title: baseline_45familylinkage_GM07051_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07051&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM07051.

source_name: Lymphoblastoid cell lines derived from GM07051


title: baseline_45familylinkage_GM07341_rep1

status: Public on Sep 21 2010

type: RNA

city: Philadelphia

first: Renuka

last: Nayak

state: PA

address: 3516 Civic Center Blvd

country: USA

institute: HHMI, University of Pennsylvania

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07341&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM07341.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16-18 hr at 45C on Affymetrix GeneChip Human HG-Focus Target Array (U95v2). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix print default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Lymphoblastoid cell lines derived from GM07341

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

growth_protocol: The cells were grown at a density of 500,000 cells/ ml in RPMI 1640 with 15% FBS, 1% penicillin-streptomycin, 2mM L-glutamine at 37°C in a humidified 5% CO2 chamber.

extract_protocol: RNA was extracted using the Rneasy Mini-Kit (Qiagen) as per the manufacturer's instructions

tag: coriell cell line repository identifier

tag: cell type

value: lymphoblastoid


title: baseline_45familylinkage_GM07054_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07054&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM07054.

source_name: Lymphoblastoid cell lines derived from GM07054


title: baseline_45familylinkage_GM07351_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07351&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM07351.

source_name: Lymphoblastoid cell lines derived from GM07351


title: baseline_45familylinkage_GM07352_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07352&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM07352.

source_name: Lymphoblastoid cell lines derived from GM07352


title: baseline_45familylinkage_GM07341_rep2


title: baseline_45familylinkage_GM07062_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07062&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM07062.

source_name: Lymphoblastoid cell lines derived from GM07062


title: baseline_45familylinkage_GM07344_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07344&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM07344.

source_name: Lymphoblastoid cell lines derived from GM07344


title: baseline_45familylinkage_GM07345_rep2

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07345&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM07345.

source_name: Lymphoblastoid cell lines derived from GM07345


title: baseline_45familylinkage_GM07051_rep2


title: baseline_45familylinkage_GM07052_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07052&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM07052.

source_name: Lymphoblastoid cell lines derived from GM07052


title: baseline_45familylinkage_GM07055_rep2

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07055&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM07055.

source_name: Lymphoblastoid cell lines derived from GM07055


title: baseline_45familylinkage_GM07055_rep1


title: baseline_45familylinkage_GM07050_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07050&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM07050.

source_name: Lymphoblastoid cell lines derived from GM07050


title: baseline_45familylinkage_GM07049_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07049&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM07049.

source_name: Lymphoblastoid cell lines derived from GM07049


title: baseline_45familylinkage_GM07046_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07046&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM07046.

source_name: Lymphoblastoid cell lines derived from GM07046


title: baseline_45familylinkage_GM07047_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07047&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM07047.

source_name: Lymphoblastoid cell lines derived from GM07047


title: baseline_45familylinkage_GM07048_rep2

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07048&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM07048.

source_name: Lymphoblastoid cell lines derived from GM07048


title: baseline_45familylinkage_GM07044_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07044&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM07044.

source_name: Lymphoblastoid cell lines derived from GM07044


title: baseline_45familylinkage_GM07061_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07061&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM07061.

source_name: Lymphoblastoid cell lines derived from GM07061


title: baseline_45familylinkage_GM07039_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07039&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM07039.

source_name: Lymphoblastoid cell lines derived from GM07039


title: baseline_45familylinkage_GM07038_rep2

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07038&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM07038.

source_name: Lymphoblastoid cell lines derived from GM07038


title: baseline_45familylinkage_GM07056_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07056&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM07056.

source_name: Lymphoblastoid cell lines derived from GM07056


title: baseline_45familylinkage_GM07040_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07040&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM07040.

source_name: Lymphoblastoid cell lines derived from GM07040


title: baseline_45familylinkage_GM07042_rep2

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07042&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM07042.

source_name: Lymphoblastoid cell lines derived from GM07042


title: baseline_45familylinkage_GM07045_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07045&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM07045.

source_name: Lymphoblastoid cell lines derived from GM07045


title: baseline_45familylinkage_GM07049_rep2


title: baseline_45familylinkage_GM07056_rep2


title: baseline_45familylinkage_GM07042_rep1


title: baseline_45familylinkage_GM07048_rep1


title: baseline_45familylinkage_GM07033_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07033&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM07033.

source_name: Lymphoblastoid cell lines derived from GM07033


title: baseline_45familylinkage_GM07034_rep2

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07034&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM07034.

source_name: Lymphoblastoid cell lines derived from GM07034


title: baseline_45familylinkage_GM07034_rep1


title: baseline_45familylinkage_GM07031_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07031&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM07031.

source_name: Lymphoblastoid cell lines derived from GM07031


title: baseline_45familylinkage_GM07027_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07027&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM07027.

source_name: Lymphoblastoid cell lines derived from GM07027


title: baseline_45familylinkage_GM07036_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07036&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM07036.

source_name: Lymphoblastoid cell lines derived from GM07036


title: baseline_45familylinkage_GM07038_rep1


title: baseline_45familylinkage_GM07028_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07028&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM07028.

source_name: Lymphoblastoid cell lines derived from GM07028


title: baseline_45familylinkage_GM07046_rep2

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07046&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM07046.

source_name: Lymphoblastoid cell lines derived from GM07046


title: baseline_45familylinkage_GM07029_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07029&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM07029.

source_name: Lymphoblastoid cell lines derived from GM07029


title: baseline_45familylinkage_GM07032_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07032&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM07032.

source_name: Lymphoblastoid cell lines derived from GM07032


title: baseline_45familylinkage_GM07035_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07035&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM07035.

source_name: Lymphoblastoid cell lines derived from GM07035


title: baseline_45familylinkage_GM07029_rep2


title: baseline_45familylinkage_GM07025_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07025&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM07025.

source_name: Lymphoblastoid cell lines derived from GM07025


title: baseline_45familylinkage_GM07030_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07030&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM07030.

source_name: Lymphoblastoid cell lines derived from GM07030


title: baseline_45familylinkage_GM07026_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07026&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM07026.

source_name: Lymphoblastoid cell lines derived from GM07026


title: baseline_45familylinkage_GM07031_rep2


title: baseline_45familylinkage_GM07024_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07024&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM07024.

source_name: Lymphoblastoid cell lines derived from GM07024


title: baseline_45familylinkage_GM07021_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07021&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM07021.

source_name: Lymphoblastoid cell lines derived from GM07021


title: baseline_45familylinkage_GM07022_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07022&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM07022.

source_name: Lymphoblastoid cell lines derived from GM07022


title: baseline_45familylinkage_GM07022_rep2


title: baseline_45familylinkage_GM07023_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07023&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM07023.

source_name: Lymphoblastoid cell lines derived from GM07023


title: baseline_45familylinkage_GM07020_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07020&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM07020.

source_name: Lymphoblastoid cell lines derived from GM07020


title: baseline_45familylinkage_GM07017_rep2

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07017&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM07017.

source_name: Lymphoblastoid cell lines derived from GM07017


title: baseline_45familylinkage_GM07019_rep2

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07019&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM07019.

source_name: Lymphoblastoid cell lines derived from GM07019


title: baseline_45familylinkage_GM07017_rep1


title: baseline_45familylinkage_GM07019_rep1


title: baseline_45familylinkage_GM07018_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07018&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM07018.

source_name: Lymphoblastoid cell lines derived from GM07018


title: baseline_45familylinkage_GM07015_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07015&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM07015.

source_name: Lymphoblastoid cell lines derived from GM07015


title: baseline_45familylinkage_GM07014_rep2

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07014&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM07014.

source_name: Lymphoblastoid cell lines derived from GM07014


title: baseline_45familylinkage_GM07013_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07013&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM07013.

source_name: Lymphoblastoid cell lines derived from GM07013


title: baseline_45familylinkage_GM07008_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07008&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM07008.

source_name: Lymphoblastoid cell lines derived from GM07008


title: baseline_45familylinkage_GM07006_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07006&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM07006.

source_name: Lymphoblastoid cell lines derived from GM07006


title: baseline_45familylinkage_GM07014_rep1


title: baseline_45familylinkage_GM07011_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07011&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM07011.

source_name: Lymphoblastoid cell lines derived from GM07011


title: baseline_45familylinkage_GM07012_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07012&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM07012.

source_name: Lymphoblastoid cell lines derived from GM07012


title: baseline_45familylinkage_GM07010_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07010&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM07010.

source_name: Lymphoblastoid cell lines derived from GM07010


title: baseline_45familylinkage_GM07013_rep2


title: baseline_45familylinkage_GM07005_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07005&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM07005.

source_name: Lymphoblastoid cell lines derived from GM07005


title: baseline_45familylinkage_GM07009_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07009&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM07009.

source_name: Lymphoblastoid cell lines derived from GM07009


title: baseline_45familylinkage_GM07003_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07003&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM07003.

source_name: Lymphoblastoid cell lines derived from GM07003


title: baseline_45familylinkage_GM07000_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07000&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM07000.

source_name: Lymphoblastoid cell lines derived from GM07000


title: baseline_45familylinkage_GM07001_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07001&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM07001.

source_name: Lymphoblastoid cell lines derived from GM07001


title: baseline_45familylinkage_GM07016_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07016&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM07016.

source_name: Lymphoblastoid cell lines derived from GM07016


title: baseline_45familylinkage_GM07002_rep2

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07002&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM07002.

source_name: Lymphoblastoid cell lines derived from GM07002


title: baseline_45familylinkage_GM07002_rep1


title: baseline_45familylinkage_GM07000_rep2


title: baseline_45familylinkage_GM06999_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM06999&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM06999.

source_name: Lymphoblastoid cell lines derived from GM06999


title: baseline_45familylinkage_GM06997_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM06997&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM06997.

source_name: Lymphoblastoid cell lines derived from GM06997


title: baseline_45familylinkage_GM07004_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM07004&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM07004.

source_name: Lymphoblastoid cell lines derived from GM07004


title: baseline_45familylinkage_GM06985_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM06985&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM06985.

source_name: Lymphoblastoid cell lines derived from GM06985


title: baseline_45familylinkage_GM06998_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM06998&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM06998.

source_name: Lymphoblastoid cell lines derived from GM06998


title: baseline_45familylinkage_GM06985_rep2


title: baseline_45familylinkage_GM06993_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM06993&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM06993.

source_name: Lymphoblastoid cell lines derived from GM06993


title: baseline_45familylinkage_GM06990_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM06990&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM06990.

source_name: Lymphoblastoid cell lines derived from GM06990


title: baseline_45familylinkage_GM06988_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM06988&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM06988.

source_name: Lymphoblastoid cell lines derived from GM06988


title: baseline_45familylinkage_GM06995_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM06995&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM06995.

source_name: Lymphoblastoid cell lines derived from GM06995


title: baseline_45familylinkage_GM06986_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM06986&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM06986.

