title: hESC.conventional_wa09_rep56_HT12v4


title: lung_K255

status: Public on Oct 21 2015

type: RNA

city: Tampa

first: Steven

last: Eschrich

state: FL

address: 12902 Magnolia Drive

department: Biostatistics & Bioinformatics

country: USA

institute: Moffitt Cancer Center

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

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

data_processing: IRON normalization was performed on the dataset, batch corrected for RNA quality using PLS

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: lung adenocarcinoma

label_protocol: Samples were amplified and labeled using a custom automated version of the NuGEN Ovation v2 with WB (whole blood) reagents protocol (using Ribo-SPIA amplification). The labeled molecules are biotinylated-cRNA. Sample amplification and labeling were performed by LabCorp Clinical Trials-Genomic Services in Seattle, Washington.

extract_protocol: Samples are processed in parallel in 96-well plates to minimize potential variation. Reaction purification is achieved using magnetic binding beads for cDNA and Qiagen RNeasy kits for cRNA purification. Isolated total RNA samples were assayed for quality (Agilent Bioanalyzer) and yield (Ribogreen) metrics prior to amplification.

tag: gender

value: F

tag: race

value: WHITE

value: Non Spanish/Hispanic

value: Missing

value: Dead

tag: Stage

value: WT

value: Mut


title: lung_K192

value: Ever

value: Alive


title: hESC.conventional_sivf022_rep158_HT12v3

city: La Jolla

first: Kristopher

middle: L.

last: Nazor

state: CA

address: 10550 North Torrey Pines Road

department: Regenerative Medicine

institute: The Scripps Research Institute

hyb_protocol: 750 ng labeled RNA/sample was hybridized to HT-12v3 Expression BeadChips (Illumina, Inc.).

scan_protocol: Arrays were imaged using HiScan using standard recommended Illumina scanner settings.

data_processing: In GenomeStudio, probes were filtered for those detected at p<0.01 in at least 1 sample and exported for normalization in R using robust spline normalization (RSN).

label_protocol: 200 ng RNA per sample was amplified using the Total PrepTM RNA Amplification Kit (Illumina, Inc.) according to manufacturer’s protocol.

extract_protocol: Total RNA was extracted from snap-frozen sample pellets (Ambion mirVana Kit, Life Technologies, Inc.) according to the manufacturer’s protocol. RNA quantity (QubitTM RNA BR Assay Kits, Life Technologies, Inc.) and quality (RNA6000 Nano Kit and Bioanalyzer 2100, Agilent) was determined to be optimal for each sample prior to further processing.

tag: derivation type


title: hESC.conventional_wa09_rep57_HT12v4

hyb_protocol: 750 ng labeled RNA/sample was hybridized to HT-12v4 Expression BeadChips (Illumina, Inc.).


title: lung_K066


title: hESC.conventional_sivf021_rep153_HT12v3


title: lung_K180

value: M


title: hESC.conventional_wa09_rep53_HT12v4


title: hESC.conventional_wa09_rep54_HT12v4


title: lung_K185


title: lung_K239


title: hESC.conventional_wa09_rep50_HT12v4


title: lung_K008

value: SpliceSite


title: hESC.conventional_wa09_rep51_HT12v4


title: hESC.conventional_sivf020_rep151_HT12v3


title: hESC.conventional_sivf019_rep149_HT12v3


title: hESC.conventional_sivf020_rep152_HT12v3


title: hESC.conventional_sivf040_rep170_HT12v3


title: hESC.conventional_sivf021_rep154_HT12v3


title: hESC.conventional_sivf021_rep155_HT12v3


title: lung_K063


title: hESC.conventional_sivf020_rep150_HT12v3


title: lung_K381


title: hESC.conventional_wa09_rep52_HT12v4


title: lung_K147


title: hESC.conventional_wa09_rep48_HT12v4


title: lung_K272


title: hESC.conventional_wa09_rep49_HT12v4


title: hESC.conventional_sivf019_rep148_HT12v3


title: lung_K382


title: hESC.conventional_wa09_rep46_HT12v4


title: hESC.conventional_wa09_rep47_HT12v4


title: hESC.conventional_sivf019_rep147_HT12v3


title: hESC.conventional_sivf019_rep146_HT12v3


title: lung_K378


title: hESC.conventional_sivf018_rep145_HT12v3


title: lung_K091


title: hESC.conventional_sivf017_rep140_HT12v3


title: lung_K129


title: hESC.conventional_wa09_rep42_HT12v4


title: hESC.conventional_wa09_rep41_HT12v4


title: lung_K021


title: hESC.conventional_sivf017_rep141_HT12v3


title: hESC.conventional_sivf015_rep137_HT12v3


title: hESC.conventional_wa09_rep39_HT12v4


title: hESC.conventional_sivf018_rep143_HT12v3


title: hESC.conventional_sivf017_rep142_HT12v3


title: hESC.conventional_wa09_rep38_HT12v4


title: hESC.conventional_wa09_rep40_HT12v4


title: lung_K288

value: VIETNAMESE


title: hESC.conventional_wa09_rep44_HT12v4


title: lung_K118


title: lung_K127


title: hESC.conventional_sivf018_rep144_HT12v3


title: lung_K158


title: hESC.conventional_sivf015_rep138_HT12v3


title: hESC.conventional_sivf014_rep136_HT12v3


title: hESC.conventional_wa07_rep36_HT12v4


title: lung_K439


title: hESC.conventional_wa09_rep43_HT12v4


title: hESC.conventional_wa07_rep37_HT12v4


title: hESC.conventional_sivf016_rep139_HT12v3


title: lung_K347


title: hESC.conventional_wa01_rep34_HT12v4


title: hESC.conventional_sivf007_rep133_HT12v3


title: hESC.conventional_sivf011_rep135_HT12v3


title: hESC.conventional_subihd1_rep32_HT12v4


title: hESC.conventional_wa09_rep45_HT12v4


title: lung_K011


title: lung_K233


title: hESC.conventional_sivf043_rep29_HT12v4


title: hESC.conventional_wa01_rep35_HT12v4


title: lung_K114


title: hESC.conventional_sivf006_rep132_HT12v3


title: hESC.conventional_sivf005_rep128_HT12v3


title: hESC.conventional_subihd1_rep31_HT12v4


title: lung_K160


title: lung_K380

value: Never


title: hESC.conventional_sivf005_rep129_HT12v3


title: hESC.conventional_uc06_rep33_HT12v4


title: lung_K444


title: hESC.conventional_sivf005_rep130_HT12v3


title: hESC.conventional_sivf004_rep127_HT12v3


title: lung_K040


title: hESC.conventional_subi1_rep30_HT12v4


title: hESC.conventional_sivf025_rep26_HT12v4


title: hESC.conventional_sivf006_rep131_HT12v3


title: hESC.conventional_sivf027_rep27_HT12v4


title: lung_K431


title: hESC.conventional_sivf022_rep24_HT12v4


title: hESC.conventional_sivf015_rep22_HT12v4


title: hESC.conventional_sivf019_rep23_HT12v4


title: lung_K212


title: hESC.conventional_sivf003_rep125_HT12v3


title: lung_K244


title: hESC.conventional_sivf029_rep28_HT12v4


title: lung_K077


title: hESC.conventional_sivf002_rep124_HT12v3


title: lung_K314


title: lung_K062

value: ASIAN INDIAN OR PAKISTANI


title: lung_K245


title: hESC.conventional_sivf007_rep134_HT12v3


title: hESC.conventional_sivf003_rep126_HT12v3


title: hESC.conventional_sivf002_rep123_HT12v3


title: hESC.conventional_shhes2_rep20_HT12v4


title: hESC.conventional_sivf024_rep25_HT12v4


title: hESC.conventional_sivf002_rep21_HT12v4


title: hESC.conventional_sivf001_rep121_HT12v3


title: hESC.conventional_sivf002_rep122_HT12v3


title: lung_K101


title: hESC.conventional_sivf001_rep118_HT12v3


title: hESC.conventional_hes3_rep14_HT12v4


title: hESC.conventional_sivf001_rep115_HT12v3


title: hESC.conventional_sivf001_rep120_HT12v3


title: lung_K134


title: hESC.conventional_mel1_rep17_HT12v4


title: hESC.conventional_sivf001_rep117_HT12v3


title: hESC.conventional_genea02_rep13_HT12v4


title: hESC.conventional_sivf001_rep116_HT12v3


title: hESC.conventional_hues9_rep15_HT12v4


title: lung_K422


title: hESC.conventional_cyt49_rep11_HT12v4


title: lung_K031


title: lung_K056


title: lung_K083


title: lung_K202


title: hESC.conventional_mel1_rep16_HT12v4


title: hESC.conventional_cyt49_rep12_HT12v4


title: hESC.conventional_miz6_rep111_HT12v3


title: hESC.conventional_mel1_rep19_HT12v4


title: lung_K374


title: hESC.conventional_miz6_rep113_HT12v3


title: hESC.conventional_miz6_rep114_HT12v3


title: lung_K324


title: hESC.conventional_miz6_rep112_HT12v3


title: lung_K042


title: hESC.conventional_cyt49_rep5_HT12v4


title: hESC.conventional_cyt49_rep10_HT12v4


title: hESC.conventional_cyt49_rep6_HT12v4


title: lung_K070


title: lung_K254


title: hESC.conventional_miz4_rep108_HT12v3


title: hESC.conventional_miz4_rep107_HT12v3


title: lung_K279


title: hESC.conventional_miz4_rep105_HT12v3


title: hESC.conventional_cyt49_rep7_HT12v4


title: hESC.conventional_miz4_rep110_HT12v3


title: hESC.conventional_cyt49_rep9_HT12v4


title: hESC.conventional_cyt49_rep4_HT12v4


title: hESC.conventional_cyt49_rep8_HT12v4


title: hESC.conventional_miz4_rep106_HT12v3


title: lung_K337

value: BLACK


title: hESC.conventional_miz4_rep109_HT12v3


title: lung_K110

value: UNKNOWN


title: lung_K248


title: hESC.conventional_miz4_rep104_HT12v3


title: lung_K451


title: lung_K166


title: hESC.conventional_miz4_rep103_HT12v3


title: lung_K469


title: hESC.conventional_bg02_rep1_HT12v4


title: lung_K002


title: hESC.conventional_sivf001_rep119_HT12v3


title: hESC.conventional_mel1_rep18_HT12v4


title: lung_K402


title: lung_K435


title: hESC.conventional_miz4_rep102_HT12v3


title: hESC.conventional_cm7_rep2_HT12v4


title: hESC.blastomere_ucsfb4_rep1_HT12v4


title: hESC.blastomere_ucsfb9_rep2_HT12v4


title: hESC.conventional_miz4_rep99_HT12v3


title: hESC.conventional_miz4_rep98_HT12v3


title: hESC.blastomere_ucsfb3_rep2_HT12v4


title: hESC.conventional_miz4_rep101_HT12v3


title: lung_K236


title: hESC.blastomere_ucsfb5_rep2_HT12v4


title: hESC.conventional_mel4_rep97_HT12v3


title: hESC.blastomere_ucsfb1_rep1_HT12v4


title: hESC.conventional_mel4_rep96_HT12v3


title: lung_K226


title: lung_K228


title: hESC.blastomere_ucsfb7_rep1_HT12v4


title: lung_K470


title: lung_K188


title: lung_K389


title: hESC.conventional_mel3_rep95_HT12v3


title: lung_K024


title: SUM52PE FGF10 Rep2

city: Cambridge

first: Kerstin

last: Meyer

address: Robinson Way

department: Cancer Research UK Cambridge Institute

country: United Kingdom

institute: University of Cambridge

hyb_protocol: Standard Illumina hybridisation protocol.

scan_protocol: Standard Illumina scanning protocol using an Illumina BeadArray reader.

data_processing: Raw image files were processed and analysed using the Beadarray R package. The data was corrected for spatial artifacts, log (base 2) transformed, and quantile normalised. Note: detection p-values are not available.

label: Biotin

source_name: SUM52PE cell line treated with estrogen and FGF10

label_protocol: Standard Illumina label protocol.

growth_protocol: MCF-7 human breast cancer cells were cultured in DMEM (Invitrogen) supplemented with 10% FBS and antibiotics. ZR751, T47D and BT474 human breast cancer cells were cultured in RPMI (Invitrogen) supplemented with 10% FBS and antibiotics. SUM52PE human breast cancer cells were cultured in Ham/F-12 (Invitrogen) supplemented with 10% FBS, 5 μg/ml insulin, 1 μg/ml hydrocortisone and antibiotics. All cells were maintained at 37°C, 5% CO2. Cell synchronisation via estrogen deprivation was carried out for three consecutive days in phenol red-free media supplemented with 5% charcoal dextran-treated FBS and antibiotics, with media changed every 24 h.

extract_protocol: RNA was extracted using the miRNeasy spin column kit (QIAGEN) and quality checked using an RNA 6000 Nano chip on a 2100 Bioanalyser (Agilent). 250ng RNA (RIN>7) was used for cRNA amplification and labelling using the Illumina TotalPrep-96 kit (Ambion 4397949).

