title: arp_1_Input

status: Public on Aug 31 2018

type: SRA

city: Atlanta

first: Roger

middle: B

last: Deal

state: GA

address: 1510 Clifton Rd NE

department: Biology

country: USA

institute: Emory University

library_source: genomic

data_processing:
Raw reads were aligned to the Arabidopsis TAIR10 genome using Bowtie2 with default parameters
Mapped reads were filtered to remove those mapping to organelle genomes, and reads with a mapping quality score of q>2 were retained for further analysis.
Peaks were identified in ChIP-seq datasets using the Findpeaks function of the Homer package, using the parameter "-region" and the matched input dataset as the reference. Peaks were called on each replicate H2A.Z ChIP-seq dataset from wild-type and mbd9 mutants, and on H4Ac ChIP-seq datasets from wild-type. Bed files of the peaks are included for these specific datasets they were called in.
Datasets not used for peak calling were also analyzed by examining normalized reads (in bigwig files) across gene bodies or at the regions identified as peaks in other datasets.
To produce bigwig files (.bw), all the filtered ChIP-seq bam files generated with a given antibody (H2A.Z or H4Ac) were first scaled to the same number of reads. These scaled bam files were converted to the bigwig format using a bin size of 1 base pair.
Genome_build: Arabidopsis thaliana TAIR10
Supplementary_files_format_and_content: .bed files containing peaks for the specific histone mark as defined using the findPeaks function of the Homer software package.

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: arp6-1 mutant_Aliquot before IP

growth_protocol: All plants were grown under 16hr light/8 hr dark cycles at 20C on 1/2 MS plates for seedling collection.

extract_protocol:
Chromatin immunoprecipitation was performed as described (in Gendrel at al. (2005) Nature Methods 2), followed by isolation of immunoprecipitated DNA using the QIagen PCR purification kit
Antibody-specific immunoprecipitated DNAs were converted to sequencing libraries through a limited number of PCR cycles using indexed primers, followed by purification of library fragments using SPRI beads.

treatment_protocol: Six-day-old seedlings, not including roots, were collected and cross-linked with 1% formaldehyde under vacuum for 15 minutes.

tag: ecotype background

tag: genotype/variation

value: arp6-1 mutant

tag: tissue

value: 6 day old seedling

tag: chromatin immunopurification

value: None - Aliquot before IP


title: mbd_1_Input

source_name: mbd9-1 mutant_Aliquot before IP

value: mbd9-1 mutant


title: wt_1_Input

source_name: wild type_Aliquot before IP

value: wild type


title: THP-1_LC53_8h_rep2

type: RNA

city: Taipei

first: George

last: Hsiao

address: No. 250, Wu-Hsing Str

department: Pharmacology

country: Taiwan

institute: Taipei Medical University

hyb_protocol: Fluorescent targets were hybridized to the Human Whole Genome OneArray® with Phalanx hybridization buffer using Phalanx Hybridization System. After 16 hrs hybridization at 50 ℃, non-speciﬁc binding targets were washed away.

scan_protocol: The arrays were scanned by Agilent G2505C scanner (635nm power 100 ) and quantify the fluoresence intensity.

data_processing: The signal intensity of each spot was loaded into Rosetta Resolver System® (Rosetta Biosoftware) to process data analysis. The error model of Rosetta Resolver System® could remove both systematic and random errors form the data. We ﬁltered out spots that the ﬂag is less than 0. Spots that passed the criteria were normalized by 50% media scaling normalization method.Normalize intensities: Median scaling performed on data set without flagged and control data. Merge technical replicate data: Average intensity values calculated on technical replicates.

molecule: total RNA

organism: Homo sapiens

source_name: THP-1, pretreated LC53, then LPS 8h

label_protocol: 1 µg of total RNA was reverse-transcribed and amplified using Amino Allyl aRNA Amplification Kit (Phalanx Biotech Group, Taiwan) and Cy5 dyes (GE, Piscataway, NJ, USA).

growth_protocol: THP-1 cells (1×10^6 cells/ml; 3 ml/well in 6 well plate) were cultured in 0.5% FBS/RPMI 1640 medium before various treatment.

extract_protocol: RNA extraction by Trizol. RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧7).

treatment_protocol: THP-1 cells were pretreated with or without LC53 (5 μM) for 15min and subsequently stimulated with 50 ng/ml LPS for 8 hours.

tag: treatment

value: pretreated LC53 then LPS

tag: cell type

value: monocyte

tag: cell line


title: THP-1_LPS_8h_rep2

source_name: THP-1, LPS stimulation, 8h

value: LPS


title: THP-1_resting_8h_rep2

source_name: THP-1, control, 8h

value: control


title: THP-1_resting_8h_rep1


title: THP-1_LC53_8h_rep1


title: THP-1_LPS_8h_rep1


title: High_S13

city: Jefferson

first: Vikrant

last: Vijay

state: AR

address: 3900 NCTR Road

department: Division of Systems Biology

institute: US FDA National Center for Toxicological Research

description: Total RNA from Testis of PND 30 male rats exposed perinatally to 30000 ppm HMB was used for gene expression

hyb_protocol: Only the cRNAs with yields >1.65 µg and specific activities > 9.0 pmol of dye per µg cRNA were used for hybridization. Equal amounts (600 ng) of purified Cy3-labeled cRNA were hybridized to Agilent SurePrint G3 rat 8 × 60K microarrays (8 arrays per slide) following the Agilent One-Color Microarray-Based Gene Expression Analysis Protocol (V5.5, Agilent Technologies, Inc.) for 17 hours at 65°C in a hybridization oven.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%). The resulting images were analyzed by quantifying the Cy3 fluorescence intensity at each of the 62,976 spots (features) on each array using the Agilent Feature Extraction Software (Version 10.7.3) with default parameters (protocol GE1_107_Sep09) to obtain background subtracted and spatially detrended Processed Signal intensities. The median fluorescence intensity of all the pixels within each feature was taken as the intensity value for that feature.

data_processing: A total of 15 raw data files for 15 samples (5 arrays for each control and treated rats) were obtained from the Agilent Feature Extraction Software. An excel spreadsheet containing raw intensity data for all 15 samples was used as an input file for further data preprocessing and normalization using SAS 9.4 (SAS institute Inc., Cary, NC). There were 62,976 features (probes) on each array. Controls were removed and average probe intensity was calculated for each probe, and then data was normalized using 75th percentile scaling.

organism: Rattus norvegicus

source_name: Whole Testis, male, PND 30, HMB-30000ppm, replicate 3

label_protocol: Total RNAs (500ng) were labeled with cyanine dye (Cy3) using the Agilent One Color Low RNA Input Linear Amplification Kit according to the manufacturer’s protocol (Agilent Technologies, Inc.) followed by RNAeasy column purification (QIAGEN, Valencia, CA). For each reaction, cRNA yields and specific activities were determined using the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Eleven to thirteen-week-old time-mated female Sprague-Dawley rats from Harlan Laboratories (Indianapolis, IN, USA) were received in the NCTR's study laboratory on gestational day (GD) 3 (day of vaginal plug detection was designated as GD 0) where they were housed individually under controlled conditions with a 12:12 h light–dark cycle, 23 ± 3°C room temperature, and 50 ± 20% relative humidity. After birth, male offspring were also kept under same conditions as the dams.

extract_protocol: RNA samples from testis of PND 30 rats (1 male pup/litter; N=5 litters/group) were extracted using the miRNeasy Kit (Qiagen, Valencia CA, USA). After extraction, the concentration of each RNA sample was determined using a NanoDrop 2000c spectrophotometer (version 3.0.1, Thermo Fisher Scientific Inc, Wilmington DE, USA). RNA samples with RNA Integrity Numbers (RINs) of 8.0 or above were used for gene expression measurements.

treatment_protocol: From gestational day (GD) 6 until postnatal day (PND) 21, the dams (n = 25, per group) were provided ad libitum low-phytoestrogen chow (Purina 5K96; Purina Mills LLC, St Louis, MO, USA) containing 0 (control), 3000, or 30000 ppm HMB (Catalog #HH13-026; Ivy Fine Chemicals, Cherry Hill, NJ, USA).` Dietary administration of HMB to the dams was terminated on PND 21, and male offspring were weaned on PND 28. The male offspring were exposed to HMB via chow and milk. The male offspring were euthanized on PND 30. All animal procedures were approved by the NCTR Institutional Animal Care and Use Committee and adhered to the Guide for the Care and Use of Laboratory Animals prescribed by the National Research Council.

tag: strain

value: Sprague-Dawley

value: Testis

tag: gender

value: Male

tag: age

value: Postnatal day (PND) 30


title: High_S16

source_name: Whole Testis, male, PND 30, HMB-30000ppm, replicate 5


title: High_S14

source_name: Whole Testis, male, PND 30, HMB-30000ppm, replicate 4


title: High_S12

source_name: Whole Testis, male, PND 30, HMB-30000ppm, replicate 2


title: High_S11

source_name: Whole Testis, male, PND 30, HMB-30000ppm, replicate 1


title: genomic DNA from sample WC62

type: genomic

city: Callaghan

first: Nikola

last: Bowden

state: NSW

address: University Dr

department: School of Medicine and Public Health

country: Australia

institute: University of Newcastle

description: Melanoma cell line

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protoc

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Raw methylated and unmethylated were loaded from idat files using the Chip Analysis Methylation Pipeline (ChAMP) package in R. Probes that had a detection p-value of <0.01 were filtered out along with probes on the X and Y chromosomes, probes overlapping with SNPs and those that align to multiple sites. Array was normalised using single sample normalisation (ssNoob) and batch correction corrected using ComBat in ChAMP.

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

growth_protocol: Cell lines were grown in  1X DMEM (5% FBS)  at 37°C and 5% CO2

extract_protocol: Genomic DNA was extracted from cell lines using Quick DNA Universal Kit (Zymo Research). A total of 1 µg of DNA for each cell line was bisulfite converted using the EZ DNA Methylation Kit (Zymo)


title: Low_S10

description: Total RNA from Testis of PND 30 male rats exposed perinatally to 3000 ppm HMB was used for gene expression

source_name: Whole Testis, male, PND 30, HMB-3000ppm, replicate 5


title: genomic DNA from sample WC77

description: Melanoma cell line


title: genomic DNA from sample WC93

description: Melanoma cell line


title: Low_S09

source_name: Whole Testis, male, PND 30, HMB-3000ppm, replicate 4


title: genomic DNA from sample WC66

description: Melanoma cell line


title: Control_S05

description: Total RNA from Testis of PND 30 male rats exposed perinatally to 0 ppm HMB was used for gene expression

source_name: Whole Testis, male, PND 30, untreated, replicate 5


title: genomic DNA from sample WC46

description: Melanoma cell line


title: Low_S07

source_name: Whole Testis, male, PND 30, HMB-3000ppm, replicate 2


title: genomic DNA from sample WC56

description: Melanoma cell line


title: Low_S06

source_name: Whole Testis, male, PND 30, HMB-3000ppm, replicate 1


title: Control_S04

source_name: Whole Testis, male, PND 30, untreated, replicate 4


title: genomic DNA from sample WC75

description: Melanoma cell line


title: genomic DNA from sample WC48

description: Melanoma cell line


title: genomic DNA from sample MME4405

description: Melanoma cell line


title: genomic DNA from sample WC54

description: Melanoma cell line


title: genomic DNA from sample SKEML28

description: Melanoma cell line


title: High_A68

description: Total RNA from Prostate of PND 30 male rats exposed perinatally to 30000 ppm HMB was used for gene expression

source_name: Whole Prostate, male, PND 30, HMB-30000ppm, replicate 5

extract_protocol: RNA samples from prostate of PND 30 rats (1 male pup/litter; N=5 litters/group) were extracted using the miRNeasy Kit (Qiagen, Valencia CA, USA). After extraction, the concentration of each RNA sample was determined using a NanoDrop 2000c spectrophotometer (version 3.0.1, Thermo Fisher Scientific Inc, Wilmington DE, USA). RNA samples with RNA Integrity Numbers (RINs) of 8.0 or above were used for gene expression measurements.