source_name: Lymphoblastoid cell lines derived from GM06986


title: baseline_45familylinkage_GM06991_rep2

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM06991&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM06991.

source_name: Lymphoblastoid cell lines derived from GM06991


title: baseline_45familylinkage_GM06996_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM06996&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM06996.

source_name: Lymphoblastoid cell lines derived from GM06996


title: baseline_45familylinkage_GM06983_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM06983&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM06983.

source_name: Lymphoblastoid cell lines derived from GM06983


title: baseline_45familylinkage_GM06992_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM06992&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM06992.

source_name: Lymphoblastoid cell lines derived from GM06992


title: baseline_45familylinkage_GM06993_rep2


title: baseline_45familylinkage_GM06991_rep1


title: baseline_45familylinkage_GM06981_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM06981&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM06981.

source_name: Lymphoblastoid cell lines derived from GM06981


title: baseline_45familylinkage_GM06994_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM06994&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM06994.

source_name: Lymphoblastoid cell lines derived from GM06994


title: baseline_45familylinkage_GM06987_rep2

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM06987&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM06987.

source_name: Lymphoblastoid cell lines derived from GM06987


title: SUDHL4_2

city: Miami

first: Maria

middle: Eugenia

last: Figueroa

state: FL

address: 1501 NW 10th Ave, BRB 709A, Locator code C227

department: Human Genetics

institute: University of Miiami

hyb_protocol: See Roche NimbleGen website and Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319. for details

scan_protocol: Scanning was performed using a GenePix 4000B scanner (Axon Instruments) as previously described in Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319.

data_processing: Raw data files (pair files) were processed with Roche NimbleGen's version of the RMA algorithm (without background correction) in NimbleScan 2.3 software. Probe sets that showed at least a 1.8 log-ratio expression change from CP-treated samples after the administration of RI-BPI (BPI-treated samples) were used to generate a BPI gene expression (GE) signature. We subtracted the BPI-GE signature of BPI-responsive cells (OCI-Ly7, OCI-Ly10, Farage, SUDHL6 and SU-DHL4) from the BPI-GE signature of BPI-resistant cells (Pfeiffer, Toledo, OCI-Ly4 and Karpas422).

source_name: SUDHL4 Replicate #2

label_protocol: Random priming with 9-mers pre-labeled with either Cy3 or Cy5 according to manufacturer's instructions using the NimbleGen Dual-Color DNA Labeling Kit (cat # 05223547001)

extract_protocol: Rneasy Plus Mini kit (Qiagen)

value: DLBCL cell line

tag: treatment group

value: Treated with control peptide

value: Treated with Bcl6 inhibitor peptide


title: AVG_Signal-31 -CTR METH b (7)

city: Baltimore

first: Jean Lud

last: Cadet

state: MD

address: 251 Bayview Blvd, Suite 200

department: Molecular Neuropsychiatry Research Branch

institute: NIDA, IRP

description: SAMPLE 30

hyb_protocol: Microarray hybridization.  Microarray hybridization was carried out using Illumina’s RatRef-12 Expression BeadChips arrays (22, 523 probes) (Illumina Inc., San Diego, CA). In brief, a 600 ng aliquot of total RNA from each striatal sample was amplified using Ambion’s Illumina RNA Amplification kit (cat. no. IL1791; Ambion, Austin, TX). Single-stranded RNA (cRNA) was generated and labeled by incorporating biotin-16-UTP (Roche Diagnostics GmbH, Mannheim, Germany, cat. no. 11388908910). 750 ng of each cRNA sample were hybridized to Illumina arrays at 55 oC overnight according to the Illumina Whole-Genome Gene Expression Protocol for BeadStation (Illumina Inc., San Diego, CA, cat. # 11201828).

scan_protocol: Hybridized biotinylated cRNA was detected with Cyanine3-streptavidin (Amersham Biosciences, Piscataway, NJ, cat. #146065) and quantified using Illumina's BeadStation 500GX Genetic Analysis Systems scanner.

data_processing: The microarray data reported in the manuscript are in accordance with MIAME guidelines. The Illumina BeadStudio software was used to measure fluorescent hybridization signals. Data were extracted by BeadStudio (Illumina, San Diego, CA) and then analyzed using GeneSpring software v. 7.3.1 (Silicon Genetics, Redwood City, CA, USA). Raw data were imported into GeneSpring and normalized using global normalization. The normalized data were used to identify changes in gene expression in these 4 group comparisons.  A gene was identified as changed if it showed increased or decreased expression according to an arbitrary cut-off of 1.7-fold changes at p < 0.025.   In previous studies, genes identified by similar criteria were consistently validated by quantitative PCR (Krasnova et al., 2008; Cadet et al., 2009; Jayanthi et al., 2009).

organism: Rattus norvegicus

source_name: Striatal Brain Tissue

label_protocol: Brains were quickly removed,   tissues were dissected on ice, snap frozen on dry ice, and stored at -80°C until used in HPLC, microarray, and quantitative PCR experiments.   The experimental groups were labelled as: saline-treated controls (SC), METH-treated controls (MC), non-lesioned side of saline-treated 6-OHDA-injected rats (SNL), lesioned side of saline-treated 6-OHDA-injected rats (SL), non-lesioned side of METH-treated 6-OHDA-injected animals (MNL), and lesioned side of METH-treated 6-OHDA-injected animals (ML).

growth_protocol: Animals. Male Sprague-Dawley rats (Charles Rivers Laboratories, Raleigh, NC), weighing g at the beginning of the experiments were used in the present study. Animals were housed in a humidity- and temperature-controlled room and were given free access to food and water. All animal procedures were performed according to the National Institutes of Health Guide for the Care and Use of Laboratory Animals and were approved by the local Animal Care Committee.

extract_protocol: METH treatment and tissue collection. One week after measuring METH-induced rotation, the animals were divided into two groups based on METH-induced rotation. The two matched groups of animals were injected with either saline or METH (2.5 mg/kg, intraperitoneally) and then sacrificed two hours after the injection. Additional control animals that had not gotten 6-OHDA injections were also used.  Their brains were quickly removed,   tissues were dissected on ice, snap frozen on dry ice, and stored at -80°C until used in HPLC, microarray, and quantitative PCR experiments.   The experimental groups were: saline-treated controls (SC), METH-treated controls (MC), non-lesioned side of saline-treated 6-OHDA-injected rats (SNL), lesioned side of saline-treated 6-OHDA-injected rats (SL), non-lesioned side of METH-treated 6-OHDA-injected animals (MNL), and lesioned side of METH-treated 6-OHDA-injected animals (ML).  HPLC. For monoamine analysis, the brain regions were homogenized in 0.01M HClO4 and centrifuged at 14, 000 x g for 15 min. DA, 3,4-dihydroxyphenylacetic acid (DOPAC), homovanillic acid (HVA), 5-HT and 5-hydroxyindoleacetic acid (5-HIAA) levels were analyzed in the brain tissue extracts using HPLC with electrochemical detector (Krasnova et al., 2007).      RNA extraction. Total RNA was isolated using Qiagen RNeasy Midi kit (Qiagen, Valencia, CA) according to the manufacturer's instructions. RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) and showed no degradation.

treatment_protocol: 6-OHDA lesioning. Unilateral lesions were performed under anesthesia with chloral hydrate (400 mg/kg, i.p.).  After immobilization on a stereotaxic frame (model 940; David Kopf Instruments), a hole was drilled in the skull for injections of 6-OHDA in the medial forebrain bundle (MFB).  6-OHDA (2 µg/µl x 5 µl in 0.9% NaCl containing 0.2 mg/ml ascorbic acid) was unilaterally injected into the left medial forebrain bundle (-4.4 mm AP, 1.2 mm ML relative to bregma and 8.4 mm below skull) over 4 minutes.  At the end of each injection, the micropipette was left in place for an additional 5 min and then withdrawn slowly to prevent reflux of the solution.

tag: treatment

value: Meth Control

tag: strain

value: Sprague Dawley


title: baseline_45familylinkage_GM06994_rep2


title: baseline_45familylinkage_GM06980_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM06980&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM06980.

source_name: Lymphoblastoid cell lines derived from GM06980


title: LY10_2

source_name: LY10 Replicate #2


title: baseline_45familylinkage_GM06982_rep1

description:
http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM06982&PgId=166
Gene expression data at baseline from lymphoblastoid cells of individual GM06982.

source_name: Lymphoblastoid cell lines derived from GM06982


title: AVG_Signal-21 -6-OHDA SAL L (20)

description: SAMPLE 20

value: Saline Lesion


title: SUDHL6_2

source_name: SUDHL6 Replicate #2


title: AVG_Signal-32 -CTR METH b (14)

description: SAMPLE 31


title: AVG_Signal-26 -CTR SAL a (8a)

description: SAMPLE 25

value: Saline Control


title: AVG_Signal-30 -CTR METH a (13)

description: SAMPLE 29


title: LY7_2

source_name: LY7 Replicate #2


title: FARAGE_1

source_name: FARAGE Replicate #1


title: AVG_Signal-29 -CTR METH a (5)

description: SAMPLE 28


title: SUDHL4_1

source_name: SUDHL4 Replicate #1


title: AVG_Signal-28 -CTR SAL b (16)

description: SAMPLE 27


title: AVG_Signal-23 -6-OHDA SAL L (28)

description: SAMPLE 22


title: AVG_Signal-20 -6-OHDA SAL L (12)

description: SAMPLE 19


title: FARAGE_2

source_name: FARAGE Replicate #2


title: KARPAS422_1

source_name: KARPAS422 Replicate #1


title: baseline_45familylinkage_GM06987_rep1


title: AVG_Signal-22 -6-OHDA SAL L (24)

description: SAMPLE 21


title: TOLEDO_1

source_name: TOLEDO Replicate #1


title: AVG_Signal-27 -CTR SAL a (15)

description: SAMPLE 26


title: LY10_1

source_name: LY10 Replicate #1


title: PFEIFFER_1

source_name: PFEIFFER Replicate #1


title: AVG_Signal-19 - 6-OHDA SAL L (4)

description: SAMPLE 18


title: AVG_Signal-24 -6-OHDA SAL L (32)

description: SAMPLE 23


title: SUDHL6_1

source_name: SUDHL6 Replicate #1


title: AVG_Signal-25 -CTR SAL a (6)

description: SAMPLE 24


title: decitabine treated HL60 cells replicate 3 (methylation, MeDIP)

type: genomic

city: Rome

first: Emiliano

last: Fabiani

address: L.go A. Gemelli 10

department: Hematology

country: Italy

institute: Università Cattolica del Sacro Cuore

description: hl60 dac 5mC 6.CEL

hyb_protocol: All hybridization reactions were performed using GeneChip Fluidics Station 450 (Affymetrix, USA).

