title: S2_tandem_Trp_Fl_10_R5

data_processing:
Raw sequence files were preprocessed using Trimmomatic (Bolger et al. 2014) to remove Illumina adaptor sequences, remove low-quality reads and trim low-quality bases.
The trimmed reads were then aligned using QuasR (using Bowtie as an aligner) (Gaidatzis et al. 2014; Langmead et al. 2009) against a bisulfite index.
Context-independent cytosine methylation call was performed using QuasR.
Custom R functions were developed to determine context-dependent (CG, GC) average methylation.
Genome_build: Release 5 (dm3)
Supplementary_files_format_and_content: genome_wide_methylation_average_dm3.txt: Tab-delimited text file providing single C methylation genome wide for S2 and OSC replicates.

source_name: S2, flavopiridol inhibition

growth_protocol: Schneider S2 cells were grown at 25 degrees in Schneider's Drosophila medium (LifeTech: 21720-001) supplemented with 10% FBS. OSC cells were grown at 25 degrees in Shields and Sang M3 Insect Medium (Sigma, S8398) supplemented with 1% insulin, 1% glutathione, 10% heat-inactivated FBS, and 10% Fly Extract.

extract_protocol:
Footprinting protocol was adapted from (Bell et al. 2010; Kelly et al. 2012). 2.5 10^6 Drosophila cells (S2 or OSC) were resuspended in ice-cold lysis buffer (10mM Tris, 10mM NaCl, 3mM Mgcl2, 0.1mM EDTA, 0.5% NP40), incubated 10 min on ice, spun down. Nuclei were washed (10mM Tris, 10mM NaCl, 3mM Mgcl2, 0.1mM EDTA) and resuspended in McviPI reaction buffer (NEB). The nuclei were then incubated with 200U of McviPI (NEB-M0227L) at 30°C for 7.5 min (in presence of 0.6mM SAM, and 300mM Sucrose). The reaction was resuplemented with 100U of McviPI and 128 pmol of SAM before a second incubation round of 30°C for 7.5 min. 10mM MgCl2, 128pmol of SAM and 60U of SssI were added for a third incubation round of 30°C for 7.5 min. Reaction was stopped by adding a SDS-containing buffer (20mM Tris, 600mM NaCl, 1%SDS 10mM EDTA), DNA was extracted after overnight Proteinase K (200 µg/ml) digestion at 55°C. For single treatments, only one of the enzymes was used in the same conditions.
Whole-genome bisulfite libraries were prepared using Illumina TruSeq DNA sample preparation kit following manufacturer recommendation. 5g of sheared DNA (Covaris) was used as an input for end-repair and A-tailing. Methylated adaptors were ligated and large DNA fragments (400-600bp) were selected on a low melting agarose gel (BIO-RAD -161-3107). The extracted material was used as an input for bisulfite conversion (Qiagen - 59104). The converted DNA was amplified by 10 cycles of PCR using Pfu Cx HotStart (Agilent - 600410) using Illumina primers. PCR product was purified using AMPureXP beads (Beckman Coulter - A63880) and controlled on Bioanalyser High sensitivity (Agilent 5067-4626). The samples were run on an Illumina HiSeq 2500 generating 150bp paired-end reads. Amplicon bisulfite sequencing was performed as previously described (Baubec et al. 2015). Bisulfite amplicons libraries were prepared using NEBNext ChIP kit and sequenced on a MiSeq instrument generating 250bp paired-end reads.

value: flavopiridol inhibition

tag: footprint conditions

value: McviPI and SssI footprint

value: amplicon bisulfite sequencing


title: Tumor at diagnosis. Patient p54

status: Public on Aug 21 2017

type: SRA

city: Vienna

first: Fikret

last: Rifatbegovic

address: Zimmermannplatz 10

department: Tumor biology

country: Austria

institute: Children's Cancer Research Institute

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
T54d

library_source: transcriptomic

data_processing:
RNA-seq reads were mapped with GSNAP v2014-12- 28 [20147302] (“-- maxsearch=100 -- npaths=1 -- max-mismatches=1 --novelsplicing=0 “) to human reference genome build GRCh37. Known SNPs and splice sites were extracted from dbSNP build 138 and Ensembl GRCh37 build 75, respectively.
DESeq2-normalized fragments per million (FPM), log2 scale
Genome_build: hg19
Supplementary_files_format_and_content: DESeq expression matrix (log2)

molecule: total RNA

organism: Homo sapiens

source_name: Tumor

extract_protocol:
miRNeasy Micro Kit
30 ng of total RNA was used for cDNA synthesis following the NEBNext® UltraT RNA Library Prep Kit for Illumina® protocol (New England BioLabs). From the point when cDNA was synthesized, the library was completed in an automated way at the EMBL Genomics Core Facility (Heidelberg, Germany) following the manufacture's protocol.

tag: cell type

value: Tumor cells from the primary tumor


title: OSC_tandem_R2_1

status: Public on Jun 23 2017

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

description: Processed data file: genome_wide_methylation_average_dm3.txt.gz

library_source: genomic

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: OSC, untreated

treatment_protocol: Transcription inhibition was performed as previously described (Henriques et al. 2013). Triptolide and/or flavopiridol were added at a final concentration of 10uM(BM to the culture media for the indicated time (0, 2.5, 5, 10, 20, 40 minutes). Heat shock was performed in S2 cells as previously described (Wirbelauer  et al. 2005). Temperature was quickly raised by mixing equivalent amount of cell containing medium at 25C(BC with pre-warmed medium (BC). The mix was incubated for 1 min at 37C(BC. After heat shock (HS), cells were let to recover for 5 min.Transcription inhibition (Trp, Fl) inhibition was performed 2.5 minutes prior heat-shock.

tag: cell line

value: OSC (Ovarian Somatic Cells)

tag: treatment

tag: sample type

value: whole-genome bisulfite sequencing


title: OSC_tandem_R2_2


title: S2_scRNA_Trp_5_R1

description:
nascent RNA
short RNA sequencing

data_processing:
After alignment against drosophila and mouse genomes (see above for details). Reads were counted in a window around TSSs [-100:200] using the qCount function of QuasR (Gaidatzis et al., 2014). To reduce potential contamination with full-length transcripts we used the second read from the pair representing the 3’ of the transcript for counting. Pairs having insert length>180bp were excluded.  We used the mouse spike-ins to perform inter-sample normalization and enable quantification of the global effects expected to occur upon inhibition of transcription. Under the Assumption that read counts from the mouse should be constant across samples; reads counts from each fly sample were normalized by the sum of the reads detected at mouse promoters within the same sample. Abundance of scRNA at each time-point was calculated relative to the respective amount before inhibition. This relative level was calculated for each replicate separately to correct for batch variations.
Genome_build: Dm3
Supplementary_files_format_and_content: bigwig files

source_name: S2 - Schneider cells

growth_protocol: Schneider S2 cells were grown at 25 degrees in Schneider’s Drosophila medium (LifeTech:21720-001) supplemented with 10%FBS. OSC cells were grown at 25 degrees in Shields and Sang M3 Insect Medium (Sigma, S8398) supplemented with 1% insulin, 1% glutathione, 10% heat-inactivated FBS, and 10% Fly Extract.

extract_protocol: scRNA protocol was adapted fron Nechaev et al, Science 2010.For each condition 20 10^6 of Triptolide treated drosophila cells were spiked with 2 10^6 untreated mouse embryonic stem cells. scRNA protocol was adapted from (Nechaev et al., 2010). Cells were re-suspended in ice-cold lysis buffer (10mM Tris (pH=7.4), 10mM NaCl, 3mM Mgcl2, 0.1mM EDTA, 0.5% NP40), incubated 10min on ice, span down. Nuclei were washed with ice cold (10mM Tris (pH=7.4), 10mM NaCl, 3mM Mgcl2, 0.1mM EDTA) and nuclear pellets were dissolved in Trizol (Thermofisher). RNA was size selected (17-200bp) using a two-step column purification strategy (RNA clean and concentrator, Zymo-R1016). 10μg of purified RNA was successively treated by 5’ dephosphorylation  - 20U at 37°C for 30min (Epicentre - RP8092H); 5’ terminator exonuclease - 1U in Buffer A at 30°C for 60min (Epicentre - TER51020); cap-clip decapping enzyme – 5U  at 37°C for 90min. After each reaction, short RNA was column purified (RNA clean and concentrator, Zymo-R1016). The resulting RNA was used for library preparation using TruSeq small RNA library  (Illumina). Libraries were purified on 6% TBE gels (150-300bp – Novex - EC6265BOX). Size distribution of the libraries were controlled on Bioanalyser High sensitivity (Agilent 5067-4626). Two biologically independent inhibition time courses were performed. The samples were run on an Illumina NextSeq generating 38bp paired-end reads.

value: S2 (Schneider cells)

value: short RNA sequencing

value: Triptolide inhibition


title: Tumor at diagnosis. Patient p50

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
T50d


title: S2_tandem_Trp_Fl_10_R4


title: S2_tandem_Trp_Fl_10_R3


title: OSC_tandem_R1_2


title: OSC_tandem_R1_1


title: S2_tandem_R2_2

source_name: S2, untreated


title: Tumor at diagnosis. Patient p02

description:
mRNA profiles of a Ewings Sarcoma cellline (clone of A673 with inducible sh EWS-FLI1 knockdown) treated with control sponge
T02d


title: S2_tandem_Trp_10_R4

source_name: S2, triptolide inhibition

value: triptolide inhibition


title: S2_tandem_R2_1


title: S2_tandem_Trp_10_R5


title: S2_tandem_Trp_10_R3


title: S2_tandem_R1_2


title: S2_tandem_C_R3


title: Subject_262: CALGB1061075-1_D-11

status: Public on Oct 16 2018

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

country: USA

institute: University of North Carolina at Chapel Hill

description: Fresh-frozen RNA was isolated with Qiagen RNAeasy kit. Illumina TruSeq RNA Sample Preparation Kit (RS-122-2001 or RS-122-2002)

data_processing:
Basecalls by Casava
Alignment by MapSplice2
Genome to transcriptome coordiantes by UBU (https://github.com/mozack/ubu/wiki)
Gene expression estimates by RSEM using Sept 2011 UCSC knownGene transcript definitions
More information on the pipeline can be found here: https://webshare.bioinf.unc.edu/public/mRNAseq_TCGA/
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited matrix of gene level count estimates
Purity-filtered reads were aligned to the human reference GRCh38/hg38 genome using Spliced Transcripts Aligned to a Reference (STAR) version 2.4.2a
Transcript (GENCODE v22) abundance estimates were generated by Salmon version 0.6.030 in ‘-quant’ mode, based on the STAR alignments
Fixed upper quartile normalization
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: tab-delimited, normalized, transcript abundance estimates

molecule: polyA RNA

source_name: Breast

tag: tissue

value: breast cancer


title: Subject_213: CALGB1052578-1_H28

extract_protocol: Fresh-frozen RNA was isolated with Qiagen RNAeasy kit. Illumina TruSeq RNA Sample Preparation Kit (RS-122-2001 or RS-122-2002)


