title: IRP2 immunoprecipitation brain replica 2

type: other

city: Heidelberg

first: Mayka

last: Sanchez

address: Meyerhofstrasse 1

institute: EMBL

description: All the microarray procedures were conducted at the EMBL Genomics Core Facility using standard Affymetrix protocols.  In brief, approximately 120ng of immunoprecipitated RNA was used as input to a two-step amplification procedure to generate biotin-labeled RNA fragments for hybridization to the Affymetrix GeneChip Mouse Genome 430 2.0 array (Eukaryotic Sample and Array Processing manual 701024 Rev.3).

hyb_protocol: Biotin-labeled RNA fragments were hybridized to Affymetrix GeneChip Mouse Genome 430 2.0 array by the EMBL Genomics Core Facility according to the Standard Affymetrix Two Cycle protocol (Eukaryotic Sample and Array Processing manual 701024 Rev.3).

scan_protocol: Affymetrix GeneChip Mouse Genome 430 2.0 arrays were scanned by the EMBL Genomics Core Facility according to the Standard Affymetrix  protocol (Eukaryotic Sample and Array Processing manual 701024 Rev.3).

data_processing: Intensity values for the hybridizations were obtained either using RMA, calculations done in bioconductor  (www.bioconductor.org) or MAS5, calculated using Affymetrix GCOS package. MAS5 calculated intensities were further quantile normalized using bioconductor.

molecule: other

source_name: RNA: from Ip (mouse brain); Protein: Recombinant His-tagged IRP2; Antibody: anti-His tag

label_protocol: Immunopreciptated RNA was used as input to a two-step amplification procedure to generate biotin-labeled RNA fragments for hybridization to the Affymetrix GeneChip Mouse Genome 430 2.0 array  by the EMBL Genomics Core Facility according to the Standard Affymetrix Two Cycle protocol (Eukaryotic Sample and Array Processing manual 701024 Rev.3).

growth_protocol:
Recombinant protein:
IRP2 fused to six His tag at its N-terminus was produced in E. coli and purified as described in Sanchez at al., 2007 Nat. Protoc.
Medium: LB
Antibiotic: Ampicillin
Temperature: 25C

extract_protocol: Reference Sanchez at al., 2007 Nat. Protoc. In brief, Affymetrix microarrays were used to determine the mRNA composition of mRNPs obtained by immunoprecipitation with IRPs (iron regulatory proteins). In brief, total RNA was extracted from the brain of six C57BL6/J mice using Trizol reagent. The mice (8-10 weeks old) were fed with an iron-normal diet. For each tissue, the RNA samples were pooled and the immunoprecipitations were carried out combining 50 µg of total RNA with purified recombinant His-tagged IRP2  produced in E.coli and a mouse monoclonal anti-His tag antibody. A control reaction in which the recombinant IRP2 was omited was performed in parallel (referred with the word “control” in the title). 120 ng of RNA recovered from the immunoprecipitate were used for microarray analysis.

value: mix (female and male) recombinant protein produced in E. coli.

tag: antibody

value: monoclonal anti-His tag


title: IRP2 control immunoprecipitation brain replica 2

status: Public on Dec 09 2011

country: Germany

label: Biotin

organism: Mus musculus

treatment_protocol: The mice (8-10 weeks old) were fed with an iron-normal diet.

tag: strain

tag: gender


title: 16131 days old chimpanzee prefrontal cortex batch 2

type: RNA

city: Leipzig

first: Mehmet

last: Somel

address: Deutscher Platz 6

department: Evolutionary Genetics

institute: Max Planck Institute for Evolutionary Anthropology

description: MicroRNA expression data from post-mortem PFC of a 16131 days old chimpanzee individual

hyb_protocol: The hybridization mix was prepared using the Human miRNA Microarray kit (Agilent Technologies) following the manufacturer's instructions. Labeled miRNA from each sample was hybridized to one Agilent-021827 Human microRNA Microarray (v3, based on the Sanger miRBase Release 12.0). Hybridization was performed at 55C for 20h. Washing was performed using the Gene Expression Wash Buffer kit (Agilent Technologies) following the manufacturer's instructions. For human and chimpanzee, the microarray experiments were carried out in two batches. Batches were balanced with respect to samples' age.

scan_protocol: Arrays were scanned by a DNA microarray scanner (Agilent G2565BA).

data_processing: The Agilent G4462AA Feature Extraction software (v10.7.3.1) was used for image analysis with default settings. In the original analysis we processed the data using the following steps (i) the data was log2 transformed and normalized, separately for each brain region dataset, (ii) we removed samples with low detection values (total detected miRNAs <200) and two samples that appeared as outliers in a principle components analysis (samples Ptr_CBC_525days_indv12_batch1, Hsa_CBC_1630days_indv5_batch2, Hsa_CBC_2922days_indv31_batch2, Hsa_CBC_8364days_indv32_batch2, Mml_CBC_3389days_indv25_batch1, Hsa_CBC_2days_indv1_batch2),  (iii) we removed any batch effects by equalizing the mean expression level across batches, (iv) we calculated the mean profile per biological replicate, (v) we excluded any miRNAs that showed any sequence difference in their mature sequences among the 3 species. For this, we first extracted miRNA precursor sequences in chimpanzee and macaque genomes (panTro3 and rheMac2, respectively) corresponding to human precursors using BLAT (Kent 2002) and then aligned these by ClustalW2 (http://www.ebi.ac.uk/Tools/msa/clustalw2) to extract the orthologous mature sequences. The processed miRNA datasets are available as supplementary files on the Series record.

molecule: total RNA

organism: Pan troglodytes

source_name: Dissected post-mortem chimpanzee prefrontal cortex

label_protocol: 100 ng of dephosphorylated RNA was labeled with Cyanine 3-pCp following standard Agilent protocols.

extract_protocol: Total RNA was extracted from dissected CBC and PFC samples (humans, n=14; chimpanzees, n=11; macaques, n=8, respectively; Table S1), using the Ambion® mirVana miRNA isolation kit. Two individuals in human PFC and CBC sets and 5 individuals in chimpanzee PFC and CBC sets were measured in both batches to estimate the technical variance.

treatment_protocol: We used prefrontal cortex (PFC) and cerebellar cortex (CBC) samples from postmortem brains of human, chimpanzee, and rhesus macaque individuals of different age. Human samples were obtained from the NICHD Brain and Tissue Bank for Developmental Disorders at the University of Maryland, USA, the Netherlands Brain Bank, Amsterdam, Netherlands, and the Chinese Brain Bank Center, Wuhan, China. Informed consent for use of human tissues for research was obtained in writing from all donors or their next of kin. All subjects were defined as normal by forensic pathologists at the corresponding brain bank. All subjects suffered sudden death with no prolonged agonal state. Chimpanzee samples were obtained from the Yerkes Primate Center, GA, USA, the Anthropological Institute & Museum of the University of Zürich-Irchel, Switzerland, and the Biomedical Primate Research Centre, the Netherlands. Rhesus macaque samples were obtained from the Suzhou Experimental Animal Center, China. All non-human primates used in this study suffered sudden deaths for reasons other than their participation in this study and without any relation to the tissue used. CBC dissections were made from the cerebellar cortex. PFC dissections were made from the frontal part of the superior frontal gyrus. All samples contained an approximately 2:1 grey matter to white matter volume ratio.

tag: age

value: 16131 days old

tag: Sex

value: F

tag: tissue

value: prefrontal cortex of the brain

tag: batch

tag: individual no


title: Wild-type liver, biological rep1

city: San Antonio

first: Masahiro

last: Morita

state: Texas

address: 4939 Charles Katz Drive

department: Department of Molecular Medicine

country: USA

institute: University of Texas Health Science Center at San Antonio

description: Gene expression data from wild-type liver

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16hr at 45C on Gene Chip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with RMA as normalization method.

source_name: Mouse liver, 12-week-old, 24hr Fasted

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA.

growth_protocol: Mice were housed in cages, maintained on a 12-hr light-dark cycle, and had access to water ad libitum. Mice were fed a normal chow diet (CA-1, CLEA Japan Inc.).

extract_protocol: Total RNA were extracted with ISOGEN according to manufacture's protocol (Nippon Gene) and purified with RNeasy Kit (Qiagen).

treatment_protocol: For fasting, mice were housed individually and deprived of food.

value: Male

tag: genotype

value: Wild-type

value: liver


title: Rhesus macaque - superior frontal gyrus - 153 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 153 days old Rhesus macaque individual
Mml_153days_batch1

hyb_protocol: Hybridization to Affymetrix® Human Gene 1.0 ST arrays was carried out following standard Affymetrix protocols. The RNA extraction and hybridization was carried out in two batches for human and macaque samples. Batches were relatively balanced with respect to age. Batch 2_2 indicates addition to macaque batch 2.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneChip Scanner 3000.

