title: dbdb Chow_RPWAT_FGF21 PEG_0.75mpk_Day 2_REP02

description:
Gene expression data of retroperitoneal white adipose tissue (RPWAT) from db/db mice treated biweekly with low dose of PEG30-FGF21 Q108 (BIW, 0.75mpk) with tissue taken approximately 30 hours post a single dose (2day time point).
RPWAT_db_pFGF21_LD_d2_2


title: dbdb Chow_RPWAT_FGF21_Day 2_REP01

status: Public on Nov 18 2013

type: RNA

city: Boston

first: eric

last: muise

state: MA

address: 33 Ave Louis Pasteur

department: Genetics and Pharmacogenomics

country: USA

institute: Merck

description:
Gene expression data of retroperitoneal white adipose tissue (RPWAT) from db/db mice treated twice daily with wild-type FGF21 (BID, 1.25mpk) with tissue taken approximately 6 hours post last dose (2day time point).
RPWAT_db_wtFGF21_d2_1

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

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

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

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: RPWAT

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

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

tag: strain

tag: genotype/variation

value: db/db

tag: age

value: 8 weeks

tag: diet

value: chow

tag: treatment protocol

tag: time

value: 6 hrs post last dose (2day time point)

tag: tissue

value: retroperitoneal white adipose tissue


title: dbdb Chow_RPWAT_FGF21 PEG_2.5mpk_Day 2_REP02

description:
Gene expression data of retroperitoneal white adipose tissue (RPWAT) from db/db mice treated biweekly with high dose of PEG30-FGF21 Q108 (BIW, 2.5mpk) with tissue taken approximately 30 hours post a single dose (2day time point).
RPWAT_db_pFGF21_HD_d2_2

value: 30 hrs post a single dose (2day time point)


title: dbdb Chow_RPWAT_FGF21 PEG_2.5mpk_Day 2_REP05

description:
Gene expression data of retroperitoneal white adipose tissue (RPWAT) from db/db mice treated biweekly with high dose of PEG30-FGF21 Q108 (BIW, 2.5mpk) with tissue taken approximately 30 hours post a single dose (2day time point).
RPWAT_db_pFGF21_HD_d2_5


title: dbdb Chow_RPWAT_FGF21 PEG_0.75mpk_Day 2_REP03

description:
Gene expression data of retroperitoneal white adipose tissue (RPWAT) from db/db mice treated biweekly with low dose of PEG30-FGF21 Q108 (BIW, 0.75mpk) with tissue taken approximately 30 hours post a single dose (2day time point).
RPWAT_db_pFGF21_LD_d2_3


title: dbdb Chow_RPWAT_FGF21 PEG_2.5mpk_Day 5_REP03

description:
Gene expression data of retroperitoneal white adipose tissue (RPWAT) from db/db mice treated biweekly with high dose of PEG30-FGF21 Q108 (BIW, 2.5mpk) with tissue taken approximately 30 hours post the second dose (5day time point).
RPWAT_db_pFGF21_HD_d5_3

value: 30 hrs post the second dose (5day time point)


title: dbdb Chow_RPWAT_FGF21 PEG_2.5mpk_Day 2_REP03

description:
Gene expression data of retroperitoneal white adipose tissue (RPWAT) from db/db mice treated biweekly with high dose of PEG30-FGF21 Q108 (BIW, 2.5mpk) with tissue taken approximately 30 hours post a single dose (2day time point).
RPWAT_db_pFGF21_HD_d2_3


title: dbdb Chow_RPWAT_FGF21 PEG_2.5mpk_Day 5_REP05

description:
Gene expression data of retroperitoneal white adipose tissue (RPWAT) from db/db mice treated biweekly with high dose of PEG30-FGF21 Q108 (BIW, 2.5mpk) with tissue taken approximately 30 hours post the second dose (5day time point).
RPWAT_db_pFGF21_HD_d5_5


title: dbdb Chow_RPWAT_FGF21 PEG_2.5mpk_Day 5_REP01

description:
Gene expression data of retroperitoneal white adipose tissue (RPWAT) from db/db mice treated biweekly with high dose of PEG30-FGF21 Q108 (BIW, 2.5mpk) with tissue taken approximately 30 hours post the second dose (5day time point).
RPWAT_db_pFGF21_HD_d5_1


title: dbdb Chow_RPWAT_FGF21 PEG_0.75mpk_Day 5_REP01

description:
Gene expression data of retroperitoneal white adipose tissue (RPWAT) from db/db mice treated biweekly with low dose of PEG30-FGF21 Q108 (BIW, 0.75mpk) with tissue taken approximately 30 hours post the second dose (5day time point).
RPWAT_db_pFGF21_LD_d5_1


title: dbdb Chow_RPWAT_FGF21 PEG_2.5mpk_Day 2_REP04

description:
Gene expression data of retroperitoneal white adipose tissue (RPWAT) from db/db mice treated biweekly with high dose of PEG30-FGF21 Q108 (BIW, 2.5mpk) with tissue taken approximately 30 hours post a single dose (2day time point).
RPWAT_db_pFGF21_HD_d2_4


title: dbdb Chow_IWAT_vehicle_Day 5_REP04

description:
Gene expression data of inguinal white adipose tissue (IWAT) from db/db mice treated twice daily with vehicle (saline) with tissue taken approximately 6 hours post last dose (5day time point).
IWAT_db_Veh_d5_4

source_name: IWAT

value: twice daily with vehicle (saline)

value: 6 hrs post last dose (5day time point)

value: inguinal white adipose tissue


title: dbdb Chow_RPWAT_FGF21 PEG_0.75mpk_Day 5_REP03

description:
Gene expression data of retroperitoneal white adipose tissue (RPWAT) from db/db mice treated biweekly with low dose of PEG30-FGF21 Q108 (BIW, 0.75mpk) with tissue taken approximately 30 hours post the second dose (5day time point).
RPWAT_db_pFGF21_LD_d5_3


title: dbdb Chow_RPWAT_FGF21 PEG_0.75mpk_Day 5_REP05

description:
Gene expression data of retroperitoneal white adipose tissue (RPWAT) from db/db mice treated biweekly with low dose of PEG30-FGF21 Q108 (BIW, 0.75mpk) with tissue taken approximately 30 hours post the second dose (5day time point).
RPWAT_db_pFGF21_LD_d5_5


title: dbdb Chow_IWAT_vehicle_Day 5_REP05

description:
Gene expression data of inguinal white adipose tissue (IWAT) from db/db mice treated twice daily with vehicle (saline) with tissue taken approximately 6 hours post last dose (5day time point).
IWAT_db_Veh_d5_5


title: dbdb Chow_IWAT_vehicle_Day 5_REP03

description:
Gene expression data of inguinal white adipose tissue (IWAT) from db/db mice treated twice daily with vehicle (saline) with tissue taken approximately 6 hours post last dose (5day time point).
IWAT_db_Veh_d5_3


title: dbdb Chow_RPWAT_FGF21_Day 2_REP04

description:
Gene expression data of retroperitoneal white adipose tissue (RPWAT) from db/db mice treated twice daily with wild-type FGF21 (BID, 1.25mpk) with tissue taken approximately 6 hours post last dose (2day time point).
RPWAT_db_wtFGF21_d2_4


title: dbdb Chow_RPWAT_FGF21 PEG_0.75mpk_Day 2_REP05

description:
Gene expression data of retroperitoneal white adipose tissue (RPWAT) from db/db mice treated biweekly with low dose of PEG30-FGF21 Q108 (BIW, 0.75mpk) with tissue taken approximately 30 hours post a single dose (2day time point).
RPWAT_db_pFGF21_LD_d2_5


title: dbdb Chow_RPWAT_FGF21 PEG_0.75mpk_Day 2_REP01

description:
Gene expression data of retroperitoneal white adipose tissue (RPWAT) from db/db mice treated biweekly with low dose of PEG30-FGF21 Q108 (BIW, 0.75mpk) with tissue taken approximately 30 hours post a single dose (2day time point).
RPWAT_db_pFGF21_LD_d2_1


title: dbdb Chow_IWAT_vehicle_Day 2_REP05

description:
Gene expression data of inguinal white adipose tissue (IWAT) from db/db mice treated twice daily with vehicle (saline) with tissue taken approximately 6 hours post last dose (2day time point).
IWAT_db_Veh_d2_5


title: dbdb Chow_IWAT_vehicle_Day 5_REP02

description:
Gene expression data of inguinal white adipose tissue (IWAT) from db/db mice treated twice daily with vehicle (saline) with tissue taken approximately 6 hours post last dose (5day time point).
IWAT_db_Veh_d5_2


title: dbdb Chow_IWAT_vehicle_Day 2_REP01

description:
Gene expression data of inguinal white adipose tissue (IWAT) from db/db mice treated twice daily with vehicle (saline) with tissue taken approximately 6 hours post last dose (2day time point).
IWAT_db_Veh_d2_1


title: dbdb Chow_IWAT_vehicle_Day 2_REP03

description:
Gene expression data of inguinal white adipose tissue (IWAT) from db/db mice treated twice daily with vehicle (saline) with tissue taken approximately 6 hours post last dose (2day time point).
IWAT_db_Veh_d2_3


title: dbdb Chow_IWAT_FGF21_Day 2_REP02

description:
Gene expression data of inguinal white adipose tissue (IWAT) from db/db mice treated twice daily with wild-type FGF21 (BID, 1.25mpk) with tissue taken approximately 6 hours post last dose (2day time point).
IWAT_db_wtFGF21_d2_2


title: dbdb Chow_IWAT_FGF21_Day 2_REP03

description:
Gene expression data of inguinal white adipose tissue (IWAT) from db/db mice treated twice daily with wild-type FGF21 (BID, 1.25mpk) with tissue taken approximately 6 hours post last dose (2day time point).
IWAT_db_wtFGF21_d2_3


title: dbdb Chow_IWAT_FGF21_Day 5_REP03

description:
Gene expression data of inguinal white adipose tissue (IWAT) from db/db mice treated twice daily with wild-type FGF21 (BID, 1.25mpk) with tissue taken approximately 6 hours post last dose (5day time point).
IWAT_db_wtFGF21_d5_3


title: dbdb Chow_IWAT_FGF21_Day 5_REP01

description:
Gene expression data of inguinal white adipose tissue (IWAT) from db/db mice treated twice daily with wild-type FGF21 (BID, 1.25mpk) with tissue taken approximately 6 hours post last dose (5day time point).
IWAT_db_wtFGF21_d5_1


title: dbdb Chow_IWAT_vehicle_Day 2_REP04

description:
Gene expression data of inguinal white adipose tissue (IWAT) from db/db mice treated twice daily with vehicle (saline) with tissue taken approximately 6 hours post last dose (2day time point).
IWAT_db_Veh_d2_4


title: dbdb Chow_IWAT_vehicle_Day 5_REP01

description:
Gene expression data of inguinal white adipose tissue (IWAT) from db/db mice treated twice daily with vehicle (saline) with tissue taken approximately 6 hours post last dose (5day time point).
IWAT_db_Veh_d5_1


title: dbdb Chow_IWAT_FGF21 PEG_2.5mpk_Day 5_REP05

description:
Gene expression data of inguinal white adipose tissue (IWAT) from db/db mice treated biweekly with high dose of PEG30-FGF21 Q108 (BIW, 2.5mpk) with tissue taken approximately 30 hours post the second dose (5day time point).
IWAT_db_pFGF21_HD_d5_5


title: dbdb Chow_IWAT_vehicle_Day 2_REP02

description:
Gene expression data of inguinal white adipose tissue (IWAT) from db/db mice treated twice daily with vehicle (saline) with tissue taken approximately 6 hours post last dose (2day time point).
IWAT_db_Veh_d2_2


title: dbdb Chow_IWAT_FGF21_Day 2_REP01

description:
Gene expression data of inguinal white adipose tissue (IWAT) from db/db mice treated twice daily with wild-type FGF21 (BID, 1.25mpk) with tissue taken approximately 6 hours post last dose (2day time point).
IWAT_db_wtFGF21_d2_1


title: dbdb Chow_IWAT_FGF21_Day 2_REP05

description:
Gene expression data of inguinal white adipose tissue (IWAT) from db/db mice treated twice daily with wild-type FGF21 (BID, 1.25mpk) with tissue taken approximately 6 hours post last dose (2day time point).
IWAT_db_wtFGF21_d2_5


title: dbdb Chow_IWAT_FGF21_Day 2_REP04

description:
Gene expression data of inguinal white adipose tissue (IWAT) from db/db mice treated twice daily with wild-type FGF21 (BID, 1.25mpk) with tissue taken approximately 6 hours post last dose (2day time point).
IWAT_db_wtFGF21_d2_4


