title: kidney biopsy, archetype1111


title: kidney biopsy, archetype1110

status: Public on Jul 10 2017

type: RNA

city: Edmonton

first: Jessica

last: Chang

address: 250 Heritage Medical Research Centre

department: Medicine

country: Canada

institute: University of Alberta

hyb_protocol: Amplified RNA (10ug) was hybridized for 16 hr at 45C on GeneChip® PrimeView™ Human Gene Expression Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Gene Array Scanner 3000 7G (Affymetrix) and processed with GeneChip® Command Console® Software (AGCC) (Affymetrix).

data_processing: Microarray data files were preprocessed using robust multi-chip averaging (RMA) implemented in Bioconductor.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: kidney biopsy

label_protocol: Total RNA (0.5µg) was labeled using GeneChip 3' IVT Express Labeling kit. Quality of labeled aRNA was assessed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) before hybridization to GeneChip® PrimeView™ Human Gene Expression Array (Affymetrix, Santa Clara, CA).

growth_protocol: All human kidney biopsies taken for clinical indication during the period specified above were included. Tissue was immediately placed in RNAlater.

extract_protocol: Tissue was homogenized in 0.5ml of Trizol reagent (Invitrogen, Carlsbad, CA) and total RNA was extracted and purified using the RNeasy Micro Kit (Qiagen, Ontario, Canada) (average yield 8µg/core, RNA integrity number >7).

treatment_protocol: The immunosuppressive treatment of the patients before the biopsy was based on individual treatment regiments; the treatment after the biopsy was adjusted based on the histopathological diagnosis.

tag: tissue

value: kidney

tag: archetype cluster

value: AKI

tag: g

tag: cg

tag: i

tag: ci

tag: t

tag: ct

tag: v

tag: cv

tag: ah

tag: ptc

tag: in i-ifta set n=234?

tag: mmdx

value: NR


title: kidney biopsy, archetype1119

value: GN


title: kidney biopsy, archetype1113

value: Bord.


title: kidney biopsy, archetype111

value: TG


title: kidney biopsy, archetype1126


title: kidney biopsy, archetype1115

value: ABMR


title: kidney biopsy, archetype1124

value: TCMR


title: kidney biopsy, archetype1123

value: Mixed


title: kidney biopsy, archetype1109


title: kidney biopsy, archetype1121

value: BK


title: kidney biopsy, archetype1108

value: ABMRsusp


title: kidney biopsy, archetype1102

value: Pos


title: kidney biopsy, archetype1107


title: kidney biopsy, archetype1105


title: kidney biopsy, archetype112

value: Other


title: kidney biopsy, archetype1106


title: kidney biopsy, archetype1112

value: NOMOA


title: kidney biopsy, archetype1104


title: kidney biopsy, archetype1101


title: kidney biopsy, archetype1103

value: Not done


title: kidney biopsy, archetype1100


title: kidney biopsy, archetype110


title: kidney biopsy, archetype1095


title: kidney biopsy, archetype1130


title: kidney biopsy, archetype1098


title: kidney biopsy, archetype1099


title: kidney biopsy, archetype11


title: kidney biopsy, archetype1088


title: kidney biopsy, archetype1086


title: kidney biopsy, archetype1094


title: kidney biopsy, archetype1090


title: kidney biopsy, archetype1089


title: kidney biopsy, archetype1087


title: kidney biopsy, archetype1097


title: kidney biopsy, archetype109


title: kidney biopsy, archetype1091


title: kidney biopsy, archetype1093


title: kidney biopsy, archetype1084


title: kidney biopsy, archetype1079


title: kidney biopsy, archetype1078


title: kidney biopsy, archetype1077


title: kidney biopsy, archetype1085


title: kidney biopsy, archetype1081


title: kidney biopsy, archetype108


title: kidney biopsy, archetype1076


title: kidney biopsy, archetype1096


title: kidney biopsy, archetype1082


title: kidney biopsy, archetype1092


title: kidney biopsy, archetype1080


title: kidney biopsy, archetype1083


title: kidney biopsy, archetype1075


title: kidney biopsy, archetype1074

value: neg


title: kidney biopsy, archetype106


title: kidney biopsy, archetype1060


title: kidney biopsy, archetype1066


title: kidney biopsy, archetype107

value: IFTA


title: kidney biopsy, archetype1064

value: kidney


title: kidney biopsy, archetype1062


title: kidney biopsy, archetype1069


title: kidney biopsy, archetype1059


title: kidney biopsy, archetype1070


title: kidney biopsy, archetype1055


title: kidney biopsy, archetype1058


title: kidney biopsy, archetype1052


title: kidney biopsy, archetype1056


title: kidney biopsy, archetype1063


title: kidney biopsy, archetype1053

value: DiabNeph


title: kidney biopsy, archetype1067


title: kidney biopsy, archetype1061


title: kidney biopsy, archetype1065

value: AKI


title: kidney biopsy, archetype1048


title: kidney biopsy, archetype1049


title: kidney biopsy, archetype1051


title: kidney biopsy, archetype105


title: kidney biopsy, archetype1047


title: kidney biopsy, archetype1054


title: kidney biopsy, archetype1050


title: kidney biopsy, archetype1068


title: kidney biopsy, archetype1057


title: kidney biopsy, archetype1072


title: kidney biopsy, archetype1071


title: kidney biopsy, archetype1073


title: kidney biopsy, archetype1043


title: kidney biopsy, archetype1040


title: kidney biopsy, archetype1036


title: kidney biopsy, archetype1045


title: kidney biopsy, archetype1042

value: GN


title: kidney biopsy, archetype1031

value: NR


title: kidney biopsy, archetype1038


title: kidney biopsy, archetype1044


title: kidney biopsy, archetype1037


title: kidney biopsy, archetype1041


title: kidney biopsy, archetype103


title: kidney biopsy, archetype1034


title: kidney biopsy, archetype1039


title: kidney biopsy, archetype1028


title: kidney biopsy, archetype1032


title: kidney biopsy, archetype104


title: kidney biopsy, archetype1035


title: kidney biopsy, archetype1029


title: kidney biopsy, archetype1021


title: kidney biopsy, archetype1033


title: kidney biopsy, archetype1022


title: kidney biopsy, archetype1027


title: kidney biopsy, archetype102


title: kidney biopsy, archetype1026


title: kidney biopsy, archetype1025


title: kidney biopsy, archetype1024


title: kidney biopsy, archetype1020


title: kidney biopsy, archetype1023


title: kidney biopsy, archetype1030


title: kidney biopsy, archetype1018


title: kidney biopsy, archetype1008


title: kidney biopsy, archetype1010


title: kidney biopsy, archetype1012


title: kidney biopsy, archetype1015

value: Bord.


title: kidney biopsy, archetype1009

value: TG

value: pos trace


title: kidney biopsy, archetype1016


title: kidney biopsy, archetype1019


title: kidney biopsy, archetype1003

value: ABMR


title: kidney biopsy, archetype1013


title: kidney biopsy, archetype1007


title: kidney biopsy, archetype101


title: kidney biopsy, archetype1006

value: TCMR


title: mH2A2_HepG2_ChIPseq

status: Public on Mar 21 2017

type: SRA

city: Badalona

first: Roberto

last: Malinverni

state: Barcelona

address: Josep Carreras Building, Ctra de Can Ruti,

country: Spain

institute: Josep Carreras Leukaemia Research Institute

description: Sample 2

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2 version 2.0.6 with the following configurations (  --sensitive -S  -t -p8)
Data were filtered using the following specifications: sickle (ver. 1.2) se   -t sanger   -l 24 -n -q 25. cutadapt (ver.1.1 ) -e 0.1 -O 5 -m 24 -a GATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGC -a GATCGGAAGAGCGGTTCA -a TCGTATGCCGTCTTCTGC -a GCAGGAATGCCGAGACCGATC -a CGGTTCAGCAGGAATGCCGAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGA -a CGGTTCAGCAGGAATGCCGA -a GATCGGAAGAGCGGTTCAGC -a AGGAATGCCGAGACCGA  -a AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTGAAAAA -a AGATCGGAAGAGCGGTTCAGCAGGAATGC -a CGAGACCGATCTCGTATGCCGTCTTCTGCTTG -a AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAA -a AGATCGGAAGAGCGTCGTGTAGGGAAA -a AGTGTAGATCTCGGTGGTCGCCGTATCATT
Peaks were called using: MACS (ver.1.4.2)   -f BAM -g hs  --bw 300  -p 1.00e-5 -w -S  --nomodel and SICER (ver. 1.1)   hs19  2 400 250 0.75 1600 0.01
Genome_build: hg19
Supplementary_files_format_and_content: BigWig

molecule: genomic DNA

source_name: Hepatocellular carcinoma

growth_protocol: HCT116 and HepG2 cells were cultured in Dulbecco’s modified Eagle medium (DMEM, Gibco) supplemented with 10% fetal bovine serum (FBS) (Gibco), 1% penicillin-streptomycin, 1% glutamamine at 37°C in 5% CO2.

extract_protocol:
Formaldehyde was added to the culture medium to a final concentration of 1%. Cross-linking was allowed to proceed for 10 min at room temperature and stopped by addition of glycine at a final concentration of 0.125 M, followed by an additional incubation for 5 min. Fixed cells were washed twice with TBS (20 mM Tris at pH 7.4, 150 mM NaCl) and harvested in SDS Buffer (50 mM Tris at pH 8.1, 0.5% SDS, 100 mM NaCl, 5 mM EDTA, and protease inhibitors). Cells were pelleted by centrifugation, and suspended in 4 mL of IP Buffer (100 mM Tris at pH 8.6, 0.3% SDS, 1.7% Triton X-100, and 5 mM EDTA). Cells were disrupted by sonication. The lysate was then diluted with IP buffer to a final volume of 9 mL. For each immunoprecipitation, diluted lysate was precleared by addition of blocked protein A beads. Samples were immunoprecipitated overnight at 4°C with polyclonal antibodies specific for either macroH2A1 (3 ug), macroH2A2 (3 ug). Before the immunoprecipitation, a fraction of precleared lysate was saved as input material. Immune complexes were recovered by adding 30 uL of blocked protein A beads and incubated for 2 h at 4°C. Beads were washed and eluted, and cross links were reversed as described by Aparicio (1999). This included successive washes in 1 mL of Mixed Micelle Buffer (20 mM Tris at pH 8.1, 150 mM NaCl, 5 mM EDTA, 5% w/v sucrose, 1% Triton X-100, and 0.2% SDS), Buffer 500 (50 mM HEPES at pH 7.5, 0.1% w/v deoxycholic acid, 1% Triton X-100, 500 mM NaCl, and 1 mM EDTA), LiCl Detergent Wash Buffer (10 mM Tris at pH 8.0, 0.5% deoxycholic acid, 0.5% NP-40, 250 mM LiCl, and 1 mM EDTA), and TE (pH 7.5). The eluted material was phenol/chloroform-extracted and ethanol-precipitated. DNA was resuspended in 50 uL of waternand quantified with PicoGreen.
Libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

tag: chip antibody

value: anti-macroH2A2 (Buschbeck et al., 2009, PMID:19734898)


title: input_HepG2_ChIPseq

description: Sample 3

value: none (input)


title: kidney biopsy, archetype1017


title: kidney biopsy, archetype1001


title: kidney biopsy, archetype1002


title: kidney biopsy, archetype1004


title: kidney biopsy, archetype1014

value: Pos


title: kidney biopsy, archetype100


title: mH2A1_HepG2_ChIPseq

description: Sample 1

value: anti-macroH2A1 (Buschbeck et al., 2009, PMID:19734898)


title: kidney biopsy, archetype1011


title: kidney biopsy, archetype1


title: Wnt4_d/d_31553

status: Public on Mar 04 2017

city: RTP

first: Franco

last: Demayo

state: NC

address: 111 TW Alexander Drive

country: USA

institute: NIEHS

description: Wnt4 conditional knockout

hyb_protocol: The arrays were hybridized for 16 hours at 45°C with rotation at 60 rpm in the Affymetrix GeneChip Hybridization Oven 640. The arrays were washed and stained with a streptavidin, R-phycoerythrin conjugate stain using the Affymetrix GeneChip Fluidics Station 450. Signal amplification was done using biotinylated anti-streptavidin.