title: S2_tandem_HS_Fl_R3

source_name: S2, flavopiridol inhibition and heat shock

value: flavopiridol inhibition and heat shock


title: S2_SssI_R1

value: SssI footprint


title: S2_tandem_HS_Fl_R2


title: S2_tandem_HS_Fl_R1


title: S2_tandem_R1_1


title: S2_tandem_HS_Trp_R5

source_name: S2, triptolide inhibition and heat shock

value: triptolide inhibition and heat shock


title: S2_McviPI_R1

value: McviPI footprint


title: S2_tandem_HS_Trp_R4


title: S2_scRNA_Trp_2_R1

description:
nascent RNA
short RNA sequencing


title: S2_tandem_HS_R4

source_name: S2, heat shock

value: heat shock


title: S2_tandem_HS_Trp_R3


title: S2_tandem_HS_Trp_Fl_R2

source_name: S2, triptolide and flavopiridol inhibition and heat shock


title: S2_tandem_HS_Trp_R2


title: S2_tandem_HS_R5


title: S2_tandem_Trp_R2


title: S2_tandem_C_R2


title: S2_tandem_HS_R2


title: S2_tandem_C_R1


title: S2_tandem_Trp_Fl_2_R2

source_name: S2, triptolide and flavopiridol inhibition

value: triptolide and flavopiridol inhibition


title: S2_tandem_Trp_Fl_10_R2


title: S2_tandem_HS_R1


title: S2_tandem_Trp_Fl_0_R2


title: S2_tandem_Trp_Fl_20_R1


title: S2_tandem_Trp_Fl_5_R2


title: S2_tandem_Trp_Fl_20_R2


title: S2_tandem_Trp_Fl_10_R1


title: S2_tandem_Trp_Fl_5_R1


title: S2_tandem_Trp_R1


title: S2_tandem_Trp_Fl_0_R1


title: S2_tandem_Fl_20_R2

value: flavopiridol inhibition


title: S2_tandem_Fl_40_R2

value: McviPI and SssI footprint


title: S2_tandem_HS_R3

value: amplicon bisulfite sequencing


title: S2_tandem_Fl_30_R2


title: S2_tandem_Fl_0_R2


title: S2_tandem_Fl_10_R2


title: S2_tandem_Trp_20_R1


title: S2_tandem_Trp_10_R1


title: S2_tandem_HS_Trp_Fl_R1

value: triptolide and flavopiridol inhibition and heat shock


title: S2_tandem_HS_Trp_R1


title: S2_tandem_Trp_0_R1


title: S2_tandem_Trp_5_R1


title: S2_tandem_Fl_40_R1


title: S2_tandem_Fl_20_R1


title: S2_tandem_Trp_2_R1


title: S2_tandem_Fl_30_R1


title: S2_tandem_Trp_Fl_2_R1


title: S2_tandem_Fl_0_R1


title: S2_tandem_Fl_10_R1


title: S2_tandem_Trp_20_R2


title: S2_tandem_Trp_0_R2


title: S2_tandem_Trp_5_R2


title: S2_tandem_Trp_2_R2


title: S2_tandem_Trp_10_R2


title: NBPAT38

status: Public on Mar 15 2017

type: RNA

city: Moscow

first: Maria

middle: Vladimirovna

last: Suntsova

address: Miklukho-Maklaya, 16/10

department: Department of Genetics and Postgenomic Technologies

country: Russia

institute: M.M. Shemyakin and Yu.A. Ovchinnikov  Institute of  bioorganic chemistry of the Russian Academy of Sciences

description:
patient #38
SAMPLE 32

hyb_protocol: Hybridization was performed according to CustomArray ElectraSense™ Hybridization and Detection protocol. Hybridization mix contained 2.5 ug of labeleled DNA library, 6X SSPE, 0.05% Tween-20, 20mM EDTA, 5x Denhardt solution, 100 ng/ul sonicated calf thymus gDNA, 0,05% SDS. Hybridization mix was incubated with chip overnight at 50ºC.

scan_protocol: Hybridization efficiency was detected electrochemically using CustomArray ElectraSense™ Detection Kit and ElectraSense™ 4X2K/12K Reader.

data_processing: Data was quantile normalized using R statistical programming language and 'preprocessCore' library

label: biotin

source_name: Neuroblastoma

label_protocol: Complete Whole Transcriptome Amplification WTA2 Kit  (Sigma) was used for reverse transcription and library amplification. Manufacturers protocol was modified by adding to amplification reaction dNTP mix containing biotinylated dUTP, resulting to final proportion dTTP/biotin-dUTP as 5/1.

extract_protocol: Total  RNA was extracted with Magnetic Beads Total Nucleic Acid Isolation Kit for FFPE (Sileks, Russia) according to manufacturer instruction. RNA was quantified using Nanodrop.

tag: tumor localisation

value: Right adrenal gland


title: NBPAT37

description:
patient #37
SAMPLE 31

value: left side of retroperitoneum


title: NBPAT7

description:
patient #7
SAMPLE 39

value: Unknown


title: NBPAT39

description:
patient #39
SAMPLE 33

value: abdominal region


title: NBPAT6

description:
patient #6
SAMPLE 38

value: retroperitoneum


title: NBPAT5

description:
patient #5
SAMPLE 37


title: NBPAT41

description:
patient #41
SAMPLE 36


title: NBPAT36

description:
patient #36
SAMPLE 30

value: Left adrenal gland


title: NBPAT33

description:
patient #33
SAMPLE 27


title: NBPAT40

description:
patient #40
SAMPLE 35


title: NBPAT35

description:
patient #35
SAMPLE 29


title: NBPAT27

description:
patient #27
SAMPLE 20


title: NBPAT28

description:
patient #28
SAMPLE 21

value: Liver


title: NBPAT3

description:
patient #3
SAMPLE 23

value: metastasis in lymphatic node


title: NBPAT34

description:
patient #34
SAMPLE 28


title: NBPAT29

description:
patient #29
SAMPLE 22


title: NBPAT30

description:
patient #30
SAMPLE 24

value: Metastasis in lymphatic node


title: NBPAT4

description:
patient #4
SAMPLE 34

value: right side of retroperitoneum


title: NBPAT8

description:
patient #8
SAMPLE 40


title: NBPAT9

description:
patient #9
SAMPLE 41


title: NBPAT31

description:
patient #31
SAMPLE 25

value: right-side of retroperitoneum


title: NBPAT32

description:
patient #32
SAMPLE 26


title: NBPAT23

description:
patient #23
SAMPLE 16


title: NBPAT20

description:
patient #20
SAMPLE 13


title: NBPAT22

description:
patient #22
SAMPLE 15


title: NBPAT21

description:
patient #21
SAMPLE 14

value: left-side of retroperitoneum


title: NBPAT26

description:
patient #26
SAMPLE 19


title: NBPAT25

description:
patient #25
SAMPLE 18

value: left side of hemithorax


title: NBPAT24

description:
patient #24
SAMPLE 17

value: metastasis in liver


title: NBPAT17

description:
patient #17
SAMPLE 9


title: NBPAT2

description:
patient #2
SAMPLE 12


title: NBPAT15

description:
patient #15
SAMPLE 7


title: NBPAT14

description:
patient #14
SAMPLE 6

value: right-side of abdominal cavity


title: NBPAT16

description:
patient #16
SAMPLE 8


title: NBPAT12

description:
patient #12
SAMPLE 4


title: NBPAT11

description:
patient #11
SAMPLE 3

value: Adrenal gland


title: NBPAT19

description:
patient #19
SAMPLE 11

value: metastasis in retroperitoneum, primary tumour originated in adrenal gland


title: NBPAT1

description:
patient #1
SAMPLE 1


title: NeuCrest3

status: Public on Mar 08 2017

description: SAMPLE 3

data_processing: The data were normalized using quantile normalization in R.

source_name: Embryonic adrenal glands

tag: individual

value: fetus 3

value: embryonic adrenal glands

value: embryonic neural crest cells


title: NBPAT13

description:
patient #13
SAMPLE 5


title: NeuCrest4

description: SAMPLE 4

value: fetus 4


title: NeuCrest1

description: SAMPLE 1

value: fetus 1


title: Norm 3_12_2

description: SAMPLE 5

source_name: Adrenal cortex

value: Patient #3

value: Adrenal cortex


title: Norm 3_12_1

description: SAMPLE 4


title: Norm 2_12

description: SAMPLE 2

value: Patient #2


title: Norm 2_13

description: SAMPLE 3

source_name: Adrenal marrow

value: Adrenal marrow


title: Norm 3_13_2

description: SAMPLE 7


title: Single neuron 20

status: Public on May 26 2016

city: Shanghai

first: Kunshan

last: Zhang

address: 389 Xincun Road

department: Stem cell Translational Research center

country: China

institute: Tongji Hospital, Tongji University

description:
Sample name: cell_20
Patch-seq
Processed data file: single_neuron_exp.txt

data_processing:
Clean reads were aligned to hg19 with TopHat2 (Kim et al., 2013).
Gene expression levels were estimated by Cufflinks (Ghosh and Chan, 2016).
Genome DNA sequence and gene annotation were downloaded from iGenome (ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Homo_sapiens/UCSC/hg19/Homo_sapiens_UCSC_hg19.tar.gz).
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: single_neuron_exp.txt: Tab-delimited text file contains gene expression level of each single neuron (FPKM).

source_name: hES/hiPS-derived neuron

growth_protocol: hiPSCs and hESCs were differentiated into functional neurons following a modified version of published step-wise differentiation protocol(s). hESC- as well as hiPSC-derived neural stem/progenitor cell (NSC/NPC) colonies formed rosettes and expressed neural precursor markers Nestin and Sox2. Rapid conversion of hESC and hiPSC into functional induced neuronal (iN) cells could be achieved in less than two weeks by overexpression of exogenous Ngn2 or ASCL1/DLX2. The efficiencies of NPC differentiation into Tuj1-positive neurons were similar amongst all lines and were consistently close to 90% from culture to culture. Upon co-culture with mouse astrocytes, hESC/iPSC-derived neurons expressed mature neuronal markers.

extract_protocol:
After recording, the wider tip of another pipette filled with no more than 0.5 µL sterilized cell harvest solution containing (in mmol/L) 144 K-gluconate, 3 MgCl2, 0.5 EGTA and 10 HEPES (pH 7.20 and 295 mOsm/kg) was gently attached to the recorded cell, then a light suction (negative pressure) was applied, through a glass syringe (Thomas Scientific) connected to the pipette. The suction lasted until the entire cell entered the tip of the pipette. The moment the complete cell had been visually located inside the tip, the pipette was quickly removed from the bath. Content of the harvest pipette was expelled into a 0.2 mL PCR tube containing 4.5-µL pre-prepared lysis buffer.
Preparation of single-cell cDNAs was performed based on previously published protocols with modifications at several steps.

value: hES/hiPS-derived neuron


title: Single neuron 17

description:
Sample name: cell_17
Patch-seq
Processed data file: single_neuron_exp.txt


title: Neuroblastoma cell line STA-NB-15 (replacement BAM)

status: Public on Jan 09 2017

description: mRNA profiles of the corresponding sample

source_name: Primary neuroblastoma cell line established at the Children's Cancer Research Institute

growth_protocol: See SAMPLES section

extract_protocol:
miRNeasy Micro Kit
RNA-Seq, New England Biolab kit with polyA enrichment

treatment_protocol: No treatment

tag: growth

value: grown in MEMa


title: Neuroblastoma cell line STA-NB-7 (replacement BAM)


title: Neuroblastoma cell line STA-NB-6 (3) (replacement BAM)


title: NeuCrest2

description: SAMPLE 2

value: fetus 2


title: Single neuron 18

description:
Sample name: cell_18
Patch-seq
Processed data file: single_neuron_exp.txt


title: Norm 1_14

description: SAMPLE 1

value: Patient #1


title: NBPAT10

description:
patient #10
SAMPLE 2

value: postmediastinum


title: Single neuron 15

description:
Sample name: cell_15
Patch-seq
Processed data file: single_neuron_exp.txt


title: NBPAT18

description:
patient #18
SAMPLE 10

value: left-side of retroperitoneum


title: Single neuron 16

description:
Sample name: cell_16
Patch-seq
Processed data file: single_neuron_exp.txt


title: Norm 3_13_1

description: SAMPLE 6


title: Single neuron 13

description:
Sample name: cell_13
Patch-seq
Processed data file: single_neuron_exp.txt


title: Single neuron 14

description:
Sample name: cell_14
Patch-seq
Processed data file: single_neuron_exp.txt


title: Single neuron 12

description:
Sample name: cell_12
Patch-seq
Processed data file: single_neuron_exp.txt


title: Single neuron 19

description:
Sample name: cell_19
Patch-seq
Processed data file: single_neuron_exp.txt


title: Single neuron 10

description:
Sample name: cell_10
Patch-seq
Processed data file: single_neuron_exp.txt


title: Single neuron 11

description:
Sample name: cell_11
Patch-seq
Processed data file: single_neuron_exp.txt


title: Single neuron 8

description:
Sample name: cell_8
Patch-seq
Processed data file: single_neuron_exp.txt


title: Single neuron 9

description:
Sample name: cell_9
Patch-seq
Processed data file: single_neuron_exp.txt


title: Single neuron 5

description:
Sample name: cell_5
Patch-seq
Processed data file: single_neuron_exp.txt


title: Single neuron 6

description:
Sample name: cell_6
Patch-seq
Processed data file: single_neuron_exp.txt


title: Single neuron 4

description:
Sample name: cell_4
Patch-seq
Processed data file: single_neuron_exp.txt


title: 49T: 24 month old tricep muscle rep8

status: Public on May 12 2016

city: Lausanne

first: Jerome

last: Feige

address: EPFL Innovation Park, Building H

department: Musculo-Skeletal Health

institute: Nestle Institute Of Health Sciences

data_processing:
Illumina Casava 1.8 software used for basecalling and demultiplexing.
Sequenced reads were trimmed for adaptor sequence, and mapped to Rnor 6.0 whole genome using RNA-STAR v2.3.0e with parameters --genomeLoad NoSharedMemory --runThreadN 12
Counts within genes were generated using HTSeq, mode union, strand no, annotation file Rattus_norvegicus.Rnor_6.0.80.gtf
Genome_build: RGSC Rnor_6.0
Supplementary_files_format_and_content: tab-delimited text file including counts per gene for each sample quantified by HTSeq