value: Prostate


title: genomic DNA from sample MELRM

description: Melanoma cell line

source_name: Mel-RM

value: Mel-RM


title: Control_S02

source_name: Whole Testis, male, PND 30, untreated, replicate 2


title: Control_S01

source_name: Whole Testis, male, PND 30, untreated, replicate 1


title: genomic DNA from sample WC123

description: Melanoma cell line


title: Control_S03

source_name: Whole Testis, male, PND 30, untreated, replicate 3


title: genomic DNA from sample WC65

description: Melanoma cell line


title: High_A14

source_name: Whole Prostate, male, PND 30, HMB-30000ppm, replicate 2


title: High_A67

source_name: Whole Prostate, male, PND 30, HMB-30000ppm, replicate 4


title: genomic DNA from sample WC86

description: Melanoma cell line


title: Low_A64

description: Total RNA from Prostate of PND 30 male rats exposed perinatally to 3000 ppm HMB was used for gene expression

source_name: Whole Prostate, male, PND 30, HMB-3000ppm, replicate 4


title: Low_A82

source_name: Whole Prostate, male, PND 30, HMB-3000ppm, replicate 5


title: High_A13

source_name: Whole Prostate, male, PND 30, HMB-30000ppm, replicate 1


title: High_A66

source_name: Whole Prostate, male, PND 30, HMB-30000ppm, replicate 3


title: Low_A06

source_name: Whole Prostate, male, PND 30, HMB-3000ppm, replicate 2


title: genomic DNA from sample MM200

description: Melanoma cell line


title: Control_A70

description: Total RNA from Prostate of PND 30 male rats exposed perinatally to 0 ppm HMB was used for gene expression

source_name: Whole Prostate, male, PND 30, untreated, replicate 3


title: Low_S08

source_name: Whole Testis, male, PND 30, HMB-3000ppm, replicate 3


title: Low_A62

source_name: Whole Prostate, male, PND 30, HMB-3000ppm, replicate 3


title: Control_A93

source_name: Whole Prostate, male, PND 30, untreated, replicate 5


title: Low_A05

source_name: Whole Prostate, male, PND 30, HMB-3000ppm, replicate 1


title: Control_A01

source_name: Whole Prostate, male, PND 30, untreated, replicate 1


title: normal brain 4

city: shanghai

first: chun

last: luo

address: 415# fengyang road

department: neurosurgery

country: China

institute: changzheng hospital

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies).

source_name: normal brain

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). Briefly, total RNA from each sample was linearly amplified and labeled with Cy3-UTP. The Labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis

value: brain

tag: diagnosis

value: normal


title: normal brain 5


title: Control_A72

source_name: Whole Prostate, male, PND 30, untreated, replicate 4


title: glioblastoma 2

source_name: glioblastoma

value: glioblastoma


title: normal brain 3


title: normal brain 1


title: glioblastoma 1


title: glioblastoma 3


title: normal brain 2


title: glioblastoma 5


title: Control_A02

source_name: Whole Prostate, male, PND 30, untreated, replicate 2


title: glioblastoma 4


title: glioblastoma 5_miRNA

description:
microRNA
T5

hyb_protocol: The Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to array manual

scan_protocol: The slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=50 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, differentially expressed miRNAs with statistical significance were identified through Volcano Plot filtering

label_protocol: The miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling


title: PSC27-PTX-treated-rep 3

city: Shanghai

first: Yu

last: Sun

address: 320 Yueyang Rd, Life Sciences Building A #1508

department: Shanghai Institute of Nutrition and Health

institute: Chinese Academy of Sciences

description: PSC27 expression 7 days after treatment by 1 uM paclitaxel for 12 hrs

hyb_protocol: One μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

data_processing:
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization,Combat between the groups of error correction and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies).
After quantile normalization of the raw data, LncRNAs and mRNAs that at least 11 out of 21 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Hierarchical Clustering and combined analysis were performed using homemade scripts.

source_name: PSC27 PTX-treated, 1 uM paclitaxel for 12 hrs ,replicate 3

label_protocol: Sample labeling was performed according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a mixture of oligo(dT) and random primers (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: PSC27 cells were grown in prostate stromal cell complete (PSCC) media supplemented with 10% FBS and 1% antibiotics.

extract_protocol: Total RNAs were prepared with a RNeasy Miniprep kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: For experimental groups, cells were either treated with either ionizing radiation (Cs137) for 10Gy, 50 ug/ml bleomycin for 6 hours, 1 uM mitoxantrone for 24 hours, 5 uM docetaxel for 12 hours, 1 uM paclitaxel for 12 hours, or 100 nM vincristine for 12 hours.

value: Normal human prostate

value: Primary stromal cells


title: PSC27-PTX-treated-rep 2

source_name: PSC27 PTX-treated, 1 uM paclitaxel for 12 hrs, replicate 2


title: glioblastoma 2_miRNA

description:
microRNA
T2


title: glioblastoma 4_miRNA

description:
microRNA
T4


title: PSC27-MIT-treated-rep 2

description: PSC27 expression 7 days after treatment by 1 uM mitoxantrone for 24 hrs

source_name: PSC27 MIT-treated, 1 uM mitoxantrone for 24 hrs, replicate 2


title: glioblastoma 1_miRNA

description:
microRNA
T1


title: PSC27-VCR-treated-rep 3

description: PSC27 expression 7 days after treatment by 100 nM vincristine for 12 hrs

source_name: PSC27 VCR-treated, 100 nM vincristine for 12 hrs, replicate 3


title: 487 ILW backfat, mRNA

city: Bologna

first: Roberta

last: Davoli

state: Bologna

address: Viale G. Fanin, 46

department: DISTAL

country: Italy

institute: Bologna University

description:
pig_backfat_487
Sample_487AC485
Castrated male
processed data file: raw_counts_variants.txt
processed data file: normalized_counts_variants.txt

library_source: transcriptomic

data_processing:
Reads with an overall sequence mean Phred quality lower than 30, reads with more than two nt (nucleotides) with quality lower than 20 and reads with uncalled bases were also discarded. Reads between 15 and 30 nt long were selected by means of the HTSEQ package.
The selected reads were mapped using BOWTIE v.0.12.7. We used the Sscrofa 10.2 genome as a reference.
Cleaned sequencing data were processed by the MIR&MORE software pipeline. The two branches of the pipeline are devoted to perform the quantification and the characterization of known miRNAs and the discovery of mature miRNAs in known precursor sequences.
MiRDeep2 v 0.0.5 was then run using default parameters. miRDeep2 predictions were filtered restricting to precursors with miRDeep2 score greater than 1.0, length greater than or equal to 50 nt and predicted probability of being a miRNA greater than 60%.
Read counts were normalized across all the samples according to the DESeq2 (v1.4.5) approach. Small RNAs represented by less than ten normalized reads considering all samples were excluded from further analysis. Short RNA differential expression was assessed by DESeq2, considering significant those variations with FDR < 0.05.
A custom target prediction was performed by the application of the MIRANDA )v 3.3a) method using the transcript sequences detected on the same samples.
Genome_build: Sscrofa10.2
Supplementary_files_format_and_content: raw_counts_variants.txt: Semicolon-delimited text file formatted as a matrix table of raw reads.
Supplementary_files_format_and_content: normalized_counts_variants.txt: Semicolon-delimited text file formatted as a matrix table of normalized reads.

organism: Sus scrofa

source_name: backfat

growth_protocol: All animals were housed in the same environment and fed the same diet.

extract_protocol:
Total RNA was extracted with Trizol (Invitrogen) according to the manufacturer's instruction. Results of the extraction were quantified using a Nanodrop ND-1000 spectrophotometer (Nanodrop Technologies) and the quality of the extracted RNA was assayed using an Agilent 2100 BioAnalyzer (Agilent Technologies).
The mRNA library was prepared using the TruSeq Small RNA kit (Illumina) and version 3 of the reagents, following the manufacturer's suggested protocol.
The libraries were individually tagged and sequenced on an Illumina GAII as 100 bp long single-end reads using two samples per lane.

treatment_protocol: Backfat sample was collected in a commercial slaughterhouse. The sample was immediately frozen in liquid nitrogen and stored at -80C in a deep freezer until RNA isolation.

tag: breed

value: Italian Large White

value: neuter

value: backfat

tag: backfat deposition

value: low

value: 241 days

tag: weight


title: PSC27-RAD-treated-rep 3

description: PSC27 expression 7 days after treatment by ionizing radiation (Cs137) for 10Gy

source_name: PSC27 RAD-treated, ionizing radiation (Cs137) for 10Gy, replicate 3


title: 489 ILW backfat, mRNA

description:
pig_backfat_489
Sample_489AC487
Castrated male
processed data file: raw_counts_variants.txt
processed data file: normalized_counts_variants.txt

value: high


title: PSC27-MIT-treated-rep 3

source_name: PSC27 MIT-treated, 1 uM mitoxantrone for 24 hrs, replicate 3


title: PSC27-VCR-treated-rep 1

source_name: PSC27 VCR-treated, 100 nM vincristine for 12 hrs, replicate 1


title: PSC27-TXT-treated-rep 3

description: PSC27 expression 7 days after treatment by 5 uM docetaxel for 12 hrs

source_name: PSC27 TXT-treated, 5 uM docetaxel for 12 hrs, replicate 3


title: PSC27-PTX-treated-rep 1

source_name: PSC27 PTX-treated, 1 uM paclitaxel for 12 hrs, replicate 1


title: PSC27-BLEO-treated-rep 1

description: PSC27 expression 7 days after treatment by 50 ug/ml bleomycin for 6 hrs

source_name: PSC27 BLEO-treated, 50 ug/ml bleomycin for 6 hrs, replicate 1


title: PSC27-RAD-treated-rep 2

source_name: PSC27 RAD-treated, ionizing radiation (Cs137) for 10Gy, replicate 2


title: PSC27-VCR-treated-rep 2

source_name: PSC27 VCR-treated, 100 nM vincristine for 12 hrs, replicate 2


title: PSC27-TXT-treated-rep 1

source_name: PSC27 TXT-treated, 5 uM docetaxel for 12 hrs, replicate 1


title: PSC27-Control-rep 3

description: PSC27 control expression (untreated)

source_name: PSC27 control, replicate 3


title: PSC27-Control-rep 2

description: PSC27 control expression (untreated)

source_name: PSC27 control, replicate 2


title: glioblastoma 3_miRNA

description:
microRNA
T3

source_name: glioblastoma


title: PSC27-BLEO-treated-rep 2

source_name: PSC27 BLEO-treated, 50 ug/ml bleomycin for 6 hrs, replicate 2


title: 488 ILW backfat, mRNA

description:
pig_backfat_488
Sample_488AC486
processed data file: raw_counts_variants.txt
processed data file: normalized_counts_variants.txt

value: female

value: 244 days


title: PSC27-TXT-treated-rep 2

source_name: PSC27 TXT-treated, 5 uM docetaxel for 12 hrs, replicate 2


title: PSC27-RAD-treated-rep 1

source_name: PSC27 RAD-treated, ionizing radiation (Cs137) for 10Gy, replicate 1


title: PSC27-MIT-treated-rep 1

source_name: PSC27 MIT-treated, 1 uM mitoxantrone for 24 hrs, replicate 1


title: 490 ILW backfat, mRNA

description:
pig_backfat_490
Sample_490AC488
Castrated male
processed data file: raw_counts_variants.txt
processed data file: normalized_counts_variants.txt

source_name: backfat

value: 235 days


title: PSC27-BLEO-treated-rep 3

source_name: PSC27 BLEO-treated, 50 ug/ml bleomycin for 6 hrs, replicate 3


title: 486 ILW backfat, mRNA

description:
pig_backfat_486
Sample_486U139
processed data file: raw_counts_variants.txt
processed data file: normalized_counts_variants.txt

value: 249 days


title: PSC27-Control-rep 1

description: PSC27 control expression (untreated)