title: dbdb Chow_IWAT_FGF21 PEG_2.5mpk_Day 2_REP05

description:
Gene expression data of inguinal white adipose tissue (IWAT) from db/db mice treated biweekly with high dose of PEG30-FGF21 Q108 (BIW, 2.5mpk) with tissue taken approximately 30 hours post a single dose (2day time point).
IWAT_db_pFGF21_HD_d2_5


title: dbdb Chow_IWAT_FGF21_Day 5_REP05

description:
Gene expression data of inguinal white adipose tissue (IWAT) from db/db mice treated twice daily with wild-type FGF21 (BID, 1.25mpk) with tissue taken approximately 6 hours post last dose (5day time point).
IWAT_db_wtFGF21_d5_5


title: dbdb Chow_IWAT_FGF21_Day 5_REP04

description:
Gene expression data of inguinal white adipose tissue (IWAT) from db/db mice treated twice daily with wild-type FGF21 (BID, 1.25mpk) with tissue taken approximately 6 hours post last dose (5day time point).
IWAT_db_wtFGF21_d5_4


title: dbdb Chow_IWAT_FGF21 PEG_2.5mpk_Day 5_REP01

description:
Gene expression data of inguinal white adipose tissue (IWAT) from db/db mice treated biweekly with high dose of PEG30-FGF21 Q108 (BIW, 2.5mpk) with tissue taken approximately 30 hours post the second dose (5day time point).
IWAT_db_pFGF21_HD_d5_1


title: dbdb Chow_IWAT_FGF21 PEG_0.75mpk_Day 5_REP05

description:
Gene expression data of inguinal white adipose tissue (IWAT) from db/db mice treated biweekly with low dose of PEG30-FGF21 Q108 (BIW, 0.75mpk) with tissue taken approximately 30 hours post the second dose (5day time point).
IWAT_db_pFGF21_LD_d5_5


title: dbdb Chow_IWAT_FGF21 PEG_0.75mpk_Day 5_REP04

description:
Gene expression data of inguinal white adipose tissue (IWAT) from db/db mice treated biweekly with low dose of PEG30-FGF21 Q108 (BIW, 0.75mpk) with tissue taken approximately 30 hours post the second dose (5day time point).
IWAT_db_pFGF21_LD_d5_4


title: dbdb Chow_IWAT_FGF21 PEG_2.5mpk_Day 5_REP04

description:
Gene expression data of inguinal white adipose tissue (IWAT) from db/db mice treated biweekly with high dose of PEG30-FGF21 Q108 (BIW, 2.5mpk) with tissue taken approximately 30 hours post the second dose (5day time point).
IWAT_db_pFGF21_HD_d5_4


title: dbdb Chow_IWAT_FGF21 PEG_0.75mpk_Day 5_REP02

description:
Gene expression data of inguinal white adipose tissue (IWAT) from db/db mice treated biweekly with low dose of PEG30-FGF21 Q108 (BIW, 0.75mpk) with tissue taken approximately 30 hours post the second dose (5day time point).
IWAT_db_pFGF21_LD_d5_2


title: dbdb Chow_IWAT_FGF21 PEG_2.5mpk_Day 5_REP02

description:
Gene expression data of inguinal white adipose tissue (IWAT) from db/db mice treated biweekly with high dose of PEG30-FGF21 Q108 (BIW, 2.5mpk) with tissue taken approximately 30 hours post the second dose (5day time point).
IWAT_db_pFGF21_HD_d5_2


title: dbdb Chow_IWAT_FGF21 PEG_2.5mpk_Day 2_REP02

description:
Gene expression data of inguinal white adipose tissue (IWAT) from db/db mice treated biweekly with high dose of PEG30-FGF21 Q108 (BIW, 2.5mpk) with tissue taken approximately 30 hours post a single dose (2day time point).
IWAT_db_pFGF21_HD_d2_2


title: dbdb Chow_IWAT_FGF21 PEG_2.5mpk_Day 5_REP03

description:
Gene expression data of inguinal white adipose tissue (IWAT) from db/db mice treated biweekly with high dose of PEG30-FGF21 Q108 (BIW, 2.5mpk) with tissue taken approximately 30 hours post the second dose (5day time point).
IWAT_db_pFGF21_HD_d5_3


title: dbdb Chow_IWAT_FGF21 PEG_2.5mpk_Day 2_REP04

description:
Gene expression data of inguinal white adipose tissue (IWAT) from db/db mice treated biweekly with high dose of PEG30-FGF21 Q108 (BIW, 2.5mpk) with tissue taken approximately 30 hours post a single dose (2day time point).
IWAT_db_pFGF21_HD_d2_4


title: dbdb Chow_IWAT_FGF21 PEG_2.5mpk_Day 2_REP03

description:
Gene expression data of inguinal white adipose tissue (IWAT) from db/db mice treated biweekly with high dose of PEG30-FGF21 Q108 (BIW, 2.5mpk) with tissue taken approximately 30 hours post a single dose (2day time point).
IWAT_db_pFGF21_HD_d2_3


title: dbdb Chow_IWAT_FGF21 PEG_2.5mpk_Day 2_REP01

description:
Gene expression data of inguinal white adipose tissue (IWAT) from db/db mice treated biweekly with high dose of PEG30-FGF21 Q108 (BIW, 2.5mpk) with tissue taken approximately 30 hours post a single dose (2day time point).
IWAT_db_pFGF21_HD_d2_1


title: dbdb Chow_IWAT_FGF21 PEG_0.75mpk_Day 5_REP03

description:
Gene expression data of inguinal white adipose tissue (IWAT) from db/db mice treated biweekly with low dose of PEG30-FGF21 Q108 (BIW, 0.75mpk) with tissue taken approximately 30 hours post the second dose (5day time point).
IWAT_db_pFGF21_LD_d5_3


title: dbdb Chow_IWAT_FGF21 PEG_0.75mpk_Day 2_REP03

description:
Gene expression data of inguinal white adipose tissue (IWAT) from db/db mice treated biweekly with low dose of PEG30-FGF21 Q108 (BIW, 0.75mpk) with tissue taken approximately 30 hours post a single dose (2day time point).
IWAT_db_pFGF21_LD_d2_3


title: dbdb Chow_RPWAT_FGF21_Day 2_REP03

description:
Gene expression data of retroperitoneal white adipose tissue (RPWAT) from db/db mice treated twice daily with wild-type FGF21 (BID, 1.25mpk) with tissue taken approximately 6 hours post last dose (2day time point).
RPWAT_db_wtFGF21_d2_3


title: dbdb Chow_IWAT_FGF21 PEG_0.75mpk_Day 5_REP01

description:
Gene expression data of inguinal white adipose tissue (IWAT) from db/db mice treated biweekly with low dose of PEG30-FGF21 Q108 (BIW, 0.75mpk) with tissue taken approximately 30 hours post the second dose (5day time point).
IWAT_db_pFGF21_LD_d5_1


title: dbdb Chow_IWAT_FGF21 PEG_0.75mpk_Day 2_REP04

description:
Gene expression data of inguinal white adipose tissue (IWAT) from db/db mice treated biweekly with low dose of PEG30-FGF21 Q108 (BIW, 0.75mpk) with tissue taken approximately 30 hours post a single dose (2day time point).
IWAT_db_pFGF21_LD_d2_4


title: dbdb Chow_EWAT_FGF21_Day 5_REP05

description:
Gene expression data of epididymal white adipose tissue (EWAT) from db/db mice treated twice daily with wild-type FGF21 (BID, 1.25mpk) with tissue taken approximately 6 hours post last dose (5day time point).
EWAT_db_wtFGF21_d5_5

source_name: EWAT

value: epididymal white adipose tissue


title: dbdb Chow_IWAT_FGF21 PEG_0.75mpk_Day 2_REP05

description:
Gene expression data of inguinal white adipose tissue (IWAT) from db/db mice treated biweekly with low dose of PEG30-FGF21 Q108 (BIW, 0.75mpk) with tissue taken approximately 30 hours post a single dose (2day time point).
IWAT_db_pFGF21_LD_d2_5


title: dbdb Chow_EWAT_vehicle_Day 5_REP02

description:
Gene expression data of epididymal white adipose tissue (EWAT) from db/db mice treated twice daily with vehicle (saline) with tissue taken approximately 6 hours post last dose (5day time point).
EWAT_db_Veh_d5_2


title: dbdb Chow_IWAT_FGF21 PEG_0.75mpk_Day 2_REP01

description:
Gene expression data of inguinal white adipose tissue (IWAT) from db/db mice treated biweekly with low dose of PEG30-FGF21 Q108 (BIW, 0.75mpk) with tissue taken approximately 30 hours post a single dose (2day time point).
IWAT_db_pFGF21_LD_d2_1


title: dbdb Chow_EWAT_FGF21_Day 5_REP02

description:
Gene expression data of epididymal white adipose tissue (EWAT) from db/db mice treated twice daily with wild-type FGF21 (BID, 1.25mpk) with tissue taken approximately 6 hours post last dose (5day time point).
EWAT_db_wtFGF21_d5_2


title: dbdb Chow_EWAT_FGF21_Day 2_REP05

description:
Gene expression data of epididymal white adipose tissue (EWAT) from db/db mice treated twice daily with wild-type FGF21 (BID, 1.25mpk) with tissue taken approximately 6 hours post last dose (2day time point).
EWAT_db_wtFGF21_d2_5


title: dbdb Chow_EWAT_vehicle_Day 5_REP01

description:
Gene expression data of epididymal white adipose tissue (EWAT) from db/db mice treated twice daily with vehicle (saline) with tissue taken approximately 6 hours post last dose (5day time point).
EWAT_db_Veh_d5_1


title: dbdb Chow_EWAT_vehicle_Day 2_REP03

description:
Gene expression data of epididymal white adipose tissue (EWAT) from db/db mice treated twice daily with vehicle (saline) with tissue taken approximately 6 hours post last dose (2day time point).
EWAT_db_Veh_d2_3


title: dbdb Chow_EWAT_FGF21_Day 5_REP04

description:
Gene expression data of epididymal white adipose tissue (EWAT) from db/db mice treated twice daily with wild-type FGF21 (BID, 1.25mpk) with tissue taken approximately 6 hours post last dose (5day time point).
EWAT_db_wtFGF21_d5_4


title: dbdb Chow_EWAT_vehicle_Day 5_REP03

description:
Gene expression data of epididymal white adipose tissue (EWAT) from db/db mice treated twice daily with vehicle (saline) with tissue taken approximately 6 hours post last dose (5day time point).
EWAT_db_Veh_d5_3


title: dbdb Chow_EWAT_vehicle_Day 5_REP04

description:
Gene expression data of epididymal white adipose tissue (EWAT) from db/db mice treated twice daily with vehicle (saline) with tissue taken approximately 6 hours post last dose (5day time point).
EWAT_db_Veh_d5_4


title: dbdb Chow_EWAT_FGF21_Day 2_REP01

description:
Gene expression data of epididymal white adipose tissue (EWAT) from db/db mice treated twice daily with wild-type FGF21 (BID, 1.25mpk) with tissue taken approximately 6 hours post last dose (2day time point).
EWAT_db_wtFGF21_d2_1


title: dbdb Chow_EWAT_vehicle_Day 2_REP05

description:
Gene expression data of epididymal white adipose tissue (EWAT) from db/db mice treated twice daily with vehicle (saline) with tissue taken approximately 6 hours post last dose (2day time point).
EWAT_db_Veh_d2_5


title: dbdb Chow_EWAT_vehicle_Day 5_REP05

description:
Gene expression data of epididymal white adipose tissue (EWAT) from db/db mice treated twice daily with vehicle (saline) with tissue taken approximately 6 hours post last dose (5day time point).
EWAT_db_Veh_d5_5


title: dbdb Chow_EWAT_vehicle_Day 2_REP01

description:
Gene expression data of epididymal white adipose tissue (EWAT) from db/db mice treated twice daily with vehicle (saline) with tissue taken approximately 6 hours post last dose (2day time point).
EWAT_db_Veh_d2_1


title: dbdb Chow_EWAT_FGF21_Day 5_REP01

description:
Gene expression data of epididymal white adipose tissue (EWAT) from db/db mice treated twice daily with wild-type FGF21 (BID, 1.25mpk) with tissue taken approximately 6 hours post last dose (5day time point).
EWAT_db_wtFGF21_d5_1


title: dbdb Chow_EWAT_vehicle_Day 2_REP04

description:
Gene expression data of epididymal white adipose tissue (EWAT) from db/db mice treated twice daily with vehicle (saline) with tissue taken approximately 6 hours post last dose (2day time point).
EWAT_db_Veh_d2_4


title: dbdb Chow_EWAT_FGF21_Day 2_REP04

description:
Gene expression data of epididymal white adipose tissue (EWAT) from db/db mice treated twice daily with wild-type FGF21 (BID, 1.25mpk) with tissue taken approximately 6 hours post last dose (2day time point).
EWAT_db_wtFGF21_d2_4


