title: Subpopulation P5 (CD24+CD29hi) from virgin wild type FVB mice, IFNa treated replicate 2

source_name: Luminal progenitor enriched P5 population of wild type virgin mice

extract_protocol:
Cell preparation: Single cell suspensions were prepared from the mammary glands of virgin wild type and transgenic mice using mechanical and enzymatic dissociation as detail described in Tiede BJ et al., 2009, PLoS ONE 4(11): e8035. doi:10.1371/journal.pone.0008035. After collection cells were plated in mammosphere 3D conditions (Chakrabarti R et al. 2014 Nat Cell Bio (10):1004-15, 1-13. doi: 10.1038/ncb3040.), treated with 1000U/ml IFNa and harvestd after 8 days.
FACS sorting: Various subpopulations of mammary epithelial cells were sorted using flow cytometry based on combination of a set of surface markers. The marker profiles and FACS gating parameters are detailed in Tiede BJ et al., 2009, PLoS ONE 4(11): e8035. doi:10.1371/journal.pone.0008035
Total RNA were extracted using RNAeasy mini-prep kit from miRVANA kit

tag: subpopulation

value: luminal progenitor

tag: ifna treatment

value: IFNa treated

value: Mix of 11 mouse cell lines


title: Subpopulation P4 (CD24+CD29hi) from virgin wild type FVB mice, control replicate 2

status: Public on May 05 2017

type: RNA

city: Plainsboro

first: Yong

last: Wei

state: NJ

address: LTL227 Wathington Road

department: Molecular Biology

country: USA

institute: Princeton University

hyb_protocol: Each cy5 labeled testing sample was mixed with equal amount cy3-labeled reference sample and fragmented and blocked (Agilent Gene Expression Hybridization Kit),  and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software (version 11.0).

data_processing: Agilent Feature Extraction Software (v 11.0) was used for background subtraction and linear Lowess normalization.

molecule: total RNA

organism: Mus musculus

source_name: MaSC enriched P4 population of wild type virgin mice

label_protocol: The testing RNA samples and universal mouse reference RNA (Agilent) were labeled with CTP-cy5 and CTP-cy3, respectively, Using Agilent Quick Amp Labeling Kit.

tag: strain

value: FVB/N-J

value: MaSC

value: control

source_name: Universal Mouse Reference RNA

tag: cell line


title: Subpopulation P4 (CD24+CD29hi) from virgin wild type FVB mice, IFNa treated replicate 2


title: Subpopulation P4 (CD24+CD29hi) from virgin wild type FVB mice, control replicate 1


title: Subpopulation P4 (Lin-CD24+CD29hi) from virgin wild type FVB mice, replicate 3

hyb_protocol: Using  Agilent’s miRNA Complete Labeling and Hyb Kit, labeled total RNA samples were mixed with blocking reagent and RPM hybridization buffer and assembled with miRNA array for hybridization. The hybridization assembly were rotate at 20rpm in 55C oven for 20hrs. The array were washed with prewarmed washing buffers and dried for scan.

data_processing: Agilent Feature Extraction Software (v 11.0) was used to extract the signal and GeneSpring v13 were used to process the data. The processing is using Agilent technology miRNA 46065 with Threshold 1.0, logbase 2, Normalization shift to 90 percentile and baseline transformation is conducted based on median of all samples.

label_protocol: The testing RNA samples were labeled with Cy3-pCp using Agilent’s miRNA Complete Labeling and Hyb Kit. Briefly, total RNA is dephosphrylated with CIP and then ligated to Cy3-pCp with T4-RNA ligase. Labeled RNA sample were purified and dried.

extract_protocol:
Cell preparation protocol: Single cell suspensions were prepared from the mammary glands of virgin wild type and transgenic mice using mechanical and enzymatic dissociation as detail described in Tiede BJ et al., 2009, PLoS ONE 4(11): e8035. doi:10.1371/journal.pone.0008035
FACS sorting protocol: Various subpopulations of mammary epithelial cells were sorted using flow cytometry based on combination of a set of surface markers. The marker profiles and FACS gating parameters are detailed in Tiede BJ et al., 2009, PLoS ONE 4(11): e8035. doi:10.1371/journal.pone.0008035
miRNA enriched Total RNA were extracted using mirVana™ miRNA Isolation Kit from Ambion

tag: mg condition

value: Virgin

tag: enrichment

value: MaSC enriched P4 population

tag: genotype/variation

value: wild type


title: Subpopulation P4 (CD24+CD29hi) from virgin wild type FVB mice, IFNa treated replicate 1


title: Subpopulation P5 (CD24+CD29hi) from virgin wild type FVB mice, control replicate 1


title: Subpopulation P5 (CD24+CD29hi) from virgin wild type FVB mice, IFNa treated replicate 1


title: Subpopulation P5 (CD24+CD29hi) from virgin wild type FVB mice, control replicate 2


title: HMLE cells engineered with LEX-miR199a, replicate 2

description: See Agilent Cat#740000 for product details

scan_protocol: Scanned on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software (v11.0.1.1).

data_processing: Agilent Feature Extraction Software (v11.0.1.1) was used for background subtraction and linear Lowess normalization.

organism: Homo sapiens

source_name: HMLE cells

extract_protocol:
Cell preparation protocol: HMLE cells were infected with lentiviral vectors expressing miR-199a. Virus containing the empty vector were used as control. Cells were treated and selected with puromycin and the overexpression of miR-199a was confirmed by qPCR.
Total RNA were extracted using RNAeasy mini-prep kit from Qiagen

value: HMLE

tag: type

value: Human Mammary epithelial Cell

tag: exogenous manipulation

source_name: Universal human Reference RNA

tag: cell lines

value: Mix of 10 human cell lines


title: Lgr5 positive subpopulation from P4 (CD24+CD29hi), replicate 3

description: See Agilent Cat#740100 for product details

source_name: MaSC

extract_protocol:
Cell preparation protocol: Single cell suspensions were prepared from the mammary glands of virgin mice using mechanical and enzymatic dissociation as detail described in Tiede BJ et al., 2009, PLoS ONE 4(11): e8035. doi:10.1371/journal.pone.0008035
FACS sorting protocol: Various subpopulations of mammary epithelial cells were sorted using flow cytometry based on combination of a set of surface markers and the expression of EGFP.  The marker profiles are detailed in Tiede BJ et al., 2009, PLoS ONE 4(11): e8035. doi:10.1371/journal.pone.0008035 and Plaks 2013 (PMID: 23352663). FACS gating parameters are detailed in Plaks 2013 (PMID: 23352663).  Specifically, Lin-CD24+CD29hiGFP+ is Lgr5 positive P4 and Lin-CD24+CD29hiGFP- is Lgr5 negative P4.
Total RNA were extracted using RNAeasy mini-prep kit from Qiagen

tag: lgr5 status

value: positive


title: HMLE cells engineered with LEX empty vector (Control), replicate 2

value: LEX


title: Lgr5 negative subpopulation from P4 (CD24+CD29hi), replicate 2

value: Negative


title: Lgr5 negative subpopulation from P4 (CD24+CD29hi), replicate 3


title: Lgr5 positive subpopulation from P4 (CD24+CD29hi), replicate 2


title: HMLE cells engineered with LEX-miR199a, replicate 1


title: Lgr5 positive subpopulation from P4 (CD24+CD29hi), replicate 1


title: Lgr5 negative subpopulation from P4 (CD24+CD29hi), replicate 1


title: HMLE cells engineered with enforce expression of mutant LCOR LXXLL, replicate 1