data_processing: Affymetrix microarray image data were collected with Affymetrix GeneChip Operating Software version 1.1 using default parameters. To identify array probes that contain mismatches among species, we mapped HuGene-1_0-st probe sequences (http://www.affymetrix.com/Auth/analysis/downloads/na23/wtgene/HuGene-1_0-st-v1.probe.tab.zip) to the human (hg18), chimpanzee (panTro2), and rhesus macaque (rheMac2) genomes using BLAT (http://genome.ucsc.edu/FAQ/FAQblat.html). Based on these alignments, we only included probes which matched all three genomes perfectly and at a single location (27% of the original array probes). Intensities of probes that passed this mask were corrected for background using the antigenomic probes with the same GC content; the latter are used as an estimator of the unspecific background hybridization (http://www.affymetrix.com/support/technical/whitepapers/exon_background_correction_whitepaper.pdf). Probe intensities were then log-transformed and quantile normalized. Intensity values per transcript were calculated by median polishing. To determine whether the signal intensity of a given probe was above the expected level of background noise, we compared each probe's signal intensity to a distribution of signal intensities of the antigenomic probes with the same GC content (a GC-bin). For each GC-bin, except the ones with the most extreme GC content, the numbers of antigenomic probes are close to 1,000. We considered a probe signal as detected if its intensity is higher than 95% of the background probes' intensities (see PMID: 17456239). In each array, we considered a transcript as “detected” if more than 50% of probes and at least 8 probes per transcript were detected. We considered a transcript as “expressed” if it was detected in >70% of human, chimpanzee or macaque individuals.

label: biotin

organism: Macaca mulatta

source_name: Dissected Rhesus macaque post-mortem superior frontal gyrus

label_protocol: Biotinylated cRNA were prepared from 2 microg. total RNA following standard Affymetrix protocols.

extract_protocol: Trizol extraction of total RNA from 100 mg of tissue was performed according to the manufacturer's instructions. RNA integrity number (RIN) was measured by the Agilent® 2100 Bioanalyzer.

treatment_protocol: All human postmortem brain tissue samples were obtained from the NICHD Brain and Tissue Bank for Developmental Disorders (NICHDBB)(Baltimore, MD, USA). All subjects were defined as normal controls by forensic pathologists at the NICHDBB. No subjects with prolonged agonal state were used. Chimpanzee samples were obtained from the Yerkes Primate Center (Atlanta, GA, USA), from the Biomedical Primate Research Centre (Rijswijk, Netherlands) and from the Anthropological Institute of the University of Zurich (Switzerland). Rhesus macaque brains were obtained from the SuZhou Experimental Animal Center (SuZhou, China). The dissections were made from the cortical region approximately corresponding to Brodmann area 9 of the prefrontal cortex (the superior frontal gyrus). We aimed to make dissections that contain 2:1 grey:white matter (60-70% grey matter).

value: 153 days

value: m

value: superior frontal gyrus of the brain

tag: post-mortem interval (hours)

tag: rna integrity number (rin)


title: Rhesus macaque - superior frontal gyrus - 10220 days old (batch1)

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 10220 days old Rhesus macaque individual
Mml_10220days_batch1

value: f


title: IRP2 immunoprecipitation brain replica 1


title: Rhesus macaque - superior frontal gyrus - 10220 days old (batch2)

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 10220 days old Rhesus macaque individual
Mml_10220days_batch2


title: 10220 days old macaque cerebellar cortex batch 1

description: MicroRNA expression data from post-mortem CBC of a 10220 days old macaque individual

source_name: Dissected post-mortem macaque cerebellar cortex

value: 10220 days old

value: cerebellar cortex of the brain


title: IRP2 control immunoprecipitation bone marrow replica 2

source_name: RNA: from Ip (mouse bone marrow); Protein: Recombinant His-tagged IRP2; Antibody: anti-His tag

extract_protocol: Reference Sanchez at al., 2007 Nat. Protoc. In brief, Affymetrix microarrays were used to determine the mRNA composition of mRNPs obtained by immunoprecipitation with IRPs (iron regulatory proteins). In brief, total RNA was extracted from the bone marrow of six C57BL6/J mice using Trizol reagent. The mice (8-10 weeks old) were fed with an iron-normal diet. For each tissue, the RNA samples were pooled and the immunoprecipitations were carried out combining 50 µg of total RNA with purified recombinant His-tagged IRP2  produced in E.coli and a mouse monoclonal anti-His tag antibody. A control reaction in which the recombinant IRP2 was omited was performed in parallel (referred with the word “control” in the title). 120 ng of RNA recovered from the immunoprecipitate were used for microarray analysis.


title: Human - superior frontal gyrus - 9277 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 9277 days old human individual
Hsa_9277days_batch1

organism: Homo sapiens

source_name: Dissected Human post-mortem superior frontal gyrus

value: 9277 days


title: Human - superior frontal gyrus - 94 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 94 days old human individual
Hsa_94days_batch2

value: 94 days


title: 7 days old macaque prefrontal cortex batch 1

description: MicroRNA expression data from post-mortem PFC of a 7 days old macaque individual

source_name: Dissected post-mortem macaque prefrontal cortex

value: 7 days old

value: M


title: 7 days old macaque cerebellar cortex batch 1

description: MicroRNA expression data from post-mortem CBC of a 7 days old macaque individual


title: IRP2 control immunoprecipitation brain replica 1

value: mix (female and male) recombinant protein produced in E. coli.

value: monoclonal anti-His tag


title: IRP2 control immunoprecipitation bone marrow replica 1

source_name: RNA: from Ip (mouse bome marrow); Protein: Recombinant His-tagged IRP2; Antibody: anti-His tag


title: Human - superior frontal gyrus - 8364 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 8364 days old human individual
Hsa_8364days_batch2

value: 8364 days


title: 1 days old macaque prefrontal cortex batch 1

description: MicroRNA expression data from post-mortem PFC of a 1 days old macaque individual

value: 1 days old

value: prefrontal cortex of the brain


title: 4 days old human prefrontal cortex batch 1

description: MicroRNA expression data from post-mortem PFC of a 4 days old human individual

source_name: Dissected post-mortem human prefrontal cortex

value: 4 days old


title: 1 days old macaque cerebellar cortex batch 1

description: MicroRNA expression data from post-mortem CBC of a 1 days old macaque individual


title: Human - superior frontal gyrus - 787 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 787 days old human individual
Hsa_787days_batch2

value: 787 days


title: Human - superior frontal gyrus - 5105 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 5105 days old human individual
Hsa_5105days_batch1

value: 5105 days


title: 4 days old human cerebellar cortex batch 1

description: MicroRNA expression data from post-mortem CBC of a 4 days old human individual

source_name: Dissected post-mortem human cerebellar cortex


title: Human - superior frontal gyrus - 4 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 4 days old human individual
Hsa_4days_batch1

value: 4 days

value: m


title: IRP2 immunoprecipitation bone marrow replica 2

description: All the microarray procedures were conducted at the EMBL Genomics Core Facility using standard Affymetrix protocols.  In brief, approximately 120ng of immunoprecipitated RNA was used as input to a two-step amplification procedure to generate biotin-labeled RNA fragments for hybridization to the Affymetrix GeneChip Mouse Genome 430 2.0 array (Eukaryotic Sample and Array Processing manual 701024 Rev.3).


title: 34 days old human cerebellar cortex batch 2

description: MicroRNA expression data from post-mortem CBC of a 34 days old human individual

value: 34 days old


title: Human - superior frontal gyrus - 6111 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 6111 days old human individual
Hsa_6111days_batch2

value: 6111 days

value: superior frontal gyrus of the brain


title: Human - superior frontal gyrus - 35770 days old (batch2)

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 35770 days old human individual
Hsa_35770days_batch2


title: IRP2 immunoprecipitation bone marrow replica 1


title: IRP2 control immunoprecipitation spleen replica 1

source_name: RNA: from Ip (mouse spleen iron deficient); Protein: Recombinant His-tagged IRP2; Antibody: anti-His tag

growth_protocol:
IRP2 fused to six His tag at its N-terminus was produced in E. coli and purified as described in Sanchez at al., 2007 Nat. Protoc.
Medium: LB
Antibiotic: Ampicillin
Temperature: 25C

extract_protocol: Reference Sanchez at al., 2007 Nat. Affymetrix microarrays were used to determine the mRNA composition of mRNPs obtained by immunoprecipitation with IRPs (iron regulatory proteins). In brief, total RNA was extracted from the spleen of four C57BL6/J mice using Trizol reagent. The mice were fed with an iron poor diet (<10mg/kg, Altromin Spezialfutter GmbH & Co, Lage, Germany) for 21 days starting from weaning age. For each tissue, the RNA samples were pooled and the immunoprecipitations were carried out combining 50 µg of total RNA with purified recombinant His-tagged IRP2 produced in E.coli and a mouse monoclonal anti-His tag antibody. A control reaction in which the recombinant IRP2 as omitted was performed in parallel (referred with the word “control” in the title). 120 ng of RNA recovered from the immunoprecipitate were used for microarray analysis.


title: IRP2 immunoprecipitation spleen replica 2

treatment_protocol: The mice were fed with an iron poor diet (<10mg/kg, Altromin Spezialfutter GmbH & Co, Lage, Germany) for 21 days starting from weaning age.


title: IRP2 control immunoprecipitation spleen replica 2


title: Human - superior frontal gyrus - 35770 days old (batch1)

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 35770 days old human individual
Hsa_35770days_batch1


title: 2 days old human cerebellar cortex batch 1

description: MicroRNA expression data from post-mortem CBC of a 2 days old human individual

value: 2 days old

value: cerebellar cortex of the brain


title: 2 days old human cerebellar cortex batch 2


title: 19 days old human cerebellar cortex batch 2

description: MicroRNA expression data from post-mortem CBC of a 19 days old human individual

value: 19 days old

value: F


title: 2 days old human prefrontal cortex batch 1

description: MicroRNA expression data from post-mortem PFC of a 2 days old human individual

value: M


title: 94 days old human prefrontal cortex batch 1

description: MicroRNA expression data from post-mortem PFC of a 94 days old human individual

value: 94 days old


title: 94 days old human cerebellar cortex batch 1

description: MicroRNA expression data from post-mortem CBC of a 94 days old human individual


title: Human - superior frontal gyrus - 32850 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 32850 days old human individual
Hsa_32850days_batch2

value: f


title: Human - superior frontal gyrus - 443 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 443 days old human individual
Hsa_443days_batch2

value: 443 days


title: Human - superior frontal gyrus - 2 days old (batch2)