title: dbdb Chow_EWAT_FGF21_Day 2_REP03

description:
Gene expression data of epididymal white adipose tissue (EWAT) from db/db mice treated twice daily with wild-type FGF21 (BID, 1.25mpk) with tissue taken approximately 6 hours post last dose (2day time point).
EWAT_db_wtFGF21_d2_3


title: dbdb Chow_EWAT_vehicle_Day 2_REP02

description:
Gene expression data of epididymal white adipose tissue (EWAT) from db/db mice treated twice daily with vehicle (saline) with tissue taken approximately 6 hours post last dose (2day time point).
EWAT_db_Veh_d2_2


title: dbdb Chow_IWAT_FGF21 PEG_0.75mpk_Day 2_REP02

description:
Gene expression data of inguinal white adipose tissue (IWAT) from db/db mice treated biweekly with low dose of PEG30-FGF21 Q108 (BIW, 0.75mpk) with tissue taken approximately 30 hours post a single dose (2day time point).
IWAT_db_pFGF21_LD_d2_2


title: dbdb Chow_EWAT_FGF21_Day 2_REP02

description:
Gene expression data of epididymal white adipose tissue (EWAT) from db/db mice treated twice daily with wild-type FGF21 (BID, 1.25mpk) with tissue taken approximately 6 hours post last dose (2day time point).
EWAT_db_wtFGF21_d2_2


title: dbdb Chow_EWAT_FGF21 PEG_2.5mpk_Day 5_REP04

description:
Gene expression data of epididymal white adipose tissue (EWAT) from db/db mice treated biweekly with high dose of PEG30-FGF21 Q108 (BIW, 2.5mpk) with tissue taken approximately 30 hours post the second dose (5day time point).
EWAT_db_pFGF21_HD_d5_4


title: dbdb Chow_EWAT_FGF21_Day 5_REP03

description:
Gene expression data of epididymal white adipose tissue (EWAT) from db/db mice treated twice daily with wild-type FGF21 (BID, 1.25mpk) with tissue taken approximately 6 hours post last dose (5day time point).
EWAT_db_wtFGF21_d5_3


title: dbdb Chow_EWAT_FGF21 PEG_2.5mpk_Day 5_REP05

description:
Gene expression data of epididymal white adipose tissue (EWAT) from db/db mice treated biweekly with high dose of PEG30-FGF21 Q108 (BIW, 2.5mpk) with tissue taken approximately 30 hours post the second dose (5day time point).
EWAT_db_pFGF21_HD_d5_5


title: dbdb Chow_EWAT_FGF21 PEG_2.5mpk_Day 5_REP03

description:
Gene expression data of epididymal white adipose tissue (EWAT) from db/db mice treated biweekly with high dose of PEG30-FGF21 Q108 (BIW, 2.5mpk) with tissue taken approximately 30 hours post the second dose (5day time point).
EWAT_db_pFGF21_HD_d5_3


title: dbdb Chow_EWAT_FGF21 PEG_2.5mpk_Day 2_REP04

description:
Gene expression data of epididymal white adipose tissue (EWAT) from db/db mice treated biweekly with high dose of PEG30-FGF21 Q108 (BIW, 2.5mpk) with tissue taken approximately 30 hours post a single dose (2day time point).
EWAT_db_pFGF21_HD_d2_4


title: dbdb Chow_EWAT_FGF21 PEG_0.75mpk_Day 5_REP04

description:
Gene expression data of epididymal white adipose tissue (EWAT) from db/db mice treated biweekly with low dose of PEG30-FGF21 Q108 (BIW, 0.75mpk) with tissue taken approximately 30 hours post the second dose (5day time point).
EWAT_db_pFGF21_LD_d5_4


title: dbdb Chow_EWAT_FGF21 PEG_0.75mpk_Day 2_REP03

description:
Gene expression data of epididymal white adipose tissue (EWAT) from db/db mice treated biweekly with low dose of PEG30-FGF21 Q108 (BIW, 0.75mpk) with tissue taken approximately 30 hours post a single dose (2day time point).
EWAT_db_pFGF21_LD_d2_3


title: dbdb Chow_EWAT_FGF21 PEG_2.5mpk_Day 5_REP01

description:
Gene expression data of epididymal white adipose tissue (EWAT) from db/db mice treated biweekly with high dose of PEG30-FGF21 Q108 (BIW, 2.5mpk) with tissue taken approximately 30 hours post the second dose (5day time point).
EWAT_db_pFGF21_HD_d5_1


title: dbdb Chow_EWAT_FGF21 PEG_2.5mpk_Day 2_REP03

description:
Gene expression data of epididymal white adipose tissue (EWAT) from db/db mice treated biweekly with high dose of PEG30-FGF21 Q108 (BIW, 2.5mpk) with tissue taken approximately 30 hours post a single dose (2day time point).
EWAT_db_pFGF21_HD_d2_3


title: dbdb Chow_EWAT_FGF21 PEG_2.5mpk_Day 2_REP05

description:
Gene expression data of epididymal white adipose tissue (EWAT) from db/db mice treated biweekly with high dose of PEG30-FGF21 Q108 (BIW, 2.5mpk) with tissue taken approximately 30 hours post a single dose (2day time point).
EWAT_db_pFGF21_HD_d2_5


title: dbdb Chow_EWAT_FGF21 PEG_0.75mpk_Day 5_REP01

description:
Gene expression data of epididymal white adipose tissue (EWAT) from db/db mice treated biweekly with low dose of PEG30-FGF21 Q108 (BIW, 0.75mpk) with tissue taken approximately 30 hours post the second dose (5day time point).
EWAT_db_pFGF21_LD_d5_1


title: dbdb Chow_EWAT_FGF21 PEG_2.5mpk_Day 5_REP02

description:
Gene expression data of epididymal white adipose tissue (EWAT) from db/db mice treated biweekly with high dose of PEG30-FGF21 Q108 (BIW, 2.5mpk) with tissue taken approximately 30 hours post the second dose (5day time point).
EWAT_db_pFGF21_HD_d5_2


title: dbdb Chow_EWAT_FGF21 PEG_2.5mpk_Day 2_REP01

description:
Gene expression data of epididymal white adipose tissue (EWAT) from db/db mice treated biweekly with high dose of PEG30-FGF21 Q108 (BIW, 2.5mpk) with tissue taken approximately 30 hours post a single dose (2day time point).
EWAT_db_pFGF21_HD_d2_1


title: dbdb Chow_EWAT_FGF21 PEG_0.75mpk_Day 5_REP02

description:
Gene expression data of epididymal white adipose tissue (EWAT) from db/db mice treated biweekly with low dose of PEG30-FGF21 Q108 (BIW, 0.75mpk) with tissue taken approximately 30 hours post the second dose (5day time point).
EWAT_db_pFGF21_LD_d5_2


title: dbdb Chow_EWAT_FGF21 PEG_0.75mpk_Day 5_REP03

description:
Gene expression data of epididymal white adipose tissue (EWAT) from db/db mice treated biweekly with low dose of PEG30-FGF21 Q108 (BIW, 0.75mpk) with tissue taken approximately 30 hours post the second dose (5day time point).
EWAT_db_pFGF21_LD_d5_3


title: dbdb Chow_BAT_vehicle_Day 5_REP04

description:
Gene expression data of brown adipose tissue (BAT) from db/db mice treated twice daily with vehicle (saline) with tissue taken approximately 6 hours post last dose (5day time point).
BAT_db_Veh_d5_4

source_name: BAT

value: brown adipose tissue


title: dbdb Chow_BAT_vehicle_Day 5_REP05

description:
Gene expression data of brown adipose tissue (BAT) from db/db mice treated twice daily with vehicle (saline) with tissue taken approximately 6 hours post last dose (5day time point).
BAT_db_Veh_d5_5


title: dbdb Chow_EWAT_FGF21 PEG_2.5mpk_Day 2_REP02

description:
Gene expression data of epididymal white adipose tissue (EWAT) from db/db mice treated biweekly with high dose of PEG30-FGF21 Q108 (BIW, 2.5mpk) with tissue taken approximately 30 hours post a single dose (2day time point).
EWAT_db_pFGF21_HD_d2_2


title: dbdb Chow_BAT_vehicle_Day 2_REP04

description:
Gene expression data of brown adipose tissue (BAT) from db/db mice treated twice daily with vehicle (saline) with tissue taken approximately 6 hours post last dose (2day time point).
BAT_db_Veh_d2_4


title: dbdb Chow_EWAT_FGF21 PEG_0.75mpk_Day 2_REP05

description:
Gene expression data of epididymal white adipose tissue (EWAT) from db/db mice treated biweekly with low dose of PEG30-FGF21 Q108 (BIW, 0.75mpk) with tissue taken approximately 30 hours post a single dose (2day time point).
EWAT_db_pFGF21_LD_d2_5


title: dbdb Chow_BAT_vehicle_Day 2_REP05

description:
Gene expression data of brown adipose tissue (BAT) from db/db mice treated twice daily with vehicle (saline) with tissue taken approximately 6 hours post last dose (2day time point).
BAT_db_Veh_d2_5


title: dbdb Chow_EWAT_FGF21 PEG_0.75mpk_Day 5_REP05

description:
Gene expression data of epididymal white adipose tissue (EWAT) from db/db mice treated biweekly with low dose of PEG30-FGF21 Q108 (BIW, 0.75mpk) with tissue taken approximately 30 hours post the second dose (5day time point).
EWAT_db_pFGF21_LD_d5_5


title: dbdb Chow_BAT_vehicle_Day 5_REP03

description:
Gene expression data of brown adipose tissue (BAT) from db/db mice treated twice daily with vehicle (saline) with tissue taken approximately 6 hours post last dose (5day time point).
BAT_db_Veh_d5_3


title: dbdb Chow_EWAT_FGF21 PEG_0.75mpk_Day 2_REP02

description:
Gene expression data of epididymal white adipose tissue (EWAT) from db/db mice treated biweekly with low dose of PEG30-FGF21 Q108 (BIW, 0.75mpk) with tissue taken approximately 30 hours post a single dose (2day time point).
EWAT_db_pFGF21_LD_d2_2


title: dbdb Chow_BAT_vehicle_Day 5_REP01

description:
Gene expression data of brown adipose tissue (BAT) from db/db mice treated twice daily with vehicle (saline) with tissue taken approximately 6 hours post last dose (5day time point).
BAT_db_Veh_d5_1


title: dbdb Chow_EWAT_FGF21 PEG_0.75mpk_Day 2_REP04

description:
Gene expression data of epididymal white adipose tissue (EWAT) from db/db mice treated biweekly with low dose of PEG30-FGF21 Q108 (BIW, 0.75mpk) with tissue taken approximately 30 hours post a single dose (2day time point).
EWAT_db_pFGF21_LD_d2_4


title: dbdb Chow_BAT_vehicle_Day 2_REP02

description:
Gene expression data of brown adipose tissue (BAT) from db/db mice treated twice daily with vehicle (saline) with tissue taken approximately 6 hours post last dose (2day time point).
BAT_db_Veh_d2_2


title: dbdb Chow_BAT_vehicle_Day 5_REP02

description:
Gene expression data of brown adipose tissue (BAT) from db/db mice treated twice daily with vehicle (saline) with tissue taken approximately 6 hours post last dose (5day time point).
BAT_db_Veh_d5_2


title: dbdb Chow_EWAT_FGF21 PEG_0.75mpk_Day 2_REP01

description:
Gene expression data of epididymal white adipose tissue (EWAT) from db/db mice treated biweekly with low dose of PEG30-FGF21 Q108 (BIW, 0.75mpk) with tissue taken approximately 30 hours post a single dose (2day time point).
EWAT_db_pFGF21_LD_d2_1


title: dbdb Chow_BAT_vehicle_Day 2_REP03

description:
Gene expression data of brown adipose tissue (BAT) from db/db mice treated twice daily with vehicle (saline) with tissue taken approximately 6 hours post last dose (2day time point).
BAT_db_Veh_d2_3


title: dbdb Chow_IWAT_FGF21_Day 5_REP02

description:
Gene expression data of inguinal white adipose tissue (IWAT) from db/db mice treated twice daily with wild-type FGF21 (BID, 1.25mpk) with tissue taken approximately 6 hours post last dose (5day time point).
IWAT_db_wtFGF21_d5_2


title: dbdb Chow_BAT_FGF21_Day 5_REP04

description:
Gene expression data of brown adipose tissue (BAT) from db/db mice treated twice daily with wild-type FGF21 (BID, 1.25mpk) with tissue taken approximately 6 hours post last dose (5day time point).
BAT_db_wtFGF21_d5_4


title: dbdb Chow_BAT_FGF21 PEG_2.5mpk_Day 5_REP02

description:
Gene expression data of brown adipose tissue (BAT) from db/db mice treated biweekly with high dose of PEG30-FGF21 Q108 (BIW, 2.5mpk) with tissue taken approximately 30 hours post the second dose (5day time point).
BAT_db_pFGF21_HD_d5_2


