RA-36 PB after/before Tocilizumab

source_name: RA-36 PB after treatment

source_name: RA-36 PB before treatment


title: RA-38 PB before/after Tocilizumab


title: RA-34 PB after/before Tocilizumab

source_name: RA-34 PB after treatment

source_name: RA-34 PB before treatment


title: RA-35 PB after/before Tocilizumab

source_name: RA-35 PB after treatment

source_name: RA-35 PB before treatment


title: RA-36 PB before/after Tocilizumab


title: RA-35 PB before/after Tocilizumab


title: RA-30 PB before/after Tocilizumab

source_name: RA-30 PB before treatment

source_name: RA-30 PB after treatment


title: RA-37 PB after/before Tocilizumab

source_name: RA-37 PB after treatment

source_name: RA-37 PB before treatment


title: RA-31 PB before/after Tocilizumab

source_name: RA-31 PB before treatment

source_name: RA-31 PB after treatment


title: RA-34 PB before/after Tocilizumab


title: RA-41 PB before/after Tocilizumab


title: RA-27 PB after/before Tocilizumab

source_name: RA-27 PB after treatment

source_name: RA-27 PB before treatment


title: RA-33 PB after/before Tocilizumab

source_name: RA-33 PB after treatment

source_name: RA-33 PB before treatment


title: RA-29 PB before/after Tocilizumab

source_name: RA-29 PB before treatment

source_name: RA-29 PB after treatment


title: RA-32 PB before/after Tocilizumab

source_name: RA-32 PB before treatment

source_name: RA-32 PB after treatment


title: RA-33 PB before/after Tocilizumab


title: RA-30 PB after/before Tocilizumab


title: RA-32 PB after/before Tocilizumab


title: RA-37 PB before/after Tocilizumab


title: RA-31 PB after/before Tocilizumab


title: RA-28 PB before/after Tocilizumab

source_name: RA-28 PB before treatment

source_name: RA-28 PB after treatment


title: RA-29 PB after/before Tocilizumab


title: RA-27 PB before/after Tocilizumab


title: RA-28 PB after/before Tocilizumab


title: RA-26 PB after/before Tocilizumab

source_name: RA-26 PB after treatment

source_name: RA-26 PB before treatment


title: RA-26 PB before/after Tocilizumab


title: RA-24 PB after/before Tocilizumab

source_name: RA-24 PB after treatment

source_name: RA-24 PB before treatment


title: RA-25 PB before/after Tocilizumab

source_name: RA-25 PB before treatment

source_name: RA-25 PB after treatment


title: RA-18 PB after/before Tocilizumab

source_name: RA-18 PB after treatment

source_name: RA-18 PB before treatment


title: RA-23 PB before/after Tocilizumab

source_name: RA-23 PB before treatment

source_name: RA-23 PB after treatment


title: RA-16 PB after/before Tocilizumab

source_name: RA-16 PB after treatment

source_name: RA-16 PB before treatment


title: RA-16 PB before/after Tocilizumab


title: RA-25 PB after/before Tocilizumab


title: RA-20 PB after/before Tocilizumab

source_name: RA-20 PB after treatment

source_name: RA-20 PB before treatment


title: RA-22 PB after/before Tocilizumab

source_name: RA-22 PB after treatment

source_name: RA-22 PB before treatment


title: RA-18 PB before/after Tocilizumab


title: RA-20 PB before/after Tocilizumab


title: RA-15 PB before/after Tocilizumab

source_name: RA-15 PB before treatment

source_name: RA-15 PB after treatment


title: RA-23 PB after/before Tocilizumab


title: RA-21 PB before/after Tocilizumab

source_name: RA-21 PB before treatment

source_name: RA-21 PB after treatment


title: RA-22 PB before/after Tocilizumab


title: RA-17 PB after/before Tocilizumab

source_name: RA-17 PB after treatment

source_name: RA-17 PB before treatment


title: RA-21 PB after/before Tocilizumab


title: RA-19 PB after/before Tocilizumab

source_name: RA-19 PB after treatment

source_name: RA-19 PB before treatment


title: RA-13 PB before/after Tocilizumab

source_name: RA-13 PB before treatment

source_name: RA-13 PB after treatment


title: RA-24 PB before/after Tocilizumab

source_name: RA-24 PB before treatment

source_name: RA-24 PB after treatment


title: RA-14 PB after/before Tocilizumab

source_name: RA-14 PB after treatment

source_name: RA-14 PB before treatment


title: RA-19 PB before/after Tocilizumab


title: RA-12 PB before/after Tocilizumab

source_name: RA-12 PB before treatment

source_name: RA-12 PB after treatment


title: RA-8 PB after/before Tocilizumab

source_name: RA-8 PB after treatment

source_name: RA-8 PB before treatment


title: RA-8 PB before/after Tocilizumab


title: RA-14 PB before/after Tocilizumab


title: RA-3 PB before/after Tocilizumab

source_name: RA-3 PB before treatment

source_name: RA-3 PB after treatment


title: RA-12 PB after/before Tocilizumab


title: RA-11 PB after/before Tocilizumab

source_name: RA-11 PB after treatment

source_name: RA-11 PB before treatment


title: RA-9 PB before/after Tocilizumab

source_name: RA-9 PB before treatment

source_name: RA-9 PB after treatment


title: RA-5 PB after/before Tocilizumab

source_name: RA-5 PB after treatment

source_name: RA-5 PB before treatment


title: RA-3 PB after/before Tocilizumab


title: RA-17 PB before/after Tocilizumab

source_name: RA-17 PB before treatment

source_name: RA-17 PB after treatment


title: RA-11 PB before/after Tocilizumab


title: RA-10 PB after/before Tocilizumab

source_name: RA-10 PB after treatment

source_name: RA-10 PB before treatment


title: RA-10 PB before/after Tocilizumab


title: RA-6 PB after/before Tocilizumab

source_name: RA-6 PB after treatment

source_name: RA-6 PB before treatment


title: RA-15 PB after/before Tocilizumab

source_name: RA-15 PB after treatment

source_name: RA-15 PB before treatment


title: RA-9 PB after/before Tocilizumab


title: RA-4 PB after/before Tocilizumab

source_name: RA-4 PB after treatment

source_name: RA-4 PB before treatment


title: RA-4 PB before/after Tocilizumab


title: RA-6 PB before/after Tocilizumab


title: RA-7 PB before/after Tocilizumab

source_name: RA-7 PB before treatment

source_name: RA-7 PB after treatment


title: RA-13 PB after/before Tocilizumab

source_name: RA-13 PB after treatment

source_name: RA-13 PB before treatment


title: RA-1 PB before/after Tocilizumab

source_name: RA-1 PB before treatment

source_name: RA-1 PB after treatment


title: RA-2 PB before/after Tocilizumab

source_name: RA-2 PB before treatment

source_name: RA-2 PB after treatment


title: RA-2 PB after/before Tocilizumab


title: RA-5 PB before/after Tocilizumab

source_name: RA-5 PB before treatment

source_name: RA-5 PB after treatment


title: RA-7 PB after/before Tocilizumab


title: whole_brain_het_male_rep4

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum München GmbH

description: replicate 4

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol using HiScan

data_processing: The data were normalised using quantile normalisation with Illumina Genomestudio 2011.1

label: biotin

organism: Mus musculus

source_name: brain

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy midi kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with gel electrophoreses.

tag: strain/background

value: brain

tag: genotype

value: heterozygote

tag: allel

tag: age

value: 23 weeks

tag: mouse id

tag: Sex


title: whole_brain_het_male_rep3

description: replicate 3


title: forebrain_wt_male_rep3

description: Replicate 3

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol using HiScan.

data_processing: The data were normalised using quantile normalisation with Illumina GenomeStudio 2011.1.

source_name: forebrain, male, wildtype

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy midi kits in accordance with the prescribed protocol provided with the kit. Quality control was performed with gel electrophoreses.

value: wildtype

value: forebrain


title: whole_brain_wt_male_rep3

description: replicate 3

value: wild type


title: RA-1 PB after/before Tocilizumab


title: whole_brain_wt_male_rep2

description: replicate 2


title: whole_brain_het_male_rep2

description: replicate 2


title: forebrain_het_female_rep2

description: Replicate 2

source_name: forebrain, female, heterozygote


title: forebrain_het_female_rep1

description: Replicate 1


title: forebrain_wt_male_rep2

description: Replicate 2


title: forebrain_hom_male_rep2

description: Replicate 2

source_name: forebrain, male, homozygote

value: homozygote


title: whole_brain_wt_male_rep1

description: replicate 1


title: forebrain_het_male_rep2

description: Replicate 2

source_name: forebrain, male, heterozygote


title: forebrain_hom_female_rep2

description: Replicate 2

source_name: forebrain, female, homozygote


title: forebrain_het_male_rep3

description: Replicate 3


title: forebrain_hom_female_rep1

description: Replicate 1


title: forebrain_wt_female_rep2

description: Replicate 2

source_name: forebrain, female, wildtype


title: forebrain_het_female_rep3

description: Replicate 3


title: forebrain_wt_female_rep1

description: Replicate 1


title: OCIS 46

city: Duarte

first: Charles

middle: David

last: Warden

state: CA

address: 1500 East Duarte Rd

department: Department of Molecular and Cellular Biology

country: USA

institute: City of Hope

description: vaginal tissue sample

hyb_protocol: 600ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human Gene Expression 8x60K v2 arrays (G4851B, Design ID 039494) 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 immediately put the slides with Agilent barcode facing up in a slide holder with an ozone-barrier slide cover on top of the array.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60K array(Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%). Raw data were extracted using the Agilent Feature Extraction software, version 10.7.3.1., protocol GE1_107_Sep09.

data_processing: Microarray expression values were calculated using the gProcessed Signal, which was normalized via log2 transformation and quantile normalization in Partek® Genomics Suite (v.6.6, Partek Inc, St. Louis, MO). Control probe expression levels were removed during normalization.  Expression changes due to batch effects between arrays have been removed.

source_name: Subject 5003_Anterior_Proximal_Left

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 25ng RNA using the One-Color Low Input Quick Amp Labeling 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: Samples were thawed on ice and mixed by repeat pipet disruption with 70% ethanol according to the procedure described in the technical protocol of the RNeasy Mini Kit (QIAGEN), which was used for subsequent purification according to the manufacturer instructions. This included an on-column DNase digestion with the RNase-free DNase kit (QIAGEN). The total RNAs were eluted once with 50 µL of RNase-free water.

