title: Liver from db/db F2 mouse at 5 weeks of age [158]

tag: gender

tag: insulin uiu per ml

tag: nmr lean

tag: nmr %fat

tag: mesenteric g


title: Liver from db/db F2 mouse at 5 weeks of age [150]

status: Public on Dec 29 2011

type: RNA

city: Los Angeles

first: Calvin

last: Pan

address: 675 Charles Young Dr South

country: USA

institute: UCLA

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: Expression measurements were background-adjusted, normalized, and summarized with RMA implemented in R

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: F2 mouse at 5 weeks

label_protocol: Standard Affymetrix procedures

growth_protocol: F2 mice, group housed until 5 weeks or 12 weeks of age

extract_protocol: Liver biopsy samples were snap frozen and stored at -80oC. Total RNA was extracted from the tissue using Trizol reagent (Invitrogen).

treatment_protocol: Chow diet

tag: strain

value: B57BL/6 X DBA/2

value: Male

tag: age

value: 5 weeks

tag: plasma glucose mg per dl

tag: trglycerides mg per dl

tag: total chol mg per dl

tag: hdl chol mg per dl

tag: unesterified chol mg per dl

tag: free fatty acids mg per dl

tag: bodyweight g

tag: nmr fat

tag: gonadal g

tag: retroperitoneal g

tag: subcutaneous g

tag: livernmrfat g

tag: livernmrlean g

tag: livernmr%fat


title: Liver from db/db F2 mouse at 5 weeks of age [144]

tag: gender

value: Female

tag: insulin uiu per ml

tag: nmr lean

tag: nmr %fat

tag: mesenteric g


title: Liver from db/db F2 mouse at 5 weeks of age [147]

tag: strain

tag: age

tag: plasma glucose mg per dl

tag: trglycerides mg per dl

tag: total chol mg per dl


title: Liver from db/db F2 mouse at 5 weeks of age [149]

tag: hdl chol mg per dl

tag: unesterified chol mg per dl

tag: free fatty acids mg per dl

tag: bodyweight g

tag: nmr fat


title: Liver from db/db F2 mouse at 5 weeks of age [137]

tag: gonadal g

tag: retroperitoneal g

tag: subcutaneous g

tag: livernmrfat g

tag: livernmrlean g


title: Liver from db/db F2 mouse at 5 weeks of age [134]

tag: gender

tag: insulin uiu per ml

tag: nmr lean

tag: nmr %fat

tag: livernmr%fat


title: Liver from db/db F2 mouse at 5 weeks of age [135]

tag: strain

tag: age

tag: plasma glucose mg per dl

tag: trglycerides mg per dl

tag: mesenteric g


title: female floral bud sample from September 2005, rep5

city: Monticello

first: Joshua

last: Adams

state: AR

address: PO Box 3468

department: Forest Resources

institute: University of Arkansas-Monticello

description:
female-5
Gene expression of preformed leaf tissue

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

scan_protocol: GeneChips were scanned using Genechip Scanner 3000 (Affymetrix).

data_processing: Pre-processing was done using the Robust Multichip Average using Affy package version 1.6 in the VioC 1.8 release of  Bioconductor and run in the R environment.

organism: Populus deltoides

source_name: female floral buds Populus deltoides sampled in  September 2005

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Samples were collected from a 30-year old male Populus deltoides tree growing next to a stream in August 8, 2005. Samples were collected from a 10-year old female Populus deltoides tree growing next to the same stream in September 12, 2005. Samples were taken at approximately 9am on both dates.

extract_protocol: RNA was extracted with a hot-borate method (Wan and Wilkins; 1994) followed by a Dnase I digestion and clean-up using Rneasy Mini Kit (Quigen, Valencia, CA).

treatment_protocol: NA, samples represent wild-type tissues

tag: tissue

value: bud

value: sexually mature tree

value: female

tag: collection date

value: September

tag: block


title: Liver from db/db F2 mouse at 5 weeks of age [142]

tag: total chol mg per dl

tag: hdl chol mg per dl

tag: unesterified chol mg per dl

tag: free fatty acids mg per dl

tag: bodyweight g

tag: nmr fat

tag: gonadal g

tag: retroperitoneal g


title: female floral bud sample from September 2005, rep1

description:
female-1
Gene expression of preformed leaf tissue

tag: gender


title: female floral bud sample from September 2005, rep3

description:
female-3
Gene expression of preformed leaf tissue


title: female floral bud sample from September 2005, rep4

description:
female-4
Gene expression of preformed leaf tissue


title: Liver from db/db F2 mouse at 5 weeks of age [143]

tag: strain

tag: insulin uiu per ml

tag: nmr lean

tag: nmr %fat

tag: subcutaneous g

tag: livernmrfat g

tag: livernmrlean g

tag: livernmr%fat


title: Liver from db/db F2 mouse at 5 weeks of age [130]

tag: age

tag: plasma glucose mg per dl

tag: trglycerides mg per dl

tag: total chol mg per dl

tag: mesenteric g


title: Liver from db/db F2 mouse at 5 weeks of age [140]

tag: hdl chol mg per dl

tag: unesterified chol mg per dl

tag: free fatty acids mg per dl

tag: bodyweight g

tag: nmr fat


title: Liver from db/db F2 mouse at 5 weeks of age [133]

tag: strain

tag: gender

tag: insulin uiu per ml

tag: gonadal g

tag: retroperitoneal g


title: Liver from db/db F2 mouse at 5 weeks of age [139]

tag: nmr lean

tag: nmr %fat

tag: subcutaneous g

tag: livernmrfat g

tag: livernmrlean g


title: Liver from db/db F2 mouse at 5 weeks of age [132]

tag: age

tag: plasma glucose mg per dl

tag: trglycerides mg per dl

tag: total chol mg per dl

tag: livernmr%fat


title: Liver from db/db F2 mouse at 5 weeks of age [141]

tag: hdl chol mg per dl

tag: unesterified chol mg per dl

tag: free fatty acids mg per dl

tag: bodyweight g

tag: mesenteric g


title: female floral bud sample from September 2005, rep2

description:
female-2
Gene expression of preformed leaf tissue

tag: tissue

tag: gender

tag: collection date

tag: block


title: Liver from db/db F2 mouse at 5 weeks of age [131]

tag: strain

tag: insulin uiu per ml

tag: nmr fat

tag: nmr lean

tag: nmr %fat

tag: gonadal g

tag: retroperitoneal g

tag: subcutaneous g


title: Liver from db/db F2 mouse at 5 weeks of age [136]

tag: age

tag: plasma glucose mg per dl

tag: trglycerides mg per dl

tag: total chol mg per dl

tag: hdl chol mg per dl

tag: livernmrfat g

tag: livernmrlean g

tag: livernmr%fat


title: Liver from db/db F2 mouse at 5 weeks of age [128]

tag: gender

tag: unesterified chol mg per dl

tag: free fatty acids mg per dl

tag: bodyweight g

tag: mesenteric g


title: Liver from db/db F2 mouse at 5 weeks of age [138]

tag: strain

tag: insulin uiu per ml

tag: nmr fat

tag: nmr lean

tag: nmr %fat


title: male floral bud sample from August 2005, rep5

description:
male-5
Gene expression of preformed leaf tissue

source_name: male floral buds Populus deltoides sampled in  August 2005

tag: tissue

tag: age

value: male

tag: collection date

value: August

tag: block


title: male floral bud sample from August 2005, rep1

description:
male-1
Gene expression of preformed leaf tissue


title: Liver from db/db F2 mouse at 5 weeks of age [127]

tag: plasma glucose mg per dl

tag: trglycerides mg per dl

tag: total chol mg per dl

tag: hdl chol mg per dl

tag: gonadal g

tag: retroperitoneal g

tag: subcutaneous g

tag: livernmrfat g


title: Liver from db/db F2 mouse at 5 weeks of age [125]

tag: strain

tag: gender

tag: unesterified chol mg per dl

tag: free fatty acids mg per dl

tag: bodyweight g

tag: mesenteric g

tag: livernmrlean g

tag: livernmr%fat


title: floral bud sample from August 2006, rep3

description: Gene expression of preformed leaf tissue

source_name: male floral buds Populus deltoides sampled in 2020

growth_protocol: Samples were collected from a 30-year old male Populus deltoides tree growing next to a stream. Samples were taken for months April through August at the end of the second week of the month.

tag: tissue

tag: age

tag: collection date

tag: block


title: male floral bud sample from August 2005, rep3

description:
male-3
Gene expression of preformed leaf tissue


title: male floral bud sample from August 2005, rep4

description:
male-4
Gene expression of preformed leaf tissue


title: floral bud sample from August 2006, rep1

source_name: male floral buds Populus deltoides sampled in 2018


title: Liver from db/db F2 mouse at 5 weeks of age [126]

tag: plasma glucose mg per dl

tag: insulin uiu per ml

tag: trglycerides mg per dl

tag: total chol mg per dl

tag: hdl chol mg per dl

tag: nmr fat

tag: nmr lean

tag: nmr %fat


title: Liver from db/db F2 mouse at 5 weeks of age [129]

tag: strain

tag: gender

tag: unesterified chol mg per dl

tag: free fatty acids mg per dl

tag: gonadal g

tag: retroperitoneal g

tag: subcutaneous g

tag: livernmrfat g


title: Liver from db/db F2 mouse at 5 weeks of age [123]

tag: age

tag: bodyweight g

tag: mesenteric g

tag: livernmrlean g

tag: livernmr%fat


title: floral bud sample from August 2006, rep2

source_name: male floral buds Populus deltoides sampled in 2019

tag: tissue

tag: collection date

tag: block


title: Liver from db/db F2 mouse at 5 weeks of age [124]

tag: plasma glucose mg per dl

tag: insulin uiu per ml

tag: trglycerides mg per dl

tag: total chol mg per dl

tag: hdl chol mg per dl

tag: nmr fat

tag: nmr lean

tag: nmr %fat


title: floral bud sample from July 2006, rep2

source_name: male floral buds Populus deltoides sampled in 2016

value: July


title: floral bud sample from July 2006, rep1

source_name: male floral buds Populus deltoides sampled in 2015


title: floral bud sample from June 2006, rep2

source_name: male floral buds Populus deltoides sampled in 2013

value: June


title: male floral bud sample from August 2005, rep2

description:
male-2
Gene expression of preformed leaf tissue

tag: gender


title: floral bud sample from July 2006, rep3

source_name: male floral buds Populus deltoides sampled in 2017

tag: age


title: Liver from db/db F2 mouse at 5 weeks of age [116]

tag: strain

tag: unesterified chol mg per dl

tag: free fatty acids mg per dl

tag: bodyweight g

tag: gonadal g

tag: retroperitoneal g

tag: subcutaneous g

tag: livernmrfat g


title: floral bud sample from June 2006, rep3

source_name: male floral buds Populus deltoides sampled in 2014

tag: tissue

tag: collection date

tag: block


title: floral bud sample from May 2006, rep2

source_name: male floral buds Populus deltoides sampled in 2010

value: May


title: floral bud sample from May 2006, rep1

source_name: male floral buds Populus deltoides sampled in 2009


title: floral bud sample from June 2006, rep1

source_name: male floral buds Populus deltoides sampled in 2012


title: floral bud sample from May 2006, rep3

source_name: male floral buds Populus deltoides sampled in 2011


title: Liver from db/db F2 mouse at 5 weeks of age [114]

tag: plasma glucose mg per dl

tag: insulin uiu per ml

tag: trglycerides mg per dl

tag: total chol mg per dl

tag: hdl chol mg per dl

tag: mesenteric g

tag: livernmrlean g

tag: livernmr%fat


title: Liver from db/db F2 mouse at 5 weeks of age [120]

tag: strain

tag: gender

tag: age

tag: unesterified chol mg per dl

tag: free fatty acids mg per dl

tag: nmr fat

tag: nmr lean

tag: nmr %fat


title: Liver from db/db F2 mouse at 5 weeks of age [112]

tag: bodyweight g

tag: gonadal g

tag: retroperitoneal g

tag: subcutaneous g

tag: livernmrfat g


title: Liver from db/db F2 mouse at 5 weeks of age [122]

tag: plasma glucose mg per dl

tag: insulin uiu per ml

tag: trglycerides mg per dl

tag: total chol mg per dl

tag: hdl chol mg per dl


title: Liver from db/db F2 mouse at 5 weeks of age [115]

tag: strain

tag: gender

tag: mesenteric g

tag: livernmrlean g

tag: livernmr%fat


title: Liver from db/db F2 mouse at 5 weeks of age [109]

tag: age

tag: unesterified chol mg per dl

tag: free fatty acids mg per dl

tag: nmr fat

tag: nmr lean


title: Liver from db/db F2 mouse at 5 weeks of age [106]

tag: bodyweight g

tag: nmr %fat

tag: gonadal g

tag: retroperitoneal g

tag: subcutaneous g


title: Liver from db/db F2 mouse at 5 weeks of age [121]

tag: plasma glucose mg per dl

tag: insulin uiu per ml

tag: trglycerides mg per dl

tag: total chol mg per dl

tag: livernmrfat g


title: Liver from db/db F2 mouse at 5 weeks of age [111]

tag: strain

tag: gender

tag: hdl chol mg per dl

tag: mesenteric g

tag: livernmrlean g


title: Liver from db/db F2 mouse at 5 weeks of age [102]

tag: age

tag: unesterified chol mg per dl

tag: free fatty acids mg per dl

tag: nmr fat

tag: livernmr%fat


title: Liver from db/db F2 mouse at 5 weeks of age [107]

tag: bodyweight g

tag: nmr lean

tag: nmr %fat

tag: gonadal g

tag: retroperitoneal g


title: Liver from db/db F2 mouse at 5 weeks of age [101]

tag: plasma glucose mg per dl

tag: insulin uiu per ml

tag: trglycerides mg per dl

tag: total chol mg per dl

tag: subcutaneous g


title: Liver from db/db F2 mouse at 5 weeks of age [100]

tag: strain

tag: gender

tag: hdl chol mg per dl

tag: mesenteric g

tag: livernmrfat g


title: Liver from db/db F2 mouse at 5 weeks of age [104]

tag: age

tag: unesterified chol mg per dl

tag: free fatty acids mg per dl

tag: nmr fat

tag: livernmrlean g


title: Overexpression empty vector control for CO2 leaves, Rep 3

description: Gene expression of leaf tissue

data_processing: Pre-processing was done using the Robust Multichip Average using the Affy package version 1.6 in the BioC 1.8 release of Bioconductor and run in the R environment.