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 (Affymetrix, USA).

data_processing: The MeDIP.CEL files for biological triplicates of HL60 mock and DAC-treated were log2 transformed, normalized and imported into the Partek Genomic Suite software (PGS), according to the manufacturer’s instructions. The baseline signal normalization was obtained through subtraction of log2 IN signal intensity at each of 4.2 million array probes. The differences between treated and control samples were performed using a t-Test (p-value 0.05). Significantly enriched regions were obtained by the MAT algorithm (Model-based Analysis of Tiling arrays) and the following cut-offs: minimum genomic region 600 nucleotides, minimum 10 probes, p-value threshold 0.05 and state 0 ignored.

molecule: genomic DNA

source_name: decitabine treated HL60 cells + MeDIP

label_protocol: ChIP on chip kit following Affymetrix protocol

growth_protocol: The human acute myeloid leukemia cell line HL60 was maintained in Iscove's Modified Dulbecco's Medium (IMDM) supplemented with 20% heat inactivated Fetal Bovine Serum (FBS), 2 mM L-Glutamine and 1x Penicilin Streptomycin solution, and incubated in humidified atmosphere containing 5% CO2 at 37°C.

extract_protocol: DNA was extracted using the QIAamp DNA Mini Kit (Qiagen AG). Methylated DNA Immunoprecipitation (MeDIP) assay  was performed according to Weber et al (Nature Genetics 2005), with minor modifications. Following sonication of DNA (10 µg, 200-1000 bp fragments) extracted from mock and DAC-treated HL60 cells, methyl-CpG island enrichment was performed using an anti-5-Methylcytidine Antibody (GeneTex Inc). The relative enrichment of methyl-CpG DNA was evaluated and validated by a semi-quantitative real-time PCR (≥400 enrichment-folds) using specific primers for hypermethylated gene DAPK1.

treatment_protocol: HL60 cells placed at a density of 1 x 105 cells/mL were treated with 1 µM decitabine or the same volume of vehicle (mock sample) for 3 days, replacing the medium and adding decitabine or vehicle every 24h. Each experiment was performed in triplicate.

value: HL60 acute myeloid leukemia cell line


title: mock treated HL60 cells replicate 3 (methylation, MeDIP)

description: hl60 mock 5mC 5.CEL

source_name: mock treated HL60 cells + MeDIP


title: mock treated HL60 cells replicate 1 (methylation, total DNA)

description: hl60 mock 1.CEL

source_name: mock treated HL60 cells


title: mock treated HL60 cells replicate 2 (methylation, MeDIP)

description: hl60 mock 5mC 2.CEL


title: decitabine treated HL60 cells replicate 1 (methylation, total DNA)

description: hl60 dac 3.CEL

source_name: decitabine treated HL60 cells


title: decitabine treated HL60 cells replicate 2 (methylation, MeDIP)

description: hl60 dac 5mC 4.CEL


title: AVG_Signal-16 -6-OHDA SAL NL (23)

description: SAMPLE 16

source_name: Striatal Brain Tissue

value: Saline Non Lesion


title: LY7_1

source_name: LY7 Replicate #1


title: AVG_Signal-09 -6-OHDA METH L (22)

description: SAMPLE 9

value: Meth Lesion


title: AVG_Signal-15 -6-OHDA SAL NL (19)

description: SAMPLE 15


title: AVG_Signal-14 - 6-OHDA SAL NL (11)

description: SAMPLE 14


title: AVG_Signal-06 -6-OHDA METH NL (29)

description: SAMPLE 6

value: Meth Non Lesion


title: AVG_Signal-11 -6-OHDA METH L (30).

description: SAMPLE 11


title: AVG_Signal-10 -6-OHDA METH L (26)

description: SAMPLE 10


title: AVG_Signal-02 -6-OHDA METH NL (9)

description: SAMPLE 2


title: AVG_Signal-05 -6-OHDA METH NL (25b)

description: SAMPLE 5


title: AVG_Signal-01 -6-OHDA METH NL (1)

description: SAMPLE 1


title: AVG_Signal-12 -6-OHDA METH L (18)

description: SAMPLE 12


title: AVG_Signal-04 -6-OHDA METH NL (21)

description: SAMPLE 4


title: AVG_Signal-07 -6-OHDA METH L (2)

description: SAMPLE 7


title: screen 2: VEGF0B

city: Utrecht

first: Guy

last: Roukens

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description:
Untreated HUVECS repeat 2
4765861087_C
Non-normalized data is available in the GSE19335_non-normalized.txt' file, which is linked to the Series GSE19335 record as a supplementary file.

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: in R package beadarray, quantile normalization and VST transformation.

source_name: Primary HUVEC, untreated

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

growth_protocol: Huvecs were grown in EGM2 medium (Lonza)

extract_protocol: Total RNA was isolated using Trizol according to manufacturers protocol and subsequently purified by using RNEasy minikit (Qiagen)

value: Primary HUVEC (Human Umbilical Vein Endothelial Cells)

value: untreated


title: Monocyte_Uninfected_rep1

city: marseille

first: adil

last: ef

address: 27 bd jean Moulin

country: France

institute: URMITE

description: raw data file: 2486_Mo_UI_1.txt

hyb_protocol: Performed according to Agilent's protocol

scan_protocol: Scan performed by DNA microarray scanner (Agilent Technologies)

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1 (Agilent) using default parameters.

source_name: blood, 2-hour incubation, uninfected control

label_protocol: RNA was amplified and labeled with Cy3 using Agilent Low RNA Input Fluorescent Linear Amplification Kit

growth_protocol: O. tsutsugamushi strain Kato was propagated in L929 cells cultivated in MEM supplemented with 5% FBS and 2 mM L-glutamine. Monocytes were isolated by adherence

extract_protocol: Total RNA was extracted  using RNeasy Mini kit and DNase digestion

treatment_protocol: Monocytes were stimulated or not with O. tsutsugamushi for 2 hours before RNA extraction

tag: tissue

value: whole blood

value: monocyte

tag: infection

value: uninfected


title: Monocyte_Uninfected_rep2

description: raw data file: 2486_Mo_UI_3.txt


title: IGR wildtype H3 density 2

city: Gothenburg

first: Claes

middle: M

last: Gustafsson

address: Medcinaregatan 9A

department: Department of Medical biochemistry and cell biology

country: Sweden

institute: Gothenburg University

description: ChIP-DNA from the wildtype strain was hybridized on a Eurogentec array together with input DNA from the same preparation to evaluate genomic sites occupied by histone 3.

hyb_protocol: Both labeled DNA populations were hybridized onto the Eurogentec IGR+ORF arrays at 42°C overnight together with 10 ug of salmon sperm DNA.

scan_protocol: Arrays were scanned using a Versarray scanner and processed using Imagene.

data_processing: Data analysis using Genespring GX software (v.7.3, Agilent Technologies) was carried out as follows: measurements less than 0.01 were set to 0,01, data was normalized to the 50th percentile and filtered on flags.

organism: Schizosaccharomyces pombe

source_name: Wildtype anti-H3 ChIP

label_protocol: 500 ng of amplified IP- and input DNA were labeled using Cy3-dCTP or Cy5-dCTP, and both samples were hybridized together to IGR + ORF arrays (Eurogentec) (Wiren et al., 2005). At least three independent ChIP-on-chip experiments were performed in each case, with dye-swap carried out in order to correct for dye bias.

extract_protocol:
For ChIP-on-chip experiments, cells were grown to mid-log phase in YES (5 g/l yeast extract, 30 g/l glucose and 0,1 g/l each of adenine, leucine, histidine, uracil, lysine, arginine and glutamine). 2*108 cells were fixed in 1 % formaldehyde for 30’, quenched in 125 mM glycine, harvested and washed twice in ice-cold PBS. Cells were resuspended in lysis buffer (150 mM NaCl, 0,1 % SDS, 1 % Triton X-100, 0,1 % Na-deoxycholate, 1 mM EDTA and 50 mM Hepes-KOH, pH 7,5) with protease inhibitors and lysed in the FastPrep machine (FP120, BIO101 Savant) with 1 volume of glass beads. The extracts were sonicated (Bioruptor UCD-200, Diagenode) to chromatin fragments of 600-1500 bp. Antibodies used for chromatin immunoprecipitation were -H3 (ab1791, Abcam) and -myc (M4439, Sigma). These were used with 30 l of protein A sepharose slurry (17-5280-01, GE Healthcare) or 50 l protein A beads (P-3391, Sigma).
 Crosslinks were reversed by overnight incubation at 65 C, the immunoprecipitated DNA was treated with proteinase K and purified by phenol-chloroform extraction followed by ethanol precipitation. After RNAse A treatment, 2 l of 40 l was used as a template for realtime-PCR (Lightcycler 2.0, Roche). Enrichment was assessed against a negative control IP performed without antibody.

tag: Strain

value: wildtype.

tag: Grown in rich medium (YES).

tag: ChIP performed using anti-H3 antibody.

source_name: Wildtype input DNA

tag: Grown in rich medium (YES). Input DNA


title: Monocyte_Uninfected_rep4

description: raw data file: 2487_Mo_UI_3.txt


title: ORF wildtype H3 density 1

source_name: Wildtype anti-H3 ChIP DNA

tag: Grown in rich medium (YES). Input DNA.


title: screen 2: VEGF0A

description:
Untreated HUVECS repeat 1
4765861087_A
Non-normalized data is available in the GSE19335_non-normalized.txt' file, which is linked to the Series GSE19335 record as a supplementary file.


title: Monocyte_Infected_rep4

description: raw data file: 2487_Mo_I_4.txt

source_name: blood, 2-hour O.tsutsugamushi infection

value: Orientia tsutsugamushi


title: LY4_1

source_name: LY4 Replicate #1

value: DLBCL cell line

value: Treated with control peptide


title: ORF Wildtype H3 density 2

value: wildtype. Grown in rich medium (YES).

value: wildtype. Grown in rich medium (YES). Input DNA.


title: screen 2: VEGF30A

description:
HUVECS treated with VEGF-A for 30 minutes repeat 1
4765861087_I
Non-normalized data is available in the GSE19335_non-normalized.txt' file, which is linked to the Series GSE19335 record as a supplementary file.

source_name: Primary HUVEC, VEGF, 30 minutes

value: VEGF, 30 minutes


title: Monocyte_Infected_rep3

description: raw data file: 2487_Mo_I_2.txt


title: Monocyte_Infected_rep1

description: raw data file: 2486_Mo_I_2.txt


title: ORF hrp1 H3 density 2

description: ChIP-DNA from a delta-hrp1 strain was hybridized on a Eurogentec array together with input DNA from the same preparation to evaluate the histone 3 density in the strain.