source_name: HMLE

extract_protocol:
MDA-MB-231 and HMLE cells were infected with lentiviral vectors of either LKO1 vectorred shRNAs targeting LCOR or LEX vectorred variety LCOR cDNAs. Virus containing the empty vector were used as control. Cells were treated and selected with puromycin and the expression of LCOR and its variants were determined by qRT-PCR and Western blot to confirm the designed manipulation.
Total RNA were extracted using RNAeasy mini-prep kit from Qiagen

value: LEX-LCOR-LXXLL


title: HMLE cells engineered with LEX empty vector (Control), replicate 1


title: HMLE cells engineered with enforce expression of mutant LCOR HTH, replicate 2

value: LEX-LCOR-△HTH


title: HMLE cells engineered with enforce expression of mutant LCOR LXXLL, replicate 2


title: HMLE cells engineered with enforce expression of wildtype LCOR, replicate 2

value: LEX-LCOR


title: CELF1 KD replicate 1

status: Public on Sep 01 2015

type: SRA

city: Albuquerque

first: Viswanathan

last: Palanisamy

state: NM

address: 2325 Camino de Salud NE,

department: Internal Medicine

institute: University of New Mexico

library_source: transcriptomic

data_processing:
Illumina casava software was used for base calling
Sequencer FASTQ files were aligned individually  to human whole genome build Hg19 using TopHat v0.1.0
Novel isoform and Isoform comparisons were performed using cuffcompare v1.1.0
Differential gene expression was quantified using cuffdiff v1.1.0
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited .txt files of FPKM values and fold changes

source_name: UMSCC-74B oral cancer cell line

growth_protocol: Cell were maintained in DMEM 10%FBS in 2% penicillin/streptomycin

extract_protocol:
Total RNA was isolated from cells using Qiagen RNAeasy kit (cat#
RNA-seq libraries were constructed using Illumina's standard library creation protocol

treatment_protocol: Cells were treated with CELF1 siRNA or control siRNA and total RNA was isolated after 48hours

tag: cell type

value: Tongue squamous cell carcinoma

tag: sirna

value: CELF1 siRNA


title: WT replicate 1

value: control siRNA


title: HMLE cells engineered with empty pLEX-MCS vector, replicate 2


title: HMLE cells engineered with pLKO1 driven shRNA#1 targeting LCOR (KD1)


title: Subpopulation P4 (CD24+CD29hi) from virgin wild type FVB mice, replicate 5

scan_protocol: Scanned on an Agilent G2565BA scanner. Images were quantified using Agilent Feature Extraction Software (version 9.5.3.1).

data_processing: Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and linear Lowess normalization.

extract_protocol:
Cell preparation protocol: Single cell suspensions were prepared from the mammary glands of virgin wild type and transgenic mice using mechanical and enzymatic dissociation as detail described in Tiede BJ et al., 2009, PLoS ONE 4(11): e8035. doi:10.1371/journal.pone.0008035
FACS sorting protocol: Various subpopulations of mammary epithelial cells were sorted using flow cytometry based on combination of a set of surface markers. The marker profiles and FACS gating parameters are detailed in Tiede BJ et al., 2009, PLoS ONE 4(11): e8035. doi:10.1371/journal.pone.0008035
Total RNA were extracted using RNAeasy mini-prep kit from Qiagen

value: FVB/N-J

value: MaSC

value: Mix of 11 mouse cell lines


title: HMLE cells engineered with enforce expression of mutant LCOR HTH, replicate 1


title: Subpopulation P5 (CD24+CD29hi) from virgin wild type FVB mice, replicate 5

value: Virgin

value: luminal progenitor


title: Subpopulation P5 (CD24+CD29hi) from virgin wild type FVB mice, replicate 4

value: wild type


title: MDA-MB231 cells engineered with pLKO1 driven shRNA#1 targeting LCOR (KD1)

value: Breast cancer


title: HMLE cells engineered with empty pLEX-MCS vector, replicate 1

value: HMLE

value: Human Mammary epithelial Cell

value: Mix of 10 human cell lines


title: MDA-MB231 cells engineered with empty pLKO1 vector (Control)


title: Subpopulation P4 (CD24+CD29hi) from virgin wild type FVB mice, replicate 3


title: MED1 hMADS white rep1, day 19

status: Public on Dec 12 2014

city: Odense M

first: Anne

last: Loft

address: Campusvej 55

department: Biochemistry & Molecular Biology

country: Denmark

institute: University of Southern Denmark

library_source: genomic

data_processing:
Alignment:
Sequence reads were trimmed and collapsed using FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). Bowtie (Langmead B, et al., Genome Biol. 10:R25) was used to align each collapsed library to the human reference genome (version hg19) with the following parameters: “-m 3 –best –strata”, with all other parameters default.
Peak finding and visualization:
BedGraph files were created using HOMER (Heinz S, et al. 2010. Mol. Cell 38:576 –589)  for visualization of binding profiles.
Genome_build: hg19

molecule: genomic DNA

source_name: human adipose-derived stem cells

growth_protocol: Human multipotent adipose-derived stem (hMADS-3) cells were cultured in DMEM (Lonza, low glucose) supplemented with 10% fetal bovine serum (Lonza), 10 mM Hepes, 2 mM L-glutamine (Lonza), penicillin (62.5 μg/ml), streptomycin (100 μg/ml), and 2.5 ng/ml hFGF2 (Peprotech).

extract_protocol:
ChIP experiments were performed in mature hMADS adipocytes essentially as previously described (Siersbæk et al. 2012, MCB, 32: 3452-3463). For cross-linking of chromatin, 0.2 mM disuccinimidyl glutarate (DSG) was applied (Proteochem, Denver, CO) for 45 min followed by cross-linking using 1% formaldehyde for 10 min.
ChIP-seq libraries were constructed according to the manufacturer's instructions (Illumina) as described in (Nielsen R, Mandrup S, 2014 Genome-Wide Profiling of Transcription Factor Binding and Epigenetic Marks in Adipocytes by ChIP-seq. Methods in Enzymology 2014, Vol. 537, pp. 261-279).

treatment_protocol: Two days post confluence (day 0) hMADS cells were induced to differentiate in DMEM/Ham`s F12 (Lonza) supplemented with 10 μg/ml transferrin, 1 μM dexamethasone, 500 μM 3-isobutyl-1-methylxanthine (MIX), 0.85 μM insulin, and 0.2 nM T3. At day 3 of differentiation, MIX and dexamethasone were omitted from the media and 0.5 μM rosiglitazone was added until day 9 of differentiation and again from day 13-16 for induction of brite adipocytes. Control white adipocytes were treated with DMSO from day 13-16. From day 16 and forth the differentiation medium of both white and brite adipocytes was depleted of rosiglitazone. White and brite hMADS adipocytes were harvested on day 19, unless stated otherwise.