organism: Populus tremula x Populus alba

source_name: leaves of 1-2 year old poplar sampled in April 2007

growth_protocol: For 35S samples, leaf tissues were collected approximately at 9 AM.  All plants were of the approximate same developmental stage and were about 2-3 year old.

tag: tissue

value: leaf

tag: line

value: juvenile tree

tag: collection date

tag: block


title: Liver from db/db F2 mouse at 5 weeks of age [99]

tag: plasma glucose mg per dl

tag: insulin uiu per ml

tag: trglycerides mg per dl

tag: bodyweight g

tag: nmr lean

tag: nmr %fat

tag: gonadal g

tag: retroperitoneal g

tag: livernmr%fat


title: Liver from db/db F2 mouse at 5 weeks of age [103]

tag: strain

tag: gender

tag: age

tag: total chol mg per dl

tag: hdl chol mg per dl

tag: unesterified chol mg per dl

tag: mesenteric g

tag: subcutaneous g

tag: livernmrfat g


title: floral bud sample from April 2006, rep3

source_name: male floral buds Populus deltoides sampled in 2008

tag: tissue

tag: collection date

value: April

tag: block


title: Liver from db/db F2 mouse at 5 weeks of age [98]

source_name: F2 mouse at 5 weeks

tag: plasma glucose mg per dl

tag: insulin uiu per ml

tag: trglycerides mg per dl

tag: free fatty acids mg per dl

tag: bodyweight g

tag: nmr fat

tag: nmr lean

tag: livernmrlean g


title: floral bud sample from April 2006, rep2

source_name: male floral buds Populus deltoides sampled in 2007

tag: age


title: Overexpression empty vector control for CO2 leaves, Rep 2

description: Gene expression of leaf tissue

tag: line


title: Liver from db/db F2 mouse at 5 weeks of age [95]

tag: strain

tag: gender

tag: total chol mg per dl

tag: hdl chol mg per dl

tag: unesterified chol mg per dl

tag: nmr %fat

tag: gonadal g

tag: retroperitoneal g

tag: livernmr%fat


title: Liver from db/db F2 mouse at 5 weeks of age [94]

tag: plasma glucose mg per dl

tag: insulin uiu per ml

tag: trglycerides mg per dl

tag: mesenteric g

tag: subcutaneous g

tag: livernmrfat g


title: Overexpression CO2, Rep 1

description: Gene expression of leaf tissue

tag: tissue

tag: age

tag: collection date

tag: block


title: floral bud sample from April 2006, rep1

source_name: male floral buds Populus deltoides sampled in 2006


title: Overexpression empty vector control for CO1 leaves, Rep 1

description: Gene expression of leaf tissue

source_name: leaves of 2-3 year old poplar sampled in May 2006

tag: line


title: Overexpression empty vector control for CO2 leaves, Rep 1

description: Gene expression of leaf tissue


title: Overexpression CO2, Rep 3

description: Gene expression of leaf tissue


title: Overexpression empty vector control for CO1 leaves, Rep 3

description: Gene expression of leaf tissue


title: Overexpression empty vector control for CO1 leaves, Rep 2

description: Gene expression of leaf tissue


title: Overexpression CO2, Rep 4

description: Gene expression of leaf tissue


title: Overexpression empty vector control for CO1 leaves, Rep 4

description: Gene expression of leaf tissue


title: Liver from db/db F2 mouse at 5 weeks of age [93]

tag: strain

tag: gender

tag: total chol mg per dl

tag: hdl chol mg per dl

tag: free fatty acids mg per dl

tag: bodyweight g

tag: nmr fat

tag: nmr lean

tag: livernmrlean g


title: Overexpression CO2, Rep 2

description: Gene expression of leaf tissue


title: Liver from db/db F2 mouse at 5 weeks of age [97]

tag: plasma glucose mg per dl

tag: insulin uiu per ml

tag: trglycerides mg per dl

tag: unesterified chol mg per dl

tag: nmr %fat

tag: gonadal g

tag: retroperitoneal g

tag: mesenteric g

tag: livernmr%fat


title: Overexpression CO1, Rep 3

description: Gene expression of leaf tissue

tag: line

tag: tissue

tag: age

tag: collection date

tag: block


title: Liver from db/db F2 mouse at 5 weeks of age [91]

tag: strain

tag: gender

tag: total chol mg per dl

tag: hdl chol mg per dl

tag: free fatty acids mg per dl

tag: bodyweight g

tag: nmr fat

tag: subcutaneous g

tag: livernmrfat g


title: Overexpression CO1, Rep 1

description: Gene expression of leaf tissue


title: normal_76006

city: Bethesda

first: Natalia

last: Shulzhenko

state: MD

address: 9000 Rockville Pike

department: Laboratory of Cellular and Molecular Immunology

institute: NIAID, USA

hyb_protocol: Test and reference samples were co-hybridized following previously described protocols (Morgun et al., 2006, PMID: 16794196)

scan_protocol: Images were scanned by GenePix4100A Scanner (Axon Instruments/Molecular Devices).

data_processing: After subtraction of local background, we used the following filtering criteria using BRB Array Tools: spots with diameter greater than 10; nonflagged spots, genes found in at least 70% of arrays. Minimal intensity cut-off was based on third quartile intensities of negative control spots. Lowess intensity-dependent normalization was used to adjust for differences in labeling intensities of the Cy3 and Cy5 dyes.

organism: Homo sapiens

source_name: normal sample

label_protocol: One microgram of total RNA were amplified in two rounds before the hybridization process, all steps following previously described protocols (Morgun et al., 2006, PMID: 16794196).

extract_protocol: Total RNA were isolated from each biopsy using TRIzol Reagent (Invitrogen) according to standard protocol.

value: normal uterine cervix

source_name: pool of tumor samples (reference)

value: pool of cervical cancer biopsies


title: Overexpression empty vector control for CO2 leaves, Rep 4

description: Gene expression of leaf tissue


title: Overexpression CO1, Rep 2

description: Gene expression of leaf tissue


title: Overexpression CO1, Rep 4

description: Gene expression of leaf tissue


title: Liver from db/db F2 mouse at 5 weeks of age [92]

value: B57BL/6 X DBA/2

value: Male

tag: plasma glucose mg per dl

tag: insulin uiu per ml

tag: trglycerides mg per dl

tag: unesterified chol mg per dl

tag: nmr lean

tag: nmr %fat

tag: gonadal g

tag: retroperitoneal g

tag: livernmrlean g


title: normal_75073

tag: tissue


title: normal_76004


title: normal_75072


title: normal_75074


title: Liver from db/db F2 mouse at 5 weeks of age [90]

tag: strain

tag: gender

tag: age

value: 5 weeks

tag: total chol mg per dl

tag: mesenteric g

tag: livernmr%fat


title: Liver from db/db F2 mouse at 5 weeks of age [83]

tag: hdl chol mg per dl

tag: free fatty acids mg per dl

tag: bodyweight g

tag: nmr fat

tag: subcutaneous g

tag: livernmrfat g


title: normal_75075


title: normal_75071


title: Liver from db/db F2 mouse at 5 weeks of age [89]

tag: plasma glucose mg per dl

tag: insulin uiu per ml

tag: trglycerides mg per dl

tag: unesterified chol mg per dl

tag: nmr lean

tag: nmr %fat


title: Liver from db/db F2 mouse at 5 weeks of age [81]

tag: strain

tag: gender

tag: gonadal g

tag: retroperitoneal g

tag: livernmrlean g


title: normal_76005

tag: tissue


title: Liver from db/db F2 mouse at 5 weeks of age [86]

value: Female

tag: age

tag: total chol mg per dl

tag: hdl chol mg per dl

tag: free fatty acids mg per dl

tag: mesenteric g

tag: livernmr%fat


title: Liver from db/db F2 mouse at 5 weeks of age [79]

tag: plasma glucose mg per dl

tag: insulin uiu per ml

tag: bodyweight g

tag: nmr fat

tag: subcutaneous g

tag: livernmrfat g


title: normal_75052


title: Liver from db/db F2 mouse at 5 weeks of age [85]

tag: strain

tag: gender

tag: trglycerides mg per dl

tag: unesterified chol mg per dl

tag: nmr lean

tag: nmr %fat


title: normal_75056

tag: tissue


title: normal_75058


title: Liver from db/db F2 mouse at 5 weeks of age [87]

tag: age

tag: total chol mg per dl

tag: hdl chol mg per dl

tag: gonadal g

tag: retroperitoneal g

tag: livernmrlean g


title: normal_75059


title: normal_75057


title: Liver from db/db F2 mouse at 5 weeks of age [82]

tag: plasma glucose mg per dl

tag: insulin uiu per ml

tag: free fatty acids mg per dl

tag: bodyweight g

tag: mesenteric g

tag: livernmr%fat


title: normal_75055


title: normal_75054


title: Liver from db/db F2 mouse at 5 weeks of age [80]

tag: strain

tag: gender

tag: trglycerides mg per dl

tag: nmr fat

tag: subcutaneous g

tag: livernmrfat g


title: Liver from db/db F2 mouse at 5 weeks of age [78]

tag: age

tag: total chol mg per dl

tag: unesterified chol mg per dl

tag: nmr lean

tag: nmr %fat


title: normal_75051

tag: tissue


title: Liver from db/db F2 mouse at 5 weeks of age [88]

tag: plasma glucose mg per dl

tag: insulin uiu per ml

tag: hdl chol mg per dl

tag: gonadal g

tag: retroperitoneal g

tag: livernmrlean g


title: Liver from db/db F2 mouse at 5 weeks of age [77]

tag: strain

tag: gender

tag: free fatty acids mg per dl

tag: bodyweight g

tag: mesenteric g

tag: livernmr%fat


title: Liver from db/db F2 mouse at 5 weeks of age [68]

tag: age

tag: trglycerides mg per dl

tag: total chol mg per dl

tag: nmr fat

tag: subcutaneous g

tag: livernmrfat g


title: normal_75047

tag: tissue


title: normal_75049


title: normal_75048


title: Liver from db/db F2 mouse at 5 weeks of age [74]

tag: plasma glucose mg per dl

tag: insulin uiu per ml

tag: hdl chol mg per dl

tag: unesterified chol mg per dl

tag: nmr lean

tag: nmr %fat


title: Liver from db/db F2 mouse at 5 weeks of age [72]

tag: strain

tag: gender

tag: free fatty acids mg per dl

tag: gonadal g

tag: retroperitoneal g

tag: livernmrlean g


title: Liver from db/db F2 mouse at 5 weeks of age [69]

tag: age

tag: trglycerides mg per dl

tag: total chol mg per dl

tag: bodyweight g

tag: mesenteric g

tag: livernmr%fat


title: Liver from db/db F2 mouse at 5 weeks of age [67]

tag: plasma glucose mg per dl

tag: insulin uiu per ml

tag: nmr fat

tag: subcutaneous g

tag: livernmrfat g


title: 4374 - MEF- 1

city: Saint Louis

first: Jianxin

last: Bao

institute: Washington University

hyb_protocol: 750ug of each aRNA in water (5ul) was suspended in Illumina “HYB” buffer (10ul) and heated to 65C for five minutes, then allowed to cool to room temperature.  The samples were applied to Mouse8v2 Expression BeadChips and hybridized at 58C for 16-20 hours at high humidity.  Arrays were washed according to Illumina standard protocol.

scan_protocol: Arrays were scanned on an Illumina BeadArray Reader.  Laser power and PMT voltage were kept constant for Cy3 scans.  Images were quantitated by Illumina Beadscan, v3.