treatment_protocol: Estrogen deprived cells were stimulated with 1 nM estradiol (Sigma); 100ng/mL FGF10 (Invitrogen) for a period of 6 h.

tag: cell line

tag: cell type

value: breast cancer


title: hESC.conventional_mel3_rep93_HT12v3


title: BT474 E2 Rep1

source_name: BT474 cell line treated with estrogen


title: SUM52PE Starved Rep3

source_name: SUM52PE cell line treated with vehicle


title: hESC.conventional_mel3_rep94_HT12v3


title: lung_K393

value: F


title: BT474 FGF10 Rep1

source_name: BT474 cell line treated with estrogen and FGF10


title: lung_K206

value: WHITE


title: hESC.conventional_mel2_rep89_HT12v3


title: lung_K373

value: Non Spanish/Hispanic


title: hESC.conventional_mel3_rep91_HT12v3


title: SUM52PE Starved Rep2


title: BT474 E2 Rep2


title: hESC.conventional_mel3_rep92_HT12v3


title: BT474 FGF10 Rep2


title: SUM52PE E2 Rep3

source_name: SUM52PE cell line treated with estrogen


title: BT474 Starved Rep2

source_name: BT474 cell line treated with vehicle


title: hESC.conventional_mel2_rep90_HT12v3


title: hESC.conventional_mel2_rep88_HT12v3


title: lung_K148

value: Missing


title: hESC.conventional_mel2_rep86_HT12v3


title: lung_K232


title: hESC.conventional_mel2_rep87_HT12v3


title: hESC.conventional_mel1_rep82_HT12v3


title: lung_K073


title: lung_K061


title: lung_K189

value: Dead


title: hESC.conventional_miz4_rep100_HT12v3


title: hESC.conventional_mel1_rep85_HT12v3


title: lung_K069

value: WT


title: SUM52PE FGF10 Rep3


title: hESC.conventional_mel1_rep81_HT12v3


title: hESC.conventional_mel1_rep83_HT12v3


title: lung_K081

value: Mut


title: BT474 Starved Rep1


title: lung_K112

value: Ever


title: hESC.conventional_mel1_rep80_HT12v3


title: BT474 FGF10 Rep3


title: hESC.conventional_csc14_rep3_HT12v4


title: lung_K053

value: Alive


title: hESC.conventional_mel1_rep77_HT12v3


title: BT474 Starved Rep3


title: hESC.conventional_mel1_rep79_HT12v3


title: hESC.conventional_mel1_rep84_HT12v3


title: lung_K327


title: lung_K308

value: M


title: BT474 E2 Rep3


title: SUM52PE E2 Rep1


title: hESC.conventional_mel1_rep78_HT12v3


title: lung_K257


title: hESC.conventional_hues7_rep76_HT12v3


title: lung_K006


title: SUM52PE FGF10 Rep1


title: lung_K468


title: hESC.conventional_hues16_rep72_HT12v3


title: hESC.conventional_hues16_rep74_HT12v3


title: hESC.conventional_hues13_rep71_HT12v3


title: lung_K187


title: lung_K405


title: lung_K210


title: hESC.conventional_hes4_rep68_HT12v3


title: lung_K149


title: hESC.conventional_hues16_rep73_HT12v3


title: lung_K394


title: hESC.conventional_hes4_rep70_HT12v3


title: lung_K015


title: lung_K218


title: lung_K196


title: lung_K428


title: lung_K406


title: hESC.conventional_hes3_rep65_HT12v3


title: hESC.conventional_hes3_rep64_HT12v3


title: hESC.conventional_hes4_rep69_HT12v3


title: lung_K001


title: hESC.conventional_hues7_rep75_HT12v3


title: lung_K071

value: SpliceSite


title: hESC.conventional_hes4_rep66_HT12v3


title: hESC.conventional_hes3_rep63_HT12v3


title: lung_K334


title: hESC.conventional_hes2_rep53_HT12v3


title: hESC.conventional_hes3_rep60_HT12v3


title: hESC.conventional_hes2_rep58_HT12v3


title: lung_K151


title: lung_K097


title: lung_K247


title: hESC.conventional_hes2_rep56_HT12v3


title: lung_K139


title: lung_K453


title: hESC.conventional_hes2_rep55_HT12v3


title: lung_K403


title: hESC.conventional_hes2_rep54_HT12v3


title: hESC.conventional_hes3_rep59_HT12v3


title: hESC.conventional_hes4_rep67_HT12v3


title: lung_K297


title: lung_K412


title: lung_K213


title: hESC.conventional_hes2_rep52_HT12v3


title: hESC.conventional_hes3_rep62_HT12v3


title: hESC.conventional_hes3_rep61_HT12v3


title: lung_K375


title: hESC.conventional_hes2_rep57_HT12v3


title: lung_K438


title: hESC.conventional_fes61_rep49_HT12v3


title: hESC.conventional_hes2_rep50_HT12v3


title: hESC.conventional_fes29_rep46_HT12v3


title: hESC.conventional_hes2_rep51_HT12v3


title: lung_K204


title: hESC.conventional_fes22_rep42_HT12v3


title: lung_K034


title: hESC.conventional_fes30_rep48_HT12v3


title: hESC.conventional_fes22_rep41_HT12v3


title: lung_K132


title: lung_K349


title: hESC.conventional_fes22_rep39_HT12v3


title: hESC.conventional_fes22_rep40_HT12v3


title: hESC.conventional_fes29_rep43_HT12v3


title: lung_K333


title: lung_K287


title: lung_K084


title: lung_K300


title: lung_K299


title: lung_K173


title: hESC.conventional_esih3_rep37_HT12v3


title: lung_K462


title: lung_K460


title: lung_K282


title: hESC.conventional_fes29_rep44_HT12v3


title: lung_K041


title: hESC.conventional_fes30_rep47_HT12v3


title: hESC.conventional_fes29_rep45_HT12v3


title: hESC.conventional_esih3_rep36_HT12v3


title: lung_K411


title: lung_K195


title: hESC.conventional_esi053_rep35_HT12v3


title: lung_K285


title: lung_K136


title: hESC.conventional_esi051_rep34_HT12v3


title: lung_K352


title: hESC.conventional_esi017_rep31_HT12v3


title: lung_K032


title: hESC.conventional_esi049_rep33_HT12v3


title: hESC.conventional_csc14_rep30_HT12v3


title: lung_K087


title: hESC.conventional_cm8_rep26_HT12v3


title: lung_K113


title: hESC.conventional_cm8_rep28_HT12v3


title: lung_K007


title: lung_K216


title: hESC.conventional_esi035_rep32_HT12v3


title: lung_K330


title: lung_K156


title: hESC.conventional_csc14_rep29_HT12v3


title: hESC.conventional_cm7_rep24_HT12v3


title: hESC.conventional_cm2_rep21_HT12v3


title: lung_K423


title: lung_K313


title: lung_K296


title: hESC.conventional_cm6_rep22_HT12v3


title: hESC.conventional_cm6_rep23_HT12v3


title: hESC.conventional_cm7_rep25_HT12v3


title: lung_K343


title: hESC.conventional_esih3_rep38_HT12v3


title: lung_K240


title: lung_K267


title: hESC.conventional_cm14_rep18_HT12v3


title: hESC.conventional_cm14_rep19_HT12v3


title: hESC.conventional_bg03_rep13_HT12v3


title: lung_K362


title: lung_K354


title: lung_K401


title: hESC.conventional_bg03_rep14_HT12v3


title: hESC.conventional_cm2_rep20_HT12v3


title: hESC.conventional_cm11_rep17_HT12v3


title: hESC.conventional_cm8_rep27_HT12v3


title: hESC.conventional_bg02_rep9_HT12v3


title: lung_K028


title: lung_K316


title: lung_K291


title: hESC.conventional_bg02_rep11_HT12v3


title: hESC.conventional_cm1_rep16_HT12v3


title: hESC.conventional_bg02_rep12_HT12v3


title: lung_K119


title: lung_K054


title: lung_K022


title: lung_K241


title: lung_K302


title: lung_K194


title: hESC.conventional_bg02_rep8_HT12v3


title: hESC.conventional_bg02_rep10_HT12v3


title: hESC.conventional_cm1_rep15_HT12v3


title: hESC.conventional_bg02_rep7_HT12v3


title: lung_K427


title: hESC.conventional_bg01v_rep4_HT12v3


title: hESC.conventional_bg01v_rep5_HT12v3


title: lung_K193


title: lung_K277


title: lung_K179


title: hESC.conventional_bg01v_rep3_HT12v3


title: lung_K050


title: hESC.conventional_bg01_rep2_HT12v3


title: lung_K459


title: hESC.blastomere_ucsfb9_rep1_HT12v3


title: hESC.conventional_bg02_rep6_HT12v3


title: hESC.blastomere_ucsfb8_rep1_HT12v3


title: lung_K078


title: hESC.conventional_bg01_rep1_HT12v3


title: hESC.blastomere_ucsfb8_rep2_HT12v3


title: lung_K305


title: hESC.blastomere_ucsfb6_rep1_HT12v3


title: LNCAP_EB_3

city: Brisbane

first: Colleen

last: Nelson

state: Queensland

address: 199 Ipswich Road

department: Institute of Health and Biomedical Innovation; Vancouver Prostate Centre

country: Australia

institute: Queensland University of Technology; University of British Columbia

hyb_protocol: 1650 ng of the labeled cRNA were hybridised onto a custom Agilent oligo microarray at 65°C for 17 hours.

scan_protocol: Arrays were scanned on an Agilent scanner (G2565CA) using the Agilent Scan Control Software (A.8.4.1) and feature extraction was performed using the Agilent Feature Extraction Software (10.7).

data_processing: A quantile between-array normalization was applied and differential expression was determined using the Bayesian adjusted t-statistic linear model of the 'Linear Models for Microarray Data' (LIMMA) package in R.

source_name: LNCaP prostate cancer cell line, eusynstyelamide B

label_protocol: 150 ng of total RNA was amplified and labelled using the Agilent Low Input Quick Amp Labeling Kit according to the manufacturer's protocol.

growth_protocol: LNCaP cells were seeded at 2.0 x 10^5 cells per well into 6-well plates in phenol-red free RPMI-1640 medium + 5% fetal calf serum and cultured for 24 h at 37°C in an atmosphere containing 5% CO2 before treatment.

extract_protocol: Total cellular RNA was extracted using the Qiagen RNeasy Mini Kit including on-column DNase-I treatment.

treatment_protocol: Cells were either left untreated or were treated with 5 μM eusynstyelamide B (EB) in DMSO or with 0.1% DMSO alone for 24 h. Triplicates of each condition were prepared for microarray profiling.

value: LNCaP

value: prostate cancer cell line

tag: treatment

value: eusynstyelamide B


title: LNCAP_DMSO_2

source_name: LNCaP prostate cancer cell line, DMSO

value: DMSO


title: hESC.blastomere_ucsfb7_rep2_HT12v3


title: lung_K276


title: hESC.blastomere_ucsfb7_rep1_HT12v3


title: LNCAP_UT_3

source_name: LNCaP prostate cancer cell line, untreated

value: untreated


title: lung_K425


title: lung_K400


title: hESC.blastomere_ucsfb9_rep2_HT12v3


title: lung_K030


title: lung_K074


title: LNCAP_UT_2


title: hESC.blastomere_ucsfb5_rep1_HT12v3


title: LNCAP_EB_2


title: LNCAP_DMSO_3


title: LNCAP_EB_1


title: hESC.blastomere_ucsfb4_rep2_HT12v3


title: LNCAP_DMSO_1


title: hESC.blastomere_ucsfb3_rep2_HT12v3


title: hESC.blastomere_ucsfb1_rep2_HT12v3


title: BLT2 S18D2

status: Public on Oct 20 2015

city: Tokyo

first: Takehiko

last: Yokomizo

address: Hongo 2-1-1, Bunkyo-ku

department: Biochemistry

country: Japan

institute: Juntendo University School of Medicine

description: Cells cultured in DMEM for 2h following to calcium starvation for 18h

hyb_protocol: Following fragmentation and labeling, cDNA were hybridized using GeneChip Hybridization Kit (Affymetrix)

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

data_processing: The data were analyzed uisng Affymetrix Expression Console Software (GC-RMA) and global scaling as normalization method.

organism: Canis lupus familiaris

source_name: MDCK cells

label_protocol: Biotinylated cDNA was labeled with The Ambion WT Expression Kit and GeneChip WT Terminal Labeling Kit (Affymetrix) according to the manufacturer’s protocol.