label: Cy 3

source_name: delta-hrp1 anti-H3 ChIP

extract_protocol:
For ChIP-on-chip experiments, cells were grown to mid-log phase in YES (5 g/l yeast extract, 30 g/l glucose and 0,1 g/l each of adenine, leucine, histidine, uracil, lysine, arginine and glutamine). 2*108 cells were fixed in 1 % formaldehyde for 30’, quenched in 125 mM glycine, harvested and washed twice in ice-cold PBS. Cells were resuspended in lysis buffer (150 mM NaCl, 0,1 % SDS, 1 % Triton X-100, 0,1 % Na-deoxycholate, 1 mM EDTA and 50 mM Hepes-KOH, pH 7,5) with protease inhibitors and lysed in the FastPrep machine (FP120, BIO101 Savant) with 1 volume of glass beads. The extracts were sonicated (Bioruptor UCD-200, Diagenode) to chromatin fragments of 600-1500 bp. Antibodies used for chromatin immunoprecipitation were anti-H3 (ab1791, Abcam) and anti-c-myc (M4439, Sigma). These were used with 30 ul of protein A sepharose slurry (17-5280-01, GE Healthcare) or 50 ul protein A beads (P-3391, Sigma).
Crosslinks were reversed by overnight incubation at 65 degrees C, the immunoprecipitated DNA was treated with proteinase K and purified by phenol-chloroform extraction followed by ethanol precipitation. After RNAse A treatment, 2 ul of 40 ul was used as a template for realtime-PCR (Lightcycler 2.0, Roche). Enrichment was assessed against a negative control IP performed without antibody.

tag: Grown in rich medium (YES)

tag: ChIP performed using anti-H3 antibody

label: Cy 5

source_name: delta-hrp1 input DNA

tag: Input DNA


title: Muscle_t10_basal_rep7_techrep

city: Sharnbrook

first: Natalie

last: Hiscock

address: Colworth House

country: United Kingdom

institute: Unilever R&D

description: Gene Expression analysis of vastus lateralis muscle, post inactivity, basal

hyb_protocol: The labeled cRNA was hybridized using Agilent's Hybridization Kit to the Whole Human Genome Oligo Arrays. The slides were then washed in Wash Solution 1 (0.005% Triton X-102), Wash Solution 2 (0.005% Triton X-102) acetonitrile and finally contained in Agilent's Stabilization and Drying Solution

scan_protocol: The slides were scanned with the Agilent G2565BA Microarray Scanner System. For data extraction and quality control, the Agilent G2567AA Feature Extraction Software (v.10.5.1.1) was used.

data_processing: Whole genome microarray analysis was performed on RNA extracted from biopsies collected from the vastus lateralis muscle before bed rest in the basal (T0-B) and insulin-stimulated state (T0-I), after bed rest in the basal (T10-B) and insulin-stimulated state (t10-I) and in the basal state after 30 d retraining (T40-B). A comparison of basal gene expression between T0-B, T10-B and T40-B was performed to identify genes up or downregulated after bed rest, and to assess the effect of re-training on the expression of these genes. A second analysis compared gene expression changes in response to insulin before (T0-B v T0-I) and after (T10-B v T10-I) bed rest. The data were analyzed using Genespring GX 7.3 Expression Analysis software (Agilent Technologies). Text tab delimited raw files were imported into Genespring. Standard data transformation, chip and gene normalisations were applied, in addition to standard QC procedures. gProcessedSignal after normalization by shift to 75th percentile and baseline transformation to median of all samples is provided in the Sample data table below. Volcano plot analysis was used to identify differentially expressed genes in both comparisons, using both p<0.05 and </> 1.2 fold change filters. Differentially expressed gene lists were exported into Ingenuity Pathway Analysis (Ingenuity Systems) to identify common functional and signalling pathways represented in the gene lists.

label_protocol: RNA from muscle tissue and Agilent One-Color RNA Spike-In RNA were labeled with reagents supplied in the Agilent Quick Amp Labeling Kit, One-Color. The labeled cRNA was then purified with the RNeasy Mini Kit (Qiagen Ltd, Crawley, UK).

extract_protocol: Skeletal muscle samples were collected in all participants in both the basal and insulin stimulated state before and after bed rest, but only in the basal state after four weeks of retraining. Muscle biopsies were collected from the vastus lateralis muscle using a Bergstrom needle with suction under local anesthesia (1% lidocaine). Biopsies were immediately frozen in liquid nitrogen and transferred to a -80ºC freezer. Extraction of total RNA and genomic DNA from the muscle biopsies was performed with TRI reagent (Sigma-Aldrich, St. Louis, MO, USA). Both RNA and DNA were quantified by spectrophotometric analysis and RNA used for the microarray analysis was quality-assessed by the Agilent Bioanalyser 2100 using the RNA 6000 Nano Assay Kit (Agilent Technologies, Wokingham, Berkshire, UK).

treatment_protocol: Ten young healthy Caucasian men (24-27 years) were recruited to the study. Subjects were requested to abstain from strenuous physical activity and alcohol consumption three days prior to the examination. To ensure standardized conditions, all subjects were provided with a nutritionally standardized diet three days prior to the first experimental day and during the bed rest with adjusted caloric content to ensure weight stability. All subjects were admitted to Steno Diabetes Center for ten days and were not permitted to deviate from a half-recumbent position during this period. Toilet visits, limited to a total of 15 minutes per day, were allowed. Study subjects were allowed to use a laptop computer, watch television and read in the bed. Body weight of all subjects was recorded every morning throughout the intervention to ensure weight stability. After bed rest a DXA scan and a VO2max test was again performed. For ethical reasons and for the purpose of studying reversibility of changes in DNA methylation, gene expression and protein levels, all subjects completed a four-week retraining program after the 9 days of bed rest. The program consisted of supervised cycle ergometry 30 min/day, 5 days/week on 70% of subjects’ VO2max

value: skeletal muscle


title: Muscle_t10_basal_rep9_techrep

source_name: vastus lateralis muscle, post inactivity, basal


title: IGR hrp1 H3 density 3


title: Muscle_t10_insulin_rep6_techrep

description: Gene Expression analysis of vastus lateralis muscle, post inactivity, insulin treated


title: Muscle_t40_basal_rep4_techrep

description: Gene Expression analysis of vastus lateralis muscle, post re-training, basal


title: IGR wildtype H3 density 1

value: wildtype

tag: Input DNA.


title: Muscle_t0_insulin-rep8_techrep

description: Gene Expression analysis of vastus lateralis muscle, pre inactivity, insulin treated


title: ORF med15 H3 density 2

description: ChIP-DNA from a delta-med15 strain was hybridized on a Eurogentec array together with input DNA from the same preparation to evaluate the histone 3 density in the strain.

source_name: delta-med15 anti-H3 ChIP

label_protocol: 500 ng of amplified IP- and input DNA were labeled using Cy3-dCTP or Cy5-dCTP, and both samples were hybridized together to IGR + ORF arrays (Eurogentec) (Wiren et al., 2005). At least two independent ChIP-on-chip experiments were performed in each case, with dye-swap carried out in order to correct for dye bias.

source_name: delta-med15 input DNA


title: IGR hrp1 H3 density 2

source_name: delta-hrp1 input dna


title: Muscle_t10_basal_rep10


title: Muscle_t0_basal_rep1_techrep

description: Gene Expression analysis of vastus lateralis muscle, pre inactivity, basal


title: ORF hrp1 H3 density 1


title: IGR med15 H3 density 2


title: Muscle_t0_basal_rep5_techrep

source_name: vastus lateralis muscle, pre inactivity, basal


title: ORF med15 H3 density 1


title: ORF Med15-myc binding 3

description: ChIP-DNA from a Med15-myc strain was hybridized on a Eurogentec array together with input DNA from the same preparation to evaluate genomic sites bound by Med15.

source_name: a-myc ChIP DNA

tag: Strain Med15-myc was grown in rich medium (YES). a-myc was used for chromatin IP and DNA purified.

source_name: Input DNA

tag: Strain Med15-myc was grown in rich medium (YES). Total (=input) DNA was purified.


title: AVG_Signal-17 -6-OHDA SAL NL (27)

description: SAMPLE 17

source_name: Striatal Brain Tissue

value: Saline Non Lesion

value: Sprague Dawley


title: IGR hrp1 H3 density 1


title: Muscle_t40_basal_rep1_techrep

source_name: vastus lateralis muscle, post re-training, basal


title: Muscle_t0_basal_rep10


title: Muscle_t10_insulin_rep10

source_name: vastus lateralis muscle, post inactivity, insulin treated


title: IGR med15 H3 density 1


title: screen 2: VEGF30B

description:
HUVECS treated with VEGF-A for 30 minutes repeat 2
4765861087_K
Non-normalized data is available in the GSE19335_non-normalized.txt' file, which is linked to the Series GSE19335 record as a supplementary file.

tag: cell type


title: Muscle_t40_basal_rep9


title: AVG_Signal-13 - 6-OHDA SAL NL (3)

description: SAMPLE 13


title: ORF hrp1 H3 density 3


title: Monocyte_Uninfected_rep3

description: raw data file: 2487_Mo_UI_1.txt

source_name: blood, 2-hour incubation, uninfected control


title: AVG_Signal-03 -6-OHDA METH NL (17)

description: SAMPLE 3

value: Meth Non Lesion


title: Monocyte_Infected_rep2

description: raw data file: 2486_Mo_I_4.txt


title: Muscle_t0_insulin-rep6_techrep

source_name: vastus lateralis muscle, pre inactivity, insulin treated


title: Muscle_t10_basal_rep9


title: AVG_Signal-08 -6-OHDA METH L (10)

description: SAMPLE 8

value: Meth Lesion


title: ORF Med15-myc binding 2


title: Muscle_t0_insulin-rep9


title: gld-2(RNAi), biological replicate 3

city: Madison

first: Judith

last: Kimble

state: WI

address: 433 Babcock Drive

department: HHMI / Biochemistry

institute: University of Wisconsin-Madison

description: Gene expression data from gld-2(RNAi) adult hermaphrodite

hyb_protocol: Following fragmentation, 100% or up to 10 µg of amplified RNA (aRNA) were hybridized in the GeneChip 640 Hybridization Oven (Affymetrix). GeneChips were washed and stained in GeneChip Fluidics Station 450 (Affymetrix) .

scan_protocol: Arrays were scanned using GC3000 G7 scanner (Affymetrix)

data_processing: The data were analyzed with GeneChip Operating Software (GCOS) v.1.4. For IP samples, the data were scaled based on the control AFFX probe sets and the trimmed mean target intensity of each array was arbitrarily set to 5000. For total RNA samples, global scaling was applied and the trimmed mean target intensity of each array was arbitrarily set to 1000.

organism: Caenorhabditis elegans

source_name: C. elegans gld-2(RNAi) adult extracts

label_protocol: Biotinylated cRNAs were prepared using the MessageAmp Biotin-II Enhanced kit (Ambion) according the manufacturer's instructions from 1ug total RNA or up to 200 ng coimmunoprecipitated RNA

growth_protocol: Synchronized adults were grown at 20C until 15 hours after L4 stage.