organism: Rattus norvegicus

extract_protocol:
mRNA was extracted using the miRNeasy kit from Qiagen, following the manufacturer's instructions.
TruSeq RNA Library Preparation Kit v2

tag: strain

value: Wistar

tag: gender

value: male

value: tricep muscle

tag: age (months)

tag: animal id


title: 50T: 24 month old tricep muscle rep9


title: 45G: 24 month old gastrocnemius muscle rep5

value: gastrocnemius muscle


title: 45T: 24 month old tricep muscle rep5


title: Single neuron 1

description:
Sample name: cell_1
Patch-seq
Processed data file: single_neuron_exp.txt


title: 46G: 24 month old gastrocnemius muscle rep6


title: Single neuron 2

description:
Sample name: cell_2
Patch-seq
Processed data file: single_neuron_exp.txt


title: 47T: 24 month old tricep muscle rep7


title: 49G: 24 month old gastrocnemius muscle rep8


title: Single neuron 3

description:
Sample name: cell_3
Patch-seq
Processed data file: single_neuron_exp.txt


title: 46T: 24 month old tricep muscle rep6


title: 50G: 24 month old gastrocnemius muscle rep9


title: 44T: 24 month old tricep muscle rep4


title: 42T: 24 month old tricep muscle rep2


title: 44G: 24 month old gastrocnemius muscle rep4


title: 42G: 24 month old gastrocnemius muscle rep2


title: 43G: 24 month old gastrocnemius muscle rep3


title: 43T: 24 month old tricep muscle rep3


title: 41T: 24 month old tricep muscle rep1


title: 41G: 24 month old gastrocnemius muscle rep1


title: 19T: 18 month old tricep muscle rep9


title: 18T: 18 month old tricep muscle rep8


title: 20G: 18 month old gastrocnemius muscle rep10


title: Single neuron 7

description:
Sample name: cell_7
Patch-seq
Processed data file: single_neuron_exp.txt


title: 19G: 18 month old gastrocnemius muscle rep9


title: 47G: 24 month old gastrocnemius muscle rep7


title: 17T: 18 month old tricep muscle rep7


title: 18G: 18 month old gastrocnemius muscle rep8


title: 16T: 18 month old tricep muscle rep6


title: 17G: 18 month old gastrocnemius muscle rep7


title: 14T: 18 month old tricep muscle rep4


title: 15G: 18 month old gastrocnemius muscle rep5


title: 15T: 18 month old tricep muscle rep5


title: 13T: 18 month old tricep muscle rep3


title: 13G: 18 month old gastrocnemius muscle rep3


title: 14G: 18 month old gastrocnemius muscle rep4


title: 16G: 18 month old gastrocnemius muscle rep6


title: 12T: 18 month old tricep muscle rep2


title: 12G: 18 month old gastrocnemius muscle rep2


title: 11G: 18 month old gastrocnemius muscle rep1


title: 11T: 18 month old tricep muscle rep1


title: 20T: 18 month old tricep muscle rep10


title: 08G: 8 month old gastrocnemius muscle rep8


title: 09G: 8 month old gastrocnemius muscle rep9


title: 10T: 8 month old tricep muscle rep10


title: 07T: 8 month old tricep muscle rep7


title: 07G: 8 month old gastrocnemius muscle rep7


title: 09T: 8 month old tricep muscle rep9


title: 10G: 8 month old gastrocnemius muscle rep10


title: 06T: 8 month old tricep muscle rep6


title: 05G: 8 month old gastrocnemius muscle rep5


title: 04T: 8 month old tricep muscle rep4


title: 05T: 8 month old tricep muscle rep5


title: 06G: 8 month old gastrocnemius muscle rep6


title: 02G: 8 month old gastrocnemius muscle rep2


title: 04G: 8 month old gastrocnemius muscle rep4


title: 02T: 8 month old tricep muscle rep2


title: 08T: 8 month old tricep muscle rep8


title: 01T: 8 month old tricep muscle rep1


title: 03T: 8 month old tricep muscle rep3


title: 03G: 8 month old gastrocnemius muscle rep3


title: 01G: 8 month old gastrocnemius muscle rep1


title: EXP-608: Blood_TCGA-AB-2825

status: Public on May 14 2015

city: Rockville

first: Mervi

last: Heiskanen

state: MD

address: 9609 Medical Center Drive, 1W378

department: CBIIT

institute: NCI

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

source_name: Primary Blood Derived Cancer

tag: age

tag: french-american-british classification

tag: Sex

value: FEMALE

tag: organism part

value: Blood

tag: cytogenetic

value: Normal

value: BONE MARROW


title: EXP-608: Blood_TCGA-AB-2908

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

value: MALE


title: EXP-608: Blood_TCGA-AB-2898

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

value: Trisomy 8


title: EXP-608: Blood_TCGA-AB-2823

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


title: EXP-608: Blood_TCGA-AB-2910

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


title: EXP-608: Blood_TCGA-AB-2927


title: EXP-608: Blood_TCGA-AB-2938


title: EXP-608: Blood_TCGA-AB-2983

value: M0 Undifferentiated


title: EXP-608: Blood_TCGA-AB-2966


title: EXP-608: Blood_TCGA-AB-2873


title: EXP-608: Blood_TCGA-AB-2924


title: EXP-608: Blood_TCGA-AB-2947


title: EXP-608: Blood_TCGA-AB-2971


title: EXP-608: Blood_TCGA-AB-2894


title: EXP-608: Blood_TCGA-AB-3000


title: EXP-608: Blood_TCGA-AB-2911

value: Complex (greater than or equal to 3 distinct abnormalities)


title: EXP-608: Blood_TCGA-AB-2915


title: EXP-608: Blood_TCGA-AB-2948


title: EXP-608: Blood_TCGA-AB-2935


title: EXP-608: Blood_TCGA-AB-2870


title: EXP-608: Blood_TCGA-AB-2964


title: EXP-608: Blood_TCGA-AB-2981


title: EXP-608: Blood_TCGA-AB-2901


title: EXP-608: Blood_TCGA-AB-2879


title: EXP-608: Blood_TCGA-AB-2933


title: EXP-608: Blood_TCGA-AB-2950


title: EXP-608: Blood_TCGA-AB-2909

value: Not Classified


title: EXP-608: Blood_TCGA-AB-2965


title: EXP-608: Blood_TCGA-AB-2899


title: EXP-608: Blood_TCGA-AB-2959


title: EXP-608: Blood_TCGA-AB-2878


title: EXP-608: Blood_TCGA-AB-2903


title: EXP-608: Blood_TCGA-AB-2869


title: EXP-608: Blood_TCGA-AB-2954


title: EXP-608: Blood_TCGA-AB-2919


title: EXP-608: Blood_TCGA-AB-2988


title: EXP-608: Blood_TCGA-AB-2867


title: EXP-608: Blood_TCGA-AB-2949


title: EXP-608: Blood_TCGA-AB-2978


title: EXP-608: Blood_TCGA-AB-3006


title: EXP-608: Blood_TCGA-AB-2936


title: EXP-608: Blood_TCGA-AB-2912


title: EXP-608: Blood_TCGA-AB-2887


title: EXP-608: Blood_TCGA-AB-2986


title: EXP-608: Blood_TCGA-AB-2921


title: EXP-608: Blood_TCGA-AB-2995


title: EXP-608: Blood_TCGA-AB-2967


title: EXP-608: Blood_TCGA-AB-2874


title: EXP-608: Blood_TCGA-AB-2982


title: EXP-608: Blood_TCGA-AB-2973


title: EXP-608: Blood_TCGA-AB-2882


title: EXP-608: Blood_TCGA-AB-2956


title: EXP-608: Blood_TCGA-AB-2945


title: EXP-608: Blood_TCGA-AB-2934


title: EXP-608: Blood_TCGA-AB-2889


title: EXP-608: Blood_TCGA-AB-2979


title: EXP-608: Blood_TCGA-AB-2925


title: EXP-608: Blood_TCGA-AB-2913


title: EXP-608: Blood_TCGA-AB-2884


title: EXP-608: Blood_TCGA-AB-2930


title: EXP-608: Blood_TCGA-AB-2939


title: EXP-608: Blood_TCGA-AB-2883


title: EXP-608: Blood_TCGA-AB-2941


title: EXP-608: Blood_TCGA-AB-2955


title: EXP-608: Blood_TCGA-AB-2871


title: EXP-608: Blood_TCGA-AB-2976


title: EXP-608: Blood_TCGA-AB-2969


title: EXP-608: Blood_TCGA-AB-2917


title: EXP-608: Blood_TCGA-AB-2972


title: EXP-608: Blood_TCGA-AB-2892


title: EXP-608: Blood_TCGA-AB-2987


title: EXP-608: Blood_TCGA-AB-2904


title: EXP-608: Blood_TCGA-AB-2872


title: EXP-608: Blood_TCGA-AB-2980


title: EXP-608: Blood_TCGA-AB-2890


title: EXP-608: Blood_TCGA-AB-2937


title: EXP-608: Blood_TCGA-AB-2940


title: EXP-608: Blood_TCGA-AB-2952


title: EXP-608: Blood_TCGA-AB-2975


title: EXP-608: Blood_TCGA-AB-2923


title: EXP-608: Blood_TCGA-AB-2886


title: EXP-608: Blood_TCGA-AB-2942


title: EXP-608: Blood_TCGA-AB-2985


title: EXP-608: Blood_TCGA-AB-2984


title: EXP-608: Blood_TCGA-AB-2897


title: EXP-608: Blood_TCGA-AB-2896


title: EXP-608: Blood_TCGA-AB-2970


title: EXP-608: Blood_TCGA-AB-2891


title: EXP-608: Blood_TCGA-AB-2900


title: EXP-608: Blood_TCGA-AB-2885


title: EXP-608: Blood_TCGA-AB-2998


title: EXP-608: Blood_TCGA-AB-2996


title: EXP-608: Blood_TCGA-AB-2928


title: BenSer1

status: Public on Apr 10 2015

city: Camperdown

first: Jeff

last: Holst

state: NSW

address: Building 93, Royal Prince Alfred Hospital, Missenden Rd

country: Australia

institute: Centenary Institute

data_processing:
Paired-end RNA-sequencing reads were trimmed and mapped to annotated human genome (hg19/GRCh37.p13) using Tophat2 with default settings.
For each gene, the number of reads were counted and normalized to the library size.
The threshold for expression was set at 5 reads in at least one experimental group. Exact tests were applied to compare differences in the means of read-counts from 4 replicates between the treated and untreated group.
The gene expression levels were estimated in CPM (count-per-million-read).
The sequencing reads were mapped to hg19 using the bowtie2 default setting. Htseq 0.6.2p2 was applied to count number of reads within each gene. Differential expression was measured by DESeq package of R
Genome_build: hg19
Supplementary_files_format_and_content: Normalized abundance measurements. Differential expression of each gene.

source_name: prostate cancer

growth_protocol: PC-3 cells were cultured in RPMI 1640 medium containing 10% (v/v) fetal bovine serum (FBS), penicillin-streptomycin solution and 1 mM sodium pyruvate. Cells were maintained at 37°C in an atmosphere containing 5% CO2.

extract_protocol:
Cells harvested and total RNA was extracted from cells using Trizol. RNA quality was confirmed (RIN values 9.8-10) using RNA 6000 Nano Chips on an Agilent 2100 Bioanalyzer (Agilent Technologies).
Libraries were prepared using TruSeq Stranded Total RNA kit (Illumina, San Diego) and paired end sequencing was performed on an Illumina HiSeq 2500 at The Kinghorn Cancer Centre (Sydney).

treatment_protocol: PC-3 cells were incubated in the presence or absence of GPNA or BenSer for 48 h

value: BenSer

value: prostate

tag: cell type

value: cancer cell


title: BenSer2

tag: cell line


title: EXP-608: Blood_TCGA-AB-2856


title: Patient 4080

status: Public on May 07 2015

city: Amsterdam

first: Costa

last: Bachas

address: CCA 4.28, De Boelelaan 1117

department: Pediatric Oncology/ Hematology

country: Netherlands

institute: VU University Medical Center

description: primary pediatric relapsed AML bone marrow specimen

hyb_protocol: Following fragmentation, 10 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Human Genome U133 Array Set HG-U133 Plus 2.0. After sample hybridization, GeneChips were stained using phycoerythrin-conjugated streptavidine in an Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneArray Scanner.

data_processing: The CEL files for these samples were read into R using the affy package and normalized at probe-level with vsn (Huber et al, Bioinformatics 2002). Measurements were summarized per probe set using median polish.