scan_protocol: The stained arrays were scanned on the Affymetrix GeneChip Scanner 3000.

data_processing: The images were analyzed and quality control metrics recorded using Affymetrix Command Console software version 3.0.0. Microarray CEL files were analyzed using dChip (www.dchip.org, PM-MM model, Quantile normalization)

organism: Mus musculus

source_name: Wnt4 conditional knockout

label_protocol: Samples were labeled using the standard Affymetrix linear amplification protocol using the 3′ IVT Express Kit. 250 ng of total RNA was reverse transcribed to produce double-stranded cDNA. The cDNA product was used as a template for the vitro transcription reaction, producing biotin-labeled cRNA. The labeled cRNA was tested for integrity on the Agilent Bioanalyzer and quantified using the NanoDrop ND-1000 spectrophotometer. 15.0 µg of the labeled cRNA was fragmented and re-checked for concentration and size. Hybridization cocktails containing Affymetrix spike-in controls and 15.0 ug of each fragmented, labeled cRNA were loaded onto Affymetrix GeneChip Mouse 430 2.0 arrays.

growth_protocol: All mice were maintained under pathogen-free conditions. Animal handling and surgery was performed according to the NIH Guide for the Care and Use of Laboratory Animals. All procedures and protocols were approved by the Institutional Animal Care and Use Committee at Baylor College of Medicine. Typical cohorts consisted of 5–10 mice unless specified otherwise.

extract_protocol: Total RNA was isolated using RNeasy kits (Qiagen) from day 1 decidual uteri (see above) according to manufacturer's instructions and three groups of two were pooled for each condition. The integrity of all RNA samples were tested with the Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: Mice were subject to ovariectomy followed by the decidualization inducing procedure as described in PMID: 17515606.

tag: genotype/variation

value: Wnt4 d/d

value: day 1 decidual uteri


title: kidney biopsy, archetype1005

tag: tissue


title: FOXO1-targeting siRNA (siFOXO1) EPC [HESC 42]

status: Public on Jan 25 2017

library_source: transcriptomic

data_processing:
Raw reads were mapped to human genome hg19 and splice junction sites with Bowtie (version 0.12.7) and TopHat (version 2.0.0) with the strand-specific model that matches our dUTP library construction protocol.
Read counts to each gene were calculated by HTSeq using the default model.
Differential gene expression was analyzed with R (v2.14.0) and the Bioconductor edgeR package (edgeR_2.4.6). A false discovery rate (FDR) of 0.05 was used as the cutoff for significant differential expression.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include log2 fold change (logFC), log2 counts-per-million (logCPM), p value, and FDR.

source_name: endometrium

growth_protocol: DMEM F12, 10% fetal bovine serum, antibiotic-antimycotic, HEPES and NaHCO3

extract_protocol:
Ambion RiboPure kit (Life Technologies)
TruSeq

treatment_protocol: Three primary human endometrial cell lines (HESC 46, 42, 36) were  transfected with 60 nM siRNA (non-targeting,  PGR-targeting, or FOXO1-targeting) with Lipofectamine RNAiMax for 48 hours. Cells were subsequently treated with 10nM 17β-estradiol, 100nM medroxyprogesterone acetate, and 1mM  cAMP in OPTI-MEM I  reduced serum media supplemented with 2% stripped fetal bovine serum and antibiotic and antimycotics for 72 hours, with media replenished after 48 hours.

tag: cell type

value: primary human endometrial cells

tag: passages

tag: health status

value: healthy, proliferative phase


title: kidney biopsy, archetype1000

value: kidney

tag: archetype cluster

tag: g

tag: cg

tag: i


title: non-targeting siRNA  (siNT) EPC [HESC 32]


title: non-targeting siRNA  (siNT) EPC [HESC 42]


title: Wnt4_d/d_31554

description: Wnt4 conditional knockout


title: non-targeting siRNA  (siNT) Vehicle [HESC 42]


title: Wnt4_f/f_31549

description: Wnt4 control

source_name: Wnt4 control

value: Wnt4 f/f


title: EGFR_d/d_26797

description: EGFR conditional knockout

source_name: EGFR conditional knockout

value: EGFR d/d


title: EGFR_d/d_26796

description: EGFR conditional knockout


title: Wnt4_f/f_31551

description: Wnt4 control


title: FOXO1-targeting siRNA (siFOXO1) EPC [HESC 32]


title: PGR-targeting siRNA (siPGR) EPC [HESC 32]


title: kidney biopsy, archetype10

tag: ci

tag: t

tag: ct

tag: v


title: PGR-targeting siRNA (siPGR) EPC [HESC 46]


title: PGR-targeting siRNA (siPGR) EPC [HESC 42]


title: FOXO1-targeting siRNA (siFOXO1) EPC [HESC 46]


title: non-targeting siRNA  (siNT) EPC [HESC 46]


title: non-targeting siRNA  (siNT) Vehicle [HESC 46]


title: Wnt4_f/f_31550

description: Wnt4 control


title: EGFR_f/f_26794

description: EGFR control

source_name: EGFR control

value: EGFR f/f


title: EGFR_d/d_26798

description: EGFR conditional knockout


title: kidney biopsy, archetype1046

value: NOMOA

tag: cv

tag: ah

tag: ptc

tag: in i-ifta set n=234?


title: non-targeting siRNA  (siNT) Vehicle [HESC 32]


title: EGFR_f/f_26793

description: EGFR control

tag: genotype/variation


title: EGFR_f/f_26795

description: EGFR control

tag: tissue


title: PFC_WT70_3_3

status: Public on Jan 01 2017

city: Nijmegen

first: Jo Huiqing

last: Zhou

address: Geert Grooteplein 26/28

country: Netherlands

institute: Radboud University

data_processing:
42bp reads were mapped to the rat genome build rn4 using bwa version 0.6.1
BedGraph tracks were generated from BAM files using 'bedtools genomecov', normalized using the '-scale' option
Genome_build: rn4
Supplementary_files_format_and_content: Gzip-compressed bedgraph files that can be uploaded to the UCSC genome browser as custom tracks.
Supplementary_files_format_and_content: Tab-separated file with normalized Ensembl gene expression values in Fragments per Kilobase per Million mapped reads (FPKM) for all samples, as calculated by the cufflinks program.

organism: Rattus norvegicus

source_name: PFC, WT70

extract_protocol:
RNA extraction was carried out using RNeasy lipid tissue kit (QIAGEN, Venlo, The Netherlands)
2.5 μg RNA was used for rRNA depletion using the Ribo‐Zero rRNA Removal Kit (Human/Mouse/Rat, Epicentre, Madison, Wisconsin, USA) according to the manufacturer's recommendations. RNA fragmentation reactions were performed using fragmentation buffer (5x; 200 mM Tris‐Ac, 500 mM potassium‐Ac, 150 mM magnesium‐Ac, pH 8.2) in a final concentration of 1x per reaction. Fragmentation reactions were incubated at 95°C for 4 min on a thermal cycler and placed on ice for 10 min. Fragmented rRNA-depleted RNA was purified using ethanol precipitation, First and second strand synthesis was performed as described by Kouwenhoven and colleagues (2015). samples were prepared for sequencing by end repair of 5 ng total DNA as measured by Qubit dsDNA HS (Invitrogen). NEXTflex adaptors (Bioo scientific, Austin, Texas, USA) were ligated to the DNA fragments, followed by post-ligation cleanup using Agencourt AMPure XP beads (Beckman Coulter, Woerden, The Netherlands), library amplification by PCR (10 cycles) and size selection (∼300 bp) using Agencourt AMPure XP beads (Beckman Coulter). Quality control of DNA libraries prepared for sequencing was performed by qPCR and by running the products on a Bioanalyzer (Bio-Rad, Veenendaal, The Netherlands). Cluster generation and sequencing (50 bp, single end reads) was performed with the Illumina HiSeq 2000 sequencer according to standard Illumina protocols. Samples were sequenced to a depth of approximately 29 million reads per sample. Reads were aligned to the rn4 rat genome assembly using the gsnap program

tag: strain

value: Wistar

value: WT

tag: developmental stage

value: Post-natal day 70

value: prefrontal cortex


title: PFC_WT70_2_3


title: PFC_WT35_11_4

source_name: PFC, WT35

value: Post-natal day 35


title: PFC_WT70_4_1


title: PFC_WT35_8_4


title: PFC_WT70_2_2


title: PFC_WT70_3_1


title: PFC_WT35_11_1


title: primary_keratinocytes_rep4

description:
Gene expression of primary keratiocyte
N4

hyb_protocol: After fragmentation, 1650 ng of labeled cRNA from each sample was hybridized in in situ hybridization oven (Agilent) for 17 h at 65ÂºC and washed during 1 min at rt in Gene Expression Wash Buffer 1 (Agilent) and 1 min at 37 ÂºC with Gene Expression Wash buffer 2 (Agilent).

scan_protocol: The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).

data_processing: Raw data was corrected for background noise using the normexp method. Quantile normalization was applied to assure comparability across samples.