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 2 days old human individual
Hsa_2days_batch2

value: 2 days


title: IRP2 control immunoprecipitation liver replica 2

source_name: RNA: from Ip (mouse liver iron deficient); Protein: Recombinant His-tagged IRP2; Antibody: anti-His tag

extract_protocol: Reference Sanchez at al., 2007 Nat. Affymetrix microarrays were used to determine the mRNA composition of mRNPs obtained by immunoprecipitation with IRPs (iron regulatory proteins). In brief, total RNA was extracted from the liver of four C57BL6/J mice using Trizol reagent. The mice were fed with an iron poor diet (<10mg/kg, Altromin Spezialfutter GmbH & Co, Lage, Germany) for 21 days starting from weaning age. For each tissue, the RNA samples were pooled and the immunoprecipitations were carried out combining 50 µg of total RNA with purified recombinant His-tagged IRP2 produced in E.coli and a mouse monoclonal anti-His tag antibody. A control reaction in which the recombinant IRP2 as omitted was performed in parallel (referred with the word “control” in the title). 120 ng of RNA recovered from the immunoprecipitate were used for microarray analysis.

value: mix (female and male) recombinant protein produced in E. coli.

value: monoclonal anti-His tag


title: 4415 days old chimpanzee prefrontal cortex batch 2

description: MicroRNA expression data from post-mortem PFC of a 4415 days old chimpanzee individual

value: 4415 days old

value: prefrontal cortex of the brain


title: Human - superior frontal gyrus - 32120 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 32120 days old human individual
Hsa_32120days_batch1

value: m


title: Human - superior frontal gyrus - 34 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 34 days old human individual
Hsa_34days_batch1

value: 34 days


title: IRP2 immunoprecipitation liver replica 1

value: monoclonal anti-His tag.


title: IRP2 immunoprecipitation liver replica 2


title: IRP2 control immunoprecipitation duodenum replica 2

source_name: RNA: from Ip (mouse duodenum iron deficient); Protein: Recombinant His-tagged IRP2; Antibody: anti-His tag

extract_protocol: Reference Sanchez at al., 2007 Nat. Affymetrix microarrays were used to determine the mRNA composition of mRNPs obtained by immunoprecipitation with IRPs (iron regulatory proteins). In brief, total RNA was extracted from the duodenum of four C57BL6/J mice using Trizol reagent. The mice were fed with an iron poor diet (<10mg/kg, Altromin Spezialfutter GmbH & Co, Lage, Germany) for 21 days starting from weaning age. For each tissue, the RNA samples were pooled and the immunoprecipitations were carried out combining 50 µg of total RNA with purified recombinant His-tagged IRP2 produced in E.coli and a mouse monoclonal anti-His tag antibody. A control reaction in which the recombinant IRP2 as omitted was performed in parallel (referred with the word “control” in the title). 120 ng of RNA recovered from the immunoprecipitate were used for microarray analysis.


title: Human - superior frontal gyrus - 2922 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 2922 days old human individual
Hsa_2922days_batch1

value: 2922 days

value: superior frontal gyrus of the brain


title: 4361 days old chimpanzee prefrontal cortex batch 1

description: MicroRNA expression data from post-mortem PFC of a 4361 days old chimpanzee individual

value: 4361 days old


title: Human - superior frontal gyrus - 2 days old (batch1)

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 2 days old human individual
Hsa_2days_batch1


title: 4361 days old chimpanzee cerebellar cortex batch 1

description: MicroRNA expression data from post-mortem CBC of a 4361 days old chimpanzee individual

source_name: Dissected post-mortem chimpanzee cerebellar cortex

value: cerebellar cortex of the brain


title: IRP2 immunoprecipitation duodenum replica 2

description: All the microarray procedures were conducted at the EMBL Genomics Core Facility using standard Affymetrix protocols.  In brief, approximately 120ng of immunoprecipitated RNA was used as input to a two-step amplification procedure to generate biotin-labeled RNA fragments for hybridization to the Affymetrix GeneChip Mouse Genome 430 2.0 array (Eukaryotic Sample and Array Processing manual 701024 Rev.3).


title: IRP2 control immunoprecipitation liver replica 1


title: IRP2 immunoprecipitation duodenum replica 1


title: IRP2 control immunoprecipitation duodenum replica 1


title: Human - superior frontal gyrus - 28692 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 28692 days old human individual
Hsa_28692days_batch2


title: 3389 days old macaque cerebellar cortex batch 1

description: MicroRNA expression data from post-mortem CBC of a 3389 days old macaque individual

value: 3389 days old


title: 3389 days old macaque prefrontal cortex batch 1

description: MicroRNA expression data from post-mortem PFC of a 3389 days old macaque individual

value: M


title: Human - superior frontal gyrus - 29200 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 29200 days old human individual
Hsa_29200days_batch1


title: 8104 days old macaque prefrontal cortex batch 1

description: MicroRNA expression data from post-mortem PFC of a 8104 days old macaque individual

value: 8104 days old


title: 8104 days old macaque cerebellar cortex batch 1

description: MicroRNA expression data from post-mortem CBC of a 8104 days old macaque individual


title: 8364 days old human cerebellar cortex batch 2

description: MicroRNA expression data from post-mortem CBC of a 8364 days old human individual

value: 8364 days old


title: 16 days old macaque prefrontal cortex batch 1

description: MicroRNA expression data from post-mortem PFC of a 16 days old macaque individual

value: 16 days old


title: Human - superior frontal gyrus - 19457 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 19457 days old human individual
Hsa_19457days_batch1


title: IRP1 control immunoprecipitation bone marrow replica 1

scan_protocol: Affymetrix GeneChip Mouse Genome 430 2.0 arrays were scanned by the EMBL Genomics Core Facility according to the Standard Affymetrix protocol (Eukaryotic Sample and Array Processing manual 701024 Rev.3).

source_name: RNA: from Ip (mouse bone marrow); Protein: Recombinant His-tagged IRP1; Antibody: anti-IRP1

growth_protocol:
IRP1 fused to six His tag at its N-terminus was produced in E. coli and purified as described in Sanchez at al., 2007 Nat. Protoc.
Medium: LB
Antibiotic: Ampicillin
Temperature: 37C

extract_protocol: Reference Sanchez at al., 2007 Nat. Protoc. In brief, Affymetrix microarrays were used to determine the mRNA composition of mRNPs obtained by immunoprecipitation with IRPs (iron regulatory proteins). In brief, total RNA was extracted from the bone marrow of six C57BL6/J mice using Trizol reagent. The mice (8-10 weeks old) were fed with an iron-normal diet. For each tissue, the RNA samples were pooled and the immunoprecipitations were carried out combining 50 µg of total RNA with purified recombinant IRP1 produced in E.coli and a rabbit polyclonal anti-IRP1 antibody . A control reaction in which the recombinant IRP1 was omited was performed in parallel (referred with the word “control” in the title). 120 ng of RNA recovered from the immunoprecipitate were used for microarray analysis.

value: rabbit polyclonal anti-IRP1


title: IRP1 immunoprecipitation brain replica 1

source_name: RNA: from Ip (mouse brain); Protein: Recombinant His-tagged IRP1; Antibody: anti-IRP1

extract_protocol: Reference Sanchez at al., 2007 Nat. Protoc. In brief, Affymetrix microarrays were used to determine the mRNA composition of mRNPs obtained by immunoprecipitation with IRPs (iron regulatory proteins). In brief, total RNA was extracted from the brain of six C57BL6/J mice using Trizol reagent. The mice (8-10 weeks old) were fed with an iron-normal diet. For each tissue, the RNA samples were pooled and the immunoprecipitations were carried out combining 50 µg of total RNA with purified recombinant IRP1 produced in E.coli and a rabbit polyclonal anti-IRP1 antibody . A control reaction in which the recombinant IRP1 was omited was performed in parallel (referred with the word “control” in the title). 120 ng of RNA recovered from the immunoprecipitate were used for microarray analysis.

value: mix (female and male) recombinant protein produced in E. coli.


title: Human - superior frontal gyrus - 21204 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 21204 days old human individual
Hsa_21204days_batch2


title: Human - superior frontal gyrus - 1630 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 1630 days old human individual
Hsa_1630days_batch2

value: 1630 days

value: f


title: Human - superior frontal gyrus - 204 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 204 days old human individual
Hsa_204days_batch1

value: 204 days


title: IRP1 immunoprecipitation bone marrow replica 1


title: Human - superior frontal gyrus - 24090 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 24090 days old human individual
Hsa_24090days_batch1

value: m


title: IRP1 immunoprecipitation brain replica 2


title: IRP1 control immunoprecipitation brain replica 2


title: Human - superior frontal gyrus - 19 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 19 days old human individual
Hsa_19days_batch2

value: 19 days


title: IRP1 control immunoprecipitation bone marrow replica 2


title: 16 days old macaque cerebellar cortex batch 1

description: MicroRNA expression data from post-mortem CBC of a 16 days old macaque individual


title: IRP1 control immunoprecipitation brain replica 1


title: IRP2 immunoprecipitation spleen replica 1

value: monoclonal anti-His tag


title: IRP1 control immunoprecipitation spleen replica 2

source_name: RNA: from Ip (mouse spleen iron deficient); Protein: Recombinant His-tagged IRP1; Antibody: anti-IRP1

extract_protocol: For each tissue, the RNA samples were pooled and the immunoprecipitations were carried out combining 50 µg of total RNA with purified recombinant IRP1 produced in E.coli and a rabbit polyclonal anti-IRP1 antibody. A control reaction in which the recombinant IRP1 was omitted was performed in parallel (referred with the word “control” in the title). 120 ng of RNA recovered from the immunoprecipitate were used for microarray analysis.