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

value: human BLT2 overexpression-MDCK

value: cells cultured in DMEM for 2h following to calcium starvation for 18h


title: BLT2 S18D2+12-HHT

description: Cells cultured in DMEM containing 200 nM 12-HHT for 2h following to calcium starvation for 18h

value: cells cultured in DMEM containing 200 nM 12-HHT for 2h following to calcium starvation for 18h


title: Mock S2

description: Cells cultured in SMEM for 2h

value: Mock-MDCK

value: cells cultured in SMEM for 2h


title: Mock S18D2+12-HHT


title: hESC.blastomere_ucsfb2_rep2_HT12v3


title: LNCAP_UT_1


title: hESC.blastomere_ucsfb6_rep2_HT12v3


title: hESC.blastomere_ucsfb5_rep2_HT12v3


title: hESC.blastomere_ucsfb2_rep1_HT12v3


title: Mock S18

description: Cells cultured in SMEM for 18h

value: cells cultured in SMEM for 18h


title: BLT2 S18

description: Cells cultured in SMEM for 18h


title: BLT2 0h

description: Cells cultured in DMEM containing 10% FCS

value: cells cultured in DMEM containing 10% FCS


title: Mock 0h


title: Mock S18D2

description: Cells cultured in DMEM for 2h after calcium starvation for 18h

value: cells cultured in DMEM for 2h after calcium starvation for 18h


title: hESC.blastomere_ucsfb4_rep1_HT12v3


title: hESC.blastomere_ucsfb3_rep1_HT12v3


title: hESC.blastomere_ucsfb1_rep1_HT12v3


title: Hep3B_UV_10J_replicate3_Dyeswap

city: barcelona

first: BELEN

last: MINANA

state: barcelona

address: dr aiguader 88

department: GENE REGULATION, STEM CELLS AND CANCER

country: Spain

institute: Center for genomic regulation

hyb_protocol: Slides were hybridized following manufacturer protocol, with the exception that we hybridized 6 micrograms of each amplified cRNA sample and the Agilent hybridization oven was set to 60ºC.

scan_protocol: Fluorescent images were obtained using the G2565BA Microarray Scanner System (Agilent) with 100% laser power and 100% PMT settings and 16-bit TIFF images, one for each channel, were quantified using GenePix Pro 6.0 microarray analysis software (Molecular Devices, www.moleculardevices.com).

data_processing: Raw data were processed using SAPO (http://bioinfo.ciberehd.org/SAP.ang.htm) and CGEM (http://bioinfo.ciberehd.org/CGEM.ang.html) alternative splicing analysis tools, obtaining lowess normalized log2ratios. Mean foreground and background intensities were extracted from the red (Cy5) and green (Cy3) channels for every spot on the microarray. The background intensities are used to correct the foreground intensities for local variation on the array surface, resulting in corrected red and green intensities.

source_name: human hepatoma Hep3B cells untreated

label_protocol: Sample was labeled using the Quick-Amp labeling kit, no dye (Agilent 5190-0447) and cyanine 5-CTP and cyanine 3-CTP (Perkin-Elmer NEL580, NEL581). Purified using Quiagen RNeasy mini kit. Quality control assessed by Agilent Bioanalyzer 2100.

growth_protocol: Hep3B cells were grown in IMDM medium supplemented with 10% fetal bovine serum, penicillin and streptomycin (Gibco), and maintained at 37°C in humidified 5% CO2 atmosphere.

extract_protocol: Total RNA was isolated using the RNAspin Mini Kit (GE Healthcare). An additional treatment with DNAse was performed using the TURBO DNA-free Kit  (Ambion inc).    Quality assessment of Total RNA samples were analyzed using the Agilent Bioanalyzer 2100 and the RNA 6000 LabChip Kit (Agilent) with the Eukaryote Total RNA Nano Assay.

treatment_protocol: Human hepatoma Hep3B cells were Hep3B cells were washed two times with PBS and then irradiated with 10J/m2 UV light; fresh medium was immediately added after the irradiation and the cells were incubated at 37 C and collected 6 hours after the treatment for the RNA preparation.

value: hepatoma

source_name: Hep3B cells treated with 10 J/m2 UV light


title: Hep3B_UV_10J_replicate2_Dyeswap


title: BLT2 S2

description: Cells cultured in SMEM for 2h


title: Hep3B_UV_10J_replicate1_Dyeswap


title: Hep3B_UV_10J_replicate1

source_name: human hepatoma Hep3B cells treated with 10 J/m2 UV light

source_name: Hep3B cells untreated


title: Hep3B_UV_10J_replicate3


title: LAP_replicate1_Dyeswap

source_name: LAP-35 cells untreated

growth_protocol: LAP-35 and SK-N-MC cells were grown in IMDM medium supplemented with 10% fetal bovine serum, penicillin and streptomycin (Gibco), and maintained at 37°C in humidified 5% CO2 atmosphere.

treatment_protocol: Ewing Sarcoma cells were plated at 50%-60% confluence 16 h before UV light irradiation (UVC 10 J/m2). Fresh medium was immediately added after the treatment and the cells were harvested at 6 hours after the irradiation.

value: Ewing sarcoma

source_name: LAP-35 cells treated with 10 J/m2 UV light


title: Hep3B_UV_10J_replicate2


title: LAP_replicate2_Dyeswap


title: LAP_replicate3


title: SK_replicate3_Dyeswap

source_name: SK_N_MC cells untreated

source_name: SK_N_MC cells treated with 10 J/m2 UV light


title: SK_replicate1


title: E14.5_Lung_Yy1flox/flox;Shh+/Cre_rep3.

city: Lausanne

first: Eric

middle: R

last: Paquet

state: Vaud

address: Station 15  CH - 1015

department: Life sciences

country: Switzerland

institute: EPFL

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing: Data were pre-processed and normalized using the affymetrix power tool using the rma-sketch method

organism: Mus musculus

source_name: E14.5  lung

label_protocol: Standard Affymetrix Labeling protocol

extract_protocol: Total RNA was extracted with Trizol reagent (Invitrogen) followed by DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. Quantification by Nanodrop.

tag: genotype

tag: developmental stage

tag: tissue

value: Lung


title: SK_replicate2


title: LAP_replicate1


title: LAP_replicate3_Dyeswap


title: E14.5_Lung_Dicerflox/flox;Shh+/Cre_rep3.

value: Dicerflox/flox;Shh+/Cre


title: SK_replicate2_Dyeswap


title: SK_replicate3


title: SK_replicate1_Dyeswap


title: E14.5_Lung_Dicerflox/flox;Shh+/Cre_rep1.


title: E14.5_Lung_Shh+/Cre_rep2.

value: Shh+/Cre


title: E14.5_Lung_Dicerflox/flox;Shh+/Cre_rep4.


title: E14.5_Lung_Yy1flox/flox;Shh+/Cre_rep4.


title: E14.5_Lung_Shh+/Cre_rep3.


title: E14.5_Lung_Shh+/Cre_rep4.


title: E14.5_Lung_Yy1flox/flox;Shh+/Cre_rep1.


title: E14.5_Lung_Dicerflox/flox;Shh+/Cre_rep2.


title: E14.5_Lung_Yy1flox/flox;Shh+/Cre_rep2.


title: E14.5_Lung_Shh+/Cre_rep1.


title: LAP_replicate2


title: human blastocyst S14_aCGH

type: genomic

city: Oxford

first: Dagan

last: Wells

address: 8000 Alec Issigonis Way

institute: University of Oxford

description: The reference samples are male or female reference DNA as provided by Illumina, as part of the standard 24sure package. The combined file represents results against both references. Raw data files are provided for each reference type.

hyb_protocol: After centrifugal precipitation, samples were dissolved in hybridization mix at 75°C for 10 minutes, and incubated overnight at 47°C on the arrays in closed incubation chambers with 50% formamide. The slides were washed 10min in 2xSSC/0.05% Tween20, 10 min 1xSSC, 5min 0.1%SSC at 60°C and 1min in 0.1%SSC at RT

scan_protocol: Microarray slides were scanned using an InnoScan 700 scanner (Innopsys, France). Images were stored as .TIFF files.

data_processing: Images were analysed using BlueFuse Multi v3.1 software (Illumina, USA).

molecule: genomic DNA

source_name: whole human blastocyst

label_protocol: 5 µL of PreAmp mastermix were added to each sample and incubated at 95°C for 2 mins, and then cycled for 12 times at 95°C for 15 sec,15°C for 50 sec, 25°C for 40 sec, 35°C for 30 sec, 65°C for 40 sec, 75°C for 40 sec. 60 µL of Amplification Mastermix were added to each sample and incubated at 95°C for 2 minutes, then cycled 14 times at 95°C for 15 sec, 65°C for 1 min and 75°C for 1 min. Labelling was done following standard 24sure v3 protocol. Briefly, samples were mixed with 5 µL of random primers and denaturated for 5 min at 94°C. Afterwards, samples were mixed with 12 µL of Cy3/Cy5 labelling master mix and incubated at 37°C for 4 hours.

growth_protocol: Embryos used in this study were donated by couples undergoing IVF treatment at the Oxford Fertility Unit, UK. All patients underwent conventional controlled ovarian hyperstimulation and oocyte collection was performed following follicle triggering by 10,000 IU recombinant hCG (Ovitrelle, Merck Serono, Germany). Collected oocytes were inseminated by exposure to fixed concentration of partner’s treated sperm sample or by intracytoplasmic sperm injection (ICSI). Fresh embryos were individually cultured in 50 µL microdrops of Cleavage medium (COOK, Australia) up until Day 3 post fertilization and then moved to 50 µL microdrops of Blastocyst medium (COOK, Australia) until donation. Donated cleavage-stage frozen embryos were thawed using standard commercial kit (COOK thawing media) and then cultured to blastocyst stage using Blastocyst medium (COOK, Australia). Incubation parameters were 37˚C and 6% CO2 and 5% O2.  Fresh embryos were donated on day 5 or 6 post insemination, whilst frozen embryos were donated at various stages between 24 and 72 hrs post insemination. Frozen embryos were thawed and cultured to day 5 or 6 until a full cavity was present.

extract_protocol: All extraction, amplification, labeling and hybridisation steps were performed according to Illumina SurePlex and 24sure protocols. 3 µL of Cell Extraction Buffer were added to each sample. 5 µL of Extraction Mastermix were added to each sample. Incubation at 75°C for 10 minutes, 95°C for 4 minutes then hold at RT.

treatment_protocol: Whole embryos were placed into sterile 0.2 mL PCR tubes in less than 2 µL PBS solution.

value: blastocyst

source_name: reference Male/Female or combined

tag: control type

value: reference DNA


title: Monocyte-derived macrophage control replicate 3

city: Iowa City

first: Thomas

middle: B

last: Bair

state: IA

address: 335 EMRB

institute: University of Iowa

hyb_protocol: The resulting biotin-labeled cDNA was mixed with Affymetrix eukaryotic hybridization buffer, placed onto Affymetrix Human Exon 1.0 ST arrays (Part No. 900650), and incubated at 45º C for 18 h with 60 rpm rotation in an Affymetrix Model 640 Genechip Hybridization Oven.  Following hybridization, the arrays were washed, stained with streptavidin-phycoerythrin (Molecular Probes, Inc., Eugene, OR), signal amplified with antistreptavidin antibody (Vector Laboratories, Inc., Burlingame, CA) using the Affymetrix Model 450 Fluidics Station.

scan_protocol: Arrays were scanned with the Affymetrix Model 3000 scanner with 7G upgrade and data were collected using the using the GeneChip operating software (GCOS) v1.4.

data_processing:
Microarray data was assessed by paired t-test analysis using R statistical software (http://www.R-project.org). Data was assessed for quality using a normalized unscaled standard error (NUSE) analysis. A 2-fold change in gene expression and p value of 0.01 was considered significant
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: Purified monocytes

label_protocol: Five micrograms of this product were fragmented (average fragment size = 85 bases) and biotin labeled using the NuGEN FL-Ovation cDNA Biotin Module (NuGEN Technologies, Cat. #4200) per the manufacturer’s recommended protocol

growth_protocol: Monocytes were purified from PBMCs by adherence and cultured and differentiated in the presence of human 50 ng/mL M-CSF for 6 days following isolation.

extract_protocol: RNA was isolated using the mirVana miRNA Isolation kit followed by clean-up and DNase I treatment using the DNA-free kit from Ambion following the manufacturer's protocol. Quality control was performed using an Experion Automated Electrophoresis Station (Bio-Rad). 50 nanograms total RNA were converted to SPIA amplified cDNA using the WT-Ovation Pico RNA Amplification System, v2 according to the manufacturer’s recommended protocol. The amplified SPIA cDNA product was purified through a QIAGEN QIAquick PCR Purification column according to modifications from NuGEN.

treatment_protocol: Six days following isolation, media was refreshed with M-CSF with or without 20 ng/mL human IFNg for 24 hours.

value: Monocyte-derived macrophage

tag: ifng

value: no


title: Monocyte-derived macrophage interferon-g inhibited

value: yes


title: human blastocyst S8_aCGH


title: 7402R [R]

city: Beijing

first: Sisi

last: Ma

state: Beijing

address: 5 Dong Dan San Tiao

department: National Laboratory of Medical Molecular Biology

country: China

institute: Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College

description: expression of microRNA

hyb_protocol: After stopping the labeling procedure, the Hy3™-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to array manual. The total 25 μL mixture from Hy3™-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min. Then hybridized to the microarray for 16-20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA). Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon).

scan_protocol: Scanning is performed with the Axon GenePix 4000B microarray scanner. GenePix pro V6.0 is used to read the raw intensity of the image.