value: human adipose-derived stem cells

tag: chip antibody

value: MED1 (M-255; sc-8998; Santa Cruz)


title: MED1 hMADS brite rep2, day 19

data_processing:
Alignment:
Sequence reads were collapsed using FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). Bowtie (Langmead B, et al., Genome Biol. 10:R25) was used to align each collapsed library to the human reference genome (version hg19) with the following parameters: “-m 3 –best –strata”, with all other parameters default.
Peak finding and visualization:
BedGraph files were created using HOMER (Heinz S, et al. 2010. Mol. Cell 38:576 –589)  for visualization of binding profiles.
Genome_build: hg19


title: MED1 hMADS brite rep1, day 19


title: MED1 hMADS white rep2, day 19


title: HMLE cells engineered with empty pLKO1 vector (Control)


title: Subpopulation P5 (CD24+CD29hi) from virgin wild type FVB mice, replicate 3


title: PPARgamma hMADS brite rep2, day 19

data_processing:
Alignment:
Sequence reads were collapsed using FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). Bowtie (Langmead B, et al., Genome Biol. 10:R25) was used to align each collapsed library to the human reference genome (version hg19) with the following parameters: “-m 3 –best –strata”, with all other parameters default.
Peak finding and visualization:
Regions enriched for PPARγ signal in white and brite hMADS adipocytes were identified using HOMER (Heinz S, et al. 2010. Mol. Cell 38:576–589) with the “-factor” and “-size given” settings and a 0.1% FDR threshold. An additional stringency filter was applied, so only peaks >15 fold over the matching input control were kept for further analyses. Merged peak files were generated from the individual PPARγ peak files if the center of two or more peaks were within 250 bp. Peaks from these merged peak files were only included if having more than 30 tags per 10 M tags in a 400 bp window around the center of each merged peak. BedGraph files were created using HOMER for visualization of binding profiles.
Differential signal intensity in PPARγ binding sites and super-enhancers:
Differential signal intensity in PPARγ binding regions in white and brite hMADS adipocytes was determined using paired analyses with EdgeR (Robinson et al. 2010, Bioinformatics 26: 139-140). A FDR<0.1 was used to determine differential PPARγ occupancy in identified PPARγ peak regions, whereas a FDR<0.01 was applied to test PPARγ super-enhancers for differential H3K27ac occupancy.
Genome_build: hg19

value: anti-PPARγ (H-100, sc-7196; Santa Cruz)


title: Input hMADS brite rep1, day 19

data_processing:
Alignment:
Sequence reads were collapsed using FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). Bowtie (Langmead B, et al., Genome Biol. 10:R25) was used to align each collapsed library to the human reference genome (version hg19) with the following parameters: “-m 3 –best –strata”, with all other parameters default.
Peak finding and visualization:
BedGraph files were created using HOMER (Heinz S, et al. 2010. Mol. Cell 38:576 –589)  for visualization of binding profiles
Genome_build: hg19

value: None (input)


title: Input hMADS white rep1, day 19


title: PPARgamma hMADS white rep2, day 19


title: PPARgamma hMADS brite rep1, day 19

data_processing:
Alignment:
Sequence reads were trimmed and collapsed using FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). Bowtie (Langmead B, et al., Genome Biol. 10:R25) was used to align each collapsed library to the human reference genome (version hg19) with the following parameters: “-m 3 –best –strata”, with all other parameters default.
Peak finding and visualization:
Regions enriched for PPARγ signal in white and brite hMADS adipocytes were identified using HOMER (Heinz S, et al. 2010. Mol. Cell 38:576–589) with the “-factor” and “-size given” settings and a 0.1% FDR threshold. An additional stringency filter was applied, so only peaks >15 fold over the matching input control were kept for further analyses. Merged peak files were generated from the individual PPARγ peak files if the center of two or more peaks were within 250 bp. Peaks from these merged peak files were only included if having more than 30 tags per 10 M tags in a 400 bp window around the center of each merged peak. BedGraph files were created using HOMER for visualization of binding profiles.
Differential signal intensity in PPARγ binding sites and super-enhancers:
Differential signal intensity in PPARγ binding regions in white and brite hMADS adipocytes was determined using paired analyses with EdgeR (Robinson et al. 2010, Bioinformatics 26: 139-140). A FDR<0.1 was used to determine differential PPARγ occupancy in identified PPARγ peak regions, whereas a FDR<0.01 was applied to test PPARγ super-enhancers for differential H3K27ac occupancy.
Genome_build: hg19


title: 4TO7 pMSCV-puro Vector Replicate 1

status: Public on Dec 23 2014

source_name: 4TO7 pMSCV-puro stable cell line

growth_protocol: Cells were grown at 37C in 5%CO2 using DMEM media supplemented with 10%FBS + 1mM L-glutamine. Cells were passaged every 3 days and grown for several passages before RNA extraction.

extract_protocol: Total RNA was extracted using the miRVana total RNA isolation kit (Ambion) using the manufacturer's instructions.

tag: tumor type

value: mammary tumor


title: 4TO7 pMSCV-puro Vector Replicate 2


title: Subpopulation P4 (CD24+CD29hi) from virgin wild type FVB mice, replicate 4


title: HMLE cells engineered with enforce expression of wildtype LCOR, replicate 1

value: LEX-LCOR


title: 4TO7 pMSCV-miR-23b/27b/24 Replicate 1

source_name: 4TO7 pMSCV-miR-23b/27b/24 stable cell line


title: PPARgamma hMADS white rep1, day 19


title: 4TO7 pMSCV-miR-23b/27b/24 Replicate 2


title: HMLEN Vector Control; replicate 1

status: Public on Dec 01 2014

description:
See Agilent Catalog #740000 for detail
Stable cell lines were generated using pLEX based lentivirus system and selected for puromycin resistance. Cells were then cultured without puromycin in normal mammaliam cell culture condition till they were about 90% conflunecy before harvesting.

source_name: HMLEN cells transduced with pLEX-MCS vector

label_protocol: The testing RNA samples and universal human reference RNA (Agilent) were labeled with CTP-cy5 and CTP-cy3, respectively, Using Agilent Quick Amp Labeling Kit.

extract_protocol: Total RNA were extracted using RNAeasy mini-prep kit from Qiagen

value: HMLEN

tag: treatment

value: Vector Control

tag: emt phenotype

value: Epithelial

tag: colony formation ability

value: Weak

tag: sample type

value: Universal Mouse Reference RNA


title: HMLEN-SNAIL/FBXO11, replicate 2

source_name: HMLEN cells transduced with pLEX-SNAIL amd pLEX-FBXO11 lentiviruses.


title: 4T1-Vector Control

description:
See Agilent Cat#740100 for product details
Stable cell lines were generated using pLEX based lentivirus system and selected for puromycin resistance. Cells were then cultured without puromycin in normal mammaliam cell culture condition till they were about 90% conflunecy before harvesting.

source_name: 4T1 cells transduced with pLEX-MCS vector lentivirus

tag: invasion ability

value: Low

value: Mix of 11 mouse cell lines


title: 4T1-SNAI1 & FBXO11 double expression

source_name: 4T1 cells transduced with pLEX-SNAIL amd pLEX-FBXO11 lentiviruses.

tag: cell line

value: SNAI1 & FBXO11 double expression


title: 4T1-SNAI1 overexpression

source_name: 4T1 cells transduced with pLEX-SNAIL and pLEX-MCS lentiviruses.

value: SNAI1 overexpression

value: Mesenchymal

value: High


title: HMLEN-SNAIL; replicate 1

source_name: HMLEN cells transduced with pLEX-SNAIL and pLEX-MCS lentiviruses.