tag: subject id

value: vaginal tissue

tag: tissue location (a-p)

value: Anterior

tag: tissue location (p-d)

value: Proximal

tag: tissue location (l-r)

value: Left


title: OCIS 45

description: vaginal tissue sample


title: OCIS 48

description: vaginal tissue sample

source_name: Subject 5006_Posterior_Proximal_Right

value: Posterior

value: Right


title: forebrain_wt_male_rep1

description: Replicate 1

value: male


title: OCIS 43

description: vaginal tissue sample

source_name: Subject 5006_Posterior_Distal_Right

value: Distal


title: OCIS 44

description: vaginal tissue sample

source_name: Subject 5006_Posterior_Distal_Left


title: forebrain_hom_male_rep3

description: Replicate 3


title: forebrain_het_male_rep1

description: Replicate 1


title: forebrain_hom_male_rep1

description: Replicate 1


title: OCIS 42

description: vaginal tissue sample

source_name: Subject 5006_Posterior_Proximal_Left


title: whole_brain_het_male_rep1

description: replicate 1


title: OCIS 39

description: vaginal tissue sample

source_name: Subject 5006_Posterior_Interior

value: Interior


title: OCIS 41

description: vaginal tissue sample


title: OCIS 38

description: vaginal tissue sample

source_name: Subject 5006_Anterior_Distal_Left


title: OCIS 40

description: vaginal tissue sample

source_name: Subject 5006_Posterior_Exterior

value: Exterior


title: OCIS 30

description: vaginal tissue sample

source_name: Subject 5005_Anterior_Distal_Left


title: OCIS 31

description: vaginal tissue sample

source_name: Subject 5005_Posterior_Interior


title: OCIS 34

description: vaginal tissue sample

source_name: Subject 5005_Posterior_Proximal_Left


title: OCIS 35

description: vaginal tissue sample

source_name: Subject 5006_Anterior_Proximal_Right


title: OCIS 36

description: vaginal tissue sample

source_name: Subject 5006_Anterior_Proximal_Left


title: OCIS 37

description: vaginal tissue sample

source_name: Subject 5006_Anterior_Distal_Right


title: OCIS 28

description: vaginal tissue sample

source_name: Subject 5005_Anterior_Proximal_Left


title: OCIS 26

description: vaginal tissue sample

source_name: Subject 5004_Posterior_Distal_Left


title: OCIS 33

description: vaginal tissue sample

source_name: Subject 5005_Posterior_Proximal_Right


title: OCIS 22

description: vaginal tissue sample

source_name: Subject 5004_Posterior_Exterior


title: OCIS 23

description: vaginal tissue sample

source_name: Subject 5004_Posterior_Proximal_Right


title: OCIS 24

description: vaginal tissue sample

source_name: Subject 5004_Posterior_Proximal_Left


title: OCIS 16

description: vaginal tissue sample

source_name: Subject 5003_Posterior_Exterior


title: OCIS 29

description: vaginal tissue sample

source_name: Subject 5005_Anterior_Distal_Right


title: OCIS 25

description: vaginal tissue sample

source_name: Subject 5004_Posterior_Distal_Right


title: OCIS 19

description: vaginal tissue sample

source_name: Subject 5003_Posterior_Middle_Right

value: Middle


title: OCIS 21

description: vaginal tissue sample

source_name: Subject 5004_Posterior_Interior


title: OCIS 13

description: vaginal tissue sample

source_name: Subject 5003_Anterior_Distal_Right


title: OCIS 17

description: vaginal tissue sample

source_name: Subject 5003_Posterior_Proximal_Right


title: OCIS 18

description: vaginal tissue sample

source_name: Subject 5003_Posterior_Proximal_Left


title: OCIS 9

description: vaginal tissue sample

source_name: Subject 5002_Posterior_Interior


title: OCIS 10

description: vaginal tissue sample

source_name: Subject 5002_Posterior_Exterior


title: OCIS 20

description: vaginal tissue sample

source_name: Subject 5003_Posterior_Middle_Left


title: OCIS 14

description: vaginal tissue sample

source_name: Subject 5003_Anterior_Distal_Left


title: OCIS 15

description: vaginal tissue sample

source_name: Subject 5003_Posterior_Interior


title: OCIS 27

description: vaginal tissue sample

source_name: Subject 5005_Anterior_Proximal_Right


title: OCIS 12

description: vaginal tissue sample


title: OCIS 11

description: vaginal tissue sample

source_name: Subject 5003_Anterior_Proximal_Right


title: E11_2hours_PMA_Rep_2

city: Atlanta

first: Gregory

middle: B

last: Lesinski

state: GA

address: 1365C Clifton Rd. NE

department: Hematology and Medical Oncology

institute: Winship Cancer Institute of Emory University

description: Gene expression data from PMA stimulated E11

hyb_protocol: Carried out by Expression Analysis (Durham, NC, USA) following standard Affymetrix protocols.

data_processing: The data were analyzed with Affymetrix GeneChip Operating Software (GCOS1.x) by Expression Analysis

label: Biotin

source_name: KG1a-PRKCB2-GFP Clone E11, 2 hour PMA

growth_protocol: Cells were maintained in complete media (Isocove's Modified Dulbecco's Media + 100 U/ml penicillin/streptomycin + 100 mM L-Glutamine + 20% fetal calf serum)

extract_protocol: Material was isolated using RNeasy mini-columns (Qiagen)

treatment_protocol: Cells were left untreated or treated with PMA (phorbol 12-myristate 13-acetate) at 10 ng/ml for 2 hours

tag: tissue of origin

value: AML-blast

value: Male

value: 59 years

tag: source

value: Generated from ATCC purchased KG1a

tag: cell line

value: 2 hrs PMA stimulated

tag: clone


title: E9_Untreated_Rep_2

description: Gene expression data from unstimulated E9

scan_protocol: Carried out by Expression Analysis (Durham, NC, USA) following standard Affymetrix protocols.

source_name: KG1a-PRKCB2-GFP Clone E9, untreated

tag: gender

value: untreated


title: E11_Untreated_Rep_2

description: Gene expression data from unstimulated E11

source_name: KG1a-PRKCB2-GFP Clone E11, untreated

label_protocol: Carried out by Expression Analysis (Durham, NC, USA) following standard Affymetrix protocols.


title: OCIS 8

description: vaginal tissue sample

source_name: Subject 5001_Posterior_Interior_Left

tag: tissue

value: vaginal tissue


title: E9_Untreated_Rep_1

tag: treatment


title: OCIS 7

description: vaginal tissue sample

source_name: Subject 5001_Posterior_Interior_Right


title: E11_Untreated_Rep_1


title: E9_2hours_PMA_Rep_1

description: Gene expression data from PMA stimulated E9

source_name: KG1a-PRKCB2-GFP Clone E9, 2 hour PMA


title: OCIS 6

description: vaginal tissue sample

source_name: Subject 5001_Posterior_Exterior


title: E9_2hours_PMA_Rep_2


title: OCIS 4

description: vaginal tissue sample

source_name: Subject 5001_Anterior_Distal_Left

value: Anterior


title: KG1a_Untreated

description: Gene expression data from unstimulated KG1a

source_name: KG1a, untreated

value: ATCC


title: KG1a_2hours_PMA

description: Gene expression data from PMA stimulated KG1a

source_name: KG1a, 2 hour PMA


title: KG1_2hours_PMA

description: Gene expression data from PMA stimulated KG1

source_name: KG1, 2 hour PMA


title: OCIS 2

description: vaginal tissue sample

source_name: Subject 5001_Anterior_Proximal_Left

value: Proximal

value: Left


title: 8h UV Replicate 1

city: Berlin

first: Carla

last: Winterling

address: Charitéplatz 1

institute: Max Planck Institute for Infection Biology

hyb_protocol: according to the supplier's protocol

scan_protocol: 5-μm resolution using a G2565CA high-resolution laser microarray scanner (Agilent Technologies) with XDR extended range

data_processing: Raw microarray image data were analyzed with the Image Analysis/Feature Extraction software G2567AA v. A.10.5.1 (Agilent Technologies) using default settings

source_name: Untreated cells

label_protocol: RNA labeling was performed with the Low RNA Input Linear Amplification Kit PLUS (Agilent Technologies). In brief, mRNA was reverse transcribed and amplified using an oligo-dT-T7 promoter primer, and cRNA was subsequently labeled with Cyanine 3-CTP or Cyanine 5-CTP.

growth_protocol: The A549 human lung epithelial cell line (CCL-185, ATCC-LGC) was grown in DMEM media (Invitrogen) supplemented with 4mM l-glutamine, 4mM sodium pyruvate and 10% fetal calf serum (FCS, Biochrom) at 37°C and 5% CO2.

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

treatment_protocol: Supernatants of A/WSN/33 (H1N1) virus infected A549 cells (MOI 5, 8hpi) were exposed to UV light for 5 min and then used to stimulate A549 cells for 8 h

tag: cell type

value: Human lung epithelial cells

source_name: UV exposed cells


title: OCIS 5

description: vaginal tissue sample

source_name: Subject 5001_Posterior_Interior

value: Posterior


title: 8h UV Replicate 2


title: 8h Infection Replicate 1

source_name: Uninfected Cells

treatment_protocol: A549 cells were washed with PBS and then infected with viruses at MOI 1 in infection buffer (PBS supplemented with 0.2% bovine serum albumin) for 60 min at room temperature. Cells were incubated for the indicated time periods at 37 °C in DMEM supplemented with 0.2% bovine serum albumin, 4 mM l-glutamine and antibiotics.

source_name: Cells 8h infected with Influenza


title: 24h Infection Replicate 2

source_name: Cells 24h infected with Influenza


title: E11_2hours_PMA_Rep_1

source_name: KG1a-PRKCB2-GFP Clone E11, 2 hour PMA


title: 24h Infection Replicate 1


title: 4h UV Replicate 2

treatment_protocol: Supernatants of A/WSN/33 (H1N1) virus infected A549 cells (MOI 5, 4hp.i.) were exposed to UV light for 5 min and then used to stimulate A549 cells for 4 h


title: Eomes+ NK cells biological rep 3

city: Lyon

first: Thierry

last: Walzer

address: 21 avenue tony garnier

country: France

institute: CIRI, centre international de recherche en infectiologie

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized  on Affymetrix HT MG-430 PM arrays

scan_protocol: standard Affymetrix protocol

data_processing: Affymetrix CEL files were analyzed in R 3.01 using the Bioconductor 2.12 suite of packages. Raw probe signals were background corrected using the maximum likelihood estimation of the normal-exponential mixture model (Silver et al., 2009 - limma 3.16.3) and normalized using the variance stabilization normalization (Huber et al., 2002 - vsn 3.28.0) followed by a quantile normalization (Bolstad et al., 2003). Summarization was performed using the median-polish (Irizarry et al., 2003 - affyPLM 1.36.0).