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, significant differentially expressed miRNAs between two groups were identified through Fold change and P-value. Differentially expressed miRNAs between two samples were filtered through Fold change. Finally, hierarchical clustering was performed to show distinguishable miRNA expression profiling among samples.

source_name: TRAIL-resistant Bel-7402 cells

label_protocol: Hy3 labeled cRNA was prepared from 1 ug RNA using the miRCURYTM Array Power Labeling kit (Cat #208032-A, Exiqon) according to the manufacturer's instructions.

extract_protocol: Total RNA of TRAIL-sensitive and TRAIL-resistant Bel-7402 cells was extracted from cells using Trizol (Invitrogen, CA, USA) reagent. Total RNA from each sample was quantified and quality assuranced by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

value: hepatoma cell line

tag: phentoype

value: TRAIL-resistant


title: human blastocyst S7_aCGH


title: human blastocyst S5_aCGH


title: 7402S [C]

description: expression of microRNA

source_name: TRAIL-sensitive Bel-7402 cells

value: TRAIL-sensitive


title: Monocyte-derived macrophage interferon-g inhibited replicate 2


title: human blastocyst S2_aCGH


title: Monocyte-derived macrophage control


title: Monocyte-derived macrophage interferon-g inhibited replicate 1


title: human blastocyst S1_aCGH


title: human blastocyst S12_aCGH


title: Monocyte-derived macrophage interferon-g inhibited replicate 3


title: Alveolar macrophage interferon-g inhibited sample replicate 1

source_name: bronchial lavage cells

growth_protocol: Cells were obtained from a bronchial lavage.  Cells were cultured in the presence of 50 ng/mL of human M-CSF for 24 hrs after isolation

extract_protocol: RNA was isolated using the mirVana miRNA Isolation kit folllowed by clean-up and DNase I treatment using the DNA-free kit from Ambion following the manufacturer's protocol. Quality control was performed using an Experion Automated Electrophoresis Station (Bio-Rad). 50 nanograms total RNA were converted to SPIA amplified cDNA using the WT-Ovation Pico RNA Amplification System, v2 according to the manufacturer’s recommended protocol. The amplified SPIA cDNA product was purified through a QIAGEN QIAquick PCR Purification column according to modifications from NuGEN.

treatment_protocol: Twenty-four hours after isolation in the presence of M-CSF, media was refreshed with M-CSF with or without 20 ng/mL human IFNg for an additional 24 hrs.

value: Alveolar macrophage


title: Alveolar macrophage interferon-g inhibited sample


title: Monocyte-derived macrophage control replicate 1


title: human blastocyst S4_aCGH


title: human blastocyst S13_aCGH


title: Alveolar macrophage control replicate 2


title: human blastocyst S10_aCGH


title: human blastocyst S9_aCGH


title: human blastocyst S3_aCGH


title: Alveolar macrophage interferon-g inhibited sample replicate 2


title: Alveolar macrophage control replicate 1


title: Human Met-5A cells exposed to Strep. Pneumoniae strain D39 replicate 2

city: Nottingham

first: Patrick

middle: Jason

last: Tighe

state: Nottinghamshire

address: University Hospital

department: School of Molecular Medical Sciences

institute: The University of Nottingham

hyb_protocol: Microarray slide hybridisation and data analysis. Microarrays were washed sequentially with 0.2% (w/v) SDS buffer,  PBS containing 0.1M sodium borohydride, 0.2% SDS (w/v), water and ethanol (100%). Microarray hybridizations were done on a HS48000 hybridization station (Tecan Ltd., Switzerland), using an automated program and 0.1-4 X SSC/0.1-0.2% (w/v) SDS buffer solutions as recommended by the manufacturer.Slides were scanned on an Agilent BA scanner (Agilent Technologies, USA) and two digital images were obtained for each array, which were overlaid using the manufacturer’s software.

scan_protocol: Arrays were scanned using an Axon Genepix 4200AL slide scanner. Images were exported to and analyzed using GenePix® Pro v6.0 software (Molecular Devices LLC, USA) and the median of duplicate spots was calculated for each image and raw data were expressed as a log ratio of Cy5/Cy3 (sample/control probe). Intra- and inter-array global LOWESS normalization was done in J- Express Pro software (MolMine, Norway) and ratios were then used to rank genes and calculate fold changes. A False Discovery Rate (FDR) limit of ≤ 5% was applied to the gene lists and genes with an FDR above this cut-off were excluded from analysis

data_processing: Log Ratio datalog [(cy5/cy3)] Raw GPR files were cleaned and filtered using  J Express Pro (Norwegian Bioinformatics Platform and Norwegian Microarray Consortium in collaboration (http://www.molmine.com)), using the median  feature signal - local background for both colours.  internal spike controls and  blank features were  removed.  Data was  filtered using  sequential filters to remove features of with FLAGS<0, feature diameter of <45um, A global Lowess normalization was applied, and secondary filtering removing any features where both normalised CY5 AND Cy3 signals contained less that 70% of feature pixels above  local background + 2 SD.  For final analysis only data which was present in all replicate arrays was used.  Data from the replicates was averaged for input into Ingenuity Pathway analysis for pathway centric exploration.

source_name: Human Met 5A cell line

label_protocol: Synthesis and purification of human cDNA and in-vitro transcription to yield amino-allyl RNA (aRNA). All  reagents  and  consumables  used  in  the  preparation  of  human  microarray probes were provided in an Amino Allyl MessageAmp™ II aRNA proprietary kit (Ambion, USA). cDNA first and second strand synthesis and purification using a cDNA filter cartridge was done following the manufacturer’s instructions (Ambion).  Purified cDNA was transcribed in the presence of amino-allyl labelled uracil triphosphate (aaUTP) to yield amino-allyl- labelled RNA (aRNA),  which was purified using a manufacturer’s proprietary filter cartridge. Incorporation of amino allyl-labelled UTP was confirmed by measurement on a Nanodrop spectrophotometer. Test aRNA samples were dye-coupled to Cy3, whilst control aRNA was labelled with Cy5, following the manufacturer’s instructions. Dye-labelled aRNA samples were purified using aRNA filter cartridges and the frequency of dye incorporation was measured on the Nanodrop spectrophotometer. For each slide to be hybridized and prior to use, 500ng of both test sample and control sample aRNA was fragmented using proprietary fragmentation buffer (Ambion) according to the manufacturer’s instructions. Samples were placed on ice and 2µl of lithium heparin and 1µl of Cot-I human DNAse (Ambion) was added to inhibit non-specific probe hybridization. Finally, pre-heated (50°C) Schott 1X hybridisation buffer was added to the probe just prior to slide hybridization.

growth_protocol: The pleural mesothelial cell (PMC) line Met-5A (ATC-CRL-9444, LGC Standards, UK) was grown in Medium 199 containing Earles’ balanced salt solution, glutamine, HEPES and sodium carbonate (Lonza, UK), supplemented with 10% (v/v) decomplemented foetal bovine serum (dFBS), 3.3nM epidermal growth factor, 870nM insulin and 400nM hydrocortisone (Sigma-Aldrich, UK). Serotype 2 capsule polysaccharide expressing Streptococcus pneumoniae strain D39 (NCTC 7466) bacteria were grown on Columbia Blood Agar Plates (E&O Laboratories Ltd., UK),incubated overnight at 37°C and 5% (v/v) CO2 in the presence of optochin discs (Mast Group, UK) to confirm culture purity. For Met-5A infection experiments for microarray analyses, D39 was grown in liquid Brain Heart Infusion (BHI) medium (Oxoid, UK) to mid-log phase, the cultures were centrifuged (2500g, 10 min at room temperature (RT) and washed once in 10ml of warm phosphate buffered saline (PBS, pH7.4).

extract_protocol: Met-5A infected and control (uninfected and trypsin-treated) cell monolayers were disrupted by the addition of lysis buffer RLT (700µl/flask). Host cell RNA was extracted from the lysates using the RNeasy Minikit (Qiagen, UK), following the manufacturer’s instructions.

treatment_protocol: Met-5A cells were seeded (~10^6 cells/ml) to confluence in 30×75 cm2 cell culture flasks (Greiner) and infected with Streptococcus pneumoniae strain D39 at a MOI (multiplicity of infection of bacteria to cell) of 200 in Medium 199 containing 1% (v/v) dFBS for 2h at 37 oC.

value: Met 5A

tag: infection status

value: infected with S. pneumnoniae strain D39 at a MOI of 200 for 2h

value: control (uninfected) culture


title: Human Met-5A cells exposed to Strep. Pneumoniae strain D39 replicate 3


title: Monocyte-derived macrophage control replicate 2


title: Human Met-5A cells exposed to Strep. Pneumoniae strain D39 replicate 5


title: Alveolar macrophage control


title: Human Met-5A cells exposed to Strep. Pneumoniae strain D39 replicate 4


title: PCC6803_∆nsiR4::oex_12hCuSO4_rep2

city: Freiburg

first: Stephan

last: Klähn

state: Baden-Würtemberg

address: Schänzlestrasse 1

department: Institute of Biology III

country: Germany

institute: University of Freiburg

hyb_protocol: The labelled RNA was fragmented and hybridized as described by the manufacturer's instructions for Agilent one color microarrays with 1.65 µg of labeled RNA

scan_protocol: Arrays were scanned on the Agilent Technologies Scanner G2505B, using Agilent Feature Extraction Software 10.7.3.1 and the protocols GE1_107_Sep09  for Cy3 labelled arrays

data_processing: Raw data were processed with the R package Limma. Median signal intensity was quantile normalized.

organism: Synechocystis sp. PCC 6803

source_name: cells from liquid culture grown for 12 h in presence of 2 µM CuSO4

label_protocol: The RNA was labeled directly, without cDNA synthesis in 2 µg aliquots with the Kreatech “ULS labeling kit for Agilent gene expression arrays” with Cy3 according to the manufacturers protocol.

growth_protocol: For the generation of nsiR4 mutants, we used the glucose-tolerant strain Synechocystis 6803 (GT-Kazusa) provided from N. Murata (National Institute for Basic Biology, Okazaki, Japan). Cultivation was performed in Cu2+-free BG11 medium buffered with 20 mM TES, pH 8.0 at 30°C under continuous white light illumination of 50–80 μmol quanta m−2 s−1 and gentle agitation. Mutant strains were grown in presence of the corresponding antibiotics.

extract_protocol: Synechocystis 6803 cells were collected by rapid filtration on hydrophilic polyethersulfone filters (Pall Supor 800 Filter, 0.8 µm). Filters covered with cells were dissolved in 1 ml PGTX (Pinto et al., 2009; BMC Mol Biol 10: 79) and RNA was extracted as described (Hein et al., 2013; RNA Biol 10: 852–864).

treatment_protocol: To induce the ectopic expression of NsiR4, 2 µM CuSO4 was added to the cultures.

tag: genotype/variation


title: PCC6803_∆nsiR4::oex_12hCuSO4_rep1


title: PCC6803_∆nsiR4_12hCuSO4_rep1


title: CNE2Z transfected with control shRNA, biological rep2

first: jinfeng

last: meng

address: No. 27, Taiping Road, Haidian District

description:
N-3
Gene expression data from the human nasopharyngeal carcinoma cell line CNE2Z transfected with control shRNA.

hyb_protocol: For Single Probe Array the final concentration of fragmented cRNA was 0.05 μg/μL. Hybridization Cocktail was performed according to the manufacturer's instructions of Eukaryotic Hybridization Control Kit and Hybridization, Wash and Stain Kit (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using GeneChip® Scanner 3000.

data_processing: Raw feature data from microarrays were subsequently corrected for background and normalized, and the log2 intensity expression summary values for each probe set were calculated using Robust Multiplechip Average (RMA). Significantly altered genes following AGO2 knockdown were analyzed by significance analysis of microarray (SAM, version 3.01), and the P values of the t test were calculated for each gene. Multiple hypothesis testing was performed to calculate the false discovery rates (FDRs) through the Bioconductor package Qvalue (http://www.bioconductor.org). Significantly altered genes following AGO2 knockdown were investigated for biological processes and signaling pathways using the cytoscape plug-in of Reactome FI.

source_name: CNE2Z transfected with control shRNA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2011, Affymetrix).

growth_protocol: The human nasopharyngeal carcinoma cell line CNE2Z was maintained in RPMI 1640 (Gibco-BRL, USA) supplemented with 10% fetal bovine serum (HyClone, USA) at 37°C under a 5% CO2 atmosphere.