data_processing: Quantitated data was imported into Illumina GenomeStudio software.  On-slide spot replicates were averaged by GenomeStudio and individual spot probe was reported.

source_name: MEF cells

label_protocol: Immobilized, biotinylated aRNAs were detected by staining with cy3 Steptavidin (1ug cy3-SA per 1 ml of Illumina “Block E1”) for 10 minutes at room temperature.

growth_protocol: Mouse ES, iPS and OKM cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM; Gibco, Grand Island, NY) supplemented with 15% FBS (Gibco, Grand Island, NY), 100 μM beta-mercaptoethanol, 2 mM non-essential amino acid, 2 mM L-glutamine, 2 mM HEPES, and 10 ng/ml leukemia inhibitory factor (LIF) (Chemicon, Temecula, CA) on mitomycin C-treated primary MEF cells. MEF cells were cultured in DMEM+10% FBS

extract_protocol: Total RNA was extracted by SV Total RNA Isolation kit (Promega, Madison, WI) according to the protocol described in the kit. Total RNA quality was then determined by Agilent 2100 bioanalyzer (Agilent Technologies) according to manufacturer’s recommendations.

tag: strain

tag: cell type

value: MEF cells


title: normal_75050

tag: tissue


title: Liver from db/db F2 mouse at 5 weeks of age [70]

tag: gender

tag: hdl chol mg per dl

tag: unesterified chol mg per dl

tag: free fatty acids mg per dl

tag: nmr lean

tag: nmr %fat

tag: gonadal g


title: Liver from db/db F2 mouse at 5 weeks of age [65]

tag: age

tag: trglycerides mg per dl

tag: total chol mg per dl

tag: bodyweight g

tag: retroperitoneal g

tag: mesenteric g

tag: livernmrlean g


title: 4383 - 3F-SOX2-CD1- 2

source_name: iPS cells

tag: strain

value: iPS cells


title: Liver from db/db F2 mouse at 5 weeks of age [73]

tag: plasma glucose mg per dl

tag: insulin uiu per ml

tag: nmr fat

tag: subcutaneous g

tag: livernmrfat g

tag: livernmr%fat


title: 4378 - 3F-CD1- 1

source_name: OKM cells

tag: cell type

value: OKM cells


title: Liver from db/db F2 mouse at 5 weeks of age [71]

tag: gender

tag: hdl chol mg per dl

tag: unesterified chol mg per dl

tag: free fatty acids mg per dl

tag: nmr lean

tag: nmr %fat


title: Liver from db/db F2 mouse at 5 weeks of age [66]

tag: age

tag: trglycerides mg per dl

tag: total chol mg per dl

tag: bodyweight g

tag: gonadal g

tag: retroperitoneal g


title: 4371 - R26- 2

source_name: ES cells

tag: strain

value: ES cells


title: 4385 - 3F-SOX2-CD1- 4


title: Liver from db/db F2 mouse at 5 weeks of age [64]

tag: plasma glucose mg per dl

tag: insulin uiu per ml

tag: nmr fat

tag: mesenteric g

tag: subcutaneous g

tag: livernmrlean g


title: Liver from db/db F2 mouse at 5 weeks of age [108]

tag: gender

tag: hdl chol mg per dl

tag: unesterified chol mg per dl

tag: livernmrfat g

tag: livernmr%fat


title: 4373 - R26- 4

tag: cell type


title: Liver from db/db F2 mouse at 5 weeks of age [62]

tag: age

tag: trglycerides mg per dl

tag: total chol mg per dl

tag: free fatty acids mg per dl

tag: nmr lean

tag: nmr %fat


title: Liver from db/db F2 mouse at 5 weeks of age [63]

tag: strain

tag: plasma glucose mg per dl

tag: insulin uiu per ml

tag: bodyweight g

tag: gonadal g

tag: retroperitoneal g


title: 4376 - MEF- 3


title: 4380 - 3F-CD1- 3


title: Liver from db/db F2 mouse at 5 weeks of age [60]

tag: gender

tag: hdl chol mg per dl

tag: nmr fat

tag: mesenteric g

tag: subcutaneous g

tag: livernmrlean g


title: Liver from db/db F2 mouse at 5 weeks of age [58]

tag: age

tag: trglycerides mg per dl

tag: unesterified chol mg per dl

tag: livernmrfat g

tag: livernmr%fat


title: Liver from db/db F2 mouse at 5 weeks of age [56]

tag: strain

tag: total chol mg per dl

tag: free fatty acids mg per dl

tag: nmr lean

tag: nmr %fat


title: Liver from db/db F2 mouse at 5 weeks of age [57]

tag: plasma glucose mg per dl

tag: insulin uiu per ml

tag: bodyweight g

tag: gonadal g

tag: retroperitoneal g


title: 4382 - 3F-SOX2-CD1- 1

tag: cell type


title: 4372 - R26- 5


title: 4379 - 3F-CD1- 2


title: 4370 - R26- 1


title: Liver from db/db F2 mouse at 5 weeks of age [55]

tag: gender

tag: hdl chol mg per dl

tag: nmr fat

tag: mesenteric g

tag: subcutaneous g

tag: livernmrlean g


title: 4377 - MEF- 4

tag: strain


title: EC50-4_EC10-4_F.candida_2-phenITC

city: Amsterdam

first: Elaine

last: van Ommen Kloeke

address: De Boelelaan 1085

department: Animal Ecology

country: Netherlands

institute: VU University

hyb_protocol: Agilent Gene Expression Hybridization Kit (Agilent Technologies) was used for hybridization, which was done at 65°C for 17 hours rotating at 10 rpm in an incubator. After hybridization the arrays were washed using Gene Expression Wash Buffer Kit (Agilent Technologies).

scan_protocol: The arrays were scanned on an Agilent DNA microarray scanner (Agilent Technologies), and fluorescence intensities were measured with Feature Extraction (9.1.3.1) Software (Agilent Technologies).

data_processing: Pre-processing and normalization was done using the limma package in the R (2.9.0) software environment (http://www.r-project.org/), which consisted of normexp background correction (set off = 30), loess normalization and aquantile normalization. Contrast ratios were obtained by fitting linear models using empirical Bayes methods.

organism: Folsomia candida

source_name: 2-phenylethyl ITC spiked soil - EC50 exposure

label_protocol: 500 ng input was used for amplification and labeling with the Agilent Low-Input Fluorescent Linear Amplification Kit (Agilent Technologies), according to the manufacturer’s guidelines with slightest modification that the transcription (labeling) reactions were done in half amounts of volume. Labeled/amplified cRNA was purified using RNeasy (Qiagen).

extract_protocol: Total RNA was extracted from all animals (~30) per jar, using SV Total RNA isolation System (Promega).

value: Berlin

tag: age

value: 25 days old

tag: tissue

value: Pool of approximately thirty animals

tag: treatment

value: exposed for 2 days in a jar containing LUFA 2.2 soil spiked with 2-phenylethyl isothiocyanate EC50 (10.7 nmol/g (DW)).

source_name: 2-phenylethyl ITC spiked soil - EC10 exposure

value: exposed for 2 days in a jar containing LUFA 2.2 soil spiked with 2-phenylethyl isothiocyanate EC10 (6.21 nmol/g (DW)).


title: Liver from db/db F2 mouse at 5 weeks of age [59]

tag: trglycerides mg per dl

tag: total chol mg per dl

tag: unesterified chol mg per dl

tag: free fatty acids mg per dl

tag: nmr lean

tag: nmr %fat

tag: livernmrfat g

tag: livernmr%fat


title: 4384 - 3F-SOX2-CD1- 3

tag: cell type


title: Liver from db/db F2 mouse at 5 weeks of age [50]

tag: gender

tag: plasma glucose mg per dl

tag: insulin uiu per ml

tag: hdl chol mg per dl

tag: bodyweight g

tag: nmr fat

tag: gonadal g

tag: retroperitoneal g


title: 4375 - MEF- 2

tag: strain


title: Liver from db/db F2 mouse at 5 weeks of age [53]

tag: age

tag: trglycerides mg per dl

tag: total chol mg per dl

tag: mesenteric g

tag: subcutaneous g

tag: livernmrlean g


title: Liver from db/db F2 mouse at 5 weeks of age [51]

tag: unesterified chol mg per dl

tag: free fatty acids mg per dl

tag: nmr lean

tag: nmr %fat

tag: livernmrfat g

tag: livernmr%fat


title: 4381 - 3F-CD1- 4

tag: cell type


title: Liver from db/db F2 mouse at 5 weeks of age [52]

tag: gender

tag: plasma glucose mg per dl

tag: insulin uiu per ml

tag: hdl chol mg per dl

tag: bodyweight g

tag: nmr fat


title: EC50-3_C4_F.candida_2-phenITC

tag: strain

tag: age

tag: tissue

tag: treatment

source_name: Control soil exposure

value: exposed for 2 days in a jar containing LUFA 2.2 soil non-spiked (control).


title: Liver from db/db F2 mouse at 5 weeks of age [96]

tag: trglycerides mg per dl

tag: total chol mg per dl

tag: unesterified chol mg per dl

tag: gonadal g

tag: retroperitoneal g

tag: mesenteric g

tag: subcutaneous g

tag: livernmrlean g


title: EC10-3_EC50-2_F.candida_2-phenITC


title: Liver from db/db F2 mouse at 5 weeks of age [49]

tag: gender

tag: plasma glucose mg per dl

tag: free fatty acids mg per dl

tag: nmr lean

tag: nmr %fat

tag: livernmrfat g

tag: livernmr%fat


title: Liver from db/db F2 mouse at 5 weeks of age [61]

tag: strain

tag: age

tag: insulin uiu per ml

tag: hdl chol mg per dl

tag: bodyweight g

tag: nmr fat


title: EC10-2_AC4_F.candida_2-phenITC

tag: tissue

tag: treatment

source_name: Acetone Control soil exposure

value: exposed for 2 days in a jar containing LUFA 2.2 soil spiked with only acetone (acetone control).


title: Liver from db/db F2 mouse at 5 weeks of age [47]

tag: trglycerides mg per dl

tag: total chol mg per dl

tag: unesterified chol mg per dl

tag: gonadal g

tag: retroperitoneal g

tag: mesenteric g

tag: subcutaneous g


title: Liver from db/db F2 mouse at 5 weeks of age [48]

tag: gender

tag: plasma glucose mg per dl

tag: free fatty acids mg per dl

tag: nmr lean

tag: nmr %fat

tag: livernmrfat g

tag: livernmrlean g


title: Liver from db/db F2 mouse at 5 weeks of age [44]

tag: strain

tag: age

tag: insulin uiu per ml

tag: hdl chol mg per dl

tag: bodyweight g

tag: nmr fat

tag: livernmr%fat


title: Liver from db/db F2 mouse at 5 weeks of age [45]

tag: trglycerides mg per dl

tag: total chol mg per dl

tag: unesterified chol mg per dl

tag: gonadal g

tag: retroperitoneal g


title: Liver from db/db F2 mouse at 5 weeks of age [37]

tag: gender

tag: plasma glucose mg per dl

tag: free fatty acids mg per dl

tag: mesenteric g

tag: subcutaneous g


title: AC2_C3_F.candida_2-phenITC

tag: strain

tag: tissue

tag: treatment


title: Liver from db/db F2 mouse at 5 weeks of age [46]

tag: age

tag: insulin uiu per ml

tag: hdl chol mg per dl

tag: nmr lean

tag: nmr %fat

tag: livernmrfat g

tag: livernmrlean g


title: C2_EC10-1_F.candida_2-phenITC


title: Liver from db/db F2 mouse at 5 weeks of age [41]

tag: trglycerides mg per dl

tag: total chol mg per dl

tag: unesterified chol mg per dl

tag: bodyweight g

tag: nmr fat

tag: gonadal g

tag: livernmr%fat


title: Liver from db/db F2 mouse at 5 weeks of age [38]

tag: strain

tag: gender

tag: plasma glucose mg per dl

tag: free fatty acids mg per dl

tag: retroperitoneal g

tag: mesenteric g

tag: subcutaneous g


title: Liver from db/db F2 mouse at 5 weeks of age [39]

tag: age

tag: insulin uiu per ml

tag: hdl chol mg per dl

tag: nmr lean

tag: nmr %fat


title: AC3_EC50-1_F.candida_2-phenITC

tag: tissue

tag: treatment


title: C1_AC1_F.candida_2-phenITC


title: Liver from db/db F2 mouse at 5 weeks of age [33]

tag: trglycerides mg per dl

tag: total chol mg per dl

tag: unesterified chol mg per dl

tag: bodyweight g

tag: nmr fat

tag: livernmrfat g

tag: livernmrlean g


title: Liver from db/db F2 mouse at 5 weeks of age [40]

tag: strain

tag: gender

tag: plasma glucose mg per dl

tag: free fatty acids mg per dl

tag: gonadal g

tag: retroperitoneal g

tag: livernmr%fat


title: Liver from db/db F2 mouse at 5 weeks of age [36]

tag: age

tag: insulin uiu per ml

tag: hdl chol mg per dl

tag: nmr lean

tag: nmr %fat

tag: mesenteric g

tag: subcutaneous g


title: Liver from db/db F2 mouse at 5 weeks of age [30]

tag: trglycerides mg per dl

tag: total chol mg per dl

tag: unesterified chol mg per dl

tag: bodyweight g

tag: nmr fat


title: Liver from db/db F2 mouse at 5 weeks of age [35]

tag: strain

tag: gender

tag: plasma glucose mg per dl

tag: livernmrfat g

tag: livernmrlean g


title: Liver from db/db F2 mouse at 5 weeks of age [28]

tag: age

tag: free fatty acids mg per dl

tag: gonadal g

tag: retroperitoneal g

tag: livernmr%fat


title: Liver from db/db F2 mouse at 5 weeks of age [34]

tag: insulin uiu per ml

tag: hdl chol mg per dl

tag: nmr lean

tag: nmr %fat

tag: mesenteric g


title: Ctrl siRNA 3d 1

description:
HeLa21
5937290010_I

hyb_protocol: Illumina BeadChip

scan_protocol: Illumina BeadChip

data_processing: AVG_Signal values generated by Bead studio software were imported into BRB Array Tools and median normalized before statistical comparisons

label_protocol: amplification and labeling was performed using Ambion Illumina Total Prep RNA amplification kit

extract_protocol: RNA was isolated using RNAeasy kit (Qiagen).