source_name: Primary human keratinocytes (PHK)

label_protocol: 500 ng of total RNA from each sample were amplified by Oligo-dT-T7 reverse transcription and labeled by in vitro transcription with T7 RNA polymerase in the presence of Cy3-CTP using the Quick Amp Labeling kit (Agilent) and purified using RNAeasy columns (Qiagen, Hilden, Germany)

extract_protocol: Total RNAs were prepared with Qiagen Rneasy minikit according to manufacturers protocol, (DNase 500 ng)

value: neonatal foreskin

tag: gender

value: male


title: transformed_keratinocytes_rep3

description:
Gene expression of transformed keratiocyte
T3


title: xenograft_derived_keratinocytes_rep2

description:
Gene expression of xenograft tumor
Ts4.2


title: PFC_WT35_10_2


title: PFC_WT35_10_4


title: immortalized_keratinocytes_rep4

description:
Gene expression of immortalized keratiocyte
IM4


title: immortalized_keratinocytes_rep1

description:
Gene expression of immortalized keratiocyte
IM1


title: immortalized_keratinocytes_rep2

description:
Gene expression of immortalized keratiocyte
IM2


title: primary_keratinocytes_rep3

description:
Gene expression of primary keratiocyte
N3


title: immortalized_keratinocytes_rep3

description:
Gene expression of immortalized keratiocyte
IM3


title: transformed_keratinocytes_rep4

description:
Gene expression of transformed keratiocyte
T4


title: xenograft_derived_keratinocytes_rep1

description:
Gene expression of xenograft tumor
Ts4.1


title: transformed_keratinocytes_rep1

description:
Gene expression of transformed keratiocyte
T1


title: PFC_WT21_16_2

source_name: PFC, WT21

value: Post-natal day 21


title: transformed_keratinocytes_rep2

description:
Gene expression of transformed keratiocyte
T2


title: primary_keratinocytes_rep1

description:
Gene expression of primary keratiocyte
N1


title: xenograft_derived_keratinocytes_rep3

description:
Gene expression of xenograft tumor
Ts4.3


title: primary_keratinocytes_rep2

description:
Gene expression of primary keratiocyte
N2


title: Wnt4_d/d_31552

description: Wnt4 conditional knockout

value: Wnt4 d/d


title: PFC_WT21_15_3


title: PFC_WT21_15_2


title: PFC_WT21_14_1


title: PFC_WT14_20_4

source_name: PFC, WT14

value: Post-natal day 14


title: PFC_WT21_14_3


title: PFC_WT8_27_2

source_name: PFC, WT8

value: Post-natal day 8


title: PFC_WT8_27_4


title: PFC_WT14_21_3


title: PFC_WT8_26_1


title: JG_02

city: Baltimore

first: Jeffrey

middle: G.

last: Gardner

state: MD

address: 1000 Hilltop Circle

department: Department of Biological Sciences

institute: University of Maryland - Baltimore County

description: glucose - exponential - rep 2

data_processing:
The raw sequence data generated was converted into FASTQ files using Illumina CASSAVA 1.8.2, which were then imported into CLC Genomics Workbench 7.5.1. Low quality base pairs were trimmed from the ends and the sequence reads were mapped to the C. japonicus reference genome with RPKM values calculated for genes. Log2 transformation and quantile normalization was performed for the RPKM values and a Student’s T-test conducted to compare gene expression between various groups of samples. Additional analysis and visualization of the data was performed using ArrayStar.
Genome_build: GCA_000019225.1
Supplementary_files_format_and_content: Tab-delimited text file includes comparative analysis (fold change) for glucose vs cellobiose (exponential) samples

organism: Cellvibrio japonicus

source_name: bacterial cell pellet

growth_protocol: MOPS defined medium

extract_protocol:
Standard extraction protocols
Sstandard Illumina protocols

treatment_protocol: 95%EtOH:5%Phenol to stop cellular metabolism

tag: protocol

value: glucose - exponential


title: JG_05

description: glucose - stationary - rep2

value: glucose - stationary


title: JG_06

description: glucose - stationary - rep3


title: JG_04

description: glucose - stationary - rep1


title: JG_03

description: glucose - exponential - rep 3


title: PFC_WT14_19_1


title: PFC_WT14_20_2


title: PFC_WT8_25_2


title: JG_01

description: glucose - exponential - rep 1


title: GATA2ff_P41

status: Public on Oct 05 2016

description: Gene expression data from ovariectomized P4 treated Gata2 f/f uterus horn

hyb_protocol: The fragmented, labeled cRNA (15 ug) was hybridized to Affymetrix mouse genome 430 2.0 arrays.

scan_protocol: Scanning was done using an Affymetrix 3000 with autoloading scanner performed using Affymetrix protocols.

data_processing: Partek Genomics Suite 6.6 was used to perform the RMA background correction. The quantile normalization was done with all Genechips (n=6).

source_name: progesterone treated

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

growth_protocol: Mice were grown to 6 weeks old prior to be ovariectomized and progesterone/oil treatment.

extract_protocol: QIAGEN RNeasy total RNA isolation kit.

treatment_protocol: Mice were ovariectomized at 6 weeks of age. Two weeks later, ovariectomized mice were injected with either vehicle (sesame oil) or progesterone (in sesame oil, 1 mg per mouse in 100 μl) and mice were sacrificed 6 hours after the injection.

value: GATA2 f/f

value: female

tag: age

value: 8 weeks old

value: mixed background

value: ovariectomized uterus


title: GATA2ff_Oil2

description: Gene expression data from ovariectomized Oil treated Gata2 f/f uterus horn

source_name: Oil treated


title: 190_B

status: Public on Feb 09 2016

city: Cleveland

first: Vinay

last: Varadan

state: OH

address: 2103 Cornell Rd

department: Case Comprehensive Cancer Center

institute: Case Western Reserve University

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

source_name: HER2+ Breast Cancer_baseline

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

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

treatment_protocol: The 03-311 trial was conducted at the Dana Farber Cancer Institute and the Yale Comprehensive Cancer Center (YCCC). Once a patient signed informed consent, pretreatment tumor biopsies were obtained, then she received a loading dose of trastuzumab (8 mg/kg). Repeat tumor biopsies were obtained approximately 14 days later, after which the patient started treatment with either vinorelbine 25 mg/m2 weekly x 12 weeks (NH) or docetaxel 75 mg/m2 and carboplatin AUC 6 every 3 weeks (TCH) with trastuzumab 2 mg/kg weekly for 12 weeks (TCH); the choice of chemotherapy regimen and subsequent surgical management of the breast and axilla were at the discretion of the treating physicians.

tag: subject id

tag: patient status

value: HER2+ Breast Cancer

tag: timepoint

value: baseline

tag: response at surgery

value: OBJR

tag: er status

value: Neg

tag: pr status


title: 189_B


title: GATA2ff_Oil3


title: 189_P

source_name: HER2+ Breast Cancer_post

value: post


title: 191_B


title: 187_B

value: pCR


title: GATA2ff_P43


title: 196_B


title: 191_P


title: 192_P


title: 194_P

value: Pos


title: 195_P


title: 187_P


title: 190_P


title: 195_B


title: 185_P


title: 192_B


title: GATA2ff_P42


title: 184_P

value: NOR


title: GATA2ff_Oil1


title: 184_B


title: 196_P


title: 194_B


title: 197_B


title: 197_P


title: 185_B


title: 182_P


title: 181_B


title: 161_B


title: 165_P


title: 170_B


title: 170_P


title: 182_B


title: 169_B


title: 154_B


title: 181_P


title: 153_B


title: 166_B


title: 154_P


title: 153_P


title: 162_B


title: 157_B


title: 152_P


title: 160_B


title: 166_P


title: 164_P


title: 169_P


title: 164_B


title: 165_B


title: 156_B


title: 161_P


title: 160_P


title: 157_P


title: 162_P


title: 156_P


title: PFC_WT14_20_6

value: Wistar

value: WT

value: Post-natal day 14

value: prefrontal cortex


title: PFC_WT8_25_3

value: Post-natal day 8


title: 151_P


title: 143_B


title: 148_P


title: 135_P


title: 137_P


title: 152_B


title: 139_P


title: 148_B


title: 151_B


title: 142_P


title: 139_B


title: 134_P


title: 145_P


title: 149_P


title: 133_P


title: 146_P


title: 143_P


title: 135_B


title: 137_B


title: 145_B


title: 132_P


title: 147_P


title: 142_B


title: 147_B


title: 133_B


title: 140_P


title: 146_B


title: 134_B


title: 140_B


title: 149_B


title: 132_B


title: 129_B


title: 130_B


title: 125_P


title: Adult_Hip_fluox2_RNAseq

status: Public on Jan 22 2016

data_processing:
36bp reads were mapped to the rat genome build rn4 using Illumina's eland software in January and March 2012.
Differential expression analysis was done with Genomatix software (www.genomatix.de)
Wiggle tracks were generated from raw sequence read BED files using an in-house Perl script.
Genome_build: rn4
Supplementary_files_format_and_content: Gzip-compressed wiggle files that can be uploaded to the UCSC genome browser as custom tracks.
Supplementary_files_format_and_content: Tab-separated file with differentially expressed transcripts as determined by Genomatix software (with P < 0.05 and Fold Change > 1.5), including raw read counts and normalized expression values per transcript for all samples (two treatments and two controls).

molecule: polyA RNA

source_name: hippocampus

extract_protocol:
RNA extraction was carried out using RNeasy lipid tissue kit (QIAGEN, Venlo, The Netherlands)
Total RNA was subjected to two rounds of poly(A) selection (Oligotex mRNA Mini Kit; QIAGEN), followed by DNaseI treatment (QIAGEN) and fragmentation by hydrolysis (5× fragmentation buffer: 200mM Tris acetate, pH8.2, 500mM potassium acetate and 150mM magnesium acetate) at 94°C for 90 s. Fragmented mRNA was purified (RNeasy MinElute Kit; QIAGEN) and used for cDNA synthesis with 5 μg random hexamers by Superscript III Reverse Transcriptase (Invitrogen Life technologies, Bleiswijk, The Netherlands). Double stranded cDNA synthesis was performed in second strand buffer (Invitrogen) according to the manufacturer's recommendations and purified using the Minelute Reaction Cleanup Kit (QIAGEN) according to the manufacturer's protocol. DNA samples were prepared for RNA-seq by end repair of 20 ng DNA as measured by Qubit dsDNA HS (Invitrogen). Adaptors were ligated to DNA fragments, followed by size selection (~300 bp) and 14 cycles of PCR amplification. Quality control of DNA libraries prepared for sequencing was made by qPCR and by running the products on a Bioanalyzer (Bio-Rad, Veenendaal, The Netherlands). Cluster generation and sequencing (36 bp, single read) was performed with the Illumina Genome Analyzer IIx (GAIIx) platform according to standard Illumina protocols. Samples were sequenced to a depth of approximately 15 million uniquely mapped tags per sample. Sequences were aligned to the rat rn4 reference genome with the Illumina Analysis Pipeline allowing one mismatch. Only the tags aligning to one position on the genome were considered for further analysis. The output data were converted to Browser Extensible Data (BED) files for downstream analysis and Wiggle (WIG) files for viewing.

treatment_protocol: Rats 2 received fluoxetine (12 mg/kg/day) or 1% methylcellulose  (Genfarma B.V. Maarssen, The Netherlands) by oral gavage from PND 67 to 88 in a volume of 5 ml/kg

tag: treatment

value: Fluoxetine


title: Adult_Hip_methyl2_RNAseq

value: Methylcellulose


title: Adult_Hip_methyl1_RNAseq


title: Adult_Hip_fluox1_RNAseq


title: 125_B


title: 126_B


title: 122_P


title: 123_P


title: 120_P


title: 128_B


title: 123_B


title: 128_P


title: 122_B


title: 126_P


title: 129_P


title: 130_P


title: 119_B


title: 120_B


title: patient73

status: Public on Nov 11 2015

city: Sudbury

first: Baoqing

last: Guo

state: ON

address: 41 Ramsey Lake Road

department: Tumor Biology

institute: Advanced Medical Research Institute of Canada

description: one color labeling, one array per sample

hyb_protocol: Microarray hybridization process was conducted as per description by Agilent one-clour Microarray-based gene expression Analysis

scan_protocol: After hybridization, the microarray slides were scanned by using an Agilent G2505C scanner as discribed in Agilent manual.