title: 449 days old macaque prefrontal cortex batch 1

description: MicroRNA expression data from post-mortem PFC of a 449 days old macaque individual

value: 449 days old

value: prefrontal cortex of the brain


title: Human - superior frontal gyrus - 14309 days old

description:
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30  days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem superior frontal gyrus of a 14309 days old human individual
Hsa_14309days_batch2

value: superior frontal gyrus of the brain


title: IRP1 immunoprecipitation bone marrow replica 2

description: All the microarray procedures were conducted at the EMBL Genomics Core Facility using standard Affymetrix protocols.  In brief, approximately 120ng of immunoprecipitated RNA was used as input to a two-step amplification procedure to generate biotin-labeled RNA fragments for hybridization to the Affymetrix GeneChip Mouse Genome 430 2.0 array (Eukaryotic Sample and Array Processing manual 701024 Rev.3).


title: 449 days old macaque cerebellar cortex batch 1

description: MicroRNA expression data from post-mortem CBC of a 449 days old macaque individual

value: cerebellar cortex of the brain


title: Experimental,biological rep2 G6

city: Hyderabad

first: kotakonda

last: Arunasri

state: Andhra Pradesh

address: Habsiguda

country: India

institute: Centre for Cellular and Molecular biology

description: Gene expression data of E.coli in LB+glycerol medium

hyb_protocol: The DNA micro array chips were hybridized with the labelled cDNA using the Affymetrix protocol (www.affymetrix.com).

scan_protocol: Microarray slides were then scanned using Affymetrix 428 Array Scanner and GCOS software to obtain images of the chips and further processed to get intensity cell files for the probe sets.

data_processing: The intensity cell files were then imported, normalized for background correction using PLIER and data analysed using Gene Spring 11.5 software.

organism: Escherichia coli

source_name: E.coli, grown in LB+ glycerol to0.8OD

label_protocol: The cDNA was fragmented with DNAse 1 (Promega Corporation, Madison, USA) and then labeled with biotin at the 3’ end using the labeling reagent from Affymetrix (CA, USA) and Terminal transferase enzyme (Promega).

growth_protocol: Escherichia coli was grown aerobically in Luria-Bertani (LB) broth at 30°C in an incubator shaker at 150 r.p.m.

extract_protocol: RNA was isolated from the culture by using the Qiagen RNeasy mini-prep kit.cDNA was synthesized using 5-10 µg/ml of RNA and the first strand cDNA synthesis kit from Invitrogen (Invitrogen Bioservices India Pvt. Ltd., Bangalore).

treatment_protocol: To study gene expression in the presence and absence of glycerol, LB was supplemented with 10% (v/v) glycerol. Medium without glycerol served as a control.

value: Escherichia coli

tag: growth medium

value: LB+glycerol medium


title: IRP1 immunoprecipitation spleen replica 1


title: IRP1 control immunoprecipitation spleen replica 1


title: 9277 days old human prefrontal cortex batch 1

description: MicroRNA expression data from post-mortem PFC of a 9277 days old human individual

value: 9277 days old

value: M


title: Experimental,biological rep2 G5


title: 9277 days old human cerebellar cortex batch 1

description: MicroRNA expression data from post-mortem CBC of a 9277 days old human individual


title: IRP1 immunoprecipitation spleen replica 2


title: Experimental,biological rep2 G4


title: Experimental,biological rep1 G3


title: 1487 days old macaque prefrontal cortex batch 1

description: MicroRNA expression data from post-mortem PFC of a 1487 days old macaque individual

value: 1487 days old


title: Experimental,biological rep1 G2


title: Wild type embryonic (E11.5) esophagus replicate 1

city: Camden

first: Xiaoxin

middle: Luke

last: Chen

state: NJ

address: 403 Haddon Avenue

institute: Coriell Institute for Medical Research

description: Biological replicate 1 of 3 wild type embryonic day 11.5 esophageal tissue

hyb_protocol: Cy3 or Cy5 labeled, linearly amplified cRNA samples were hybridized with Gene Expression Hybridization Kit (Agilent p/n 5188-5242) according to the user guide.

scan_protocol: Scanned on an Agilent Microarray Scanner p/n G2565BA Agilent Feature Extraction Software 9.1

data_processing: Agilent Feature Extraction Software 9.1 was used for background subtraction and LOWESS normalization.

source_name: Whole esophagus of C57BL/6J mouse at E11.5

label_protocol: 1 µg of total RNA were labled with Agilent Low RNA Input Linear Amplification Kit, PLUS, Two-Color (Agilent p/n 5188-5340) according to the provided protocol.

growth_protocol: animal care: The mice were bred in-house to generate embryos and offsprings of proper genotypes. Mice were PCR-genotyped according to protocols provided by the original developers.

extract_protocol:
sample harvest: Esophagi of E11.5, E15.5, P0, P7, and adult (8 weeks old) mice were dissected and snap-frozen for extraction of total RNA
Total RNA was extracted from mouse esophageal tissue using RNeasy Fibrous Tissue Mini Kit (Qiagen; Valencia, CA).

value: Embryonic day 11.5

value: whole esophagus

source_name: Agilent's Universal Mouse Reference RNA

tag: cell type

value: 11 mouse cell lines


title: 1487 days old macaque cerebellar cortex batch 1

description: MicroRNA expression data from post-mortem CBC of a 1487 days old macaque individual

source_name: Dissected post-mortem macaque cerebellar cortex


title: IRP1 control immunoprecipitation liver replica 1

source_name: RNA: from Ip (mouse liver iron deficient); Protein: Recombinant His-tagged IRP1; Antibody: anti-IRP1

value: mix (female and male) recombinant protein produced in E. coli.

value: rabbit polyclonal anti-IRP1


title: IRP1 immunoprecipitation liver replica 2


title: IRP1 control immunoprecipitation liver replica 2


title: Nrf2-/- adult (8 weeks) esophageal epithelium replicate 3

description: Biological replicate 3 of 3 Nrf2-/-  adult esophageal epithelium

source_name: Esophageal epithelium of adult Nrf2-/- mouse

value: Adult (8 weeks)

value: esophageal epithelium

value: Nrf2-/- on C57BL/6J background


title: Nrf2-/- adult (8 weeks) esophageal epithelium replicate 2

description: Biological replicate 2 of 3 Nrf2-/-  adult esophageal epithelium


title: control, biological rep2 C6

description: Gene expression data of E.coli in LB medium

source_name: E.coli, grown in LB to0.8OD

value: LB medium


title: 2922 days old human cerebellar cortex batch 2

description: MicroRNA expression data from post-mortem CBC of a 2922 days old human individual

value: 2922 days old


title: IRP1 immunoprecipitation liver replica 1


title: IRP1 control immunoprecipitation duodenum replica 2

source_name: RNA: from Ip (mouse duodenum iron deficient); Protein: Recombinant His-tagged IRP1; Antibody: anti-IRP1


title: 1630 days old human cerebellar cortex batch 1

description: MicroRNA expression data from post-mortem CBC of a 1630 days old human individual

value: 1630 days old

value: F


title: control, biological rep2 C5

value: Escherichia coli


title: IRP1 immunoprecipitation duodenum replica 2

label_protocol: Immunopreciptated RNA was used as input to a two-step amplification procedure to generate biotin-labeled RNA fragments for hybridization to the Affymetrix GeneChip Mouse Genome 430 2.0 array  by the EMBL Genomics Core Facility according to the Standard Affymetrix Two Cycle protocol (Eukaryotic Sample and Array Processing  manual 701024 Rev.3).


title: MB-1398

type: genomic

city: HEIDELBERG

first: Paul

middle: A.

last: Northcott

address: Im Neuenheimer Feld 280

institute: German Cancer Research Center (DKFZ)

description:
Hybridized to Affy SNP6.0
MB-G-Pri

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: As per manufacturer (Affymetrix)

data_processing: CEL files were quantile normalized and modelled using the dChip algorithm.

molecule: genomic DNA

source_name: brain tumor: tissue

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: High molecular weight genomic DNA was extracted using standard SDS/Proteinase K digestion, followed by phenol extraction and ethanol precipitation.