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

treatment_protocol: A mixture of constructs including three AGO2 shRNAs or the control shRNA construct was transfected into CNE2Z cells using Lipofectamine 2000 (Invitrogen, USA). The efficiency of RNA interfering was assessed by Western blot analysis.

value: nasopharyngeal carcinoma cell line

value: poorly differentiated

tag: cell morphology

value: adherent epithelial cells

tag: shRNA

value: control


title: CNE2Z transfected with AGO2 shRNAs, biological rep3

description:
S-4
Gene expression data from the human nasopharyngeal carcinoma cell line CNE2Z transfected with AGO2 shRNAs.

source_name: CNE2Z transfected with AGO2 shRNAs


title: GBM052_Rc

city: Suwon

first: Hyun Goo

last: Woo

address: 164 Worldcup-ro Yeongtong-gu

country: South Korea

institute: Ajou University School of Medicine

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

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

extract_protocol: RNA was extracted with mirVana miRNA Isolation kit with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: gender

value: GBM

tag: subgroup


title: GBM051_Rc


title: TE rep 1

hyb_protocol: Individual samples were brought to a total volume of 5 µl adding RNase-free water, mixed and left at RT for 10 minutes, then resuspended. 10 µL of previously heated HYB solution were added to each sample. Illumine BeadChips were prepared according to manufacturer’s instructions. 15 µL of sample were added to each hybridisation chambers and incubated for 16 hours at 58°C with rocker speed at 5. On the next day, slides were collected from hybridising oven and cover slides removed in E1BC buffer. Slides were then submerged in high temperature Wash buffer for 10 minutes. Slides were immediately transferred into the staining dish containing E1BC and placed on an orbital shaker for 5 minutes at the highest speed possible. The slides were then transferred into 100% ethanol and shaken for 10 minutes in an orbital shaker and transferred to E1BC wash for 2 minutes agitating. Reactions were blocked by submerging the slides in Block E1 buffer and agitating for 10 minutes. Slides were then stained with streptavidin-Cy3 by submersion and agitation for 10 minutes at RT and then washed in E1BC buffer for 5 minutes before drying in a centrifuge for 4 minutes.

scan_protocol: BeadChips were then scanned using an Illumina HiScan device.

data_processing:
Raw data were imported into the R statistical software for further processing and analysis using BioConductor packages. Raw signal intensities were background corrected prior to being transformed and normalised using the “*vsn*” package. The background intensity range was defined by a set of several hundred negative control probes on the array, designed with no match in the human genome.
Probes were assigned a detection p-value, based on their signal overlap with the background distribution. A detection p-value <0.05 was used to define probes expressed above background levels. Probes with signals above background levels in all of the samples were classified as expressed. These were annotated with gene information using the relevant BioConductor annotation package.

source_name: Human Trophectoderm

label_protocol: Purified mRNA was amplified using TargetAmp 2-Round Biotin-aRNA Amplification Kit 3.0 (Epicentre, Illumina) following manufacturer’s instructions. Briefly, this kit allows two subsequent in vitro transcription reactions and the incorporation of Biotin labeled nucleotides in the last step, starting from purified RNA. As suggested by the manufacturer, SuperScript III and SuperScript II Reverse Transcriptase (Invitrogen, Life Technologies, USA) were used for 1st strand cDNA synthesis in the first and second amplification rounds. RNA Clean & Concentrator-5 Kit (Zymo Research) was used for RNA purification after the first round of in vitro transcription. Final Biotin-aRNA purification was performed using RNeasy MinElute Cleanup Kit (Qiagen, Germany). No freezing step was performed during the procedure to avoid sample degradation. Total RNA output was measured by spectrophotometry analysis using a Nanodrop device (Thermo Fisher, USA). Aliquots of all samples were normalized to 150 ng/µL to allow microarray hybridization.

extract_protocol: The mRNA from the samples was isolated using RNaqueous-Micro Kit (Life Technologies) and following manufacturer’s instructions. Briefly, after ethanol-based cell lysis, cellular content was filtered using a Micro Filter Cartridge and centrifugation. The filtered products were washed with commercial solution prior to elution. RNA was then collected and treated for DNA digestion. The RNA was collected with the supernatant and placed in a new RNAse-free PCR tube.

treatment_protocol: Fully expanded human blastocysts were placed in 10 µL microdrops of filtered PBS. Embryos were anchored to a holding pipette (Cook, Australia) while part of the zona pellucida corresponding to the ICM was removed by laser pulse (Research Instruments, UK). Using a 35 µm Blastomere aspiration pipette (Cook, Australia) gentle aspiration was applied and the portion containing the ICM was extracted from the zona pellucida. At need, small laser pulses were applied to the TE to facilitate the detachment of the biopsied sample from the rest of the embryo. Three biopsied ICM samples and the corresponding TE were individually transferred to sterile PCR tubes in 2.5 µL of PBS solution and kept at 4˚C to minimize cellular degradation before storing at –80˚C.

value: embryo TE


title: TE rep 3


title: TE rep 2


title: CNE2Z transfected with AGO2 shRNAs, biological rep1

description:
S-2
Gene expression data from the human nasopharyngeal carcinoma cell line CNE2Z transfected with AGO2 shRNAs.


title: PCC6803_∆nsiR4_12hCuSO4_rep2


title: ICM rep 3

source_name: Human Inner Cell Mass

value: embryo ICM


title: CNE2Z transfected with AGO2 shRNAs, biological rep2

description:
S-3
Gene expression data from the human nasopharyngeal carcinoma cell line CNE2Z transfected with AGO2 shRNAs.


title: ICM rep 2


title: ICM rep 1


title: CNE2Z transfected with control shRNA, biological rep3

description:
N-4
Gene expression data from the human nasopharyngeal carcinoma cell line CNE2Z transfected with control shRNA.


title: PCC6803_NsiR4oex_12hCuSO4_rep2


title: GBM050_Rc


title: PCC6803_WT_12hCuSO4_rep2

value: WT


title: PCC6803_NsiR4oex_12hCuSO4_rep1


title: CNE2Z transfected with control shRNA, biological rep1

description:
N-2
Gene expression data from the human nasopharyngeal carcinoma cell line CNE2Z transfected with control shRNA.


title: SK-N-AS-tet, MYCN, t=96, rep3

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

country: Netherlands

institute: msterdam UMC and University of Amsterdam

description: SKNAS-MYCN were grown under standard conditions and harvested at different timepoints after addition of doxycycline.

hyb_protocol: 10 µg of labeled cRNA was hybridized to Affymetrix Human genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protocol.

data_processing: Expression data (CEL files) were normalized with the MAS5.0 algorithm (target signal = 100) using GCOS software (Affymetrix).

source_name: SK-N-AS, MYCN, time 96

label_protocol: RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.

growth_protocol: SK-N-AS cells were cultured in DMEM (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.

extract_protocol: Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol.

treatment_protocol: To induce MYCN in SK-N-AS-tet-MYCN, doxycycline was addded to the medium.

value: SK-N-AS

value: Neuroblastoma

tag: mycn expression

value: inducible


title: SK-N-AS-tet, MYCN, t=192, rep3

source_name: SK-N-AS, MYCN, time 192


title: GBM049_Rc


title: SK-N-AS-tet, MYCN, t=48, rep3

source_name: SK-N-AS, MYCN, time 48


title: GBM045_Pr

description: Matched Recurrent_GBM051

value: M

tag: age

tag: cohort

value: SNU


title: GBM046_Pr

description: Matched Recurrent_GBM052

value: F


title: GBM044_Pr

description: Matched Recurrent_GBM050


title: GBM048_Rc


title: PCC6803 ∆ndhD3/ndhD4/cmpA/sbtA LC 24h rep2

source_name: cells from liquid culture grown for 24h at LC

growth_protocol: The glucose-tolerant strain Synechocystis sp. PCC 6803 was used as the WT (obtained from N. Murata, National Institute for Basic Biology, Okazaki, Japan). Cultures were grown in BG11 medium (Rippka et al., 1979; J Gen Microbiol 111: 1–61) buffered with 20 mM TES–KOH to pH 8.0 under conditions given before (Schwarz et al., 2011; Plant Physiol 155: 1640–1655). The ∆ndhD3/ndhD4/cmpA/sbtA mutant (= ∆4) was obtained from Prof. Teruo Ogawa (Biocenter of the University of Nagoya, Japan) and grown as WT but in presence of the corresponding, selective antibiotics.

treatment_protocol: For CO2-shift experiments, cells were pre-cultivated with air enriched with 5% CO2 (defined as high CO2, HC). Then, cells were harvested by centrifugation (5 min at 3000 g, 20°C). The pellet was washed and re-suspended in fresh BG11 medium of pH 7.0 at an optical density of 0.8 at 750 nm (OD750). After 1 h cultivation under HC, CO2 limitation was set by shifting the exponentially growing cultures to bubbling with ambient air containing 0.035% CO2 (defined as low CO2, LC).

tag: strain


title: GBM042_Pr

description: Matched Recurrent_GBM048


title: GBM037_Rc

value: Chonnam


title: GBM038_Pr

description: Matched Recurrent_GBM039


title: GBM043_Pr

description: Matched Recurrent_GBM049


title: GBM039_Rc


title: Human Met-5A cells exposed to Strep. Pneumoniae strain D39 replicate 1

tag: cell line

value: Met 5A

value: infected with S. pneumnoniae strain D39 at a MOI of 200 for 2h


title: PCC6803 ∆ndhD3/ndhD4/cmpA/sbtA LC 24h rep1


title: SK-N-AS-tet, MYCN, t=8, rep3

source_name: SK-N-AS, MYCN, time 8

tag: cell type


title: PCC6803_WT_12hCuSO4_rep1


title: SK-N-AS-tet, MYCN, t=24, rep3

source_name: SK-N-AS, MYCN, time 24


title: GBM034_Pr

description: Matched Recurrent_GBM035


title: PCC6803 ∆ndhD3/ndhD4/cmpA/sbtA LC 3h rep1

source_name: cells from liquid culture grown for 3h at LC


title: GBM036_Pr

description: Matched Recurrent_GBM037


title: PCC6803 ∆ndhD3/ndhD4/cmpA/sbtA LC 3h rep2


title: human blastocyst S11_aCGH

source_name: whole human blastocyst

value: blastocyst

source_name: reference Male/Female or combined

value: reference DNA


title: GBM031_Rc

value: AJOU


title: human blastocyst S6_aCGH


title: SK-N-AS-tet, MYCN, t=4, rep3

source_name: SK-N-AS, MYCN, time 4


title: SK-N-AS, mock, t=192

description: SKNAS-pcDNA6TR (mock) were grown under standard conditions and harvested at different timepoints after addition of doxycycline.

source_name: SK-N-AS, mock, time 192

value: mock


title: GBM035_Rc

value: GBM


title: SK-N-AS-tet, MYCN, t=0, rep3

source_name: SK-N-AS, MYCN, time 0


title: PCC6803 ∆ndhD3/ndhD4/cmpA/sbtA HC rep2

source_name: cells from liquid culture grown at HC


title: GBM029_Rc


title: GBM027_Rc


title: GBM028_Rc


title: GBM030_Pr

description: Matched Recurrent_GBM031


title: PCC6803 ∆ndhD3/ndhD4/cmpA/sbtA HC rep1


title: SK-N-AS, mock, t=24

source_name: SK-N-AS, mock, time 24


title: SK-N-AS, mock, t=48

source_name: SK-N-AS, mock, time 48


title: SK-N-AS, mock, t=96

source_name: SK-N-AS, mock, time 96


title: GBM026_Rc


title: GBM023_Pr

description: Matched Recurrent_GBM028


title: PCC6803 WT LC 24h rep2


title: GBM025_Pr


title: PCC6803 WT LC 3h rep2


title: SK-N-AS, mock, t=8

source_name: SK-N-AS, mock, time 8


title: GBM017_Pr


title: GBM022_Pr

description: Matched Recurrent_GBM027


title: PCC6803 WT LC 24h rep1


title: GBM018_Pr


title: SK-N-AS, mock, t=0

source_name: SK-N-AS, mock, time 0


title: PCC6803 WT LC 3h rep1


title: PCC6803 WT HC rep1


title: GBM015_Pr


title: GBM016_Rc


title: GBM021_Pr


title: SK-N-AS, mock, t=4

source_name: SK-N-AS, mock, time 4


title: GBM014_Pr


title: PCC6803 WT HC rep2


title: SK-N-AS-tet, MYCN, t=96, rep2

source_name: SK-N-AS, MYCN, time 96


title: SK-N-AS-tet, MYCN, t=192, rep2

source_name: SK-N-AS, MYCN, time 192


title: GBM013_Pr


title: SK-N-AS-tet, MYCN, t=4, rep2


title: SK-N-AS-tet, MYCN, t=48, rep2

source_name: SK-N-AS, MYCN, time 48


title: GBM010_Rc


title: PCC6803_∆ndhR_LC_24h_rep2

source_name: ∆ndhR_liquid cell culture grown for 24h at LC

growth_protocol: The glucose-tolerant strain Synechocystis sp. PCC 6803 was used as the WT (obtained from N. Murata, National Institute for Basic Biology, Okazaki, Japan). Cultures were grown in BG11 medium (Rippka et al., 1979; J Gen Microbiol 111: 1-61) buffered with 20 mM TES-KOH to pH 8.0 under conditions given before (Schwarz et al., 2011; Plant Physiol 155: 1640–1655). The mutant ∆slr1594::Km (hereafter ∆ndhR), in which the gene slr1594 is disrupted by insertion of an aphII gene, was obtained from Prof. Teruo Ogawa (Biocenter of the University of Nagoya, Japan) and grown in kanamycin (Km) supplemented media (final concentration 50 µg ml-1).