source_name: PSC27 control, replicate 1


title: 483 ILW backfat, mRNA

description:
pig_backfat_483
Sample_483U136
processed data file: raw_counts_variants.txt
processed data file: normalized_counts_variants.txt

value: 250 days


title: normal brain 4_miRNA

description:
microRNA
N4

source_name: normal brain


title: normal brain 3_miRNA

description:
microRNA
N3


title: 482 ILW backfat, mRNA

description:
pig_backfat_482
Sample_482U135
processed data file: raw_counts_variants.txt
processed data file: normalized_counts_variants.txt

value: 237 days


title: 480 ILW backfat, mRNA

description:
pig_backfat_480
Sample_480U074
processed data file: raw_counts_variants.txt
processed data file: normalized_counts_variants.txt

value: 243 days


title: normal brain 1_miRNA

description:
microRNA
N1

value: brain

value: normal


title: 479 ILW backfat, mRNA

description:
pig_backfat_479
Sample_479U134
Castrated male
processed data file: raw_counts_variants.txt
processed data file: normalized_counts_variants.txt


title: normal brain 2_miRNA

description:
microRNA
N2


title: 477 ILW backfat, mRNA

description:
pig_backfat_477
Sample_477u076
Castrated male
processed data file: raw_counts_variants.txt
processed data file: normalized_counts_variants.txt


title: 476 ILW backfat, mRNA

description:
pig_backfat_476
Sample_476U969
processed data file: raw_counts_variants.txt
processed data file: normalized_counts_variants.txt


title: 478 ILW backfat, mRNA

description:
pig_backfat_478
Sample_478U077
processed data file: raw_counts_variants.txt
processed data file: normalized_counts_variants.txt

value: 239 days


title: 475 ILW backfat, mRNA

description:
pig_backfat_475
Sample_475U968
Castrated male
processed data file: raw_counts_variants.txt
processed data file: normalized_counts_variants.txt

value: 233 days


title: 474 ILW backfat, mRNA

description:
pig_backfat_474
Sample_474U967
Castrated male
processed data file: raw_counts_variants.txt
processed data file: normalized_counts_variants.txt

value: Italian Large White


title: 485 ILW backfat, mRNA

description:
pig_backfat_485
Sample_485U138
processed data file: raw_counts_variants.txt
processed data file: normalized_counts_variants.txt


title: 481 ILW backfat, mRNA

description:
pig_backfat_481
Sample_481U075
Castrated male
processed data file: raw_counts_variants.txt
processed data file: normalized_counts_variants.txt

value: neuter


title: 484 ILW backfat, mRNA

description:
pig_backfat_484
Sample_484U137
Castrated male
processed data file: raw_counts_variants.txt
processed data file: normalized_counts_variants.txt

value: backfat


title: 473 ILW backfat, mRNA

description:
pig_backfat_473
Sample_473U966
processed data file: raw_counts_variants.txt
processed data file: normalized_counts_variants.txt

value: low

value: 247 days


title: normal brain 5_miRNA

description:
microRNA
N5


title: Breast cancer tissue [T194] copy number

city: Mexico

first: Sandra

middle: Lorena

last: Romero-Cordoba

state: Mexico

address: Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan. México, D.F.

department: Cancer Genomics

country: Mexico

institute: National Instute of Genomic Medicine

description: Hybridized to SNP6 Affymetrix

hyb_protocol: DNA was digested with NspI and StyI enzymes (New England Biolabs), ligated to the respective Affymetrix adapters using T4 DNA ligase (New England Biolabs) amplified (Clontech), purified using magnetic beads (Agencourt), labeled, fragmented, and hybridized to the arrays

scan_protocol: As per manufacturer (Affymetrix)

data_processing:
Background correction and extraction of raw fluorescence intensity were performed with the Affymetrix Genotyping Console. To generate the copy number profiles we used the “Copy Number Inference” pipeline implemented in genepattern: (http://genepattern.broadinstitute.org/gp/pages/index.jsf). In brief, probe-level signal intensities from Affymetrix SNP6 (cel files) were normalized to a uniform brightness and merged to obtain values for each probe set using SNP File Creator. These intensities measurements were converted into a copy number call by the Copy Number Inference model. After reducing the noise by subtracting out the variation that is also seen within the normal samples (peripheral blood), the CBS segmentation algorithm identifies regions in the genome that have a uniform underlying copy number, creating a segmentation file. Finally, we identified the significantly somatic alterations with GISTIC using the cnv segmentation results.
Matched normalized SCNA and SNPs

label: biotin

source_name: Breast tumor

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: DNA from peripheral blood lymphocytes was extracted with the QIAamp DNA Blood Maxi Kit (Qiagen, Valencia, CA), according to manufacturer’s instructions

value: Breast cancer tissue

value: Somatic cell fraction

tag: population

value: Mexican hispanic


title: Breast cancer tissue [T190] copy number

description: Hybridized to SNP6 Affymetrix


title: Breast cancer tissue [T191] copy number

description: Hybridized to SNP6 Affymetrix


title: Breast cancer tissue [T196] copy number

description: Hybridized to SNP6 Affymetrix


title: Breast cancer tissue [T198] copy number

description: Hybridized to SNP6 Affymetrix


title: Breast cancer tissue [T200] copy number

description: Hybridized to SNP6 Affymetrix


title: Breast cancer tissue [T189] copy number

description: Hybridized to SNP6 Affymetrix


title: Breast cancer tissue [T187] copy number

description: Hybridized to SNP6 Affymetrix


title: SINET_Case15_liver_array3

city: Göteborg

first: Anna

last: Rehammar

address: Chalmers Tvärgata 3

department: Department of Mathematical Sciences

country: Sweden

institute: Chalmers University of Technology

hyb_protocol: Labeled samples were hybridized to 8x15K human miRNA microarrays (V3) (G4470C; Design ID 021827; Agilent Technologies)

scan_protocol: Arrays were scanned using an Agilent G2565BA Microarray Scanner (Agilent Technologies).

data_processing: Images were read and processed using Feature Extraction software v10.7.1.1 (Agilent Technologies). The microarrays were background corrected using the normexp method and normalized using the quantile-quantile method.

source_name: liver metastasis

label_protocol: cDNA synthesis, labeling, and hybridization were performed according to the One-Color Microarray-Based miRNA Complete labeling and hybridization protocol (v2.1) (Agilent Technologies).

extract_protocol: RNA was isolated from fresh-frozen biopsies using the miRNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol.

tag: case

value: Case 15


title: Breast cancer tissue [T193] copy number

description: Hybridized to SNP6 Affymetrix


title: Breast cancer tissue [T192] copy number

description: Hybridized to SNP6 Affymetrix


title: Breast cancer tissue [T186] copy number

description: Hybridized to SNP6 Affymetrix


title: SINET_Case1_primary_array2

source_name: primary tumor

value: Case 1


title: SINET_Case23_liver_array2

value: Case 23


title: PIP2-2

city: Trondheim

first: Per

last: Winge

address: Høgskoleringen 5e

department: Department of Biology

country: Norway

institute: Norwegian University of Science and Technology

description:
Two color microarray. Biological replicas are dye-swapped between slides.
Rosette leaves treated with PIP2 peptide for 3 hours compared to rosette leaves treated with MQ water and 0.02% Silwet L-77 for 3 hours (replica 2)

hyb_protocol: Hybridization was performed with the Gene Expression Hybridization Kit (Agilent p/n 5188-5242). 825 ng cRNA from both MQ-silwet treated plants and peptide-treated plants were used. The cRNA mixture was fragmented and hybridized on Arabidopsis (V4) Gene Expression Microarray 4x44K arrays in a rotary oven at 65°C in ~15 h. The slides were washed with Gene Expression Wash Buffer 1 (Agilent p/n 5188-5325), Gene Expression Wash Buffer 2 (Agilent p/n 5188-5326), acetonitrile (VWR International) and Stabilization and Drying Solution (Agilent Technologies) according to the manufacturer’s instructions.

scan_protocol: The slides were scanned at 5 µm resolution on an Agilent DNA microarray scanner (Agilent Technologies).

data_processing: Prior to the statistical analysis spots from control spikes, landmarks and genes with low expression (absent) were filtered out. The data were analysed using the limma package (Smyth, 2004) and the R statistical data analysis program package (R 3.0.3). No background subtraction was performed and data were normalized by the global loess normalization method. The Benjamini and Hochberg’s method to control the false discovery rate was used to identify differentially regulated genes (Benjamini and Hochberg, 1995). Genes with dye bias effects were removed and genes with an adjusted p-value less than 0.05 were regarded as significantly differentially expressed. The study is MIAME compliant.

source_name: Treatment of rosette leaves with MQ water and 0.02% Silwet L-77 (3 hours), 2 week stage

label_protocol: Total RNA (~0.2 µg) was reverse transcribed, amplified and labelled using the Low Input Quick Amp Labeling Kit, two-color, (Agilent p/n 5190-2306) (Agilent Technologies, USA). cRNA from the MQ-silwet and peptide-treated plants (PIP1 or PIP2 peptide) were alternately labelled with Cy3 or Cy5.

growth_protocol: Seeds of Col-0 ecotype were surface-sterilised and sown out on half-strength MS plates at a density of 20 seeds per Petri dish (14 cm diameter), and stratified for 3 days at 4°C. Plates were grown under a 16 h photoperiod (70 µmol m-2 s-1) at 22°C for two weeks.

extract_protocol: 100 mg frozen plant tissue each from four biological replicas were homogenised using TissueLyser II (Qiagen, Hilden, Germany) for 2 x 2 minutes at 25 Hz. Total RNA was extracted with the Spectrum Plant Total RNA kit (Sigma-Aldrich, Saint Louis, USA) as described by the supplier, but with lysis solution being added to the plant tissue between the two disruption cycles. An on-column DNase digestion was performed using the RNase-Free DNase Set (Qiagen, Hilden, Germany).

treatment_protocol: Seedlings were treated by spraying with an aqueous peptide solution (100 nM) supplemented with 0.02% silwet L-77 (Lehle Seeds, UK). Control seedlings were sprayed with MQ water with 0.02% silwet L-77. Whole rosettes were collected 3 h after treatment, snap-frozen in liquid nitrogen, and stored at -80°C.

tag: ecotype

value: Rosette leaves, 2 week stage

source_name: PIP2 peptide treatment of rosette leaves (3 hours), 2 week stage


title: Breast cancer tissue [T178] copy number

description: Hybridized to SNP6 Affymetrix


title: Breast cancer tissue [T184] copy number

description: Hybridized to SNP6 Affymetrix


title: Breast cancer tissue [T176] copy number

description: Hybridized to SNP6 Affymetrix


title: SINET_Case14_primary_array2

value: Case 14


title: PIP1-2

description:
Two color microarray. Biological replicas are dye-swapped between slides.
Rosette leaves treated with PIP1 peptide for 3 hours compared to rosette leaves treated with MQ water and 0.02% Silwet L-77 for 3 hours (replica 2)

source_name: PIP1 peptide treatment of rosette leaves (3 hours), 2 week stage


title: PIP2-3

description:
Two color microarray. Biological replicas are dye-swapped between slides.
Rosette leaves treated with PIP2 peptide for 3 hours compared to rosette leaves treated with MQ water and 0.02% Silwet L-77 for 3 hours (replica 3)


title: Breast cancer tissue [T175] copy number

description: Hybridized to SNP6 Affymetrix


title: PIP2-1

description:
Two color microarray. Biological replicas are dye-swapped between slides.
Rosette leaves treated with PIP2 peptide for 3 hours compared to rosette leaves treated with MQ water and 0.02% Silwet L-77 for 3 hours (replica 1)


title: SINET_Case5_primary_array1

value: Case 5


title: SINET_Case8_primary_array2

value: Case 8


title: SINET_Case27_liver_array1

value: Case 27


title: Breast cancer tissue [T174] copy number

description: Hybridized to SNP6 Affymetrix


title: Breast cancer tissue [T172] copy number

description: Hybridized to SNP6 Affymetrix


title: PIP1-3

description:
Two color microarray. Biological replicas are dye-swapped between slides.
Rosette leaves treated with PIP1 peptide for 3 hours compared to rosette leaves treated with MQ water and 0.02% Silwet L-77 for 3 hours (replica 3)