title: dbdb Chow_BAT_FGF21 PEG_2.5mpk_Day 5_REP05

description:
Gene expression data of brown adipose tissue (BAT) from db/db mice treated biweekly with high dose of PEG30-FGF21 Q108 (BIW, 2.5mpk) with tissue taken approximately 30 hours post the second dose (5day time point).
BAT_db_pFGF21_HD_d5_5


title: dbdb Chow_BAT_FGF21_Day 2_REP02

description:
Gene expression data of brown adipose tissue (BAT) from db/db mice treated twice daily with wild-type FGF21 (BID, 1.25mpk) with tissue taken approximately 6 hours post last dose (2day time point).
BAT_db_wtFGF21_d2_2


title: dbdb Chow_BAT_FGF21_Day 5_REP03

description:
Gene expression data of brown adipose tissue (BAT) from db/db mice treated twice daily with wild-type FGF21 (BID, 1.25mpk) with tissue taken approximately 6 hours post last dose (5day time point).
BAT_db_wtFGF21_d5_3


title: dbdb Chow_BAT_FGF21_Day 2_REP04

description:
Gene expression data of brown adipose tissue (BAT) from db/db mice treated twice daily with wild-type FGF21 (BID, 1.25mpk) with tissue taken approximately 6 hours post last dose (2day time point).
BAT_db_wtFGF21_d2_4


title: dbdb Chow_BAT_FGF21_Day 2_REP05

description:
Gene expression data of brown adipose tissue (BAT) from db/db mice treated twice daily with wild-type FGF21 (BID, 1.25mpk) with tissue taken approximately 6 hours post last dose (2day time point).
BAT_db_wtFGF21_d2_5


title: dbdb Chow_BAT_vehicle_Day 2_REP01

description:
Gene expression data of brown adipose tissue (BAT) from db/db mice treated twice daily with vehicle (saline) with tissue taken approximately 6 hours post last dose (2day time point).
BAT_db_Veh_d2_1


title: dbdb Chow_BAT_FGF21_Day 5_REP01

description:
Gene expression data of brown adipose tissue (BAT) from db/db mice treated twice daily with wild-type FGF21 (BID, 1.25mpk) with tissue taken approximately 6 hours post last dose (5day time point).
BAT_db_wtFGF21_d5_1


title: dbdb Chow_BAT_FGF21_Day 5_REP02

description:
Gene expression data of brown adipose tissue (BAT) from db/db mice treated twice daily with wild-type FGF21 (BID, 1.25mpk) with tissue taken approximately 6 hours post last dose (5day time point).
BAT_db_wtFGF21_d5_2


title: dbdb Chow_BAT_FGF21_Day 2_REP01

description:
Gene expression data of brown adipose tissue (BAT) from db/db mice treated twice daily with wild-type FGF21 (BID, 1.25mpk) with tissue taken approximately 6 hours post last dose (2day time point).
BAT_db_wtFGF21_d2_1


title: dbdb Chow_BAT_FGF21_Day 2_REP03

description:
Gene expression data of brown adipose tissue (BAT) from db/db mice treated twice daily with wild-type FGF21 (BID, 1.25mpk) with tissue taken approximately 6 hours post last dose (2day time point).
BAT_db_wtFGF21_d2_3


title: PD1222 in Cu-L replicate 3

city: Norwich

first: Matthew

middle: John

last: Sullivan

state: Norfolk

address: Earlham Road

department: School of Biological Sciences

country: United Kingdom

institute: University of East Anglia

hyb_protocol: CyDye-labelled DNA samples were mixed with hybridisation buffer (Morpholine-4-ethanesulfonic acid (MES) hydrate (pH 6.5)  50 mM, Sodium chloride 1 M, 99% Formamide 20% (w/v), EDTA 20 mM, Triton X-100  1% (w/v)) and applied to microarray slides in a tight chamber at 55°C for 60 hours at 8 rpm

scan_protocol: Scanned on an GenePix 4000B scanner (Axon Instruments, Inc.).Images were quantified using Axon GenePix Pro7

data_processing: BABAR R-package was used in R v2.9.2 (Alston et al 2010, BMC Bioinformatics 11:73) was used for background subtraction and LOWESS normalization.

organism: Paracoccus denitrificans PD1222

source_name: PD1222 in Cu-L media replicate 3

label_protocol: Total RNA  (10 μg) was converted to cDNA and fluorescently labelled by random priming to incorporate Cy5-dCTP (Amersham) using reverse transcriptase (AffinityScript, Stratagene).

growth_protocol: The media was inoculated with 1/1000 of over night culture and grown to OD600=0.4 at 30 C without agitation.

extract_protocol: Total RNA extracted using Promega SV total RNA extration kit following manufacturer's instructions

treatment_protocol: The cells were treated with cold ethanol 20%, phenol 1% and left 30min on ice prior centrifugation.

tag: genotype

value: Wild type

source_name: Wild Type in LB


title: dbdb Chow_BAT_FGF21 PEG_0.75mpk_Day 5_REP04

description:
Gene expression data of brown adipose tissue (BAT) from db/db mice treated biweekly with low dose of PEG30-FGF21 Q108 (BIW, 0.75mpk) with tissue taken approximately 30 hours post the second dose (5day time point).
BAT_db_pFGF21_LD_d5_4


title: dbdb Chow_BAT_FGF21 PEG_0.75mpk_Day 5_REP05

description:
Gene expression data of brown adipose tissue (BAT) from db/db mice treated biweekly with low dose of PEG30-FGF21 Q108 (BIW, 0.75mpk) with tissue taken approximately 30 hours post the second dose (5day time point).
BAT_db_pFGF21_LD_d5_5


title: dbdb Chow_BAT_FGF21 PEG_0.75mpk_Day 5_REP03

description:
Gene expression data of brown adipose tissue (BAT) from db/db mice treated biweekly with low dose of PEG30-FGF21 Q108 (BIW, 0.75mpk) with tissue taken approximately 30 hours post the second dose (5day time point).
BAT_db_pFGF21_LD_d5_3


title: dbdb Chow_BAT_FGF21 PEG_2.5mpk_Day 5_REP03

description:
Gene expression data of brown adipose tissue (BAT) from db/db mice treated biweekly with high dose of PEG30-FGF21 Q108 (BIW, 2.5mpk) with tissue taken approximately 30 hours post the second dose (5day time point).
BAT_db_pFGF21_HD_d5_3


title: dbdb Chow_BAT_FGF21 PEG_0.75mpk_Day 2_REP05

description:
Gene expression data of brown adipose tissue (BAT) from db/db mice treated biweekly with low dose of PEG30-FGF21 Q108 (BIW, 0.75mpk) with tissue taken approximately 30 hours post a single dose (2day time point).
BAT_db_pFGF21_LD_d2_5


title: dbdb Chow_BAT_FGF21 PEG_2.5mpk_Day 2_REP01

description:
Gene expression data of brown adipose tissue (BAT) from db/db mice treated biweekly with high dose of PEG30-FGF21 Q108 (BIW, 2.5mpk) with tissue taken approximately 30 hours post a single dose (2day time point).
BAT_db_pFGF21_HD_d2_1


title: dbdb Chow_BAT_FGF21 PEG_2.5mpk_Day 2_REP02

description:
Gene expression data of brown adipose tissue (BAT) from db/db mice treated biweekly with high dose of PEG30-FGF21 Q108 (BIW, 2.5mpk) with tissue taken approximately 30 hours post a single dose (2day time point).
BAT_db_pFGF21_HD_d2_2


title: dbdb Chow_BAT_FGF21 PEG_2.5mpk_Day 2_REP04

description:
Gene expression data of brown adipose tissue (BAT) from db/db mice treated biweekly with high dose of PEG30-FGF21 Q108 (BIW, 2.5mpk) with tissue taken approximately 30 hours post a single dose (2day time point).
BAT_db_pFGF21_HD_d2_4


title: dbdb Chow_BAT_FGF21 PEG_2.5mpk_Day 5_REP01

description:
Gene expression data of brown adipose tissue (BAT) from db/db mice treated biweekly with high dose of PEG30-FGF21 Q108 (BIW, 2.5mpk) with tissue taken approximately 30 hours post the second dose (5day time point).
BAT_db_pFGF21_HD_d5_1


title: dbdb Chow_BAT_FGF21 PEG_2.5mpk_Day 2_REP03

description:
Gene expression data of brown adipose tissue (BAT) from db/db mice treated biweekly with high dose of PEG30-FGF21 Q108 (BIW, 2.5mpk) with tissue taken approximately 30 hours post a single dose (2day time point).
BAT_db_pFGF21_HD_d2_3


title: dbdb Chow_BAT_FGF21 PEG_0.75mpk_Day 2_REP04

description:
Gene expression data of brown adipose tissue (BAT) from db/db mice treated biweekly with low dose of PEG30-FGF21 Q108 (BIW, 0.75mpk) with tissue taken approximately 30 hours post a single dose (2day time point).
BAT_db_pFGF21_LD_d2_4


title: dbdb Chow_BAT_FGF21 PEG_2.5mpk_Day 5_REP04

description:
Gene expression data of brown adipose tissue (BAT) from db/db mice treated biweekly with high dose of PEG30-FGF21 Q108 (BIW, 2.5mpk) with tissue taken approximately 30 hours post the second dose (5day time point).
BAT_db_pFGF21_HD_d5_4


title: dbdb Chow_BAT_FGF21 PEG_0.75mpk_Day 5_REP02

description:
Gene expression data of brown adipose tissue (BAT) from db/db mice treated biweekly with low dose of PEG30-FGF21 Q108 (BIW, 0.75mpk) with tissue taken approximately 30 hours post the second dose (5day time point).
BAT_db_pFGF21_LD_d5_2


title: dbdb Chow_BAT_FGF21 PEG_2.5mpk_Day 2_REP05

description:
Gene expression data of brown adipose tissue (BAT) from db/db mice treated biweekly with high dose of PEG30-FGF21 Q108 (BIW, 2.5mpk) with tissue taken approximately 30 hours post a single dose (2day time point).
BAT_db_pFGF21_HD_d2_5


title: dbdb Chow_BAT_FGF21 PEG_0.75mpk_Day 5_REP01

description:
Gene expression data of brown adipose tissue (BAT) from db/db mice treated biweekly with low dose of PEG30-FGF21 Q108 (BIW, 0.75mpk) with tissue taken approximately 30 hours post the second dose (5day time point).
BAT_db_pFGF21_LD_d5_1


title: dbdb Chow_BAT_FGF21 PEG_0.75mpk_Day 2_REP02

description:
Gene expression data of brown adipose tissue (BAT) from db/db mice treated biweekly with low dose of PEG30-FGF21 Q108 (BIW, 0.75mpk) with tissue taken approximately 30 hours post a single dose (2day time point).
BAT_db_pFGF21_LD_d2_2


title: PD1222 in Cu-H replicate 1

source_name: PD1222 in Cu-H media replicate 1


title: dbdb Chow_BAT_FGF21 PEG_0.75mpk_Day 2_REP01

description:
Gene expression data of brown adipose tissue (BAT) from db/db mice treated biweekly with low dose of PEG30-FGF21 Q108 (BIW, 0.75mpk) with tissue taken approximately 30 hours post a single dose (2day time point).
BAT_db_pFGF21_LD_d2_1


title: dbdb Chow_BAT_FGF21 PEG_0.75mpk_Day 2_REP03

description:
Gene expression data of brown adipose tissue (BAT) from db/db mice treated biweekly with low dose of PEG30-FGF21 Q108 (BIW, 0.75mpk) with tissue taken approximately 30 hours post a single dose (2day time point).
BAT_db_pFGF21_LD_d2_3


title: PD1222 in Cu-L replicate 2

source_name: PD1222 in Cu-L media replicate 2


title: PD1222 in Cu-H replicate 2

source_name: PD1222 in Cu-H media replicate 2


title: PD1222 in Cu-H replicate 3

source_name: PD1222 in Cu-H media replicate 3


title: Normal-N_AJ1

city: New York

first: Mayte

last: Suarez-Farinas

state: NY

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

hyb_protocol: RNA was hybridized to HGU133 Plus 2.0 chips to measure relative gene expression.

scan_protocol: Hewlett-Packard GeneArray Scanner

data_processing: Preprocessing was carried out using GCRMA (through gcrma package from R/Bioconductor). Since samples were processed using two different kits, Combat was used to eliminate the batch effect. However, the presence of genes with small variance precluded successful estimation of the parameters in the sophisticated model used by Combat in this dataset. To circumvent this issue, genes with SD<0.2 were eliminated prior to Combat adjustment of the batch effect.

organism: Homo sapiens

source_name: human skin biopsy

label_protocol: GeneChip Affymetrix protocol

extract_protocol: Total RNA was extracted using miRNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol with on-column DNase digestion

tag: condition

value: Normal

tag: patient

value: Normal skin biopsy

tag: kit

value: Ovation


title: Psoriasis-287

value: Psoriasis

value: LS skin biopsy


title: Normal-N_AJ3


title: Psoriasis-252


title: Discoid Lupus-L9

value: Discoid Lupus


title: Psoriasis-292


title: PD1222 in Cu-L replicate 1

source_name: PD1222 in Cu-L media replicate 1


title: Normal-N_AJ2


title: Discoid Lupus-L5


title: Discoid Lupus-L3


title: Discoid Lupus-L2


title: dbdb Chow_BAT_FGF21_Day 5_REP05

description:
Gene expression data of brown adipose tissue (BAT) from db/db mice treated twice daily with wild-type FGF21 (BID, 1.25mpk) with tissue taken approximately 6 hours post last dose (5day time point).
BAT_db_wtFGF21_d5_5

value: db/db

value: 8 weeks

value: chow


title: Discoid Lupus-L4


title: Discoid Lupus-L8


title: Discoid Lupus-L1


title: mari5

type: genomic

city: Tartu

first: Mait

last: Metspalu

address: Riia 23

country: Estonia

institute: Estonian Biocentre

description: Genomic DNA extracted from blood was genotyped using Human610-Quad v1.0 BeadChip (Illumina).