value: ∆ndhR (∆slr1594::Km)

tag: time point

value: 24h after shift to LC (low CO2 conditions; air)


title: GBM012_Rc

tag: tissue


title: GBM011_Rc


title: SK-N-AS-tet, MYCN, t=8, rep2

source_name: SK-N-AS, MYCN, time 8


title: PCC6803_∆ndhR_LC_24h_rep1


title: GBM009_Rc


title: PCC6803_∆ndhR_LC_24h_rep3


title: PCC6803_∆ndhR_LC_3h_rep2

source_name: ∆ndhR_liquid cell culture grown for 3h at LC

value: 3h after shift to LC (low CO2 conditions; air)


title: PCC6803_∆ndhR_HC_rep1

source_name: ∆ndhR_liquid cell culture grown at HC

value: grown at HC (high CO2 concentrations) for 1hr


title: SK-N-AS-tet, MYCN, t=24, rep2

source_name: SK-N-AS, MYCN, time 24

value: SK-N-AS

value: Neuroblastoma


title: PCC6803_∆ndhR_HC_rep2


title: PCC6803_∆ndhR_LC_3h_rep1


title: GBM008_Pr


title: PCC6803_WT_LC_24h_rep2

source_name: WT_liquid cell culture grown for 24h at LC

value: WT


title: GBM007_Pr

description: Matched Recurrent_GBM029

value: M


title: SK-N-AS-tet, MYCN, t=24, rep1

value: inducible


title: GBM006_Pr

description: Matched Recurrent_GBM012


title: PCC6803_WT_LC_24h_rep1


title: SK-N-AS-tet, MYCN, t=0, rep2

source_name: SK-N-AS, MYCN, time 0


title: GBM005_Pr

value: F


title: SK-N-AS-tet, MYCN, t=96, rep1


title: SK-N-AS-tet, MYCN, t=192, rep1


title: Huh7.5 - HCV - 25HC - bio rep 3 - tech rep 1

status: Public on Oct 19 2015

city: Ottawa

first: John

middle: Paul

last: Pezacki

state: ON

address: 150 Louis-Pasteur Pvt

department: Chemistry and Biomolecular Sciences

country: Canada

institute: University of Ottawa

description: The miRCURY LNA microRNA Array (v11.0) probe sets (Exiqon) were spotted in duplicate onto epoxysilane coated Nexterion® slide E (Schott).

hyb_protocol: RNA were hybridized in a Advalytix Slidebooster SB400 hybridization station at 56°C overnight

scan_protocol: The arrays were scanned on a GenePix 4200A Scanner (Molecular Devices).

data_processing: Data extraction and image analysis were performed using GenePix Pro Software (Molecular Devices).  Replicate spots from same array were averaged.  Missing spots or high background portions of arrays were flagged manually and omitted from downstream analysis.  Quantile normalization was subsequently performed using the preprocessCore library of the Bioconductor package in the R environment on the signal intensities extracted from all the human microRNA probe-associated signal intensities.

label: 550 Oyster

source_name: Huh7.5 hepatoma cells

label_protocol: Total RNA (3 μg) was labelled using the Oyster-550 based Flashtag RNA labelling kit (Genisphere)

growth_protocol: Huh7.5 cells were grown in DMEM supplemented with 5% FCS, and pen/strep.

extract_protocol: mirVana miRNA isolation kit was used to extract total RNA, in accordance with the manufacturer's instructions.

treatment_protocol: Huh7.5 cells were mock infected or infected with JFH1T HCV (MOI = 0.1).  48 hours post-transfection, cells were treated with 5 μM 25-HC.  24 hours post-treatment, total RNA was isolated from cells.


title: Huh7.5 - HCV - 25HC - bio rep 3 - tech rep 2


title: Huh7.5 - HCV - 25HC - bio rep 2


title: GBM004_Pr

description: Matched Recurrent_GBM010


title: PCC6803_WT_LC_3h_rep2

source_name: WT_liquid cell culture grown for 3h at LC


title: SK-N-AS-tet, MYCN, t=48, rep1


title: Huh7.5 - HCV - 25HC - bio rep 1 - tech rep 1


title: Huh7.5 - HCV - vehicle - bio rep 2 - tech rep 2


title: HCV infection - bio rep 3

treatment_protocol: Huh7.5 cells were mock infected or infected with JFH1T HCV (MOI = 0.1).  72 hours post-infection, total RNA was isolated from cells.

tag: hcv


title: Huh7.5 - HCV - vehicle - bio rep 1 - tech rep 1


title: Huh7.5 - HCV - vehicle - bio rep 1 - tech rep 2


title: Huh7.5 - HCV - 25HC - bio rep 1 - tech rep 2


title: GBM003_Pr

description: Matched Recurrent_GBM009


title: PCC6803_WT_LC_3h_rep1


title: PCC6803_WT_HC_rep2

source_name: WT_liquid cell culture grown at HC


title: SK-N-AS-tet, MYCN, t=4, rep1

source_name: SK-N-AS, MYCN, time 4


title: HCV infection - bio rep 1 - tech rep 2


title: GBM001_Pr


title: HCV infection - bio rep 1 - tech rep 1


title: Mock infection - bio rep 3


title: Mock infection - bio rep 2


title: Mock infection - bio rep 1


title: Huh7.5 - HCV - vehicle - bio rep 2 - tech rep 1


title: HCV infection - bio rep 2


title: SK-N-AS-tet, MYCN, t=0, rep1


title: PCC6803_WT_HC_rep1


title: AX80

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

data_processing: The data were processed and normalised using quantile normalization with BeadStudio software

source_name: formalin-fixed paraffin-embedded tissue

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

tag: t

tag: n

value: pos

tag: grade

value: III

tag: er

tag: pgr

value: neg

tag: event

tag: time to relapse


title: BA09


title: AZ76


title: BQ87


title: AZ67


title: AZ68

value: II


title: AZ83


title: AZ74


title: BQ88


title: AX96


title: BQ90


title: AX89


title: AZ82


title: HT-29 cell incubation

city: Nanchang

first: Yaoping

last: Wu

state: Jiangxi

address: Nanchang University 235 Nanjingong Road

institute: Nanchang Univ.

description: replicate 1

scan_protocol: Standard Illumina scaning protocol

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

source_name: HT-29 cell

growth_protocol: HT-29 cell were cultured in 75cm2 flasks and maintained in DMEM medium with inactivated 10% fetal bovine serum. Before incubation with Bifidobacterium, the DMEM medium was removed and washed twice.

extract_protocol: Total RNA was isolated with Trizol Total RNA reagent. RNA quality was assessed by ratios A260/A280 close to 2

treatment_protocol: Bifidobacterium bifidum ATCC 29521 strain was cultured in MRS mto 108 CFU/ml. After centrifugation, bacterium precipitate washed twice by sterile PBS buffer, then, added to 75cm2 flasks for incubation for 3 hours. HT-29 cell grown without Biffdobacterium were used as controls.

tag: protocol

value: incubation with Bifidobacterium bifidum ATCC 29521


title: AZ75


title: AZ81


title: HT-29 cell no incubation

description: replicate 1

value: no incubation


title: BA06


title: AX74


title: BA07


title: BD43


title: AX88


title: BA10


title: AX87


title: BQ86


title: BQ81


title: AX75


title: BS48


title: AX95


title: AZ72


title: AX78


title: BA13


title: BD41


title: AX91


title: AX90


title: AZ79


title: AZ70


title: AX84


title: BD39


title: AZ84


title: AZ78


title: BD40


title: BQ79


title: AZ80


title: AX85


title: BQ83


title: BS49


title: SScESO_18_Upper

city: Lebanon

first: Tammara

last: Wood

state: NH

address: WTRB 674

department: Biomedical Data Science

institute: Dartmouth Medical School

description:
Test_SScESO_18_Upper
Esophageal sample

hyb_protocol: Fragmentation Buffer and Hybridization Buffer (Agilent Gene Expression Hybridization Kit) were added, and samples applied to Agilent-014850 Whole Human Genome microarrays.

scan_protocol: Scanned on Axon scanner.

data_processing:
Images were quantified using GenePix Pro.
Log(base2) of R/G Lowess Normalized Ratio (Mean), data were multiplied by -1 to convert to Log2(Cy3/Cy5) ratios, probes with > 20% data were removed, missing values were imputed using a k-nearest neighbors algorithm, non-parametric ComBat was used to adjust batch effects, genes were median-centered.

source_name: human esophageal biopsy, upper, dcSSc

label_protocol: 200ng of total RNA was reverse transcribed using Agilent Quick-Amp Labeling Kit and labeled with Perkin Elmer Cy3.

extract_protocol: Total RNA extracted using RNeasy Fibrous Tissue Mini following manufacturer's protocol.

treatment_protocol: Storage of human tissue in RNAlater.

tag: case/control

value: case

value: esophageal biopsy

tag: biopsy site

value: upper

tag: batch

tag: systemic sclerosis subtype

value: dcSSc

tag: patient/control id

value: patient 18

source_name: Universal Human Reference (UHR)

extract_protocol: RNA extracted from cell lines.

tag: sample type

value: reference


title: SScESO_19_Upper

description:
Test_SScESO_19_Upper
Esophageal sample

value: patient 19


title: AX92

tag: age


title: SScESO_19_Lower

description:
Test_SScESO_19_Lower
Esophageal sample

source_name: human esophageal biopsy, lower, dcSSc

tag: tissue

value: lower


title: SScESO_18_Lower

description:
Test_SScESO_18_Lower
Esophageal sample


title: AZ69


title: AZ85


title: AZ77


title: SScESO_17_Upper

description:
Test_SScESO_17_Upper
Esophageal sample

source_name: human esophageal biopsy, upper, lcSSc

value: lcSSc

value: patient 17


title: SScESO_17_Lower

description:
Test_SScESO_17_Lower
Esophageal sample

source_name: human esophageal biopsy, lower, lcSSc


title: AX82


title: BA11


title: SScESO_15_Lower

description:
Test_SScESO_15_Lower
Esophageal sample

value: patient 15


title: SScESO_15_Upper

description:
Test_SScESO_15_Upper
Esophageal sample


title: SScESO_13_Lower

description:
Test_SScESO_13_Lower
Esophageal sample

value: patient 13


title: SScESO_12_Lower

description:
Test_SScESO_12_Lower
Esophageal sample

value: patient 12


title: SScESO_13_Upper

description:
Test_SScESO_13_Upper
Esophageal sample


title: SScESO_08_Lower

description:
Test_SScESO_08_Lower
Esophageal sample

value: patient 08


title: SScESO_08_Upper

description:
Test_SScESO_08_Upper
Esophageal sample


title: SScESO_14_Lower

description:
Test_SScESO_14_Lower
Esophageal sample

value: patient 14


title: SScESO_14_Upper

description:
Test_SScESO_14_Upper
Esophageal sample


title: SScESO_09_Lower

description:
Test_SScESO_09_Lower
Esophageal sample

value: patient 09


title: SScESO_11_Upper

description:
Test_SScESO_11_Upper
Esophageal sample

value: patient 11


title: SK-N-AS-tet, MYCN, t=8, rep1

source_name: SK-N-AS, MYCN, time 8

tag: cell line

value: SK-N-AS

tag: cell type

value: Neuroblastoma

tag: mycn expression

value: inducible


title: SScESO_06_Lower

description:
Test_SScESO_06_Lower
Esophageal sample

value: case

value: esophageal biopsy

value: patient 06


title: BA05

tag: t

tag: n

value: neg

tag: grade

value: II

value: pos


title: SScESO_05_Lower

description:
Test_SScESO_05_Lower
Esophageal sample

value: lower

value: lcSSc

value: patient 05

value: reference


title: SScESO_04_Upper

description:
Test_SScESO_04_Upper
Esophageal sample

value: upper

value: patient 04


title: SScESO_06_Upper

description:
Test_SScESO_06_Upper
Esophageal sample


title: SScESO_11_Lower

description:
Test_SScESO_11_Lower
Esophageal sample

value: dcSSc


title: SScESO_03_Upper

description:
Test_SScESO_03_Upper
Esophageal sample

value: patient 03


title: GERD_04_Upper

description:
Test_GERD_04_Upper
GERD Control

source_name: human esophageal biopsy, upper, control

value: control

value: control 04


title: GERD_03_Upper

description:
Test_GERD_03_Upper
GERD Control

value: control 03


title: SScESO_04_Lower

description:
Test_SScESO_04_Lower
Esophageal sample

value: case


title: GERD_06_Lower

description:
Test_GERD_06_Lower
GERD Control

source_name: human esophageal biopsy, lower, control

value: esophageal biopsy

value: control 06


title: GERD_07_Lower

description:
Test_GERD_07_Lower
GERD Control

value: control 07


title: SScESO_05_Upper

description:
Test_SScESO_05_Upper
Esophageal sample


title: SScESO_01_Lower

description:
Test_SScESO_01_Lower
Esophageal sample

value: patient 01


title: SScESO_02_Lower

description:
Test_SScESO_02_Lower
Esophageal sample

value: patient 02


title: GERD_07_Upper

description:
Test_GERD_07_Upper
GERD Control


title: SScESO_01_6mo_Lower

description:
Test_SScESO_01_6mo_Lower
Esophageal sample

value: lower


title: GERD_04_Lower

description:
Test_GERD_04_Lower
GERD Control


title: SScESO_09_Upper

description:
Test_SScESO_09_Upper
Esophageal sample

value: lcSSc

value: patient 09


title: SScESO_01_Upper

description:
Test_SScESO_01_Upper
Esophageal sample

value: reference


title: SScESO_02_Upper

description:
Test_SScESO_02_Upper
Esophageal sample

value: upper


title: SScESO_03_Lower

description:
Test_SScESO_03_Lower
Esophageal sample


title: GERD_06_Upper

description:
Test_GERD_06_Upper
GERD Control


title: SScESO_01_6mo_Upper

description:
Test_SScESO_01_6mo_Upper
Esophageal sample


title: GERD_05_Upper

description:
Test_GERD_05_Upper
GERD Control

value: control 05


title: GERD_02_Lower

description:
Test_GERD_02_Lower
GERD Control

value: control 02


title: GERD_02_Upper

description:
Test_GERD_02_Upper
GERD Control


title: GERD_03_Lower

description:
Test_GERD_03_Lower
GERD Control


title: GERD_01_Upper

description:
Test_GERD_01_Upper
GERD Control

value: control 01


title: d6DE-null-2

first: Arne

middle: Wyndham

last: Mould

state: Oxfordshire

address: Warneford Hospital

department: Psychiatry

institute: Oxford University

description: Lhx1 null d6 DE replicate 2

data_processing: Rank invariant normalization using Gene Expression Module V1.9.0 of Illumina GenomeStudio