title: SINET_Case14_primary_array1


title: SINET_Case15_primary_array1


title: Breast cancer tissue [T169] copy number

description: Hybridized to SNP6 Affymetrix


title: SINET_Case6_primary_array1

value: Case 6


title: Breast cancer tissue [T168] copy number

description: Hybridized to SNP6 Affymetrix


title: SINET_Case23_liver_array1


title: Breast cancer tissue [T166] copy number

description: Hybridized to SNP6 Affymetrix


title: SINET_Case15_liver_array2


title: PIP1-1

description:
Two color microarray. Biological replicas are dye-swapped between slides.
Rosette leaves treated with PIP1 peptide for 3 hours compared to rosette leaves treated with MQ water and 0.02% Silwet L-77 for 3 hours (replica 1)


title: Breast cancer tissue [T165] copy number

description: Hybridized to SNP6 Affymetrix


title: SINET_Case25_lymphnode_array1

source_name: lymph node metastasis

value: Case 25


title: SINET_Case7_primary_array1

value: Case 7


title: SINET_Case16_liver_array1

value: Case 16


title: Breast cancer tissue [T160] copy number

description: Hybridized to SNP6 Affymetrix


title: SINET_Case3_primary_array1

value: Case 3


title: SINET_Case32_liver_array1

value: Case 32


title: SINET_Case8_primary_array1


title: SImucosa_6

source_name: normal small intestine mucosa

value: normal


title: SINET_Case7_liver_array1


title: SINET_Case13_primary_array1

value: Case 13


title: SINET_Case18_liver_array1

value: Case 18


title: Breast cancer tissue [T150] copy number

description: Hybridized to SNP6 Affymetrix

value: Breast cancer tissue

value: Somatic cell fraction

value: Mexican hispanic


title: Breast cancer tissue [T155] copy number

description: Hybridized to SNP6 Affymetrix


title: Breast cancer tissue [T154] copy number

description: Hybridized to SNP6 Affymetrix


title: SINET_Case14_liver_array1


title: Breast cancer tissue [T149] copy number

description: Hybridized to SNP6 Affymetrix


title: SINET_Case8_liver_array1


title: Breast cancer tissue [T146] copy number

description: Hybridized to SNP6 Affymetrix


title: Breast cancer tissue [T143] copy number

description: Hybridized to SNP6 Affymetrix


title: SINET_Case37_liver_array1

value: Case 37


title: Breast cancer tissue [T144] copy number

description: Hybridized to SNP6 Affymetrix


title: SINET_Case11_primary_array1

value: Case 11


title: SINET_Case2_primary_array1

value: Case 2


title: Breast cancer tissue [T142] copy number

description: Hybridized to SNP6 Affymetrix


title: Breast cancer tissue [T141] copy number

description: Hybridized to SNP6 Affymetrix


title: SINET_Case13_liver_array1


title: Breast cancer tissue [T140] copy number

description: Hybridized to SNP6 Affymetrix


title: SINET_Case33_liver_array1

value: Case 33


title: Breast cancer tissue [T137] copy number

description: Hybridized to SNP6 Affymetrix


title: Breast cancer tissue [T138] copy number

description: Hybridized to SNP6 Affymetrix


title: Breast cancer tissue [T125] copy number

description: Hybridized to SNP6 Affymetrix


title: Breast cancer tissue [T135] copy number

description: Hybridized to SNP6 Affymetrix


title: SINET_Case34_liver_array1

value: Case 34


title: SINET_Case29_liver_array1

value: Case 29


title: Breast cancer tissue [T129] copy number

description: Hybridized to SNP6 Affymetrix


title: SINET_Case19_liver_array1

value: Case 19


title: Breast cancer tissue [T124] copy number

description: Hybridized to SNP6 Affymetrix


title: SImucosa_5


title: SINET_Case15_liver_array1

value: Case 15


title: SINET_Case30_liver_array1

value: Case 30


title: SImucosa_4


title: Breast cancer tissue [T123] copy number

description: Hybridized to SNP6 Affymetrix


title: SINET_Case28_liver_array1

value: Case 28


title: SImucosa_3


title: SINET_Case31_liver_array1

value: Case 31


title: SINET_Case36_lymphnode_array1

value: Case 36


title: Breast cancer tissue [T121] copy number

description: Hybridized to SNP6 Affymetrix


title: SINET_Case35_liver_array1

value: Case 35


title: Breast cancer tissue [T120] copy number

description: Hybridized to SNP6 Affymetrix


title: SINET_Case17_liver_array1

value: Case 17


title: Breast cancer tissue [T126] copy number

description: Hybridized to SNP6 Affymetrix

value: Breast cancer tissue


title: Breast cancer tissue [T113] copy number

description: Hybridized to SNP6 Affymetrix

value: Somatic cell fraction


title: SINET_Case22_liver_array1

value: Case 22


title: Breast cancer tissue [T110] copy number

description: Hybridized to SNP6 Affymetrix

value: Mexican hispanic


title: SINET_Case24_primary_array1

value: Case 24


title: Breast cancer tissue [T108] copy number

description: Hybridized to SNP6 Affymetrix


title: SImucosa_1

value: normal


title: Breast cancer tissue [T105] copy number

description: Hybridized to SNP6 Affymetrix


title: Breast cancer tissue [T122] copy number

description: Hybridized to SNP6 Affymetrix


title: Breast cancer tissue [T106] copy number

description: Hybridized to SNP6 Affymetrix


title: Breast cancer tissue [T98] copy number

description: Hybridized to SNP6 Affymetrix


title: SINET_Case26_liver_array1

value: Case 26


title: Breast cancer tissue [T94] copy number

description: Hybridized to SNP6 Affymetrix


title: SINET_Case4_primary_array1

value: Case 4


title: SINET_Case1_primary_array1

value: Case 1


title: Breast cancer tissue [T85] copy number

description: Hybridized to SNP6 Affymetrix


title: SINET_Case21_liver_array1

value: Case 21


title: Breast cancer tissue [T95] copy number

description: Hybridized to SNP6 Affymetrix


title: SImucosa_2


title: Breast cancer tissue [T83] copy number

description: Hybridized to SNP6 Affymetrix


title: SINET_Case10_primary_array1

value: Case 10


title: Breast cancer tissue [T82] copy number

description: Hybridized to SNP6 Affymetrix


title: Breast cancer tissue [T116] copy number

description: Hybridized to SNP6 Affymetrix


title: Breast cancer tissue [T81] copy number

description: Hybridized to SNP6 Affymetrix


title: Breast cancer tissue [T80] copy number

description: Hybridized to SNP6 Affymetrix


title: SINET_Case20_liver_array1

value: Case 20


title: Breast cancer tissue [T97] copy number

description: Hybridized to SNP6 Affymetrix


title: Breast cancer tissue [T77] copy number

description: Hybridized to SNP6 Affymetrix


title: Breast cancer tissue [T76] copy number

description: Hybridized to SNP6 Affymetrix


title: Breast cancer tissue [T75] copy number

description: Hybridized to SNP6 Affymetrix


title: Breast cancer tissue [T73] copy number

description: Hybridized to SNP6 Affymetrix


title: SINET_Case12_primary_array1

value: Case 12


title: Breast cancer tissue [T71] copy number

description: Hybridized to SNP6 Affymetrix


title: Breast cancer tissue [T69] copy number

description: Hybridized to SNP6 Affymetrix


title: SINET_Case9_primary_array1

value: Case 9


title: FOXD1 knockdown #2 A375 melanoma cell line rep2

city: heidelberg

first: Lionel

last: Larribere

address: im neuenheimer Feld

country: Germany

institute: DKFZ

description:
A375 siFOXD1-2B
replicate 2
101194680007_C

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with IlluminaGUI in R

source_name: melanoma patient

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

extract_protocol: mRNA was isolated with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Clean-up and DNase I treatment was included. Quality control was performed with Agilent Bioanalyzer.

value: A375 melanoma cell line

tag: biomaterial provider

value: generated at DKFZ

value: FOXD1 knockdown #2


title: Breast cancer tissue [T62] copy number

description: Hybridized to SNP6 Affymetrix

value: Breast cancer tissue


title: Breast cancer tissue [T58] copy number

description: Hybridized to SNP6 Affymetrix

value: Somatic cell fraction


title: Breast cancer tissue [T59] copy number

description: Hybridized to SNP6 Affymetrix


title: FOXD1 knockdown #1 A375 melanoma cell line rep3

description:
A375 siFOXD1-1C
replicate 3
101194680007_H

value: FOXD1 knockdown #1


title: FOXD1 knockdown #1 MeWo melanoma cell line rep1

description:
MeWo siFOXD1-1A
replicate 1
101194620038_B

value: MeWo melanoma cell line


title: control A375 melanoma cell line rep3

description:
A375 siCTL_C
replicate 3
101194680007_G

value: control


title: FOXD1 knockdown #2  MeWo melanoma cell line rep2

description:
MeWo siFOXD1-2B
replicate 2
101194620038_L


title: control A375 melanoma cell line rep1

description:
A375 siCTL_A
replicate 1
101194620038_D


title: FOXD1 knockdown #2 A375 melanoma cell line rep1

description:
A375 siFOXD1-2A
replicate 1
101194620038_F


title: FOXD1 knockdown #1 A375 melanoma cell line rep2

description:
A375 siFOXD1-1B
replicate 2
101194680007_B


title: FOXD1 knockdown #2 A375 melanoma cell line rep3

description:
A375 siFOXD1-2C
replicate 3
101194680007_I


title: control A375 melanoma cell line rep2

description:
A375 siCTL_B
replicate 2
101194680007_A


title: FOXD1 knockdown #1 A375 melanoma cell line rep1

description:
A375 siFOXD1-1A
replicate 1
101194620038_E


title: FOXD1 knockdown #2  MeWo melanoma cell line rep1

description:
MeWo siFOXD1-2A
replicate 1
101194620038_C


title: control MeWo melanoma cell line rep2

description:
MeWo siCTL_B
replicate 2
101194620038_J


title: Breast cancer tissue [T74] copy number

description: Hybridized to SNP6 Affymetrix

value: Mexican hispanic


title: Breast cancer tissue [T55] copy number

description: Hybridized to SNP6 Affymetrix


title: FOXD1 knockdown #1 MeWo melanoma cell line rep2

description:
MeWo siFOXD1-1B
replicate 2
101194620038_K


title: Breast cancer tissue [T48] copy number

description: Hybridized to SNP6 Affymetrix


title: control MeWo melanoma cell line rep1

description:
MeWo siCTL_A
replicate 1
101194620038_A


title: Breast cancer tissue [T47] copy number

description: Hybridized to SNP6 Affymetrix


title: Breast cancer tissue [T50] copy number

description: Hybridized to SNP6 Affymetrix


title: Breast cancer tissue [T45] copy number

description: Hybridized to SNP6 Affymetrix


title: Breast cancer tissue [T44] copy number

description: Hybridized to SNP6 Affymetrix


title: Breast cancer tissue [T40] copy number

description: Hybridized to SNP6 Affymetrix


title: Breast cancer tissue [T39] copy number

description: Hybridized to SNP6 Affymetrix


title: Breast cancer tissue [T43] copy number

description: Hybridized to SNP6 Affymetrix


title: human melanoma cell line MeWo

description:
MeWo
no replicate
9878593057_L

value: human melanoma cell line MeWo

value: Nice uni.


title: human melanoma cell line A375

description:
A375
no replicate
9985187156_A

value: human melanoma cell line A375

value: ATCC


title: Breast cancer tissue [T38] copy number

description: Hybridized to SNP6 Affymetrix


title: Skmel 28 human melanoma cell line_clone with no SETDB1 amplification

description:
SK-NL-SETDB1
no replicate
8986302012_E


title: Breast cancer tissue [T37] copy number

description: Hybridized to SNP6 Affymetrix


title: Breast cancer tissue [T36] copy number

description: Hybridized to SNP6 Affymetrix


title: human melanoma cell line MZ7

description:
MZ7
no replicate
9985187156_C

value: human melanoma cell line MZ7

value: Bonn uni.