source_name: bone marrow or peripheral blood sample from child with acute myeloid leukemia

label_protocol: Biotinylated cRNA was produced according tot the Affymetrix protocol with the ENZO IVT labeling kit, using 5 ug total RNA as input (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: in patient/vivo

extract_protocol: Total RNA was isolated out of leukemic cells using Trizol reagent (GIBCO BRL, Life Technologies). Quality of RNA was checked using an Agilent 2100 Bio-analyzer.

treatment_protocol: If required, samples were enriched for leukemic cells were isolated by sucrose density centrifugation and non-leukemic cells were eliminated as previously described

tag: diagnosis

value: primary pediatric relapsed acute myeloid leukemia

tag: cytogenetic aml subgroup

value: AML-ETO

tag: flt3/itd mutation status

value: wild type

tag: npm1 mutation status

tag: ras mutation status

tag: kit mutation status

value: mutated

tag: cebpa mutation status

tag: wt1 mutation status


title: Patient 4752

value: Other


title: Patient 4935

value: MLL


title: GPNA2

tag: treatment

value: GPNA

tag: tissue


title: Patient 3593


title: Patient 4951


title: EXP-608: Blood_TCGA-AB-2943

tag: age

value: FEMALE

value: Blood


title: EXP-608: Blood_TCGA-AB-2876

tag: french-american-british classification

value: Normal

value: BONE MARROW


title: Patient 4095


title: Patient 3340

value: CN-AML


title: Patient 4093

value: Complex


title: Patient 3364


title: Patient 3357


title: Patient 4749


title: Patient 3343


title: Patient 3376


title: Patient 4091


title: Patient 4602


title: Patient 3344


title: GPNA1


title: WT2

description:
cmp_ben.txt
cmp_gpna.txt


title: WT1

description:
cmp_ben.txt
cmp_gpna.txt


title: Patient 4807

value: Del 7


title: EXP-608: Blood_TCGA-AB-3007

tag: Sex

value: MALE


title: AML with t(8;21), AML1-ETO (06-011456)

status: Public on Sep 27 2014

city: München

first: Torsten

last: Haferlach

address: Max-Lebsche-Platz 31

country: Germany

institute: MLL Munich leukemia laboratory

hyb_protocol: according MILE study target preparation SOP v1.11

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

data_processing: The data were analyzed with Affymetrix GeneChip Operating Software using Affymetrix default analysis settings.

extract_protocol: Isolation of total RNA was performed with the Qiagen RNeasy MinElute Cleanup Kit according to the manufacturer's instructions.

tag: gender

value: female

value: Bone Marrow

value: positive

tag: condition

value: AML with t(8;21), AML1-ETO


title: AML with complex aberrant karyotype, del(5q) (06-011151)

label_protocol: according MILE study target preparation SOP v1.11

value: male

value: negative


title: AML with other chromosomal aberrations, del(5q), trisomy 8 (06-012547)


title: AML with complex aberrant karyotype, untypical, therapy-related (06-008150)


title: AML with t(8;16), therapy-related (07-000562)

value: AML with t(8;16), therapy-related


title: AML with del(5q) sole (06-011441)

value: AML with del(5q) sole


title: AML with t(11q23)/MLL, t(9;11), MLL-AF9, therapy-related (06-011192)


title: AML with normal karyotype (06-011336)

value: AML with normal karyotype


title: AML with complex aberrant karyotype, del(5q) (06-011020)


title: AML with normal karyotype (06-009591)


title: AML with trisomy 13 sole (06-010739)

value: AML with trisomy 13 sole


title: AML with complex aberrant karyotype, del(5q) (06-009692)


title: AML with complex aberrant karyotype, del(5q) (06-009753)

value: not available


title: AML with inv(16)/t(16;16), CBFB-MYH11, therapy-related (06-006242)


title: AML with t(15;17), PML-RARA, FAB M3/M3v (06-007073)

value: AML with t(15;17), PML-RARA, FAB M3/M3v


title: AML with t(11q23)/MLL, t(11;19) (06-007959)


title: AML with complex aberrant karyotype (06-007227)

value: AML with complex aberrant karyotype


title: AML with del(5q) + 1 additional aberration (06-007650)


title: AML with other chromosomal aberrations (06-007054)

value: AML with other chromosomal aberrations


title: AML with normal karyotype (06-010069)


title: AML with complex aberrant karyotype, del(5q) (06-009246)


title: AML with trisomy 13 sole (06-007368)


title: AML with complex aberrant karyotype, del(5q) (06-006904)


title: AML with complex aberrant karyotype, del(5q) (06-010085)


title: AML with complex aberrant karyotype, del(5q) (06-007053)


title: AML with t(8;21), AML1-ETO (06-009385)


title: AML with t(8;16) (06-011296)

value: AML with t(8;16)


title: AML with normal karyotype (06-006241)


title: AML with complex aberrant karyotype, untypical (06-006187)


title: AML with del(5q) sole (06-004494)


title: AML with t(15;17), PML-RARA, FAB M3 (06-004360)

value: AML with t(15;17), PML-RARA, FAB M3


title: AML with normal karyotype (06-004286)


title: Patient 4705

value: primary pediatric relapsed acute myeloid leukemia

value: AML-ETO

value: wild type


title: AML with del(9q) sole (06-004209)

value: female

value: Bone Marrow

value: AML with del(9q) sole


title: AML with t(11q23)/MLL, t(9;11), MLL-AF9 (06-004030)

value: male

value: negative

value: AML with t(11q23)/MLL, t(9;11), MLL-AF9


title: AML with complex aberrant karyotype, untypical (06-004023)


title: AML with other chromosomal aberrations (06-004073)


title: AML with complex aberrant karyotype, del(5q) (06-003403)


title: AML with normal karyotype (06-004024)

value: AML with normal karyotype


title: AML with t(15;17), PML-RARA, FAB M3/M3v (06-005907)

value: positive


title: AML with complex aberrant karyotype, del(5q) (06-003077)


title: AML with other chromosomal aberrations, trisomy 21 sole (06-005899)


title: AML with t(8;21), AML1-ETO (06-003874)

value: AML with t(8;21), AML1-ETO


title: AML with other chromosomal aberrations (06-003076)


title: AML with normal karyotype (06-003678)


title: AML with normal karyotype (06-004046)


title: AML with t(11q23)/MLL, t(11;19), MLL-ENL, therapy-related (06-003943)


title: AML with complex aberrant karyotype, untypical, therapy-related (06-003455)


title: AML with normal karyotype (06-002845)


title: AML with inv(16)/t(16;16), CBFB-MYH11 (06-003402)

value: AML with inv(16)/t(16;16), CBFB-MYH11


title: AML with complex aberrant karyotype, del(5q) (06-003104)


title: AML with trisomy 13 sole (06-002466)

value: AML with trisomy 13 sole


title: AML with other chromosomal aberrations, monosomy 7, trisomy 13 (06-003568)


title: AML with complex aberrant karyotype, untypical (06-003552)


title: AML with normal karyotype (06-002316)


title: AML with normal karyotype (06-002793)


title: AML with other chromosomal aberrations (06-004221)

value: AML with other chromosomal aberrations


title: AML with normal karyotype (06-003102)


title: AML with complex aberrant karyotype, del(5q) (06-002107)


title: AML with normal karyotype (06-002789)


title: AML with normal karyotype (06-001832)


title: AML with t(8;21), AML1-ETO, therapy-related (06-001032)


title: AML with normal karyotype (06-001006)


title: AML with other chromosomal aberrations (06-000501)


title: AML with normal karyotype (06-000720)


title: AML with normal karyotype (06-000592)


title: AML with t(8;21), AML1-ETO (06-001698)


title: AML with normal karyotype (06-001961)


title: AML with normal karyotype (06-000470)


title: AML with normal karyotype (06-000650)


title: AML with normal karyotype (06-000398)


title: AML with t(6;9) (06-001758)

value: AML with t(6;9)


title: AML with normal karyotype (06-000374)


title: AML with normal karyotype (06-000032)


title: AML with complex aberrant karyotype, del(5q) (06-001218)


title: AML with normal karyotype (06-000408)


title: AML with complex aberrant karyotype, del(5q) (06-000131)


title: AML with normal karyotype (06-001430)


title: AML with t(8;21), AML1-ETO (06-000424)


title: AML with trisomy 8 sole (06-000844)

value: AML with trisomy 8 sole


title: AML with normal karyotype (06-000767)


title: AML with complex aberrant karyotype, del(5q) (06-000990)

value: not available


title: AML with trisomy 13 sole (06-000619)


title: AML with normal karyotype (06-000406)


title: AML with normal karyotype (06-000155)


title: AML with other chromosomal aberrations, trisomy 8, trisomy 19 (06-000102)


title: AML with t(6;9) (06-000840)


title: AML with normal karyotype (06-000645)


title: AML with normal karyotype (06-001402)


title: AML with normal karyotype (06-000005)


title: AML with normal karyotype (06-000121)


title: AML with complex aberrant karyotype, del(5q) (05-003727)


title: AML with complex aberrant karyotype, untypical (05-003710)


title: AML with trisomy 8 sole (05-003735)


title: AML with other chromosomal aberrations, trisomy 21 sole (06-000004)


title: AML with normal karyotype (05-003631)


title: AML with del(5q) sole (05-003745)

value: AML with del(5q) sole


title: AML with normal karyotype (05-003094)


title: AML with t(15;17), PML-RARA, FAB M3 (05-003533)

value: AML with t(15;17), PML-RARA, FAB M3


title: AML with t(8;21), AML1-ETO, therapy-related (05-003319)

value: female


title: AML with normal karyotype (05-003014)

value: Bone Marrow


title: AML with other chromosomal aberrations (05-003623)


title: AML with inv(16)/t(16;16), CBFB-MYH11 (05-003503)


title: AML with other chromosomal aberrations, trisomy 14 sole (05-003164)


title: AML with t(15;17), PML-RARA, FAB M3/M3v (05-002434)

value: AML with t(15;17), PML-RARA, FAB M3/M3v


title: AML with t(8;21), AML1-ETO (05-002811)


title: AML with complex aberrant karyotype, del(5q) (05-002769)

value: male


title: AML with trisomy 8 sole (05-003269)

value: negative


title: AML with normal karyotype (05-002631)


title: AML with normal karyotype (05-002780)


title: AML with normal karyotype (05-003194)


title: AML with normal karyotype (05-002609)


title: AML with monosomy 7 sole (05-002574)

value: AML with monosomy 7 sole


title: AML with t(8;21), AML1-ETO (05-003455)


title: AML with normal karyotype (05-002339)

value: AML with normal karyotype


title: AML with other chromosomal aberrations (05-002236)


title: AML with normal karyotype (05-002237)

value: positive


title: AML with other chromosomal aberrations (05-003260)


title: AML with trisomy 11 sole (05-002233)

value: AML with trisomy 11 sole


title: AML with normal karyotype (05-002095)


title: AML with other chromosomal aberrations, therapy-related (05-001941)


title: AML with complex aberrant karyotype, untypical (05-001737)


title: AML with trisomy 8 sole (05-001866)


title: AML with normal karyotype (05-001789)


title: AML with t(11q23)/MLL, t(9;11), MLL-AF9, therapy-related (05-001507)


title: AML with complex aberrant karyotype, del(5q) (05-001197)


title: AML with complex aberrant karyotype, untypical (05-001939)


title: AML with complex aberrant karyotype, del(5q) (05-001354)


title: AML with normal karyotype, therapy-related (05-001146)


title: AML with other chromosomal aberrations (05-001647)


title: AML with trisomy 8 sole (05-001140)


title: AML with normal karyotype (05-001251)


title: AML with complex aberrant karyotype, del(5q) (05-000976)


title: AML with other chromosomal aberrations, del(9q), trisomy 21 (05-001646)


title: AML with normal karyotype, therapy-related (05-000703)


title: AML with normal karyotype (05-000646)


title: AML with monosomy 7 sole (05-000666)


title: AML with normal karyotype (05-000600)


title: AML with normal karyotype (05-001046)


title: AML with trisomy 8 sole (05-001056)


title: AML with normal karyotype (05-000637)


title: AML with complex aberrant karyotype, del(5q) (05-001004)


title: AML with other chromosomal aberrations (05-000854)


title: AML with complex aberrant karyotype, del(5q) (05-000784)


title: AML with normal karyotype (05-001353)


title: AML with t(15;17), PML-RARA, FAB M3v/M3 (05-000713)

value: AML with t(15;17), PML-RARA, FAB M3v/M3


title: AML with normal karyotype (05-000705)


title: AML with complex aberrant karyotype, del(5q) (05-001132)


title: AML with complex aberrant karyotype, del(5q) (05-000685)


title: AML with complex aberrant karyotype (05-000764)

value: AML with complex aberrant karyotype


title: AML with t(11q23)/MLL, t(10;11), MLL-AF10 (05-000590)


title: AML with inv(16)/t(16;16), CBFB-MYH11 (05-000405)

value: AML with inv(16)/t(16;16), CBFB-MYH11


title: AML with other chromosomal aberrations (05-000081)

value: AML with other chromosomal aberrations


title: AML with monosomy 7 sole (05-000118)


title: AML with complex aberrant karyotype, del(5q) (05-000449)


title: AML with normal karyotype (05-000549)


title: AML with other chromosomal aberrations (05-000402)


title: AML with t(8;21), AML1-ETO (05-000260)

value: AML with t(8;21), AML1-ETO


title: AML with complex aberrant karyotype, untypical (05-000510)


title: AML with normal karyotype (05-000221)


title: PC_H3

status: Public on Dec 06 2013

city: Gliwice

first: Magdalena

last: Olbryt

address: Wybrzerze AK 15

department: Center for Translational Research and Molecular Biology of Cancer

country: Poland

institute: Cancer Center and Institute of Oncology

description: PC-3 prostate cancer cells exposed to experimental chronic hypoxia (1% oxygen) for 72 h, biological replica 3

hyb_protocol: Following fragmentation, 16 μg of cRNA were hybridized for 16 hr at 45ºC on GeneChip Human Genome U133 Plus 2.0 Array (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Arrays were scanned by GeneChip Scanner 3000 and the data was acquired using GCOS 1.2 software (Affymetrix).