source_name: definitive endoderm cultures

label_protocol: Total RNA was labeled according to the standard Illumina protocol

growth_protocol: Embryonic stem cells differentiated to definitive endoderm using Activin-A

extract_protocol: RNA was extracted with QIAGEN Rneasy mini kit and DNase I treatment on-column in accordance with the prescribed protocol provided with the kit.

tag: genotype

value: ES cells


title: d6DE-null-4

description: Lhx1 null d6 DE replicate 2


title: d6DE-null-3

description: Lhx1 null d6 DE replicate 2


title: GERD_01_Lower

description:
Test_GERD_01_Lower
GERD Control

value: control


title: AZ71

value: pos

value: II

tag: er

tag: pgr

tag: event

tag: time to relapse


title: d5DE-cont-4

description: Control d5 DE replicate 4


title: d6DE-null-1

description: Lhx1 null d6 DE replicate 1


title: d5DE-cont-3

description: Control d5 DE replicate 3


title: d5DE-null-2

description: Lhx1 null d5 DE replicate 2


title: d5DE-null-1

description: Lhx1 null d5 DE replicate 1


title: d5DE-null-4

description: Lhx1 null d5 DE replicate 4


title: d6DE-cont-4

description: Control d6 DE replicate 4


title: d6DE-cont-2

description: Control d6 DE replicate 2


title: d6DE-cont-3

description: Control d6 DE replicate 3


title: d5DE-cont-1

description: Control d5 DE replicate 1


title: d6DE-cont-1

description: Control d6 DE replicate 1


title: d5DE-cont-2

description: Control d5 DE replicate 2


title: miR-185 mimic, bio rep 2

description: Gene expression data from Huh7.5 cells transfected with miR-185 mimic

hyb_protocol: 5.5 ug of cDNA were hybridized for 16 hr at 45C on Human Gene 2.0 ST microarrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450_0002.

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

data_processing: The data was analyzed with the Affymetrix Expression Console using Affymetrix default analysis settings (RMA) and Affymetrix Transcriptome Analysis Console.

label: Biotin Allonamide Triphosphate

label_protocol: Biotinylated cDNA were prepared from 400 ng RNA using the Affymetrix WT Plus Kit.

growth_protocol: Huh7.5 cells were maintained in DMEM supplemented with 10% FBS, 1X non essential amino acids, and pen/strep.

extract_protocol: 72 hours post-transfection, total RNA was isolated using Qiagen RNeasy Kit, as per manufacturer's protocol.

treatment_protocol: Huh7.5 cells were transfected with 100 nM control or miR-185 mimics (Ambion) using Lipofectamine RNAiMax, as per manufacturer's instructions.


title: d5DE-null-3

description: Lhx1 null d5 DE replicate 3


title: Ctrl mimic, bio rep 1

description: Gene expression data from Huh7.5 cells transfected with control mimic


title: miR-185 mimic, bio rep 1

source_name: Huh7.5 cells transfected with miR-185 mimic


title: ZR751_MPA_rep4

status: Public on Oct 18 2015

city: Woodville South

first: Eleanor

middle: F

last: Need

state: SA

address: 28 Woodville Rd

department: Discipline of Surgery

institute: The University of Adelaide

hyb_protocol: Standard Illumina hybridisation protocol

scan_protocol: Standard Illumina Scanning protocol

data_processing: Data was normalised using rank variant normalisation in bead studio. For publication, this data was then normalised using variance stabilisation normalisation, corrected with ComBat, filtered to likely expressed transcripts and then subjected to linear model fitting as implemented in the bioconductor Limma package in R.

label_protocol: biotinylated cDNA was prepared using 1ug of total RNA according to standard Illumina protocols

growth_protocol: Cells were sourced from ATCC and used at passage 16. Cells were grown in RPMI 1640 (Life Technologies) supplemented with 10% FBS (Sigma-Aldrich)

extract_protocol: Total RNA was isolated using a Qiagen Rneasy RNA extraction kit, incorporating Dnase on-column digestion according to manufacturer's instructions

treatment_protocol: Cells were plated at 500,000 cells per well in 6 well plates in phenol red free RPMI 1640 (Life Technologies) supplemented with 10% dextran charcoal stripped FBS (Sigma-Aldrich), and treated with 10nM E2 where indicated (E2L). Cells were subsequently treated for 16h with the nominated hormone(s).

value: breast cancer cells

tag: treatment group

value: 16h 10nM medroxyprogesterone acetate


title: ZR751_P_rep1

value: 16h 10nM progesterone


title: Ctrl mimic, bio rep 2

source_name: Huh7.5 cells transfected with control mimic


title: ZR751_P_rep4


title: ZR751_E2s_rep4

value: 16h 10nM estradiol


title: ZR751_DHT_rep3

value: 16h 10nM dihydrotestosterone


title: ZR751_vcvc_16hr_rep3

description: RNA isolation with Qiagen Rneasy kit + Dnase digestion

hyb_protocol: Standard Affymetrix hybridisation protocol

data_processing: Raw data was processed in R using bioconductor and Limma. Array data was normalized using RMA

source_name: Breast cancer ZR751 cells plated in 1 part per million vehicle (ethanol) for 72 hours, overlayed with 1part per million vehicle (ethanol) for 16hrs. Replicate 3.

label_protocol: Biotinylated cDNA was prepared from 300ng RNA according to standard Affymetrix protocols

growth_protocol: Cells were routinely passaged in RPMI1640 supplemented with 10% FBS. ZR-75-1 cells (passage 16; ATCC) were plated at 500,000 cells/well in 6 well plates in phenol red free RPMI1640 (Life Technologies) supplemented with 10% dextran-charcoal stripped FBS (Hyclone) and treated with hormones as described for each sample. RNA extracted at the timepoints indicated, DNAse treated on column using Qiagen RNeasy kit. An aliquot of each sample was used to synthesise cDNA to validate treatment effects. RNA quality was assessed for each sample via bioanalyser, with an average RIN of  9.6 (range 8.8 to 9.9).

extract_protocol: Extraction was performed using Qiagen Rneasy kit and on-column Dnase digestion according to manufacturer's instructions.

treatment_protocol: Cells were treated using an overlay method involving treatment with 10X concetrated hormone mixture at 1:10 of the cell culture volume, followed by gentle swirling. Treatment times were staggered, and the RNA was isolated as a batch at the culmination of the experiment.

tag: treatment

value: breast cancer

tag: biosample number

tag: bioproject id

tag: time


title: ZR751_EpVC_8hr_rep3

source_name: Breast cancer ZR751 cells pretreated with 10nM E2 for 72 hours, overlayed with 1part per million vehicle (ethanol) for 8hrs. Replicate 3.

tag: tissue


title: ZR751_E2s_P_rep1

tag: cell line

value: 16h 10nM estradiol cotreated with 16h 10nM progesterone


title: ZR751_E2L_P_rep1

tag: cell type

value: 72h 10nM estradiol cotreated with 10nM progesterone for final 16h


title: ZR751_EpVC_4hr_rep2

source_name: Breast cancer ZR751 cells pretreated with 10nM E2 for 72 hours, overlayed with 1part per million vehicle (ethanol) for 4hrs. Replicate 2.


title: ZR751_vcvc_16hr_rep1

source_name: Breast cancer ZR751 cells plated in 1 part per million vehicle (ethanol) for 72 hours, overlayed with 1part per million vehicle (ethanol) for 16hrs. Replicate 1.


title: ZR751_DHT_rep2


title: ZR751_DHT_rep1


title: ZR751_VC_rep3

value: 16h eqivalent vehicle (ethanol; 2 parts per million)


title: ZR751_E2L_P_rep4


title: ZR751_EpVC_4hr_rep3

source_name: Breast cancer ZR751 cells pretreated with 10nM E2 for 72 hours, overlayed with 1part per million vehicle (ethanol) for 4hrs. Replicate 3.


title: ZR751_EpVC_4hr_rep1

source_name: Breast cancer ZR751 cells pretreated with 10nM E2 for 72 hours, overlayed with 1part per million vehicle (ethanol) for 4hrs. Replicate 1.


title: ZR751_E2L_P_rep3


title: ZR751_vcvc_16hr_rep2

source_name: Breast cancer ZR751 cells plated in 1 part per million vehicle (ethanol) for 72 hours, overlayed with 1part per million vehicle (ethanol) for 16hrs. Replicate 2.


title: ZR751_EpVC_8hr_rep2

source_name: Breast cancer ZR751 cells pretreated with 10nM E2 for 72 hours, overlayed with 1part per million vehicle (ethanol) for 8hrs. Replicate 2.


title: ZR751_E2s_MPA_rep2

value: 16h 10nM estradiol cotreated with 16h 10nM medroxyprogesterone acetate


title: ZR751_E2s_MPA_rep4


title: ZR751_MPA_rep2


title: ZR751_E2s_MPA_rep3


title: ZR751_EpVC_8hr_rep1

source_name: Breast cancer ZR751 cells pretreated with 10nM E2 for 72 hours, overlayed with 1part per million vehicle (ethanol) for 8hrs. Replicate 1.


title: ZR751_E2s_P_rep4


title: ZR751_EpVC_16hr_rep2

source_name: Breast cancer ZR751 cells pretreated with 10nM E2 for 72 hours, overlayed with 1part per million vehicle (ethanol) for 16hrs. Replicate 2.


title: ZR751_EpVC_16hr_rep1

source_name: Breast cancer ZR751 cells pretreated with 10nM E2 for 72 hours, overlayed with 1part per million vehicle (ethanol) for 16hrs. Replicate 1.


title: ZR751_MPA_rep1


title: ZR751_E2s_rep3


title: ZR751_VC_rep4


title: ZR751_EpP_8hr_rep2

source_name: Breast cancer ZR751 cells pretreated with 10nM E2 for 72 hours, overlayed with 10nM progesterone for 8hrs. Replicate 2.


title: ZR751_EpP_8hr_rep3

source_name: Breast cancer ZR751 cells pretreated with 10nM E2 for 72 hours, overlayed with 10nM progesterone for 8hrs. Replicate 3.


title: ZR751_EpVC_16hr_rep3

source_name: Breast cancer ZR751 cells pretreated with 10nM E2 for 72 hours, overlayed with 1part per million vehicle (ethanol) for 16hrs. Replicate 3.


title: ZR751_DHT_rep4


title: ZR751_E2s_DHT_rep1

value: 16h 10nM estradiol cotreated with 16h 10nM dihydrotestosterone


title: ZR751_EpP_4hr_rep2

source_name: Breast cancer ZR751 cells pretreated with 10nM E2 for 72 hours, overlayed with 10nM progesterone for 4hrs. Replicate 2.


title: ZR751_EpP_4hr_rep3

source_name: Breast cancer ZR751 cells pretreated with 10nM E2 for 72 hours, overlayed with 10nM progesterone for 4hrs. Replicate 3.


title: ZR751_EpP_4hr_rep1

source_name: Breast cancer ZR751 cells pretreated with 10nM E2 for 72 hours, overlayed with 10nM progesterone for 4hrs. Replicate 1.


title: ZR751_E2s_rep2


title: ZR751_E2s_rep1


title: ZR751_EpP_8hr_rep1

source_name: Breast cancer ZR751 cells pretreated with 10nM E2 for 72 hours, overlayed with 10nM progesterone for 8hrs. Replicate 1.