title: Breast cancer tissue [T34] copy number

description: Hybridized to SNP6 Affymetrix


title: human melanoma cell line HT144

description:
HT144
no replicate
8136640001_I

value: human melanoma cell line HT144


title: Breast cancer tissue [T31] copy number

description: Hybridized to SNP6 Affymetrix


title: Breast cancer tissue [T28] copy number

description: Hybridized to SNP6 Affymetrix


title: Breast cancer tissue [T29] copy number

description: Hybridized to SNP6 Affymetrix


title: Breast cancer tissue [T30] copy number

description: Hybridized to SNP6 Affymetrix


title: Breast cancer tissue [T27] copy number

description: Hybridized to SNP6 Affymetrix


title: hiPSC rep3

description:
D1_3
replicate 3
9347704022_J

source_name: healthy donor

value: hiPSC


title: Breast cancer tissue [T41] copy number

description: Hybridized to SNP6 Affymetrix


title: hiPSC rep1

description:
D1_1
replicate 1
8986302012_A


title: hiPSC rep2

description:
D1_2
replicate 2
9347704022_I


title: Breast cancer tissue [T26] copy number

description: Hybridized to SNP6 Affymetrix


title: Breast cancer tissue [T17] copy number

description: Hybridized to SNP6 Affymetrix


title: Breast cancer tissue [T16] copy number

description: Hybridized to SNP6 Affymetrix


title: Breast cancer tissue [T13] copy number

description: Hybridized to SNP6 Affymetrix


title: Breast cancer tissue [T15] copy number

description: Hybridized to SNP6 Affymetrix


title: Breast cancer tissue [T9] copy number

description: Hybridized to SNP6 Affymetrix


title: Breast cancer tissue [T6] copy number

description: Hybridized to SNP6 Affymetrix


title: Breast cancer tissue [T18] copy number

description: Hybridized to SNP6 Affymetrix


title: Breast cancer tissue [T4] copy number

description: Hybridized to SNP6 Affymetrix


title: Breast cancer tissue [T2] copy number

description: Hybridized to SNP6 Affymetrix


title: S276A_IL1_rep2

city: Cleveland

last: Stark

state: OH

address: 9500 Euclid Avenue

department: Cancer Biology

institute: Cleveland Clinic Lerner Research Institute

data_processing: The data were normalised using quantile normalisation with Illumina GenomeStudio Software 2011.1 Gene Expression Module.

label_protocol: Biotinylated cRNA were prepared with the TargetAmpNano Labeling kit for Illumina Expression BeadChip.

growth_protocol: HMECs immortalized with human telomerase reverse transcriptase (Clontech) were grown in Medium 171 with mammary epithelial growth supplement (Invitrogen). All cultures were kept in 5% CO2 at 37°C.

extract_protocol: RNA was extracted with RNAeasy Kit from Qiagen. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: HME cells deprived of EGF-containing supplements overnight were treated with or without 100 ng/mL EGF (Millipore) or 10 ng/mL IL-1β (Peprotech) for 4 h.

value: human mammary epithelial cells (HMEC)

tag: genotype/variation

tag: treated with

value: 10 ng/mL IL-1 4 h


title: WT_IL1_rep2

value: wildtype


title: S276A_IL1_rep1


title: WT_IL1_rep1


title: WT_UT_rep1

value: none (untreated)


title: WT_EGF_rep2

value: 100 ng/mL EGF 4 h


title: S276A_EGF_rep2


title: WT_UT_rep2


title: WT_EGF_rep1


title: S276A_UT_rep1


title: S276A_EGF_rep1


title: S276A_UT_rep2


title: Breast cancer tissue [T1] copy number

description: Hybridized to SNP6 Affymetrix

tag: tissue

value: Breast cancer tissue

value: Somatic cell fraction


title: Breast cancer tissue [T5] copy number

description: Hybridized to SNP6 Affymetrix


title: Buffy coat from peripheral blood [C198] copy number

description: Hybridized to SNP6 Affymetrix

source_name: Blood from breast cancer patient

value: Buffy coat from peripheral blood

value: Germinal cell fraction


title: Buffy coat from peripheral blood [C200] copy number

description: Hybridized to SNP6 Affymetrix

value: Mexican hispanic


title: Buffy coat from peripheral blood [C194] copy number

description: Hybridized to SNP6 Affymetrix


title: Buffy coat from peripheral blood [C196] copy number

description: Hybridized to SNP6 Affymetrix


title: Buffy coat from peripheral blood [C193] copy number

description: Hybridized to SNP6 Affymetrix


title: Buffy coat from peripheral blood [C192] copy number

description: Hybridized to SNP6 Affymetrix


title: Buffy coat from peripheral blood [C191] copy number

description: Hybridized to SNP6 Affymetrix


title: Buffy coat from peripheral blood [C190] copy number

description: Hybridized to SNP6 Affymetrix


title: Buffy coat from peripheral blood [C189] copy number

description: Hybridized to SNP6 Affymetrix


title: Buffy coat from peripheral blood [C187] copy number

description: Hybridized to SNP6 Affymetrix


title: Si HDAC2 1-2

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

country: Japan

institute: CyberomiX Inc

description: Gene expression of differentiated CMs 30 days after the initial differentiation treated by siHDAC2

hyb_protocol: Manufacturer's protocol

scan_protocol: Slides were scanned on the G2565CA Microarray Scanner System (Agilent).

data_processing: GeneSpring GX. Signals were normalized to percentile.

source_name: day30 CMs siHDAC2-1 sample2

label_protocol: Manufacturer's protocol

growth_protocol: Undifferentiated iPSCs were dissociated, and then suspended in StemPro34 medium supplemented with Y-27632 and BMP4 and allowed to form EBs by being placed into 96-well dish. On day 1, media, which included activin A, BMP4 and bFGF, were added into the wells. On day 3, EBs were collected and dissociated, and then suspended in differentiation media supplemented with VEGF and  IWP-3. Approximately 10000-20000 cells were put in each well to again form aggregates for 4 days. On day 7, the media were changed to StemPro 34 media supplemented with VEGF and bFGF. For the maintenance of iPSC-CMs, the culture media were refed every 2-3 days.

extract_protocol: RNA was prepared using the miRNeasy Purification kit (Qiagen) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: After cardiac differentiation, we collected GFP positive cardiomyocytes by FACS sorting on day9, 21, and 30. Additionally, we compared differences of gene expressions between CORIN highly expressed cairomyocytes and low expressed cardiomyocytes. Moreover, we checked the effects of HDAC2 for cardiac maturaion.

value: Differentiated cells from human induced pluripotent stem cells

value: female


title: MS645_500_rep2

city: new york

first: MING-MING

last: ZHOU

state: NY

address: 1425 madison ave

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequencing short reads were mapped to the reference genome assembly (Hg19) using TopHat (version 2.0.8)
HT-seq was used to find read counts across genes.
Differentially expressed genes were identified using DESeq2
Tdf files were generated using IGVTools.
Genome_build: Hg19
Supplementary_files_format_and_content: tab-delimited text file containing raw counts and tdf files for each sample

source_name: Triple-negative breast cancer (TNBC) cell line, MS645 500 nM for 18 hrs

growth_protocol: MDA-MB-231 cells were grown in DMEM with 10% FBS at 37°C in the incubator containing 5% CO2.

extract_protocol:
Total RNA was extracted using NucleoSpin® RNA (Macherey-Nagel).
RNA libraries were prepared for sequencing using standard Illumina protocols by sequencing cores.

treatment_protocol: MDA-MB-231 cells were treated with DMSO or compounds (final DMSO concentration 1‰) for 18 hours.

tag: agent

tag: dose

tag: time

value: 18 hrs

tag: platform

value: Epigenomics Core of Weill Cornell


title: JQ1_500_rep2

source_name: Triple-negative breast cancer (TNBC) cell line, JQ1 500 nM for 18 hrs

tag: cell line


title: MS645_50_rep2

source_name: Triple-negative breast cancer (TNBC) cell line, MS645 50 nM for 18 hrs

value: 50 nM


title: Si NC-1

description: Gene expression of differentiated CMs 30 days after the initial differentiation treated by siNegative control

source_name: day30 CMs siNegative control sample1

tag: cell type

tag: gender


title: Si NC-3

source_name: day30 CMs siNegative control sample3


title: Si HDAC2 2-2

source_name: day30 CMs siHDAC2-2 sample2


title: Si HDAC2 2-3

source_name: day30 CMs siHDAC2-2 sample3


title: JQ1_50_rep2

source_name: Triple-negative breast cancer (TNBC) cell line, JQ1 50 nM for 18 hrs


title: Buffy coat from peripheral blood [C186] copy number

description: Hybridized to SNP6 Affymetrix


title: Si HDAC2 1-3

source_name: day30 CMs siHDAC2-1 sample3


title: Si HDAC2 2-1

source_name: day30 CMs siHDAC2-2 sample1


title: Si NC-2

source_name: day30 CMs siNegative control sample2


title: CORIN low

description: Gene expression of differentiated CMs 30 days after the initial differentiation with low CORIN expression

source_name: day30 CMs CORIN low


title: Si HDAC2 1-1

source_name: day30 CMs siHDAC2-1 sample1


title: day30-CMs

description: Gene expression of differentiated cells 30 days after the initial differentiation

source_name: differentiated CMs day30


title: DMSO_rep2

source_name: Triple-negative breast cancer (TNBC) cell line, DMSO for 18 hrs

value: DMSO

value: control


title: day21-CMs

description: Gene expression of differentiated cells 21 days after the initial differentiation

source_name: differentiated CMs day21


title: CORIN high

description: Gene expression of differentiated CMs 30 days after the initial differentiation with high CORIN expression

source_name: day30 CMs CORIN high


title: day3

description: Gene expression of differentiated cells 3 days after the initial differentiation

source_name: differentiated cells day3


title: day5

description: Gene expression of differentiated cells 5 days after the initial differentiation

source_name: differentiated cells day5


title: day9-CMs

description: Gene expression of differentiated cells 9 days after the initial differentiation

source_name: differentiated CMs day9


title: day0

description: Gene expression of undifferentiated iPSC

source_name: Human induced pluripotent stem cell line  (201B7 MHC-GFP)

value: Undifferentiated human induced pluripotent stem cells


title: Buffy coat from peripheral blood [C184] copy number

description: Hybridized to SNP6 Affymetrix

source_name: Blood from breast cancer patient


title: MS645_500_rep1

source_name: Triple-negative breast cancer (TNBC) cell line, MS645 500 nM for 18 hrs


title: MS645_50_rep1

source_name: Triple-negative breast cancer (TNBC) cell line, MS645 50 nM for 18 hrs


title: JQ1_500_rep1

source_name: Triple-negative breast cancer (TNBC) cell line, JQ1 500 nM for 18 hrs


title: Buffy coat from peripheral blood [C178] copy number

description: Hybridized to SNP6 Affymetrix


title: MS645_500_rep0

value: Mount Sinai sequencing core


title: Buffy coat from peripheral blood [C175] copy number

description: Hybridized to SNP6 Affymetrix


title: DMSO_rep1


title: MS645_50_rep0


title: 1772200100_H01

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

institute: Karolinska Institutet

data_processing:
Read processing was performed as described (Islam et al., Nat Methods. 2014 Feb;11(2):163-6), except that we removed any RNA molecule (i.e. Unique Molecular Identifier) supported only by a single read ("singleton molecules"). This removed a large number of false positive molecules, artefacts that can arise by sequencing error, PCR-induced mutations or translocations and cross-contamination.
The first 6 bases of each read represent the random Unique Molecular Identifier used for molecule counting. After follows three or more Gs, stemming from the template switching at the mRNA 5' end during first strand cDNA sythesis.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: total number of detected mRNA molecules from each gene in each cell