extract_protocol: Trizol followed by RNeasy MinElute columns (Qiagen), following the manufacturer's instructions.

treatment_protocol: Adults were washed extensively and used to prepare extracts

tag: developmental stage

value: adult

tag: gender

value: hermaphrodite

value: whole  animal

tag: sample type

value: total RNA


title: ORF Med15-myc binding 1


title: Muscle_t0_insulin-rep10

tag: tissue


title: gld-2(RNAi), biological replicate 2

tag: strain


title: Muscle_t0_insulin-rep4_techrep


title: Muscle_t40_basal_rep10


title: IGR Med15-myc binding 1

source_name: a-myc IP

tag: Strain

tag: ChIP performed using a-myc.

source_name: input DNA


title: Muscle_t40_basal_rep8


title: wild-type total RNA, biological replicate 2

description: Gene expression data from wild-type adult hermaphrodite

source_name: C. elegans wild-type adult extracts

value: wild-type (N2 Bristol strain)


title: wild-type total RNA, biological replicate 4


title: wild-type total RNA, biological replicate 3


title: IGR Med15-myc 2

source_name: Med15-myc IP DNA

source_name: IGR Med15-myc input DNA


title: Muscle_t0_insulin-rep8


title: Muscle_t10_insulin_rep8


title: gld-2(RNAi), biological replicate 1


title: Muscle_t10_insulin_rep9


title: IGR Med15-myc ChIP 3

source_name: IGR Med15-myc ChIP DNA


title: Muscle_t0_basal_rep8


title: RNP-8 rnp-8(q784)-IP, biological replicate 3

description: mRNA associated with RNP-8

source_name: C. elegans rnp-8(q784) adult extracts used to immunoprecipitate RNP-8

value: RNA from RNP-8 immunoprecipitation

tag: antibody


title: Muscle_t0_basal_rep9


title: mock treated HL60 cells replicate 3 (expression)

description: HL60 exp mock3.CEL

data_processing: The expression array .CEL files for HL60 mock and DAC treated cells were imported in PGS using the Gene Expression Workflow tool, after GC-RMA normalization and log2 transformation.

source_name: mock treated HL60 cells

label_protocol: IVT express kit (Affymetrix)following manifacturer's instructions

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen, AG).

value: HL60 acute myeloid leukemia cell line


title: Muscle_t10_basal_rep8

source_name: vastus lateralis muscle, post inactivity, basal


title: Muscle_t40_basal_rep7


title: mock treated HL60 cells replicate 1 (expression)

description: HL60 exp mock1.CEL


title: Muscle_t10_insulin_rep7


title: RNP-8 rnp-8(q784)-IP, biological replicate 2

description: mRNA associated with RNP-8


title: RNP-8 rnp-8(q784)-IP, biological replicate 1

description: mRNA associated with RNP-8


title: RNP-8 wt-IP, biological replicate 3

description: mRNA associated with RNP-8

source_name: C. elegans wild-type adult extracts used to immunoprecipitate RNP-8

value: wild-type


title: decitabine treated HL60 cells replicate 2 (expression)

description: HL60 exp dac2.CEL

source_name: decitabine treated HL60 cells


title: Muscle_t0_insulin-rep7


title: RNP-8 wt-IP, biological replicate 1

description: mRNA associated with RNP-8


title: Muscle_t10_insulin_rep6


title: wild-type total RNA, biological replicate 1


title: Muscle_t10_basal_rep7


title: decitabine treated HL60 cells replicate 3 (expression)

description: HL60 exp dac3.CEL


title: RNP-8 wt-IP, biological replicate 2

description: mRNA associated with RNP-8


title: GLD-2 gld-2(RNAi)-IP, biological replicate 2

description: mRNA associated with GLD-2

source_name: C. elegans gld-2(RNAi) adult extracts used to immunoprecipitate GLD-2

value: RNA from GLD-2 immunoprecipitation


title: Muscle_t40_basal_rep6

source_name: vastus lateralis muscle, post re-training, basal


title: GLD-2 gld-2(RNAi)-IP, biological replicate 1

description: mRNA associated with GLD-2


title: Muscle_t0_basal_rep7

source_name: vastus lateralis muscle, pre inactivity, basal


title: GLD-2 gld-2(RNAi)-IP, biological replicate 4

description: mRNA associated with GLD-2


title: Affymetrix expression in med15 2

description: Gene expression in the delta-med15 S. pombe strain was analysed using the Affymetrix GeneChip Yeast Genome 2.0 array.

hyb_protocol: According to the GeneChip expression analysis technical manual that is available for download at www.affymetrix.com.

data_processing: After the ExpressionStat algorithm, data was imported into Genespring GX (Agilent technologies), per-gene normalized to median and filtered on flags.

label_protocol: Labeling was performed according to the GeneChip expression analysis technical manual that is available for download at www.affymetrix.com.

extract_protocol: RNA was isolated from mid-log phase cultures according to Xue et al. 2004 (Yeast 21(1):25-39).

value: delta-med15. Cells were grown to mid-log phase in rich medium.


title: GLD-2 gld-2(RNAi)-IP, biological replicate 3

description: mRNA associated with GLD-2


title: decitabine treated HL60 cells replicate 1 (expression)

description: HL60 exp dac1.CEL


title: Control DLD-1 cells (not induced)

city: Leipzig

first: Levin

last: Böhlig

address: Semmelweisstr. 14

country: Germany

institute: University of Leipzig

description: This sample includes the gene expression of DLD-1 cells which were stably transfected with a tet-off expression system for p53 wildtype (Yu J et al., Proc Natl Acad Sci USA 1999; 96:14517-22). These cells were cultured with Tetracyclin (p53wt off).

hyb_protocol: Standard Affymetrix hybridization procedure

scan_protocol: Standard Affymetrix scan procedure

data_processing: Values were generated by normalizing signals with the MAS5 algorithm

source_name: Control DLD-1 cells (not induced)

label_protocol: Standard Affymetrix labelling procedure

extract_protocol: Trizol preparation

value: colon carcinoma

tag: cell line

tag: genotype/variation

value: stably tranfected with tet-off regulated p53 wildtype

tag: treatment

value: cultured with Tetracyclin (p53wt off)


title: Muscle_t0_insulin-rep6

source_name: vastus lateralis muscle, pre inactivity, insulin treated

value: skeletal muscle


title: Muscle_t10_basal_rep6


title: p53 expressing DLD-1 cells (induced)

description: This sample includes the gene expression of DLD-1 cells which were stably transfected with a tet-off expression system for p53 wildtype (Yu J et al., Proc Natl Acad Sci USA 1999; 96:14517-22). These cells were cultured without Tetracyclin for 9h (p53wt on).

source_name: p53 expressing DLD-1 cells (induced)


title: Affymetrix expression in med15

scan_protocol: According to the GeneChip expression analysis technical manual that is available for download at www.affymetrix.com.


title: Affymetrix expression in hrp1 2

description: Gene expression in the delta-hrp1 S. pombe strain was analysed using the Affymetrix GeneChip Yeast Genome 2.0 array.

value: delta-hrp1. Cells were grown to mid-log phase in rich medium.


title: Muscle_t0_basal_rep6


title: GLD-2 wt-IP, biological replicate 4

description: mRNA associated with GLD-2

source_name: C. elegans wild-type adult extracts used to immunoprecipitate GLD-2


title: Affymetrix expression in hrp1 1

source_name: delta-hrp1 strain


title: GLD-2 wt-IP, biological replicate 3

description: mRNA associated with GLD-2


title: GLD-2 wt-IP, biological replicate 1

description: mRNA associated with GLD-2


title: Muscle_t40_basal_rep5


title: GLD-2 wt-IP, biological replicate 2

description: mRNA associated with GLD-2


title: mock treated HL60 cells replicate 2 (expression)

description: HL60 exp mock2.CEL


title: Affymetrix expression in wildtype 1

description: Gene expression in the wildtype S. pombe strain was analysed using the Affymetrix GeneChip Yeast Genome 2.0 array.

source_name: Wildtype (711)

value: 711. Cells were grown to mid-log phase in rich medium.


title: Muscle_t10_insulin_rep4

source_name: vastus lateralis muscle, post inactivity, insulin treated


title: Muscle_t0_insulin-rep5


title: Affymetrix expression in wildtype 2


title: Muscle_t10_basal_rep5


title: liver_stuff_rep2

hyb_protocol: hybridation during 17 hours at 37°C with a low agitation (10rpm)

scan_protocol: Agilent's Feature Extraction v.10.5.1

data_processing: normalization method by quantile

organism: Mus musculus

source_name: stuff mouse

label_protocol: protocol one color from agilent

extract_protocol: kit RNeasy from Qiagen

value: BALBc

value: female

value: liver

tag: treatment group


title: liver_control_rep2

source_name: control mouse

value: control


title: Muscle_t40_basal_rep4


title: Muscle_t10_insulin_rep5


title: Muscle_t0_basal_rep5


title: liver_control_rep1


title: liver_stuff_rep1


title: Muscle_t0_basal_rep4


title: Muscle_t10_basal_rep4


title: MEP_induced_rep4

city: New York

first: Jeffrey

middle: Ohmann

last: Bush

state: NY

address: One Gustave Levy Place, Box 1020

department: Developmental and Regenerative Biology

institute: Mount Sinai School of Medicine

description:
4032131007_E
Induced with 2 ug/ml pre-clustered ephrin-B1-Fc for 60 minutes.