title: ZR751_E2s_DHT_rep3


title: ZR751_EpP_16hr_rep2

source_name: Breast cancer ZR751 cells pretreated with 10nM E2 for 72 hours, overlayed with 10nM progesterone for 16hrs. Replicate 2.


title: ZR751_E2s_DHT_rep2


title: ZR751_EpP_16hr_rep3

source_name: Breast cancer ZR751 cells pretreated with 10nM E2 for 72 hours, overlayed with 10nM progesterone for 16hrs. Replicate 3.


title: ZR751_P_rep3


title: E2s_MPA_rep2

data_processing: Data was normalised using cubic spline normalisation in bead studio. For publication, data was normalised using variance stabilisation normalisation, corrected with ComBat, filtered to likely expressed transcripts and then subjected to linear model fitting as implemented in the bioconductor Limma package in R.

source_name: T47D breast cancer cells, 10nM estradiol and medroxyprogesterone acetate treated 16h, rep 2

growth_protocol: Cells were grown in RPMI 1640 supplemented with 10% FBS

treatment_protocol:
hormone treatment: Plated in hormone stripped medium (Phenol red free RPMI1640 supplemented with 10% dextran charcoal stripped FCS) for 56h, followed by treatment with 10nM estradiol and 10nM medroxyprogesterone acetate for 16h. Replicate 2
Cells were plated at 500,000 cells per well in 6 well plates in phenol red free RPMI 1640 supplemented with 10% dextran charcoal stripped FBS and incubated for 56h. Cells were subsequently treated for 16h with the nominated hormone(s).

value: breast cancer cell line


title: E2s_MPA_rep1

source_name: T47D breast cancer cells, 10nM estradiol and medroxyprogesterone acetate treated 16h, rep 1

treatment_protocol:
hormone treatment: Plated in hormone stripped medium (Phenol red free RPMI1640 supplemented with 10% dextran charcoal stripped FCS) for 56h, followed by treatment with 10nM estradiol and 10nM medroxyprogesterone acetate for 16h. Replicate 1
Cells were plated at 500,000 cells per well in 6 well plates in phenol red free RPMI 1640 supplemented with 10% dextran charcoal stripped FBS and incubated for 56h. Cells were subsequently treated for 16h with the nominated hormone(s).


title: Myoblasts Subject6 Control

city: Stockholm

last: Rullman

address: C1:82 Karolinska University Hospital, Huddinge

department: Laboratory Medicine

country: Sweden

institute: Karolinska Institutet

description: Primary proliferating myoblasts isolated from Vastus lateralis muscle treated with vehicle for 24h. Cells isolated from Subject 6

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix HG U133 plus2 3'  array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The probe-set level intensities of the arrays were normalized using the Robust Multi-array Analysis method (RMA) implemented within the R statistical software environment using the ‘affy’ package (Bioconductor project).

source_name: Primary proliferating myoblasts, Subject 6, Control

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

growth_protocol: Isolated human myoblasts were cultured in DMEM-F12 Glutamax containing 20% FBS and 1% ABAM (high-serum media) at 37° C, 5% CO2. Culture dishes were coated with collagen I (Gibco® Collagen I, Bovine 5 mg/mL Invitrogen) diluted to a final concentration of 50 μg/mL in 0.02 M acetic acid according to the manufacturers manual. Myoblasts were taken through serial passages to increase cell numbers prior to experimentation. All myoblasts were used for experimentation at passage 4-5. For experimentation, myoblasts were harvested and transferred to collagen I coated 6-well plates at a density of 8 x 10^4 cells per well.

treatment_protocol: Low-serum media containing 100 nM 1,25(OH)2D3, or vehicle alone for 24 h.

value: Primary proliferating myoblasts

value: Vastus lateralis

value: Control

tag: subject

value: Subject 6


title: ZR751_EpM_8hr_rep3

source_name: Breast cancer ZR751 cells pretreated with 10nM E2 for 72 hours, overlayed with 10nM medroxyprogesterone acetate for 8hrs. Replicate 3.


title: ZR751_P_rep2


title: ZR751_EpM_8hr_rep2

source_name: Breast cancer ZR751 cells pretreated with 10nM E2 for 72 hours, overlayed with 10nM medroxyprogesterone acetate for 8hrs. Replicate 2.


title: ZR751_EpM_8hr_rep1

source_name: Breast cancer ZR751 cells pretreated with 10nM E2 for 72 hours, overlayed with 10nM medroxyprogesterone acetate for 8hrs. Replicate 1.


title: ZR751_EpP_16hr_rep1

source_name: Breast cancer ZR751 cells pretreated with 10nM E2 for 72 hours, overlayed with 10nM progesterone for 16hrs. Replicate 1.


title: Myoblasts Subject6 Vitamin D

description: Primary proliferating myoblasts isolated from Vastus lateralis muscle treated with Vitamin D for 24h. Cells isolated from Subject 6

source_name: Primary proliferating myoblasts, Subject 6, Vitamin D

value: Vitamin D


title: ZR751_E2L_P_rep2

value: breast cancer cells


title: Myoblasts Subject5 Control

description: Primary proliferating myoblasts isolated from Vastus lateralis muscle treated with vehicle for 24h. Cells isolated from Subject 5

source_name: Primary proliferating myoblasts, Subject 5, Control

value: Subject 5


title: ZR751_MPA_rep3

value: 16h 10nM medroxyprogesterone acetate


title: Myoblasts Subject4 Control

description: Primary proliferating myoblasts isolated from Vastus lateralis muscle treated with vehicle for 24h. Cells isolated from Subject 4

source_name: Primary proliferating myoblasts, Subject 4, Control

value: Subject 4


title: Myoblasts Subject5 Vitamin D

description: Primary proliferating myoblasts isolated from Vastus lateralis muscle treated with Vitamin D for 24h. Cells isolated from Subject 5

source_name: Primary proliferating myoblasts, Subject 5, Vitamin D


title: E2s_MPA_rep3

source_name: T47D breast cancer cells, 10nM estradiol and medroxyprogesterone acetate treated 16h, rep 3

treatment_protocol:
hormone treatment: Plated in hormone stripped medium (Phenol red free RPMI1640 supplemented with 10% dextran charcoal stripped FCS) for 56h, followed by treatment with 10nM estradiol and 10nM medroxyprogesterone acetate for 16h. Replicate 3
Cells were plated at 500,000 cells per well in 6 well plates in phenol red free RPMI 1640 supplemented with 10% dextran charcoal stripped FBS and incubated for 56h. Cells were subsequently treated for 16h with the nominated hormone(s).


title: Myoblasts Subject4 Vitamin D

description: Primary proliferating myoblasts isolated from Vastus lateralis muscle treated with Vitamin D for 24h. Cells isolated from Subject 4

source_name: Primary proliferating myoblasts, Subject 4, Vitamin D


title: Myoblasts Subject3 Vitamin D

description: Primary proliferating myoblasts isolated from Vastus lateralis muscle treated with Vitamin D for 24h. Cells isolated from Subject 3

source_name: Primary proliferating myoblasts, Subject 3, Vitamin D

value: Subject 3


title: ZR751_E2s_P_rep3


title: ZR751_EpM_4hr_rep3

source_name: Breast cancer ZR751 cells pretreated with 10nM E2 for 72 hours, overlayed with 10nM medroxyprogesterone acetate for 4hrs. Replicate 3.

value: breast cancer


title: E2s_PROG_rep1

source_name: T47D breast cancer cells, 10nM estradiol and progesterone treated 16h, rep 1

treatment_protocol:
hormone treatment: Plated in hormone stripped medium (Phenol red free RPMI1640 supplemented with 10% dextran charcoal stripped FCS) for 56h, followed by treatment with 10nM estradiol and 10nM progesterone for 16h. Replicate 1
Cells were plated at 500,000 cells per well in 6 well plates in phenol red free RPMI 1640 supplemented with 10% dextran charcoal stripped FBS and incubated for 56h. Cells were subsequently treated for 16h with the nominated hormone(s).


title: ZR751_EpM_4hr_rep2

source_name: Breast cancer ZR751 cells pretreated with 10nM E2 for 72 hours, overlayed with 10nM medroxyprogesterone acetate for 4hrs. Replicate 2.


title: E2s_DHT_rep3

source_name: T47D breast cancer cells, 10nM estradiol and dihydrotestosterone treated 16h, rep 3

treatment_protocol:
hormone treatment: Plated in hormone stripped medium (Phenol red free RPMI1640 supplemented with 10% dextran charcoal stripped FCS) for 56h, followed by treatment with 10nM estradiol and 10nM dihydrotestosterone for 16h. Replicate 3
Cells were plated at 500,000 cells per well in 6 well plates in phenol red free RPMI 1640 supplemented with 10% dextran charcoal stripped FBS and incubated for 56h. Cells were subsequently treated for 16h with the nominated hormone(s).


title: Myoblasts Subject2 Vitamin D

description: Primary proliferating myoblasts isolated from Vastus lateralis muscle treated with Vitamin D for 24h. Cells isolated from Subject 2

source_name: Primary proliferating myoblasts, Subject 2, Vitamin D

value: Subject 2


title: ZR751_EpM_4hr_rep1

source_name: Breast cancer ZR751 cells pretreated with 10nM E2 for 72 hours, overlayed with 10nM medroxyprogesterone acetate for 4hrs. Replicate 1.


title: E2s_PROG_rep2

source_name: T47D breast cancer cells, 10nM estradiol and progesterone treated 16h, rep 2

treatment_protocol:
hormone treatment: Plated in hormone stripped medium (Phenol red free RPMI1640 supplemented with 10% dextran charcoal stripped FCS) for 56h, followed by treatment with 10nM estradiol and 10nM progesterone for 16h. Replicate 2
Cells were plated at 500,000 cells per well in 6 well plates in phenol red free RPMI 1640 supplemented with 10% dextran charcoal stripped FBS and incubated for 56h. Cells were subsequently treated for 16h with the nominated hormone(s).


title: ZR751_VC_rep2


title: Myoblasts Subject3 Control

description: Primary proliferating myoblasts isolated from Vastus lateralis muscle treated with vehicle for 24h. Cells isolated from Subject 3

source_name: Primary proliferating myoblasts, Subject 3, Control


title: E2s_DHT_rep1

source_name: T47D breast cancer cells, 10nM estradiol and dihydrotestosterone treated 16h, rep 1

treatment_protocol:
hormone treatment: Plated in hormone stripped medium (Phenol red free RPMI1640 supplemented with 10% dextran charcoal stripped FCS) for 56h, followed by treatment with 10nM estradiol and 10nM dihydrotestosterone for 16h. Replicate 1
Cells were plated at 500,000 cells per well in 6 well plates in phenol red free RPMI 1640 supplemented with 10% dextran charcoal stripped FBS and incubated for 56h. Cells were subsequently treated for 16h with the nominated hormone(s).


title: ZR751_EpM_16hr_rep2

source_name: Breast cancer ZR751 cells pretreated with 10nM E2 for 72 hours, overlayed with 10nM medroxyprogesterone acetate for 16hrs. Replicate 2.


title: E2s_PROG_rep3

source_name: T47D breast cancer cells, 10nM estradiol and progesterone treated 16h, rep 3

treatment_protocol:
hormone treatment: Plated in hormone stripped medium (Phenol red free RPMI1640 supplemented with 10% dextran charcoal stripped FCS) for 56h, followed by treatment with 10nM estradiol and 10nM progesterone for 16h. Replicate 3
Cells were plated at 500,000 cells per well in 6 well plates in phenol red free RPMI 1640 supplemented with 10% dextran charcoal stripped FBS and incubated for 56h. Cells were subsequently treated for 16h with the nominated hormone(s).


title: E2s_DHT_rep2

source_name: T47D breast cancer cells, 10nM estradiol and dihydrotestosterone treated 16h, rep 2

treatment_protocol:
hormone treatment: Plated in hormone stripped medium (Phenol red free RPMI1640 supplemented with 10% dextran charcoal stripped FCS) for 56h, followed by treatment with 10nM estradiol and 10nM dihydrotestosterone for 16h. Replicate 2
Cells were plated at 500,000 cells per well in 6 well plates in phenol red free RPMI 1640 supplemented with 10% dextran charcoal stripped FBS and incubated for 56h. Cells were subsequently treated for 16h with the nominated hormone(s).


title: ZR751_EpM_16hr_rep3

source_name: Breast cancer ZR751 cells pretreated with 10nM E2 for 72 hours, overlayed with 10nM medroxyprogesterone acetate for 16hrs. Replicate 3.


title: T47D_MPA_rep2

source_name: T47D breast cancer cells, 10nM medroxyprogesterone acetate treated 16h, rep 2

treatment_protocol:
hormone treatment: Plated in hormone stripped medium (Phenol red free RPMI1640 supplemented with 10% dextran charcoal stripped FCS) for 56h, followed by treatment with 10nM medroxyprogesterone acetate for 16h. Replicate 2
Cells were plated at 500,000 cells per well in 6 well plates in phenol red free RPMI 1640 supplemented with 10% dextran charcoal stripped FBS and incubated for 56h. Cells were subsequently treated for 16h with the nominated hormone(s).