organism: Mus musculus

extract_protocol:
After the recording, weak negative pressure was applied in order to aspirate the recorded cells into the glass capillary patch electrode. Using positive pressure the pipette content was quickly ejected into a 1 μL drop of RNase-free lysis buffer. placed on the side of a 0.2 mL RNase free tight-lock tube (TubeOne). The sample was rapidly spun down (5-10 s) and stored at −80 before reverse transcription (RT).
20 microL lysis buffer (0.15% Triton X-100, 1 U/microL TaKaRa RNase inhibitor, 4 microM reverse transcription primer C1-P1-T31, 5% C1 Loading Reagent and 1:50,000 Life Technologies ERCC  Spike-In Mix 1), reverse transcription mix (1x SuperScript II First-Strand Buffer supplemented with 3 mM MgCl2, 1.5 mM dNTP, 4 mM DTT, 3.3% C1 Loading Reagent, 1.8 microM template-switching oligo C1-P1-RNA-TSO, 1.5 U/microL TaKaRa RNase inhibitor and 18 U/microL Life Technologies Superscript II reverse transcriptase) and PCR mix (1.1x Clontech Advantage2 PCR buffer, 440 microM dNTP, 530 nM PCR primer C1-P1-PCR-2, 5% C1 Loading Reagent and 2x Advantage2 Polymerase Mix) were added to wells. The plate was put in the Fluidigm C1 and the mRNA Seq: RT + Amp (1772x/1773x) script was executed, which took about 8.5 hours and included lysis, reverse transcription and 21 cycles of PCR. When the run finished, the amplified cDNA was harvested in a total of 13 microL C1 Harvesting Reagent and quantified on an Agilent BioAnalyzer. The typical yield was 1 ng/microL. Amplified cDNA was simultaneously fragmented and barcoded by tagmentation, i.e. using Tn5 DNA transposase to transfer adapters to the target DNA. 96 different 10x transposome stocks (6.25 microM barcoded adapter C1-TN5-x, 40% glycerol, 6.25 microM Tn5 transposase, where x denotes a well-specific barcode) were prepared, each with a different barcode sequence.  6 microL harvested cDNA was mixed with 5 microL tagmentation buffer (50 mM TAPS-NaOH pH 8.5, 25 mM MgCl2 and 50% DMF), 11.5 microL nuclease-free water and 2.5 microL 10x transposome stock. The mix was incubated for 5 minutes at 55 degeees C then cooled on ice. 100 microL Dynabeads MyOne Streptavidin C1 beads were washed in 2xBWT (10 mM Tris HCl pH 7.5, 1 mM EDTA, 2 M NaCl, 0.02% Tween-20) then resuspended in 2 mL 2xBWT. 20 microL beads was added to each well and incubated at room temperature for 5 minutes. All fractions were pooled, the beads were immobilized and the supernatant removed (thus removing all internal fragments, and retaining only the 5'- and 3'-most fragments). The beads were then resuspended in 100 microL TNT (20 mM Tris pH 7.5, 50 mM NaCl, 0.02% Tween), washed in 100 microL Qiagen Qiaquick PB, then twice in 100 microL TNT. The beads were then resuspended in 100 microL restriction mix (1x NEB NEBuffer 4, 0.4 U/microL PvuI-HF enzyme), designed to cleave 3' fragments carrying the PvuI recognition site. The mix was incubated for one hour at 37 degrees C, then washed three times in TNT. Finally, the single-stranded library was eluted by resuspending the beads in 100 microL 100 mM NaOH, incubating for 5 minutes, removing the beads, then adding 100 microL 100 mM HCl and 50 microL Neutralization buffer (200 mM Tris pH 7.5, 0.05% Tween-20). At this point, the typical yield was 1-5 nM single-stranded library. Aliquots were rom these were run on  with 187ds_).

treatment_protocol: Whole-cell patch-clamp recordings were performed as previously described (Muñoz-Manchado et al., Cereb. Cortex 26 (2016), pp. 96-105) on 5HT3aEGFP, Pvalbcre::RCE and Pvalbcre::tdTomato animals. Prior to brain dissection, animals were transcardially perfused using ice-cold oxygenated cutting solution (in mM): 87 NaCl, 2.5 KCl, 1.25 NaH2PO4, 26 NaHCO3, 75 sucrose, 12.5 glucose. Electrophysiological parameters were acquired using depolarizing and hyperpolarizing current steps.

tag: strain

tag: age (days)

value: dorso-lateral striatum

tag: cell id

value: Th


title: 1772200100_H05

value: Npy/Mia


title: 1772200100_G03

value: No


title: JQ1_50_rep0

source_name: Triple-negative breast cancer (TNBC) cell line, JQ1 50 nM for 18 hrs


title: JQ1_500_rep0


title: Breast cancer tissue [T79] copy number

description: Hybridized to SNP6 Affymetrix

source_name: Breast tumor

value: Breast cancer tissue

value: Somatic cell fraction

tag: population


title: Buffy coat from peripheral blood [C176] copy number

description: Hybridized to SNP6 Affymetrix

value: Buffy coat from peripheral blood

value: Germinal cell fraction


title: 1772200100_G02

value: Pthlh


title: DMSO_rep0


title: human melanoma cell line SKmel103

description:
SKmel103
no replicate
9985134004_I

source_name: melanoma patient

value: human melanoma cell line SKmel103

value: Madrid, CNIO


title: Buffy coat from peripheral blood [C174] copy number

description: Hybridized to SNP6 Affymetrix

value: Mexican hispanic


title: 1772200100_F06

value: Pvcre


title: Buffy coat from peripheral blood [C172] copy number

description: Hybridized to SNP6 Affymetrix


title: Buffy coat from peripheral blood [C169] copy number

description: Hybridized to SNP6 Affymetrix


title: 1772200100_F04


title: Jacket_Tumor

city: Cambridge

first: Elin

middle: S.

last: Agoston

state: Massachusetts

address: 675 West Kendall Street

institute: Cellaria Biosciences

description: Tumor used to derive Jacket model

hyb_protocol: The biotinylated fragments are added to a hybridization solution containing a biotinylated control oligonucleotide (for quality control), and hybridized to a microarray chip overnight at 49°C.

scan_protocol: The chips are then transferred to a fluidics instrument that performs washes to remove DNA that has not hybridized to its complementary oligonucleotide probe. The bound DNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE) followed by biotinylated anti-streptavidin, followed by SAPE. Each DNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensitites of the fluorescent emissions are captured.

data_processing:
BRLMM genotyping was performed using the Affymetrix Genotyping Console with the following parameters: Score threshold of 0.5, Prior size of 10000, DM Threshold of 0.17. Additional CEL files were added to each analysis to successfully generate prior.
The genotyping results are presented for each sample as well as the confidence values.

source_name: Lung tumor tissue

label_protocol: The fragemented PCR products are labeled with a single biotin at each free 3'OH using terminal deoxynucleotidyl transferase and a dideoxy biotinylated nuceloside triphosphate.

growth_protocol: Cells were grown to reach the desired number of population doublings and extracts were harvested at 80% confluency

extract_protocol: Cell monolayers were lysed directly in RLT+ buffer and homogenized with TissueRuptor rotor-stator homogenizer (Qiagen). Frozen tissues were homogenized by rotor-stator directly in RLT+ buffer.

tag: tissue of origin

value: Lung

tag: clinical diagnosis

value: Adenocarcinoma of the lung

tag: ajcc/iuicc stage

value: IB


title: Jacket_40PD

description: Jacket lung cancer cell line- 40 population doublings

source_name: Lung cancer cell line


title: Jacket_20PD

description: Jacket lung cancer cell line- 20 population doublings


title: Jacket_150PD

description: Jacket lung cancer cell line- 150 population doublings


title: 1772200100_F02


title: DF68_25PD

description: DF68 extended primary culture- 23 population doublings

source_name: Ovarian cancer ascites

value: Ovary

value: Recurrent adenocarcinoma of the ovary

value: III


title: JQ1_50_rep1

value: 50 nM

value: 18 hrs

value: Epigenomics Core of Weill Cornell


title: DF68_Ascites

description: DF68 High grade serous ascites primary cells


title: DF30_23PD

description: DF30 extended primary culture- 23 population doublings

value: Primary peritoneal

value: Primary peritoneal high grade serous carcinoma


title: 1772200100_G04

value: dorso-lateral striatum

value: Th


title: DF30_Ascites

description: DF30 High grade serous ascites primary cells


title: 1772200100_F01

value: Pthlh


title: Ferry_40PD

description: Ferry colon cancer cell line- 40 population doublings

source_name: Colon cancer cell line

value: Colon

value: Adenocarcinoma of the large intestine

value: IIA


title: Ferry_20PD

description: Ferry colon cancer cell line- 20 population doublings


title: Buffy coat from peripheral blood [C165] copy number

description: Hybridized to SNP6 Affymetrix

value: Buffy coat from peripheral blood

value: Germinal cell fraction

value: Mexican hispanic


title: Wood_Tumor

description: Tumor used to derive Wood model

source_name: Breast tumor tissue

value: Breast

value: Infiltrating ductal and lobular carcinoma of the breast


title: 1772200100_E06

value: Pvcre


title: Buffy coat from peripheral blood [C160] copy number

description: Hybridized to SNP6 Affymetrix


title: Ferry_Tumor

description: Ferry colon cancer cell line- 150 population doublings

source_name: Colon tumor tissue


title: 1772200100_E03

value: No


title: Buffy coat from peripheral blood [C166] copy number

description: Hybridized to SNP6 Affymetrix


title: 1772200100_E04


title: Wood_150PD

description: Wood breast cancer cell line- 150 population doublings

source_name: Breast cancer cell line


title: Buffy coat from peripheral blood [C155] copy number

description: Hybridized to SNP6 Affymetrix


title: Wood_40PD

description: Wood breast cancer cell line- 40 population doublings


title: Wood_20PD

description: Wood breast cancer cell line- 20 population doublings


title: 1772200100_E02


title: Buffy coat from peripheral blood [C168] copy number

description: Hybridized to SNP6 Affymetrix


title: Buffy coat from peripheral blood [C154] copy number

description: Hybridized to SNP6 Affymetrix


title: 1772200100_E01


title: Buffy coat from peripheral blood [C150] copy number

description: Hybridized to SNP6 Affymetrix


title: 1772200100_D03

value: Cck+Vip


title: Buffy coat from peripheral blood [C149] copy number

description: Hybridized to SNP6 Affymetrix


title: 1772200100_D02


title: Buffy coat from peripheral blood [C144] copy number

description: Hybridized to SNP6 Affymetrix


title: Buffy coat from peripheral blood [C143] copy number

description: Hybridized to SNP6 Affymetrix


title: Buffy coat from peripheral blood [C142] copy number

description: Hybridized to SNP6 Affymetrix


title: 1772200100_C02


title: 1772200100_C06


title: Buffy coat from peripheral blood [C141] copy number

description: Hybridized to SNP6 Affymetrix


title: 1772200100_C01


title: Buffy coat from peripheral blood [C140] copy number

description: Hybridized to SNP6 Affymetrix


title: Buffy coat from peripheral blood [C146] copy number

description: Hybridized to SNP6 Affymetrix


title: 1772200100_D01


title: Atorvastatin tumor-bearing colon epithelium 1

city: Philadelphia

first: Margie

last: Clapper

state: PA

address: 333 Cottman Ave

institute: Fox Chase Cancer Center

description:
total laser microdissected RNA
Gene expression of atorvastatin-treated tumor-bearing normal colon epithelium, replicate 1

hyb_protocol: 1.65 ug of Cy-3 labeled cRNA targets is hybridized onto Agilent 4x44k whole genome arrays for 17 hours at 65º C and washed according to Agilent procedure.

scan_protocol: The hybridized slides are scanned at 5µm resolution on Agilent scanner (Agilent)  G2505B.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: normal colon epithelium from tumor-bearing mouse, astorvastatin treatment for 7 days

label_protocol: 10 ng total laser microdissected RNA samples were subjected to two rounds of liner RNA amplification, amino allyl labeled and hybridized to the Agilent Mouse Whole Genome 4x44 microarrrays according to the manufacturer's instructions (Agilent Technologies, Santa Clara, CA ). For each condition, 3-4 biological replicate samples were used for microarray experiments.