value: SNAIL

value: Strong

value: Mix of 10 human cell lines


title: HMLEN-SNAIL/FBXO11, replicate 1


title: Subpopulation P4 (CD24+CD29hi) from pregnant wild type FVB mice, replicate 1

status: Public on Aug 19 2014

source_name: MaSC enriched P4 population of wild type Pregnant mice

extract_protocol:
Cell preparation protocol: Single cell suspensions were prepared from the mammary glands of virgin and pregnant wild type and transgenic mice using mechanical and enzymatic dissociation as detail described in Tiede BJ et al., 2009, PLoS ONE 4(11): e8035. doi:10.1371/journal.pone.0008035
FACS sorting protocol: Various subpopulations of mammary epithelial cells were sorted using flow cytometry based on combination of a set of surface markers and/or GFP expression. The marker profiles and FACS gating parameters are detailed in Tiede BJ et al., 2009, PLoS ONE 4(11): e8035. doi:10.1371/journal.pone.0008035
Total RNA were extracted using RNAeasy mini-prep kit from Qiagen

tag: strain

value: FVB/N-J

value: wild type

tag: mg condition

value: pregnant

value: MaSC


title: Subpopulation P6 (CD24lo) from pregnant wild type FVB mice, replicate 1

source_name: Differentiated MEC P6 population of wild type Pregnant mice

tag: genotype/variation

tag: enrichment


title: Subpopulation P6 (CD24lo) from virgin wild type FVB mice, replicate 1

source_name: Differentiated MEC P6 population of wild type virgin mice

value: Virgin

source_name: Universal Mouse Reference RNA


title: Subpopulation P6 (CD24lo) from pregnant wild type FVB mice, replicate 2


title: Subpopulation P5 (CD24+CD29hi) from virgin wild type FVB mice, replicate 2

source_name: Luminal progenitor enriched P5 population of wild type virgin mice

value: luminal progenitor


title: Subpopulation P4 (CD24+CD29hi) from virgin wild type FVB mice, replicate 1

source_name: MaSC enriched P4 population of wild type virgin mice


title: Lin-/GFPlo subpopulation from virgin FVB-Luciferase (L2G85) mice

source_name: MaSC depeleted GFPlo population from L2G85 mice

value: FVB/N-Luciferase transgenic mouse L2G85

value: transgenic mouse L2G85


title: Subpopulation P4 (CD24+CD29hi) from pregnant wild type FVB mice, replicate 2


title: Subpopulation P5 (CD24+CD29hi) from pregnant wild type FVB mice, replicate 2

source_name: Luminal progenitor enriched P5 population of wild type Pregnant mice


title: Subpopulation P5 (CD24+CD29hi) from pregnant wild type FVB mice, replicate 1


title: Subpopulation P4 (CD24+CD29hi) from virgin wild type FVB mice, replicate 2


title: Subpopulation P5 (CD24+CD29hi) from virgin wild type FVB mice, replicate 1


title: Total MECs from from virgin DNP63 heterozygous mice

source_name: Total MECs from DNP63 KO heterozygous virgin mice

extract_protocol:
cell preparation:  Single cell suspensions were prepared from the mammary glands of virgin mice using mechanical and enzymatic dissociation as detail described in Tiede BJ et al., 2009, PLoS ONE 4(11): e8035. doi:10.1371/journal.pone.0008035
FACS sorting protocol:  Various subpopulations of mammary epithelial cells were sorted using flow cytometry based on combination of a set of surface markers. The marker profiles and FACS gating parameters are detailed in Tiede BJ et al., 2009, PLoS ONE 4(11): e8035. doi:10.1371/journal.pone.0008035
Total RNA were extracted using RNAeasy mini-prep kit from Qiagen

value: DNP63 KO heterozygous


title: Total MECs from from virgin wild type mice

source_name: Total MECs from wild type virgin mice

value: Mix of 11 mouse cell lines


title: Subpopulation P5 (CD24+CD29lo) from virgin DNP63 heterozygous mice

source_name: Luminal progenitor enriched P5 population of DNP63 KO heterozygous virgin mice


title: Lin-/GFPhi subpopulation from virgin FVB-Luciferase (L2G85) mice

source_name: MaSC enriched GFPhi population from L2G85 mice


title: Subpopulation P5 (CD24+CD29lo) from virgin wild type mice


title: Subpopulation P4 (CD24+CD29hi) from virgin DNP63 heterozygous mice

source_name: MaSC enriched P4 population of DNP63 KO heterozygous virgin mice


title: Subpopulation P4 (CD24+CD29hi) from virgin wild type mice


title: WTA PyMT tumor cells infected with empty vector, treated with CPT, replicate 3

status: Public on Aug 12 2014

description: See Agilent Cat#740100 for reference product details

treatment_protocol: PYMT tumor cell lines, i.e KO2 and WTA, were established from correponding mouse models. Cell were infected with lenti-viral vectors carrying OE or KD expression constructs. Cells were selected with FACS sorting with GFP for rescue samples and puromycin treatment for shRNA samples, respectively. All cells were treated with 50uM CPT for 36 hrs

tag: genotype

value: FVB

tag: tumor model

value: PYMT

tag: exogenous manipulation

value: 50uM CPT for 36 hrs

tag: reference


title: WTA PyMT tumor cells with Snd1 shRNA KD, treated with CPT, replicate 3


title: WTA PyMT tumor cells with Snd1 shRNA KD, treated with CPT, replicate 2


title: RAW264.7 cells treated with 50ng/mL RANKL 2 days Rep1

status: Public on Oct 14 2013

hyb_protocol: Array was crosslinked by 700mJ UV, then blocked in Roche Blocking Agent at 65C for 35 min. Labeled samples were mixed with 2x Enhanced Hybridization Buffer according to manufacturer's protocol and hybridized to array in humidified chamber overnight at 52C.

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.7.5).

data_processing: Median intensity value were substracted by median background signal values. The spots with lower than background values are removed. Median values of remaining probes for each channel were averaged across all arrays to develop a normalization constant for each array using Microsoft Excel 2008. Log2 ratio of normalized Cy3/Cy5 data were calculated and represents the changes in expression.

label_protocol: 5 ug of total RNA was polyA tailed using 1ul polyA Polymerase, then ligated with 2uL T4 DNA ligase with 25uM Cy3 or Cy5 using the Ncode multispecies miRNA microarray kit following manufacturer's instructions.

growth_protocol: Cells were maintained in an undifferentiated state in DMEM + 10% FBS

extract_protocol: Total RNA extracted using miRVANA kit following manufacturer's instructions

treatment_protocol: Cells were treated with 10uL PBS in 2 mL DMEM plus 10% FBS to maintain an undifferentiated state

tag: cell type

value: Immortalized monocyte/macrophage cell

tag: treated with

value: none (untreated control)

source_name: RAW264.7_RANKL for 2 days

growth_protocol: Cells were grown for 2 days in 50ng/mL RANKL.

treatment_protocol: Cells were treated with 50ng/ml mouse RANKL in 2 mL DMEM + 10%FBS.

value: 50ng/ml mouse RANKL for 2 days


title: RAW264.7 cells treated with 50ng/mL RANKL 6 days Rep1

source_name: RAW264.7_RANKL for 6 days

growth_protocol: Cells were grown for 6 days in 50ng/mL RANKL.

value: 50ng/ml mouse RANKL for 6 days


title: RAW264.7 cells treated with TSU-Pr1 vs TSU-PR1-B2 conditioned media

description: TSU

source_name: RAW264.7_TSU-Pr1 conditioned media for 6 days

growth_protocol: Cells were differentiated into osteoclasts after treatment with conditioned media for 6 days.