data_processing: The CEL files were pre-processed using the GC-RMA algorithm available in R environment as the Bioconductor gcrma package.

source_name: PC-3 cells exposed to chronic hypoxia

label_protocol: Total RNA (5 μg) was used for synthesis of double stranded cDNA according to manufacturer's instructions. Half of the cDNA volume was used for synthesis of biotynylated cRNA with reagents recommended by Affymetrix.

growth_protocol: The human cancer cells were grown in CO2 incubator at 37°C in the following culture media: PC-3 - RPMI (Sigma-Aldrich) supplemented with 10% fetal bovine serum (FBS; Gibco BRL), SK-OV-3 - McCoy’s medium (Sigma-Aldrich) supplemented with 10% FBS (Gibco BRL), WM793B - 2% Tu medium (Sigma-Aldrich) supplemented with 2% FBS (Gibco BRL), bovine insulin (0.005 mg/ml) and 1.68 mmol/l CaCl2 (Sigma-Aldrich).

extract_protocol: Total RNA was isolated using Rneasy Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Hypoxic conditions were introduced by incubating the cells in 1% oxygen using oxygen flow-regulated incubator for 72 h (chronic hypoxia) or for 4/12 hour periods of 1% oxygen interchanged with periods of 21% oxygen (cycling hypoxia). Control cells were cultured in standard conditions (21% oxygen) for 72 h.

tag: cell type

value: PC-3 human prostate cancer cell line

value: ATCC, CRL-1440


title: PC-3_Geraniol, rep3

status: Public on Nov 25 2013

city: Seoul

first: Ju-Hong

last: Jeon

state: Seoul

address: 28 Yongon-Dong, Chongno-Gu

department: Department of Physiology and Biomedical Sciences

country: South Korea

institute: Seoul National University College of Medicine

description: Geraniol effect on gene expression profile in PC-3 cells.

hyb_protocol: Following fragmentation, 5.5 ug of framented cDNA were hybridized for about 17 hr at 45℃ on Human Gene 1.0 ST arrays. The hybridized probe arrays were stained and washed with the GeneChip® Hybridization, Wash and Stain Kit using the Fluidics Station 450 (Affymetrix).

scan_protocol: The stained GeneChips were scanned with a GeneChip® Scanner 3000+ 7G (Affymetrix) at 570 nm.

data_processing: Raw data were normalized using the Single Channel Array Normalization (Piccolo et al. 2012, PMID: 22959562) method, which is implemented as a Bioconductor package (http://www.bioconductor.org/packages/release/bioc/html/SCAN.UPC.html). As part of the normalization process, a custom chip-definition (CDF)  file from the BrainArray resource was used to map genes based on updated genome mappings and excludes inaccurate or wrongly annotated probes. Microarray probes to 11,931 genes.

source_name: Prostate cancer cell line PC-3, geraniol

label_protocol: The Affymetrix GeneChip® procedure for generation of the biotin-labeled single-stranded cDNA by in vitro transcription were performed according to the manufacturer's instructions from 300ng total RNA (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Rev.5). Protocol was performed using the Whole Transcript Sense Target Labeling and Control Reagents (Affymetrix 900652).

growth_protocol: The cells were maintained under DMEM medium containing 10% FBS.

extract_protocol: Total RNA was extracted from the cells and processed according to the manufacturer's guideline (Affymetrix).

treatment_protocol: Compounds were dissolved in ethanol as a vehicle at 0.1% working concentration and treated in PC-3 cells. Vehicle-treated PC-3 cells were used as a control.

tag: cell line

value: androgen-independent prostate carcinoma cell line

value: geraniol


title: PC-3_Linalool, rep3

description: Linalool effect on gene expression profile in PC-3 cells.

source_name: Prostate cancer cell line PC-3, linalool

value: linalool


title: PC-3_Icilin, rep2

description: icilin effect on gene expression profile in PC-3 cells.

source_name: Prostate cancer cell line PC-3, icilin

value: icilin


title: PC-3_Icilin, rep3


title: PC-3_Geraniol, rep1


title: PC-3_Geraniol, rep2


title: PC_C3

description: PC-3 prostate cancer cells  exposed to experimental cycling hypoxia (interchanging 1% and 21% oxygen) for 72 h, biological replica 3

source_name: PC-3 cells exposed to cycling hypoxia

value: ATCC, CRL-1437


title: PC-3_Cineol, rep2

description: Cineol effect on gene expression profile in PC-3 cells.

source_name: Prostate cancer cell line PC-3, cineol

value: cineol


title: PC-3_Icilin, rep1


title: AML with normal karyotype (05-000482)

value: male

value: Bone Marrow

value: negative


title: PC-3_Linalool, rep2


title: PC_H1

description: PC-3 prostate cancer cells  exposed to experimental chronic hypoxia (1% oxygen) for 72 h, biological replica 1

value: ATCC, CRL-1438


title: PC_K3

description: PC-3 prostate cancer cells cultured in control conditions (21% oxygen), biological replica 3

source_name: control PC-3 cells

value: ATCC, CRL-1443


title: PC-3_Linalool, rep1


title: PC-3_Cineol, rep3


title: PC_K1

description: PC-3 prostate cancer cells cultured in control conditions (21% oxygen), biological replica 1

value: ATCC, CRL-1441


title: PC_C2

description: PC-3 prostate cancer cells  exposed to experimental cycling hypoxia (interchanging 1% and 21% oxygen) for 72 h, biological replica 2

value: ATCC, CRL-1436


title: PC_C1

description: PC-3 prostate cancer cells  exposed to experimental cycling hypoxia (interchanging 1% and 21% oxygen) for 72 h, biological replica 1

value: ATCC, CRL-1435


title: PC_H2

description: PC-3 prostate cancer cells exposed to experimental chronic hypoxia (1% oxygen) for 72 h, biological replica 2

value: ATCC, CRL-1439


title: PC_K2

description: PC-3 prostate cancer cells cultured in control conditions (21% oxygen), biological replica 2

value: PC-3 human prostate cancer cell line

value: ATCC, CRL-1442


title: PC-3_Menthol, rep3

description: Menthol effect on gene expression profile in PC-3 cells.

source_name: Prostate cancer cell line PC-3, menthol

value: androgen-independent prostate carcinoma cell line

value: menthol


title: PC-3_Vehicle, rep1

description: Vehicle effect on gene expression profile in PC-3 cells.

source_name: Prostate cancer cell line PC-3, vehicle control

value: ethanol vehicle


title: PC-3_Menthol, rep1


title: PC-3_Vehicle, rep3


title: PC-3_Vehicle, rep2


title: Chromatin IP for HA in MCF-7 cells transfected with HA-LRH1 vector Replicate 2

status: Public on Aug 01 2013

first: Koen

last: Flach

address: Plesmanlaan 121

institute: NKI

data_processing:
Reads were aligned to hg19 using BWA with the default settings
Peak calling was done using chip sample versus whole cell extract by MACS version 1.3.7.1
Peaks were called using MACS using a p-value cutoff of 1e-7
Genome_build: hg19

source_name: MCF-7 cells

growth_protocol: MCF-7 cells were routinely cultured in DMEM containing 10% FCS.

extract_protocol:
After fixation and cell lysis, lysates were clarified from sonicated nuclei.Lysate was immunoprecipitated for Estrogen Receptor or HA and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Cells were transfected with double-stranded RNA oligonucleotides using the Lipofectamine RNAiMax reverse transfection method (Invitrogen, UK), according to manufacturer’s protocols. ON-TARGETplus SMARTpool for LRH-1 (LU-003430, Thermofisher) or Control si

value: breast cancer

tag: chip antibody

value: HA (sc-7392; Santa Cruz)


title: 794178

status: Public on Oct 30 2013

city: St. Louis

first: Jacqueline

last: Payton

state: MO

address: 660 S. Euclid Ave

department: Pathology and Immunology

institute: Washington University School of Medicine

description: A study that used high-throughput sequencing of the bone marrow (tumor) and skin of acute myeloid leukemia patients.

hyb_protocol: according to manufacturer's protocol

data_processing: MAS5, scaled to array mean of 1500

source_name: AML bone marrow

label_protocol: according to manufacturer's protocol

extract_protocol: Trizol reagent standard protocol

value: AML bone marrow

tag: fab

value: M

tag: race

value: C

tag: age on study

tag: karyotype

value: Normal


title: PC-3_Menthol, rep2


title: 914247


title: 729805

value: Poor Risk Cytogenetic Abnormality


title: Chromatin IP for HA in MCF-7 cells transfected with pcDNA vector Replicate 2


title: 605322


title: 405655

value: Complex


title: Chromatin IP for ERα in MCF-7 cells transfected with a LRH-1 siRNA Replicate 2

value: ERα (Santa Cruz; sc-543)


title: Chromatin IP for ERα in MCF-7 cells transfected with a LRH-1 siRNA Replicate 1


title: Chromatin IP for ERα in MCF-7 cells transfected with a control siRNA Replicate 2


title: 578179


title: 348685

value: F


title: 866660


title: PC-3_Cineol, rep1

value: cineol


title: 723101

value: nc

value: A


title: 303642


title: 632729

value: Poor Risk


title: 806794


title: 123804


title: 115225


title: 193139

value: AA


title: 499862


title: 861663


title: Chromatin IP for ERα in MCF-7 cells transfected with a control siRNA Replicate 1


title: 868442


title: 100232


title: 617776


title: 766126


title: LatB_2hr_3

status: Public on May 01 2013

city: Ann Arbor

first: Richard

middle: R.

last: Neubig

state: MI

address: 1150 W. Med. Ctr. Dr.

department: Pharmacology

institute: University of Michigan

description: Gene expression data from PC-3 prostate cancer cells treated with Latrunculin B for 2 hr

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix 3000 7G GeneChip Scanner with Autoloader

data_processing: Data was analyzed using the limma and affy Bioconductor packages implemented in the R-statistical environment. RMA was used to normalize the data and fit log2 transformed expression values

source_name: PC-3 prostate cancer 2hr LatB

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: Triplicate cultures of human PC-3 prostate cancer cells (9 x 10^5) in 60 mm dishes were grown in 10% FBS for 24 hours then were serum starved for 24 hours (0.5% FBS).

extract_protocol: Total RNA was isolated using the RNAqueous® kit from Ambion.

treatment_protocol: At t=0 hr or t=22 hr, DMSO (1%) or compounds (CCG-1423 3 uM, Latrunculin B 0.5 uM, or DRB 50 uM) were added . Cells were harvested at t=24 hr.  Samples treated for 2 hr (CCG-1423, LatB, or DRB) or 24 hr (DMSO, CCG-1423, LatB, or DRB) were all compared to results for the 24 hr DMSO treatment.