tag: tumor type

value: medulloblastoma

tag: tumor source

value: primary tumor

tag: patient gender

value: Male

tag: patient age at diagnosis

tag: medulloblastoma subgroup


title: control, biological rep2 C4

tag: strain


title: Experimental,biological rep1 G1

value: LB+glycerol medium


title: MB-1384

description:
Hybridized to Affy SNP6.0
MB-E-Pri

value: Female

value: SHH


title: Wild type adult (8 weeks) esophageal epithelium replicate 3

description: Biological replicate 3 of 3 wild type adult esophageal epithelium

source_name: Esophageal epithelium of adult C57BL/6J mouse

value: 11 mouse cell lines


title: 1630 days old human cerebellar cortex batch 2

source_name: Dissected post-mortem human cerebellar cortex

value: cerebellar cortex of the brain


title: Wild type embryonic (E11.5) esophagus replicate 2

description: Biological replicate 2 of 3 wild type embryonic day 11.5 esophageal tissue

value: Embryonic day 11.5

value: whole esophagus


title: Wild type adult (8 weeks) esophageal epithelium replicate 2

description: Biological replicate 2 of 3 wild type adult esophageal epithelium

value: Adult (8 weeks)

value: esophageal epithelium


title: MB-1395

description:
Hybridized to Affy SNP6.0
MB-F-Met

value: metastatic tumor


title: MB-1394

description:
Hybridized to Affy SNP6.0
MB-F-Pri


title: MB-1399

description:
Hybridized to Affy SNP6.0
MB-G-Met


title: 443 days old human cerebellar cortex batch 2

description: MicroRNA expression data from post-mortem CBC of a 443 days old human individual

value: 443 days old

value: M


title: control, biological rep1 C2

value: LB medium


title: MB-1385

description:
Hybridized to Affy SNP6.0
MB-E-Met


title: control, biological rep1 C1

value: Escherichia coli


title: 2313 days old chimpanzee prefrontal cortex batch 1

description: MicroRNA expression data from post-mortem PFC of a 2313 days old chimpanzee individual

source_name: Dissected post-mortem chimpanzee prefrontal cortex

value: 2313 days old

value: F

value: prefrontal cortex of the brain


title: 1630 days old human prefrontal cortex batch 1

description: MicroRNA expression data from post-mortem PFC of a 1630 days old human individual

source_name: Dissected post-mortem human prefrontal cortex

value: 1630 days old


title: IRP1 immunoprecipitation duodenum replica 1

description: All the microarray procedures were conducted at the EMBL Genomics Core Facility using standard Affymetrix protocols.  In brief, approximately 120ng of immunoprecipitated RNA was used as input to a two-step amplification procedure to generate biotin-labeled RNA fragments for hybridization to the Affymetrix GeneChip Mouse Genome 430 2.0 array (Eukaryotic Sample and Array Processing manual 701024 Rev.3).

extract_protocol: Reference Sanchez at al., 2007 Nat. Protoc. Affymetrix microarrays were used to determine the mRNA composition of mRNPs obtained by immunoprecipitation with IRPs (iron regulatory proteins). In brief, total RNA was extracted from the duodenum of four C57BL6/J mice using Trizol reagent. The mice were fed with an iron poor diet (<10mg/kg, Altromin Spezialfutter GmbH & Co, Lage, Germany) for 21 days starting from weaning age. For each tissue, the RNA samples were pooled and the immunoprecipitations were carried out combining 50 µg of total RNA with purified recombinant IRP1 produced in E.coli and a rabbit polyclonal anti-IRP1 antibody. A control reaction in which the recombinant IRP1 was omitted was performed in parallel (referred with the word “control” in the title). 120 ng of RNA recovered from the immunoprecipitate were used for microarray analysis.

tag: gender

value: mix (female and male) recombinant protein produced in E. coli.

tag: antibody

value: rabbit polyclonal anti-IRP1


title: 2313 days old chimpanzee cerebellar cortex batch 1

description: MicroRNA expression data from post-mortem CBC of a 2313 days old chimpanzee individual

source_name: Dissected post-mortem chimpanzee cerebellar cortex

tag: age

tag: Sex


title: Wild type adult (8 weeks) esophageal epithelium replicate 1

description: Biological replicate 1 of 3 wild type adult esophageal epithelium

tag: tissue

value: 11 mouse cell lines


title: Nrf2-/-Keap1-/- postnatal (P7) esophagus replicate 3

description: Biological replicate 3 of 3 Nrf2-/-Keap1-/- postnatal day 7 esophagi

source_name: Whole esophagus of Nrf2-/-Keap1-/- mouse at P7

value: Postnatal day 7

value: Nrf2-/-Keap1-/- on C57BL/6J background


title: MB-1324

description:
Hybridized to Affy SNP6.0
MB-D-Met

value: medulloblastoma

value: Male

value: Group D


title: IRP1 control immunoprecipitation duodenum replica 1


title: control, biological rep1 C3


title: 39 days old chimpanzee prefrontal cortex batch 1

description: MicroRNA expression data from post-mortem PFC of a 39 days old chimpanzee individual

value: 39 days old

tag: batch

tag: individual no


title: Nrf2-/-Keap1-/- postnatal (P7) esophagus replicate 2

description: Biological replicate 2 of 3 Nrf2-/-Keap1-/- postnatal day 7 esophagi

value: whole esophagus


title: 39 days old chimpanzee prefrontal cortex batch 2

value: M


title: 39 days old chimpanzee cerebellar cortex batch 1

description: MicroRNA expression data from post-mortem CBC of a 39 days old chimpanzee individual

value: cerebellar cortex of the brain


title: MB-523

description:
Hybridized to Affy SNP6.0
MB-B-Met1

value: metastatic tumor

value: Group C


title: 8 days old chimpanzee prefrontal cortex batch 2

description: MicroRNA expression data from post-mortem PFC of a 8 days old chimpanzee individual

value: 8 days old


title: MB-522

description:
Hybridized to Affy SNP6.0
MB-B-Pri

value: primary tumor


title: Nrf2-/-Keap1-/- postnatal (P7) esophagus replicate 1

description: Biological replicate 1 of 3 Nrf2-/-Keap1-/- postnatal day 7 esophagi


title: mdm 328 Ttn-

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

description: quadriceps RNA of mouse 328 without Titin-mutation

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 4, from SAS. Gene expression profiling was performed using arrays of HGU133_2 -type from Affymetrix. A Custom CDF Version 11 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized using RMA.

source_name: mouse 328 without Ttn-mutation

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

extract_protocol: RNA was isolated from quadriceps using Trizol®-Reagent (Gibco brl). and Qiagen RNeasy Kit

value: B6C3Fe a/a-Ttnmdm/J

tag: genotype

value: Titin wild type

value: quadriceps


title: Nrf2-/- adult (8 weeks) esophageal epithelium replicate 1

description: Biological replicate 1 of 3 Nrf2-/-  adult esophageal epithelium

value: Adult (8 weeks)

value: esophageal epithelium

value: Nrf2-/- on C57BL/6J background

value: 11 mouse cell lines


title: mdm 335 Ttn-

description: quadriceps RNA of mouse 335 without Titin-mutation

source_name: mouse 335 without Ttn-mutation


title: mdm 326 Ttn+

description: quadriceps RNA of mouse 326 with Titin-mutation

source_name: mouse 326 with Ttn-mutation

value: Titin mutant


title: Keap1-/- postnatal (P7) esophagus replicate 3

description: Biological replicate 3 of 3 Keap1-/- postnatal day 7 esophagi

source_name: Whole esophagus of Keap1-/- mouse at P7

value: Postnatal day 7

value: Keap1-/- on C57BL/6J background


title: Keap1-/- postnatal (P7) esophagus replicate 1

description: Biological replicate 1 of 3 Keap1-/- postnatal day 7 esophagi

value: whole esophagus

source_name: Agilent's Universal Mouse Reference RNA


title: 45 days old chimpanzee prefrontal cortex batch 2

description: MicroRNA expression data from post-mortem PFC of a 45 days old chimpanzee individual

value: 45 days old

value: F

value: prefrontal cortex of the brain


title: Keap1-/- postnatal (P7) esophagus replicate 2

description: Biological replicate 2 of 3 Keap1-/- postnatal day 7 esophagi


title: MB-579

description:
Hybridized to Affy SNP6.0
MB-C-Met

value: medulloblastoma

value: metastatic tumor

value: Female

value: Group D


title: 1 days old chimpanzee prefrontal cortex batch 1

description: MicroRNA expression data from post-mortem PFC of a 1 days old chimpanzee individual

value: 1 days old


title: MB-1323

description:
Hybridized to Affy SNP6.0
MB-D-Pri

value: primary tumor

value: Male


title: Nrf2-/- postnatal (P7) esophagus replicate 3

description: Biological replicate 3 of 3 Nrf2-/- postnatal day 7 esophagi

source_name: Whole esophagus of Nrf2-/- mouse at P7


title: Nrf2-/- postnatal (P7) esophagus replicate 2

description: Biological replicate 2 of 3 Nrf2-/- postnatal day 7 esophagi


title: Nrf2-/- postnatal (P7) esophagus replicate 1

description: Biological replicate 1 of 3 Nrf2-/- postnatal day 7 esophagi


title: 1 days old chimpanzee cerebellar cortex batch 1

description: MicroRNA expression data from post-mortem CBC of a 1 days old chimpanzee individual

value: cerebellar cortex of the brain


title: MB-525

description:
Hybridized to Affy SNP6.0
MB-B-Met3

value: Group C


title: 787 days old human cerebellar cortex batch 1

description: MicroRNA expression data from post-mortem CBC of a 787 days old human individual

value: 787 days old


title: 787 days old human prefrontal cortex batch 1

description: MicroRNA expression data from post-mortem PFC of a 787 days old human individual


title: MB-528

description:
Hybridized to Affy SNP6.0
MB-A-Met1


title: 0 days old chimpanzee cerebellar cortex batch 1

description: MicroRNA expression data from post-mortem CBC of a 0 days old chimpanzee individual