growth_protocol: Male Apc+/Min-FCCC mice were subjected to colonscopy at 6-8 weeks of age.  Based on the results of the colonscopic exam, mice were categorized as tumor-free and tumor bearing.  Tumor-bearing mice were randomly assigned to the untreated control and sulindac/atorvastatin groups.  Tumor-free mice were randomly assigned to the atorvastatin-treated and control groups.

extract_protocol: Total RNA is isolated using TRIzol reagent (Invitrogen, Carlsbad, CA) and further purified by RNeasy kit (Qiagen, Valencia, CA) according to manufacturer’s instructions.  The quality of total RNA is assessed by the ratios OD260/OD280 and OD260/OD230 and using an Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA).

treatment_protocol: Sulindac/atorvastatin (300 ppm/100 ppm) and atorvastatin (100 ppm) were supplemeted into meal form of Harlan Teklad 2018SX chow.  Mice were provided untreated or drug-supplemented chow for 7 days before euthanasia.

value: colon normal epithelial cells


title: Atorvastatin colon epithelium 2

source_name: normal colon epithelium from tumor-free mouse_astorvastatin for 7 days

tag: strain background

tag: Sex

value: male

tag: age

value: 6-8 weeks

tag: mouse group

value: tumor-free

value: astorvastatin for 7 days


title: 1772200100_B04

tag: tissue

value: dorso-lateral striatum


title: Atorvastatin tumor-bearing  colon epithelium 4

description:
total laser microdissected RNA
Gene expression of atorvastatin-treated tumor-bearing  normal colon epithelium, replicate 4


title: Atorvastatin tumor-bearing  colon epithelium 2

description:
total laser microdissected RNA
Gene expression of atorvastatin-treated tumor-bearing  normal colon epithelium, replicate 2


title: 1772200100_C12

value: Pthlh


title: Atorvastatin colon epithelium 3

tag: treated with


title: Buffy coat from peripheral blood [C138] copy number

description: Hybridized to SNP6 Affymetrix


title: Sulindac/Atorvastatin Tumor 4

source_name: colon adenomas_sulindac/atorvastatin for 7 days

value: tumor-bearing

value: sulindac/atorvastatin for 7 days

value: colon adenoma cells


title: Atorvastatin tumor-bearing  colon epithelium 3

description:
total laser microdissected RNA
Gene expression of atorvastatin-treated tumor-bearing  normal colon epithelium, replicate 3


title: 1772200100_B03


title: Atorvastatin colon epithelium 4


title: Sulindac/Atorvastatin Tumor 2


title: Buffy coat from peripheral blood [C137] copy number

description: Hybridized to SNP6 Affymetrix

source_name: Blood from breast cancer patient

value: Buffy coat from peripheral blood

value: Germinal cell fraction


title: Atorvastatin colon epithelium 1


title: 1772200100_B02


title: Sulindac/Atorvastatin Tumor 3


title: Buffy coat from peripheral blood [C135] copy number

description: Hybridized to SNP6 Affymetrix

value: Mexican hispanic


title: Sulindac/Atorvastatin Tumor 1


title: 1772200100_B01

value: Th


title: Buffy coat from peripheral blood [C129] copy number

description: Hybridized to SNP6 Affymetrix


title: 1772200100_A03


title: Buffy coat from peripheral blood [C126] copy number

description: Hybridized to SNP6 Affymetrix


title: 1772200100_A02


title: Control Tumor 1

source_name: untreated colon adenoma

value: none (untreated control)


title: ESCs_L3mbtl2_rep4

city: Sendai

first: Yohei

last: Hayashi

state: Miyagi

address: 4-1 Seiryo-machi, Aobaku

department: Institute of Development, Aging and Cancer

institute: Tohoku University

hyb_protocol: 1.65ug of Cy3-labelled cRNAs from each sample were fragmented and hybridized to microarrays according to the manufacturer's instructions using the Gene Expression Hybridization kit (Agilent 5188-5242) and Agilent hybridization oven. After hybridization, microarrays were washed using the Gene Expression Wash Pack (Agilent 5188-5327).

scan_protocol: The microarrays were scanned using the Agilent DNA microarray scanner (Agilent G2505C); the spot signals were quantified using Feature Extraction software.

data_processing: Data was normalized by 75 percentile shift and analyzed by GeneSpring GX (Agilent).

source_name: ESCs_L3mbtl2 siRNA

label_protocol: Cy3-labeled cRNA samples were prepared using the Agilent Low Input Quick Amp Labeling Kit (one-color) (5190-2305) and RNA Spike-In Kit (one-color) (5188-5282) according to the manufacturer's instructions. Input was 100 ng of total RNA from each sample.

extract_protocol: Total RNA was purified using the RNeasy micro kit according to the manufacturer's instructions.

value: Embryonic stem cell (Vasa::Venus Tg)

tag: genotype/variation

value: L3mbtl2 siRNA


title: Buffy coat from peripheral blood [C125] copy number

description: Hybridized to SNP6 Affymetrix


title: Control Tumor 3


title: ESCs_AllStars_rep4

source_name: ESCs_control siRNA

value: control siRNA


title: Buffy coat from peripheral blood [C124] copy number

description: Hybridized to SNP6 Affymetrix


title: ESCs_L3mbtl2_rep3

value: male


title: ESCs_AllStars_rep3


title: 1772100100_H11

value: No


title: Control Tumor 2

value: 6-8 weeks


title: ESCs_L3mbtl2_rep2


title: ESCs_AllStars_rep2


title: Buffy coat from peripheral blood [C123] copy number

description: Hybridized to SNP6 Affymetrix


title: 1772100100_H10


title: Buffy coat from peripheral blood [C122] copy number

description: Hybridized to SNP6 Affymetrix


title: 1772200100_A01


title: ESCs_AllStars_rep1


title: 1772100100_H09


title: ESCs_L3mbtl2_rep1


title: Buffy coat from peripheral blood [C120] copy number

description: Hybridized to SNP6 Affymetrix


title: human lung tumor PC14 cells alone [D30_7]

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

country: Israel

institute: Tel Aviv University

description:
D30_7_PC14
PC14 control

hyb_protocol: according to the instruction manual, as described in the Affymetrix website

data_processing: RMA normalization, summarization by mean

growth_protocol: PC14 cells were maintained as monolayer culture in eagle minimum essential medium (MEM-EAGLE, Biological industries) supplemented with 10% fetal bovine serum, 5% L-glutamine 5% sodium pyruvate, 5% nonessential amino acids, 5% MEM vitamin solution, and 5% penicillin-streptomycin. Cells were maintained at 37°C in a humidified 5% CO2 incubator. Conditioned immortalized mice astrocytes were maintained as monolayer culture in dulbecco's modified eagle medium (DMEM, Biological industries) supplemented with 10% fetal bovine serum, 5% L-glutamine 5% sodium pyruvate, 5% nonessential amino acids, 10% vitamin solution, and 5% penicillin-streptomycin. Cells were maintained at 33°C in a humidified 8% CO2  incubator.

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

treatment_protocol:
co-culture: Astrocytes and PC14 cells were co-cultured in MEM-EAGLE medium supplemented with 10% fetal bovine serum, 5% L-glutamine 5% sodium pyruvate, 5% nonessential amino acids, 5% MEM vitamin solution, and 5% penicillin-streptomycin at a tumor cell-astrocyte ratio of 1:1 onto 35-mm-diameter well of six-well tissue culture multiwell dish. Cells were incubated at 37ºC in a humidified 5% CO2 incubator for six hours.
TW: PC14 cells were prevented from directly contacting astrocytes by a semi-permeable 0.2 µm-pore transwell membrane (Costar). Briefly, astrocytes (2.5×105, in 1 ml of medium) were plated in the lower chamber and PC14 cells  (4×10^5, in 1 ml of medium) were added to the upper compartment (in 6-well plates). The cells were incubated for six hours at 37°C

tag: cell line

value: lung adenocarcinoma cell line

tag: cultured

value: alone


title: human lung tumor PC14 cells cultured (direct contact) with astrocytes [D31_9]

description:
D31_9_PC14_CoC
PC14 co-culture

scan_protocol: according to the instruction manual, as described in the Affymetrix website

source_name: PC14 direct contact_coculture

tag: cell type

value: (direct contact) with astrocytes


title: human lung tumor PC14 cells cultured in transwell (TW) with astrocytes [D32_11]

description:
D32_11_PC14_TW
PC14 TW

source_name: PC14 transwell_coculture

label_protocol: according to the instruction manual, as described in the Affymetrix website

value: in transwell (TW) with astrocytes


title: 1772100100_H08

tag: strain

value: dorso-lateral striatum

value: Pthlh


title: Buffy coat from peripheral blood [C116] copy number

description: Hybridized to SNP6 Affymetrix

value: Buffy coat from peripheral blood


title: human lung tumor PC14 cells alone [D27_1]

description:
D27_1_PC14
PC14 control


title: human lung tumor PC14 cells cultured (direct contact) with astrocytes [D28_3]

description:
D28_3_PC14_CoC
PC14 co-culture


title: 1772100100_H06

tag: age (days)


title: 1772100100_H05

tag: cell id


title: Buffy coat from peripheral blood [C113] copy number

description: Hybridized to SNP6 Affymetrix

value: Germinal cell fraction

tag: population


title: IMCs, co-cultured, 24h, rep 2

first: Cindy

last: Lin

address: 3601 Spruce Street

institute: Wistar Institute

description: Myeloma co-cultured with Myeloid cells, replicate 2

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Data was normalized and log2-transformed using RMA algorithm

source_name: IMCs, co-cultured, 24h

label_protocol: Standard Affymetrix protocol

growth_protocol: DP42 MM cells were cultured alone or with mouse B cells or neutrophils for 24h.

treatment_protocol: Co-cultured cells were flow sorted into their respective populations, rinsed with PBS and placed into Trizol solution.

tag: coculture

value: neutrophils (IMC)


title: Buffy coat from peripheral blood [C121] copy number

description: Hybridized to SNP6 Affymetrix

value: Mexican hispanic


title: 1772100100_H04


title: human lung tumor PC14 cells cultured in transwell (TW) with astrocytes [D29_5]

description:
D29_5_PC14_TW
PC14 TW


title: Buffy coat from peripheral blood [C110] copy number

description: Hybridized to SNP6 Affymetrix


title: IMCs, co-cultured, 24h, rep 1

description: Myeloma co-cultured with Myeloid cells, replicate 1


title: DP42 MM cells, rep 2

description: Control experiment with no co-culturing, replicate 2

source_name: DP42 MM cells


title: B-cells, co-cultured, 24h, rep 2

description: Myeloma co-cultured with B-cell, replicate 2

source_name: B-cells, co-cultured, 24h

value: B-cells


title: Buffy coat from peripheral blood [C108] copy number

description: Hybridized to SNP6 Affymetrix


title: B-cells, co-cultured, 24h, rep 1

description: Myeloma co-cultured with B-cell, replicate 1


title: DP42 MM cells, rep 1

description: Control experiment with no co-culturing, replicate 1


title: Buffy coat from peripheral blood [C106] copy number

description: Hybridized to SNP6 Affymetrix


title: Triple negative breast cancer cell line HS578

description: miRNA expression data from triple negative tumors.

hyb_protocol: Total RNA was labeled with Flashtag HSR kit and hybridized to the Affymetrix GeneChip

scan_protocol: Washed and stain processes were performed in the GeneChip Fluidics Station 450. The probe arrays were scanned using an Affymetrix GeneChip Scanner 3000 7G

data_processing: Computational analysis of the microarray data Cel files was processed with the Oligo library in R Bioconductor. Microarray background correction and normalization was done using Robust Multichip Analysis (RMA) and quantile algorithm, respectively. To define subgroups a non-hierarchical analysis was performed by a non-negtaive matrix factorization (NMF). Differentially expression patterns between triple negative tumors, subtypes and other immunophenotypes were determined using the limma package to perform an adjusted Student’s t-test using a Bayesian estimation of the variance.