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48°C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol, dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Image data was analyzed using Genomestudio v2011.1 with GT module 1.9.4 (Illumina).

label: Cy3, Cy5

molecule: genomic DNA

source_name: blood

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37°C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from blood was performed using standard extraction protocols.

value: blood

tag: gender

value: Male

tag: population

value: Maris

tag: region

value: Europe


title: mari7


title: mari9


title: mari6


title: mari12


title: mari3


title: mari13


title: Selkup87

description: Genomic DNA extracted from blood was genotyped using Human660W-Quad v1.0 Genotyping BeadChip (Illumina).

value: Selkups

value: Siberia


title: mari15


title: mari11


title: mari10


title: even3777

value: Female

value: Evens


title: Psoriasis-Patient-L

value: PS-L

value: Affy


title: Psoriasis-Patient-M

value: PS-M


title: mari8


title: Psoriasis-Patient-K

value: Psoriasis

value: PS-K


title: even3776


title: Psoriasis-Patient-J

value: PS-J

value: LS skin biopsy


title: Selkup83


title: Psoriasis-Patient-O

value: PS-O


title: Psoriasis-Patient-I

value: PS-I


title: Selkup3a

value: blood


title: mari14

value: Male


title: Psoriasis-Patient-H

value: PS-H


title: altai389

value: Altaians


title: Psoriasis-Patient-N

value: PS-N


title: altai80

value: Siberia


title: Psoriasis-Patient-F

value: PS-F


title: GhrhKO_006

first: William

middle: R

last: Swindell

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard University

description: liver tissue from Ghrh-KO mice

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse Genome 430 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray TM Scanner 3000.

data_processing: Robust Multichip Average (RMA)

source_name: liver

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

growth_protocol: Ghrh-KO mice and wild-type controls (on a mixed C57BL6 and 129SV background) were bred in a closed colony, housed under standard conditions (12-hr. light/12-hr. dark cycling and 20-23 degrees C), and fed Lab Diet Formula 5001 (23% protein, 4.5% fat, 6% fiber) (Nestle Purina, St. Louis, MO).

extract_protocol: RNA was extracted using QIAGEN mini kits

treatment_protocol: Male mice were fasted for 6-8 hours and then sacrificed by CO2 inhalation. Upon sacrifice, livers were collected and samples were stored in RNAlater (Qiagen cat. no. 76106) and placed at 4 degrees C for 24 hours before transitioning to -20 degrees C. All samples were disrupted using a rotor-stator homogenizer and RNA extractions were performed using the Qiagen RNeasy Fibrous Tissue kit (Qiagen cat. no. 74704), with on-column DNAase digestion (Qiagen cat. no. 79254). Extracted RNA was quantified using the NanoDrop spectrophotometer and RNA quality was evaluated using the Agilent Bioanalyzer.

value: Ghrh-KO

value: liver

value: male

value: mixed C57BL6 and 129SV


title: Psoriasis-Patient-G

value: Psoriasis

value: PS-G

value: Affy


title: Selkup15a

value: Female

value: Selkups


title: Psoriasis-Patient-E

value: PS-E

value: LS skin biopsy


title: GhrhKO_005

description: liver tissue from Ghrh-KO mice


title: mari4

value: blood

value: Male

value: Maris

value: Europe


title: mari1


title: Selkup59

value: Siberia


title: Psoriasis-Patient-D

value: PS-D


title: Selkup82


title: Psoriasis-Patient-C

value: PS-C


title: Normal_001

description: liver tissue from control littermates

value: Control (wild-type)

value: liver


title: NK_resting_wt3

city: Rehovot

first: Joseph

last: Lotem

department: Molecular genetics

country: Israel

institute: Weizmann institute of science

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials and protocol. Fluidics washing protoco is FS450_000.7

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G.

data_processing: Data was analyzed using Partek Genomics Suite software.  Pre-background Ajustment: Adjust for GC Content. Background Correction: GCRMA Background Correction. Normalization: Quantile Normalization.

source_name: spleen

label_protocol: cDNA samples were generated and labeled using Affymetrix cDNA synthesis and labeling kit.

growth_protocol: Mouse splenic NK cells freshly isolated and FACS sorted.

extract_protocol: Total RNA was isolated using the RNeasy micro kit (Qiagen) according to manufacturer’s instructions.

treatment_protocol: NK cells were enriched by negative selection using NK cell isolation kit (R&D) and then FACS sorted to obtain DX5+ cells.

tag: cell type

value: NK cells

value: 6 weeks

value: Runx3 +/+

tag: Sex

value: male and female

value: ICR


title: mari2


title: a39

value: Female

value: Estonians


title: GhrhKO_004

description: liver tissue from Ghrh-KO mice

value: Ghrh-KO

value: male

value: mixed C57BL6 and 129SV


title: Psoriasis-Patient-B

value: Psoriasis

value: PS-B

value: LS skin biopsy

value: Affy


title: altai377

value: blood

value: Altaians

value: Siberia


title: NK_resting_wt1

value: NK cells


title: Psoriasis-Patient-A

value: PS-A


title: NK_resting_wt2

value: 6 weeks

value: Runx3 +/+


title: NK_resting_ko3

value: Runx3 -/-

value: male and female

value: ICR


title: NK_resting_ko1


title: CD8_IL2_ko3

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials and protocol. Fluidics washing protocol is FS450_0007.

data_processing: Data was analyzed using Partek Genomics Suite software.  Pre-background Ajustment: Adjust for GC Content. Background Correction: RMA Background Correction. Normalization: Quantile Normalization.

label_protocol: cDNA samples were generated and labeled using Affymetrix WT-cDNA synthesis and labeling kit.

growth_protocol: Mouse CD8+ splenic T cells were isolated from WT and Runx3-/- mice and TCR-activated on anti-CD3-coated plates and soluble anti-CD28 for 2 days as published (Cruz-Guilloty et al., J Exp Med 206: 51-59, 2009). Cells were then diluted into fresh medium supplemented with 100u/ml human recombinant IL-2 (Beit Haemek, Israel) and cultured for 4 days. Cultured Runx3-/- CD8+ T cells were further sorted to remove CD4+CD8- T cells.

treatment_protocol: WT CD8+ T cells were isolated to >95% purity using positive selection on anti-CD8 magnetic beads (BD). Runx3-/- CD8+ T cells cells were also positively selected and further FACS sorted to remove CD11c+CD8+ dendritic cells.

value: CD8+ T cells


title: Kazakh73cp

value: Male

value: Kazakhs

value: Central Asia


title: CD8_IL2_ko2

value: male


title: Normal_002

description: liver tissue from control littermates

value: Control (wild-type)

value: liver

value: mixed C57BL6 and 129SV


title: NK_IL15_wt2

growth_protocol: Mouse splenic NK cells freshly isolated and cultured with IL-2 or IL-15.

treatment_protocol: NK cells were enriched by negative selection using NK cell isolation kit (R&D) and cultured for 7 days with 1000 u/ml recombinant human IL-2 (Beit-Haemek, Israel) or mouse IL-15 (Peprotec, Israel).

tag: treatment

value: male or female


title: NK_IL15_wt1

tag: strain


title: NK_IL15_ko2


title: Kazakh70cp

value: blood


title: NK_IL15_ko1

value: NK cells


title: Normal_003

description: liver tissue from control littermates

tag: genotype/variation


title: CD8_IL2_ko1

tag: age


title: Kazakh67cp


title: kazakh164

value: Female


title: kazakh178


title: NK_IL2_ko1

value: 6 weeks


title: NK_IL2_ko3


title: NK_IL2_wt3

value: Runx3 +/+


title: Dolgan3845

value: Dolgans

value: Siberia


title: CD8_IL2_wt2

value: ICR


title: Kazakh63cp


title: Selkup121

value: Selkups


title: NK_IL2_wt1


title: CD8_IL2_wt3

value: CD8+ T cells


title: CD8_IL2_wt1


title: Kazakh56cp

value: Male

value: Kazakhs


title: NK_resting_ko2

value: Runx3 -/-

value: male and female


title: CD8_resting_ko2

growth_protocol: Mouse CD8+ splenic T cells freshly isolated and FACS sorted.

value: male


title: NK_IL2_ko2


title: CD8_resting_ko1


title: altai406

value: Russians


title: MU_Mi

city: Genoa

first: Adriana

middle: Agnese

last: Amaro

address: Largo Rosanna Benzi 10

department: Molecular Pathology

country: Italy

institute: IRCCS Ospedale Policlinico SAN MARTINO - IST - NATIONAL CANCER RESEARCH INSTITUTE

description: SAMPLE 19

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: Affymetrix Expression Console

source_name: Uveal melanoma

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

extract_protocol: Total RNA was extracted from the tissue lysate using an miRNeasy mini kit (Qiagen).

tag: disease state

value: Uveal melanoma

value: eye tumor

value: female


title: CD8_resting_wt3


title: Kazakh65cp

value: blood

value: Central Asia


title: MU_66

description: SAMPLE 16


title: Kazakh52cp


title: MU_78

description: SAMPLE 18


title: CD8_resting_wt1

value: 6 weeks

value: Runx3 +/+


title: Kazakh54cp


title: Kazakh62cp


title: Kazakh44cp


title: NK_IL2_wt2

value: NK cells

value: male or female


title: Kazakh48cp


title: MU_62

description: SAMPLE 13


title: MU_63

description: SAMPLE 14


title: Kazakh36cp


title: MU_67

description: SAMPLE 17


title: Kazakh46cp


title: CD8_resting_wt2

value: ICR


title: MU_50

description: SAMPLE 11


title: KirgizKGN84

value: Female

value: Kyrgyzians


title: MU_60

description: SAMPLE 12


title: MU_64

description: SAMPLE 15


title: MU_46

description: SAMPLE 9


title: Kazakh34cp

value: Male

value: Kazakhs


title: Kazakh32cp


title: MU_47

description: SAMPLE 10


title: CD8_resting_ko3

value: CD8+ T cells

value: Runx3 -/-


title: KirgizKGN66


title: MU_45

description: SAMPLE 8


title: Kazakh58cp


title: MU_42

description: SAMPLE 7


title: KirgizKGN71


title: kirgiz35


title: MU_41

description: SAMPLE 6

value: male


title: kirgiz37


title: KirgizKGN82


title: KirgizKGN62


title: MU_39

description: SAMPLE 5

value: Uveal melanoma


title: KirgizKGN8


title: ee53

description: Genomic DNA extracted from blood was genotyped using HumanHap650Yv3 Genotyping BeadChip (HumanHap650Yv3_A) (Illumina).

value: Estonians

value: Europe


title: MU_38

description: SAMPLE 4

value: eye tumor


title: MU_35

description: SAMPLE 2

value: female


title: kirgiz31

value: blood

value: Central Asia


title: kirgiz30


title: MU_37

description: SAMPLE 3


title: kirgiz34


title: MU_28

description: SAMPLE 1


title: ee149


title: ee45


title: ee144


title: PBMC_pre_rep14

status: Public on Nov 17 2013

city: Piscataway

first: Howard

last: Kipen

state: NJ

address: 170 Frelinghuysen Road

institute: University of Medicine and Dentistry-Robert Wood Johnson Medical School

description:
Gene Expression before exposure
124_1G.txt

hyb_protocol: 1.65 ug of Cy3-labelled cDNA was fragmented at 37°C for 30 minutes in a reaction volume of 20ul containing 2ul of Fragmentation Buffer and 1.5ul Fragmentation Enzyme following the manufacturers instructions. On completion of the fragmentation reaction, 55ul of Agilent 2X hybridization buffer and 11ul of Agilent 10X Blocking Agent and 34 ul of NuGEN Blocking reagent was added to 10ul of fragmented Cy3 labeled cDNA. The target was hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 40 hours at 65 °C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 °C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