treatment_protocol: Cells were treated with 2 mL DMEM that had been conditioned by TSU-Pr1 human prostate tumor cells for 2 days. RAW264.7 cells were cultured in the conditioned media for a total of 6 days with meida changes every 2 days.

value: TSU-Pr1 conditioned media for 6 days

source_name: RAW264.7_TSU-PR1-B2 conditioned media for 6 days

treatment_protocol: Cells were treated with 2 mL DMEM that had been conditioned by TSU-Pr1-B2 human prostate tumor cells for 2 days. RAW264.7 cells were cultured in the conditioned media for a total of 6 days with meida changes every 2 days.

value: TSU-PR1-B2 conditioned media for 6 days


title: RAW264.7 cells treated with 4T1 vs 4T1.2 conditioned media Rep2

source_name: RAW264.7_4T1 condition media for 6 days

treatment_protocol: Cells were treated with 2 mL DMEM that had been conditioned by 4T1 mouse mammary tumor cells for 2 days. RAW264.7 cells were cultured in the conditioned media for a total of 6 days with meida changes every 2 days.

value: 4T1 condition media for 6 days

source_name: RAW264.7_4T1.2 conditioned media for 6 days

treatment_protocol: Cells were treated with 2 mL DMEM that had been conditioned by 4T1.2 mouse mammary tumor cells for 2 days. RAW264.7 cells were cultured in the conditioned media for a total of 6 days with meida changes every 2 days.

value: 4T1.2 conditioned media for 6 days


title: RAW264.7 cells treated with 50ng/mL RANKL 6 days Rep2


title: RAW264.7 cells treated with 50ng/mL RANKL 2 days Rep2


title: WTA PyMT tumor cells infected with empty vector, treated with CPT, replicate 1

value: wild type


title: SPM13-CPT

source_name: MTDH-KO2-PYMT tumor cell rescue with mutant Mtdhspm13-ires2-GFP lenti-vector,treated with CPT, the Mtdh carries W391D point mutation

value: MTDH-KO

value: LmPGK-mMtdhspm13-ires2-GFP, the MTDH carries W391D point mutation


title: WTA PyMT tumor cells with Snd1 shRNA KD, treated with CPT, replicate 1

source_name: Universal Mouse Reference RNA


title: Primary Sertoli Vehicle rep1

status: Public on Feb 01 2014

city: Stanford

first: Kazuteru

last: Hasegawa

address: Lorry Lokey Stem Cell Research Building (SIM1), G2165 265 Campus Drive

institute: Stanford University

description: Gene expression after 24hr in vehicle-treated primary Sertoli cells

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 50 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 50 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%)

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_95 and Grid:014868_D_20070207) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Primary Sertoli cells, Vehicle, 24h, replicate1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.4 µg RNA using the Low Input Quick Amp Labeling Kit, one-color (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Isolated Sertoli cells were cultured with F12/DMEM mixed with 10μg/ml Insulin , 5μg/ml Transferrin  and 5ng/ml Epidermal growth factor at 34oC. Medium was changed at day 2, 4 and stimulation started at day 5.

extract_protocol: Total RNA was extracted with RNeasy mini kit  (QIAGEN, Valencia, CA) according to the manufacture's protocol.

treatment_protocol: Isolated primary Sertoli cells were incubated with 20ng bFGF, 10uM PD0325901 or vehicle for 24 hours.

value: Primary Sertoli cells

value: Vehicle


title: RAW264.7 cells treated with 4T1 vs 4T1.2 conditioned media Rep1


title: MTDH-CPT

source_name: MTDH-KO2-PYMT tumor cell rescue with Mtdh-ires2-GFP lenti-vector, treated with CPT

value: Mix of 11 mouse cell lines


title: Primary Sertoli PD0325901 rep1

description: Gene expression after 24hr in PD0325901-treated primary Sertoli cells

source_name: Primary Sertoli cells, PD, 24h, replicate1


title: Primary Sertoli Vehicle rep2

source_name: Primary Sertoli cells, Vehicle, 24h, replicate2


title: WTA PyMT tumor cells infected with empty vector, treated with CPT, replicate 2

value: FVB


title: Primary Sertoli bFgf rep2

description: Gene expression after 24hr in bFGF-treated primary Sertoli cells

source_name: Primary Sertoli cells, bFgf, 24h, replicate2

value: bFGF


title: Primary Sertoli bFgf rep1

source_name: Primary Sertoli cells, bFgf, 24h, replicate1


title: Primary Sertoli PD0325901 rep2

source_name: Primary Sertoli cells, PD, 24h, replicate2


title: WT ELF5 infecetd MDA-MB-231 cell, replicate 2

status: Public on Sep 20 2012

description: Biological replicate 2, wild type Elf5 infected MDA-MB231 cells

label_protocol: The testing RNA samples and universal human reference RNA (Strategene) were labeled with CTP-cy5 and CTP-cy3, respectively, with Agilent Quick Amp Labeling Kit.

growth_protocol: Standard cloning process was used to clone coding sequence of Elf5 or DNA binding domain mutant Elf5 in pLEX vector. Lentivirus were produced in 293T cells.

treatment_protocol: MDA-MB231cells were infected with lentivirus containing either wild type or mutant Elf5 (in pLEX vector), and selected for 10 days with puromycin.

tag: tissue

value: breast cancer

source_name: Human universal reference RNA (Strategene)

value: mixed


title: WT ELF5 infecetd MDA-MB-231 cell, replicate 3

description: Biological replicate 3, wild type Elf5 infected MDA-MB231 cells


title: Control (mut-Elf5) infected MDA-MB-231 cell, replicate 2

description: Biological replicate 2, mutant Elf5 infected MDA-MB231 cells


title: Control (mut-Elf5) infected MDA-MB-231 cell, replicate 3

description: Biological replicate 3, mutant Elf5 infected MDA-MB231 cells


title: WT ELF5 infecetd MDA-MB-231 cell, replicate 1

description: Biological replicate 1, wild type Elf5 infected MDA-MB231 cells


title: Control (mut-Elf5) infected MDA-MB-231 cell, replicate 1

description: Biological replicate 1, mutant Elf5 infected MDA-MB231 cells


title: Tubules IV-VI-dnRARa-2

status: Public on Jul 01 2012

description: Gene expression 5 days after Lentiviral injection

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

source_name: Seminiferous tubules at stages IV-VI, dnRARa, 5 days

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.20 µg RNA using the One-Color Low RNA Input Linear Amplification kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

treatment_protocol: Primary Sertoli cells were treated with 1mM RA for 24 hours. Lentivirus were injected into adult testes 5 days before disection.

value: Seminiferous tubule

tag: age

value: 6-8 week

tag: treatment

value: dnRARa


title: Tubules IX-XII-dnRARa-2

source_name: Seminiferous tubules at stages IX-XII, dnRARa, 5 days


title: ELF5 infected LM2 cell, replicate 2

description: Biological replicate 2, ELF5 infected LM2

growth_protocol: Standard cloning process was used to clone coding sequence of Elf5 or GFP in pLEX vector. Lentivirus were produced in H293T cells.or GFP control plasmid (pLEX vector),

treatment_protocol: LM2 cells were infected with lentivirus containing either Elf5 (in pLEX vector), and selected for 10 days with puromycin.