source_name: Cell line

growth_protocol: 3×106 cells were cultured in medium DMEM supplemented at 37ºC on 5% CO2

extract_protocol: Total RNA including the small fraction was isolated using RecoverAll™ Total Nucleic Acid Isolation Kit for FFPE

treatment_protocol: Paraffin embedded tissue from breast cancer tumors in adjuvance

value: Cell line model  HS578T

tag: subtype

value: Triple Nevative/ Basal A

tag: miRNA subtype

value: Caucasian


title: Triple negative breast cancer TN87

source_name: Macrodissection of FFPE breast cancer tumor

label_protocol: Total RNA was labeled with Flashtag HSR kit and hybridized to the Affymetrix GeneChip

value: breast cancer tissue

value: Triple Nevative

value: Mexico Hispanic


title: 1772100100_H03


title: Triple negative breast cancer TN86


title: 1772100100_H02


title: Triple negative breast cancer TN83


title: Buffy coat from peripheral blood [C105] copy number

description: Hybridized to SNP6 Affymetrix


title: Triple negative breast cancer cell line 231

value: Cell line model  MDA MB 231

value: Triple Nevative/ Basal B


title: Triple negative breast cancer TN84


title: Triple negative breast cancer cell line 468

value: Cell line model MDA MB 468

value: Black


title: 1772100100_H01

value: dorso-lateral striatum

value: Th


title: Triple negative breast cancer TN82


title: Triple negative breast cancer TN77


title: 1772100100_G12

value: Pthlh


title: Triple negative breast cancer TN85


title: Triple negative breast cancer TN80


title: Triple negative breast cancer TN78


title: Triple negative breast cancer TN81


title: 1772100100_G11


title: Buffy coat from peripheral blood [C97] copy number

description: Hybridized to SNP6 Affymetrix

value: Buffy coat from peripheral blood

value: Germinal cell fraction


title: Triple negative breast cancer TN73


title: 1772100100_G10

value: No


title: Buffy coat from peripheral blood [C95] copy number

description: Hybridized to SNP6 Affymetrix

value: Mexican hispanic


title: Buffy coat from peripheral blood [C94] copy number

description: Hybridized to SNP6 Affymetrix


title: Buffy coat from peripheral blood [C85] copy number

description: Hybridized to SNP6 Affymetrix


title: 1772100100_G09

value: Npy/Mia


title: 1772100100_G08


title: Triple negative breast cancer TN75


title: Buffy coat from peripheral blood [C98] copy number

description: Hybridized to SNP6 Affymetrix


title: Buffy coat from peripheral blood [C83] copy number

description: Hybridized to SNP6 Affymetrix


title: 1772100100_G06


title: 1772100100_G07


title: Triple negative breast cancer TN70


title: Triple negative breast cancer TN72


title: Triple negative breast cancer TN76


title: Buffy coat from peripheral blood [C81] copy number

description: Hybridized to SNP6 Affymetrix


title: Triple negative breast cancer TN66


title: Triple negative breast cancer TN71


title: Triple negative breast cancer TN67


title: Luminal B breast cancer LBtp196

value: Luminal B


title: 1772100100_G04


title: Triple negative breast cancer TN68


title: Triple negative breast cancer TN61


title: Triple negative breast cancer TN69


title: Triple negative breast cancer TN63


title: Triple negative breast cancer TN65


title: Buffy coat from peripheral blood [C80] copy number

description: Hybridized to SNP6 Affymetrix


title: Luminal B breast cancer LBtp196_2


title: 1772100100_G03


title: Buffy coat from peripheral blood [C82] copy number

description: Hybridized to SNP6 Affymetrix


title: Luminal B breast cancer LBtp186


title: Luminal B breast cancer LBtp137


title: Luminal B breast cancer LBtp149


title: 1772100100_G02


title: Buffy coat from peripheral blood [C79] copy number

description: Hybridized to SNP6 Affymetrix


title: Luminal B breast cancer LBtp13


title: Buffy coat from peripheral blood [C77] copy number

description: Hybridized to SNP6 Affymetrix


title: 1772100100_G05


title: Luminal B breast cancer LBtp55


title: 1772100100_G01


title: 1772100100_F12


title: Buffy coat from peripheral blood [C75] copy number

description: Hybridized to SNP6 Affymetrix


title: Buffy coat from peripheral blood [C74] copy number

description: Hybridized to SNP6 Affymetrix


title: Buffy coat from peripheral blood [C76] copy number

description: Hybridized to SNP6 Affymetrix


title: Luminal B breast cancer LBtp16


title: 1772100100_F11


title: 1772100100_F10


title: 1772100100_F09


title: Luminal B breast cancer LBTP105


title: Buffy coat from peripheral blood [C71] copy number

description: Hybridized to SNP6 Affymetrix


title: 1772100100_F08


title: Luminal A breast cancer LATP129

value: Luminal A


title: Luminal A breast cancer LAtp50

value: breast cancer tissue


title: Luminal A breast cancer LAtp26


title: Luminal A breast cancer LAtp40


title: Luminal A breast cancer LAtp83


title: Luminal A breast cancer LATP106


title: Luminal A breast cancer LAT28


title: Her2 breast cancer HTTP47


title: Buffy coat from peripheral blood [C59] copy number

description: Hybridized to SNP6 Affymetrix


title: Her2 breast cancer Htp85


title: Her2 breast cancer HTP166


title: 1772100100_F02


title: Luminal A breast cancer LATP125


title: Her2 breast cancer HTP108


title: 1772100100_F01

value: Pvcre


title: Buffy coat from peripheral blood [C69] copy number

description: Hybridized to SNP6 Affymetrix


title: Buffy coat from peripheral blood [C62] copy number

description: Hybridized to SNP6 Affymetrix


title: 1772100100_F03


title: s8: Notch3-sIRNA-DMSO#2

city: Columbus

first: Rajeswara

last: Arasada

address: 420 W 12th Ave

institute: Ohio State University

description: Notch3-siRNA+Control treatment

hyb_protocol: not provided

scan_protocol: not provided

data_processing: Gene-level expression were summarized by RMA summarizaiton method. Linear models were performed to detect differentially expressed genes.

label: Biotin

source_name: Notch3 KO

label_protocol: not provided

extract_protocol: Total RNA was isolated

treatment_protocol: DMSO or 0.1uM Erlotinib

value: Lung cancer cell line


title: s6: Notch1-sIRNA-DMSO#3

description: Notch1-siRNA+Control treatment

source_name: Notch1 KO


title: Buffy coat from peripheral blood [C58] copy number

description: Hybridized to SNP6 Affymetrix


title: Buffy coat from peripheral blood [C73] copy number

description: Hybridized to SNP6 Affymetrix


title: 1772100100_E12


title: 1772100100_E11


title: Buffy coat from peripheral blood [C55] copy number

description: Hybridized to SNP6 Affymetrix


title: Luminal A breast cancer LATP36

value: Mexico Hispanic


title: 1772100100_E08


title: s9: Notch3-sIRNA-DMSO#3

description: Notch3-siRNA+Control treatment


title: s5: Notch1-sIRNA-DMSO#2

description: Notch1-siRNA+Control treatment


title: s7: Notch3-sIRNA-DMSO#1

description: Notch3-siRNA+Control treatment


title: Buffy coat from peripheral blood [C50] copy number

description: Hybridized to SNP6 Affymetrix


title: s33: NTC-Erlotinib#3

description: Control siRNA+Erlotinib treatment

source_name: Erlotinib


title: s32: NTC-Erlotinib#2

description: Control siRNA+Erlotinib treatment


title: Buffy coat from peripheral blood [C48] copy number

description: Hybridized to SNP6 Affymetrix


title: Buffy coat from peripheral blood [C47] copy number

description: Hybridized to SNP6 Affymetrix


title: Buffy coat from peripheral blood [C45] copy number

description: Hybridized to SNP6 Affymetrix


title: 1772100100_E06


title: 1772100100_E05


title: Buffy coat from peripheral blood [C44] copy number

description: Hybridized to SNP6 Affymetrix


title: 1772100100_E07


title: 1772100100_E04


title: Buffy coat from peripheral blood [C43] copy number

description: Hybridized to SNP6 Affymetrix


title: s31: NTC-Erlotinib#1

description: Control siRNA+Erlotinib treatment


title: 1772100100_E03


title: Buffy coat from peripheral blood [C41] copy number

description: Hybridized to SNP6 Affymetrix


title: s26: Notch3-sIRNA-Erlotinib#5

description: Notch3-siRNA+Erlotinib treatment

source_name: Notch3 KO + Erlotinib


title: 1772100100_E02


title: s14: NTC-DMSO#2

description: Control siRNA+Control treatment

source_name: DMSO


title: s15: NTC-DMSO#3

description: Control siRNA+Control treatment


title: s13: NTC-DMSO#1

description: Control siRNA+Control treatment


title: s4: Notch1-sIRNA-DMSO#1

description: Notch1-siRNA+Control treatment


title: 1772100100_E01


title: s24: Notch1-sIRNA-Erlotinib#3

description: Notch1-siRNA+Erlotinib treatment

source_name: Notch1 KO + Erlotinib


title: Buffy coat from peripheral blood [C39] copy number

description: Hybridized to SNP6 Affymetrix

source_name: Blood from breast cancer patient


title: s23: Notch1-sIRNA-Erlotinib#2

description: Notch1-siRNA+Erlotinib treatment


title: Buffy coat from peripheral blood [C40] copy number

description: Hybridized to SNP6 Affymetrix


title: 1772100100_D11


title: Buffy coat from peripheral blood [C38] copy number

description: Hybridized to SNP6 Affymetrix


title: s27: Notch3-sIRNA-Erlotinib#6

description: Notch3-siRNA+Erlotinib treatment


title: s25: Notch3-sIRNA-Erlotinib#4

description: Notch3-siRNA+Erlotinib treatment


title: s22: Notch1-sIRNA-Erlotinib#1

description: Notch1-siRNA+Erlotinib treatment


title: TN81

description: Gene expression Affymetrix Human Transcriptome Array 2.0

hyb_protocol: Hybridization according to manufacter (Affymetrix)

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix) in the GeneChip Fluidics Station 450(Affymetrix)

data_processing: Computational analysis of the microarray data Cel files was processed with the Expression consule of Affymetrix. Microarray background correction and normalization was done using Robust Multichip Analysis (RMA) and quantile algorithm, respectively. To define Lehmann subtypes based in mRNA expression TBNCtool was computed on the data.

source_name: FFPE breast cancer tumor

label_protocol: Samples were hybridized with  Gene Chip Human Transcriptome Array (HTA) 2.0 (Affymetrix) and scanned at the INMEGEN Microarray Core Facility.

extract_protocol: From FFPE breast cancer tissues, total RNA was extracted with miRNeasy mini kit (Qiagen)

value: Triple negative breast cancer

tag: lehmann subtype

value: M


title: TN80


title: TN162


title: 1772100100_D10


title: Buffy coat from peripheral blood [C37] copy number

description: Hybridized to SNP6 Affymetrix


title: TN76

value: UNS


title: TN78

value: LAR


title: TN85


title: TN75

value: IM


title: Buffy coat from peripheral blood [C36] copy number

description: Hybridized to SNP6 Affymetrix


title: 1772100100_D09

value: dorso-lateral striatum


title: TN70


title: TN83


title: TN79


title: TN73


title: TN68


title: 1772100100_D07

value: Pthlh


title: 1772100100_D04

value: Th


title: 1772100100_D06


title: 1772100100_D03


title: Buffy coat from peripheral blood [C31] copy number

description: Hybridized to SNP6 Affymetrix

value: Buffy coat from peripheral blood

value: Germinal cell fraction


title: Buffy coat from peripheral blood [C28] copy number

description: Hybridized to SNP6 Affymetrix

value: Mexican hispanic


title: Buffy coat from peripheral blood [C34] copy number

description: Hybridized to SNP6 Affymetrix