source_name: Eomes+ NK cells

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

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

treatment_protocol: Liver NK and NKT cells were sorted by flow cytometry prior to RNA extraction

tag: strain background

tag: genotype/variation

value: Eomes-GFP reporter mice.

value: liver

value: Eomes+ NK cells

tag: facs gating

value: GFP+ NK1.1+ CD3-


title: 8h Infection Replicate 2


title: Eomes+ NK cells biological rep 2


title: Eomes+ NK cells biological rep 4


title: KG1_Untreated

description: Gene expression data from unstimulated KG1

source_name: KG1, untreated

value: AML-blast

tag: age


title: Eomes- NK cells biological rep 4

source_name: Eomes- NK cells

value: Eomes- NK cells

value: GFP- NK1.1+ CD3-


title: NKT cells biological rep 4

source_name: NKT cells

value: NKT cells

value: GFP- NK1.1+ CD3+


title: Eomes+ NK cells biological rep 1


title: 4h UV Replicate 1


title: NKT cells biological rep 2


title: Eomes- NK cells biological rep 1


title: NKT cells biological rep 3


title: Eomes- NK cells biological rep 3


title: GR-REV 6-BA EtOH 2h_replicate 1

city: Shanghai

first: Tian-Qi

last: Zhang

address: 300 Fenglin Road

department: Plant Molecular Genetics

country: China

institute: Institute of Plant Physiology and Ecology

description: Rev-GR6 CK EtoH 2h

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-028004 SurePrint G3 Human GE 8x60K array(Agilent) 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 (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 12.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

organism: Arabidopsis thaliana

source_name: GR-REV 6-BA EtOH 2h

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: 35S::FLAG-GR-rREV plants were grown on soil in 23 C long days.

extract_protocol: The aerial parts of seedlings were collected. Total RNAs were extracted RNeasy Mini Kit (Qiagen) following the manufacturer's mannual.

treatment_protocol: 10-day-old seedlings were treated with DMSO+ethanol (mock), 6-BA+ethanol, DMSO+DEX, and 6-BA DEX for 2 hours.

tag: transgenic plants

value: aerial parts of seedlings

tag: treated with

value: 6-benzylaminopurine (6-BA)+ethanol for 2hrs


title: GR-REV 6-BA EtOH 2h_replicate 2

description: REV-GR 6


title: GR-REV 6-BA DEX 2h_replicate 1

description: Rev-GR8 CK DEX 2h

source_name: GR-REV 6-BA DEX 2h

value: 6-BA+DEX for 2 hrs


title: GR-REV DMSO DEX 2h_replicate 1

description: Rev-GR7DMSO DEX 2h

source_name: GR-REV DMSO DEX 2h

value: dexamethasone +DMSO for 2hrs


title: GR-REV DMSO EtOH 2h_replicate 2

description: REV-GR 5

source_name: GR-REV DMSO EtOH 2h

value: DMSO+ethanol (mock)


title: GR-REV 6-BA DEX 2h_replicate 2

description: REV-GR 8


title: NKT cells biological rep 1


title: GR-REV DMSO DEX 2h_replicate 2

description: REV-GR 7


title: GR-REV DMSO EtOH 2h_replicate 1

description: Rev-GR5DMSO EtoH 2h


title: MLII knock-in osteoblasts, biological rep2

city: Hamburg

first: Thomas

last: Streichert

address: Martinistr. 52, Campus Forschung N27, 2. OG

department: Institute For Clinical Chemistry / Central Laboratories

institute: University Medical Center Hamburg-Eppendorf

description: Gene expression data from mutant osteoblasts.

hyb_protocol: For hybridization, 15 µg of fragmented cRNA were incubated with the chip in 200 µl of hybridization solution in Hybridization Oven 640 (Affymetrix) at 45°C for 16 hours. GeneChips were then washed and stained with the Affymetrix Fluidics Station 450 according to the GeneChip Expression Wash, Stain and Scan Manual using the GeneChip Hybridization, Wash and Stain Kit (Affymetrix).

scan_protocol: Microarrays were scanned with the Affymetrix GeneChip Scanner 7G.

data_processing: Signals were processed using GCOS (v.1.4; Affymetrix). The GCOS software was used to scale the samples to a target signal of 200 and perform pairwaise comparisons.

source_name: primary cultured osteoblasts from knock-in (KI) mice

label_protocol: First strand cDNA synthesis with 100 ng of total RNA, synthesis of biotin-labeled cRNA and clean-up was carried out using the 3′ IVT Express Kit (Affymetrix).

growth_protocol: Primary osteoblasts were isolated from calvaria of 5-day-old mice and differentiated by ascorbic acid and beta-glycerophosphate for 10 days.

extract_protocol: Total RNA was isolated from primary cultured osteoblasts using GeneJET™ RNA Purification Kit (Fermentas) according to the manufacturer's protocol.

tag: tissue origin

value: calvaria

tag: cell-type

value: primary osteoblasts

tag: differentiation stage

value: at day 10 of differentiation

tag: strain

value: mixed C57Bl/6-129/SvJ (Kollmann, K., et al. Lysosomal dysfunction causes neurodegeneration in mucolipidosis II 'knock-in' mice. Brain 135, 2661-2675 (2012))

tag: genotype

value: mutant (Gnptabc.3082insC)


title: x782

city: New Haven

first: Shilpa

last: Hattangadi

state: CT

address: 333 Cedar Street LMP 2073

department: Pediatric Hematology-Oncology

institute: Yale School of Medicine

description: Sample 1

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Gene Expression Microarrays (G2519F-014868) for 17 hours at 65Â°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 (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE2-v5 and Grid: 10.1.1.1) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: after Xpo7 knockdown

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

growth_protocol: Murine fetal liver erythroid precursors (Ter119-negative cells) were isolated from C57Bl6 E14.5 embryos by magnetic depletion with Ter119 beads and infected with retroviruses containing shRNA constructs against Xpo7.

extract_protocol: RNA was prepared using the Qiagen RNAEasy Purification kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations.  The protocol includes lysis of blood precursor cells and an on-column DNase digestion. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Cells were cultured in Epo-containing media (2U/mL) for 36hrs until they were fully differentiated and then sorted for GFP+ (infected cells) in order to isolate total RNA to be used for the profiling.

tag: developmental stage

value: Xpo7 knockdown

source_name: before Xpo7 knockdown

value: wild type control


title: wild-type osteoblasts, biological rep2

description: Gene expression data from primary cultured osteoblasts (wild-type).

source_name: primary cultured osteoblasts from wild-type (WT) mice

value: wild-type


title: MLII knock-in osteoblasts, biological rep1


title: RNA_Hu2640_B

city: Stockholm

first: Karl

last: Ekwall

address: Alfred Nobels Alle 7

country: Sweden

institute: Karolinska Inst

description:
RNA from htb1-K119R S. pombe; replicate 2.
Results file: RNA_Hu2640_F.bar
Results file: RNA_Hu2640_R.bar
Additional results file: RNA_Hu2640_F.txt
Additional results file: RNA_Hu2640_R.txt

hyb_protocol: Hybridised to Affymetrix GeneChip S. pombe Tiling 1.0FR array at the Affymetrix core facility at Novum (http://apt.bea.ki.se) according to standard Affymetrix protocols.

scan_protocol: Scanned at the Affymetrix core facility at Novum (http://apt.bea.ki.se) according to standard Affymetrix protocols.

data_processing:
CEL files were analysed using Affymetrix Tiling Analysis Software (TAS) v1.1. Replicate samples were subjected to quantile normalization (separate) and linear scaling to 100. Probe signals were generated using a bandwidth of 100 and assigned to S. pombe genome coordinates (Sanger 2007) and reported in separate BAR files for forward (F) and reverse (R) strand.
Results files in BAR format were generated using Affymetrix Tiling Analysis Software (TAS) v1.1. and contain log2 values for each probe.
Additional results files in txt format were generated using Affymetrix Tiling Analysis Software (TAS) v1.1. and contain log2 values for each probe.

organism: Schizosaccharomyces pombe

source_name: RNA, htb1-K119R

label_protocol: RNA was treated according to the Affymetrix total RNA labelling protocol (http://www.affymetrix.com).

growth_protocol: Liquid cultures were grown in YES media shaking at 180 rpm at 30 °C.

extract_protocol: Total RNA was extracted with hot acid phenol and chloroform. Briefly, cells were harvested by centrifugation at RT, resuspended in TES (10 mM TrisHCl pH7.5, 10 mM EDTA and 0.5% SDS) and transferred to preheated acid phenol (65 °C). After a 45 min shaking incubation at 65 °C, RNA was isolated by phenol-chloroform extraction.


title: RNA_Hu2640_A

description:
RNA from htb1-K119R S. pombe; replicate 1.
Results file: RNA_Hu2640_F.bar
Results file: RNA_Hu2640_R.bar
Additional results file: RNA_Hu2640_F.txt
Additional results file: RNA_Hu2640_R.txt


title: 10.1_clone_second_transplant

type: genomic

city: Charlestown

first: David

last: Langenau

state: MA

institute: Massachusetts General Hospital

hyb_protocol: Labeled Reference and Test samples were combined with hybridization buffer, as described in the standard Agilent protocol, and applied to microarrays enclosed in Agilent SureHyb-enable hybridization chambers. After hybridization, slides were washed sequentially in Buffer 1 and Buffer 2. Buffer 3 was not used as the scanner is in an ozone hood.

scan_protocol: Scanned on an Aglient G2505C sanner, at 2 microns

data_processing: Normalized, background subtracted data obtained from log2 of processed Red signal/Green signal. Aglient software was used.

molecule: genomic DNA

organism: Danio rerio

source_name: monoclonal zebrafish T-ALL, second transplant

label_protocol: Samples were labeled using the standard Agilent array CGH protocol with the following modifications: our experiments used 1 ug of heat denatured DNA (5 minutes at 95 degrees C) per labeling reaction in the place of the 1 ug of restriction-enzyme digested DNA, as indicated in the standard protocol. Reference samples were labeled with Cy3-dCTP and Test Samples were labeled with Cy5-dCTP.

growth_protocol: Zebrafish were handled using standard IACUC approved methods. Leukemia cells were transplanted by intraperitoneal injection.