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Data was normalized using cubic spline in Illumina Genome Studio v1.6.0 software; no background subtraction was used.

source_name: MEP cells isolated from E13.5 palatal shelves, induced

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

growth_protocol: MEP cells were isolated and grown in DMEM + 10%FBS, and passaged to P1 before induction of signaling.

extract_protocol: QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Forward signaling was induced by treatment with 2 ug/ml of ephrin-B1-Fc pre-clustered with an anti-human antibody.

value: CBA;C57BL6 N2

value: embryo

tag: age

value: palatal shelf

value: mouse embryonic palate (MEP) primary cells

value: induction with pre-clustered ephrin-B1


title: kyp ibm1

city: Ikoma

first: Soichi

last: Inagaki

state: Nara

address: 8916-5, Takayama-cho

department: Graduate School of Biological Sciences

country: Japan

institute: Nara Institute of Science and Technology

description: ChIP-chip of H3K9me2 in kyp ibm1

scan_protocol: Used Agilent Microarray Scanner.

data_processing:
Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction.
Each feature on the array has a corresponding scaled log2 ratio, which is the ratio of the signals for the ChIP and input samples cohybridized to the array. The log2 ratio is computed and scaled to center the ratio data around zero. Scaling is performed by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value.

organism: Arabidopsis thaliana

source_name: H3K9me2 ChIP DNA from kyp ibm1

label_protocol: According to standard NimbleGen protocols (www.nimblegen.com).

growth_protocol: 4 weeks on soil

extract_protocol: Leaves of 4-week-old plants were fixed as described previously (Saze et al, 2008). Chromatin immunoprecipitation (ChIP) was performed as described previously (Kimura et al, 2008), using antibody against H3K9me2 (CMA307, Kimura et al, 2008).

treatment_protocol: no treatment

tag: genotype

value: kyp ibm1 mutant

value: ChIP fraction

value: CMA307, anti-H3K9me2 antibody

tag: antibody source

value: Antibody used was directly provided from Dr. Hiroshi Kimura at Osaka Univ.

source_name: Input DNA from kyp ibm1

value: Input fraction


title: Muscle_t10_basal_rep3

source_name: vastus lateralis muscle, post inactivity, basal

value: skeletal muscle


title: kyp

description: ChIP-chip of H3K9me2 in kyp

hyb_protocol: According to standard NimbleGen protocols (www.nimblegen.com)

source_name: H3K9me2 ChIP DNA from kyp

value: kyp mutant

source_name: Input DNA from kyp


title: cmt3

description: ChIP-chip of H3K9me2 in cmt3

source_name: H3K9me2 ChIP DNA from cmt3

value: cmt3 mutant

source_name: Input DNA from cmt3


title: cmt3 ibm1

description: ChIP-chip of H3K9me2 in cmt3 ibm1

source_name: H3K9me2 ChIP DNA from cmt3 ibm1

value: cmt3 ibm1 mutant

source_name: Input DNA from cmt3 ibm1


title: Muscle_t40_basal_rep2

source_name: vastus lateralis muscle, post re-training, basal


title: Muscle_t40_basal_rep3


title: MEP_uninduced_rep1

description:
1905531021_D
Control induction.

source_name: MEP cells isolated from E13.5 palatal shelves, uninduced

value: no induction


title: cmt3_1

description: RMA-normalized

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction.

growth_protocol: 4 weeks on soil, long day.

extract_protocol: Used the Rneasy Plant Mini kit (Qiagen).

treatment_protocol: No treatment.

value: Young leaves


title: MEP_induced_rep1

description:
1905531021_E
Induced with 2 ug/ml pre-clustered ephrin-B1-Fc for 60 minutes.


title: H3_Rpb1_60

city: Boston

first: Xiaochun

last: Fan

state: MA

address: 220 Longwood Ave.

department: Biological Chemistry & Molecular Pharmacology

institute: Harvard Medical School

description: H3 ChIP from 1ug/ml Rapamycin treated cells

hyb_protocol: see GSE23778_Hybri_Tiling_Protocol.pdf for details

scan_protocol: default settings for Genechip Scanner 3000

data_processing: data were processed through MAT Johnson et al. PNAS 2006 (http://www.ncbi.nlm.nih.gov/pubmed/16895995)

label: Biotin-ddATP

organism: Saccharomyces cerevisiae

label_protocol: Dnase I treated, 50-100nt DNA was labeled with biotin-ddA

growth_protocol: yeast cells were grown in YPD to OD0.6 before fixed with 1% formaldehyde; or washed twice with water and resuspended in YP, incubated for 6hr. AA strain was grown in YPD to OD0.4 before fixed with 1% formaldehyde, or 1ug/ml rapamycin was added, cells were fixed after 60min incubation.

extract_protocol: chromatin was prepared according to Fax et al. NAR 2008 (http://www.ncbi.nlm.nih.gov/pubmed/18765474)

treatment_protocol: Wash twice with water, resuspend cells in YP and incubate for 6hr. Rapamycin was added in the final concentration of 1ug/ml.

tag: condition

value: 60min after 1ug/ml Rapamycin treatment

value: AA

tag: antibody catalog #

tag: antibody manufacturer

value: Abcam

tag: antibody lot #

source_name: Input DNA from 1ug/ml Rapamycin treated cells


title: H3_Rpb1_0

description: H3 ChIP from untreated cells

source_name: H3 ChIP from untreated cells

value: No Rapamycin treatment

source_name: Input DNA from untreated cells


title: MEP_uninduced_rep4

description:
4032131007_F
Control induction.

value: CBA;C57BL6 N2

tag: developmental stage

value: embryo

value: palatal shelf

tag: cell type

value: mouse embryonic palate (MEP) primary cells


title: ibm1

description: ChIP-chip of H3K9me2 in ibm1

source_name: H3K9me2 ChIP DNA from ibm1

value: ibm1 mutant

tag: sample type

value: ChIP fraction

value: CMA307, anti-H3K9me2 antibody

source_name: Input DNA from ibm1


title: MEP_induced_rep3

description:
4032131007_B
Induced with 2 ug/ml pre-clustered ephrin-B1-Fc for 60 minutes.

source_name: MEP cells isolated from E13.5 palatal shelves, induced

tag: strain

tag: tissue

value: induction with pre-clustered ephrin-B1


title: Muscle_t0_insulin-rep3

source_name: vastus lateralis muscle, pre inactivity, insulin treated

value: skeletal muscle


title: MEP_uninduced_rep3

description:
4032131007_C
Control induction.


title: Muscle_t10_insulin_rep2

description: Gene Expression analysis of vastus lateralis muscle, post inactivity, insulin treated


title: H3_YP

description: H3 ChIP from cells grown in YP for 6hr

source_name: H3 ChIP from cells grown in YP for 6hr

value: YP for 6hr

tag: antibody

source_name: Input DNA from cells grown in YP for 6hr


title: H3_YPD

description: H3 ChIP from cells grown in YPD

source_name: H3 ChIP from cells grown in YPD

value: YPD OD0.6

source_name: Input DNA from cells grown in YPD


title: Healthy control

city: St. Louis

first: Daniel

middle: C

last: Link

state: MO

address: 660 S. Euclid, Campus Box 8007

institute: Washington University

hyb_protocol: Labeled RNAs were hybridized to the Agilent miRNA arrays using Agilent's Complete miRNA Microarray System version 1.7.  Labeled RNAs were suspended in water, Agilent 2xHi-RPM hybridization buffer, and Agilent 10x GE Blocking Agent and hybridized for 20 hours at 55C in an Agilent rotating hybridization oven set at 10rpm.  Arrays were then washed in Agilent Gene Expression wash buffer 1 for 5 minutes at room temperature, followed by a 5 minute wash in Agilent Gene Expression wash buffer 2 at 37C.  Arrays were removed from wash solution and dried.

scan_protocol: Agilent miRNA arrays were scanned on an Agilent Microarray Scanner (B version) according to manufacturer recommendations.  Scans were performed at  5 micron resolution at both high and low sensitivity (Green pmt 100%, 5%).  Images were quantitated using Agilent Feature Extraction, v9.5.3.1.

data_processing: For each sample, Agilent Feature Extraction software generated a GeneView.txt file in which a signal value (totalgenesignal) is provided for each miRNA represented on the array.  These signal values were imported into Agilent GX v.10, and all samples were then normalized to the 75th percentile signal for all samples.

source_name: bone marrow Cd34+ cells

label_protocol: Total RNA quality was determined by Agilent 2100 bioanalyzer (Agilent Technologies) according to manufacturer’s recommendations.  miRNAs were labeled using Agilent’s Complete miRNA Microarray System version 1.7.  Total RNAs (100 ng) were first dephosphorylated with Calf Intestine Alkaline Phosphatase, and then denatured in 100% DMSO.  Samples were labeled by ligating with T4 RNA Ligase one Cyanine 3-pCp molecule to the 3' ends of the RNAs.

extract_protocol: RNA extracted using Trizol

value: Cd34+ selected cells from bone marrow

tag: disease state

value: healthy


title: AML

source_name: bone marrow

value: whole bone marrow

value: acute myelogenous leukemia


title: kyp_1

description: RMA-normalized

source_name: kyp

value: kyp mutant

value: Young leaves


title: MEP_induced_rep2

description:
1905531070_E
Induced with 2 ug/ml pre-clustered ephrin-B1-Fc for 60 minutes.

value: CBA;C57BL6 N2


title: cmt3_2

description: RMA-normalized

value: cmt3 mutant


title: MEP_uninduced_rep2

description:
1905531070_D
Control induction.

value: embryo

value: palatal shelf

value: no induction


title: wild type Col-0

description: ChIP-chip of H3K9me2 in wild type

source_name: H3K9me2 ChIP DNA from wild type Col-0

value: wild type Col-0

value: ChIP fraction

value: Antibody used was directly provided from Dr. Hiroshi Kimura at Osaka Univ.

source_name: Input DNA from wild type Col-0

value: Input fraction


title: Muscle_t10_insulin_rep1

source_name: vastus lateralis muscle, post inactivity, insulin treated

value: skeletal muscle


title: kyp_2

description: RMA-normalized


title: wild type Col-0_1

description: RMA-normalized

source_name: wild type Col-0


title: Muscle_t0_insulin-rep2

description: Gene Expression analysis of vastus lateralis muscle, pre inactivity, insulin treated


title: 8.5dpc BMS+FA treated embryos vs 8.5dpc BMS treated embryos

status: Public on Sep 20 2010

city: Roma

first: Francesca

last: Amati

address: Via Montpellier 1

department: Biomedicine and Prevention

institute: University of Rome Tor Vergata

description: MO4_28_A_130706.gpr: Cy3 BMS-treated, Cy5 CTRL embryos; MO4_29_8.5dpc_B.gpr: Cy3 CTRL embryos, Cy5 BMS-treated

hyb_protocol: The labeled cDNAs were co-hybridized to slides in duplicate, with one dye swap. Microarray slides contained about 33.000 oligonucleotides corresponding to mouse genes and transcripts (AECOM, USA, http://microarray1k.aecom.yu.edu/).

scan_protocol: Each slide was scanned on the GenePix 4000B Microarray Scanner at the optimal wavelength for theAlexa555 (F532) and Alexa647 (F635) using lasers.   The DNA spots were automatically segmented; total intensities as well as the fluorescence ratios of the two dyes for each spot were then calculated. The spots were flagged when they exhibited poor hybridization signals and when they were saturated (F635 or F532 median = 65535).

data_processing: Spots with signal to background ratio below 1.5 were filtered, together with flagged spots. We decided to subtract the local spot background signal from the foreground signal depending from the correlation of foreground to background intensity ratios, as in the method suggested by Scharpf e co-authors (Scharpf RB, Iacobuzio-Donahue CA, Sneddon JB, Parmigiani G When should one subtract background fluorescence in 2-color microarrays? Biostatistics 2007, 8: 695-707).  We removed systematic bias in the data by applying lowess and dye-swap normalizations in order to have the least possible information loss. Dye-swap normalization makes use of the reverse labelling in the two microarray replicates directly (Fang Y, Brass A, Hoyle DC, Hayes A, Bashein A, Oliver SG, Waddington D, Rattray M. A model-based analysis of microarray experimental error and normalisation. Nucleic Acids Res 2003; 31:e96.). To establish the significance of observed regulation for each gene, we used one sample t-test, and corrected the p-value for multiple comparisons controlling the false discovery rate [Benjamini Y, Hochberg Y. 1995]. Finally, only genes with a satisfactory effect (absolute value of the fold change at least ”1.5”) were considered.