value: 0 days old

value: M


title: 0 days old chimpanzee prefrontal cortex batch 2

description: MicroRNA expression data from post-mortem PFC of a 0 days old chimpanzee individual


title: MB-527

description:
Hybridized to Affy SNP6.0
MB-A-Pri


title: MB-321

description:
Hybridized to Affy SNP6.0
MB-C-Pri


title: Wild type postnatal (P7) esophagus replicate 1

description: Biological replicate 1 of 3 wild type postnatal day 7 esophagi

source_name: Whole esophagus of C57BL/6J mouse at P7

value: Postnatal day 7

value: 11 mouse cell lines


title: Wild type postnatal (P7) esophagus replicate 3

description: Biological replicate 2 of 3 wild type postnatal day 7 esophagi

value: whole esophagus


title: 0 days old chimpanzee prefrontal cortex batch 1


title: 525 days old chimpanzee prefrontal cortex batch 1

description: MicroRNA expression data from post-mortem PFC of a 525 days old chimpanzee individual

value: 525 days old

value: F


title: Wild type postnatal (P7) esophagus replicate 2


title: Wild type postnatal (P0) esophagus replicate 2

description: Biological replicate 2 of 3 wild type postnatal day 0 esophagi

source_name: Whole esophagus of C57BL/6J mouse at P0

value: Postnatal day 0


title: 525 days old chimpanzee prefrontal cortex batch 2

value: prefrontal cortex of the brain


title: MB-529

description:
Hybridized to Affy SNP6.0
MB-A-Met2

value: medulloblastoma

value: metastatic tumor


title: Wild type embryonic (E15.5) esophagus replicate 3

description: Biological replicate 1 of 3 wild type embryonic day 15.5 esophageal tissue

source_name: Whole esophagus of C57BL/6J mouse at E15.5

value: Embryonic day 15.5


title: Wild type postnatal (P0) esophagus replicate 1

description: Biological replicate 1 of 3 wild type postnatal day 0 esophagi


title: Wild type postnatal (P0) esophagus replicate 3

description: Biological replicate 3 of 3 wild type postnatal day 0 esophagi


title: Wild type embryonic (E15.5) esophagus replicate 2


title: 525 days old chimpanzee cerebellar cortex batch 1

description: MicroRNA expression data from post-mortem CBC of a 525 days old chimpanzee individual


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_402

status: Public on Dec 08 2011

city: Bethesda

first: Yuelin

middle: Jack

last: Zhu

state: MD

address: 9000 Rockville Pike

department: Genetics Branch, Center for Cancer Research

institute: NCI

description: Primary

hyb_protocol: DNA was hybridized to the Illumina GoldenGate Cancer Panel I array using the standard Illumina protocol.

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

data_processing:
Cy3, Cy5, Average Beta, and detection p-values were extracted using BeadStudio software.

Unmethylated and methylated signal intensities are available in 'GSE29428_raw_data.txt', which is linked to the Series GSE29428 record as a supplementary file.

label: Cy5, Cy3

source_name: Breast_Primary, ER-

label_protocol: DNA was bisulfite converted, amplified, and labeled.

extract_protocol: Genomic DNA was extracted using standard techniques.

value: breast

tag: disease state

tag: er status

value: ER-


title: Wild type embryonic (E15.5) esophagus replicate 1

tag: cell type


title: genomic_DNA_Breast_TDLU_AJP10_0850_401

description: Terminal ductal-lobular unit (TDLU)

source_name: Breast_Terminal ductal-lobular unit (TDLU)

value: TDLU


title: MB-524

description:
Hybridized to Affy SNP6.0
MB-B-Met2

source_name: brain tumor: tissue

tag: tumor type

value: Group C


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_400

description: Primary

source_name: Breast_Primary, ER+

value: ER+


title: genomic_DNA_Breast_TDLU_AJP10_0850_399

description: Terminal ductal-lobular unit (TDLU)


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_396

description: Primary


title: mdm 325 Ttn+

description: quadriceps RNA of mouse 325 with Titin-mutation

source_name: mouse 325 with Ttn-mutation

value: B6C3Fe a/a-Ttnmdm/J

value: Titin mutant

value: quadriceps


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_397

description: Primary


title: genomic_DNA_Breast_TDLU_AJP10_0850_398

description: Terminal ductal-lobular unit (TDLU)


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_393

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_394

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_395

description: Primary


title: Wild type embryonic (E11.5) esophagus replicate 3

description: Biological replicate 3 of 3 wild type embryonic day 11.5 esophageal tissue

source_name: Whole esophagus of C57BL/6J mouse at E11.5

value: Embryonic day 11.5

value: 11 mouse cell lines


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_390

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_389

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_391

description: Primary


title: genomic_DNA_Breast_TDLU_AJP10_0850_392

description: Terminal ductal-lobular unit (TDLU)


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_385

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_387

description: Primary


title: genomic_DNA_Breast_TDLU_AJP10_0850_383

description: Terminal ductal-lobular unit (TDLU)


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_380

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_388

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_384

description: Primary


title: genomic_DNA_Breast_MET_AJP10_0850_386

description: Metastasis

source_name: Breast_Metastasis, ER-


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_382

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_377

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_376

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_374

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_378

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_373

description: Primary


title: genomic_DNA_Breast_TDLU_AJP10_0850_375

description: Terminal ductal-lobular unit (TDLU)


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_381

description: Primary


title: genomic_DNA_Breast_TDLU_AJP10_0850_372

description: Terminal ductal-lobular unit (TDLU)


title: genomic_DNA_Breast_TDLU_AJP10_0850_371

description: Terminal ductal-lobular unit (TDLU)


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_379

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_368

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_369

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_362

description: Primary


title: genomic_DNA_Breast_TDLU_AJP10_0850_361

description: Terminal ductal-lobular unit (TDLU)


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_366

description: Primary


title: genomic_DNA_Breast_TDLU_AJP10_0850_367

description: Terminal ductal-lobular unit (TDLU)


title: genomic_DNA_Breast_TDLU_AJP10_0850_365

description: Terminal ductal-lobular unit (TDLU)


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_363

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_370

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_364

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_358

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_360

description: Primary


title: genomic_DNA_Breast_TDLU_AJP10_0850_359

description: Terminal ductal-lobular unit (TDLU)


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_357

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_356

description: Primary


title: NP_Pax6_rep1

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

description: Chip-chip wildtype mouse NP cells Pax6

hyb_protocol: Hybridization was performed according to standard Nimblegen procedure

scan_protocol: Scanning was performed with NImbleScan.

data_processing: For each oligo, the log2 ratio of IP over input intensities were calculated. Arrays were then loess normalized using R and Bioconductor package limma.

source_name: Pax6 ChIP DNA from NP cells

label_protocol: According to Nimblegen guidelines

growth_protocol: Wild-type embryonic stem cells (129-C57Bl/6) and derived neuronal progenitor cells were cultured and differentiated as previously described (M. Bibel, J. Richter, E. Lacroix, Y. A. Barde, Nat Protoc 2, 1034 (2007))

extract_protocol: ChIP experiments for Pax6 were performed as previously described (Weber et al., 2007, PMID: 17334365).

value: NP cells

tag: chip antibody

value: anti-Pax6 (Covance PRB-278P)

source_name: Input DNA from NP cells

value: none, input DNA


title: NP_Pax6_rep3

description: Chip-chip wildtype mouse NP cells Pax6


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_351

description: Primary


title: genomic_DNA_Breast_MET_AJP10_0850_355

description: Metastasis

source_name: Breast_Metastasis, ER+


title: genomic_DNA_Breast_TDLU_AJP10_0850_350

description: Terminal ductal-lobular unit (TDLU)


title: 1 days old chimpanzee prefrontal cortex batch 2

description: MicroRNA expression data from post-mortem PFC of a 1 days old chimpanzee individual

source_name: Dissected post-mortem chimpanzee prefrontal cortex

extract_protocol: Total RNA was extracted from dissected CBC and PFC samples (humans, n=14; chimpanzees, n=11; macaques, n=8, respectively; Table S1), using the Ambion® mirVana miRNA isolation kit. Two individuals in human PFC and CBC sets and 5 individuals in chimpanzee PFC and CBC sets were measured in both batches to estimate the technical variance.