extract_protocol: standard phenol:chloroform isolation

tag: leukemia propagating cell frequency

source_name: whole non-tumor CG1

value: whole non-tumor CG1


title: RNA_Hu303_B

description:
RNA from WT S. pombe; replicate 2.
Results file: RNA_Hu303_F.bar
Results file: RNA_Hu303_R.bar
Additional results file: RNA_Hu303_F.txt
Additional results file: RNA_Hu303_R.txt

source_name: RNA, WT

value: WT


title: 10_primary

source_name: Myc induced zebrafish T-ALL, primary

value: Myc induced zebrafish T-ALL, primary


title: inv_28h_repli2

city: Edegem

first: Ken

last: Op de Beeck

address: Universiteitsplein 1

country: Belgium

institute: University Of Antwerp

description: replicate 2

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were quantile normalized in limma 3.14.1 for R

label_protocol: Biotinylated cRNA were prepared with the Illumina Totalprep RNA amplification kit (Life technologies)

growth_protocol: The MDA-MB-231 cells were cultured in RPMI1640 supplemented with 10% fetal bovine serum (FBS), 1% L-glutamine, 1% penicillin/streptomycin and 1% sodium pyruvate. All cell culture reagents were purchased from Invitrogen (Life Technologies, USA) unless mentioned otherwise. Cell lines were maintained at 37°C and 5% CO2/95% air in a humidified incubator. Although the MDA-MB-231 breast cancer cell line was purchased from the American Type Culture Collection (ATCC, USA) (http:// www.lgcstandards-atcc.org), cell line identity was validated in-house by short tandem repeat (STR) profiling using the Cell ID System (Promega, USA) according to the manufacturer’s instructions.

extract_protocol: Total RNA was extracted using the RNAqueousTM Micro Kit (Life Technologies, USA) for nucleic acid extraction from small cell populations. All cell populations of interest were lysed directly on the membranes without prior enzymatic detachment.

treatment_protocol: In vitro invasion experiments have been performed using a conventional 24-well Transwell system (Corning®), with 4x10^5 cells seeded on top of a 20% (v/v) Matrigel layer. Complete medium was added to the wells as chemoattractant and the Transwell plates were incubated at 37°C/5% CO2 during 20h (first timewindow) and 28h (second timewindow), as predetermined in real-time invasion assessments. An identical protocol as the above was followed for migration experiments, without application of an extracellular matrix substitute. Transwell migration plates were incubated during 6h30’ (first timewindow) and 24h (second timewindow). For both invasion and migration, the respective timeframes of incubation have immediately been followed by RNA-isolation.

tag: cell population

value: late invasive cell population

tag: cell line


title: inv_28h_repli1

description: replicate 1


title: 9.3_clone_third_transplant

source_name: monoclonal zebrafish T-ALL, third transplant

tag: tissue


title: inv_28h_repli3

description: replicate 3


title: inv_ref_28h_repli3

description: replicate 3

value: non-motile cells, reference for late invasive cell population


title: wild-type osteoblasts, biological rep1


title: inv_ref_28h_repli1

description: replicate 1


title: inv_ref_28h_repli2

description: replicate 2


title: 10.2_clone

source_name: monoclonal zebrafish T-ALL, first transplant


title: inv_20h_repli3

description: replicate 3

value: early invasive cell population


title: input_A

description:
input DNA
Results file: Cnp1_Hu2640_input.bar, H2Bub1_Hu303_input.bar, H3_WT_input.bar, H3_Hu2640_input.bar, H3K9me2_WT_input.bar, H3K9me2_Hu2640_input.bar
Additional results file: Cnp1_Hu2640_input.txt, H2Bub1_Hu303_input.txt, H3_WT_input.txt, H3_Hu2640_input.txt, H3K9me2_WT_input.txt, H3K9me2_Hu2640_input.txt

hyb_protocol: Hybridised to Affymetrix GeneChip S. pombe Tiling 1.0FR Affymetrix core facility at Novum (http://apt.bea.ki.se) according to standard Affymetrix protocols.

data_processing:
CEL.files were analysed using Affymetrix Tiling Analysis Software (TAS) v1.1. Two sample comparisons of immunoprecipitated vs. input samples or immunoprecipitated (strain 1) vs. immunoprecipitated (strain 2), quantile normalization (separate) and linear scaling to 100 was applied. Probe signals were generated using a bandwidth of 100 and assigned to S. pombe genome coordinates (Sanger 2004) and reported in BAR files.
Results files in BAR formats were generated using Affymetrix Tiling Analysis Software (TAS) v1.1. and contain log2 values for relative enrichment (ChIP vs. Input, or ChIP vs. ChIP) for each probe.
Additional results files in txt formats were generated using Affymetrix Tiling Analysis Software (TAS) v1.1. and contain log2 values for relative enrichment (ChIP vs. Input, or ChIP vs. ChIP) for each probe.

source_name: input DNA

label_protocol: A specific sequence tag was attached to immunoprecipitated DNA fragments by PCR using sequenase and random primers (5'-GTTTCCCAGTCACGATCNNNNNNNNN-3'). This DNA was amplified using Taq polymerase and a primer recognizing the specific sequence tag (5'-GTTTCCCAGTCACGATC-3') in the precence of 5 mM dUTP. PCR products were purified using Qiaquick PCR purification kit. DNA was fragmented by UDG and APE nuclease treatment and labelled with biotin by Affymetrix core facility at Novum (http://apt.bea.ki.se) according to standard Affymetrix protocols. Immunoprecipitation Assay Protocol

extract_protocol: Immunoprecipitation was done using indicated antibody from chromatin extracts prepared from mid-logarithmic phase cells at 30C. Briefly, cells were fixed in 1% formaldehyde for 30 minutes, quenched with 125 mM glycine, and washed twice in PBS. Cells were resuspended in lysis buffer (0.1% SDS, 50 mM Hepes-KOH, 1 % Triton X-100, 0.1 % sodium deoxucholate, 1 mM EDTA and 150 mM NaCl) and lysed with glass beads in a FastPrep homogenizer. The lysate was sonicated and soluble chromatin fragments with an average size of 600 bp were collected. Chromatin was immunoprecipitated with indicated antibody for 2 hours and incubated with protein A agarose beads for 1 hour. The beads were washed, chromatin eluted at with TES at 65C and crosslinks reversed at 65C over night, together with input samples. Proteins were digested with proteinase K and immunoprecipitated DNA recovered using QIAquick PCR Purification kit.

tag: chip antibody

tag: sample type

value: input DNA


title: input_B


title: 9.2_clone

value: monoclonal zebrafish T-ALL, first transplant


title: 10.1_clone_first_transplant


title: RNA_Hu303_A

description:
RNA from WT S. pombe; replicate 1.
Results file: RNA_Hu303_F.bar
Results file: RNA_Hu303_R.bar
Additional results file: RNA_Hu303_F.txt
Additional results file: RNA_Hu303_R.txt


title: 9.3_clone_first_transplant


title: inv_20h_repli2

description: replicate 2


title: H3K9me2_Hu2640_B

description:
ChIP DNA, htb1-K119R, H3K9me2
Results file: H3K9me2_Hu2640_input.bar
Results file: H3K9me2_Hu2640_WT.bar
Additional results file: H3K9me2_Hu2640_input.txt
Additional results file: H3K9me2_Hu2640_WT.txt

source_name: ChIP DNA, htb1-K119R, H3K9me2

value: H3K9me2 (07-441, lot DAM1463717, EMD Millipore)

value: ChIP DNA


title: 9.3_clone_second_transplant

value: monoclonal zebrafish T-ALL, second transplant


title: inv_20h_repli1

description: replicate 1


title: H3K9me2_Hu2640_A


title: H3_Hu2640_C

description:
ChIP DNA, htb1-K119R, H3
Results file: H3_Hu2640_input.bar
Results file: H3_Hu2640_WT.bar
Additional results file: H3_Hu2640_input.txt
Additional results file: H3_Hu2640_WT.txt

source_name: ChIP DNA, htb1-K119R, H3

value: H3 (ab1791, Abcam)


title: 8.4_clone_second_transplant


title: H3K9me2_Hu303

description:
ChIP DNA, WT, H3K9me2
Results file: H3K9me2_WT_input.bar
Results file: H3K9me2_Hu2640_WT.bar
Additional results file: H3K9me2_WT_input.txt
Additional results file: H3K9me2_Hu2640_WT.txt

source_name: ChIP DNA, WT, H3K9me2


title: inv_ref_20h_repli3

description: replicate 3

value: non-motile cells, reference for early invasive cell population


title: 9_primary


title: 9.1_clone


title: H3_Hu2640_B


title: inv_ref_20h_repli2

description: replicate 2


title: H3_Hu2640_A


title: H3_Hu29

description:
ChIP DNA, WT, H3
Results file: H3_WT_input.bar
Results file: H3_Hu2640_WT.bar
Additional results file: H3_WT_input.txt
Additional results file: H3_Hu2640_WT.txt

source_name: ChIP DNA, WT, H3


title: H3K9me2_Hu29


title: inv_ref_20h_repli1

description: replicate 1


title: H3_Hu303


title: 8.3_clone


title: 8.1_clone


title: 8.4_clone_first_transplant


title: H2Bub1_Hu303_B

description:
ChIP DNA, WT, H2Bub1
Results file: H2Bub1_Hu303_input.bar
Additional results file: H2Bub1_Hu303_input.txt

source_name: ChIP DNA, WT, H2Bub1

value: H2Bub1 (05-1312, lot NG1856943, EMD Millipore)


title: mig_24h_repli1

description: replicate 1

value: late migratory cell population


title: H2Bub1_Hu303_A


title: 8.2_clone


title: mig_6h30_repli3

description: replicate 3

value: early migratory cell population


title: mig_24h_repli2

description: replicate 2


title: mig_ref_24h_repli2

description: replicate 2

value: non-motile cells, reference for late migratory cell population


title: mig_ref_24h_repli1

description: replicate 1


title: 8_primary

value: whole non-tumor CG1


title: Cnp1_Hu2640_A

description:
ChIP DNA, htb1-K119R, Cnp1
Results file: Cnp1_Hu2640_input.bar
Results file: Cnp1_Hu2640_WT.bar
Additional results file: Cnp1_Hu2640_input.txt
Additional results file: Cnp1_Hu2640_WT.txt

source_name: ChIP DNA, htb1-K119R, Cnp1

value: Cnp1 (in house)


title: Cnp1_Hu29

description:
ChIP DNA, WT, Cnp1
Results file: Cnp1_WT_input.bar
Results file: Cnp1_Hu2640_WT.bar
Additional results file: Cnp1_WT_input.txt
Additional results file: Cnp1_Hu2640_WT.txt

source_name: ChIP DNA, WT, Cnp1

value: WT


title: Cnp1_Hu2640_B


title: Cnp1_Hu303


title: 7.3_clone


title: mig_ref_24h_repli3

description: replicate 3


title: mig_6h30_repli1

description: replicate 1


title: mig_24h_repli3

description: replicate 3


title: 7_primary

value: Myc induced zebrafish T-ALL, primary


title: 7.1_clone


title: mig_6h30_repli2

description: replicate 2


title: 6.3_clone


title: 7.4_clone


title: mig_ref_6h30_repli2

description: replicate 2

value: non-motile cells, reference for early migratory cell population


title: Patient 5

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

country: Spain

institute: CIC bioGUNE

hyb_protocol: Whole-Genome Gene Expression Direct Hybridization Illumina Inc.'s protocol

scan_protocol: BeadScan Illumina Inc.