value: LM2 (MDA-MB231 subline)


title: Tubules IV-VI-dnRARa-1


title: Tubules IX-XII-Venus-1

source_name: Seminiferous tubules at stages IX-XII, Venus, 5 days, 5 days

value: Venus


title: Control (GFP) infected LM2 cell, replicate 2

description: Biological replicate 2, GFP infected LM2


title: Control (GFP) infected LM2 cell, replicate 1

description: Biological replicate 1, GFP infected LM2


title: Tubules IX-XII-Venus-2


title: Tubules VI-VIII-Venus-1

source_name: Seminiferous tubules at stages VII-VIII, Venus, 5 days, 5 days


title: Tubules IV-VI-Venus-1

source_name: Seminiferous tubules at stages IV-VI, Venus, 5 days


title: Tubules VI-VIII-dnRARa-2

source_name: Seminiferous tubules at stages VII-VIII, dnRARa, 5 days


title: Tubules IX-XII-dnRARa-1


title: Tubules I-III-dnRARa-2

source_name: Seminiferous tubules at stages I-III, dnRARa, 5 days


title: Tubules I-III-Venus-2

source_name: Seminiferous tubules at stages I-III, Venus, 5 days, 5 days


title: Tubules I-III-dnRARa-1


title: ELF5 infected LM2 cell, replicate 1

description: Biological replicate 1, ELF5 infected LM2


title: Tubules VI-VIII-2

source_name: Seminiferous tubules at stages VII-VIII


title: Tubules IX-XII-1

source_name: Seminiferous tubules at stages IX-XII


title: Tubules I-III-2

source_name: Seminiferous tubules at stages I-III


title: Tubules VI-VIII-dnRARa-1


title: Tubules I-III-Venus-1


title: Tubules IX-XII-2


title: HMLEN-SNAIL; replicate 2

description:
See Agilent Catalog #740000 for detail
Stable cell lines were generated using pLEX based lentivirus system and selected for puromycin resistance. Cells were then cultured without puromycin in normal mammaliam cell culture condition till they were about 90% conflunecy before harvesting.

source_name: HMLEN cells transduced with pLEX-SNAIL and pLEX-MCS lentiviruses.

value: HMLEN

value: SNAIL

tag: emt phenotype

value: Mesenchymal

tag: colony formation ability

value: Strong

source_name: Universal Mouse Reference RNA

value: Universal Mouse Reference RNA

value: Mix of 10 human cell lines


title: Tubules IV-VI-Venus-2

source_name: Seminiferous tubules at stages IV-VI, Venus, 5 days, 5 days


title: Tubules VI-VIII-Venus-2


title: Tubules IV-VI-1

source_name: Seminiferous tubules at stages IV-VI


title: Tubules VI-VIII-1


title: HMLEN Vector Control; replicate 2

source_name: HMLEN cells transduced with pLEX-MCS vector

value: Vector Control

value: Epithelial

value: Weak

tag: sample type


title: Subpopulation P6 (CD24lo) from virgin wild type FVB mice, replicate 2

source_name: Differentiated MEC P6 population of wild type virgin mice

value: FVB/N-J

value: wild type

value: Virgin

tag: cell lines

value: Mix of 11 mouse cell lines


title: Tubules IV-VI-2

tag: strain

value: Seminiferous tubule

value: 6-8 week


title: Cultured Sertoli-vehicle-2

source_name: WT Sertoli cells, Cultured with vehicle

value: Sertoli cell


title: Sertoli N3KO-FACS-1

description: Directly sorted with FACS

source_name: Nanos3KO Sertoli cells, isolated


title: Hrde sensor F4 (A)

status: Public on Jun 25 2012

city: Darlinghurst

first: Leonard

last: Goldstein

address: 384 Victoria St

country: Australia

institute: Garvan Institute of Medical Research

description: Hrde sensor in wild-type, F4 after treatment with dsRNA targeting GFP (A)

data_processing:
Fastq sequence reads with missing bases were excluded. Protocol 1: Reads were trimmed by removing the first four bases corresponding to 5' barcodes and any 3' As. Protocol 2: Reads were trimmed by removing 3' adapter sequences (TGGAATTCTCGGGTGCCAAGG) requiring a minimum of 6 overlapping bases and at most 2 mismatches. Inserts with length 18-30 nucleotides were collapsed to unique sequences, retaining the number of reads for each sequence. The C. elegans genome (assembly WS190/ce6) was downloaded from the UCSC Genome Browser website (http://genome.ucsc.edu/) (Kent et al. 2002, Fujita et al. 2010). Perfect matches to the reference genome and transgene constructs (if applicable) were identified using bowtie in -v alignment mode, allowing for multiple matches (Langmead et al. 2009).
Genome_build: WS190/ce6
Supplementary_files_format_and_content: BED files including perfect alignments to the reference genome and transgene sequences (if applicable). Entries in the 'name' column have format sequence-#reads/#alignments. The 'score' column indicates the number of mismatches.

organism: Caenorhabditis elegans

source_name: whole animal

extract_protocol: Libraries were constructed using one of two protocols as indicated in sample information. Protocol 1: Total RNA was isolated using the mirVana miRNA isolation kit (Ambion). The total RNA samples were separated on denaturing 15% polyacrylamide gels and 18-30 nt length species selected. Following poly-A tailing, small RNAs were treated with tobacco acid pyrophosphatase (Epicentre). Adapters were then ligated to the 5’ phosphate of the RNA. First-strand cDNA synthesis was performed using an oligo(dT)-adapter primer and the M-MLV reverse transcriptase. The resulting cDNAs were PCR-amplified to about 20-30 ng/μl in 18-20 PCR cycles using a high fidelity DNA polymerase. cDNA were purified using the Macherey & Nagel NucleoSpin Exctract II kit. Libraries were sequenced on the Illumina GA IIx platform. Protocol 2: Total RNA was isolated using TRIsure reagent (Bioline). Total RNA was treated with RNA 5’ polyphosphatase (Epicentre). cDNA libraries were then prepared following the TruSeq Small RNA protocol (Illumina). Libraries were size selected on Novex® 6% TBE gels (Invitrogen) and sequenced on the Illumina MiSeq platform.

value: Hrde sensor in wild-type

tag: developmental stage

tag: barcode

value: 5' barcode (CTTA)

tag: library construction

value: Protocol 1


title: Hrde sensor F1 (B)

description: Hrde sensor in wild-type, F1 after treatment with dsRNA targeting GFP (B)

tag: genotype

value: adult

value: Protocol 2


title: Cultured Sertoli-RA-2

description: Gene expression 24h after 1mM RA treatment

source_name: WT Sertoli cells, Cultured with RA, 24h

value: retinoic acid


title: hpl-2 (C)

description: hpl-2 (C)

value: young adult

value: 5' barcode (ATGA)


title: Hrde sensor nrde-2 F1 (B)

description: Hrde sensor nrde-2, F1 after treatment with dsRNA targeting GFP (B)

value: Hrde sensor in nrde-2


title: Hrde sensor P0 control (A)

description: Hrde sensor in wild-type, P0 after treatment with control vector (A)

value: 5' barcode (ACTA)


title: wild-type (C)

description: wild-type (C)

value: wild-type

value: 5' barcode (TCGA)


title: Hrde sensor P0 (A)

description: Hrde sensor in wild-type, P0 after treatment with dsRNA targeting GFP (A)

value: 5' barcode (GTAA)


title: piRNA sensor in wild-type (B)

status: Public on Jun 18 2012

description: piRNA sensor in wild-type (B)

data_processing:
Fastq entries with missing bases or barcodes not matching any of the expected sequences were excluded. Reads were trimmed by removing 5' barcodes (if applicable) and any 3'As. Inserts with length outside the relevant size range (18-30 nucleotides) were excluded. To account for differences in read depth a between-sample normalization was performed within each set of libraries (A, B, C). Size factors based on miRNA read counts were obtained essentially as in Anders et al. 2010. The library with smallest size factor was chosen as a reference. Normalization of the remaining libraries was performed by sampling sequence reads without replacement, where the total number of draws was given by # reads x reference size factor / size factor. Reads were considered miRNA reads if they were identical to the sequence of a mature miRNA (miRBase 13) (3' As were trimmed off miRNA sequences before sequence matching). Read sequences were aligned to the C. elegans genome (WS190/ce6) downloaded from the UCSC Genome Browser website (http://genome.ucsc.edu/) and transgenic sequences (if applicable). Perfect alignments were obtained using bowtie 0.12.7 allowing for multiple matches (Langmead et al. 2009).
BED files including perfect alignments to the reference genome and transgene sequences (if applicable). Entries in the 'name' column have format sequence-#reads/#alignments. The 'score' column indicates the number of mismatches.