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

data_processing: The scanned images were analyzed with Feature Extraction Software Version 9.5.3.1 (Agilent) using default parameters (protocol GE1_v5_95_Feb07 and Grid: 014850_D_F_20070207) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: PBMC, pre exposue, subject 124

label_protocol: Cyanine-3 (Cy3) labeled cDNA was prepared from 40ng of RNA using NuGEN Ovation Amplication kit and labeled and fragemented by using NuGEN FL-Ovation cDNA Fluorescent Module. Dye incorporation and cDNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: PBMC layer were collected using CPT tubes. 2ml PBMC was lysed in 6ml of Trizol LS. Add 4ml of lysed samples to a 15ml PCG tube. Add 1000ul of chroroform, close cape securely and shake vigorously by hand for 15 seconds. Then incubate on bench for 2-3 minutes. Spin samples at 3000 g at 4 degree for 15 minutes. Carefully remove the upper colourless aqueous layer to the final drop and place into a fresh tube. Add 0.75 times the volume with 100% ethanol to the aqueous phase and mix the tube gently by inversion. Pipette 700 ul of the mixture into the RNA binding column (Qiagen mini RNAeasy column). Centrifuge the column at 8000g for 15 seconds. Discard the flow through. Repeat this step until all of the aqueous phas/ethanol mixture has been trhough the column. Washing the column with 500 ul PRE buffer. Spin for 15 seconds at 8000g, discard the flow through. Wash the column again with 500ul of RPE buffer. Spin for 2 mins at 8000g and discard the flow through. To elute add 30ul nucelase free water to the center of the colunm, spin for 1 min at 8000g, dicard the column. remove 1ul for nanodrop and 1.5ul for bioanalyzer.

treatment_protocol: Each exposure session lasted 60 minutes and occurred at approximately the same time of day in the early morning. Research technicians verified adherence to health, medication and dietary criteria. An ECG was recorded; blood was drawn for physiologic endpoints (to be reported elsewhere) and RNA extraction. ECG leads were attached for continuous monitoring during exposure. Following check-in and pre-exposure testing, subjects walked approximately 40 yards and took a two story elevator ride to the CEF located in the same building. Participants were confortably seated and asked to read or study during sessions. Subjects and real-time exposure data were continuously monitored by staff.

value: PBMC


title: ee147


title: kirgiz33


title: PBMC_post_rep14

description:
Gene Expression after exposure
124_5G.txt

source_name: PBMC, post exposue, subject 124


title: kirgiz24


title: PBMC_post_rep12

description:
Gene Expression after exposure
117_5G.txt

source_name: PBMC, post exposue, subject 117


title: PBMC_pre_rep13

description:
Gene Expression before exposure
118_6G.txt

source_name: PBMC, pre exposue, subject 118


title: PBMC_post_rep13

description:
Gene Expression after exposure
118_10G.txt

source_name: PBMC, post exposue, subject 118


title: kirgiz28


title: PBMC_pre_rep11

description:
Gene Expression before exposure
114_6G.txt

source_name: PBMC, pre exposue, subject 114


title: PBMC_post_rep11

description:
Gene Expression after exposure
114_10G.txt

source_name: PBMC, post exposue, subject 114


title: kirgiz25


title: PBMC_pre_rep10

description:
Gene Expression before exposure
108_1G.txt

source_name: PBMC, pre exposue, subject 108


title: ee50


title: PBMC_post_rep8

description:
Gene Expression after exposure
103_10G.txt

source_name: PBMC, post exposue, subject 103


title: PBMC_pre_rep9

description:
Gene Expression before exposure
104_1G.txt

source_name: PBMC, pre exposue, subject 104


title: PBMC_post_rep9

description:
Gene Expression after exposure
104_5G.txt

source_name: PBMC, post exposue, subject 104


title: ee14


title: kirgiz23


title: PBMC_post_rep7

description:
Gene Expression after exposure
83_5G.txt

source_name: PBMC, post exposue, subject 83


title: PBMC_post_rep6

description:
Gene Expression after exposure
80_5G.txt

source_name: PBMC, post exposue, subject 80


title: PBMC_pre_rep6

description:
Gene Expression before exposure
80_1G.txt

source_name: PBMC, pre exposue, subject 80


title: PBMC_pre_rep8

description:
Gene Expression before exposure
103_6G.txt

source_name: PBMC, pre exposue, subject 103


title: PBMC_post_rep4

description:
Gene Expression after exposure
71_5G.txt

source_name: PBMC, post exposue, subject 71


title: PBMC_pre_rep12

description:
Gene Expression before exposure
117_1G.txt

source_name: PBMC, pre exposue, subject 117


title: PBMC_pre_rep7

description:
Gene Expression before exposure
83_1G.txt

source_name: PBMC, pre exposue, subject 83


title: kirgiz36

description: Genomic DNA extracted from blood was genotyped using Human660W-Quad v1.0 Genotyping BeadChip (Illumina).

source_name: blood


title: ee114

description: Genomic DNA extracted from blood was genotyped using HumanHap650Yv3 Genotyping BeadChip (HumanHap650Yv3_A) (Illumina).


title: PBMC_pre_rep5

description:
Gene Expression before exposure
72_6G.txt

source_name: PBMC, pre exposue, subject 72


title: PBMC_post_rep5

description:
Gene Expression after exposure
72_10G.txt

source_name: PBMC, post exposue, subject 72


title: PBMC_pre_rep4

description:
Gene Expression before exposure
71_1G,txt

source_name: PBMC, pre exposue, subject 71


title: PBMC_pre_rep3

description:
Gene Expression before exposure
65_1G.txt

source_name: PBMC, pre exposue, subject 65


title: PBMC_post_rep3

description:
Gene Expression after exposure
65_5G.txt

source_name: PBMC, post exposue, subject 65


title: ee140


title: PBMC_post_rep2

description:
Gene Expression after exposure
64_5G.txt

source_name: PBMC, post exposue, subject 64


title: uzbek96

value: Uzbeks


title: uzbek88


title: kirgiz21


title: PBMC_pre_rep1

description:
Gene Expression before exposure
58_6G.txt

source_name: PBMC, pre exposue, subject 58


title: PBMC_pre_rep2

description:
Gene Expression before exposure
64_1G.txt

source_name: PBMC, pre exposue, subject 64


title: PBMC_post_rep1

description:
Gene Expression after exposure
58_10G.txt

source_name: PBMC, post exposue, subject 58


title: Liver mbd4KO

city: Jerusalem

first: Ofra

last: sabag

address: Ein kerem

institute: The Hebrew university

description: Tissue DNA was obtained from A. Bird [Millar CB et al. 2002 - PMID:12130785]

hyb_protocol: The labeled Input and Bound DNAs were combined and hybridized for 60 h at 67°C in 15% deionized formamide to a CpG island microarray using the Agilent aCGH hybridization buffer and protocol.

scan_protocol: Arrays were washed according to the Agilent aCGH protocol, immediately scanned on an Agilent microarray scanner and processed using Agilent Feature extraction software version 9.5.

data_processing: Probe log ratio signals were Loess normalized and transformed into Z-scores according to their Tm.

source_name: Liver mbd4KO_INPUT

label_protocol: The Input and Bound DNAs were labeled using the Agilent Technologies Genomic Labeling kit Plus according to the manufacturer’s instructions. Briefly, 300ng of each sample was labeled with Cyanine-3 or Cyanine-5 dUTP and purified using microcon YM 30 columns.

extract_protocol: mouse (40µg) DNA was sonicated to an average fragment size of 300–1000 bp, precipitated with  400 mM NaCl, 2 volumes of ethanol and 1 µl glycogen. 1.5 µg were set aside as the Input fraction. DNA was denatured and anti-5-methylcytidine  monoclonal antibody (10 µl for 5 µg) was added and incubated on a rotator at 4°C overnight. 40 µl Dynabeads (Sheep anti-Mouse IgG) were prewashed  with 0.1% BSA/PBS and added to the DNA. The DNA was then washed 3 times and Ab-bound DNA resuspended and extracted with proteinase K,  phenol-chloroform and ethanol precipitation.

value: 6 months

value: liver

tag: antibody

value: anti-5-methylcytidine monoclonal antibody [Mayer W et al. 2000 - PMID:10676950, Reynaud C et al. 1992 - PMID:1739950]

source_name: Liver mbd4KO_BOUND


title: ee136

value: Male


title: Gadd45a k.d

source_name: Gadd45a k.d_INPUT

value: embryonic stem cells (ES)

value: Gadd45a knock down

source_name: Gadd45a k.d_BOUND


title: PBMC_post_rep10

description:
Gene Expression after exposure
108_5G.txt

source_name: PBMC, post exposue, subject 108


title: Spleen mbd4KO

source_name: Spleen mbd4KO_INPUT

value: spleen

source_name: Spleen mbd4KO_IBOUND


title: liver aidKO

description: Tissue DNA was obtained from W. Reik [Popp C et al. 2010 - PMID:20098412]

source_name: liver aidKO_INPUT

value: aid-/-

source_name: liver aidKO_BOUND


title: Spleen aidKO

source_name: Spleen aidKO_INPUT

source_name: Spleen aidKO_BOUND


title: kirgiz22

source_name: blood

value: Female

value: Kyrgyzians


title: ES aidKO

source_name: ES aidKO_INPUT

source_name: ES aidKO_BOUND


title: ee108

value: Estonians

value: Europe


title: ES wt

source_name: ES wt_INPUT

value: wild type

source_name: ES wt_BOUND


title: ES mbd4KO

source_name: ES mbd4KO_INPUT

source_name: ES mbd4KO_BOUND


title: colorectal cancer tissues

status: Public on Nov 16 2013

city: shanghai

first: shi

last: debing

state: shanghai

address: 270 Dongan Road

country: China

institute: Fudan University Shanghai Cancer Center

description: lncRNA and mRNA expression

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides

data_processing: Agilent Feature Extraction software (version 10.7.3.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies)

source_name: colorectal cancer tissues

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

extract_protocol: Total RNA was extracted from two pool of snap frozen colon cancer tissues and one pool of normal tissues using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol.

value: colorectal cancer tissues

value: male


title: cadmium MCF7-Cd8

city: Skövde

first: Zelmina

last: Lubovac Pilav

address: Box 408

country: Sweden

institute: University of Skövde

hyb_protocol: Affymetrix protocol

scan_protocol: GeneChip® Gene 1.0 ST Array System

data_processing:
Data was processed using Affymetrix Expression Console, gene-level RMA normalization (background correction, normalized (quantile) and summarized (MedianPolish)). Following identification of differentially expressed genes was done with SAM, using MeV-MultiExperiment Viewer
meta-probeset file: HuGene-1_0-st-v1.na32.hg19.transcript.csv

source_name: cadmium-adapted breast cancer cell lines

label_protocol: Affymetrix protocol

extract_protocol: extract protocol

tag: cell line

value: cadmium MCF7-Cd8


title: primary adjacent normal tissues

description: lncRNA and mRNA expression

source_name: primary adjacent normal tissues

tag: tissue

value: primary adjacent normal tissues


title: control MCF7-2

source_name: breast cancer cell lines


title: cadmium MCF7-Cd7

value: cadmium MCF7-Cd7


title: cadmium MCF7-Cd12

value: cadmium MCF7-Cd12


title: CFPAC Replicate 2

city: Baltimore

first: Jennifer

last: Bailey

state: MD

address: 733 N. Broadway MRB 472

department: Surgery

institute: Johns Hopkins University

description: Biological Replicate

hyb_protocol: 825 ng labeled RNA was fragmented, denatured and hybridized to the array at 60ºC for 17 hours in a hybridization oven with rotation. After hybridization, arrays were washed and dried according to the Agilent microarray processing protocol.

scan_protocol: Arrays were scanned by Agilent G2505B Scanner controlled by Agilent Scan Control 7.0 Software. Data were extracted with Agilent Feature Extraction Software.

data_processing: Partek software was used to import Agilent's ProcessedSignal values (which include background subtraction) as LogRatios.

source_name: CFPAC AAT+

label_protocol: 400 ng total RNA was amplified and labeled using Low RNA Input Fluorescent Linear Amplification Kit (Cat# 5190-0447, Agilent Technologies) with oligo dT primers (Cat# RA300A-2, System Bioscience) and cyanine-labeled CTPs (Perkin Elmer) according to manufacturer’s manual. Labeled cRNA was purified using RNeasy Mini Kit (Qiagen). RNA spike-in controls (Agilent Technologies) were added to RNA samples before amplification and labeling according to manufacturer’s protocol.

growth_protocol: CFPAC and AsPC1 cells were grown in DMEM with 10% FBS.

extract_protocol: RNA was extracted using the Rneasy mini kit from Qiagen

treatment_protocol: CFPAC and AsPC1 cells were labeling with AcTub antibody and then FACS sorted based on high or low levels of AcTub.