data_processing:
Raw data were decoded by GenomeStudio Illumina Inc. And normalization was done (1) forcePositive background correction, (2) log2 transformation and (3) quantile normalization
Normalized data includes data only for  probes (> 4000) that gave normalized signals. In addition, the data considered in this project are RNAs present in cellular vesicles, and as such, the number of probes present in these systems is quite small.

source_name: Urine: Extracellular Vesicles

label_protocol: TargetAmp™ Nano-g™ Biotin-aRNA Labeling Kit for the Illumina® System, Epicentre (Cat.Num. TAN07924)

extract_protocol: Trizol extraction of total RNA

tag: disease state

value: bladder cancer

tag: Sex

value: M

value: Urine Extracellular Vesicles


title: mig_ref_6h30_repli1

description: replicate 1


title: Patient 2

tag: age


title: mig_ref_6h30_repli3

description: replicate 3


title: Patient 3


title: Patient 4


title: Patient 1


title: 6.1_clone_first_transplant

value: monoclonal zebrafish T-ALL, first transplant


title: 6.2_clone


title: 6.1_clone_second_transplant


title: 4_primary


title: Control 5

value: control


title: 4.2_clone


title: 4.1_clone


title: 2.3_clone


title: lung at day 14

city: Nanjing

first: Chunhui

last: Ni

address: Tianyuan road No. 818

department: Department of Occupational Medicine and Environmental Health, School of Public Health

institute: Nanjing Medical University

description: miRNA expression data from lung tissue in late inflammation phase, day 14 after silica exposure.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hours at 48°C and 60 rpm on Affymetrix GeneChip miRNA Arrays. GeneChips were washed and stained in the Fluidics Station 450: Fluidics Script, FS450_0003.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Scanned images of microarray chips were analyzed using Expression Console (Affymetrix) with the default settings. Raw data were processed using different algorithms. Detected Above Background algorithm (DABG) and RMA Background Adjustment algorithm were performed in order to remove the background value.

source_name: Mouse lung tissue in late inflammation phase after silica treatment

label_protocol: FlashTag is ideally suited to label total RNA samples. For new users, 1μg of total RNA is recommended as starting point for labeling.(Genisphere Technical Support: 877.888.3DNA)

growth_protocol: specific pathogen-free conditions

treatment_protocol: The trachea of each animal was exposed under sodium pentobarbital (Dainippon Sumitomo Pharma, Osaka, Japan) anesthesia, and 50 mg/kg of silica in 0.05 ml sterile saline or 0.05 ml sterile saline was instilled intratracheally, respectively. Mice were sacrificed by excessive doses of anesthesia for the collection of lungs on days (D) 0, 3, 7, 14, 28 and 56 after silica instillation (n = 6 for each time point).

value: lung

tag: gender

value: Male

value: 6-8 weeks


title: Control 4


title: Control 3


title: Control 6


title: Control 2


title: lung at day 28

description: miRNA expression data from lung tissue in early fibrosis phase, day 28 after silica exposure.

source_name: Mouse lung tissue in fibrosis phase after silica treatment


title: 2.1_clone


title: 6_primary


title: lung at day 7

description: miRNA expression data from lung tissue in early inflammation phase, day 7 after silica exposure.

source_name: Mouse lung tissue in early inflammation phase after silica treatment


title: Control 1


title: lung at day 56

description: miRNA expression data from lung tissue in late fibrosis phase, day 56 after silica exposure.


title: 4.3_clone

source_name: whole non-tumor CG1


title: CG1_nontumor_whole_fish

source_name: CG1 zebrafish, wild-type

value: CG1 zebrafish, wild-type


title: lung at day 0

description: miRNA expression data from lung tissue without silica exposure, i.e. before silica treatment.

source_name: Mouse lung tissue before silica treatment (the control group)


title: lung at day 3

description: miRNA expression data from lung tissue in early inflammation phase, day 3 after silica exposure.


title: 1.1_clone_first_transplant


title: 1.4_clone_third_transplant

source_name: monoclonal zebrafish T-ALL, third transplant


title: 2_primary

source_name: Myc induced zebrafish T-ALL, primary


title: 1.4_clone_second_transplant

source_name: monoclonal zebrafish T-ALL, second transplant


title: 1.3_clone_first_transplant

source_name: monoclonal zebrafish T-ALL, first transplant


title: Test cell - heavy polysome#2

status: Public on Jan 28 2014

city: Nagasaki

first: Kazuo

last: Yamamoto

state: Nagasaki

address: 1-12-4 Sakamoto

department: Biomedical Research Support Center

institute: Nagasaki University School of Medical Sciences

description: Biological replicate 2 of 3. Test cells, heavy polysomal RNA.

hyb_protocol: Oligoarray control targets and GEx hybridization buffer Hi-RPM (Agilent Gene Expression Hybridization Kit) were added, and samples were applied to microarrays enclosed in Agilent SureHyb chambers. After hybridization, slides were washed sequentially.

scan_protocol: Scanned on an Agilent G2565C DNA scanner.

data_processing:
Images were quantified using Agilent Extraction Protocol GE2_107_Sept07.
The Agilent Feature Extraction text files were loaded into GeneSpring GX 11.0.1 followed by median centered normalization.

source_name: Test cell - heavy polysome#2

label_protocol: 200 ng of polysomal RNA were primed with oligo dT-T7 promoter primer at 65°C for 10 min, then reversetranscribed at 40°C for 2 h in the presence of AffinityScript RT (Agilent), and 500 µM each dATP, dTTP, dGTP, and dCTP, and used for the template for cRNA synthesis by T7 RNA polymerase in the presence of Cy5-CTP.

growth_protocol: Control and PRR16/Largen-overexpressing 293T cells were cultured in DMEM supplemented with 10% FBS in a humidified chamber at 37°C in 5% CO2.

extract_protocol: Cytoplasmic extracts prepared from exponentially-growing 293T cell clones were centrifuged on pre-chilled 10-50% sucrose gradients at 35,000 rpm for 2 hr at 4°C in a Beckman SW40Ti rotor. Gradients were fractionated and the UV-absorbance at 254 nm was continuously recorded using an ISCO fractionator (Teledyne ISCO). Light and heavy polysome fractions were prepared from three independent sucrose gradient fractionations, and RNA from each fraction was isolated using Trizol following manufacturer's instructions.

tag: cell type

value: embryonic kidney cells

tag: genotype/variation

source_name: Human reference RNA

tag: reference

value: Agilent Human Reference RNA

tag: catalog#


title: Test cell - light polysome#2

description: Biological replicate 2 of 3. Test cells, light polysomal RNA.

source_name: Test cell - light polysome#2


title: Test cell - input#2

description: Biological replicate 2 of 3. Test cells, input RNA.

source_name: Test cell - input#2


title: Test cell - heavy polysome#1

description: Biological replicate 1 of 3. Test cells, heavy polysomal RNA.

source_name: Test cell - heavy polysome#1


title: 1.2_clone_second_transplant

value: monoclonal zebrafish T-ALL, second transplant


title: Test cell - light polysome#1

description: Biological replicate 1 of 3. Test cells, light polysomal RNA.

source_name: Test cell - light polysome#1


title: 1.2_clone_first_transplant

value: whole non-tumor CG1


title: Test cell - heavy polysome#3

description: Biological replicate 3 of 3. Test cells, heavy polysomal RNA.

source_name: Test cell - heavy polysome#3


title: Test cell - input#1

description: Biological replicate 1 of 3. Test cells, input RNA.

source_name: Test cell - input#1


title: Test cell - light polysome#3

description: Biological replicate 3 of 3. Test cells, light polysomal RNA.

source_name: Test cell - light polysome#3


title: 1_primary


title: Control cell - heavy polysome#1

description: Biological replicate 1 of 3. Control cells, heavy polysomal RNA.

source_name: Control cell - heavy polysome#1

value: Control


title: Control cell - heavy polysome#2

description: Biological replicate 2 of 3. Control cells, heavy polysomal RNA.

source_name: Control cell - heavy polysome#2


title: Control cell - light polysome#2

description: Biological replicate 2 of 3. Control cells, light polysomal RNA.

source_name: Control cell - light polysome#2


title: Control cell - light polysome#1

description: Biological replicate 1 of 3. Control cells, light polysomal RNA.

source_name: Control cell - light polysome#1


title: 1.1_clone_second_transplant

source_name: whole non-tumor CG1


title: 1.4_clone_first_transplant


title: Test cell - input#3

description: Biological replicate 3 of 3. Test cells, input RNA.

source_name: Test cell - input#3


title: Control cell - heavy polysome#3

description: Biological replicate 3 of 3. Control cells, heavy polysomal RNA.

source_name: Control cell - heavy polysome#3


title: 1.3_clone_second_transplant

source_name: monoclonal zebrafish T-ALL, second transplant


title: Healthy donor LIVER20

city: roma

first: antonella

last: minutolo

address: viale del policlinico

country: Italy

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

label: SYBR Green

source_name: fresh liver

label_protocol: Human Adipogenesis RT² Profiler™ PCR Array

extract_protocol: Total RNA was extracted with RNeasy Mini Kit followed by DNase I treatment.

tag: phenotype

value: Healthy donor liver

value: liver biopsy


title: Healthy donor LIVER18


title: Healthy donor LIVER19


title: Control cell - light polysome#3

description: Biological replicate 3 of 3. Control cells, light polysomal RNA.

source_name: Control cell - light polysome#3

source_name: Human reference RNA


title: Healthy donor LIVER16


title: Healthy donor LIVER15


title: Healthy donor LIVER17


title: Healthy donor LIVER14


title: Healthy donor LIVER13


title: Healthy donor LIVER12


title: Healthy donor LIVER11


title: Healthy donor LIVER9


title: Healthy donor LIVER10


title: Healthy donor LIVER8


title: Healthy donor LIVER6


title: Healthy donor LIVER7


title: Healthy donor LIVER4


title: Healthy donor LIVER5


title: Control cell - input#2

description: Biological replicate 2 of 3. Control cells, input RNA.