treatment_protocol: For siRNA-mediated downregulation of Lamp3, Hela cells were transfected with LAMP3-specific siRNA (L-004716-01; ON-TARGETplus SMARTpool) or control siRNA (D-001810-01-05; ON-TARGETplus SMARTpool) using Dharmafect 1 transfection reagent (T-2004-01, Dharmacon [Thermo Scientific]; Lafayette, CO) according to the manufacture instructions. Following the initial 24 h transfection, cells were stimulated with IFN-alpha (Roferon-A, Hoffman-LaRoche) at the concentration of 1ng/ml and grown for 24 hr, then split, re-transfected with siRNA, and fresh medium with IFN was added. Cells were incubated for additional 24 or 48 h and collected at 48 hr and 72 hr of initial stimulation with IFN.

tag: sample type

tag: cell line

value: HeLa

tag: knockdown

value: Ctrl-siRNA

tag: time

value: 3d interferon alpha

tag: treatment

value: interferon alpha


title: Liver from db/db F2 mouse at 5 weeks of age [29]

tag: strain

value: B57BL/6 X DBA/2

tag: gender

value: 5 weeks

tag: plasma glucose mg per dl

tag: trglycerides mg per dl

tag: total chol mg per dl

tag: unesterified chol mg per dl

tag: bodyweight g

tag: nmr fat

tag: subcutaneous g

tag: livernmrfat g


title: Liver from db/db F2 mouse at 5 weeks of age [22]

value: Female

tag: age

tag: insulin uiu per ml

tag: hdl chol mg per dl

tag: free fatty acids mg per dl

tag: nmr lean

tag: nmr %fat

tag: gonadal g

tag: retroperitoneal g

tag: livernmrlean g

tag: livernmr%fat


title: Liver from db/db F2 mouse at 5 weeks of age [19]

tag: strain

tag: gender

tag: plasma glucose mg per dl

tag: trglycerides mg per dl

tag: mesenteric g


title: Liver from db/db F2 mouse at 5 weeks of age [12]

value: Male

tag: total chol mg per dl

tag: unesterified chol mg per dl

tag: bodyweight g

tag: nmr fat

tag: subcutaneous g


title: Liver from db/db F2 mouse at 5 weeks of age [20]

tag: age

tag: insulin uiu per ml

tag: hdl chol mg per dl

tag: free fatty acids mg per dl

tag: livernmrfat g


title: Lamp3 KD 4d 2

description:
HeLa20
5937290010_H

tag: sample type

tag: cell line

tag: knockdown

value: LAMP-3 siRNA

tag: time

value: 4d interferon alpha

tag: treatment


title: Liver from db/db F2 mouse at 5 weeks of age [16]

tag: strain

tag: gender

tag: plasma glucose mg per dl

tag: trglycerides mg per dl

tag: nmr lean

tag: nmr %fat

tag: gonadal g

tag: retroperitoneal g

tag: livernmrlean g

tag: livernmr%fat


title: Lamp3 KD 3d 2

description:
HeLa18
5937290010_F


title: Ctrl siRNA 4d 2

description:
HeLa24
5937290010_L


title: Liver from db/db F2 mouse at 5 weeks of age [14]

tag: age

tag: insulin uiu per ml

tag: total chol mg per dl

tag: hdl chol mg per dl

tag: unesterified chol mg per dl

tag: free fatty acids mg per dl

tag: bodyweight g

tag: nmr fat

tag: mesenteric g

tag: subcutaneous g


title: Liver from db/db F2 mouse at 5 weeks of age [26]

tag: strain

tag: gender

tag: plasma glucose mg per dl

tag: trglycerides mg per dl

tag: livernmrfat g


title: Ctrl siRNA 4d 1

description:
HeLa23
5937290010_K

tag: sample type

tag: cell line

tag: knockdown

tag: time

tag: treatment


title: Liver from db/db F2 mouse at 5 weeks of age [27]

tag: age

tag: insulin uiu per ml

tag: total chol mg per dl

tag: hdl chol mg per dl

tag: nmr lean

tag: nmr %fat

tag: gonadal g

tag: retroperitoneal g

tag: livernmrlean g

tag: livernmr%fat


title: Liver from db/db F2 mouse at 5 weeks of age [6]

tag: strain

tag: gender

tag: plasma glucose mg per dl

tag: trglycerides mg per dl

tag: unesterified chol mg per dl

tag: free fatty acids mg per dl

tag: nmr fat

tag: mesenteric g

tag: subcutaneous g


title: Lamp3 KD 4d 1

description:
HeLa19
5937290010_G

tag: sample type

tag: cell line

tag: knockdown

tag: time

tag: treatment


title: Ctrl siRNA 3d 2

description:
HeLa22
5937290010_J


title: Liver from db/db F2 mouse at 5 weeks of age [5]

tag: age

tag: insulin uiu per ml

tag: total chol mg per dl

tag: hdl chol mg per dl

tag: bodyweight g

tag: nmr lean

tag: nmr %fat

tag: gonadal g

tag: retroperitoneal g

tag: livernmrfat g


title: Liver from db/db F2 mouse at 5 weeks of age [7]

tag: strain

tag: gender

tag: plasma glucose mg per dl

tag: trglycerides mg per dl

tag: unesterified chol mg per dl

tag: free fatty acids mg per dl

tag: nmr fat

tag: mesenteric g

tag: livernmrlean g

tag: livernmr%fat


title: Lamp3 KD 3d 1

description:
HeLa17
5937290010_E

tag: sample type

tag: cell line

tag: knockdown

tag: time

tag: treatment


title: Liver from db/db F2 mouse at 5 weeks of age [21]

tag: age

tag: insulin uiu per ml

tag: total chol mg per dl

tag: hdl chol mg per dl

tag: bodyweight g

tag: nmr lean

tag: nmr %fat

tag: gonadal g

tag: retroperitoneal g

tag: subcutaneous g


title: Bone_visceral bone metastasis patient 12

city: L'Aquila

first: Mattia

last: Capulli

address: Via Vetoio Coppito 2

country: Italy

institute: University of L'Aquila

hyb_protocol: 1.5 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent hUMAN 1a Microarrays (G4110B) 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), 1 minute with 37°C GE Wash buffer 2 (Agilent) and then dried with the Agilent Stabilisation and drying solution.

scan_protocol: Slides were scanned immediately after washing on the AFFYMETRIX 428 DNA Microarray Scanner using one color scan setting for 1x22k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and ).

data_processing: Jaguar Software1 version 2.0 (Affymetrix) for the acquisition of the microarray image, scanning the cy3 fluorescence. ImaGene1 Software (BioDiscovery, Inc.) to obtain background subtracted and spatially detrended Processed Signal intensities. VectorXpression1 Version 4.1 (Invitrogen) to fully analyze the microarray data.

source_name: Bone metastasis from breast cancer patient

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).  cRNA yield were checked with a classical UV-Spectrophotometer.

extract_protocol: RNA was extracted from bone biopsies of human bone metastases using TRIzol (Invitrogen) procedure following the manufacturer’s instructions, and quantified using the invitrogen Qbit kit RNA high sensitivity and the Invitrogen Qbit spectrophotometer.

tag: gender

value: female

tag: tissue

value: bone metastasis biopsy

tag: metastasis


title: Bone_only bone metastasis_9


title: CD69-activated CD4 T cells biological replicate 3

city: Ulm

first: Karlheinz

last: Holzmann

address: Helmholtzstreet 8/1

department: Medical Faculty

country: Germany

institute: Ulm University

description: gene expression data from CD69-activated CD4 T cells from the spleen of wt B6 mice

hyb_protocol: according to Affymetrix Whole Transcript (WT) Sense Target Labeling Assay

scan_protocol: according to Affymetrix protocols using a GeneChip 3000 Scanner

data_processing: Statistical analyses were carried out using R (v. 2.12.1) (R-Development-Core-Team, 2010). Arrays have been normalized using robust multiple-array average (RMA) (Gautier et al., 2004). Expression data were analyzed using Bioconductor oligo package for R (Benilton and Irizarry, 2010). Differentially expressed genes were determined by the shrinkage T-statistic (Opgen-Rhein and Strimmer, 2007).   A one-way ANOVA test (for non-parametric) data and a t-test for two unequal variances was used. P < 0.05 was considered statistically significant.

growth_protocol: 107 CD4 enriched T cells in medium containing RPMI, 10%FCS and 1% Penicilin/Streptomycin were cultured with anti-CD3/anti-CD28 coated beads (cell:bead ratio 10:1) for 72h at 37°C

extract_protocol: RNA was prepared from peletted CD4 T cells using RNAeasy mini kit  (Qiagen, Hilden, Germany)

treatment_protocol: For CD69 activation after 24h cell culturing, anti-CD69 antibody (1:200 dilution) was added and after 48h cell culturing secoundary cross-linking antibody (1:200 dilution) was also added.

tag: genotype/variation

value: wildtype

tag: cell type

value: CD69-activated CD4 T cells

tag: strain

value: spleen


title: 4472-2 E2F3 Heterozygous

city: East Lansing

first: Eran

last: Andrechek

state: MI

address: 2120 BPS Building

department: Physiology

institute: Michigan State University

hyb_protocol: The resulting biotin-labeled RNA samples were then hybridized with Affymetrix Mouse 430A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).

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

data_processing: The data were processed using Affymetrix Expression Console to generate MAS5 data.

label: Biotin

source_name: E2F3 Heterozygous

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: All tumors are from MMTV-Myc transgenics in an FVB background.

extract_protocol: Total RNA was extracted from mouse mammary tumors using the Qiagen RNeasy Midi Kit.

treatment_protocol: Tumors were flash frozen.

value: FVB

tag: genotype

value: E2F3 heterozygous

value: mammary gland tumor


title: CD69-activated CD4 T cells biological replicate 1

source_name: CD69-activated CD4 T cells from the spleen of wt B6 mice

label_protocol: Whole Transcript (WT) Sense Target Labeling Assay


title: Bone_Only_Bone_Metastasis_32

source_name: Bone Metastases from breast cancer patient


title: Bone_only_Bone_Metastasis_28

scan_protocol: Slides were scanned immediately after washing on the AFFYMETRIX 428 DNA Microarray Scanner using one color scan setting for 1x22k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green).