data_processing:
Images were quantified and background subtraction was performed using Agilent Feature Extraction Software (version A.10.7.1.1).
All data analysis was performed using BRB-ArrayTools Version: 4.2.1 - Stable Release (January 2012) with R version 2.13.2 (2011-09-30)    Normalization: Normalize (center) each array using relative median over all genes. Used median array as reference array 1.  Exclude a gene under any of the following conditions:   Less than 20 % of expression data have at least a 1.5 -fold change in either direction from gene's median value   Percent of data missing or filtered out exceeds 50 %

source_name: human breast tumor core biopsy

label_protocol: Agilent 4×44k oligonucleotide arrays (Agilent, Product #: G4112F.) were used in our microarray experiments to compare the expression of genes between different categories. 200 ng of RNA  was used for labelling using the Quick Amp labeling kit (Agilent, #5190-0444) as described in Agilent manual.

extract_protocol: Total RNA was isolated using RNeasy Mini Kit (Qiagen), and quantity and quality were assessed using Agilent BioAnalyizer. RNA isolations with RIN at or over 5 were used for labelling.

treatment_protocol: MA.22 clinical trial accrued T3N0, any N2 or N3, and T4 breast cancer patients. Treatment was 3-weekly (Schedule A; N=47) or 2-weekly (Schedule B; N=46) regimens of epirubicin/docetaxel chemotherapy in sequential phase I/II studies, with growth factor support.  Toxicity was assessed. In phase I of each schedule, MTDs were determined based on DLT; in phase II, best clinical responses (CR/PR) and pathologic complete responses (pCR) were assessed. Six tumor biopsy cores were obtained pre-, mid-, and post-treatment: 3 cores for pathologic assessment; 3 cores for microarray studies.

value: human breast tumor core biopsy

value: pretreatment

tag: schedule

value: Schedule B

tag: clinical response

value: Partial Response (PR)

tag: estrogen-receptor

value: positive

tag: progesterone receptor

value: negative

tag: experimental batches

value: B


title: patient75

tag: tissue


title: patient72

value: Stable Disease (SD)


title: patient76


title: patient69

value: A


title: patient71


title: patient74


title: patient70


title: 119_P

value: HER2+ Breast Cancer

value: post

value: NOR

value: Neg


title: patient68


title: patient58

value: F


title: patient56


title: patient57


title: patient63


title: patient67


title: patient47

value: E


title: patient62


title: patient66


title: patient59


title: patient60


title: patient53


title: patient64


title: patient51

value: Complete Response (CR)


title: patient48


title: patient54


title: patient65


title: patient61


title: patient55


title: patient52


title: patient44

value: C


title: patient49

value: human breast tumor core biopsy

value: Progressive Disease (PD)


title: patient46

value: pretreatment

value: Schedule B


title: patient41

value: Schedule A

value: positive


title: patient50

value: Partial Response (PR)

value: negative


title: patient42


title: patient43


title: patient40


title: patient38


title: patient39


title: patient45


title: patient36


title: patient34

value: D


title: patient35


title: patient37


title: patient19


title: patient27

value: Stable Disease (SD)


title: patient23


title: patient24


title: patient31


title: patient21


title: patient28


title: patient18


title: patient30


title: patient29


title: patient32


title: patient12


title: patient15


title: patient20


title: patient22


title: patient25


title: patient26


title: patient16


title: patient17


title: patient13


title: patient14


title: patient10


title: patient08


title: patient11


title: patient09


title: patient33


title: patient07


title: patient04


title: O395_WT_RNAseq

status: Public on Oct 26 2015

city: Minneapolis

first: Shijia

last: Zhu

state: Minnesota

address: 1200 Washington Avenue S Suite #175

department: Department of Laboratory Medicine and Pathology

institute: University of Minnesota Medical School

data_processing:
RNA sequencing was performed on a HiSeq 2500 with 100bp single reads. BWA was used to map raw RNA reads for each sample to the Genbank V. cholerae N16961 reference. Reads that mapping to rRNA and tRNAs were excluded.
Genome_build: V. cholerae N16961
Supplementary_files_format_and_content: txt format; the read count for each gene

organism: Vibrio cholerae

source_name: Vibrio cholerae O395

growth_protocol: Bacterial were cultured in LB and collected at mid-exponential phase (OD600 ~0.5)

extract_protocol:
Purified mRNA was extracted from two biological replicates of exponential phase V. cholerae and converted to cDNA as previously described (Mandlik, A. et al. Cell Host Microbe 10:165-174, 2011).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: genotype/variation

value: Control


title: O395_KO_RNAseq

value: vchM Knock Out


title: C6706_WT_RNAseq

source_name: Vibrio cholerae C6706


title: WT_in_vitro_log_Bisulfite

data_processing:
Bisulfite sequencing reads were analyzed using Bismark, which output bedgraph files that describes fraction of 5mC methylation for each cytosine site.
Genome_build: V. cholerae N16961
Supplementary_files_format_and_content: .bedGraph.gz; fraction of 5mC methylation for each cytosine site

source_name: wild type cells

growth_protocol: Cells were grow in LB and collected at mid-log phase (OD ~0.5) and overnight stationary phase. In vivo cells were harvested from infected rabbit cecal fluid upon onset of symptomatic cholera (~ 18-24 hours post-infection)

extract_protocol:
Genomic DNA was extracted from two biological replicates of exponential phase, overnight stationary phase and frozen rabbit cecal fluid V. cholerae using the Wizard Genomic DNA purification kit (Promega).
Bisulfite conversion of the DNA was carried using the EZ DNA Methylation Kit (Zymo) twice to ensure high conversion efficiency. The converted DNA was then amplified by PCR using the Kapa HiFi Uracil+ polymerase for 12-15 cycles (Kapa biosystems) and sequenced on the MiSeq platform (Illumina).

tag: condition

value: exponential phase


title: WT_in_vivo_Bisulfite

value: rabbit intestinal infection


title: WT_in_vitro_stat_Bisulfite

value: stationary phase


title: C6706_KO_RNAseq


title: patient05

value: Complete Response (CR)

value: G


title: patient03

value: human breast tumor core biopsy

value: E


title: patient06

value: pretreatment


title: patient01

value: F


title: patient02

value: Schedule A


title: sample_97_11-EV-003 [expression]

status: Public on Oct 06 2015

city: Modena

first: Enrico

last: Tagliafico

state: MO

address: Via Campi 287

department: Center for Genome Research

country: Italy

institute: University of Modena and Reggio Emilia

hyb_protocol: Affymetrix Human Genome U133 Plus 2.0 array (manufacturer's protocol).

scan_protocol: Affymetrix GeneChip Scanner 3000 7G (manufacturer's protocol).

data_processing: Partek GS.

label: Biotin

source_name: Breast cancer, CHER-LOB Arm B, pre-treated

label_protocol: Affymetrix GeneChip® 3' IVT Express Kit (manufacturer's protocol).

extract_protocol: Qiagen RNeasy (manufacturer's protocol).

treatment_protocol: CHER-LOB is a phase II, randomized, multicenter, trial in which 121 patients with primary HER2-positive breast cancer were randomized to receive preoperative chemotherapy with weekly paclitaxel times 12 followed by 4 courses of 3-weekly FEC (fluorouracil, epirubicin and cyclophosphamide) plus either trastuzumab (Arm A), lapatinib (Arm B) or the combination of trastuzumab and lapatinib (Arm C). The trial design, eligibility criteria, statistical analysis, and clinical results including response, surgery outcomes and treatment safety are described in details elsewhere.

tag: disease state

value: HER2-positive breast cancer

value: breast cancer

tag: cher-lob arm

value: B

tag: arm description

value: chemotherapy+lapatinib

tag: pcr (1=yes)


title: sample_84_05-LR-004 [expression]

source_name: Breast cancer, CHER-LOB Arm A, pre-treated

value: A

value: chemotherapy+trastuzumab


title: sample_94_08-FR-07 [expression]


title: sample_90_08-ZMT-06 [expression]


title: sample_79_01-AG-015 [expression]

source_name: Breast cancer, CHER-LOB Arm C, pre-treated

value: C

value: chemotherapy+trastuzumab+lapatinib


title: sample_72_06-AD-001 [expression]


title: sample_93_08-CM-05 [expression]


title: sample_99_11-RG-005 [expression]


title: sample_96_11-EB-002 [expression]


title: sample_98_11-IS-004 [expression]


title: sample_95_05-CB-005 [expression]


title: sample_88_03-CV-002 [expression]


title: sample_87_01-PD-016 [expression]


title: sample_82_05-LF-002 [expression]


title: sample_61_11-VB-001 [expression]


title: sample_77_07-SF-002 [expression]


title: sample_45_01-AV-013 [expression]


title: sample_83_05-LA-003 [expression]


title: sample_53_08-GC-001 [expression]


title: sample_55_08-GL-002 [expression]


title: sample_51_08-FP-003 [expression]


title: sample_47_01-PJL-014 [expression]


title: sample_91_08-KA-04 [expression]


title: sample_78_07-MS-003 [expression]


title: sample_66_02-GS-005 [expression]


title: sample_44_01-WG-012 [expression]


title: sample_69_05-IL-001 [expression]


title: sample_28_01-MR-006 [expression]


title: sample_35_01-CB-07 [expression]


title: sample_209_08-MS-016 [expression]


title: sample_211_08-EM-014 [expression]


title: sample_212_08-OS-013 [expression]


title: sample_208_08-BMC-017 [expression]


title: sample_213_12-DB-007 [expression]


title: sample_206_05-GS-007 [expression]


title: sample_21_01-ES-005 [expression]


title: sample_195_01-GL-032 [expression]


title: sample_205_05-MP-006 [expression]


title: sample_183_01-PF-030 [expression]


title: sample_184_01-IR-031 [expression]


title: sample_197_02-SC-012 [expression]


title: sample_181_12-MBC-006 [expression]


title: sample_180_12-RP-005 [expression]


title: sample_178_12-AP-003 [expression]


title: sample_202_03_AM-10 [expression]


title: sample_177_12-OH-002 [expression]


title: sample_186_08-BS-012 [expression]


title: sample_196_02-AN-011 [expression]


title: sample_182_01-NF-029 [expression]


title: sample_172_11-GR-008 [expression]


title: sample_179_12-LA-004 [expression]


title: sample_185_08-GZ-010 [expression]


title: sample_171_11-GM-007_III [expression]


title: sample_176_12-GP-001 [expression]


title: sample_173_11-LT-009 [expression]


title: sample_17_02-MS-003 [expression]


title: sample_164_03-PM-009 [expression]


title: sample_163_03-MAM-008 [expression]


title: sample_158_03-ECC-003 [expression]


title: sample_162_03-MG-007 [expression]


title: sample_157_01-VV-027 [expression]


title: sample_148_02-IR-008 [expression]


title: sample_159_03-AA-004 [expression]


title: sample_150_02-CS-010 [expression]


title: sample_145_01-LF-025 [expression]


title: sample_147_06-LN-005 [expression]


title: sample_142_01-MB-022 [expression]