source_name: Control cell - input#2


title: HCV LIVER38

value: HCV+  liver


title: Healthy donor LIVER3


title: HCV LIVER40


title: wt cells treated with IFN10

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

institute: University of Torino

hyb_protocol: hybridization (Illumina), washing, and staining were performed as per manufacturer instructions

scan_protocol: Arrays were scanned on IlluminaBeadStation 500

data_processing: Probe average intensity signal was calculated with BeadStudio without background correction. Raw data were analyzed with Bioconductor using the one ChannelGUI package. Average probe intensities were log2-transformed and normalized by the lowess method. All experimental groups were filtered to have an inter-quartile range for each probe > 0.25.

source_name: MEF cells

label_protocol: Labelling was performed as per manufacturer instructions

growth_protocol: Immortalized Rictor +/+  and Rictor-/-MEFs were  maintained in DMEM supplemented with 10% FBS and gentamycin

extract_protocol: RNA was isolated using RNAeasy RNA isolation kit from Qiagen

treatment_protocol: Rictor specific siRNAs were purchased from Dharmacon and use to treat MEF cells

value: MEF

value: Rictor+/+

tag: treatment

value: 2500 U/ml of mouse IFNa for 24 hours


title: rictor KO cells11

value: Rictor-/-


title: Healthy donor LIVER1


title: Healthy donor LIVER2


title: rictor KO cells7


title: HCV LIVER39


title: HCV LIVER37


title: untreated cell9


title: HCV LIVER35


title: wt cells treated with IFN6


title: rictor KO cells with IFN8


title: HCV LIVER34


title: HCV LIVER33


title: HCV LIVER32


title: Control cell - input#3

description: Biological replicate 3 of 3. Control cells, input RNA.

source_name: Control cell - input#3


title: HCV LIVER31


title: HCV LIVER30


title: HCV LIVER29


title: wt cells treated with IFN2


title: HCV LIVER27


title: HCV LIVER26


title: HCV LIVER28


title: HCV LIVER24


title: Control cell - input#1

description: Biological replicate 1 of 3. Control cells, input RNA.

source_name: Control cell - input#1


title: HCV LIVER25


title: HCV LIVER36


title: HCV LIVER23


title: rictor KO cells with IFN12


title: HCV LIVER22


title: HCV LIVER21


title: HCV LIVER20


title: rictor KO cells3


title: HCV LIVER19


title: HCV LIVER18


title: HCV LIVER16


title: HCV LIVER17


title: HCV LIVER15


title: HCV LIVER14


title: HCV LIVER13


title: HCV LIVER12


title: HCV LIVER11


title: rictor KO cells with IFN4


title: HCV LIVER9


title: HCV LIVER8


title: untreated cell5


title: HCV LIVER5


title: HCV LIVER7


title: HCV LIVER3


title: HCV LIVER4


title: HCV LIVER1


title: HDPBMCS20

source_name: fresh PBMC

value: Healthy donor PBMC

value: PBMC


title: HDPBMCS19


title: HDPBMCS18


title: HDPBMCS17


title: HDPBMCS15


title: HDPBMCS13


title: HDPBMCS12


title: HCV LIVER2


title: HDPBMCS11


title: HDPBMCS16


title: HDPBMCS14


title: HDPBMCS7


title: HDPBMCS8


title: HDPBMCS5


title: HDPBMCS6


title: HDPBMCS9


title: HDPBMCS10


title: HCV LIVER10


title: HCV LIVER6


title: HDPBMCS4


title: HDPBMCS1


title: HD PBMCS2


title: HDPBMCS3


title: HbV PBMCS20

value: HbV+ PBMC


title: HbV PBMCS19


title: HbV PBMCS18


title: HbV PBMCS17


title: HbV PBMCS16


title: HbV PBMCS14


title: HbV PBMCS12


title: HbV PBMCS2


title: HbV PBMCS15


title: HD pbmcs20

source_name: fresh pbmc


title: HD pbmcs17


title: HbV PBMCS1


title: HbV PBMCS3


title: HbV PBMCS6


title: HbV PBMCS5


title: HbV PBMCS9


title: HbV PBMCS13


title: HD pbmcs18


title: HbV PBMCS7


title: HbV PBMCS10


title: HD pbmcs15


title: HbV PBMCS11


title: HbV PBMCS4


title: HbV PBMCS8


title: HD pbmcs11


title: HD pbmcs19


title: HD pbmcs9


title: HD pbmcs10


title: HD pbmcs16


title: HD pbmcs8


title: HD pbmcs7


title: HD pbmcs6


title: HD pbmcs1


title: HD pbmcs4


title: HD pbmcs14


title: HD pbmcs5


title: HD pbmcs3


title: HCV pbmc 37

value: HCV+ PBMC


title: HCV pbmc 36


title: HD pbmcs13


title: HD pbmcs12


title: HD pbmcs2


title: HCV pbmc 38


title: HCV pbmc 31


title: HCV pbmc 32


title: HCV pbmc 33


title: HCV pbmc 40


title: HCV pbmc 35


title: HCV pbmc 34


title: HCV pbmc 39


title: HCV pbmc 30


title: HCV pbmc 27


title: HCV pbmc 26


title: HCV pbmc 23


title: HCV pbmc 28


title: HCV pbmc 29


title: HCV pbmc 22


title: HCV pbmc 24


title: HCV pbmc 25


title: HCV pbmc 20


title: untreated cell1


title: HCV pbmc 21


title: Nanog KO iPSC, biological rep2

city: Boston

first: Benjamin

last: Schwarz

address: 185 Cambridge St.

department: Molecular Biology

institute: MGH

description: Gene expression data

hyb_protocol: Following fragmentation, 5.5 ug of cDNA were hybridized for 16 hr at 45 C on GeneChip Mouse 2.0 ST Array in an Affymetrix GeneChip Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G running Affymetrix Gene Command Console ver 3.2.

data_processing: The data were analyzed with using Affymetrix Expression Console ver 1.3.0.187 using Analysis algorithm RMA.

source_name: Nanog KO iPSC

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 73.5 ng total RNA using amplification kit Ambion WT Expression, Lot # 1303016, followed by labeling 5.5 ug cDNA using kit Affymetrix GeneChip WT Terminal Labeling, Lot # 4196729, 4207143 and 4185701.

growth_protocol: Cells were grown in ESC media, 2i/LIF media, or MEF media.

extract_protocol: RNA was islolated and extracted using the Rneasy Micro Kit (Qiagen).

treatment_protocol: Cells were harvested following trypsin treatment.

value: iPSCs

tag: genotype

value: Nanog KO

tag: strain


title: HCV pbmc 19


title: Sphingomonas sp. A1_dalgO_yeast extract_medium

city: Uji

first: Wataru

last: Hashimoto

state: Kyoto

address: Gokasho

department: Graduate School of Agriculture

institute: Kyoto University

description: This sample is of Sphingomonas. sp A1 delta-algO, a single deletion mutant grown in yeast extract medium.

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

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

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Sphingomonas sp. A1

source_name: grown yeast extract medium

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

growth_protocol: Sphingomonas sp. A1 AlgO-deficient mutant was grown to mid-log phase (O.D.600nm 0.5 to 0.6) at 30°C in 0.5% yeast extract medium (0.1% (NH4)2SO4, 0.1% KH2PO4, 0.1% Na2HPO4, 0.01% MgSO4•7H2O, and 0.5% yeast extract (pH 7.2)).

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen), and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen).

value: deletion mutant delta-algO


title: WT MEFs

description: Gene expression data

source_name: WT MEFs

value: MEFs

value: WT


title: HCV pbmc 18


title: Nanog KO MEFs

description: Gene expression data

source_name: Nanog KO MEFs


title: Sphingomonas sp. A1_dalgO_alginate_medium

description: This sample is of Sphingomonas. sp A1 delta-algO, a single deletion mutant grown in alginate medium.

source_name: grown alginate medium

growth_protocol: Sphingomonas sp. A1 AlgO-deficient mutant was grown to mid-log phase (O.D.600nm 0.5 to 0.6) at 30°C in 0.5% alginate medium (0.1% (NH4)2SO4, 0.1% KH2PO4, 0.1% Na2HPO4, 0.01% MgSO4•7H2O, 0.01% yeast extract, and 0.5% sodium alginate (pH 7.2)) .


title: HCV pbmc 16


title: WT ESCs

description: Gene expression data

source_name: WT ESCs

value: ESCs


title: HCV pbmc 15


title: WT iPSC, biological rep2

description: Gene expression data

source_name: WT iPSC


title: WT E14.5 FL SLAM LSK 10h DMSO Rep3

city: Philadelphia

first: dawson

last: gerhardt

address: BRB2/3 421 Curie Blvd.

institute: University of Pennsylvania

hyb_protocol: ssDNA was added to Affymetrix hybridization cocktails, heated at 99ºC for 2 min and hybridized for 16 h at 45ºC to Mouse Gene 2.0st GeneChips

scan_protocol: A confocal scanner was used to collect fluorescence signal after excitation at 570 nm.

data_processing:
Affymetrix.cel files (containing probe intensities) were exported from Command Console software and imported into Partek Genomics Suite (v6.6, Partek Inc., St. Louis, MO) where RMA was applied yielding normalized, log2 transformed signal intensities. Transcript IDs were filtered to exclude technical controls, leaving 34,365 IDs for differential expression analysis. To find differentially expressed genes, SAM (Significance Analysis for Microarrays, samr v2.0, Stanford University) was applied using a two-class (GSI vs DMSO) paired (by litter pool) design.
probe group file: MoGene-2_0-st.pgf
meta-probeset file: MoGene-2_0-st.mps

source_name: Fetal liver hematopoeitic stem cell (SLAM LSK)

label_protocol: ssDNA was fragmented and biotinylated by terminal transferase end labeling

growth_protocol: Livers wer dissected from WT (C57B/6) embryos at E14.5 and cultured on OP9-DL1 cells. SLAM-LSK HSCs were FACs sorted after the indicated culture time

extract_protocol: Cells were sorted into Arcturus Pico pure extraction buffer and RNA prepared per instructions on the Arcturus Pico Pure RNA isolation kit

treatment_protocol: FL cells were  cultured on OP9-DL1 cells for 4 or 10 hrs in the presence of DMS0 Gamma Secretase ihibitor (1uM)

value: fetal liver

value: HSC

value: DMSO

tag: time


title: Nanog KO iPSC, biological rep1

description: Gene expression data


title: WT E14.5 FL SLAM LSK 10h DMSO Rep4


title: WT iPSC, biological rep1

description: Gene expression data


title: WT E14.5 FL SLAM LSK 10h GSI Rep2

value: GSI


title: WT E14.5 FL SLAM LSK 10h DMSO Rep1


title: HCV pbmc 13


title: HCV pbmc 14


title: WT E14.5 FL SLAM LSK 10h DMSO Rep2


title: WT E14.5 FL SLAM LSK 10h GSI Rep1


title: WT E14.5 FL SLAM LSK 4h DMSO Rep7


title: WT E14.5 FL SLAM LSK 10h GSI Rep4


title: HCV pbmc 17


title: WT E14.5 FL SLAM LSK 10h GSI Rep3


title: HCV pbmc 11


title: HCV pbmc 12


title: WT E14.5 FL SLAM LSK 4h GSI Rep7


title: HCV pbmc 10


title: WT E14.5 FL SLAM LSK 4h GSI Rep6


title: WT E14.5 FL SLAM LSK 4h DMSO Rep5


title: HCV pbmc 9


title: HCV pbmc 7


title: HCV pbmc 8


title: HCV pbmc 6


title: WT E14.5 FL SLAM LSK 4h GSI Rep4


title: HCV pbmc 4


title: HCV pbmc 5


title: HCV pbmc 2


title: HCV pbmc 1


title: WT E14.5 FL SLAM LSK 4h DMSO Rep6


title: HD LIVER20

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://sabiosciences.com/pcrarraydataanalysis.php
For the normalization it uses the average of five housekeeping genes:ACTB.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Matrix normalized worksheet reports normalized signal (against housekeeping genes BETA ACTIN).
Fold Change worksheet reports test/control ratios average.