title: CD69-activated CD4 T cells biological replicate 2


title: 4472-3 E2F3 Heterozygous


title: wt B6 CD4 T cells biological replicate 3

description: gene expression data from CD4 T cells from the spleen of wt B6 mice

source_name: CD4T cells from the spleen of wt B6 mice

value: CD4T cells


title: 4041-4 E2F3 Heterozygous


title: 4031-1 E2F3 Heterozygous


title: CD69-/- B6 CD4 T cells biological replicate 1

description: gene expression data from CD4 T cells from the spleen of CD69-/- B6 mice

source_name: CD4T cells from the spleen of CD69-/- B6 mice


title: wt B6 CD4 T cells biological replicate 2


title: Bone_Visceral_Bone_Metastasis_26


title: 3702-1 E2F3 Heterozygous


title: 4041-1 E2F3 Heterozygous


title: 3702-2 E2F3 Heterozygous


title: 4031-3 E2F3 Heterozygous


title: 4421-1 E2F3 Heterozygous


title: 4140-3 E2F3 Heterozygous


title: 4140-1 E2F3 Heterozygous


title: CD69-/- B6 CD4 T cells biological replicate 2


title: 4032-1 E2F3 Heterozygous


title: 4472-1 E2F3 Heterozygous


title: wt B6 CD4 T cells biological replicate 1


title: 4031-2 E2F3 Heterozygous


title: CD69-/- B6 CD4 T cells biological replicate 3


title: 4040-2 E2F3 Heterozygous


title: 4013-3 E2F2 Null

source_name: E2F2 Null

value: E2F2 null


title: 4010-3 E2F2 Null


title: 4040-1 E2F3 Heterozygous


title: 4010-4 E2F2 Null


title: 3471-1 E2F3 Heterozygous


title: 4140-4 E2F3 Heterozygous


title: 4010-1 E2F2 Null


title: 4124-1 E2F2 Null


title: tumor_81564

source_name: tumor sample

value: cervical cancer biopsy

value: pool of cervical cancer biopsies


title: 4010-2 E2F2 Null


title: 4013-2 E2F2 Null


title: 4332-1 E2F2 Null


title: 3560-2 E2F2 Null


title: 4194-1 E2F3 Heterozygous


title: 4015-1 E2F2 Null


title: 4013-1 E2F2 Null


title: 4194-2 E2F3 Heterozygous


title: tumor_81565

source_name: pool of tumor samples (reference)


title: 3560-4 E2F2 Null


title: 3491-1 E2F2 Null


title: 4321-1 E2F2 Null


title: 4128-1 E2F2 Null


title: tumor_81568


title: tumor_81562


title: tumor_81561


title: tumor_81567


title: tumor_81566


title: 3491-2 E2F2 Null


title: 3560-3 E2F2 Null


title: tumor_81554


title: tumor_81557


title: tumor_81553


title: tumor_81558


title: 3497-1 E2F2 Null


title: 3497-3 E2F2 Null


title: tumor_81552


title: tumor_81551


title: tumor_81560


title: 3987-1 E2F1 Null

source_name: E2F1 Null

value: E2F1 null


title: tumor_81549


title: 3978-1 E2F1 Null


title: tumor_81550


title: tumor_81548


title: 3979-2 E2F1 Null


title: 3979-1 E2F1 Null


title: 3976-3 E2F1 Null


title: 3765-1 E2F1 Null


title: 4117-1 E2F1 Null


title: tumor_81569


title: tumor_81547


title: tumor_81559


title: 3765-2 E2F1 Null


title: tumor_76026


title: tumor_81546


title: 3975-1 E2F1 Null


title: 3985-2 E2F1 Null


title: 3500-1 E2F2 Null


title: 3895-2 E2F1 Null


title: tumor_76025


title: 3976-1 E2F1 Null


title: tumor_76019

source_name: tumor sample (pool of two samples)


title: tumor_76027


title: 4121-1 E2F1 Null


title: 3898-1 E2F1 Null


title: tumor_76016


title: tumor_76017


title: tumor_76014


title: tumor_76011


title: tumor_76028


title: tumor_76010


title: tumor_76020


title: 3274-2 E2F WT

source_name: E2F WT

value: wild-type


title: 3586-1 E2F1 Null


title: tumor_76009


title: 3587-1 E2F1 Null


title: 3886-1 E2F1 Null


title: 3894-2 E2F WT


title: 4112-2 E2F WT


title: 3886-2 E2F1 Null


title: tumor_76007


title: 4033-1 E2F WT


title: 3896-1 E2F1 Null


title: LAC5

city: Bristol

first: DAVID

last: MURPHY

state: AVON

address: Whitson Street

department: Medicine and Dentistry

country: United Kingdom

institute: University of Bristol

description: Gene expression data from 5 female rats after 11 days lactation

hyb_protocol: According to Affymetrix protocol

data_processing:
The raw data (.CEL) from each of the 24 Rat GeneChip 230 2.0 microarrays were then loaded into GeneSpring GX11 (Agilent Technologies, Stockport, UK) where it was summarized with Mas5 (which incorporates a scaling normalization) and transformed to the median of all samples. GeneSpring GX11 was also used for high-level analysis, namely principal component analysis (PCA; 34), statistical analysis, and GO exploration.
The GeneSpring-derived MAS5 data described in the publication is not included in this submission.

organism: Rattus norvegicus

source_name: 11 DAYS LACTATION

label_protocol: According to Affymetrix protocol

extract_protocol: Extracted using a Trizol based approach (see Hindmarch et al 2006 for protocol advice)

value: Sprague Dawley

tag: Sex

value: Female

tag: treatment

value: 11 DAYS LACTATION


title: 3589-1 E2F1 Null


title: LAC4


title: 3883-1 E2F WT


title: LAC3


title: CH2796

description: Gene expression data from 5 female rats after 72hours dehydration

source_name: 72 HOUR DEHYDRATED

value: 72 HOUR DEHYDRATED


title: 3880-1 E2F WT


title: 3871-1 E2F WT


title: 4112-1 E2F WT


title: 3880-3 E2F WT


title: CT4

description: Gene expression data from 5 female euhydrated control rats

source_name: EUHYDRATED CONTROL

value: EUHYDRATED CONTROL


title: 3550-1 E2F WT


title: 3880-2 E2F WT


title: 3451-1 E2F WT


title: Nodule Parenchyma rep2

city: Uji

first: Kojiro

last: Takanashi

address: Gokasho

department: Research Institute for Sustainable Humanosphere

country: Japan

institute: Kyoto University

hyb_protocol: At least 750 ng Cy3-labeled cRNA was fragmented and hybridized on a slide of Lotus japonicus 4x44K microarray at 65℃ for 17 hours. Hybridization and washing of the hybridized slide were performed according to the manufacturer’s instructions.

scan_protocol: Slides were scanned on an Agilent G2505B DNA microarray scanner.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended processed signal intensities. The processed signal intensities were log2 transformed and quantile normalized using R software.

organism: Lotus japonicus

source_name: Nodule Parencyma, replicate 2

label_protocol: One-color spike-mix was added to the total RNA prior to the labeling reaction, and labeling was performed using a Quick Amp Labeling Kit, One-Color (Agilent Technologies) in the presence of cyanine-3 (Cy3)-CTP according to the modified manufacturer’s protocol. The cyanine-3-labeled cRNA was purified by the RNeasy Mini Kit (Qiagen), and the cRNA yield was determined using the NanoDrop ND-1000 UV-VIS spectrophotomer (NanoDrop).

growth_protocol: L. japonicus MG-20 Miyakojima were grown in a cultivation chamber under a 16-h day/8-h night cycle at temperatures of 23°C. Seeds were surface-sterilized with a 1% sodium hypochloride solution for 10 min, rinsed five times with sterile distilled water, then germinated on water agar plate (0.8%). Five-day-old seedlings were transferred on sterile vermiculite with liquid 1/2 B&D medium in plant box. After 2 days plants were inoculated with M. loti MAFF303099, which had been cultured overnight in TY medium at 28°C

extract_protocol: Total RNAs were extracted from LM cells with a PicoPure RNA isolation kit (Molecular Devices) according to the instruction manual. The extracted total RNA was quantified with a Quant-iT RiboGreen RNA reagent and kit (Invitrogen) according to the manufacturer’s instructions. The quality of extracted RNA was assessed using a RNA 6000 Pico kit on an Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Nodules fixed in Farmer's fixative (EtOH : AcOH = 3 : 1) overnight at 4°C were paraffin-embedded using a microwave processor, cut to a thickness of 16 μm, and dissected by Laser Microdissection System.

value: Root Nodule Parencyma

tag: infection

value: M. loti MAFF303099

tag: cultivar

value: MG-20 Miyakojima


title: CT1


title: Nodule Parenchyma rep3

source_name: Nodule Parencyma, replicate 3


title: CT2


title: 3879-1 E2F WT

value: FVB


title: CH2792


title: Nodule Parenchyma rep1

source_name: Nodule Parencyma, replicate 1


title: LAC2


title: CH2770


title: Nodule Cortex rep2

source_name: Nodule inner cortex, replicate 2

value: Root Nodule inner cortex


title: 3885-1 E2F WT

value: mammary gland tumor


title: Nodule Cortex rep1

source_name: Nodule inner cortex, replicate 1


title: CH2793


title: CH2794


title: 3881-1 E2F WT


title: LAC1


title: 3551-1 E2F WT


title: 3883-2 E2F WT


title: Infection Zone rep3

source_name: Nodule Infection Zone, replicate 3

value: Root Nodule Infection Zone


title: CT3


title: 3872-1 E2F WT


title: Nodule Cortex rep3

source_name: Nodule inner cortex, replicate 3


title: 3449-1 E2F WT


title: Infection Zone rep1

source_name: Nodule Infection Zone, replicate 1


title: Infection Zone rep2

source_name: Nodule Infection Zone, replicate 2


title: 3275-1 E2F WT


title: Stem_LC_Rep3

status: Public on Dec 28 2011

city: Cambridge

first: Scott

last: Jelinsky

state: MA

address: 610 Main Street

department: Inflammation and Immunology

institute: Pfizer

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip RAE230 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: The data were analyzed with Microarray Suite GCOS 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: Stem Leydig Cell

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

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

value: Sprague-Dawley

value: Stem Leydig Cell


title: Stem_LC_Rep4


title: Bone_Stem_Cells_rep2

source_name: Bone Stem Cell

value: Bone Stem Cell


title: Stem_LC_Rep2


title: Immature_LC_rep1

source_name: Immature Leydig Cell

value: Immature Leydig Cell


title: Bone_Stem_Cells_rep3


title: Progenitor_LC_rep3

source_name: Progenitor Leydig Cell

value: Progenitor Leydig Cell


title: Stem_LC_Rep1


title: Stem_LC_Rep5


title: Bone_Stem_Cells_rep1


title: sphere stage zebrafish embryo_nanog-like-MO1_rep3

city: Boston

first: Cong

last: Xu

address: 1 Blackfan Circle

institute: Harvard Medical School

description:
39068902_532
It is the first of third nanog-like-MO1-injected biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed by Nimblegen using their standard protocol

scan_protocol: Scanning was performed by Nimblegen using their standard protocol

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: Danio rerio

label_protocol: Labeling was performed by Nimblegen using their standard protocol

growth_protocol: E3 fish water, 28°C

extract_protocol: RNA was extracted by Trizol reagent (Invitrogen).

tag: phenotype

value: gastrulation defect


title: Immature_LC_rep4


title: Adult_LC_rep4

source_name: Adult Leydig Cell

value: Adult Leydig Cell


title: Progenitor_LC_rep2


title: Adult_LC_rep3


title: sphere stage zebrafish embryo_control-MO_rep3

description:
39075302_532
It is the first of third control-injected biological replicates used in this experiment, each from separate cultures.

value: control-MO

value: normal


title: Progenitor_LC_rep1


title: Immature_LC_rep2


title: sphere stage zebrafish embryo_nanog-like-MO1_rep1

description:
39269802_532
It is the first of first nanog-like-MO1-injected biological replicates used in this experiment, each from separate cultures.


title: sphere stage zebrafish embryo_nanog-like-MO1_rep2

description:
39658602_532
It is the first of second nanog-like-MO1-injected biological replicates used in this experiment, each from separate cultures.


title: Adult_LC_rep2


title: sphere stage zebrafish embryo_control-MO_rep1

description:
39066902_532
It is the first of three control-injected biological replicates used in this experiment, each from separate cultures.


title: Immature_LC_rep3


title: sphere stage zebrafish embryo_control-MO_rep2

description:
39069002_532
It is the second of three control-injected biological replicates used in this experiment, each from separate cultures.


title: Adult_LC_rep1


title: Ctrl T2 [CBA mouse] biological rep4

city: Gold Coast

first: Glen

middle: C

last: Ulett

state: QLD

address: Parklands Drive

department: School of Medical Science

country: Australia

institute: Griffith University

description:
PBS2h 4-P4
P4_(MoGene-1_0-st-v1).CEL

hyb_protocol: Hybridization was performed according to the manufacturers’ instructions

scan_protocol: GeneChips were scanned using the Affymetrix 3000 7G scanner

data_processing: Raw microarray data were normalized using quantile normalization and summarized using RMA as implemented in the affy package in Bioconductor. Differentially expressed genes were identified by analyzing the data using the MAANOVA package (Wu et al., 2003) (http://www.bioconductor.org/packages/bioc/1.8/html/maanova.html)

source_name: Bladder, 2h Control

label_protocol:
Total RNA amplified into double-stranded cDNA with random hexamers tagged with a T7 promoter sequence
RNA that passed Bioanalyzer analysis was quantified and 100 ng used for cDNA synthesis. RNA-derived biotinylated sense-strand DNA was applied to the whole transcript Gene 1.0 ST Mouse Microarray and hybridization was performed according to the manufacturers’ instructions in an Affymetrix Fluidics Station 400.

growth_protocol: O/N LB culture of CFT073 UPEC at 37C was collected and concentrated into PBS by centrifugation and washes in PBS