value: 1 days old

value: F

value: prefrontal cortex of the brain


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_349

description: Primary


title: genomic_DNA_RLN_FEMALE_AJP10_0850_341


title: genomic_DNA_Breast_MET_AJP10_0850_348

description: Metastasis


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_347

description: Primary


title: genomic_DNA_RLN_FEMALE_AJP10_0850_343


title: genomic_DNA_RLN_FEMALE_AJP10_0850_345


title: genomic_DNA_RLN_FEMALE_AJP10_0850_342


title: genomic_DNA_Breast_MET_AJP10_0850_354

description: Metastasis


title: NP_Pax6_rep2

description: Chip-chip wildtype mouse NP cells Pax6


title: genomic_DNA_RLN_FEMALE_AJP10_0850_339


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_352

description: Primary


title: genomic_DNA_RLN_FEMALE_AJP10_0850_338


title: genomic_DNA_RLN_FEMALE_AJP10_0850_337


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_331

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_329

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_330

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_328

description: Primary


title: genomic_DNA_RLN_FEMALE_AJP10_0850_333


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_332

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_325

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_326

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_327

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_324

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_323

description: Primary


title: genomic_DNA_RLN_FEMALE_AJP10_0850_334


title: genomic_DNA_MESENCH_AJP10_0850_321

description: MESENCH

value: MUSCLE


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_320

description: Primary

value: breast


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_322

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_319

description: Primary

value: ER-


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_318

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_311

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_310

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_306

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_317

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_316

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_308

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_313

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_305

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_309

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_304

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_315

description: Primary


title: genomic_DNA_Breast_TDLU_AJP10_0850_314

description: Terminal ductal-lobular unit (TDLU)

value: TDLU


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_303

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_293

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_297

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_298

description: Primary


title: genomic_DNA_Breast_NOTUMREG_AJP10_0850_299

description: NOTUMREG

value: NOTUMREG


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_294

description: Primary

value: ER+


title: genomic_DNA_Breast_NOTUMREG_AJP10_0850_302

description: NOTUMREG


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_296

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_291

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_295

description: Primary


title: genomic_DNA_Breast_NOTUMREG_AJP10_0850_312

description: NOTUMREG


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_300

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_307

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_290

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_301

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_292

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_287

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_286

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_284

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_285

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_288

description: Primary


title: genomic_DNA_Breast_NOTUMREG_AJP10_0850_289

description: NOTUMREG


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_282

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_281

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_283

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_276

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_275

description: Primary


title: genomic_DNA_Breast_MET_AJP10_0850_278

description: Metastasis


title: genomic_DNA_MESENCH_AJP10_0850_279

description: MESENCH


title: genomic_DNA_Breast_MET_AJP10_0850_280

description: Metastasis


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_277

description: Primary


title: IM19_case

city: Roskilde

first: Vibe

last: Skov

address: Koegevej 7-13

department: Hematology

country: Denmark

institute: Roskilde Hospital

description: Intima media

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: The R statistical software was applied for data analysis. VSN was used for global background correction and normalization. Gene expression index calculation was done using model based index calculation (MBEI). Only perfect match probes were included in data analysis. Welch two sample t-test for paired data was used to calculate p-values.

source_name: Intima media; type 2 diabetic patient

label_protocol: One µg purified total RNA was converted to biotin-labeled aRNA using the MessageAmpTM II-Biotin single round aRNA amplification kit

extract_protocol: Frozen muscle tissue was homogenized in Trizol with a Polytron Homogenizer and total RNA was purified using TRIzol Reagent including an extra step after phase separation with chloroform. Briefly, 1 volume of phenol-chloroform-isoamylalcohol (25-24-1) was added to the aqueous phase and spun at 10.000 x g for 10 minutes at 4˚C. Then, 1 volume of chloroform was added to the aqueous phase and spun at 12.000 x g for 20 minutes at 4˚C before RNA precipitation.

tag: Intima media


title: IM122_case

description: Intima media


title: IM69_control

description: Intima media

source_name: Intima media; control subject


title: IM66_control

description: Intima media


title: IM32_control

description: Intima media


title: Lima1A_case

description: Intima media


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_274

description: Primary


title: IM70_control

description: Intima media


title: IM46_control

description: Intima media


title: IM28_control

description: Intima media


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_273

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_272

description: Primary


title: genomic_DNA_Breast_MET_AJP10_0850_271

description: Metastasis


title: IM27_case

description: Intima media


title: IM63_case

description: Intima media


title: IM29_control

description: Intima media


title: IM67_case

description: Intima media


title: IM24_control

description: Intima media


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_270

description: Primary


title: IM18_control

description: Intima media


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_269

description: Primary


title: IM17_control

description: Intima media


title: IM16_case

description: Intima media


title: IM14_case

description: Intima media


title: IM71_case

description: Intima media


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_353

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_264

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_263

description: Primary


title: genomic_DNA_Breast_TDLU_AJP10_0850_267

description: Terminal ductal-lobular unit (TDLU)


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_266

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_265

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_262

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_268

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_257

description: Primary


title: Delta-mntR 60 min with 10 microM MnCl2

first: Lauren

last: Waters

address: 18 Library Drive, Room 113

institute: National Institutes of Health

hyb_protocol: Following fragmentation, 3.5 µg of cDNA was hybridized for 16 hr at 45˚C on GeneChip E.coli Genome 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000.

data_processing: The data were analyzed with Affymetrix GeneChip operating software (1.4.0.036). Scaling: All probe set with target intensity of each array arbitrarily set to 500. Normalization: All probes set to scale factor 1.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: DmntR 60 min with 10 microM MnCl2

label_protocol: Biotinylated cDNA was prepared according to the standard Affymetrix protocol from 3.5 µg total RNA (Section 3 Prokaryotic sample and array processing).

growth_protocol: MG1655 and DmntR cultures were grown in M9 glucose media overnight at 37 ºC, diluted 1:100 in M9 glucose, and grown to OD600 ~0.5 at 37 ºC.

extract_protocol: Total RNA was isolated using the hot phenol extraction procedure.

treatment_protocol: MnCl2 was added to a final concentration of 10 μM and cells were grown for an additional time of 10 or 60 min before harvesting.

tag: gentoype

value: Delta-mntR

tag: treatment


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_259

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_258

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_261

description: Primary


title: genomic_DNA_Breast_NOTUMREG_AJP10_0850_260

description: NOTUMREG


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_255

description: Primary


title: IM13_control

description: Intima media


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_253

description: Primary


title: genomic_DNA_Breast_NOTUMREG_AJP10_0850_254

description: NOTUMREG


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_256

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_250

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_251

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_252

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_247

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_248

description: Primary


title: genomic_DNA_Breast_MET_AJP10_0850_246

description: Metastasis


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_244

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_249

description: Primary


title: MG1655 10 min with 10 microM MnCl2

source_name: MG1655 10 min with 10 microM MnCl2

value: wild type


title: MG1655 60 min with 10 microM MnCl2

source_name: MG1655 60 min with 10 microM MnCl2


title: IM12_case

description: Intima media


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_245

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_243

description: Primary


title: Delta-mntR 10 min with 10 microM MnCl2

source_name: DmntR 10 min with 10 microM MnCl2


title: TP-Pi54 challenged replicate 2

city: New Delhi

first: Dr. Tilak

middle: Raj

last: Sharma

state: Delhi

address: 38 LBS Centre IARI Pusa Campus

department: Biotechnology

institute: National Research Centre on Plant Biotechnology

description: Gene expression profile of TP-Pi54 challenged.

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: GCOS 1.2, MAS5.0 signal intensity

organism: Oryza sativa Japonica Group

source_name: Pi54-transformed line challenged

label_protocol: standard Affymetrix procedures

growth_protocol: Plants were grown in standard rice growing condition

extract_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 μg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

treatment_protocol: Total RNA was isolated by using TRIzol Reagent (Sigma) RNA samples were processed as recommended by Affymetrix (Affymetrix geneChip Expression Analysis Technical manual; Affymetrix)

value: Seedling 15 days after germination

tag: infection

value: Magnaporthe oryzae

tag: genotype/variation

value: transgenic line (TP-Pi54)


title: TP-Pi54 challenged replicate 1


title: TP-Pi54 control replicate 2

description: Gene expression profile of TP-Pi54 control.

source_name: Pi54-transformed line control

value: control


title: TP-Pi54 control replicate 1


title: TP challenged replicate 1

description: Gene expression profile of TP challenged

source_name: Untransformed challenged

value: non transgenic line Taipei 309


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_241

description: Primary

source_name: Breast_Primary, ER-


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_242

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_240

description: Primary


title: TP control replicate 1

description: Gene expression profile of control TP.

source_name: Untransformed control


title: TP challenged replicate 2

description: Gene expression profile of TP challenged.


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_238

description: Primary

source_name: Breast_Primary, ER+


title: genomic_DNA_Breast_MET_AJP10_0850_237

description: Metastasis


title: Scramble (Cy3) v Pooled (Cy5)

city: Sutton

first: Ian

last: Giddings

state: Surrey

address: 15 Cotswold Road

department: Section of Molecular Carcinogenesis

country: United Kingdom

institute: Institute of Cancer Research

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added and samples were applied to microarrays enclosed in Agilent microarray hybridization chambers. After hybridization, slides were washed sequentially.