value: CFPAC

tag: origin

value: Pancreatic Cancer

source_name: CFPAC AAT-


title: control MCF7-1


title: metastatic colorectal cancer tissues

description: lncRNA and mRNA expression

source_name: metastatic colorectal cancer tissues

value: metastatic colorectal cancer tissues


title: CELLLINE-MLS1765

city: Heidelberg

first: Marcus

last: Renner

address: Im Neuenheimer Feld 224

department: General Pathology

country: Germany

institute: Institute of Pathology

data_processing: Annotation and quantile normalization were performed using a lumi R-package (Du P et al. BMC Bioinformatics 2010, 11:587.; Du P et al. Cancer 2007, 2:1-31.)

source_name: tumor cell line

label_protocol: Expression profiling was performed using the HumanHT-12 v3 BeadArrays (Illumina) according to the manufacturers’ instructions. Quality control as well as labeling and hybridization were performed in the Core Facility of the DKFZ Heidelberg.

extract_protocol: RNA was isolated from snap-frozen tissue using Allprep DNA/RNA Mini Kit (Qiagen) according to manufacturer’s instructions. Quality control and quantification of total RNA was done with a RNA 6000 nano LabChip using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA). Only RNA with a RNA integrity number > 7 was used.

treatment_protocol: All sarcoma samples of this set were obtained prior to any cytotoxic treatment and were snap-frozen immediately after surgery. Prior to RNA extraction tumor cell content was checked by a pathologist and only samples with >80% tumor content were processed further.

tag: tumor cell line


title: CELLLINE-T449

hyb_protocol: Expression profiling was performed using the HumanHT-12 v3 BeadArrays (Illumina) according to the manufacturers’ instructions.


title: CELLLINE-HT1080

scan_protocol: Expression profiling was performed using the HumanHT-12 v3 BeadArrays (Illumina) according to the manufacturers’ instructions.


title: AsPC1 Replicate 2

description: Biological Replicate

source_name: AsPC1 AAT+

source_name: AsPC1 AAT-


title: CELLLINE-T778


title: CELLLINE-FU-DDLS-1


title: CELLLINE-HS-SY-II

value: HS-SY-II


title: CELLLINE-SW872


title: CELLLINE-MLS402


title: CELLLINE-1273


title: CELLLINE-Fuji

value: Fuji


title: cadmium MCF7-Cd6

value: cadmium MCF7-Cd6


title: ee111

source_name: blood

value: blood

value: Female


title: AsPC1 Replicate 1

description: Biological Replicate


title: CELLLINE-SYO-1


title: UPS-12

source_name: tumor sample

tag: age (yrs)

tag: sarcoma subtype

value: undifferentiated pleomorphic liposarcoma (UPS)


title: UPS-11

tag: gender

value: female


title: UPS-13


title: CELLLINE-CME

value: CME


title: UPS-10


title: UPS-07


title: UPS-05


title: ee105

tag: population

value: Estonians

value: Europe


title: uzbek80

value: Male

value: Uzbeks

tag: region

value: Central Asia


title: SS-09

value: male

value: synovial sarcoma (SS)


title: UPS-09


title: UPS-08


title: UPS-06


title: CELLLINE-STS26T


title: SS-06


title: UPS-04


title: SS-10


title: SS-05


title: SS-07


title: SS-08


title: UPS-01


title: SS-04


title: ee1


title: SS-01


title: uzbek55


title: PLS-08

value: pleomorphic liposarcoma (PLS)


title: UPS-02


title: PLS-07


title: SS-02


title: UPS-03


title: PLS-05


title: PLS-03


title: MPNST-10

value: malignant peripheral nerve sheath tumor(MPNST)


title: MPNST-05


title: MLS-09

value: myxoid liposarcoma (MLS)


title: cadmium MCF7-Cd4

value: cadmium MCF7-Cd4


title: CFPAC Replicate 1

description: Biological Replicate

value: CFPAC

value: Pancreatic Cancer


title: PLS-04


title: MPNST-09


title: PLS-01


title: MPNST-08


title: MPNST-06


title: MLS-08


title: PLS-02


title: MLS-07


title: MPNST-03


title: MPNST-04


title: MPNST-01


title: MPNST-07


title: MLS-05


title: MPNST-02


title: MLS-02


title: MLS-03


title: MLS-06


title: MLS-04


title: MLS-01


title: LMS-10

value: leiomyosarcoma (LMS)


title: MFS-07

value: myxofibrosarcoma (MFS)


title: MFS-04

value: female


title: LMS-04


title: MFS-03


title: LMS-09


title: MFS-01


title: MFS-05


title: MFS-02


title: LMS-08


title: LMS-05


title: LMS-07


title: FAT-02

source_name: normal sample

value: non-neoplastic fat


title: LMS-02


title: LMS-01


title: DDLS-12

value: dedifferentiated liposarcoma (DDLS)


title: DDLS-11


title: DDLS-09


title: LMS-06


title: DDLS-08


title: LMS-03


title: FAT-01


title: DDLS-06


title: DDLS-05


title: DDLS-03


title: DDLS-04


title: DDLS-01


title: DDLS-02


title: DDLS-10


title: DDLS-07


title: CELLLINE-T449 [methylation]

hyb_protocol: DNA methylation profiling was performed using the HumanMethylation 27k BeadArrays (Illumina) according to the manufacturers’ instructions. Quality control as well as labeling and hybridization were performed in the Core Facility of the DKFZ Heidelberg.

data_processing:
The methylation status obtained from this assay can be expressed as the ratio of fluorescence intensity of the methylated probe over the overall intensity (beta value) or the log2 ratio of the intensities of methylated probe versus unmethylated probe (M-value).
The 'qnorm.txt' file contains the quantile normalized beta values as provided by the DKFZ (German Cancer Research Center) Core Facility.
M-values were generated as described in: PMID:21118553

extract_protocol: Genomic DNA was isolated using Allprep DNA/RNA Mini Kit (Qiagen, Hilden, Germany) followed by ethanol precipitation with 5 M ammonium acetate. Bisulfite conversion was carried out by using the EZ DNA Methylation Kit (Zymo Research, Irvine, USA) according to the manufacturer’s instruction and 500 ng of the bisulfite converted genomic DNA was used with the Infinium bead array platform.


title: CELLLINE-MLS1765 [methylation]

scan_protocol: DNA methylation profiling was performed using the HumanMethylation 27k BeadArrays (Illumina) according to the manufacturers’ instructions. Quality control as well as labeling and hybridization were performed in the Core Facility of the DKFZ Heidelberg.


title: CELLLINE-HT1080 [methylation]

label_protocol: DNA methylation profiling was performed using the HumanMethylation 27k BeadArrays (Illumina) according to the manufacturers’ instructions. Quality control as well as labeling and hybridization were performed in the Core Facility of the DKFZ Heidelberg.


title: CELLLINE-T265 [methylation]


title: CELLLINE-HS-SY-II [methylation]

value: HS-SY-II


title: PLS-06


title: CELLLINE-FU-DDLS-1 [methylation]


title: CELLLINE-SYO-1 [methylation]


title: CELLLINE-T778 [methylation]


title: CELLLINE-Fuji [methylation]

value: Fuji


title: CELLLINE-STS26T [methylation]


title: UPS-13 [methylation]

value: undifferentiated pleomorphic liposarcoma (UPS)


title: UPS-12 [methylation]


title: CELLLINE-SW872 [methylation]


title: SS-03


title: CELLLINE-CME [methylation]

value: CME


title: UPS-10 [methylation]


title: CELLLINE-MLS402 [methylation]


title: UPS-11 [methylation]


title: UPS-04 [methylation]


title: UPS-01 [methylation]


title: UPS-05 [methylation]


title: UPS-06 [methylation]

value: male


title: CELLLINE-1273 [methylation]


title: UPS-03 [methylation]


title: UPS-08 [methylation]


title: UPS-07 [methylation]


title: UPS-09 [methylation]


title: SS-10 [methylation]

value: synovial sarcoma (SS)


title: SS-09 [methylation]


title: UPS-02 [methylation]


title: SS-05 [methylation]


title: PLS-07 [methylation]

value: pleomorphic liposarcoma (PLS)


title: PLS-03 [methylation]


title: SS-02 [methylation]


title: PLS-04 [methylation]


title: SS-01 [methylation]


title: SS-03 [methylation]


title: SS-04 [methylation]


title: SS-08 [methylation]


title: PLS-05 [methylation]


title: PLS-06 [methylation]


title: SS-06 [methylation]


title: SS-07 [methylation]


title: PLS-02 [methylation]


title: PLS-08 [methylation]


title: PLS-01 [methylation]


title: 3800Ga

city: Beijing

first: Yunfeng

last: Yang

state: Beijing

address: Qinghuayuan Street

department: School of Environment

institute: Tsinghua University

description: GeoChip data for soil sample collected at the 3800 m elevation grassland with grazing, replicate 1

hyb_protocol: Then DNA was dried in a SpeedVac (ThermoSavant, Milford, MA, USA) at 45°C for 45 minutes. The hybridization was carried out at 42°C for 16 hours on a MAUI hybridization station (BioMicro, Salt Lake City, UT, USA).

scan_protocol: After purification, GeoChip microarrays were scanned by a NimbleGen MS200 scanner (Roche, Madison, WI, USA) at 633 nm using a laser power and photomultiplier tube (PMT) gain of 100% and 75%, respectively.

data_processing: Signal intensities were quantified and processed using the data analysis pipeline as previously described (He et al 2010). Then processed GeoChip data were analyzed using the following steps: (i) remove the poor quality spots, which were flagged as 1 or 3 by ImaGene or with a signal to noise ratio (SNR) of less than 2.0; (ii) normalize the signal intensity of each spot by dividing the signal intensity by the total intensity of the microarray followed by multiplying by a constant; (iii) transform the data to the natural logarithmic form; and (iv) remove genes detected in only one out of three samples from the same elevation.

organism: uncultured bacterium

source_name: Soil microbes in Tibetan grasslands

label_protocol: As previously described (Yang et al 2013), DNA samples were labeled with the fluorescent dye Cy-5 using a random priming method and purified using the QIA quick purification kit (Qiagen, Valencia, CA, USA).

extract_protocol: Soil genomic DNA was extracted using a FastDNA spin kit for soil (MP Biomedical, Carlsbad, CA, USA) following the manufacturer’s instructions. To purify it, DNA extract was mixed with 2.5 volume of 100% ice cold ethanol and 0.1 volume of 3 M NaOAc (pH 5.2) prior to overnight incubation at -20°C. DNA was precipitated by centrifugation for 30 minutes at 13,000 x g. Then supernatant was decanted and washed with 1 ml of 70% ethanol. DNA was air-dried and dissolved in 50 µl of nuclease-free water. DNA quality and quantity were measured using NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies Inc., Wilmington, DE, USA) and with PicoGreen (Ahn et al 1996) using a FLUOstar Optima (BMG Labtech, Jena, Germany), respectively.

treatment_protocol: In August 2009, soil samples were collected from all of the plots. Five soil cores at a depth of 0-20 cm and diameter of 1.5 cm were randomly taken from each plot and mixed thoroughly to generate a soil sample representing the plot. Soil samples were kept on ice when transporting to laboratory, and sieved with 2 mm mesh to remove roots and stones. Soil samples were preserved at -80°C before DNA extraction.