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

treatment_protocol: Mice were catheterized using a sterile Teflon catheter and 40 microlitres of PBS containing 10^9 CFU was instilled transurethrally into the bladder. Whole bladders collected at 2h following infection

value: CBA

value: female

tag: age

value: 10 wk

value: control


title: Ctrl T2 [CBA mouse] biological rep5

description:
PBS2h 5-P5
P5_(MoGene-1_0-st-v1).CEL


title: Ctrl T2 [CBA mouse] biological rep3

description:
PBS2h 3-P3
P3_(MoGene-1_0-st-v1).CEL


title: Ctrl T2 [CBA mouse] biological rep1

description:
PBS2h 1-P1
P1_(MoGene-1_0-st-v1).CEL


title: UTI T2 [CBA mouse] biological rep4

description:
UPEC2h 4-U4
U4_(MoGene-1_0-st-v1).CEL

source_name: Bladder, 2h Infection

value: UPEC


title: UTI T2 [CBA mouse] biological rep5

description:
UPEC2h 5-U5
U5_(MoGene-1_0-st-v1).CEL


title: Ctrl T2 biological rep2

description: amplified into double-stranded cDNA with random hexamers tagged with a T7 promoter sequence

data_processing:
Raw microarray data were normalized using quantile normalization and summarized using RMA as implemented in the affy package in Bioconductor. Differentially expressed genes were identified by analyzing the data using the MAANOVA package (Wu et al., 2003) (http://www.bioconductor.org/packages/bioc/1.8/html/maanova.html)
RMA signal intensity; significant changes in gene expression identified using a shrinkage based t test together with permutation. A false discovery rate (FDR) of 0.05 was used to generate the significant gene list

label_protocol: RNA that passed Bioanalyzer analysis was quantified and 100 ng used for cDNA synthesis. RNA-derived biotinylated sense-strand DNA was applied to the whole transcript Gene 1.0 ST Mouse Microarray and hybridization was performed according to the manufacturers’ instructions in an Affymetrix Fluidics Station 400.

value: bladder


title: Ctrl T2 biological rep4


title: Ctrl T2 [CBA mouse] biological rep2

description:
PBS2h 2-P2
P2_(MoGene-1_0-st-v1).CEL


title: Ctrl T2 biological rep5


title: Ctrl T2 biological rep1


title: UTI T2 [CBA mouse] biological rep2

description:
UPEC2h 2-U2
U2_(MoGene-1_0-st-v1).CEL


title: ASML wt exosome_1

city: Heidelberg

first: Sanyukta

last: Rana

address: Im Neuenheimerfeld 365

department: Tumor Cell Biology

institute: University Hostipal Heidelberg

description: Both ASML wt exosome_1 and ASML wt exosome_2 data are from 2010-09-10_11-1388_0532.gpr

scan_protocol: done by Genomics core facility, EMBL Heidelberg using GenePix 4200A 01 Autoloader

data_processing:
The original gpr files were sorted with miRNA or the ID [sorted_*.gpr], the first sample [*_1 and *_3 samples] value corresponds to the row which appears first, and the second samples (*_2 and *_4 samples] from duplicated spot, which appears next. Both original and sorted gpr files were linked to the first (*_1 and *_3 samples) samples as Supplementary files.
Only the 346 rno_miRNA (rat miRNAs) were included in data processing/normalization.
Data was processed usng Genepix pro software at Genomix core facility, EMBL, Heidelberg.

source_name: ASML wt exosome

growth_protocol: ASML and ASML CD44v kd cells were maintained in RPMI wihout serum for 48hrs, thereafter, supernatants were collected to purify exosomes

extract_protocol: Total RNA was extracted using Trizol reagent

treatment_protocol: Exosomes were treated with 100µg/ml RNAase for 15min at 37˚C to destroy any RNA outside exosomes

tag: cell line source

value: ASML

value: wild type

value: metatsatic pancreatic adenocarcinoma


title: ASML wt exosome_3

description: Both ASML wt exosome_3 and ASML wt exosome_4 data are from 2010-09-10_11-1389_0532.gpr

hyb_protocol: done by Genomics core facility, EMBL Heidelberg


title: ASML wt exosome_2

description: Both ASML wt exosome_1 and ASML wt exosome_2 data are from 2010-09-10_11-1388_0532.gpr [available as  'ASML wt exosome_1' sample supplementary files]

label_protocol: done by Genomics core facility, EMBL Heidelberg


title: ASML CD44v kd exosome_4

description: Both ASML CD44v kd exosome_3 and ASML CD44v kd exosome_4 data are from 2010-09-10_11-1391_0532.gpr [available as  'ASML CD44v kd exosome_3' Sample Supplementary file]

source_name: ASML CD44v kd exosome

value: CD44v  knockdown


title: UTI T2 biological rep5


title: UTI T2 biological rep3


title: ASML CD44v kd exosome_2

description: Both ASML CD44v kd exosome_1 and ASML CD44v kd exosome_2 data are from 2010-09-10_11-1390_0532.gpr [available as 'ASML CD44v kd exosome_1' Sample Supplementary file]


title: ASML CD44v kd exosome_1

description: Both ASML CD44v kd exosome_1 and ASML CD44v kd exosome_2 data are from 2010-09-10_11-1390_0532.gpr


title: ASML wt exosome_4

description: Both ASML wt exosome_3 and ASML wt exosome_4 data are from 2010-09-10_11-1389_0532.gpr [available as 'ASML wt exosome_3' sample Supplementary file]


title: ASML CD44v kd exosome_3

description: Both ASML CD44v kd exosome_3 and ASML CD44v kd exosome_4 data are from 2010-09-10_11-1391_0532.gpr


title: UTI T2 [CBA mouse] biological rep3

description:
UPEC2h 3-U3
U3_(MoGene-1_0-st-v1).CEL


title: Ctrl T2 biological rep3


title: UTI T2 [CBA mouse] biological rep1

description:
UPEC2h 1-U1
U1_(MoGene-1_0-st-v1).CEL


title: UTI T2 biological rep1


title: UTI T2 biological rep2


title: UTI T2 biological rep4


title: sample 12: B12 cells kd exosomes

hyb_protocol: Standard Illumina hybridization protocol at DKFZ core facility

scan_protocol: Standard Illumina scanning protocol at DKFZ core facility

data_processing: The data were normalised at the DKFZ core facility

source_name: B12 lymph node stroma cells treated with ASML CD44v kd exosomes 24 h

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays at DKFZ core facility

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: B12 lymph node stroma cells


title: sample 10: B12 cells wt exosomes

source_name: B12 lymph node stroma cells treated with ASML exosomes 24 h


title: sample 7: B12 cells 0 treatment

source_name: B12 lymph node stroma cells


title: sample 9: B12 cells wt exosomes


title: sample 1: ASML wt exosomes

source_name: exosomes from ASML cells

value: ASML cells


title: sample 6: ASML kd exosomes

source_name: exosomes from ASML CD44v kd cells

value: ASML CD44v kd cells


title: sample 3: ASML wt exosomes


title: sample 4: ASML kd exosomes


title: sample 11: B12 cells kd exosomes


title: Negative Control siRNA, Huh7, rep2

status: Public on Dec 27 2011

first: Daekwan

last: Seo

address: 37 Convent Dr. Rm 4140

department: NCI

institute: NIH

description: Replicate 2 of 4.

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Data was processed by using Gene Expression Module v 1.1.1 in Genome Studio V2009.1 from illumina, Inc. The background noise was subtracted and quantile normalization was applied.

source_name: Huh7, control siRNA

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep RNA Amplification kit for Illumina arrays.

growth_protocol: DMEM/F - 12 (+ 10% fetal bovine serum).

extract_protocol: Total RNA was extracted with the Qiagen RNeasy Kit. Quality control and measurement were performed using NanoDrop and Agilent Bioanalyzer.

treatment_protocol: 15 nM siRNA for 48h.

tag: cell line

value: liver cancer

tag: sirna


title: CSN5 siRNA, Huh7, rep2

description: Replicate 2 of 4.

source_name: Huh7, CSN5 siRNA


title: sample 2: ASML wt exosomes


title: Negative Control siRNA, Huh7, rep4

description: Replicate 4 of 4.


title: CSN5 siRNA, Huh7, rep1

description: Replicate 1 of 4.


title: CSN5 siRNA, Huh7, rep4

description: Replicate 4 of 4.


title: LT-HSC day 2, biological replicate 2

city: Leiden

first: Martijn

middle: H

last: Brugman

address: Albinusdreef 2

department: IHB

institute: LUMC

hyb_protocol: Following fragmentation, 3.75 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to Nugen's protocols.

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

data_processing: Expression measurements were normalized and summarized using RMA in R-2.10.

source_name: LT-HSC, cultured 2 days

label_protocol: RNA was amplified using Nugen Ovation RNA amplification system V2 and labelled and fragmented using Nugen FL Ovation Biotin module v2. Fragmentation was confirmed on using an Agilent RNA 6000 nano labchip.

growth_protocol: Mouse bone marrow was collected from femurs and tibiae by crushing the bones. The cell suspension was then filtered over a 70 um filter, erythrocytes were lysed and the cells were stained for using biotinylated antibodies for lineage markers (CD127, Caltag mouse lineage mixture) as well as Sca-1 PerCPCy5.5, CD117 APC, CD34 FITC and CD135 PE all in the presence of streptavidin PECy7 and CD16/32 Fc block. After staining, cells were washed in cold PBS/1% FCS/2mM EDTA. Lineage negative, Sca-1+ CD117+ CD34- CD135- cells were sorted into Stemspan medium supplemented with 10 ng/ml mScf, 20 ng/ml mTpo, 10 ng/ml hFGF-1, 100 ng/ml hIGFBP2 and 100 ng/ml Angptl5 to a purity of >98%. After 48 hours, cells were harvested and collected in Qiagen RNeasy RLT buffer and stored at -80C.

extract_protocol: RNA was isolated using Qiagen RNeasy micro columns according to the manufacturer's instructions. RNA quality was confirmed using OD measurements on a Nanodrop spectrophotometer and using an Agilent Agilent RNA 6000 pico labchip.

value: LT-HSC (LSK, CD34-, CD135-)


title: TRANS-control vs WT-control (slide5)

city: Baton Rouge

first: Niranjan

last: Baisakh

state: LA

address: 104 Madison B Sturgis Hall

department: School of Plant, Environmental, and Soil Sciences

institute: Louisiana State University Agricultural Center

description:
Slide: Rice45K1.4.031
Pooled leaf and root tissues from one month-old seedling under hydroponics.  Vacuolar ATPase subunit c1 from halophyte grass Spartina alterniflora.

hyb_protocol: Hybridization and washing was performed as described by (Edwards et al., 2008) . Prior to hybridization, the microarray slides were 4X rehydrated at 50 °C on a water bath for ten seconds and then snap-dried at 65 °C. Next, the slides were UV cross-linked (180 mJ) in a Stratalinker (Stratagene, CA). The slides were then incubated in a 1% BSA solution in 6.6× SSC at 37°C for 40 minutes, placed in 1% SDS for five min, washed in water, and spun to dryness. The hybridization buffer was prepared using 24 μL of labeled cDNA (including both the Cy3 and Cy5 samples), 1.2 μL of 2% SDS, 3 μL of 20× SSC, and 1.8 μL of Liquid Block (Amersham Life Science, cat# 1059304). The samples were denatured for five minutes at 100 °C and placed immediately on ice. The hybridization buffer (60 ul) was loaded onto each slide under a cover slip (Lifter slip, Erie Scientific, 241x301-2-511) and incubated for 12-16 hours at 65 °C in a HYBAID mini hybridization oven. After hybridization, the slides were washed successively in three solutions (2× SSC and 0.5 % SDS at 65°C, 0.5× SSC at room temperature, and 0.2× SSC at room temperature) for five minutes each. The slides were centrifuged to dryness at 1,000 rpm for 2 minutes and scanned using a GenePix Autoloader 4200AL. The scanned images were saved as individual, 16-bit grayscale, multi-image TIFF files. The intensity values at each individual wavelength are therefore preserved for future analysis. After data extraction, the results were saved as GPR (GenePix Results) or TXT doc. files.

scan_protocol: scanned on GenePix Autoloader 4200AL

data_processing:
Normalized in 'limma' (R Project). No background adjustment. Print-tip loess using points that had less than two-fold difference within a slide (~6.3% of points dropped). Quantile method.
Normalized log ratios (cy5/cy3); p-values (P) and adjusted p-values (adjP) for effects of environment (env), genotype (genotype) and their interaction (genotypexenv)

organism: Sporobolus alterniflorus

source_name: rice plant in nutrient solution, pooled over 24h, 48h, 72h time points

label_protocol: Target preparation i.e., first strand synthesis, second strand synthesis, aRNA purification and dye labeling was performed as per the protocol described earlier (Edwards et al., 2008). For each of the four samples, 1 μg of cDNA was labeled with Cy3 or Cy5 dUTP/dCTP (Amersham Biosciences, Piscataway, NJ) followed by purification in a single spin-column (Qiagen PCR purification kit, CA), and eluted in 25 μL of water.