title: sample_160_03-PP-005 [expression]


title: sample_140_08-MR-009 [expression]


title: sample_115_01-ESA-021 [expression]


title: sample_110_01-NB-020 [expression]


title: sample_161_03-PB-006 [expression]


title: sample_107_02-BG-006 [expression]


title: sample_113_06-SF-003 [expression]


title: sample_12_02-FML-002 [expression]


title: sample_108_02-FM-007 [expression]


title: sample_149_02-MF-009 [expression]


title: sample_139_08-NC-008 [expression]


title: sample_109_01-PK-019 [expression]


title: sample_146_01-SB-026 [expression]


title: sample_103_01-VT-018 [expression]


title: sample_102_01-PDG-017 [expression]


title: sample_210_08-AT-015 [expression]


title: sample_112_06-NP-002 [expression]


title: sample_01-OR-011 [expression]


title: gray-00248: s0168

status: Public on May 20 2015

city: Rockville

first: Mervi

last: Heiskanen

address: 9609 Medical Center Drive, 1W378

department: CBIIT

institute: NCI

description: E-TABM-158-processed-data-1670335489.txt

hyb_protocol: See mage-tab files linked to series entry for additional details

source_name: mammary gland

tag: chemotherapy treatment

value: no

tag: p53 positive (ihc)

tag: Sex

value: female

tag: erbb2 positive (ihc)

tag: distal recurrence

tag: distal recurrence time

tag: organism part

value: mammary gland

tag: family history

tag: followup time

tag: ethnicity

value: Caucasian

tag: dead of disease

tag: tumor grading

tag: tumor staging

tag: hormonal therapy

value: yes

tag: estrogen receptor status

value: positive

tag: biosource type

tag: progesterone receptor status

tag: alive at endpoint

tag: node positive

tag: age at diagnosis

tag: recurrence time

tag: tumor size (mm)

tag: recurrence

tag: radiation treatment


title: gray-00248: b0165

scan_protocol: See mage-tab files linked to series entry for additional details

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: Sex

tag: erbb2 positive (ihc)

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

value: African American

tag: disease state

value: negative


title: gray-00248: b0427

data_processing: See mage-tab files linked to series entry for additional details

tag: followup time

tag: ethnicity

tag: dead of disease

tag: tumor grading

tag: tumor staging

tag: hormonal therapy

tag: estrogen receptor status

tag: biosource type

tag: progesterone receptor status


title: gray-00248: b0672

label_protocol: See mage-tab files linked to series entry for additional details

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: alive at endpoint

tag: node positive

tag: age at diagnosis

tag: recurrence time

tag: tumor size (mm)

tag: recurrence

tag: radiation treatment


title: gray-00248: b0252

extract_protocol: See mage-tab files linked to series entry for additional details

tag: Sex

tag: erbb2 positive (ihc)

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: ethnicity

tag: disease state


title: gray-00248: b0243

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: dead of disease

tag: tumor grading

tag: tumor staging

tag: hormonal therapy

tag: estrogen receptor status

tag: biosource type

tag: progesterone receptor status


title: gray-00248: b0554

tag: Sex

tag: erbb2 positive (ihc)

tag: alive at endpoint

tag: node positive

tag: age at diagnosis

tag: recurrence time

tag: tumor size (mm)

tag: recurrence

tag: radiation treatment


title: gray-00248: b0629

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: ethnicity

tag: disease state


title: gray-00248: s1511

tag: Sex

tag: erbb2 positive (ihc)

tag: dead of disease

tag: tumor grading

tag: tumor staging

tag: hormonal therapy

tag: estrogen receptor status

tag: biosource type

tag: progesterone receptor status


title: gray-00248: s1551

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: alive at endpoint

tag: node positive

tag: age at diagnosis

tag: recurrence time

tag: tumor size (mm)

tag: recurrence

tag: radiation treatment


title: gray-00248: s0059

tag: Sex

tag: erbb2 positive (ihc)

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: ethnicity

tag: disease state


title: gray-00248: s0101

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: dead of disease

tag: tumor grading

tag: tumor staging

tag: hormonal therapy

tag: estrogen receptor status

tag: biosource type

tag: progesterone receptor status


title: gray-00248: b0667

tag: Sex

tag: erbb2 positive (ihc)

tag: alive at endpoint

tag: node positive

tag: age at diagnosis

tag: recurrence time

tag: tumor size (mm)

tag: recurrence

tag: radiation treatment


title: sample_01_01-TT-001 [expression]

tag: disease state

tag: tissue

tag: cher-lob arm

tag: arm description

tag: pcr (1=yes)


title: gray-00248: b0574

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: ethnicity

tag: dead of disease

tag: tumor grading

tag: tumor staging

tag: hormonal therapy

tag: estrogen receptor status


title: gray-00248: b0244

tag: Sex

tag: erbb2 positive (ihc)

value: Other

tag: disease state

tag: biosource type

tag: progesterone receptor status

tag: alive at endpoint

tag: node positive

tag: age at diagnosis

tag: recurrence time

tag: tumor size (mm)

tag: recurrence

tag: radiation treatment


title: gray-00248: s0103

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: ethnicity

tag: dead of disease


title: gray-00248: b0694

tag: Sex

tag: erbb2 positive (ihc)

tag: tumor grading

tag: tumor staging

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: biosource type

tag: progesterone receptor status


title: gray-00248: b0772

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: alive at endpoint

tag: node positive

tag: age at diagnosis

tag: recurrence time

tag: tumor size (mm)

tag: recurrence

tag: radiation treatment


title: gray-00248: s0077

tag: Sex

tag: erbb2 positive (ihc)

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: ethnicity

tag: dead of disease


title: gray-00248: b0383

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: tumor grading

tag: tumor staging

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: biosource type

tag: progesterone receptor status


title: gray-00248: s0183

tag: Sex

tag: erbb2 positive (ihc)

tag: alive at endpoint

tag: node positive

tag: age at diagnosis

tag: recurrence time

tag: tumor size (mm)

tag: recurrence

tag: radiation treatment


title: gray-00248: s0210

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: ethnicity

tag: dead of disease


title: gray-00248: s0195

tag: Sex

tag: erbb2 positive (ihc)

tag: tumor grading

tag: tumor staging

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: biosource type

tag: progesterone receptor status


title: gray-00248: s0100

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: alive at endpoint

tag: node positive

tag: age at diagnosis

tag: recurrence time

tag: tumor size (mm)

tag: recurrence

tag: radiation treatment


title: gray-00248: s0350

tag: Sex

tag: erbb2 positive (ihc)

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: ethnicity

tag: dead of disease


title: gray-00248: b0565

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: tumor grading

tag: tumor staging

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: biosource type

tag: progesterone receptor status


title: gray-00248: s0190

tag: Sex

tag: erbb2 positive (ihc)

tag: alive at endpoint

tag: node positive

tag: age at diagnosis

tag: recurrence time

tag: tumor size (mm)

tag: recurrence

tag: radiation treatment


title: gray-00248: b0664

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: ethnicity

tag: dead of disease


title: gray-00248: s0060

tag: Sex

tag: erbb2 positive (ihc)

tag: tumor grading

tag: tumor staging

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: biosource type

tag: progesterone receptor status


title: gray-00248: s0086

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: alive at endpoint

tag: node positive

tag: age at diagnosis

tag: recurrence time

tag: tumor size (mm)

tag: recurrence

tag: radiation treatment


title: gray-00248: s0087

tag: Sex

tag: erbb2 positive (ihc)

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: ethnicity

tag: dead of disease


title: gray-00248: b0251

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: tumor grading

tag: tumor staging

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: biosource type

tag: progesterone receptor status


title: gray-00248: s0175

tag: Sex

tag: erbb2 positive (ihc)

tag: alive at endpoint

tag: node positive

tag: age at diagnosis

tag: recurrence time

tag: tumor size (mm)

tag: recurrence

tag: radiation treatment


title: gray-00248: s0067

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: ethnicity

tag: dead of disease


title: gray-00248: s0013

tag: Sex

tag: erbb2 positive (ihc)

tag: tumor grading

tag: tumor staging

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: biosource type

tag: progesterone receptor status


title: gray-00248: b0327

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: alive at endpoint

tag: node positive

tag: age at diagnosis

tag: recurrence time

tag: tumor size (mm)

tag: recurrence

tag: radiation treatment


title: gray-00248: b0394

tag: Sex

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tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: ethnicity

tag: dead of disease


title: gray-00248: s0006

tag: chemotherapy treatment

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tag: tumor grading

tag: tumor staging

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: biosource type

tag: progesterone receptor status


title: gray-00248: s0116

tag: Sex

tag: erbb2 positive (ihc)

tag: alive at endpoint

tag: node positive

tag: age at diagnosis

tag: recurrence time

tag: tumor size (mm)

tag: recurrence

tag: radiation treatment


title: gray-00248: s0205

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: ethnicity

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title: sample_143_01-MGC-023 [expression]

tag: disease state

value: HER2-positive breast cancer

tag: tissue

tag: cher-lob arm

tag: arm description

tag: pcr (1=yes)


title: sample_144_01-MPC-024 [expression]

value: breast cancer


title: gray-00248: b0512

tag: Sex

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tag: tumor grading

tag: tumor staging

tag: hormonal therapy

tag: estrogen receptor status

tag: biosource type

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title: gray-00248: s0042

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tag: distal recurrence time

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title: gray-00248: b0679

tag: Sex

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tag: tumor staging

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tag: progesterone receptor status

tag: alive at endpoint


title: gray-00248: b0671

tag: chemotherapy treatment

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tag: distal recurrence time

tag: organism part

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title: gray-00248: s0104

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title: gray-00248: b0551

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title: gray-00248: b0434

tag: Sex

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tag: distal recurrence time

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title: gray-00248: s0037

tag: chemotherapy treatment

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title: gray-00248: s0033

tag: Sex

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tag: tumor staging

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tag: progesterone receptor status

tag: alive at endpoint


title: gray-00248: s0106

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: distal recurrence

tag: distal recurrence time

tag: organism part

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tag: recurrence time

tag: tumor size (mm)


title: gray-00248: b0339

tag: Sex

tag: erbb2 positive (ihc)

tag: family history

tag: followup time

tag: ethnicity

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tag: recurrence

tag: radiation treatment


title: gray-00248: s0154

tag: chemotherapy treatment

tag: p53 positive (ihc)

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tag: tumor staging

tag: hormonal therapy

tag: estrogen receptor status

tag: biosource type

tag: progesterone receptor status

tag: alive at endpoint


title: gray-00248: s0162

tag: Sex

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tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: node positive

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tag: recurrence time

tag: tumor size (mm)


title: gray-00248: b0359

tag: chemotherapy treatment

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tag: recurrence

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title: gray-00248: b0387

tag: Sex

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tag: tumor staging

tag: hormonal therapy

tag: estrogen receptor status

tag: biosource type

tag: progesterone receptor status

tag: alive at endpoint


title: gray-00248: s0071

tag: chemotherapy treatment

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tag: distal recurrence time

tag: organism part

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title: gray-00248: b0542

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tag: recurrence

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title: gray-00248: s0176

tag: chemotherapy treatment

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tag: tumor staging

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tag: biosource type

tag: progesterone receptor status

tag: alive at endpoint


title: gray-00248: s0107

tag: Sex

tag: erbb2 positive (ihc)

tag: distal recurrence

tag: distal recurrence time

tag: organism part

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tag: recurrence time

tag: tumor size (mm)


title: gray-00248: b0374

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title: gray-00248: b0341

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tag: progesterone receptor status