value: PC-3 prostate cancer

tag: drug

value: Latrunculin B


title: LatB_2hr_2


title: CCG-1423_24hr_2

description: Gene expression data from PC-3 prostate cancer cells treated with CCG-1423 for 24 hr

source_name: PC-3 prostate cancer 24hr CCG-1423


title: LatB_24hr_2

description: Gene expression data from PC-3 prostate cancer cells treated with Latrunculin B for 24 hr

source_name: PC-3 prostate cancer 24hr LatB


title: DRB_2hr_2

description: Gene expression data from PC-3 prostate cancer cells treated with DRB for 2 hr

source_name: PC-3 prostate cancer 2hr DRB


title: DRB_24hr_3

description: Gene expression data from PC-3 prostate cancer cells treated with DRB for 24 hr

source_name: PC-3 prostate cancer 24hr DRB


title: DRB_2hr_1


title: CCG-1423_2hr_2

description: Gene expression data from PC-3 prostate cancer cells treated with CCG-1423 for 2 hr

source_name: PC-3 prostate cancer 2hr CCG-1423


title: CCG-1423_24hr_1


title: LatB_2hr_1


title: DMSO_1

description: Gene expression data from PC-3 prostate cancer cells treated with DMSO

source_name: PC-3 prostate cancer 24hr DMSO

value: DMSO control


title: CCG-1423_2hr_1


title: DRB_24hr_2


title: DRB_24hr_1


title: DRB_2hr_3


title: LatB_24hr_1


title: DMSO_2


title: CCG-1423_2hr_3


title: DMSO_3


title: CCG-1423_24hr_3


title: PC3_invivopassaged_cloneD3_CPAtreated_rep4

status: Public on Jan 23 2013

city: Munich

first: Stefan

last: Krebs

address: Feodor-Lynen-Str. 25

department: Gene Center

institute: Ludwig-Maximilian University

description:
F4-T_m
Xenograft of in vivo passaged CPA-resistant clone D3 of cell line PC3.

hyb_protocol: Fluidics Station 450.

scan_protocol: Affymetrix GeneChip Scanner 3000.

data_processing: RMA normalization and detection above background (DABG) calls by the R-package 'xps', filtered for 'present' probesets (probesets not called by DABG for at least 2 arrays in at least one group were omitted), outliers were identified by hierarchical clustering (heatmap representation).

source_name: tumor xenograft, PC3 D3, CPA

label_protocol: Affymetrix WT cDNA Synthesis and Amplification and Terminal Labeling kits.

growth_protocol: PC3 human prostate carcinoma cells (PC3-wt) (ATCC # CRL1435) and re-isolated clones PC3 A3, PC3 D3, and PC3 D4 were cultured in RPMI 1640 medium supplemented with 10% FBS. Cells were grown at 37°C in 5% CO2 in a humidified atmosphere. PC3 subclones were cultured without antibiotics for at least 3-4 passages before tumor cell implantation and were harvested when reaching approx. 70% confluence.

extract_protocol: Trizol method.

treatment_protocol: PC3 wt, PC3 A3, PC3 D3 and PC3 D4 cells were injected and grown as xenografts until they reached a mean volume of 30 mmÂ³. One group of each PC3 subclone was treated i.p. with 120mg/kg CPA.

value: PC3, clone D3

value: prostate carcinoma cells

tag: cell line conditioning

value: in vivo

value: cyclophosphamide (CPA)

tag: cpa sensitivity

value: resistant


title: PC3_invivopassaged_cloneD4_CPAtreated_rep4

description:
H4-T_m
Xenograft of in vivo passaged CPA-resistant clone D4 of cell line PC3.

source_name: tumor xenograft, PC3 D4, CPA

value: PC3, clone D4

tag: treatment


title: PC3_invivopassaged_cloneD4_CPAtreated_rep2

description:
H2-T_m
Xenograft of in vivo passaged CPA-resistant clone D4 of cell line PC3.


title: PC3_invivopassaged_cloneD4_CPAtreated_rep5

description:
H5-T_m
Xenograft of in vivo passaged CPA-resistant clone D4 of cell line PC3.


title: PC3_invivopassaged_cloneD4_CPAtreated_rep1

description:
H1-T_m
Xenograft of in vivo passaged CPA-resistant clone D4 of cell line PC3.


title: PC3_invivopassaged_cloneD3_CPAtreated_rep5

description:
F5-T_m
Xenograft of in vivo passaged CPA-resistant clone D3 of cell line PC3.


title: PC3_invivopassaged_cloneD4_untreated_rep2

description:
G2-T
Xenograft of in vivo passaged CPA-resistant clone D4 of cell line PC3.

source_name: tumor xenograft, PC3 D4, control

value: control


title: PC3_invivopassaged_cloneD4_untreated_rep1

description:
G1-T
Xenograft of in vivo passaged CPA-resistant clone D4 of cell line PC3.


title: PC3_invivopassaged_cloneD4_untreated_rep5

description:
G5-T
Xenograft of in vivo passaged CPA-resistant clone D4 of cell line PC3.


title: PC3_invivopassaged_cloneD4_untreated_rep4

description:
G4-T
Xenograft of in vivo passaged CPA-resistant clone D4 of cell line PC3.


title: PC3_invivopassaged_cloneD3_CPAtreated_rep3

description:
F3-T_m
Xenograft of in vivo passaged CPA-resistant clone D3 of cell line PC3.


title: PC3_invivopassaged_cloneD3_CPAtreated_rep2

description:
F2-T_m
Xenograft of in vivo passaged CPA-resistant clone D3 of cell line PC3.


title: PC3_invivopassaged_cloneD3_untreated_rep5

description:
E5-T
Xenograft of in vivo passaged CPA-resistant clone D3 of cell line PC3.

source_name: tumor xenograft, PC3 D3, control


title: PC3_invivopassaged_cloneA3_CPAtreated_rep2

description:
D2-T_m
Xenograft of in vivo passaged clone A3 of cell line PC3.

source_name: tumor xenograft, PC3 A3, CPA

value: PC3, clone A3

value: sensitive


title: PC3_unpassaged_CPAtreated_rep5

description:
B5-T_m
Xenograft of wt cell line PC3.

source_name: tumor xenograft, PC3 wt, CPA

value: in vitro


title: PC3_invivopassaged_cloneA3_untreated_rep4

description:
C4-T
Xenograft of in vivo passaged clone A3 of cell line PC3.

source_name: tumor xenograft, PC3 A3, control


title: PC3_unpassaged_untreated_rep4

description:
A4-T
Xenograft of wt cell line PC3.

source_name: tumor xenograft, PC3 wt, control


title: PC3_invivopassaged_cloneA3_untreated_rep1

description:
C1-T
Xenograft of in vivo passaged clone A3 of cell line PC3.


title: PC3_invivopassaged_cloneA3_untreated_rep2

description:
C2-T
Xenograft of in vivo passaged clone A3 of cell line PC3.


title: PC3_unpassaged_untreated_rep2

description:
A2-T
Xenograft of wt cell line PC3.


title: PC3_unpassaged_untreated_rep3

description:
A3-T
Xenograft of wt cell line PC3.


title: PC3_unpassaged_CPAtreated_rep1

description:
B1-T_m
Xenograft of wt cell line PC3.


title: PC3_unpassaged_untreated_rep1

description:
A1-T
Xenograft of wt cell line PC3.


title: PC3_unpassaged_CPAtreated_rep3

description:
B3-T_m
Xenograft of wt cell line PC3.


title: PC3_invivopassaged_cloneD3_untreated_rep3

description:
E3-T
Xenograft of in vivo passaged CPA-resistant clone D3 of cell line PC3.


title: PC3_invivopassaged_cloneD3_untreated_rep1

description:
E1-T
Xenograft of in vivo passaged CPA-resistant clone D3 of cell line PC3.


title: PC3_invivopassaged_cloneD3_untreated_rep2

description:
E2-T
Xenograft of in vivo passaged CPA-resistant clone D3 of cell line PC3.


title: PC3_invivopassaged_cloneA3_CPAtreated_rep3

description:
D3-T_m
Xenograft of in vivo passaged clone A3 of cell line PC3.


title: PC3_invivopassaged_cloneA3_CPAtreated_rep1

description:
D1-T_m
Xenograft of in vivo passaged clone A3 of cell line PC3.


title: PC3_unpassaged_CPAtreated_rep2

description:
B2-T_m
Xenograft of wt cell line PC3.


title: PC3_invivopassaged_cloneA3_CPAtreated_rep4

description:
D4-T_m
Xenograft of in vivo passaged clone A3 of cell line PC3.


title: PC3 Wee117AAG Rep2

status: Public on Jan 10 2013

city: Bethesda

first: Mehdi

last: Mollapour

address: 9000 Rockville Pike

department: UOB

institute: NCI-NIH

description: Gene expression data from PC3 cells treated with Wee1inhibitorII and 17AAG

hyb_protocol: Samples were hybridized to Affymetrix GeneChip microarrays overnight

scan_protocol: GeneChip were scanned on Affymetrix GeneChip scanner 3000

data_processing: Data were collected using Affymetrix AGCC software.Statistical and clustering analysis was performed with Partek Genomics Suite (6.5) software using RMA normalization algorithm.

label_protocol: RNA (100 ng) was reverse transcribed and labeled with biotin using Affymetrix 3’ IVTexpress Labeling kit following manufacturer’s protocol.

growth_protocol: The human prostate cancer cell line PC3 (ATCC) was cultured in Dulbecco's modified Eagle's minimal essential medium (DMEM; Invitrogen, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum (FBS; Invitrogen). Cells were propagated at 37°C in an atmosphere containing 5% CO2.

extract_protocol: Total RNA was isolated with RNAeasy kit from Qiagen

treatment_protocol: Wee1 inhibitor II was synthesized and 17-AAG was obtained from the National Cancer Institute (Bethesda, MD). Drug treatments were performed as follows unless otherwise stated. Cells were plated in growth media at 10% confluency 1 day prior to initiation of treatment. On the first day of treatment, Wee1 inhibitor was added to the medium so that the final concentration was 2.5 μM. Twentyfour hours later, 17-AAG was added to the medium so that the final concentration was 40 nM. For controls, an equivalent amount of vehicle was administered. Cells were harvested for analysis 48 hrs after administration of 17-AAG.

value: Wee1 inhibitor II  and 17AAG


title: PC3 17AAG Rep2

description: Gene expression data from PC3 cells treated with 17-AAG

source_name: PC3 cells treated with 17-AAG


title: PC3 Wee1 Rep3

description: Gene expression data from PC3 cells treated with Wee1inhibitorII

source_name: PC3 cells treated with Wee1inhibitorII

value: Wee1 inhibitor II


title: PC3 Control Rep2 (weak signal)

description: Gene expression data from PC3 cells Untreated

source_name: PC3 cells Untreated


title: PC3 Wee117AAG Rep1

source_name: PC3 cells treated with Wee1inhibitorII and 17AAG


title: PC3 17AAG Rep1


title: PC3 Control Rep3


title: PC3 Wee117AAG Rep3


title: PC3 Wee1 Rep2


title: PC3 17AAG Rep3


title: PC3 Wee1 Rep1


title: PC3 cells, normoxia, no treatment rep 2

status: Public on Dec 01 2012

city: Stirling

first: Iain

last: Gallagher

address: Room 4B133 Cottrell Building, University of Stirling, Airthrey Road

department: Faculty of Health Sciences and Sport

country: United Kingdom

institute: University of Stirling

description: Gene expression data from PC3 cells under normoxic conditions with no treatment

hyb_protocol: Labelled cDNA was hybridised to Affymetrix hgu133plus2 arrays using protocols provided by Nugen Inc.

scan_protocol: Arrays were scanned with default settings using an Affymetrix scanner as directed by manufacturer

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. Further data processing were performed by RMA.

source_name: PC3 cells, normoxia, no treatment rep 2

label_protocol: For microarray work reverse transcription of RNA to cDNA was carried out using the Ovation RNA Amplification system v2 (Nugen Technologies Inc, USA). 100ng of total RNA was reverse transcribed as per the manufacturer’s protocol. cDNA was purified using qiaQuick PCR purification kit (Qiagen, UK) and quantified using the Nanodrop instrument. 3.75ug of cDNA was fragmented and labelled with the FL-Ovation cDNA Biotin Module V2 (Nugen Technologies, USA) and hybridised to each Affymetrix U133+2 array

growth_protocol: PC-3 cells were cultured in RPMI 1640 media supplemented with 10% foetal calf serum, 2mM L-glutamine, penicillin 100u/ml, streptomycin 100ug/ml (all from Invitrogen, Paisley, UK).

extract_protocol: After 48 hours incubation 700µl of Qiazol lysis reagent (Qiagen, UK) was added. Cell scrapers were used to disrupt the cells and the resulting homogenate was transferred into a 1.5ml eppendorf tube. Total RNA was extracted using the RNeasy Lipid tissue mini kit with an on column DNAse step as directed by the manufacturer (Qiagen, UK).  RNA was  quantified using the Nanodrop instrument (Labtech Intl, UK). 260/230 and 260/280 ratios were assessed to examine RNA purity and integrity was assessed with the Bioanalyzer instrument (Agilent, UK).