source_name: embryonic tissue collected from BMS+FA litters at 8.5dpc

label_protocol: Synthesis of the labelled first strand cDNA was conducted according to manufacturer’s instructions (Superscript Indirect cDNA labeling system, Invitrogen, USA) with starting material of 10 µg of total RNA. The amino-allyl labeled dNTP mix was added to the reaction to generate amino-allyl labelled second strand cDNA. Following the hydrolysis reaction, single-stranded cDNA probes were purified using a Purification Module (Invitrogen). Probe mixtures where then evaporated in a vacuum centrifuge, and the cDNA pellet resuspended in 3 µL of water. The dye coupling reactions were performed by mixing the cDNA samples with AlexaFluor Dyes 555 or 647 and were incubated for a overnight in the dark. The reactions were purified with a Purification Module (Invitrogen) to remove the unincorporated/quenched dyes. After the purification, samples were combined for hybridization.

growth_protocol: Outbred CD1, Swiss mice (Charles River, Calco, Italy) were housed and mated under standard laboratory conditions that complied with Italian regulations for laboratory animal care. Pregnant mice were randomly divided into three experimental groups of 6 mice each (control, BMS-treated and BMS+FA treated group).

extract_protocol: Mouse embryos were collected at 8.5 dpc, and placentas were removed from embryonic tissue. Three to five embryos were pooled within each litter, and stored in RNAlater (Ambion) until RNA extraction. Total RNA was extracted and purified using TriZol reagent (Invitrogen), its quality and quantity was assessed using a Nanodrop spectrophotometer (Thermo Scientific) and agarose gel electrophoresis.

treatment_protocol: Administration of BMS-189453 alone and together with folic acid to pregnant mice was performed as described. (Cipollone et al., 2006; Cipollone et al., 2009). Briefly, mice received 5mg/kg body weight of BMS-189453 twice (12h interval) at 7.25/7.75 dpc by oral gavage (BMS-treated group); the BMS+FA group received the additional FA administration from 0.5 dpc until the end of pregnancy; control group received twice PBS.

source_name: embryonic tissue collected from BMS litters at 8.5dpc


title: CF_control

city: Kansas City

first: Robert

last: De Lisle

state: KS

address: 3901 Rainbow Blvd

department: Anatomy & Cell Biology

institute: Univ Kansas Med Ctr

hyb_protocol: GeneChip was prehybridized with Hybridization buffer at 45C 10min. Denatured Hybridization cocktail was applied to GeneChip. GeneChip was hybridized 16 hr at 45C in GeneChip Hybridization Oven 640. Washing and Staining: Automated process using the GeneChip Fluidics Station 400 with the Standard Array Format.

scan_protocol: Automated process conducted using the Agilent GeneArray Scanner. Pixel value = 3um Wavelength = 570nm

data_processing: Primary analysis was by GCOS with 'Scaling - All Probe Sets: Target Signal = 500'; 'Normalization – User Defined: Scale Factor = 1' using MAS 5.0.

source_name: Entire small intestine, CF, control

label_protocol: The standard labeling protocol was used.

growth_protocol: All mice were fed from weaning to sacrifice with a liquid diet (Peptamen).

extract_protocol: The entire small intestine was resected into ice cold PBS; the mesentery was trimmed and discarded; the tissue was homogenized in 8 ml Trizol and extracted to isolate total RNA.

treatment_protocol: Mice were gavaged daily with 100 ul Peptamen including 10 ug/kg body weight lubiprostone for two weeks, as indicated.

value: small intestine

value: cftr-tm1Unc (cftr null)


title: Muscle_t0_insulin-rep4


title: Muscle_t10_insulin_rep3


title: Wild_type_lubiprostone

source_name: Entire small intestine, wild type, lubiprostone treated

value: wild type

value: lubiprostone


title: trachea, SYMs-144

first: Yael

last: Strulovici-Barel

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: airway epithelial cells obtained by bronchoscopy and brushing

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-2 microg total RNA (Expression Analysis Technical Manual, 701022 Rev.2, Affymetrix).

extract_protocol: Trizol extraction and RNAeasy clean-up of total RNA was performed according to the manufacturer's instructions.

tag: Age

tag: Sex

value: F

tag: Ethnic group

value: hispanic

tag: Smoking status

value: smoker, 29 pack-years


title: trachea, smoker 093

value: M

value: black


title: Muscle_t0_basal_rep3

description: Gene Expression analysis of vastus lateralis muscle, pre inactivity, basal


title: CF_lubiprostone

source_name: Entire small intestine, CF, lubiprostone treated

tag: genotype

tag: treatment


title: Muscle_t10_basal_rep2

description: Gene Expression analysis of vastus lateralis muscle, post inactivity, basal


title: trachea, smoker 136

value: smoker, 26 pack-years


title: Muscle_t40_basal_rep1

description: Gene Expression analysis of vastus lateralis muscle, post re-training, basal


title: trachea, SYMs-127

value: smoker, 23 pack-years


title: trachea, smoker 087

value: smoker, 30 pack-years


title: Muscle_t0_basal_rep1

source_name: vastus lateralis muscle, pre inactivity, basal


title: trachea, smoker 112

value: white


title: wild type Col-0_2

description: RMA-normalized

value: wild type Col-0

value: Young leaves


title: Muscle_t0_basal_rep2


title: 8.5 Wild type embryos vs 8.5dpc BMS treated embryos

description: MO4151.gpr: Cy3 BMS-treated,  Cy5 BMS+FA -treated; MO4153.gpr: Cy3 BMS+FA treated, Cy5 BMS-treated

source_name: embryonic tissue collected from CD1 litters at 8.5dpc

value: embryo

source_name: embryonic tissue collected from BMS treated litters at 8.5dpc


title: S1587-17, acid soil, 3 days treatment, biologial rep3

city: Campinas

first: Marcelo

last: Menossi

state: SP

address: Rua Monteiro Lobato, 255, Instituto de Biologia, Departamento de Genetica, Evolucao e Bioagentes

department: Genetica, Evolucao e Bioagentes

country: Brazil

institute: Marcelo Menossi

description: Gene expression data from root apexes subjected to soil growth

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45oC on GeneChip Maize Genome Array. GeneChips were washed and stained using the Affymetrix platform.

scan_protocol: The image was acquired with Affymetrix GeneChip Scanner 3000-7G using the sotware Affymetrix Command Console.

data_processing: The data were normalized by the RMA method using R/Bioconductor.

label: Biotin

organism: Zea mays

source_name: Root apex from maize genotype S1587-17 grown in acid soil for 3 days

label_protocol: Biotinylated cRNA were prepared using 2 ug total RNA according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2006, Affymetrix).

growth_protocol: Seeds from the tropical maize (Zea mays L.) inbreed lines Cat100-6 (Al-tolerant) and S1587-17 (Al-sensitive) were obtained from the germplasm bank from the University of Campinas. Seeds were geminated for 2 days in moist filter paper and then transferred to germination plastic bags (500 mL each) filled with 1 kg of control or acid soil. Only seedlings with similar initial root length were transferred to the soil bags (20 seeds/bag). Plants were grown in a growth chamber at 26°C (light:dark period of 16:8h). The bags with the seed were weighted and then twice a day the weight was completed with distillated water to keep soil humidity at 15% (v/w).

extract_protocol: The RNA was extracted with the RNeasy Plant Mini Kit (Quiagen, USA). The RNA was evaluated on agarose/formaldehyde gel, quantified in spectrophotometer and stocked in biofreezers.

treatment_protocol: The soil used is a Dark Red Latossol from Fazenda Santa Elisa, Campinas, SP, Brazil (location 22°59’09”S 47°05’25”O, approximately 610 meter above sea level). Soil samples were taken at 20-40 cm depth, sieved through a 4mm mesh and kept inside plastic boxes protected from light. Soil analysis indicated that the original sample presented pH 4.1 and Al content of 10 mmolc/dm3. The acid soil treatment consisted of the original soil with a fertilization to avoid nutritional stress. The control soil was incubated with 0.8 g of Ca(OH)2 per Kg of soil for 1 week prior to fertilization with the same amount of nutrient provided to the acid soil. The incubation with Ca(OH)2 made the pH increase to pH 5.5 and the presence of Al was undetectable. The fertilization comprised the following nutrients (mg/Kg of soil): 56 of N; 38.75 of P; 78 of K; 32 of S; 60 of Mg; 0.5 of B; 0.5 of Cu; 0.01 of Mo; 1.0 of Zn. The acid soil also received the correction of Ca through the addition of a CaCl2 solution. This was because of the differential incubation of the control soil with Ca(OH)2. The soil was mixed several times to reduce the natural variability of the physical and chemical properties of both soils.

value: Root apex (5mm)

tag: genome/variation

tag: days of treatment

value: 3 days


title: trachea, smoker 044

value: smoker, 25 pack-years


title: S1587-17, acid soil, 3 days treatment, biologial rep2


title: S1587-17, control soil, 1 day treatment, biologial rep3

source_name: Root apex from maize genotype S1587-17 grown in control soil for 1 day

value: 1 day


title: trachea, smoker 042

value: smoker, 24 pack-years


title: small airways, SYMs-021

value: F

value: smoker, 20 pack-years


title: small airways, SYMs-171

value: smoker, 8 pack-years


title: trachea, SYMs-151

value: M

value: hispanic

value: smoker, 13 pack-years


title: Wild_type_control

source_name: Entire small intestine, wild type, control

value: small intestine

value: wild type


title: Muscle_t0_insulin-rep1

source_name: vastus lateralis muscle, pre inactivity, insulin treated

value: skeletal muscle


title: S1587-17, control soil, 3 days treatment, biologial rep3

source_name: Root apex from maize genotype S1587-17 grown in control soil for 3 days


title: small airways, SYMs-057

value: white

value: smoker, 35 pack-years


title: Muscle_t10_basal_rep1

source_name: vastus lateralis muscle, post inactivity, basal


title: Cat100-6, acid soil, 3 days treatment, biologial rep3

source_name: Root apex from maize genotype Ca100-6 grown in acid soil for 3 days


title: S1587-17, control soil, 3 days treatment, biologial rep2


title: S1587-17, acid soil, 1 day treatment, biologial rep2

source_name: Root apex from maize genotype S1587-17 grown in acid soil for 1 day


title: trachea, smoker 086

value: smoker, 33 pack-years


title: trachea, non-smoker 046

value: non-smoker


title: trachea, non-smoker 041

source_name: large airway epithelial cells obtained by bronchoscopy and brushing


title: S1587-17, control soil, 1 day treatment, biologial rep2

value: Root apex (5mm)