source_name: fresh liver

label_protocol: Human Adipogenesis RT² Profiler™ PCR Array SAbiosciences Qiagen

extract_protocol: Total RNA was extracted with RNeasy Mini Kit followed by DNase I treatment THERMO SCIENTIFIC

value: Healthy donor liver

value: liver biopsy


title: HD LIVER19


title: WT E14.5 FL SLAM LSK 4h GSI Rep5


title: WT E14.5 FL SLAM LSK 4h DMSO Rep4


title: WT E14.5 FL SLAM LSK 4h DMSO Rep2


title: WT E14.5 FL SLAM LSK 4h DMSO Rep1


title: HD LIVER18


title: HCV pbmc 3


title: HD LIVER17


title: HD LIVER16


title: WT E14.5 FL SLAM LSK 4h DMSO Rep3


title: HD LIVER15


title: WT E14.5 FL SLAM LSK 4h GSI Rep3


title: HD LIVER14


title: WT E14.5 FL SLAM LSK 4h GSI Rep1


title: HD LIVER13


title: C2C12-pMirn378_day 3_BMP2 treated_rep1

city: Nijmegen

first: Marlinda

last: Hupkes

address: Heyendaalseweg 135

department: Cell and Applied Biology

country: Netherlands

institute: Radboud University Nijmegen

description: gene expression in differentiating C2C12-pMirn378 cells treated with BMP (osteogenesis d3)

hyb_protocol: 10 µg of biotin-labeled cRNA was hybridized to a GeneChip Mouse Genome 430 2.0 array (Affymetrix) for  16 hours at 45°C at 60 rpm in a GeneChip Hybridization Oven 640 (Affymetrix). Following hybridization, the arrays were washed and stained with a GeneChip Fluidics Station 450 (Affymetrix) using the Affymetrix Hybridization Wash Stain (HWS) kit.

scan_protocol: GeneChips were laser scanned with a GeneChip Scanner 3000 7G (Affymetrix)

data_processing: Data was saved as raw image file and quantified using Affymetrix GeneChip Command Console v 1.0 (Affymetrix). This data was imported to R 2.4.1 using the Bioconductor (www.bioconductor.org) Affymetrix package. The model-based Robust Multiarray Average (RMA) algorithm was used to generate the probe set summary based on the full annotation on gene level and normalization was done according to the quantile method.

source_name: RNA from C2C12-pMirn378 cells treated with BMP (osteogenesis), day 3

label_protocol: 200 ng total RNA was amplified, labeled and fragmented using the GeneChip 3'IVT Express Kit (Affymetrix) according to the manufacturer's instructions.

growth_protocol: C2C12-pMirn0 and C2C12-pMirn378 myoblasts were plated at 2.5 x 10^4 cells/cm2 in DMEM 10% Newborn Calf Serum (NCS) and grown for 24 hrs

treatment_protocol: C2C12-pMirn0 and C2C12-pMirn378 cells were treated with or without 300 ng/ml bone morphogenetic protein 2 (BMP2) for 6 days. Total RNA was extracted on day 0, day 3 and day6.

tag: cell line


title: HD LIVER12

tag: tissue


title: C2C12-pMirn378_day 6_BMP2 treated_rep1

description: gene expression in differentiating C2C12-pMirn378 cells treated with BMP (osteogenesis d6)

source_name: RNA from C2C12-pMirn378 cells treated with BMP (osteogenesis), day 6


title: Dctr1_CTR1D300_rep1

city: Dresden

first: Astrid

last: Schuller

address: Zellescher Weg 20B

institute: TU-Dresden

description: Gene expression of Dctr1 cells over-expressing CTR1D300 after 7 hours of culture under excess copper (0.02 mM CuCl2)

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented and hybridized to the Agilent-016322 Yeast (V2) Gene Expression 8x15K Microarray (Probe Name version) using the Agilent Gene Expression Hybridization Kit following the manufacturers instructions. Hybridisation was done 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).

scan_protocol: Slides were scanned immediately after washing on the Agilent microarray confocal laser scanner (G2505B) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5µm, Dye channel is set to Green and Green PMT is set to 100%, XDR was 0.10).

data_processing: The scanned images were analyzed with Feature Extraction Software (10.7.1.1, Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 016322_D_F_20100113) to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Saccharomyces cerevisiae

source_name: Dctr1, over-expressing CTR1D300, rep1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.4 ug RNA using the One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) from 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 extraction was done with glass beads using the following RNA extraction buffer: 0.1 M NaCl (DEPC treated), 10 mM EDTA (DEPC treated), 5% SDS (DEPC treated) and 50 mM Tris/HCl, pH 7.5. Next, two PCI (50:49:1 Phenol:Chloroform:Isoamylalkohol) extraction steps and one Sevag (24:1 Chloroform:Isoamylalkohol/Chloroform) extraction step was included, followed by RNA precipitation with 0.1 volume 3 M NaOAc, pH 5.2 (DEPC treated) and 3 volumes of 96% EtOH (-20 °C). RNA pellet was washed twice (75% EtOH and 100% EtOH). Isolated RNA was purified with the RNeasy MinElute Cleanup Kit (QIAGEN). RNA quantification was done using the NanoDrop Spectrophotometer ND-100 (NanoDrop Technologies, Inc., Wilmington, DE) and RNA integrity was verified by BioAnalyzer run (Agilent RNA 6000 Nano Kit, Agilent 2100 Bioanalyzer).

treatment_protocol: Overnight cultures grown in SC-leu medium were diluted to an OD600 of 0.6 in fresh SC-leu medium with 0.02 mM CuCl2. Cells were grown at 30°C and 180 rpm for 7 h.

tag: genetic background

value: ctr1-deletion over-expressing CTR1D300


title: C2C12-pMirn378_day 6_untreated_rep1

description: gene expression in differentiating C2C12-pMirn378 cells treated without BMP (myogenesis d6)

source_name: RNA from C2C12-pMirn378 cells treated without BMP (myogenesis), day 6

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


title: Dctr1_CTR1D300_rep3

source_name: Dctr1, over-expressing CTR1D300, rep3


title: C2C12-pMirn378_d0_rep1

description: gene expression in undifferentiated C2C12-pMirn378 myoblasts (day 0)

source_name: RNA from undifferentiated C2C12-pMirn378 myoblasts, day 0


title: C2C12-pMirn0_day 6_BMP2 treated_rep1

description: gene expression in differentiating C2C12-pMirn0 cells treated with BMP (osteogenesis d6)

source_name: RNA from C2C12-pMirn0 cells treated with BMP (osteogenesis), day 6


title: C2C12-pMirn378_day 3_untreated_rep2

description: gene expression in differentiating C2C12-pMirn378 cells treated without BMP (myogenesis d3)

source_name: RNA from C2C12-pMirn378 cells treated without BMP (myogenesis), day 3


title: C2C12-pMirn378_day 3_untreated_rep1


title: C2C12-pMirn0_day 6_BMP2 treated_rep2


title: WT E14.5 FL SLAM LSK 4h GSI Rep2


title: C2C12-pMirn378_d0_rep2


title: C2C12-pMirn378_day 6_untreated_rep2


title: C2C12-pMirn378_day 3_BMP2 treated_rep2


title: Dctr1_CTR1D300_rep2

source_name: Dctr1, over-expressing CTR1D300, rep2


title: C2C12-pMirn0_day 3_BMP2 treated_rep2

description: gene expression in differentiating C2C12-pMirn0 cells treated with BMP (osteogenesis d3)

source_name: RNA from C2C12-pMirn0 cells treated with BMP (osteogenesis), day 3


title: C2C12-pMirn378_day 6_BMP2 treated_rep2


title: Dctr1_Con_rep3

description: Gene expression of Dctr1 control cells after 7 hours of culture under excess copper (0.02 mM CuCl2)

source_name: Dctr1, Control, rep3


title: HD LIVER11


title: HD LIVER10


title: Dctr1_Con_rep2

source_name: Dctr1, Control, rep2


title: C2C12-pMirn378_day 6_BMP2 treated_rep3


title: C2C12-pMirn378_day 3_untreated_rep3


title: C2C12-pMirn0_day 3_BMP2 treated_rep3


title: C2C12-pMirn378_day 6_untreated_rep3


title: HD LIVER9


title: C2C12-pMirn378_day 3_BMP2 treated_rep3


title: Dctr1_Con_rep1

source_name: Dctr1, Control, rep1


title: HD LIVER7


title: HD LIVER5


title: HD LIVER6


title: C2C12-pMirn0_day 6_BMP2 treated_rep3


title: C2C12-pMirn378_d0_rep3


title: C2C12-pMirn0_day 3_BMP2 treated_rep1


title: WT_CTR1_rep2

description: Gene expression of WT cells over-expressing CTR1 after 7 hours of culture under excess copper (0.02 mM CuCl2)

source_name: WT, over-expressing CTR1, rep2

value: wild type over-expressing CTR1


title: C2C12-pMirn0_day 3_untreated_rep3

description: gene expression in differentiating C2C12-pMirn0 cells treated without BMP (myogenesis d3)

source_name: RNA from C2C12-pMirn0 cells treated without BMP (myogenesis), day 3


title: HD LIVER8


title: WT_Con_rep3

description: Gene expression of WT control cells after 7 hours of culture under excess copper (0.02 mM CuCl2)

source_name: WT, Control, rep3

value: wild type


title: C2C12-pMirn0_day 6_untreated_rep1

description: gene expression in differentiating C2C12-pMirn0 cells treated without BMP (myogenesis d6)