tag: sourced elevations

tag: transplanted elevations

tag: grazing condition

value: Grazing

tag: vegetation landsape

value: Grassland


title: MPNST-09 [methylation]

value: malignant peripheral nerve sheath tumor (MPNST)


title: MPNST-10 [methylation]


title: 3800Gb

description: GeoChip data for soil sample collected at the 3800 m elevation grassland with grazing, replicate 2


title: MPNST-08 [methylation]


title: MFS-06


title: 3800Gc

description: GeoChip data for soil sample collected at the 3800 m elevation grassland with grazing, replicate 3


title: 3800b

description: GeoChip data for soil sample collected at the 3800 m elevation grassland without grazing, replicate 2

value: Ungrazing


title: 86c

description: GeoChip data for soil sample collected at the 3600 m elevation sourced from 3800m after 3 years transplant, from gassland without grazing, replicate 3


title: MPNST-07 [methylation]


title: MPNST-06 [methylation]


title: 3800a

description: GeoChip data for soil sample collected at the 3800 m elevation grassland without grazing, replicate 1


title: 86b

description: GeoChip data for soil sample collected at the 3600 m elevation sourced from 3800m after 3 years transplant, from gassland without grazing, replicate 2


title: 3800c

description: GeoChip data for soil sample collected at the 3800 m elevation grassland without grazing, replicate 3


title: MPNST-05 [methylation]


title: MPNST-04 [methylation]


title: 84c

description: GeoChip data for soil sample collected at the 3400 m elevation sourced from 3800m after 3 years transplant, from gassland without grazing, replicate 3


title: MLS-06 [methylation]

value: myxoid liposarcoma (MLS)


title: 84b

description: GeoChip data for soil sample collected at the 3400 m elevation sourced from 3800m after 3 years transplant, from gassland without grazing, replicate 2


title: MLS-08 [methylation]


title: MLS-07 [methylation]


title: MLS-04 [methylation]


title: MLS-03 [methylation]


title: MPNST-01 [methylation]


title: 3600Gc

description: GeoChip data for soil sample collected at the 3600 m elevation grassland with grazing, replicate 3


title: MPNST-03 [methylation]


title: 3600Ga

description: GeoChip data for soil sample collected at the 3600 m elevation grassland with grazing, replicate 1


title: 3600Gb

description: GeoChip data for soil sample collected at the 3600 m elevation grassland with grazing, replicate 2


title: 68a

description: GeoChip data for soil sample collected at the 3800 m elevation sourced from 3600m after 3 years transplant, from gassland without grazing, replicate 1


title: MLS-02 [methylation]


title: MPNST-02 [methylation]


title: 68b

description: GeoChip data for soil sample collected at the 3800 m elevation sourced from 3600m after 3 years transplant, from gassland without grazing, replicate 2


title: MLS-05 [methylation]


title: 82b

description: GeoChip data for soil sample collected at the 3200 m elevation sourced from 3800m after 3 years transplant, from gassland without grazing, replicate 2


title: 82c

description: GeoChip data for soil sample collected at the 3200 m elevation sourced from 3800m after 3 years transplant, from gassland without grazing, replicate 3


title: 86a

description: GeoChip data for soil sample collected at the 3600 m elevation sourced from 3800m after 3 years transplant, from gassland without grazing, replicate 1


title: 82a

description: GeoChip data for soil sample collected at the 3200 m elevation sourced from 3800m after 3 years transplant, from gassland without grazing, replicate 1


title: MLS-09 [methylation]


title: 84a

description: GeoChip data for soil sample collected at the 3400 m elevation sourced from 3800m after 3 years transplant, from gassland without grazing, replicate 1


title: 68c

description: GeoChip data for soil sample collected at the 3800 m elevation sourced from 3600m after 3 years transplant, from gassland without grazing, replicate 3


title: 3600b

description: GeoChip data for soil sample collected at the 3600 m elevation grassland without grazing, replicate 2


title: 3600c

description: GeoChip data for soil sample collected at the 3600 m elevation grassland without grazing, replicate 3


title: 3600a

description: GeoChip data for soil sample collected at the 3600 m elevation grassland without grazing, replicate 1


title: MLS-01 [methylation]


title: MFS-07 [methylation]


title: 64c

description: GeoChip data for soil sample collected at the 3400 m elevation sourced from 3600m after 3 years transplant, from gassland without grazing, replicate 3


title: 64a

description: GeoChip data for soil sample collected at the 3400 m elevation sourced from 3600m after 3 years transplant, from gassland without grazing, replicate 1


title: MFS-04 [methylation]


title: MFS-06 [methylation]


title: LMS-09 [methylation]

value: leiomyosarcoma (LMS)


title: LMS-07 [methylation]


title: 62c

description: GeoChip data for soil sample collected at the 3200 m elevation sourced from 3600m after 3 years transplant, from gassland without grazing, replicate 3


title: LMS-05 [methylation]


title: 62a

description: GeoChip data for soil sample collected at the 3200 m elevation sourced from 3600m after 3 years transplant, from gassland without grazing, replicate 1


title: 64b

description: GeoChip data for soil sample collected at the 3400 m elevation sourced from 3600m after 3 years transplant, from gassland without grazing, replicate 2


title: 3400Gc

description: GeoChip data for soil sample collected at the 3400 m elevation grassland with grazing, replicate 3


title: LMS-10 [methylation]


title: MFS-02 [methylation]

value: myxofibrosarcoma (MFS)


title: MFS-01 [methylation]

value: female


title: LMS-08 [methylation]


title: MFS-03 [methylation]


title: 3400GNc

description: GeoChip data for soil sample collected at the 3400 m elevation shrubland with grazing, replicate 3

value: Shrubland


title: 48c

description: GeoChip data for soil sample collected at the 3800 m elevation sourced from 3400m after 3 years transplant, from gassland without grazing, replicate 3


title: 3400GNb

description: GeoChip data for soil sample collected at the 3400 m elevation shrubland with grazing, replicate 2


title: 3400GNa

description: GeoChip data for soil sample collected at the 3400 m elevation shrubland with grazing, replicate 1


title: MFS-05 [methylation]


title: LMS-04 [methylation]


title: LMS-06 [methylation]


title: 3400Gb

description: GeoChip data for soil sample collected at the 3400 m elevation grassland with grazing, replicate 2


title: LMS-03 [methylation]


title: 62b

description: GeoChip data for soil sample collected at the 3200 m elevation sourced from 3600m after 3 years transplant, from gassland without grazing, replicate 2


title: 3400Ga

description: GeoChip data for soil sample collected at the 3400 m elevation grassland with grazing, replicate 1


title: LMS-02 [methylation]


title: 48a

description: GeoChip data for soil sample collected at the 3800 m elevation sourced from 3400m after 3 years transplant, from gassland without grazing, replicate 1


title: LMS-01 [methylation]


title: 46c

description: GeoChip data for soil sample collected at the 3600 m elevation sourced from 3400m after 3 years transplant, from gassland without grazing, replicate 3


title: 48b

description: GeoChip data for soil sample collected at the 3800 m elevation sourced from 3400m after 3 years transplant, from gassland without grazing, replicate 2


title: 46b

description: GeoChip data for soil sample collected at the 3600 m elevation sourced from 3400m after 3 years transplant, from gassland without grazing, replicate 2


title: FAT-02 [methylation]

value: non-neoplastic fat


title: 3400c

description: GeoChip data for soil sample collected at the 3400 m elevation grassland without grazing, replicate 3


title: DDLS-04 [methylation]

value: dedifferentiated liposarcoma (DDLS)


title: FAT-01 [methylation]


title: DDLS-07 [methylation]


title: 3200Gc

description: GeoChip data for soil sample collected at the 3200 m elevation grassland with grazing, replicate 3


title: DDLS-12 [methylation]


title: 46a

description: GeoChip data for soil sample collected at the 3600 m elevation sourced from 3400m after 3 years transplant, from gassland without grazing, replicate 1


title: 3200Gb

description: GeoChip data for soil sample collected at the 3200 m elevation grassland with grazing, replicate 2


title: MLS-10 [methylation]


title: 28c

description: GeoChip data for soil sample collected at the 3800 m elevation sourced from 3200m after 3 years transplant, from gassland without grazing, replicate 3


title: 28b

description: GeoChip data for soil sample collected at the 3800 m elevation sourced from 3200m after 3 years transplant, from gassland without grazing, replicate 2


title: 3400b

description: GeoChip data for soil sample collected at the 3400 m elevation grassland without grazing, replicate 2


title: DDLS-02 [methylation]


title: DDLS-06 [methylation]


title: DDLS-10 [methylation]


title: DDLS-09 [methylation]


title: DDLS-08 [methylation]


title: 42a

description: GeoChip data for soil sample collected at the 3200 m elevation sourced from 3400m after 3 years transplant, from gassland without grazing, replicate 1


title: DDLS-11 [methylation]


title: DDLS-05 [methylation]


title: DDLS-03 [methylation]


title: 3200Ga

description: GeoChip data for soil sample collected at the 3200 m elevation grassland with grazing, replicate 1


title: 3400a

description: GeoChip data for soil sample collected at the 3400 m elevation grassland without grazing, replicate 1


title: DDLS-01 [methylation]


title: 42b

description: GeoChip data for soil sample collected at the 3200 m elevation sourced from 3400m after 3 years transplant, from gassland without grazing, replicate 2


title: 42c

description: GeoChip data for soil sample collected at the 3200 m elevation sourced from 3400m after 3 years transplant, from gassland without grazing, replicate 3


title: 28a

description: GeoChip data for soil sample collected at the 3800 m elevation sourced from 3200m after 3 years transplant, from gassland without grazing, replicate 1


title: 26b

description: GeoChip data for soil sample collected at the 3600 m elevation sourced from 3200m after 3 years transplant, from gassland without grazing, replicate 2


title: 26c

description: GeoChip data for soil sample collected at the 3600 m elevation sourced from 3200m after 3 years transplant, from gassland without grazing, replicate 3


title: Muscle biopsies from trained COPD patient #42 with low Body Mass Index

city: Birmingham

last: Turan

address: University of Birmingham, Edgbaston

institute: University of Birmingham

description: Gene expression data from muscle biopsies of a trained COPD individual with low BMI.

hyb_protocol: Affymetrix GeneChip technology was performed using Human U133 Plus2 GeneChips according to the manufacturer's suggested protocols.

scan_protocol: Affymetrix Scanner 3000 7G.

data_processing: The data were quantile normalized using the R package RMA.

source_name: Trained COPD with low BMI

label_protocol: Amplification and labeling of cRNA was performed with the Affymetrix IVT labeling  kit.

extract_protocol: RNA was isolated using the RNeasy extraction kit (QIAGEN, USA) according to the manufacturer's instructions.

treatment_protocol: 8 weeks of exercise training.

value: musculus vastus lateralis

value: chronic obstructive pulmonary disease (COPD)

tag: exercise state

value: trained

tag: bmi

value: low

tag: individual


title: 26a

description: GeoChip data for soil sample collected at the 3600 m elevation sourced from 3200m after 3 years transplant, from gassland without grazing, replicate 1


title: Muscle biopsies from trained COPD patient #41 with low Body Mass Index

tag: disease state


title: 24a

description: GeoChip data for soil sample collected at the 3400 m elevation sourced from 3200m after 3 years transplant, from gassland without grazing, replicate 1


title: 3200b

description: GeoChip data for soil sample collected at the 3200 m elevation grassland without grazing, replicate 2


title: 24b

description: GeoChip data for soil sample collected at the 3400 m elevation sourced from 3200m after 3 years transplant, from gassland without grazing, replicate 2


title: 3200c

description: GeoChip data for soil sample collected at the 3200 m elevation grassland without grazing, replicate 3


title: N3D cell line Biological replicate in antisense orientation replicate 4

first: Kathleen

middle: Helen

last: Burns

address: 720 Rutland Ave Ross 524

department: Pathology

institute: Johns Hopkins University School of Medicine

description: Control experiment showing the specificity of the transposable element array.

hyb_protocol: Arrays were hybridized following the manufacturer’s protocol for 17h. Longer hybridization times up to 65 h were attempted in order to verify saturation at the recommended 17h.

scan_protocol: Arrays were washed and scanned on an Agilent 2mm scanner at 70% PMT (photomultiplier tubes) for both green and red channels. Agilent's Feature Extractor was used for generating data files.

data_processing: Probe intensities from the two-channel arrays were log2 transformed and LOESS normalized.

source_name: Control Mouse cell line N3D biological replicate 4

label_protocol: Poly-A RNA was reverse transcribed to double stranded cDNA using MMLV RT. T7 promoter was ligated to the 3’ end corresponding to poly-A. T7 was used to generate single stranded, labeled cRNA. RNA was labeled using Quick amp kit (Agilent) with Cy-dye labeled Cytosine.

extract_protocol: N1G and N3D were derived from primary breast cancer overexpressing Rat Her2/Neu in Balbc mice. Cell lines were maintained in D-MEM with 10% FBS and 100 units/ml penicillin/streptomycin. After reaching 75% confluence, Trizol was added directly onto the plates and total RNA was extracted following the standard Trizol prescribed protocol.

tag: age

tag: strain

value: Balbc

source_name: Control Mouse cell line N3D Total RNA extracted from different culture plates of same cell line replicate 4


title: Muscle biopsies from trained COPD patient #38 with low Body Mass Index

tag: tissue


title: Muscle biopsies from trained COPD patient #37 with low Body Mass Index


title: Muscle biopsies from sedentary COPD patient #42 with low Body Mass Index

description: Gene expression data from muscle biopsies of a sedentary COPD individual with low BMI.

source_name: Sedentary COPD with low BMI

value: sedentary


title: Muscle biopsies from sedentary COPD patient #39 with low Body Mass Index


title: N3D cell line Biological replicate in antisense orientation replicate 1

source_name: Control Mouse cell line N3D biological replicate 1

source_name: Control Mouse cell line N3D Total RNA extracted from different culture plates of same cell line replicate 1


title: Muscle biopsies from trained COPD patient #36 with low Body Mass Index


title: N3D cell line Biological replicate in antisense orientation replicate 2

source_name: Control Mouse cell line N3D biological replicate 2

source_name: Control Mouse cell line N3D Total RNA extracted from different culture plates of same cell line replicate 2


title: Muscle biopsies from trained COPD patient #39 with low Body Mass Index