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title: gray-00248: s0201

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title: gray-00248: s0132

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title: gray-00248: s0018

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title: gray-00248: s0109

tag: Sex

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tag: distal recurrence time

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title: gray-00248: s0229

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title: gray-00248: b0370

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tag: tumor staging

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tag: progesterone receptor status

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title: gray-00248: b0428

tag: chemotherapy treatment

tag: p53 positive (ihc)

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tag: distal recurrence time

tag: organism part

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title: gray-00248: b0334

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title: gray-00248: b0515

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title: gray-00248: s0088

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title: gray-00248: s0046

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title: gray-00248: s0025

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tag: progesterone receptor status

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title: gray-00248: s0001

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title: gray-00248: s0019

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title: gray-00248: s0136

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title: gray-00248: b0494

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tag: distal recurrence time

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title: gray-00248: b0338

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title: gray-00248: s0026

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title: gray-00248: s0177

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tag: distal recurrence time

tag: organism part

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tag: age at diagnosis

tag: recurrence time

tag: tumor size (mm)


title: gray-00248: s0146

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title: gray-00248: s0170

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title: gray-00248: b0566

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tag: distal recurrence time

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title: gray-00248: b0421

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title: gray-00248: b0502

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title: gray-00248: b0627

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title: gray-00248: s1616

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tag: progesterone receptor status

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title: gray-00248: s0138

tag: Sex

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tag: distal recurrence time

tag: organism part

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tag: recurrence time

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title: gray-00248: b0340

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title: gray-00248: s0141

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title: gray-00248: s0204

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title: gray-00248: b0305

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title: gray-00248: b0668

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title: gray-00248: s0055

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tag: distal recurrence time

tag: organism part

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title: gray-00248: b0499

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title: gray-00248: b0404

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tag: progesterone receptor status

tag: alive at endpoint


title: gray-00248: s0040

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: node positive

tag: age at diagnosis

tag: recurrence time

tag: tumor size (mm)


title: gray-00248: b0504

tag: Sex

tag: erbb2 positive (ihc)

tag: family history

tag: followup time

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tag: recurrence

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title: gray-00248: b0556

tag: chemotherapy treatment

tag: p53 positive (ihc)

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tag: tumor staging

tag: hormonal therapy

tag: estrogen receptor status

tag: biosource type

tag: progesterone receptor status

tag: alive at endpoint


title: p63_day7

status: Public on May 01 2015

data_processing:
42bp reads left after demultiplexing of original 50bp reads were mapped to the human GRCh37 genome (hg19; assembly February 2009) using BWA 0.6.1 with standard parameters.
All duplicate reads and reads mapping to multiple locations were removed.
All p63, H3K27ac and RNAPII ChIP-seq datasets (BAM files) were normalized to the same sequencing depth by randomly removing aligned reads.
P63 peaks were called using MACS2 (2.0.10.20120913) with default settings and a P value threshold of 1E-9 using input genomic DNA as background control.
H3K27ac peaks were called using MACS2 (2.0.10.20120913) using default settings for broad peak calling and a P value threshold of 1E-9 using input genomic DNA as background control.
RNAPII occupancy in RefSeq gene bodies calculated as Reads Per Kilobase per Million mapped reads (RPKM).
Wiggle tracks were generated from normalized BAM files.
Genome_build: hg19
Supplementary_files_format_and_content: Gzip-compressed wiggle files that can be uploaded to the UCSC genome browser as custom tracks.
Supplementary_files_format_and_content: MACS2 .xls output file with peak data.
Supplementary_files_format_and_content: Tab-separated RefSeq RNAPII gene body occupancy matrix containing genomic location, strand, RefSeq transcript ID, RefSeq gene ID (HUGO gene symbol), and the RPKM values for days 0, 2, 4 & 7 respectively.

source_name: Keratinocytes

growth_protocol: Skin biopsies were taken from the abdomen of healthy volunteers to set up the primary keratinocyte culture (Rheinwald and Green 1977). Keratinocytes were cultured in Keratinocyte Growth Medium (KGM) under undifferentiated conditions as previously described (Rinne et al. 2008).

extract_protocol:
ChIP-sequencing datasets were generated with an antibody recognizing the alpha isoforms of p63 (H129, Santa Cruz), an antibody that detects all forms of the large subunit of RNA polymerase II (8WG16, Santa Cruz), and a H3K27ac antibody recognizing the acetylation of the lysine 27 residue of Histone H3 (H3K27ac, Diagenode). RNAPII, p63 and H3K27ac ChIP experiments were performed as previously described (Denissov et al. 2007; Kouwenhoven et al. 2010; Smeenk et al. 2008), with a minor change of using magnetic beads (Novex by Life Technologies, Cat. No. 10008D and 10009D).
DNA samples were prepared for sequencing by end repair of 6 ng total DNA (p63 ChIP-seq, and RNAPII ChIP-seq samples) and 10 ng total DNA (H3K27ac ChIP-seq samples) as measured by Qubit (Invitrogen). Adaptors were ligated to the DNA fragments, followed by a pre-PCR of 4 cycles, size selection (∼300 bp) and subsequently 11 cycles of PCR amplification.

treatment_protocol: Differentiation of keratinocyte cultures was induced by cell contact inhibition and excluding several growth factor supplements: bovine pituitary extract (Bio Whittaker), EGF (Sigma), insulin (Sigma), and hydrocortisone (Calbiochem) from the medium. The medium was changed every second day, and before harvesting of the RNA and chromatin. Cells were collected on day 0, and on days 2, 4 and 7 after induction of differentiation.

tag: chip antibody

tag: differentiation day

tag: cell type

value: Keratinocytes


title: gray-00248: b0626

tag: Sex

tag: erbb2 positive (ihc)

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: ethnicity

tag: node positive

tag: age at diagnosis

tag: recurrence time

tag: tumor size (mm)


title: p63_day4


title: RNAPII_day0

description: HKC_L1_ChIP_RNAPII_RefSeq_RPKM_days0247.txt

value: RNAPII


title: gray-00248: s0035

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: dead of disease

tag: tumor grading

tag: tumor staging

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: biosource type

tag: progesterone receptor status

tag: recurrence

tag: radiation treatment


title: H3K27ac_day4

tag: chip antibody

tag: differentiation day

tag: cell type


title: p63_day2


title: H3K27ac_day2


title: p63_day0


title: gray-00248: s0047

tag: Sex

tag: erbb2 positive (ihc)

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: ethnicity

tag: alive at endpoint

tag: node positive

tag: age at diagnosis

tag: recurrence time


title: RNAPII_day7


title: gray-00248: b0318

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: dead of disease

tag: tumor grading

tag: tumor staging

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: biosource type

tag: progesterone receptor status

tag: tumor size (mm)

tag: recurrence


title: gray-00248: b0519

tag: Sex

tag: erbb2 positive (ihc)

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: ethnicity

tag: radiation treatment


title: gray-00248: s0050

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: dead of disease

tag: tumor grading

tag: tumor staging

tag: alive at endpoint

tag: node positive

tag: age at diagnosis

tag: recurrence time


title: gray-00248: b0344

tag: Sex

tag: erbb2 positive (ihc)

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: biosource type

tag: progesterone receptor status

tag: tumor size (mm)

tag: recurrence


title: gray-00248: s0004

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: ethnicity

tag: radiation treatment


title: gray-00248: b0354

tag: Sex

tag: erbb2 positive (ihc)

tag: dead of disease

tag: tumor grading

tag: tumor staging

tag: alive at endpoint

tag: node positive

tag: age at diagnosis

tag: recurrence time


title: gray-00248: b0336

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: biosource type

tag: progesterone receptor status

tag: tumor size (mm)

tag: recurrence


title: gray-00248: b0382

tag: Sex

tag: erbb2 positive (ihc)

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: ethnicity

tag: radiation treatment


title: gray-00248: s0181

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: dead of disease

tag: tumor grading

tag: tumor staging

tag: alive at endpoint

tag: node positive

tag: age at diagnosis

tag: recurrence time


title: gray-00248: s0084

tag: Sex

tag: erbb2 positive (ihc)

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: biosource type

tag: progesterone receptor status

tag: tumor size (mm)

tag: recurrence


title: gray-00248: b0326

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: ethnicity

tag: radiation treatment


title: RNAPII_day4

tag: chip antibody

tag: differentiation day

tag: cell type


title: gray-00248: b0433

tag: Sex

tag: erbb2 positive (ihc)

tag: dead of disease

tag: tumor grading

tag: tumor staging

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: alive at endpoint

tag: node positive

tag: age at diagnosis

tag: recurrence time


title: Input

value: Input control


title: gray-00248: s0200

tag: chemotherapy treatment

tag: p53 positive (ihc)

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: ethnicity

tag: biosource type

tag: progesterone receptor status

tag: tumor size (mm)

tag: recurrence


title: RNAPII_day2

tag: chip antibody

tag: differentiation day

tag: cell type


title: HKC_L2_day2_RNAseq

description:
HKC_L1L2_RNAseq_days0247_FPKM_genes.txt
HKC_L1L2_RNAseq_days0247_FPKM_isoforms.txt

data_processing:
42bp reads left after demultiplexing of original 50bp reads were mapped to the human genome NCBI build 37 (hg19) using gsnap version 2013-03-31.
Spliced reads were mapped based on the Ensembl 68 reference transcriptome.
Transcript quantification and differential expression analysis were done with cufflinks v2.1.1, using the RefSeq transcriptome (downloaded from UCSC genome browser website, June 2013).
Wiggle tracks were generated from read count-normalized BAM files.
Genome_build: hg19
Supplementary_files_format_and_content: Gzip-compressed wiggle files that can be uploaded to the UCSC genome browser as custom tracks.
Supplementary_files_format_and_content: Tab-separated FPKM gene expression matrix containing RefSeq gene ID, HUGO gene symbol, genomic location and the FPKM values for the 8 samples.
Supplementary_files_format_and_content: Tab-separated FPKM isoform expression matrix containing RefSeq transcript ID, RefSeq gene ID, HUGO gene symbol, genomic location and the FPKM values for the 8 samples.