source_name: RNA from C2C12-pMirn0 cells treated without BMP (myogenesis), day 6


title: C2C12-pMirn0_day 6_untreated_rep3


title: HD LIVER4

source_name: fresh liver


title: WT_Con_rep2

source_name: WT, Control, rep2


title: C2C12-pMirn0_day 6_untreated_rep2


title: HD LIVER3


title: C2C12-pMirn0_day 3_untreated_rep1


title: C2C12-pMirn0_d0_rep3

description: gene expression in undifferentiated C2C12-pMirn0 myoblasts (day 0)

source_name: RNA from undifferentiated C2C12-pMirn0 myoblasts, day 0


title: WT_Con_rep1

source_name: WT, Control, rep1


title: WT_CTR1_rep3

source_name: WT, over-expressing CTR1, rep3


title: C2C12-pMirn0_d0_rep2


title: HD LIVER2


title: HD LIVER1


title: C2C12-pMirn0_day 3_untreated_rep2


title: WT_CTR1_rep1

source_name: WT, over-expressing CTR1, rep1


title: HbV LIVER20

value: HbV+ liver


title: C2C12-pMirn0_d0_rep1


title: HbV LIVER18


title: HbV LIVER19


title: HbV LIVER17


title: HbV LIVER15


title: MYCN hemizygous tumorsphere-2

city: Nagoya

first: Yuko

last: Murakami-Tonami

address: 1-1 Kanokoden, Chikusa-ku

institute: Aichi Cancer Center

description: Gene expression data from hemizygous tumorsphere

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

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

data_processing: The data were analyzed with GeneChip Operating Softwere version 1.4 (GCOS1.4, Affymetrix) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: hemizygous tumorsphere

label_protocol: Biotinylated cRNA were prepared from 40 ng total RNA with a Two-Cycle cDNA Synthesis Kit and 3'-Amplification Reagents for IVT Labeling (Affymetrix).

growth_protocol: Those mice are kept by crossing with 129+Ter/SvJcl wild-type mice (CLEA Japan).

extract_protocol: Total RNA was isolated using an Isogen reagent (Nippon Gene).

treatment_protocol: Tissues were dissected and frozen with liquid nitrogen, and homogenized with Isogen.

value: mixed 129+Ter/SvJcl

value: tumorsphere

value: MYCN Tg hemizygote


title: MYCN hemizygous tumor-4

description: Gene expression data from hemizygous tumor

source_name: hemizygous tumor

value: tumor tissue


title: Untreated-12w-6

city: Newark

first: Selvakumar

last: Subbian

state: NJ

address: 225 Warren Street

department: Medicine

institute: PHRI, NJMS, Rutgers the State University of NJ

description:
Biological replicate
New Zealand White rabbits were infected with Mtb HN878 at about 3.2log10 (on day 0).  One group of rabbits were treated with Etanercept, starting at 4 weeks post-infection, for 4 or 8 weeks (i.e, 8 or 12 weeks post infection).

hyb_protocol: standard protocol used can be found at <http://www.cag.icph.org/downloads_page.htm#LabelingProtocols> from the center for applied genomics of the Public Health Research Institute of Rutgers university was used for all the experiments

scan_protocol: The rabbit microarray slides were scanned using Agilent scanner

data_processing: Microarray data from the scanned images were extracted using the software from Agilent technologies and downstream analysis was performed using commercial software.

organism: Oryctolagus cuniculus

source_name: Lung

label_protocol: cDNA was synthesised from total RNA using First strand synthesis kit (Invitrogen) and was labelled with either Cy3 or Cy5 using the kit from the manufacturer (Agilent Technologies)

extract_protocol: Total RNA from the rabbit lungs were isolated using TRIzol reagent (Invitrogen, CA, USA) according to the instructions of the manufacturers and purified through a Qiagen RNA kit.

treatment_protocol: Lung samples were snap frozen at -80oC before isolation of total RNA (using TRIzol method)

tag: infection

value: Mtb HN878-infected

value: untreated

value: lung

value: 12 wks post infection


title: MYCN hemizygous tumorsphere-1


title: Untreated-12w-5


title: MYCN homozygous tumor-3

description: Gene expression data from homozygous tumor

source_name: homozygous tumor

value: MYCN Tg homozygote


title: WT neurosphere-2

description: Gene expression data from WT neurosphere

source_name: WT neurosphere

value: neurosphere


title: MYCN hemizygous tumor-3


title: WT neurosphere-1


title: Etanercept-12w-3

value: Etanercept


title: Etanercept-12w-6


title: Etanercept-12w-5


title: MYCN homozygous tumor-4


title: WT ganglion-4

description: Gene expression data from WT ganglion

source_name: WT ganglion

value: ganglion


title: HbV LIVER14

value: liver biopsy


title: WT ganglion-3

description: Gene expression data from WT ganglion


title: Etanercept-12w-4


title: Untreated-12w-4


title: HbV LIVER13


title: HbV LIVER12


title: HbV LIVER11


title: HbV LIVER10


title: HbV LIVER16


title: MYCN hemizygous tumor-2


title: HbV LIVER9


title: Untreated-12w-2


title: Untreated-12w-1


title: genomic DNA from pituitary macroadenoma Sample 24

city: Los Angeles

first: Chao

last: Ling

state: California

address: 1501 San Pablo street

department: Zilkha Neurogenetic Institute

institute: University of Southern California

description:
d0413
female, invasive, pituitary

hyb_protocol: One microgram of bisulphite converted DNA per sample was used for genome-scale DNA methylation profiling, which was performed in the USC Epigenome Center using the Illumina Infinium HumanMethylation450 (HM450) Beadchip platform,

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

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

source_name: pituitary macroadenoma

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA purification was processed using DNeasy Blood & Tissue kit (Qiagen) according to the standard protocols of the manufacturer.

value: pituitary macroadenoma

tag: subtype

value: NFA

tag: knosp grade

value: female

tag: tumor type

value: invasive


title: Untreated-12w-3


title: Etanercept-12w-1


title: Etanercept-12w-2


title: HbV LIVER8

value: HbV+ liver


title: Etanercept-8w-6

value: 8 wks post infection


title: MYCN hemizygous tumor-1

value: mixed 129+Ter/SvJcl

value: MYCN Tg hemizygote


title: Untreated-8w-6

value: Mtb HN878-infected


title: WT ganglion-1

description: Gene expression data from WT ganglion

value: wild type


title: MYCN homozygous ganglion-1

description: Gene expression data from homozygous ganglion

source_name: homozygous ganglion


title: MYCN homozygous ganglion-2


title: genomic DNA from pituitary macroadenoma Sample 23

description:
d1447
female, invasive, pituitary

value: ACTH

tag: age

tag: gender


title: WT ganglion-2

description: Gene expression data from WT ganglion


title: genomic DNA from pituitary macroadenoma Sample 22

description:
d1341
female, invasive, pituitary


title: genomic DNA from pituitary macroadenoma Sample 20

description:
d8277
male, invasive , pituitary

value: GH-PRL

value: male


title: HbV LIVER5


title: HbV LIVER6


title: HbV LIVER7


title: genomic DNA from pituitary macroadenoma Sample 16

description:
d8190
male, invasive , pituitary


title: genomic DNA from pituitary macroadenoma Sample 21

description:
d8447
male, invasive , pituitary


title: genomic DNA from pituitary macroadenoma Sample 18

description:
d9620
male, invasive , pituitary


title: MYCN homozygous Mdk_KO-2

description: Gene expression data from homozygous Mdk-KO tumor

source_name: homozygous Mdk-KO tumor

value: tumor tissue

value: MYCN Tg homozygote + Mdk KO


title: genomic DNA from pituitary macroadenoma Sample 17

description:
d8279
female, invasive, pituitary


title: MYCN homozygous tumor-2

value: MYCN Tg homozygote


title: HbV LIVER4

value: liver biopsy


title: HbV LIVER3


title: Untreated-8w-5

value: untreated

value: lung


title: Etanercept-8w-5

value: Etanercept


title: Etanercept-8w-4


title: Etanercept-8w-3


title: Untreated-8w-4


title: MYCN homozygous Mdk_KO-1


title: HbV LIVER2


title: genomic DNA from pituitary macroadenoma Sample 19

description:
d9988
female, invasive, pituitary

value: pituitary macroadenoma

value: NFA

value: female

value: invasive


title: Maize_Δtin2_4day_rep3

city: Marburg

first: Regine

last: Kahmann

address: Karl-von-Frisch-Strasse 10

department: Organismic Interactions

institute: Max Planck Institute for Terrestrial Microbiology

description: Gene expression data from maize leaves infected with U. maydis SG200Δtin2

hyb_protocol: Affymetrix protocols (GeneChip® Hybridization Wash and Stain Kit; Midi_Euk2V3 protocol on GeneChip Fluidics Station 450)

scan_protocol: Affymetrix protocols (scanning on Affymetrix GSC3000G)

data_processing: Partek Genomics Suite® version 6.12. Expression values were normalized using the RMA method.

organism: Zea mays

source_name: Maize seedling leaves inoculated with U. maydis SG200Δtin2

label_protocol: Affymetrix protocols (GeneChip® Hybridization Wash and Stain Kit)

growth_protocol: Maize plants (Early Golden Bantam) were grown in a phytochamber in a 15 h/9 h light/dark cycle; light period started/ended with 1 h ramping of light intensity. Temperature was 28 and 20 °C, relative humidity 40% and 60% during light and dark periods, respectively, with 1 h ramping for both values. Plants were inoculated with H2O (mock), SG200 and SG200Δtin2

extract_protocol: Fungus infected or water-inoculated tissue from 20 plants per experiment was harvested at 4 dpi by excising a section of the third leaf between 1 and 3 cm below the injection holes. For RNA extraction, material was pooled, ground to powder under liquid nitrogen and RNA was extracted with Trizol reagent (Invitrogen). RNA was purified applying the RNeasy kit (Qiagen).

treatment_protocol: 7-day-old maize young seedlings were infected with U. maydis cell suspensions (OD600=3.0).

value: Maize leaves of young seedlings


title: genomic DNA from pituitary macroadenoma Sample 12

description:
d0266
male, noninvasive, pituitary

value: noninvasive


title: Maize_Δtin2_4day_rep2


title: genomic DNA from pituitary macroadenoma Sample 10

description:
d9827
male, noninvasive, pituitary


title: genomic DNA from pituitary macroadenoma Sample 13

description:
d0628
female, invasive, pituitary


title: MYCN homozygous tumor-1

value: mixed 129+Ter/SvJcl


title: Untreated-8w-3

value: Mtb HN878-infected

value: 8 wks post infection