treatment_protocol: On Day 0, PC-3 cells were seeded at 2x106 cells/25cm2 flask and left overnight in a 37C incubator, 5% CO2. Next day (day 1) 0.05% DMSO (Sigma–Aldrich, Gillingham, UK), 25µM of NCX1102 (NO-sulindac; donated by NicOx (Sophia Antipolis, France)), and 25µM of sulindac (NicOx) was prepared in DMSO and added to the corresponding flasks. Flasks were placed in normoxic conditions (21% O2, 37C, 5% CO2) or in hypoxic conditions (0.2% O2, 37C, 95% CO2 & 5% N2) in a PROOX 110 oxygen controller (BioSpherix Ltd., Redfield, NY) for 48hrs.

tag: oxygen level


title: PC3 cells, hypoxia, no treatment rep 1

description: Gene expression data from PC3 cells under hypoxic conditionswith no treatment

source_name: PC3 cells, hypoxia, no treatment rep 1


title: PC3 cells, hypoxia, sulindac rep 1

description: Gene expression data from PC3 cells under hypoxic conditions and treated with sulindac

source_name: PC3 cells, hypoxia, sulindac rep 1

value: sulindac


title: PC3 cells, normoxia, DMSO rep 2

description: Gene expression data from PC3 cells under normoxic conditions treated with DMSO

source_name: PC3 cells, normoxia, DMSO rep 2

value: DMSO


title: PC3 cells, normoxia, sulindac rep 1

description: Gene expression data from PC3 cells under normoxic conditions and treated with sulindac

source_name: PC3 cells, normoxia, sulindac rep 1


title: PC3 cells, normoxia, NO-sulindac rep 2

description: Gene expression data from PC3 cells under normoxic conditions and treated with NO-sulindac

source_name: PC3 cells, normoxia, NO-sulindac rep 2

value: NO-sulindac


title: PC3 Control Rep1


title: PC3 cells, hypoxia, no treatment rep 2

source_name: PC3 cells, hypoxia, no treatment rep 2


title: PC3 cells, normoxia, NO-sulindac rep 2b


title: PC3 cells, hypoxia, sulindac rep 2

source_name: PC3 cells, hypoxia, sulindac rep 2


title: PC3 cells, hypoxia, NO-sulindac rep 2b

description: Gene expression data from PC3 cells under hypoxic conditions and treated with NO-sulindac

source_name: PC3 cells, hypoxia, NO-sulindac rep 2


title: PC3 cells, hypoxia, DMSO rep 2

description: Gene expression data from PC3 cells under hypoxic conditions and treated with DMSO

source_name: PC3 cells, hypoxia, DMSO rep 2


title: PC3 cells, hypoxia, DMSO rep 1

source_name: PC3 cells, hypoxia, DMSO rep 1


title: PC3 cells, normoxia, no treatment rep 1

source_name: PC3 cells, normoxia, no treatment rep 1


title: UC_0544_1.RNA.e1.a1.lbe1

status: Public on May 24 2012

city: Lund

first: Gottfrid

last: Sjodahl

address: Medicon Village

department: Department of Translational Medicine

country: Sweden

institute: Lund Univeristy

hyb_protocol: According to the manufacturers specifications

data_processing:
Control probe filtering and background correction was performed within the BioArray Software Environment (BASE). The data was corrected for bias introduced by two different extraction methods (RNeasy and AllPrep)  by a probe-by-probe rescaling of each sample, determining the scaling factor using the median value of RNeasy samples vs the median value of AllPrep samples. The smaller sample group (AllPrep) was rescaled to the same median as the larger group (DNeasy). Using the same method, we rescaled all probes of labeling plates P1, P2, P5, and P6 to have the same median values as P4 samples, thereby correcting for an observed labeling plate bias. Following bias correction, the data was quantile normalized using the limma package (Smyth, Stat Appl Genet Mol Biol. 2004) and converted to the log2 scale. The probes were annotated to HGNC GeneSymbols using the Illumina platform annotation file and probes without gene symbol were discarded. Next, 50% of the probes with lowest intensity were discarded and the remaining probes were mean-centered. Probes annotated with the same gene symbol were merged using the median value for each gene symbol.
Normalized data in Sample tables below: Original detection p-values, along with expression values arrived at after: background correction, probe-by-probe rescaling adjustment for extraction method, probe-by-probe rescaling adjustment for labeling plate, quantile normalization, Log2 conversion, application of a 50% intensity filter and mean centering of probes.
Matrix non-normalized (linked as supplementary file on Series record): The raw intensity values subjected only to background correction.

source_name: Bladder Tumor UC_0544_1

label_protocol: Total RNA was labeled using the Illumina TotalPrep-96 RNA Amplification Kit (Ambion), following the manufacurers instructions.

extract_protocol: Total RNA was extracted using Trizol reagent followed by purification on RNeasy micro columns (Qiagen) according to the manufacturers recommendations

treatment_protocol: Urothelial carcinoma samples were collected by cold-cup biopsy from the exophytic part of the bladder tumor of patients undergoing transurethral resection at hospitals within the southern healthcare region of Sweden.

value: M

tag: age

value: Ta

value: no


title: PC3 cells, normoxia, DMSO rep 1

source_name: PC3 cells, normoxia, DMSO rep 1


title: PC3 cells, normoxia, sulindac rep 2

source_name: PC3 cells, normoxia, sulindac rep 2


title: PC3 cells, hypoxia, NO-sulindac rep 2


title: UC_0456_2.RNA.e1.a1.lbe1

scan_protocol: According to the manufacturers specifications

source_name: Bladder Tumor UC_0456_2


title: UC_0513_1b.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0513_1b

value: F


title: UC_0542_2.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0542_2


title: UC_0410_1a.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0410_1a

value: yes


title: UC_0235_3.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0235_3

value: yes (Cystectomy Stage Ta)


title: UC_0267_3.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0267_3


title: UC_0200_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0200_1


title: UC_0395_1a.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0395_1a


title: UC_0199_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0199_1

value: yes (T2)


title: UC_0196_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0196_1

value: yes (T3)


title: UC_0295_2c.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0295_2c


title: UC_0354_2c.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0354_2c


title: UC_0152_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0152_1


title: UC_0009_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0009_1


title: PC3-docetaxel resistant-rep2

status: Public on Jan 01 2012

city: Barcelona

first: Mercedes

last: Marín-Aguilera

address: Villarroel 170

country: Spain

institute: Fundació Clínic per a la Recerca Biomèdica

hyb_protocol: GeneChip Hybridization wash and stain kit

scan_protocol: GeneChip 3000 Scanner 3000 7G system; software: GeneChip  Command Console (AGCC 1.1)

data_processing: Raw expression measures were summarized after background correction and normalization steps using the rma methodology in the affy package from the Bioconductor project.

source_name: PC3 cell line resistant to docetaxel

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix IVT Labeling kit from  2ug total RNA.

growth_protocol: DU-145 and DU-145R cell lines were cultured in RPMI 1640 medium (Invitrogen), and PC-3 and PC-3R in F-12K nutrient mixture medium (Invitrogen), both supplemented with 10% fetal bovine serum.

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

treatment_protocol: The human prostate carcinoma cell lines DU-145 and PC-3 (obtained from American Tissue Culture Collection) were converted to docetaxel-resistant cells by exposing them to an initial dose of 5 nM docetaxel and culturing surviving cells during 1 yr and 6 mo, respectively, with increasing doses in an intermittent regimen. Docetaxel (Sigma) was dissolved in DMSO (10mM).

tag: disease state

value: metastatic prostate cancer

value: converted to docetaxel-resistant cells


title: PC3-2

source_name: PC3 cell line original


title: AML with normal karyotype #83

status: Public on Aug 04 2011

city: Rotterdam

first: Erdogan

last: Taskesen

address: dr. molewaterplein 50

institute: Erasmus University Medical Center (EMC)

description: CEBPAwt

hyb_protocol: Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.

scan_protocol: Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default settings and targeted intensity values at 100. Intensity values were log2 transformed and mean centered per probe set.

label: Biotin

source_name: mononuclear cells from bone marrow

label_protocol: For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using a cDNA Synthesis System kit including an oligo(dT)24 – T7 primer (Roche Applied Science, Mannheim, Germany) and Poly-A control transcripts (Affymetrix, Santa Clara, CA, USA). The generated cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The incubation steps during the cDNA synthesis, in vitro transcription reaction, and target fragmentation were performed using the Hybex Microarray Incubation System (SciGene, Sunnyvale, CA, USA) and Eppendorf ThermoStat plus instruments (Eppendorf, Hamburg, Germany).

extract_protocol: The total RNA was purified either with Qiagen RNeasy Mini kits (Qiagen, Hilden, Germany) or with TRIzol-based protocols.

treatment_protocol: Samples are from untreated patients (de novo AML)

tag: genotype/variation (cebpa single mutant, cebpa double mutant)

value: negative,negative


title: PC3-1


title: AML with normal karyotype #80

description: CEBPAwt


title: PC3 cells, COUP-TFII siRNA for 48 hr, rep2

status: Public on Oct 25 2011

city: Houston

first: Jun

last: Qin

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

hyb_protocol: Hybridization cocktails containing Affymetrix spike-in controls and 15.0ug of each fragmented, labeled cRNA were loaded onto Affymetrix GeneChip® Human U133 Plus 2.0 arrays.  The arrays were hybridized for 16 hours at 45°C with rotation at 60 rpm in the Affymetrix GeneChip® Hybridization Oven 640.

scan_protocol: The stained arrays were scanned on the Affymetrix GeneChip® Scanner 3000.  The images were analyzed and quality control metrics recorded using Affymetrix Command Console software version 3.0.0.

data_processing: The data were analyzed with dCHIP using Affymetrix default analysis settings and global scaling as normalization method. We selected differentially expressed genes using two sample comparisons according to the following criteria: lower bound of 90% confidence interval of fold change greater than 1.2.

source_name: PC3 cells

label_protocol: Samples were labeled using the new 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.

growth_protocol: PC3 cells are cultured in RPMI supplemented with 10% fetal bovine serum.

treatment_protocol: Control or COUP-TFII siRNA knockdown

value: Prostate cancer cell line

tag: sirna

value: COUP-TFII siRNA for 48 hr


title: PC3-3


title: UC_0042_2a.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0042_2a

tag: gender


title: AML 46,XY,9ph #73

description: CEBPAwt


title: AML with normal karyotype #94

description: CEBPAwt


title: AML with normal karyotype #82

description: CEBPAwt


title: PC3-docetaxel resistant-rep3


title: PC3 cells, control siRNA for 48 hr, rep1

tag: cell type

value: control siRNA for 48 hr


title: AML with normal karyotype #68

description: CEBPAwt


title: UC_0077_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0077_1


title: AML with normal karyotype #84

description: CEBPAwt


title: AML with normal karyotype #81

description: CEBPAwt


title: AML with normal karyotype #70

description: CEBPAwt


title: AML with normal karyotype #64

description: CEBPAwt


title: AML with normal karyotype #60

description: CEBPAwt


title: AML with normal karyotype #65

description: CEBPAwt


title: AML with normal karyotype #69

description: CEBPAwt


title: AML with 46,XY,inv(9)(p11q13)c #91

description: CEBPAwt


title: AML with normal karyotype #61

description: CEBPAwt


title: PC3 cells, COUP-TFII siRNA for 48 hr, rep1

tag: cell line


title: AML with normal karyotype #72

description: CEBPAwt


title: AML with normal karyotype #67

description: CEBPAwt


title: AML with normal karyotype #55

description: CEBPAwt


title: AML with normal karyotype #62

description: CEBPAwt


title: PC3 cells, control siRNA for 48 hr, rep2


title: AML 46,XY,inv(9)(p13q22)c #38

description: CEBPAwt


title: AML with normal karyotype #47

description: CEBPAwt


title: AML with normal karyotype #39

description: CEBPAwt


title: AML with normal karyotype #51

description: CEBPAwt


title: AML with normal karyotype #46

description: CEBPAwt


title: AML with normal karyotype #42

description: CEBPAwt


title: AML with normal karyotype #41

description: CEBPAwt


title: AML with normal karyotype #45

description: CEBPAwt


title: AML with normal karyotype #24

description: CEBPAwt


title: AML with normal karyotype #28

description: CEBPAwt


title: AML with normal karyotype #40

description: CEBPAwt


title: AML with normal karyotype #36

description: CEBPAwt


title: AML with normal karyotype #23

description: CEBPAwt


title: AML with normal karyotype #25

description: CEBPAwt


title: AML with normal karyotype #14

description: CEBPAdm

value: negative,positive


title: AML with normal karyotype #9

description: CEBPAdm


title: AML with normal karyotype #8

description: CEBPAdm


title: AML with normal karyotype #49

description: CEBPAwt


title: AML with normal karyotype #16

description: CEBPAdm


title: AML with normal karyotype #43

description: CEBPAwt


title: AML with normal karyotype #22

description: CEBPAdm


title: AML with normal karyotype #10

description: CEBPAdm


title: AML with normal karyotype #4

description: CEBPAsm

value: positive,negative


title: AML with normal karyotype #29

description: CEBPAwt


title: AML with normal karyotype #37

description: CEBPAwt


title: AML with normal karyotype #5

description: CEBPAsm


title: 375182

status: Public on May 20 2011

city: St Louis

address: 4320 Forest Park Avenue, Suite 211

hyb_protocol: Chips hybridized according to Manufacturer's protocol

data_processing: Data scaled to array mean of 1500

source_name: Bone marrow specimen from Tumor cells

label_protocol: Chips labeled with biotin according to Manufacturer's protocol

growth_protocol: Bone marrow specimen from tumor cells

tag: tissue

value: bone marrow

tag: Sex

value: W

tag: cytogenetics

value: normal

tag: %bm blast

tag: pb wbc@ presentation

tag: %pb blast

tag: vital status

value: Dead

tag: efs months (3.31.10)