extract_protocol:
RNA extraction was carried out using the NucleoSpin RNA II kit (740955.50; MACHEREY-NAGEL, Düren, Germany).
cDNA synthesis from 1 μg total RNA as control for RNA-seq was carried out using the iScript cDNA synthesis kit (Bio-Rad; 170-8891, CA, Hercules, USA). Starting amount of RNA-seq sample was 1 μg. rRNA depletion was performed with the Ribo-Zero rRNA Removal Kit (Human/Mouse/Rat; cat. no. MRZH11124, Epicentre, Madison, WI, USA) according to the manufacturer's instructions. RNA fragmentation reactions were performed using fragmentation buffer (5×; 200 mM Tris-Ac, 500 mM Potassium-Ac, 150 mM Magnesium-Ac) in a final concentration of 1× per reaction. Each 50 μl fragmentation reaction was incubated at 95°C for 1.5 minutes on a thermal cycler, and placed on ice for 10 minutes. Ethanol precipitation was used to purify the reactions. The fragmented rRNA depleted RNA was combined with 5 μg of random hexamers (Roche) in a final volume of 11 μl, incubated at 65°C for 5 minutes, and afterwards immediately placed on ice. The remaining reagents were added to the reaction: 4 μl 5× First strand buffer (Invitrogen), 2 μl DTT (0.1 M Invitrogen), 1 μl dNTP mix (10 mM Invitrogen), 2 μl Actinomycin D (0.1 μg/ μl Sigma), 1 μl of RNase H (40U/ml Ambion), and 1 μl SuperScript III (200 U Invitrogen). The first strand reaction was incubated at 25°C for 10 minutes, 50°C for 90 minutes, followed by deactivation at 70°C for 15 minutes, followed by MinElute Reaction Cleanup Kit (Qiagen), according to the manufacturer's protocol. The second strand was synthesized by adding 20 μl 5x Second strand buffer (Invitrogen), 4 μl 5x First strand buffer (Invitrogen), 2 μl DTT (0.1 M Invitrogen), 1 μl random hexamers (5 mg/ml Roche), dUTP mix (12.5 mM Invitrogen), 1 μl RNase H (8U/ml Ambion), 1 μl E. coli DNA polymerase I (10U/ μl Invitrogen), and 1 μl E. coli DNA ligase (10 U/μl NEB) to the purified sample (100 μl total volume). After 2 hours at 16°C, 1 μl of T4 DNA polymerase (10U/μl Promega) was added and the reaction was incubated at 16°C for 10 minutes. The ds-cDNA was purified using the MinElute Reaction Cleanup Kit (Qiagen), according to the manufacturer's protocol. DNA samples were prepared for sequencing by end repair of 5 ng total cDNA as measured by Qubit (Invitrogen). Adaptors were ligated to the DNA fragments, followed by a pre-PCR of 4 cycles, size selection (∼300 bp) and subsequently 11 cycles of PCR amplification.

tag: cell line

value: HKC L2


title: HKC_L2_day7_RNAseq


title: H3K27ac_day0


title: HKC_L1_day2_RNAseq

value: HKC L1


title: HKC_L1_day0_RNAseq


title: gray-00248: b0241

tag: Sex

tag: erbb2 positive (ihc)

tag: dead of disease

tag: tumor grading

tag: tumor staging

tag: disease state

tag: hormonal therapy

tag: estrogen receptor status

tag: alive at endpoint

tag: node positive

tag: age at diagnosis

tag: recurrence time

tag: radiation treatment


title: HKC_L1_day7_RNAseq


title: ES.Cbx8.RA

status: Public on Nov 04 2014

data_processing:
Basecalls performed using CASAVA version 1.4
alignment with mouse genome (NCBIM37/mm9) using Bowtie version 0.12.7 (Langmead et al. 2009), two mismatches were allowed for the alignment within the seed, only reads mapping to a single position in the genome were used
To detect genomic region with significant enrichment we used MACS software version 1.4.1 (Zhang et al. 2008).  For peak calling of Cbx8 in RA-treated ES cells we used a p-value cutoff of 1 x 10-4 and a FDR of 5%.
Genome_build: mm9
Supplementary_files_format_and_content: Wig are created using  file Extended tag pileup from MACS version 1.4.2 20120305 for every 10 bp

source_name: ES E14 mouse cells

growth_protocol: E14Tg2A.4 mouse ES cells were cultured as described (Creppe et al. 2012).

extract_protocol: Chromatin immunoprecipitation (ChIP) experiments were performed and analyzed essentially as previously described (Buschbeck et al. 2009).

treatment_protocol: For neuronal differentiation, 1 μM all trans retinoic acid (RA) was added directly to cells in medium without leukemia inhibitory factor. Cells were collected after 72h of RA treatment.

value: E14Tg2A.4 embryonic stem (ES)

tag: chip antibody


title: gray-00248: b0521

tag: chemotherapy treatment

value: no

tag: p53 positive (ihc)

tag: distal recurrence

tag: distal recurrence time

tag: organism part

tag: family history

tag: followup time

tag: ethnicity

tag: biosource type

tag: progesterone receptor status

tag: tumor size (mm)

tag: recurrence


title: ES.Cbx8.untreated

tag: cell type


title: H3K27ac_day7

tag: differentiation day


title: HKC_L1_day4_RNAseq

tag: cell line


title: ES.IgG

value: IgG


title: HKC_L2_day0_RNAseq


title: HKC_L2_day4_RNAseq


title: E14_ES_nt.rep3

description: Gene expression

hyb_protocol: After fragmentation, 1650 ng of labeled cRNA from each sample was hybridized in in situ hybridization oven (Agilent) for 17 h at 65°C and washed during 1 min at rt in Gene Expression Wash Buffer 1 (Agilent) and 1 min at 37 °C with Gene Expression Wash buffer 2 (Agilent).

source_name: E14, no treated, rep 3

extract_protocol: Total RNAs were prepared with Qiagen Rneasy minikit according to manufacturers protocol


title: E14_ES_RA.rep3

description: Gene expression after 72h retinoic acid

source_name: E14, retinoc acid, 72h, rep 3


title: E14_ES_RA.rep4

description: Gene expression after 72h retinoic acid

source_name: E14, retinoc acid, 72h, rep 4


title: E14_ES_nt.rep4

description: Gene expression

source_name: E14, no treated, rep 4


title: E14_ES_RA.rep2

description: Gene expression after 72h retinoic acid

source_name: E14, retinoc acid, 72h, rep 2


title: E14_ES_nt.rep1

description: Gene expression

source_name: E14, no treated, rep 1


title: E14_ES_RA.rep1

description: Gene expression after 72h retinoic acid

source_name: E14, retinoc acid, 72h, rep 1


title: BreastCancer_S264

status: Public on Jan 21 2014

city: Penzberg

first: Anton

last: Belousov

address: Nonnenwald 2

department: NCS-TTB

country: Germany

institute: Roche

hyb_protocol: Hybridization of labeled probes on the Affymetrix GeneChip Human Genome U133 Plus 2.0 Array were conducted using the GeneChip® Hybridization, Wash, and Stain Kit (Affymetrix).

scan_protocol: For this workflow a GeneChip Fluidics Station 450 and a GeneChip Scanner 3000 7G were used

source_name: breast cancer

label_protocol: A Transcriptor First Strand cDNA Synthesis Kit (Roche) was used to prepare cDNA from 100 ng of total RNA, using an anchored oligo(dT)-primer followed by a subsequent amplification step with the SYBR Green I Master on a LightCycler® 480 instrument (Roche Applied Science). Formalin-fixed paraffin-embedded tumor (FFPET)-derived RNA was amplified with the WT-Ovation™ FFPE System V2 (NuGEN). Biotin labeling of the cDNA was performed using the FL-Ovation cDNA Biotin Module V2 (NuGEN).

extract_protocol: Formalin-fixed, paraffin-embedded (FFPE) core biopsies were prospectively collected prior to treatment. The yield and purity of RNA was determined using a NanoDrop 1000 Spectrophotometer (Thermo Scientific). RNA integrity was measured using a Bioanalyzer (Agilent Technologies) with either the RNA Nano or Pico Kit, depending on sample concentration. The RNA Integrity Number (RIN) and average length of the RNA were used for sample characterization. mRNA integrity was measured using a semiquantitative reverse transcription-polymerase chain reaction assay (rtPCR). This assay is based on quantitative amplification of 5'- and 3'-end sequences of the housekeeping gene β-actin. Calculating the ratio of 3' to 5' amplicons allows for assessment of mRNA integrity: intact RNA transcripts exhibit a ratio of 1, while degraded RNA increases the ratio.

tag: centerid

tag: patid

tag: inflammatory_cells [%]

tag: invasive_tumor_area_size1 [mm]

tag: invasive_tumor_area_size2 [mm]

tag: invasive_tumor_cells [%]

tag: necrotic_cells [%]

tag: normal_epithelial_cells [%]

tag: preneoplastic_tumor_cells [%]

tag: stroma_cells [%]

tag: race

tag: er

value: ER+

tag: pr

value: PR+

tag: arm

value: HER2- CT

tag: treatment

value: neoadjuvant doxorubicin/paclitaxel (AT) followed by cyclophosphamide/methotrexate/fluorouracil (CMF)

tag: age

tag: ecog

value: pre

tag: pcr

value: pCR


title: E14_ES_nt.rep2

description: Gene expression

source_name: E14, no treated, rep 2

tag: cell type


title: BreastCancer_S265

tag: centerid

tag: patid

tag: inflammatory_cells [%]

value: Caucasian

value: RD


title: BreastCancer_S266

tag: invasive_tumor_area_size1 [mm]

tag: invasive_tumor_area_size2 [mm]

tag: invasive_tumor_cells [%]

value: ER-

value: PR-


title: BreastCancer_S262

tag: necrotic_cells [%]

tag: normal_epithelial_cells [%]

tag: preneoplastic_tumor_cells [%]

value: post


title: BreastCancer_S269

tag: race

tag: er


title: BreastCancer_S263

tag: stroma_cells [%]

tag: pr

tag: arm


title: BreastCancer_S261

tag: treatment

tag: age

tag: ecog


title: BreastCancer_S257

tag: centerid

tag: pcr


title: BreastCancer_S256

tag: patid

tag: inflammatory_cells [%]


title: BreastCancer_S259

tag: invasive_tumor_area_size1 [mm]

tag: invasive_tumor_area_size2 [mm]

value: yes


title: BreastCancer_S260

tag: invasive_tumor_cells [%]

tag: necrotic_cells [%]


title: BreastCancer_S268

value: HER2+ CT H

value: neoadjuvant doxorubicin/paclitaxel (AT) followed by cyclophosphamide/methotrexate/fluorouracil (CMF) + Trastuzumab for 1 year


title: BreastCancer_S254

tag: normal_epithelial_cells [%]

tag: preneoplastic_tumor_cells [%]


title: BreastCancer_S247

tag: race

tag: er


title: BreastCancer_S251

tag: stroma_cells [%]

tag: pr


title: BreastCancer_S258

tag: arm

tag: treatment


title: BreastCancer_S248

tag: age

tag: ecog


title: BreastCancer_S250

tag: centerid

tag: pcr


title: BreastCancer_S253

tag: patid

tag: inflammatory_cells [%]


title: BreastCancer_S231

tag: invasive_tumor_area_size1 [mm]

tag: invasive_tumor_area_size2 [mm]

value: HER2+ CT


title: BreastCancer_S234

tag: invasive_tumor_cells [%]

tag: necrotic_cells [%]


title: BreastCancer_S245

tag: normal_epithelial_cells [%]

tag: preneoplastic_tumor_cells [%]

value: no


title: BreastCancer_S246

tag: race

tag: er


title: BreastCancer_S237

tag: stroma_cells [%]