growth_protocol: One week seedlings germinated from wild type and transgenic rice cultivar 'Cocodrie' were transferred to Yoshida's nutrient solution and grown under 16h light: 8h dark. The solution was replenished weekly.

extract_protocol: Total RNA was extracted from salt stressed and unstressed WT (Cocodrie) and transgenic plants at different time points (24 h, 48 h, and 72 h) using RNeasy plant minikit (Qiagen, Valencia, CA).  For microarray experiment, total RNA quality was checked in gel as well as through Agilent 2100 bioanalyzer.  The RNA samples from different time points except recovery point were pooled for WT and SaVHAc1 plants for each of the four biological replications.  The four samples were named WT-Control (WT-C), WT-Stress (WT-S), SaVHAc1-rice-Control (SaVHAc1-rice-C), and SaVHAc1-rice-stress (SaVHAc1-rice-S).

treatment_protocol: One month-old rice seedlings (wild type and transgenic) were transferred to fresh solution with salt 150 mM NaCl (stress) or without salt (control). Leaf and root tissues were collected from stressed and control tissues at 0h, 24h, 48h, 72 h and four days after recovery. Samples at different time points were pooled for root and leaf separately for control and stress treatments. The treatment was replicated four times.

value: Cocodrie

value: transgenic SaVHAc1

tag: developmental stage

value: one month-old seedling

value: Pooled leaf and root

tag: stress

source_name: rice plant in water, pooled over 24h, 48h, 72h time points


title: WT-control vs TRANS-control (slide6)

description:
Slide: Rice45K1.4.032
Pooled leaf and root tissues from one month-old seedling under hydroponics.  Vacuolar ATPase subunit c1 from halophyte grass Spartina alterniflora.

tag: tissue


title: TRANS-control vs TRANS-saline (slide4)

description:
Slide: Rice45K1.4.030
Pooled leaf and root tissues from one month-old seedling under hydroponics.  Vacuolar ATPase subunit c1 from halophyte grass Spartina alterniflora.

source_name: rice plant in 150 mM NaCl conditions, pooled over 24h, 48h, 72h exposure

value: salt stress


title: Negative Control siRNA, Huh7, rep1

description: Replicate 1 of 4.

value: control


title: WT-control vs WT-saline (slide2)

description:
Slide: Rice45K1.4.028
Pooled leaf and root tissues from one month-old seedling under hydroponics.  Vacuolar ATPase subunit c1 from halophyte grass Spartina alterniflora.


title: WT-saline vs TRANS-control (slide1)

description:
Slide: Rice45K1.4.027
Pooled leaf and root tissues from one month-old seedling under hydroponics.  Vacuolar ATPase subunit c1 from halophyte grass Spartina alterniflora.


title: TRANS-saline vs WT-saline (slide8)

description:
Slide: Rice45K1.4.034
Pooled leaf and root tissues from one month-old seedling under hydroponics.  Vacuolar ATPase subunit c1 from halophyte grass Spartina alterniflora.


title: sample 8: B12 cells 0 treatment


title: WT-saline vs TRANS-saline (slide7)

description:
Slide: Rice45K1.4.033
Pooled leaf and root tissues from one month-old seedling under hydroponics.  Vacuolar ATPase subunit c1 from halophyte grass Spartina alterniflora.


title: Negative Control siRNA, Huh7, rep3

description: Replicate 3 of 4.


title: TRANS-saline vs WT-control (slide3)

description:
Slide: Rice45K1.4.029
Pooled leaf and root tissues from one month-old seedling under hydroponics.  Vacuolar ATPase subunit c1 from halophyte grass Spartina alterniflora.


title: LT-HSC day 2, biological replicate 1


title: sample 5: ASML kd exosomes


title: CSN5 siRNA, HepG2, rep4

description: Replicate 4 of 4.

source_name: HepG2, CSN5 siRNA


title: CSN5 siRNA, HepG2, rep2

description: Replicate 2 of 4.


title: CSN5 siRNA, Huh7, rep3

description: Replicate 3 of 4.


title: CSN5 siRNA, HepG2, rep3

description: Replicate 3 of 4.


title: CSN5 siRNA, HepG2, rep1

description: Replicate 1 of 4.


title: Negative Control siRNA, HepG2, rep3

description: Replicate 3 of 4.

source_name: HepG2, control siRNA


title: Negative Control siRNA, HepG2, rep1

description: Replicate 1 of 4.


title: Negative Control siRNA, HepG2, rep4

description: Replicate 4 of 4.


title: Negative Control siRNA, HepG2, rep2

description: Replicate 2 of 4.


title: Bangladesh_Site2_fish7

type: genomic

first: Charles

last: Lee

address: 221 Longwood Ave., EBRC-422

department: Pathology

institute: Brigham and Women's Hospital/Harvard Medical School

description: Native Reference vs. Native Test

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-enabled hybridization chambers. After hybridization, slides were washed sequential in Buffer 1 and Buffer 2. Buffere 3 was not used as the scanner is in an ozone hood.

scan_protocol: Scanned on an Agilent G2505C scanner. At 2 micorns.

data_processing: Normalized, background subtracted data obtained from log10 of processed Red signal/processed Green signal. Agilent software was used.

molecule: genomic DNA

source_name: Native Bangladesh Reference, Whole animal homogenate

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°C) per labeling reaction in 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: Laboratory animals were raised using standard IACUC approved methods. Native fish were captured and shipped from Bangladesh to the University of Exeter where they were raised using standarad approved culture methods

extract_protocol: standard phenol:chloroform isolation

value: Native Population-Bangladesh

source_name: Native Test, Site2 Fish7, Caudal fin clip


title: WIK_vs_TU

description: PooledWIK vs. Pooled TU

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

source_name: WIK, Equal DNA amounts from 10 whole animal homogenate

growth_protocol: Laboratory animals were raised using standard IACUC approved methods.

value: WIK

source_name: TU, Equal DNA amounts from 10 whole animal homogenate

value: TU


title: Bangladesh_Site2_fish3

description: Native Reference vs. Native Test

source_name: Native Test, Site2 Fish3, Caudal fin clip


title: Bangladesh_Site2_fish10

description: Native Reference vs. Native Test

source_name: Native Test, Site2 Fish10, Caudal fin clip


title: Bangladesh_Site1_fish9

description: Native Reference vs. Native Test

source_name: Native Test, Site1 Fish9, Caudal fin clip


title: AB_vs_TU

description: PooledAB vs. Pooled TU

source_name: AB, Equal DNA amounts from 10 whole animal homogenate

value: AB


title: Bangladesh_Site2_fish5

description: Native Reference vs. Native Test

source_name: Native Test, Site2 Fish5, Caudal fin clip


title: Bangladesh_Site2_fish4

description: Native Reference vs. Native Test

source_name: Native Test, Site2 Fish4, Caudal fin clip


title: Bangladesh_Site2_fish6

description: Native Reference vs. Native Test

source_name: Native Test, Site2 Fish6, Caudal fin clip


title: Bangladesh_Site2_fish2

description: Native Reference vs. Native Test

source_name: Native Test, Site2 Fish2, Caudal fin clip


title: Bangladesh_Site1_fish4

description: Native Reference vs. Native Test

source_name: Native Test, Site1 Fish4, Caudal fin clip


title: Bangladesh_Site1_fish1

description: Native Reference vs. Native Test

source_name: Native Test, Site1 Fish1, Caudal fin clip


title: Bangladesh_Site2_fish8

description: Native Reference vs. Native Test

source_name: Native Test, Site2 Fish8, Caudal fin clip


title: WIK_ZIRC_fish5

description: WIK Reference vs. WIK Test

source_name: WIK Reference, Whole animal homogenate

source_name: WIK Test, ZIRC5, Whole animal homogenate


title: Bangladesh_Site1_fish3

description: Native Reference vs. Native Test

source_name: Native Bangladesh Reference, Whole animal homogenate

source_name: Native Test, Site1 Fish3, Caudal fin clip


title: Bangladesh_Site1_fish5

description: Native Reference vs. Native Test

source_name: Native Test, Site1 Fish5, Caudal fin clip


title: WIK_ZIRC_fish6

description: WIK Reference vs. WIK Test

source_name: WIK Test, ZIRC6, Whole animal homogenate


title: Bangladesh_Site2_fish1

description: Native Reference vs. Native Test

source_name: Native Test, Site2 Fish1, Caudal fin clip


title: AB_vs_WIK

description: PooledAB vs. Pooled WIK

source_name: WIK, Equal DNA amounts from 10 whole animal homogenate


title: WIK_ZIRC_fish7

description: WIK Reference vs. WIK Test

source_name: WIK Test, ZIRC7, Whole animal homogenate


title: Bangladesh_Site2_fish9

description: Native Reference vs. Native Test

source_name: Native Test, Site2 Fish9, Caudal fin clip


title: Bangladesh_Site1_fish2

description: Native Reference vs. Native Test

source_name: Native Test, Site1 Fish2, Caudal fin clip


title: WIK_ZIRC_fish2

description: WIK Reference vs. WIK Test

source_name: WIK Test, ZIRC2, Whole animal homogenate


title: WIK_ZIRC_fish3

description: WIK Reference vs. WIK Test

source_name: WIK Test, ZIRC3, Whole animal homogenate


title: Bangladesh_Site1_fish8

description: Native Reference vs. Native Test

source_name: Native Test, Site1 Fish8, Caudal fin clip


title: WIK_ZIRC_fish4

description: WIK Reference vs. WIK Test

source_name: WIK Test, ZIRC4, Whole animal homogenate


title: LNCaP cells treated with R1881, replicate 4 [gene-level, IterPLIER]

city: Newcastle-upon-Tyne

first: Prabhakar

last: Rajan

address: Central Parkway

department: Institute of Human Genetics

institute: Newcastle University

description:
gene expression data following androgen treatment
David_Elliot_8.CEL

hyb_protocol: Samples were hybridized to Human Exon 1.0 ST Arrays (Affymetrix) overnight using kit materials as per the manufacturer's protocol

scan_protocol: Microarrays were scanned in an Affymetrix GCS 3000 7G scanner

data_processing:
Gene expression values were obtained by quantile-normalisation using Robust Multichip Analysis (RMA) with core probesets (228,940 probesets), and antigenomic background probes.  After summarization, the Student’s T-test was used to detect differential expression between control and treatment arrays.  Only probe sets that were detected above background (defined by detection above background; DABG P ≤ 0.01) were included in the analysis.  The False discovery rate (FDR) was calculated to make corrections of multiple testing, using the Q-value program {Storey, 2003}, with q < 0.005 taken to indicate statistical significance.  For detection of alternative splicing, the student’s T-test was performed on “normalized” probeset intensities, which were obtained by removal of core meta probeset intensities (gene level estimates) from extended probeset intensities (exon level estimates).  Iter-PLIER algorithm was used for gene level estimates, and the PLIER algorithm was used for exon level estimates {http://www.affymetrix.com/support/technical/whitepapers/,}.  To improve the accuracy of gene expression estimation, only those meta probesets with ≥ 11 core probes were used. Other genes were excluded from the analysis. 16,309 of 17,881 meta probesets passed this filtering.  After the T-test for differential splicing, the following filtering criteria were applied to identify differentially spliced probe sets:  a) The gene is expressed in both conditions and DABG P ≤0.01 at least in three replicates in each condition; b) The reliability of gene level estimates was tested by extracting the probe intensities for each meta probeset, obtaining an average across replicates for each condition, and ensuring good correlation (Pearson product-moment and Spearman’s rank correlation coefficient ≥ 0.7) between conditions; c) Gene expression between conditions should not exceed 10 fold (3.32 in the log2 scale); d) The T-test of normalized probe set intensities yields P ≤ 0.001 (or P ≤ 0.0005); e) The exon must have detectable expression at least in one condition.  More specifically, the DABG P-value at the probe set level must be ≤ 0.01 in three replicates in either condition. In addition, in this condition, the probe set intensity must be in an appropriate range compared with gene expression level (between 1/5 and 5, or -2.32 and 2.32 in the log2 scale).
probe group file: HuEx-1_0-st-v2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: LNCaP cells treated with 10nM R1881 for 24h

label_protocol: One microgram of total RNA was labelled according to the GeneChip Whole Transcript (WT) Sense Target Labelling Assay provided by the manufacturer (Affymetrix).

growth_protocol: LNCaP cells (ATCC CRL-1740) were maintained in RPMI-1640 with 10% Fetal Bovine Serum (FBS)

extract_protocol: Total RNA from treatment and control experiments (n = 8) was purified using RNeasy Plus Kit (Qiagen), which includes genomic DNA (gDNA) eliminator column to remove contaminating DNA accordingly to the manufacturer’s instructions.  Ribosomal RNA (rRNA) reduction was performed using the RiboMinus Kit (Invitrogen).  RNA quality was verified by analysis on the 2100 Bioanalyzer (Agilent).