tag: flt3 itd

value: ITD


title: 179223

value: F

tag: race

tag: fab


title: 987523

tag: age

value: M

value: B

value: complex [no favorable]

value: Alive


title: 923966


title: 431799


title: 255108


title: 671473


title: 128392


title: 452198

tag: flt3 d835


title: 809653


title: 254137


title: 573988


title: 869922


title: 982009


title: 997292


title: 594368


title: 757199


title: 737451


title: 434640


title: 498463


title: 514066


title: 553863


title: 470690


title: 717456


title: 595704


title: 690397


title: 499294


title: 463352


title: 740266

value: W/Nat Amer


title: 708512


title: 326772


title: 507696


title: 329614


title: 410324


title: 400830


title: 319955


title: 179016

value: complex [incl:t(15;17)]


title: 245450


title: 906708


title: 237983

value: -7 only


title: 702808


title: 303818


title: 816067


title: 700717


title: 907786


title: 180168


title: 242129


title: 817156


title: 456892


title: 750152


title: 142074


title: 103342


title: 455499

value: H


title: 202127


title: 150288


title: 224143


title: 400220


title: 989176


title: 478908


title: 545259


title: 831711


title: 962561


title: 804168


title: 146218


title: 113971

value: G590fs/ 1.5Mb deletion


title: 808642


title: 141273


title: 862507

value: Unk


title: 991612


title: 273919


title: Sample 30 - MLL/AF10

status: Public on Apr 21 2011

city: Padova

first: Andrea

last: Zangrando

address: Via Giustiniani, 3

department: Woman and Child's Health

country: Italy

institute: University of Padova

description: Gene expression data from acute myeloid leukemia with MLL/AF10 translocations at diagnosis

hyb_protocol: Following fragmentation, 12.5 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Scan GCS3000 7G

data_processing: The data were normalized using R software [www.r-ptoject.org] with BioConductor package [www.bioconductor.org]

source_name: Bone Marrow cells

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix IVT express protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2008, Affymetrix).

extract_protocol: Total RNA extracted using Trizol

tag: disease state

value: AML samples

tag: cells

value: Bone Marrow


title: 445045

value: bone marrow

value: W


title: 530962

value: -Y

value: Dead


title: Sample 36 - MLL/SEPTIN6

description: Gene expression data from acute myeloid leukemia with MLL/SEPTIN6 translocations at diagnosis


title: 593890


title: Sample 42 - MLL/ELL

description: Gene expression data from acute myeloid leukemia with MLL/ELL translocations at diagnosis


title: Sample 38 - MLL/AF9

description: Gene expression data from acute myeloid leukemia with MLL/AF9 translocations at diagnosis


title: Sample 34 - MLL/ELL


title: Sample 35 - MLL/SEPTIN6


title: Sample 33 - MLL/ENL

description: Gene expression data from acute myeloid leukemia with MLL/ENL translocations at diagnosis


title: Sample 23 - MLL/AF10


title: Sample 28 - MLL/AF9


title: Sample 25 - MLL/AF9


title: Sample 32 - MLL/AF1q

description: Gene expression data from acute myeloid leukemia with MLL/AF1q translocations at diagnosis


title: Sample 41 - MLL/ENL


title: Sample 37 - MLL/AF1q


title: Sample 27 - MLL/AF9


title: Sample 22 - MLL/AF9


title: Sample 26 - MLL/AF9


title: Sample 24 - MLL/AF10


title: Sample 20 - MLL/AF6

description: Gene expression data from acute myeloid leukemia with MLL/AF6 translocations at diagnosis


title: Sample 29 - MLL/AF9


title: Sample 31 - MLL/AF10


title: Sample 19 - MLL/AF6


title: Sample 21 - MLL/AF6


title: Sample 18 - MLL/AF6


title: Sample 17 - MLL/AF6


title: Sample 16 - MLL/AF6


title: Sample 14 - MLL/AF6


title: Sample 9 - MLL/AF9


title: Sample 11 - MLL/SEPTIN6


title: Sample 10 - MLL/ENL


title: Sample 7 - MLL/AF6


title: AML with normal karyotype #131

status: Public on Jan 01 2010

city: New York

first: Hans-Ulrich

last: Klein

state: NY

department: Neurology

institute: Columbia University Medical Center

description: MUC

data_processing: The Robust Multichip Average (RMA) algorithm as implemented in the R package affy (version 1.20.2) was applied to generate probe set level signal intensities. (Irizarry et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64)

value: negative

tag: cebpa

tag: diagnosis

value: AML with normal karyotype

tag: gender

value: female

tag: specimen type

tag: blast cell percentage

value: de novo AML


title: Sample 4 - MLL/AF10


title: Sample 13 - MLL/AF9


title: Sample 6 - MLL/AF6


title: AML with normal karyotype #137

description: MUC

value: positive


title: AML with normal karyotype #128

description: MUC

value: male


title: Sample 2 - MLL/AF10


title: AML with normal karyotype #124

description: MUC


title: AML with normal karyotype #130

description: MUC


title: AML with normal karyotype #125

description: MUC


title: AML with normal karyotype #122

description: MUC


title: AML with normal karyotype #121

description: MUC


title: Sample 5 - MLL/AF6


title: AML with normal karyotype #120

description: MUC


title: AML with normal karyotype #136

description: MUC


title: Sample 8 - MLL/AF10


title: Sample 1 -MLL/AF10


title: Sample 3 - MLL/AF9


title: AML with normal karyotype #133

description: MUC


title: AML with normal karyotype #134

description: MUC


title: Sample 12 - MLL/AF9


title: AML with normal karyotype #129

description: MUC


title: AML with normal karyotype #119

description: MUC


title: Sample 15 - MLL/AF6


title: AML with normal karyotype #126

description: MUC


title: AML with normal karyotype #115

description: MUC


title: AML with normal karyotype #117

description: MUC


title: AML with normal karyotype #114

description: MUC


title: AML with normal karyotype #103

description: MUC


title: AML with normal karyotype #112

description: MUC


title: AML with normal karyotype #97

description: MUC


title: AML with normal karyotype #106

description: MUC


title: AML with normal karyotype #109

description: MUC


title: AML with normal karyotype #116

description: MUC


title: AML with normal karyotype #96

description: MUC


title: AML with normal karyotype #108

description: MUC


title: AML with normal karyotype #101

description: MUC


title: AML with normal karyotype #105

description: MUC


title: AML with normal karyotype #104

description: MUC


title: AML with normal karyotype #92

description: MUC


title: AML with normal karyotype #98

description: MUC


title: AML with normal karyotype #102

description: MUC


title: AML with normal karyotype #110

description: MUC


title: AML with normal karyotype #100

description: MUC


title: AML with normal karyotype #118

description: MUC


title: AML with normal karyotype #95

description: MUC


title: AML with normal karyotype #113

description: MUC


title: AML with normal karyotype #111

description: MUC


title: AML with normal karyotype #107

description: MUC


title: AML with normal karyotype #84

description: MUC


title: AML with normal karyotype #83

description: MUC


title: AML with normal karyotype #82

description: MUC


title: AML with normal karyotype #89

description: MUC


title: AML with normal karyotype #91

description: MUC


title: AML with normal karyotype #88

description: MUC

value: t-AML


title: MILES stage 1 data N1_2092

status: Public on Sep 30 2009

city: Pleasanton

first: Wei-Min

last: Liu

state: CA

address: 4300 Hacienda Drive

institute: Roche Molecular Systems

data_processing: Data pre-processing included a summarization and quantile normalization step to generate probe set level signal intensities for each microarray experiment and was performed as previously published by Liu WM et al. PQN and DQN: algorithms for expression microarrays. J.Theor.Biol. 2006;243:273-278.

source_name: Leukemia patient sample

growth_protocol: not applicable

extract_protocol: The total RNA was purified either with Qiagen RNeasy Mini kits (Qiagen, Hilden, Germany) or with TRIzol-based protocols

treatment_protocol: Samples are from untreated patients.

tag: sample type

tag: leukemia class

value: Non-leukemia and healthy bone marrow


title: AML with normal karyotype #80

description: MUC


title: AML with normal karyotype #86

description: MUC


title: AML with normal karyotype #87

description: MUC


title: MILES stage 1 data N1_2086


title: MILES stage 1 data N1_2090


title: MILES stage 1 data N1_2094


title: MILES stage 1 data N1_2089


title: AML with normal karyotype #85

description: MUC


title: AML with normal karyotype #81

description: MUC


title: MILES stage 1 data N1_2088


title: MILES stage 1 data N1_2087


title: MILES stage 1 data N1_2096


title: MILES stage 1 data N1_2076


title: MILES stage 1 data N1_2095


title: MILES stage 1 data N1_2078


title: AML with normal karyotype #93

description: MUC


title: MILES stage 1 data N1_2093


title: MILES stage 1 data N1_2091


title: MILES stage 1 data N1_2082


title: MILES stage 1 data N1_2079


title: MILES stage 1 data N1_2081


title: MILES stage 1 data N1_2083


title: MILES stage 1 data N1_2067


title: MILES stage 1 data N1_2085


title: MILES stage 1 data N1_2071


title: MILES stage 1 data N1_2077


title: MILES stage 1 data N1_2080


title: MILES stage 1 data N1_2084


title: MILES stage 1 data N1_2072


title: MILES stage 1 data N1_2070


title: MILES stage 1 data N1_2074


title: MILES stage 1 data N1_2060


title: MILES stage 1 data N1_2073


title: MILES stage 1 data N1_2069


title: MILES stage 1 data N1_2061


title: MILES stage 1 data N1_2066


title: MILES stage 1 data N1_2068


title: MILES stage 1 data N1_2052


title: AML with normal karyotype #99

description: MUC


title: MILES stage 1 data N1_2062


title: MILES stage 1 data N1_2063


title: MILES stage 1 data N1_2053


title: MILES stage 1 data N1_2065


title: MILES stage 1 data N1_2059


title: MILES stage 1 data N1_2064


title: AML with normal karyotype #79

description: MUC


title: MILES stage 1 data N1_2047


title: MILES stage 1 data N1_2049


title: MILES stage 1 data N1_2046


title: MILES stage 1 data N1_2044


title: MILES stage 1 data N1_2056


title: MILES stage 1 data N1_2050


title: MILES stage 1 data N1_2042


title: MILES stage 1 data N1_2041


title: MILES stage 1 data N1_2057


title: MILES stage 1 data N1_2051


title: MILES stage 1 data N1_2048


title: MILES stage 1 data N1_2045


title: MILES stage 1 data N1_2043


title: AML with normal karyotype #94

description: MUC


title: MILES stage 1 data N1_2032


title: MILES stage 1 data N1_2038


title: MILES stage 1 data N1_2039


title: MILES stage 1 data N1_2030


title: MILES stage 1 data N1_2029


title: MILES stage 1 data N1_1284

value: AML with normal karyotype + other abnormalities


title: MILES stage 1 data N1_2027


title: MILES stage 1 data N1_2035


title: MILES stage 1 data N1_2034


title: MILES stage 1 data N1_2026


title: MILES stage 1 data N1_2024


title: MILES stage 1 data N1_1292

value: AML complex aberrant karyotype


title: MILES stage 1 data N1_2040


title: MILES stage 1 data N1_2033


title: MILES stage 1 data N1_2028


title: MILES stage 1 data N1_2036


title: MILES stage 1 data N1_2037


title: MILES stage 1 data N1_2025


title: MILES stage 1 data N1_1290


title: MILES stage 1 data N1_1291


title: MILES stage 1 data N1_1283

value: peripheral blood


title: MILES stage 1 data N1_1285


title: MILES stage 1 data N1_1277


title: MILES stage 1 data N1_1289


title: MILES stage 1 data N1_1282


title: MILES stage 1 data N1_1288


title: MILES stage 1 data N1_1267


title: MILES stage 1 data N1_1281