tag: pr


title: BreastCancer_S252

tag: arm

tag: treatment


title: BreastCancer_S244

tag: age

tag: ecog


title: BreastCancer_S226

tag: centerid

tag: pcr


title: BreastCancer_S221

tag: patid

tag: inflammatory_cells [%]


title: BreastCancer_S235

tag: invasive_tumor_area_size1 [mm]

tag: invasive_tumor_area_size2 [mm]


title: BreastCancer_S218

tag: invasive_tumor_cells [%]

tag: necrotic_cells [%]


title: BreastCancer_S230

tag: normal_epithelial_cells [%]

tag: preneoplastic_tumor_cells [%]


title: BreastCancer_S212

tag: race

tag: er


title: BreastCancer_S215

tag: stroma_cells [%]

tag: pr


title: BreastCancer_S232

tag: arm

tag: treatment


title: BreastCancer_S211

tag: age

tag: ecog


title: BreastCancer_S219

tag: centerid

tag: pcr


title: BreastCancer_S233

tag: patid

tag: inflammatory_cells [%]


title: BreastCancer_S203

tag: invasive_tumor_area_size1 [mm]

tag: invasive_tumor_area_size2 [mm]


title: BreastCancer_S207

tag: invasive_tumor_cells [%]

tag: necrotic_cells [%]


title: BreastCancer_S210

tag: normal_epithelial_cells [%]

tag: preneoplastic_tumor_cells [%]


title: BreastCancer_S205

tag: race

tag: er


title: BreastCancer_S193

tag: stroma_cells [%]

tag: pr


title: BreastCancer_S184

tag: arm

tag: treatment


title: BreastCancer_S208

tag: age

tag: ecog


title: BreastCancer_S185

tag: centerid

tag: pcr


title: BreastCancer_S241

tag: patid

tag: inflammatory_cells [%]


title: BreastCancer_S183

tag: invasive_tumor_area_size1 [mm]

tag: invasive_tumor_area_size2 [mm]


title: BreastCancer_S182

tag: invasive_tumor_cells [%]

tag: necrotic_cells [%]

value: Oriental


title: BreastCancer_S192

tag: normal_epithelial_cells [%]

tag: preneoplastic_tumor_cells [%]


title: BreastCancer_S178

tag: race

tag: er


title: BreastCancer_S156

tag: stroma_cells [%]

tag: pr


title: BreastCancer_S174

tag: arm

tag: treatment


title: BreastCancer_S175

value: ER+

tag: age

tag: ecog


title: BreastCancer_S167

tag: centerid

tag: pcr


title: BreastCancer_S179

tag: patid

tag: inflammatory_cells [%]

value: PR+


title: BreastCancer_S151

tag: invasive_tumor_area_size1 [mm]

tag: invasive_tumor_area_size2 [mm]

value: HER2- CT


title: BreastCancer_S152

tag: invasive_tumor_cells [%]

tag: necrotic_cells [%]

value: neoadjuvant doxorubicin/paclitaxel (AT) followed by cyclophosphamide/methotrexate/fluorouracil (CMF)


title: BreastCancer_S180

tag: normal_epithelial_cells [%]

tag: preneoplastic_tumor_cells [%]


title: BreastCancer_S139

tag: race

tag: er


title: BreastCancer_S153

tag: stroma_cells [%]

tag: pr

value: pre


title: BreastCancer_S170

tag: arm

tag: treatment

value: pCR


title: BreastCancer_S118

value: Caucasian

tag: age

tag: ecog


title: BreastCancer_S127

tag: centerid

tag: pcr


title: BreastCancer_S146

tag: patid

tag: inflammatory_cells [%]

value: RD


title: BreastCancer_S161

tag: invasive_tumor_area_size1 [mm]

tag: invasive_tumor_area_size2 [mm]

value: Black

value: ER-


title: BreastCancer_S149

tag: invasive_tumor_cells [%]

tag: necrotic_cells [%]

value: PR-


title: BreastCancer_S135

tag: normal_epithelial_cells [%]

tag: preneoplastic_tumor_cells [%]

value: yes

value: post


title: BreastCancer_S173

tag: race

tag: er


title: BreastCancer_S133

tag: stroma_cells [%]

tag: pr


title: BreastCancer_S166

tag: arm

value: HER2+ CT H

tag: treatment

value: neoadjuvant doxorubicin/paclitaxel (AT) followed by cyclophosphamide/methotrexate/fluorouracil (CMF) + Trastuzumab for 1 year


title: BreastCancer_S116

tag: age

tag: ecog


title: BreastCancer_S138

tag: centerid

value: no

tag: pcr


title: BreastCancer_S121

tag: patid

tag: inflammatory_cells [%]


title: BreastCancer_S130

tag: invasive_tumor_area_size1 [mm]

tag: invasive_tumor_area_size2 [mm]

value: HER2+ CT


title: BreastCancer_S129

tag: invasive_tumor_cells [%]

tag: necrotic_cells [%]

value: ER+


title: BreastCancer_S126

tag: normal_epithelial_cells [%]

tag: preneoplastic_tumor_cells [%]

value: PR+


title: BreastCancer_S120

tag: race

tag: er


title: BreastCancer_S117

tag: stroma_cells [%]

tag: pr


title: BreastCancer_S114

tag: arm

tag: treatment


title: BreastCancer_S109

tag: age

tag: ecog


title: BreastCancer_S115

tag: centerid

value: HER2- CT

tag: pcr


title: BreastCancer_S097

tag: patid

tag: inflammatory_cells [%]


title: BreastCancer_S108

tag: invasive_tumor_area_size1 [mm]

tag: invasive_tumor_area_size2 [mm]

value: neoadjuvant doxorubicin/paclitaxel (AT) followed by cyclophosphamide/methotrexate/fluorouracil (CMF)


title: BreastCancer_S113

tag: invasive_tumor_cells [%]

tag: necrotic_cells [%]


title: BreastCancer_S107

tag: normal_epithelial_cells [%]

tag: preneoplastic_tumor_cells [%]

value: pre


title: BreastCancer_S101

tag: race

tag: er


title: BreastCancer_S099

tag: stroma_cells [%]

tag: pr


title: BreastCancer_S088

tag: arm

tag: treatment


title: BreastCancer_S094

tag: age

tag: ecog


title: BreastCancer_S112

tag: centerid

tag: pcr

value: pCR


title: BreastCancer_S095

tag: patid

tag: inflammatory_cells [%]

value: Caucasian


title: BreastCancer_S069

tag: invasive_tumor_area_size1 [mm]

tag: invasive_tumor_area_size2 [mm]

value: RD


title: BreastCancer_S076

tag: invasive_tumor_cells [%]

tag: necrotic_cells [%]


title: BreastCancer_S080

tag: normal_epithelial_cells [%]

tag: preneoplastic_tumor_cells [%]


title: BreastCancer_S086

tag: race

tag: er


title: BreastCancer_S075

tag: stroma_cells [%]

tag: pr


title: BreastCancer_S067

tag: arm

tag: treatment


title: BreastCancer_S106

tag: age

tag: ecog


title: BreastCancer_S082

tag: centerid

tag: pcr


title: BreastCancer_S078

tag: patid

tag: inflammatory_cells [%]


title: BreastCancer_S087

tag: invasive_tumor_area_size1 [mm]

tag: invasive_tumor_area_size2 [mm]


title: BreastCancer_S060

tag: invasive_tumor_cells [%]

tag: necrotic_cells [%]


title: BreastCancer_S063

tag: normal_epithelial_cells [%]

tag: preneoplastic_tumor_cells [%]


title: BreastCancer_S058

tag: race

tag: er


title: BreastCancer_S070

tag: stroma_cells [%]

tag: pr


title: BreastCancer_S066

tag: arm

tag: treatment


title: BreastCancer_S057

tag: age

tag: ecog


title: BreastCancer_S054

tag: centerid

tag: pcr


title: BreastCancer_S090

tag: patid

tag: inflammatory_cells [%]


title: BreastCancer_S062

tag: invasive_tumor_area_size1 [mm]

tag: invasive_tumor_area_size2 [mm]


title: BreastCancer_S055

tag: invasive_tumor_cells [%]

tag: necrotic_cells [%]


title: BreastCancer_S053

tag: normal_epithelial_cells [%]

tag: preneoplastic_tumor_cells [%]


title: BreastCancer_S050

tag: race

tag: er


title: BreastCancer_S048

tag: stroma_cells [%]

tag: pr


title: BreastCancer_S047

tag: arm

tag: treatment


title: BreastCancer_S042

tag: age

tag: ecog


title: BreastCancer_S049

tag: centerid

tag: pcr


title: BreastCancer_S039

tag: patid

tag: inflammatory_cells [%]


title: BreastCancer_S040

tag: invasive_tumor_area_size1 [mm]

tag: invasive_tumor_area_size2 [mm]


title: BreastCancer_S043

tag: invasive_tumor_cells [%]

tag: necrotic_cells [%]


title: BreastCancer_S045

tag: normal_epithelial_cells [%]

tag: preneoplastic_tumor_cells [%]


title: BreastCancer_S033

tag: race

tag: er


title: BreastCancer_S032

tag: stroma_cells [%]

tag: pr


title: BreastCancer_S037

tag: arm

tag: treatment


title: BreastCancer_S031

tag: age

tag: ecog


title: BreastCancer_S036

tag: centerid

tag: pcr


title: BreastCancer_S035

tag: patid

tag: inflammatory_cells [%]


title: BreastCancer_S038

tag: invasive_tumor_area_size1 [mm]

tag: invasive_tumor_area_size2 [mm]


title: BreastCancer_S026

tag: invasive_tumor_cells [%]

tag: necrotic_cells [%]


title: BreastCancer_S030

tag: normal_epithelial_cells [%]

tag: preneoplastic_tumor_cells [%]


title: BreastCancer_S027

tag: race

tag: er


title: BreastCancer_S022

tag: stroma_cells [%]

tag: pr


title: BreastCancer_S021

tag: arm

tag: treatment


title: BreastCancer_S020

tag: age

tag: ecog


title: BreastCancer_S024

tag: centerid

tag: pcr


title: BreastCancer_S046

tag: patid

tag: inflammatory_cells [%]


title: BreastCancer_S023

tag: invasive_tumor_area_size1 [mm]

tag: invasive_tumor_area_size2 [mm]


title: BreastCancer_S016

tag: invasive_tumor_cells [%]

tag: necrotic_cells [%]


title: BreastCancer_S014

tag: normal_epithelial_cells [%]

tag: preneoplastic_tumor_cells [%]


title: BreastCancer_S025

tag: race

tag: er


title: BreastCancer_S018

tag: stroma_cells [%]

tag: pr


title: BreastCancer_S019

tag: arm

tag: treatment


title: BreastCancer_S017

tag: age

tag: ecog


title: BreastCancer_S012

tag: centerid

tag: pcr


title: BreastCancer_S010

tag: patid

tag: inflammatory_cells [%]


title: BreastCancer_S008

tag: invasive_tumor_area_size1 [mm]

tag: invasive_tumor_area_size2 [mm]


title: BreastCancer_S003

tag: invasive_tumor_cells [%]

tag: necrotic_cells [%]


title: BreastCancer_S011

tag: normal_epithelial_cells [%]

tag: preneoplastic_tumor_cells [%]