treatment_protocol: LNCaP cells transferred into RPMI-1640 with charcoal stripped 10% FBS (devoid of steroid) for 72 hours (control) and subqeuently were treated with 10nM R1881 for 24 hours (treatment)

value: LNCaP

tag: protocol

value: grown in media devoid of steroid, and subsequently treated with 10nM R1881 synthetic androgen analogue for 24 hours


title: LNCaP cells treated with R1881, replicate 3 [gene-level, IterPLIER]

description:
gene expression data following androgen treatment
David_Elliot_7.CEL


title: Bangladesh_Site1_fish7

description: Native Reference vs. Native Test

source_name: Native Test, Site1 Fish7, Caudal fin clip


title: WIK_ZIRC_fish9

description: WIK Reference vs. WIK Test

source_name: WIK Reference, Whole animal homogenate

source_name: WIK Test, ZIRC9, Whole animal homogenate


title: Bangladesh_Site1_fish6

description: Native Reference vs. Native Test

source_name: Native Bangladesh Reference, Whole animal homogenate

source_name: Native Test, Site1 Fish6, Caudal fin clip


title: LNCaP cells treated with R1881, replicate 1 [gene-level, IterPLIER]

description:
gene expression data following androgen treatment
David_Elliot_5.CEL


title: WIK_ZIRC_fish8

description: WIK Reference vs. WIK Test

source_name: WIK Test, ZIRC8, Whole animal homogenate


title: LNCaP cells treated with R1881, replicate 2 [exon-level, RMA]

description:
gene expression data following androgen treatment
David_Elliot_6.CEL

data_processing:
Gene expression values were obtained by quantile-normalisation using Robust Multichip Analysis (RMA) with core probesets (228,940 probesets), and antigenomic background probes.  After summarization, the Student’s T-test was used to detect differential expression between control and treatment arrays.  Only probe sets that were detected above background (defined by detection above background; DABG P ≤ 0.01) were included in the analysis.  The False discovery rate (FDR) was calculated to make corrections of multiple testing, using the Q-value program {Storey, 2003}, with q < 0.005 taken to indicate statistical significance.  For detection of alternative splicing, the student’s T-test was performed on “normalized” probeset intensities, which were obtained by removal of core meta probeset intensities (gene level estimates) from extended probeset intensities (exon level estimates).  Iter-PLIER algorithm was used for gene level estimates, and the PLIER algorithm was used for exon level estimates {http://www.affymetrix.com/support/technical/whitepapers/,}.  To improve the accuracy of gene expression estimation, only those meta probesets with ≥ 11 core probes were used. Other genes were excluded from the analysis. 16,309 of 17,881 meta probesets passed this filtering.  After the T-test for differential splicing, the following filtering criteria were applied to identify differentially spliced probe sets:  a) The gene is expressed in both conditions and DABG P ≤0.01 at least in three replicates in each condition; b) The reliability of gene level estimates was tested by extracting the probe intensities for each meta probeset, obtaining an average across replicates for each condition, and ensuring good correlation (Pearson product-moment and Spearman’s rank correlation coefficient ≥ 0.7) between conditions; c) Gene expression between conditions should not exceed 10 fold (3.32 in the log2 scale); d) The T-test of normalized probe set intensities yields P ≤ 0.001 (or P ≤ 0.0005); e) The exon must have detectable expression at least in one condition.  More specifically, the DABG P-value at the probe set level must be ≤ 0.01 in three replicates in either condition. In addition, in this condition, the probe set intensity must be in an appropriate range compared with gene expression level (between 1/5 and 5, or -2.32 and 2.32 in the log2 scale).
HuEx-1_0-st-v2.pgf
HuEx-1_0-st-v2.r2.dt1.hg18.core.mps


title: LNCaP cells treated with R1881, replicate 3 [exon-level, RMA]


title: LNCaP cells treated with R1881, replicate 2 [gene-level, IterPLIER]


title: LNCaP cells treated with R1881, replicate 1 [exon-level, RMA]


title: LNCaP cells in DCC, replicate 4 [gene-level, IterPLIER]

description:
gene expression data in basal state
David_Elliot_4.CEL

source_name: LNCaP cells in DCC media

value: grown in RPMI-1640 media with charcoal-stripped 10% FBS devoid of steroids


title: LNCaP cells in DCC, replicate 3 [gene-level, IterPLIER]

description:
gene expression data in basal state
David_Elliot_3.CEL


title: LNCaP cells in DCC, replicate 2 [exon-level, RMA]

description:
gene expression data in basal state
David_Elliot_2.CEL


title: LNCaP cells treated with R1881, replicate 4 [exon-level, RMA]


title: LNCaP cells in DCC, replicate 3 [exon-level, RMA]


title: LNCaP cells in DCC, replicate 1 [exon-level, RMA]

description:
gene expression data in basal state
David_Elliot_1.CEL


title: LNCaP cells in DCC, replicate 4 [exon-level, RMA]


title: WIK_ZIRC_fish1

description: WIK Reference vs. WIK Test

source_name: WIK Test, ZIRC1, Whole animal homogenate


title: LNCaP cells in DCC, replicate 2 [gene-level, IterPLIER]


title: LNCaP cells treated with R1881, replicate 4 [exon-level, IterPLIER]


title: WIK_BostonChildrensHospital_ZonLab_Karp_Male5

description: WIK Reference vs. WIK Test

source_name: WIK Test, KarpMale5, Whole animal homogenate


title: WIK_BostonChildrensHospital_ZonLab_Karp_Male6

description: WIK Reference vs. WIK Test

source_name: WIK Test, KarpMale6, Whole animal homogenate


title: LNCaP cells treated with R1881, replicate 3 [exon-level, IterPLIER]


title: WIK_BostonChildrensHospital_ZonLab_Karp_Male3

description: WIK Reference vs. WIK Test

source_name: WIK Test, KarpMale3, Whole animal homogenate


title: LNCaP cells in DCC, replicate 1 [gene-level, IterPLIER]


title: WIK_BostonChildrensHospital_ZonLab_ender_fish8

description: WIK Reference vs. WIK Test

source_name: WIK Test, Ender8, Whole animal homogenate


title: TU_BostonChildrensHospital_ZonLab_fish9

description: Tu Reference vs. Tu Test

source_name: Tubingen Reference, Whole animal homogenate

value: Tubingen

source_name: Tu Test, Zon9, Whole animal homogenate


title: WIK_BostonChildrensHospital_ZonLab_ender_fish3

description: WIK Reference vs. WIK Test

source_name: WIK Test, Ender3, Whole animal homogenate


title: LNCaP cells treated with R1881, replicate 4 [gene-level, RMA]


title: WIK_BostonChildrensHospital_ZonLab_Karp_Male4

description: WIK Reference vs. WIK Test

source_name: WIK Test, KarpMale4, Whole animal homogenate


title: WIK_BostonChildrensHospital_ZonLab_ender_fish4

description: WIK Reference vs. WIK Test

source_name: WIK Test, Ender4, Whole animal homogenate


title: LNCaP cells treated with R1881, replicate 2 [exon-level, IterPLIER]

source_name: LNCaP cells treated with 10nM R1881 for 24h


title: TU_BostonChildrensHospital_ZonLab_fish10

description: Tu Reference vs. Tu Test

source_name: Tu Test, Zon10, Whole animal homogenate


title: WIK_BostonChildrensHospital_ZonLab_Karp_Male2

description: WIK Reference vs. WIK Test

source_name: WIK Reference, Whole animal homogenate

source_name: WIK Test, KarpMale2, Whole animal homogenate


title: WIK_BostonChildrensHospital_ZonLab_ender_fish1

description: WIK Reference vs. WIK Test

source_name: WIK Test, Ender1, Whole animal homogenate


title: WIK_BostonChildrensHospital_ZonLab_ender_fish2

description: WIK Reference vs. WIK Test

source_name: WIK Test, Ender2, Whole animal homogenate


title: LNCaP cells treated with R1881, replicate 1 [exon-level, IterPLIER]


title: LNCaP cells treated with R1881, replicate 3 [gene-level, RMA]


title: TU_BostonChildrensHospital_ZonLab_fish8

description: Tu Reference vs. Tu Test

source_name: Tu Test, Zon8, Whole animal homogenate


title: LNCaP cells treated with R1881, replicate 2 [gene-level, RMA]


title: LNCaP cells in DCC, replicate 4 [gene-level, RMA]

source_name: LNCaP cells in DCC media


title: TU_BostonChildrensHospital_ZonLab_fish7

description: Tu Reference vs. Tu Test

source_name: Tu Test, Zon7, Whole animal homogenate


title: LNCaP cells treated with R1881, replicate 1 [gene-level, RMA]


title: LNCaP cells in DCC, replicate 4 [exon-level, IterPLIER]


title: TU_BostonChildrensHospital_ZonLab_fish5

description: Tu Reference vs. Tu Test

source_name: Tu Test, Zon5, Whole animal homogenate


title: LNCaP cells in DCC, replicate 3 [gene-level, RMA]


title: LNCaP cells in DCC, replicate 2 [gene-level, RMA]


title: LNCaP cells in DCC, replicate 1 [gene-level, RMA]


title: TU_BostonChildrensHospital_ZonLab_fish6

description: Tu Reference vs. Tu Test

source_name: Tu Test, Zon6, Whole animal homogenate


title: TU_BostonChildrensHospital_ZonLab_fish3

description: Tu Reference vs. Tu Test

source_name: Tu Test, Zon3, Whole animal homogenate


title: LNCaP cells in DCC, replicate 3 [exon-level, IterPLIER]


title: TU_HuntsmanCancerCenter_TredeLab_fish9

description: Tu Reference vs. Tu Test

source_name: Tubingen Reference, Whole animal homogenate

source_name: Tu Test, Utah9, Whole animal homogenate


title: LNCaP cells in DCC, replicate 2 [exon-level, IterPLIER]


title: TU_BostonChildrensHospital_ZonLab_fish4

description: Tu Reference vs. Tu Test

source_name: Tu Test, Zon4, Whole animal homogenate


title: TU_BostonChildrensHospital_ZonLab_fish1

description: Tu Reference vs. Tu Test

source_name: Tu Test, Zon1, Whole animal homogenate


title: TU_HuntsmanCancerCenter_TredeLab_fish8

description: Tu Reference vs. Tu Test

source_name: Tu Test, Utah8, Whole animal homogenate


title: LNCaP cells in DCC, replicate 1 [exon-level, IterPLIER]


title: TU_BostonChildrensHospital_ZonLab_fish2

description: Tu Reference vs. Tu Test

source_name: Tu Test, Zon2, Whole animal homogenate


title: TU_HuntsmanCancerCenter_TredeLab_fish6

description: Tu Reference vs. Tu Test

source_name: Tu Test, Utah6, Whole animal homogenate


title: Mut-3

city: Baltimore

first: Luigi

last: Marchionni

address: 1550 Orleans St., CRB2, Room 1M52

department: Oncology

institute: Johns Hopkins University

description: No additional description available for sample: Mut-3

hyb_protocol: Following quantification and fragmentation (50-200 nucleotides in length), cRNA was hybridized for 16 hr at 45C on Human Genome U133 Plus 2.0 array. The array was then washed and stained with streptavidin?phycoerythrin using the GeneChip Fluidics Workstation 450 (Affymetrix).

scan_protocol: The gene chip was scanned using a confocal laser scanner (Affymetrix).

data_processing: The data were analyzed at the probe level with the R/Bioconductor package affy (version 1.19.0), using the RMA algorithm.

source_name: iPrEC cell line transfected with the mutant USP2A, sample: Mut-3

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 to 15 micrograms of total RNA. Double-stranded cDNA synthesis was prepared from total RNA, purified cDNA,  and then  transcribed in vitro in presence of biotinylated ribonucleotides. The labeled cRNA was then purified on an affinity resin.

growth_protocol: Immortalized androgen receptor expressing prostate epithelial cells (iPrEC) grown in specific PrEBM medium, and and selected in 1.6 ug/ml puromycin

extract_protocol: Total RNA was purified using RNAzol (Invitrogen), purified using a DNase I (Qiagen), followed by a secondary purification using the RNEasy system (Qiagen). RNA integrity was determined the Agilent 2100 Bioanalyzer. RNA samples with a RIN score of > 8.0 were profiled.

tag: type

value: Cell culture

value: iPrEC

tag: disease state

value: Expression of mutant USP2A


title: EV-3

description: No additional description available for sample: EV-3

source_name: iPrEC cell line transfected with the empty vector, sample: EV-3

value: Transfection control


title: WT-3

description: No additional description available for sample: WT-3

source_name: iPrEC cell line transfected with the wild-type USP2A, sample: WT-3

value: Expression of wild-type USP2A


title: TU_HuntsmanCancerCenter_TredeLab_fish5

description: Tu Reference vs. Tu Test

tag: strain

source_name: Tu Test, Utah5, Whole animal homogenate


title: TU_HuntsmanCancerCenter_TredeLab_fish7

description: Tu Reference vs. Tu Test

source_name: Tu Test, Utah7, Whole animal homogenate


title: WT-2

description: No additional description available for sample: WT-2

source_name: iPrEC cell line transfected with the wild-type USP2A, sample: WT-2