title: S1587-17, acid soil, 1 day treatment, biologial rep3


title: trachea, smoker 124

value: smoker, 0.5 pack-years


title: small airways, SYMs-127

value: black

value: smoker, 23 pack-years


title: small airways, SYMs-151


title: small airways, SYMs-090

value: smoker, 10 pack-years


title: trachea, smoker 134

value: F

value: smoker, 20 pack-years


title: Cat100-6, control soil, 3 days treatment, biologial rep3

source_name: Root apex from maize genotype Ca100-6 grown in control soil for 3 days

value: 3 days


title: S1587-17, control soil, 3 days treatment, biologial rep1


title: S1587-17, acid soil, 1 day treatment, biologial rep1

value: 1 day


title: S1587-17, acid soil, 3 days treatment, biologial rep1


title: Cat100-6, acid soil, 3 days treatment, biologial rep2


title: small airways, SYMs-108

value: M

value: smoker, 57 pack-years


title: Cat100-6, control soil, 3 days treatment, biologial rep1


title: small airways, SYMs-002

value: smoker, 13 pack-years


title: Cat100-6, acid soil, 1 day treatment, biologial rep3

source_name: Root apex from maize genotype Ca100-6 grown in acid soil for 1 day


title: small airways, SYMs-144

value: hispanic

value: smoker, 29 pack-years


title: S1587-17, control soil, 1 day treatment, biologial rep1


title: small airways, SYMs-035

value: white

value: smoker, 28 pack-years


title: small airways, LODs-215

value: smoker, 40 pack-years


title: small airways, LODs-204

value: smoker, 35 pack-years


title: Cat100-6, control soil, 3 days treatment, biologial rep2

value: Root apex (5mm)


title: Cat100-6, acid soil, 3 days treatment, biologial rep1


title: Cat100-6, control soil, 1 day treatment, biologial rep3

source_name: Root apex from maize genotype Ca100-6 grown in control soil for 1 day


title: small airways, LODs-194

source_name: airway epithelial cells obtained by bronchoscopy and brushing

value: black

value: smoker, 49 pack-years


title: small airways, LODs-208

value: smoker, 11 pack-years


title: small airways, LODs-195

value: F

value: smoker, 30 pack-years


title: small airways, LODs-131

value: smoker, 7 pack-years


title: Cat100-6, control soil, 1 day treatment, biologial rep1

value: 1 day


title: small airways, LODs-164

value: M

value: smoker, 15 pack-years


title: Bone marrow (hBM)-G0 [US22502695_251485029893_1_1]

city: Indianapolis

first: Brahmananda

middle: Reddy

last: Chitteti

state: IN

address: 980 W Walnut Streeet R3-c356

institute: Indiana University School of Medicine

description: Gene expression of G0 phase cells of bone marrow derived CD34+ cells

hyb_protocol: The Cy3- labeled cDNAs were hybridized overnight (17 hours, 65°C) to an Agilent Whole Human Genome Oligo Microarrays 4 x 44K using Agilent’s recommended hybridization chamber and oven. Finally, the microarrays were washed once with 6x SSPE buffer containing 0.005% Nlauroylsarcosine for 1 min at room temperature followed by a second wash with pre-heated 0.06x SSPE buffer (37 °C) containing 0.005% N-lauroylsarcosine for 1 min. The last washing step was performed with acetonitrile for 30 sec.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies).

data_processing:
The Agilent Feature Extraction Software (FES, v.9.1) was used to read out and process the microarray image files. The software determines feature intensities (including background subtraction), rejects outliers and calculates statistical confidences. The signal intensities from the single-experiment raw data lists are normalized by dividing the intensity values by their median.
For determination of differential gene expression FES derived output data files were further analyzed using the Rosetta Resolver gene expression data analysis system (Rosetta Biosoftware). This software offers – among other features – the possibility to compare two single intensity profiles in a ratio experimen. All samples were labeled with Cy3, here, the ratio experiments are shown as control versus (vs.) sample experiments.
The gIsPosAndSignif column indicates with a value = 1 that the signal intensity is positive and significant above the background and a value = 0 that the signal intensity is not positive and significant above the background.

source_name: Bone marrow (hBM)- G0

label_protocol: 250 ng of each of the cDNAs were used as template for Cy3 labeling which was performed according to Miltenyi Biotec’s undisclosed protocol.

extract_protocol: SuperAmp RNA amplification was performed according to Miltenyi Biotec’s undisclosed procedure. Briefly, the amplification is based on a global PCR protocol using mRNA-derived cDNA. mRNA was isolated via magnetic bead technology. Amplified cDNA samples were quantified using the ND-1000 Spectrophotometer (NanoDrop Technologies). The integrity of the cDNA was checked via the Agilent 2100 Bioanalyzer platform (Agilent Technologies).

treatment_protocol: BM and UCB samples were ficolled and mononuclear cells were collected followed by CD34+ selection using Miltenyi Magnetically Activated Cell Sorting (MACS) columns according to the manufacturer’s directions (Miltenyi Biotec GmbH, Bergisch Gladbach, Germany). Mobilization was achieved by daily granulocyte colony-stimulating factor administration at 5 mg/kg (maximum of 480 mg/day) for 4 consecutive days. Apheresis was performed on day 5 and CD34+ cells were isolated by immunomagnetic selection on an Isolex 300i system (Nexell, Irvine, CA). To generate distinct and unique sets of data, we did not pool multiple samples from any tissue studied so that each sample or its replicate was from a single donor.  Purity of selected CD34+ fractions was assessed by flow-cytometric analysis with an antibody recognizing a different CD34 epitope (BD Biosciences, San Jose, CA). The efficiency of the MACS columns was over 80% and the efficiency of the Isolex 300i system exceeded 95%. All samples of selected CD34+ cells were cryopreserved prior to their use.

value: Bone marrow

value: CD34+ cells

tag: cell cycle phase


title: small airways, LODs-025

value: smoker, 26 pack-years


title: Cat100-6, acid soil, 1 day treatment, biologial rep1


title: Cat100-6, acidl soil, 1 day treatment, biologial rep2


title: HMLE, shGFP rep2

city: Cambridge

first: Piyush

middle: B.

last: Gupta

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research/MIT

description: Global gene expression signature upon salinomycin treatment

hyb_protocol: Standard Affymetrix protocol; hybridization was performed with high-throughput HT_HG-U133A arrays in 96-well format

scan_protocol: Scanned using an Affymetrix HT Scanner

data_processing: The data were RMA-normalized using the open-source R-project statistical software with bioconductor packages.

source_name: HMLE breast epithelial cells transduced with shGFP

label_protocol: Standard Affymetrix protocol

growth_protocol: Cells were grown in a 1:1 mixture of DMEM+10%FBS, insulin, hydrocortisone and MEGM.

extract_protocol: Total RNA was extracted from culture plates for each cell type using an RNeasy Mini kit coupled with an RNase-free DNase set (Qiagen).

treatment_protocol: Following retroviral transduction, cells were treated for 5 days with blasticidin (5ng/ml); after drug selection, cells were grown for at least one week prior to RNA extraction.

value: HMLE

value: breast

value: SV40ER, hTERT


title: Cat100-6, control soil, 1 day treatment, biologial rep2


title: Bone marrow (hBM)-G0 [US22502695_251485029252_1_3]


title: HMLE, Snail, rep3

source_name: HMLE breast epithelial cells transduced with Snail


title: HMLE, shGFP rep3


title: HMLE, shEcad, rep3

source_name: HMLE breast epithelial cells transduced with shEcad


title: Mobilized peripheral blood (MPB)-G1 [US22502695_251485029254_1_2]

description: Gene expression of G1 phase cells of mobilized periphearal blood derived CD34+ cells

source_name: Mobilized peripheral blood (MPB)- G1

value: Mobilized peripheral blood


title: Bone marrow (hBM)-G1 [US22502695_251485029252_1_2]

description: Gene expression of G1 phase cells of bone marrow derived CD34+ cells

source_name: Bone marrow (hBM)- G1


title: Bone marrow (hBM)-G1 [US22502695_251485029252_1_4]


title: Mobilized peripheral blood (MPB)-G0 [US22502695_251485029254_1_1]

description: Gene expression of G0 phase cells of mobilized periphearal blood derived CD34+ cells

source_name: Mobilized peripheral blood (MPB)- G0


title: HMLE, shEcad, rep2


title: Wild type 6

city: Homburg

first: Andreas

last: Keller

address: Building 60

institute: Saarland University

hyb_protocol: according to manufacturers instruction (febit biomed)

scan_protocol: Slides were scanned using a “Geniom Real Time Analyzer” (febit biomed gmbh, Heidelberg, Germany). Wizard software on standard Microsoft Windows Workstation PC was used.

data_processing: summarizing of technical replica by median and quantile normalization. Following BG correction, negative values were corrected to 1

source_name: RNA from blood

label_protocol: MPEA, microfluidic primer extension assay Biotin labeling

extract_protocol: Blood from Tff3 KO as well as WT mice was collected in RNAprotect® Animal Blood Tubes (Qiagen GmbH, Hilden). About 400-500µl of peripheral blood were obtained from each animal. Following centrifugation of the blood samples at 5000 g for 10 min at room temperature (RT), the supernatant was discarded while the pellet was resuspended in 5ml RNase free water. After a second centrifugation step at 5000 g for 10 min and RT, isolation of total RNA including miRNA was performed using the miRNeasy kit (Qiagen GmbH, Hilden).

treatment_protocol: stored at -20 degree

tag: genotype/variation

value: wild type

tag: gender

value: female


title: Bone marrow (hBM)-G0 [US22502695_251485029252_1_1]

tag: cell type


title: HMLE, shEcad, rep1


title: small airways, LODs-034

value: black

value: smoker, 18 pack-years


title: HMLE, Snail, rep1


title: Umbillical Cord blood (CB)-G1 [US22502695_251485029250_1_2]

description: Gene expression of G1 phase cells of CB derived CD34+ cells

source_name: Umbillical Cord blood (CB)- G1

value: Umbillical Cord blood


title: HMLE, Snail, rep2


title: HMLE, shGFP, rep1


title: HMLE, Gsc, rep3

source_name: HMLE breast epithelial cells transduced with Gsc


title: Wild type 5


title: Umbillical Cord blood (CB)-G1 [US22502695_251485029250_1_4]


title: HMLE, Gsc, rep2


title: Umbillical Cord blood (CB)-G0 [US22502695_251485029250_1_3]

description: Gene expression of G0 phase cells of CB derived CD34+ cells

source_name: Umbillical Cord blood (CB)- G0