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software.

data_processing: Spatial representations of the hybridization signals were examined to confirm absence of technical artifacts. The distribution of background and foreground signals and pre-normalization MA plots were examined to measure the quality of the hybridization. Low quality spots identified by the Agilent image processing software were not used in the subsequent analyses. Expression signal estimates were derived from the red (cy3) and green (cy5) Agilent Processed Signal data by normalizing using the LOESS algorithm and background correction using a fitted convolution of normal and exponential distributions.

source_name: PC3M with scrambled virus

label_protocol: Total RNA was primed with 1.2 μL of T7 Promoter Primer at 65°C for 10 min, reversed transcribed at 40°C for 2 h in the presence of 1mM dNTP mix and then labelled with Cyanine 3-CTP or Cyanine 5-CTP according to Agilent instructions

growth_protocol: PC3-M prostate cells were grown in RPMI 1640 media containing L-Glutamine (2mM),  penicillin (1000units/ml), streptomycin (100μg/ml) and 10% fetal calf serum

extract_protocol: Total RNA was extracted with a Rneasy mini kit (Qiagen) according to manufacturer's instructions

treatment_protocol: Short hairpin RNA for RPL19 cloned into a pSilencer™ 4.1-CMV neo (Ambion) expression vector and transfected into PC3-M prostate cells with SiPORT XP-1 reagent (Ambion)

tag: cell line

source_name: Pooled knockdowns


title: TP control replicate 2

description: Gene expression profile of control TP.


title: PC3M wt (Cy3) v ST (Cy5)

source_name: PC3M with stable RPL19 knockdown


title: genomic_DNA_Breast_TDLU_AJP10_0850_239

description: Terminal ductal-lobular unit (TDLU)

source_name: Breast_Terminal ductal-lobular unit (TDLU)


title: PNT2 (Cy3) v Scramble (Cy5)


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_229

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_230

description: Primary


title: ST (Cy3) v Pooled (Cy5)


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_236

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_231

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_232

description: Primary


title: genomic_DNA_Breast_NOTUMREG_AJP10_0850_235

description: NOTUMREG


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_233

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_234

description: Primary


title: PC3M wt (Cy3) v PNT2 (Cy5)


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_228

description: Primary


title: Scramble (Cy3) v ST (Cy5)


title: Pooled (Cy3) v PC3M (wt) (Cy5)


title: PNT2 (Cy3) v ST (Cy5)


title: Scramble (Cy3) v PC3M wt (Cy5)


title: Pooled (Cy3) v PNT2 (Cy5)


title: ER-positive placebo-treated patient 103

city: Pittsburgh

first: Soonmuyung

last: Paik

state: PA

address: 1307 Federal Street, Suite 303

department: Pathology

institute: NSABP Foundation

hyb_protocol: After the labeling procedure, the amplified cDNA was purified with the KREA pure columns (Kreatech Biotechnology, Amsterdam, The Netherlands) to remove the dye in excess and was then fragmented using the Affymetrix fragmentation buffer provided with the GeneChip® Sample Cleanup Module Kit (Affymetrix, Santa Clara, CA). Finally, the cDNA was purified with the Clean-up columns, provided as well with the GeneChip® Sample Cleanup Module Kit, an added to the Hybridization Cocktail. The cocktail was then subjected to an overnight pre-hybridization to an used Affymetrix Genechip U133 2.0 Plus. The day after, 900 ng of the unbound labeled cDNA mix removed from the chip were processed as raccomanded by the manufacturer and hybridized to the Agilent Whole Human Genome (4 X 44 k) array. The hybridization was performed at 65 °C for 17 hours at a rotation of 10 revolutions per minute.

scan_protocol: The slides were scanned using a DNA Microarray Scanner ( Agilent Technologies, Santa Clara, CA) and features were extracted using Agilent’s Feature Extraction Software (v 9.5.3.1).

data_processing: Single channel hybridization intensity data were compiled using commercial software (Partek Genomic Suite, St Louis, Missouri). After quantile normalization, genes with mean intensity below 500 were filtred out. Data were log2 transformed for statistical analysis.

source_name: Primary Breast cancer

label_protocol: 3 μg of the WTA product were labeled with a fluorescent dye (Cy3) using a direct chemical labeling method (ULS™ Labeling Kit with Cy3 for Agilent Gene Expression Arrays, Kreatech Biotechnology, Amsterdam, The Netherlands)

extract_protocol: Tumor areas were identified by ER immunostaining with a hematoxylin counter stain. Total RNA was isolated from 3 to 5  five μn unstained sections using the Ambion RecoverAll™ Total Nucleic Acid Isolation Kit (Applied Biosystems, Foster City, CA) and quantified using UV absorption on a spectrophotometer (NanoDrop® ND-1000). 100-200 nanograms of total RNA were converted to cDNA and amplified using a commercial service provided by Rubicon Genomics, Inc. (Ann Arbor, Mi), using the TransPlex™ Whole Transcriptome Amplification (WTA) kit.

treatment_protocol: Excised tumor specimens were formalin fixed paraffin embedeed in a routine process.

tag: histology

value: ductal

tag: ER_status (0 - negarive, 1 - positive)

tag: HER2_status (0 - negarive, 1 - positive)

tag: treatment (1 - placebo, 2- tamoxifen)


title: ER-positive placebo-treated patient 105


title: ER-positive placebo-treated patient 107

value: lobular


title: ER-positive tamoxifen-treated patient 108


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_227

description: Primary

tag: tissue


title: ER-positive placebo-treated patient 100


title: ER-negative tamoxifen-treated patient 106


title: ER-positive tamoxifen-treated patient 102


title: ER-positive placebo-treated patient 101


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_221

description: Primary


title: genomic_DNA_Breast_MET_AJP10_0850_223

description: Metastasis

source_name: Breast_Metastasis, ER+


title: genomic_DNA_Breast_TDLU_AJP10_0850_220

description: Terminal ductal-lobular unit (TDLU)


title: genomic_DNA_Breast_TDLU_AJP10_0850_219

description: Terminal ductal-lobular unit (TDLU)


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_226

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_222

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_225

description: Primary


title: ER-negative tamoxifen-treated patient 97


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_224

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_217

description: Primary


title: genomic_DNA_Breast_TDLU_AJP10_0850_218

description: Terminal ductal-lobular unit (TDLU)


title: ER-positive tamoxifen-treated patient 96


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_216

description: Primary


title: ER-positive placebo-treated patient 94


title: ER-positive placebo-treated patient 89


title: ER-positive tamoxifen-treated patient 95


title: ER-positive placebo-treated patient 88


title: ER-positive placebo-treated patient 99


title: ER-positive placebo-treated patient 92


title: ER-positive tamoxifen-treated patient 91


title: ER-positive tamoxifen-treated patient 98


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_215

description: Primary


title: ER-negative placebo-treated patient 86


title: ER-positive tamoxifen-treated patient 93


title: ER-positive placebo-treated patient 90


title: ER-positive placebo-treated patient 84


title: ER-positive placebo-treated patient 104


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_213

description: Primary


title: ER-negative placebo-treated patient 87


title: ER-positive placebo-treated patient 85


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_212

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_211

description: Primary


title: genomic_DNA_MESENCH_AJP10_0850_214

description: MESENCH


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_209

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_210

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_208

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_206

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_205

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_204

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_202

description: Primary


title: genomic_DNA_Breast_MET_AJP10_0850_207

description: Metastasis


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_201

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_200

description: Primary


title: ER-negative tamoxifen-treated patient 82


title: ER-positive placebo-treated patient 75


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_199

description: Primary


title: ER-negative tamoxifen-treated patient 81


title: ER-positive placebo-treated patient 78


title: ER-positive tamoxifen-treated patient 76


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_203

description: Primary


title: ER-negative tamoxifen-treated patient 73


title: ER-positive tamoxifen-treated patient 77


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_198

description: Primary


title: ER-positive placebo-treated patient 72


title: ER-negative placebo-treated patient 68


title: ER-positive placebo-treated patient 71


title: ER-negative placebo-treated patient 69


title: ER-positive placebo-treated patient 79


title: ER-positive placebo-treated patient 67


title: ER-positive placebo-treated patient 70


title: ER-positive placebo-treated patient 74


title: ER-positive placebo-treated patient 83


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_196

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_197

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_195

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_194

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_189

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_188

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_187

description: Primary


title: genomic_DNA_Breast_MET_AJP10_0850_191

description: Metastasis


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_192

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_190

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_185

description: Primary


title: ER-negative placebo-treated patient 64


title: ER-positive placebo-treated patient 63


title: ER-positive tamoxifen-treated patient 59


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_182

description: Primary


title: ER-positive tamoxifen-treated patient 54


title: ER-positive tamoxifen-treated patient 60


title: ER-positive placebo-treated patient 55


title: ER-negative tamoxifen-treated patient 57


title: ER-positive placebo-treated patient 66


title: ER-positive placebo-treated patient 52


title: ER-negative placebo-treated patient 50


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_183

description: Primary


title: ER-positive tamoxifen-treated patient 58


title: ER-positive tamoxifen-treated patient 61


title: ER-positive tamoxifen-treated patient 53


title: genomic_DNA_Breast_MET_AJP10_0850_186

description: Metastasis


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_181

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_193

description: Primary


title: ER-positive placebo-treated patient 65


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_179

description: Primary


title: ER-positive placebo-treated patient 56


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_180

description: Primary


title: ER-positive placebo-treated patient 51


title: genomic_DNA_Breast_MET_AJP10_0850_178

description: Metastasis


title: ER-positive placebo-treated patient 47


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_177

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_176

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_175

description: Primary


title: ER-positive placebo-treated patient 48


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_171

description: Primary


title: ER-negative tamoxifen-treated patient 44


title: ER-positive placebo-treated patient 49


title: ER-negative placebo-treated patient 46


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_169

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_173

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_184

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_172

description: Primary


title: ER-negative placebo-treated patient 45


title: ER-positive placebo-treated patient 39


title: ER-negative placebo-treated patient 38


title: ER-positive tamoxifen-treated patient 40


title: ER-positive placebo-treated patient 42


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_174

description: Primary


title: ER-positive tamoxifen-treated patient 37

value: tubular


title: ER-negative placebo-treated patient 41


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_168

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_167

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_166

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_164

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_163

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_170

description: Primary


title: ER-positive tamoxifen-treated patient 80


title: ER-positive placebo-treated patient 36


title: ER-positive placebo-treated patient 35


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_165

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_159

description: Primary


title: ER-negative tamoxifen-treated patient 33


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_158

description: Primary


title: ER-negative tamoxifen-treated patient 34


title: ER-positive placebo-treated patient 31


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_162

description: Primary


title: ER-positive placebo-treated patient 43


title: ER-positive placebo-treated patient 29