source_name: whole animal_piRNA sensor in wild-type_young adult

growth_protocol: C. elegans were grown under standard conditions at 20C The food source used was E. coli strain HB101 (Caenorhabditis Genetics Center, University of Minnesota, Twin Cities, MN, USA). We used bleaching followed by starvation-induced L1 arrest to generate synchronized cultures. The wild-type strain was Bristol N2.

extract_protocol: cDNA libraries were prepared by Vertis Biotechnologie AG (Martinsried). Briefly total RNA was extracted using the mirVana miRNA isolation kit (Ambion). Small RNAs were size selected to ~18-30 nucleotides by denaturing polyacrylamide gel fractionation. cDNA libraries that did not depend on 5'-monophosphates were constructed by tobacco acid pyrophosphatase treatment using adapters recommended for Illumina sequencing as described previously (Das et al. 2008). Each sample was labelled with a unique four base pair barcode. cDNA was purified using the NucleoSpin Extract II kit (Macherey & Nagel).

treatment_protocol: Synchronized worms were collected as young adults by washes in M9 and worm pellets were snap-frozen in liquid Nitrogen.

tag: genetic background

tag: transgene

value: piRNA sensor

value: TruSeq barcode (CGTACG)


title: piRNA sensor in wild-type 2 (C)

description: piRNA sensor in wild-type (C)

value: 5' barcode (CGAT)


title: piRNA sensor in mut-7 (C)

description: piRNA sensor in mut-7 (C)

source_name: whole animal_piRNA sensor in mut-7_young adult

value: 5' barcode (TTCA)


title: Cultured Sertoli-vehicle-1

value: Sertoli cell

value: 6-8 week


title: Sertoli WT-FACS-2

description: Directly sorted with FACS

source_name: WT Sertoli cells, isolated


title: piRNA sensor in prg-1 (B)

description: piRNA sensor in prg-1 (B)

source_name: whole animal_piRNA sensor in prg-1_young adult

value: TruSeq barcode (GGTAGC)


title: control sensor in wild-type (B)

description: control sensor in wild-type (B)

source_name: whole animal_control sensor in wild-type_young adult

value: control sensor

value: TruSeq barcode (GAGTGG)


title: Sertoli WT-FACS-1

description: Directly sorted with FACS


title: Tubules I-III-1

value: Seminiferous tubule


title: Whole testes-2

source_name: Whole testes

value: Testis


title: Sertoli N3KO-FACS-2

description: Directly sorted with FACS


title: Whole testes-1


title: Cultured Sertoli-RA-1

value: retinoic acid


title: prg-1 (A)

description: prg-1 (A)

source_name: whole animal_prg-1 mutant_young adult

value: young adult

value: 5' barcode (TACA)


title: wild-type (A)

description: wild-type (A)

source_name: whole animal_wild-type_young adult

value: 5' barcode (CGGA)


title: cured JU1580

status: Public on Jan 01 2011

description: bleached JU1580

data_processing:
Data were processed using custom perl scripts. Reads with missing bases or whose first four bases did not match the expected barcodes were excluded. Reads were trimmed by removing the first four nucleotides and any 3' As. The obtained inserts were collapsed to unique sequences, retaining the number of reads for each sequence. Sequences in the expected size range (18-30 nt) were aligned to the C. elegans genome (WS190) downloaded from the UCSC Genome Browser website (http://genome.ucsc.edu/) and the JU1580 partial virus genome using the ELAND module within the Illumina Genome Analyzer Pipeline Software, v0.3.0, allowing for up to two mismatches and up to 250 alignments for an individual sequence. Alignments with one or two mismatches were considered only if there were no alignments with less than one or two mismatches, respectively.
In the included BED files, entries in the 'name' column have format sequence-#reads/#alignments_#mismatches. The 'score' column indicates the number of mismatches.
For the purpose of this study only sequences with perfect and unambiguous alignment were considered.

growth_protocol: 4-6 90 mm plates with 15-20 adults (JU1580 or cured JU1580) were grown for 4 days at 20°C. Mixed stage animals from all plates were collected, pooled and frozen at -80°C.

extract_protocol: A cDNA library that did not depend on 5'-monophosphates was constructed by tobacco acid pyrophosphatase treatment using adapters recommended for Illumina sequencing as described previously (Das et al. 2008). Each sample was labelled with a unique four base pair barcode. cDNA was purified using the NucleoSpin Extract II kit (Macherey & Nagel).

treatment_protocol: Total RNA was extracted using the mirVana miRNA isolation kit (Ambion). Small RNAs were size selected to 18-30 nucleotides by denaturing polyacrylamide gel fractionation.

tag: infection

value: cured


title: infected JU1580

value: nodavirus-infected


title: Fam 1 Resistant Control

status: Public on Feb 14 2012

city: Bergen

first: Pablo

last: Balseiro

address: Thormøhlensgate 53

department: Institutt for Biovitenskap

country: Norway

institute: Universitet i Bergen

description:
Gene expression of family 1 injected with VHSV (0d) and with control medium (30d)
turbot2_252469810014_S01_GE1-v5_95_Feb07_1_3.txt

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul adding 1ul 25x Agilent fragmentation buffer and 5 ul 10x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction 25 ul 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the turbot custom oligo-microarray for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation

scan_protocol: Signal was captured, processed and segmented using an Agilent scanner (G2565B, AgilentTechnologies) by the Agilent Feature ExtractionSoftware (v9.5) with the protocol GE1-v5_95, extended dynamic range and preprocessing by the Agilent feature extraction v9.5.5.1. Results for fluorescence intensity data and quality annotations were imported into the GeneSpring GX version 11.0.2 (Agilent Technologies)

data_processing:
All control features (positive, negative, landing lights, etc.) were excluded from subsequent analyses. Previous to normalization, all intensity values lower than 1 were set to 1.0, normalization was carried out by percentile shift at the 75th percentile and data were filtered both by flags present and marginal and by expression to retain expression values between the 20th and 100th percentile in the raw data.
Note: If you arrange raw data file by Probe UID column, then the resultant matrix is arranged as in the GPL11161 platform (ID_Ref 1-14 is GE_Bright Corner; 15-49 is Dark Corner, 50-52 is R2_1257 and so on).

organism: Scophthalmus maximus

source_name: Head kidney, Family 1, VHSV (0d), control medium (30d)

label_protocol: Cyanine-3 (Cy3) labelled cRNA was prepared from 0.2 ug RNA using the One-Color Microarray-Based Gene Expression Analysis (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: 6 different families of turbot (Scophthalmus maximus) were obtained from a commercial fish farm. Fish were acclimated to laboratory conditions for 2 weeks. Fish were injected with VHSV (infected) or culture medium (control) and mortality rate was observed. 4 families (2 with the highest mortality rates and 2 with the lowest mortality rates) were selected for gene expression microarray analysis.

extract_protocol: 24h after the second injection, fish (n=5) of each family were sacrified, head kidney were dissected and total RNA was isolated with Trizol reagent (Invitrogen) following manufacturer's instructions. RNA was treated with DNAse I to remove contaminant genomic DNA and subsequently purified using the RNeasy mini kit (Qiagen) following manufacturer's instructions. cDNA was obtained pooling RNA from 5 fish (2 ug per fish) and using the Superscript III First-Strand Synthesis Supermix for qRT-PCR.

treatment_protocol: Fish from each of the 4 selected families were injected intraperitoneally with 100 µl of VHSV solution (106 TCID50 g-1) or the same volume of culture medium. After 30d, surviving fish (Resistant) and control fish (Naive) were splitted in two groups and re-challenged with the VHSV (Infected) or with the culture medium (Control)

tag: family

value: Head kidney

tag: injection


title: Fam 3 Resistant Control

description:
Gene expression of family 3 injected with VHSV (0d) and with control medium (30d)
turbot2_252469810026_S01_GE1-v5_95_Feb07_1_3.txt

source_name: Head kidney, Family 3, VHSV (0d), control medium (30d)

tag: tissue


title: Fam 1 Resistant Infected

description:
Gene expression of family 1 injected twice with VHSV (0d and 30d)
turbot2_252469810014_S01_GE1-v5_95_Feb07_1_4.txt

source_name: Head kidney, Family 1, VHSV (0d), VHSV (30d)

value: twice with VHSV (0d and 30d)


title: Fam 2 Resistant Infected

description:
Gene expression of family 2 injected twice with VHSV (0d and 30d)
turbot2_252469810014_S01_GE1-v5_95_Feb07_2_4.txt

source_name: Head kidney, Family 2, VHSV (0d), VHSV (30d)


title: Fam 3 Naive Control

description:
Gene expression of family 3 injected twice with control medium (0d and 30d)
turbot2_252469810026_S01_GE1-v5_95_Feb07_1_1.txt

source_name: Head kidney, Family 3, control medium (0d), control medium (30d)

value: twice with control medium (0d and 30d)


title: Fam 2 Resistant Control

description:
Gene expression of family 2 injected with VHSV (0d) and with control medium (30d)
turbot2_252469810014_S01_GE1-v5_95_Feb07_2_3.txt

source_name: Head kidney, Family 2, VHSV (0d), control medium (30d)


title: piwi n4357 n4358 rep2

description: prg-1(n4357);prg-2(n4358) double mutant young adult

hyb_protocol: According to Affymetrix protocol

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner.

data_processing: Affymetrix CEL files were read into R. Array quality control was performed using packages available from Bioconductor. Arrays were processed using the RMA function, performing background correction, quantile normalization and probe set summary.The processed data provided here were further analyzed using the limma package. Since the quality of arrays varied, array quality weights were obtained and used in the linear model fit. Probe set annotations were obtained by mapping probe sequences to annotated transcripts (extracted from C. elegans genome WS190/ce6 based on the refGene table). A transcript was assigned to a probe set if all probes mapped without mismatches in the expected order and orientation.

label: biotin

source_name: whole animal, prg-1(n4357);prg-2(n4358) double mutant, young adult

label_protocol: mRNA was labelled using the 3’IVT expression kit (Affymetrix).

extract_protocol: mRNA was extracted from 100 µl of pelleted young adult animals by using the Absolutely RNA miniprep kit (Stratagene) at the GeneCore Facility (EMBL, Heidelberg, Germany).

value: whole animal


title: Fam 3 Naive Infected

description:
Gene expression of family 3 injected with control medium (0d) and with VHSV (30d)
turbot2_252469810026_S01_GE1-v5_95_Feb07_1_2.txt

source_name: Head kidney, Family 3, control medium (0d), VHSV (30d)


title: piwi n4503 nDf57 rep2

description: prg-1(n4503);prg-2(nDf57) double mutant young adult

source_name: whole animal, prg-1(n4503);prg-2(nDf57) double mutant, young adult


title: Fam 4 Resistant Control

description:
Gene expression of family 4 injected with VHSV (0d) and with control medium (30d)
turbot2_252469810026_S01_GE1-v5_95_Feb07_2_3.txt

source_name: Head kidney, Family 4, VHSV (0d), control medium (30d)


title: Fam 4 Naive Control

description:
Gene expression of family 4 injected twice with control medium (0d and 30d)
turbot2_252469810026_S01_GE1-v5_95_Feb07_2_1.txt

source_name: Head kidney, Family 4, control medium (0d), control medium (30d)


title: Fam 3 Resistant Infected

description:
Gene expression of family 3 injected twice with VHSV (0d and 30d)
turbot2_252469810026_S01_GE1-v5_95_Feb07_1_4.txt

source_name: Head kidney, Family 3, VHSV (0d), VHSV (30d)


title: Fam 1 Naive Control

description:
Gene expression of family 1 injected twice with control medium (0d and 30d)
turbot2_252469810014_S01_GE1-v5_95_Feb07_1_1.txt

source_name: Head kidney, Family 1, control medium (0d), control medium (30d)


title: Fam 4 Resistant Infected

description:
Gene expression of family 4 injected twice with VHSV (0d and 30d)
turbot2_252469810026_S01_GE1-v5_95_Feb07_2_4.txt

source_name: Head kidney, Family 4, VHSV (0d), VHSV (30d)


title: Fam 2 Naive Control

description:
Gene expression of family 2 injected twice with control medium (0d and 30d)
turbot2_252469810014_S01_GE1-v5_95_Feb07_2_1.txt

source_name: Head kidney, Family 2, control medium (0d), control medium (30d)


title: Fam 2 Naive Infected

description:
Gene expression of family 2 injected with control medium (0d) and with VHSV (30d)
turbot2_252469810014_S01_GE1-v5_95_Feb07_2_2.txt

source_name: Head kidney, Family 2, control medium (0d), VHSV (30d)


title: Fam 4 Naive Infected

description:
Gene expression of family 4 injected with control medium (0d) and with VHSV (30d)
turbot2_252469810026_S01_GE1-v5_95_Feb07_2_2.txt

source_name: Head kidney, Family 4, control medium (0d), VHSV (30d)


title: N2 rep3

description: wild-type young adult

source_name: whole animal, wild-type, young adult

value: wild-type


title: Fam 1 Naive Infected

description:
Gene expression of family 1 injected with control medium (0d) and with VHSV (30d)
turbot2_252469810014_S01_GE1-v5_95_Feb07_1_2.txt

source_name: Head kidney, Family 1, control medium (0d), VHSV (30d)


title: piwi n4503 nDf57 rep1


title: WT_GFPp_rep3

status: Public on Mar 22 2010

description: GFP+ cells from wild-type embryos

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, according to manufacturer instructions.

data_processing: Affymetrix CEL files were read into R. Array quality control was performed using packages available from Bioconductor. Arrays were processed using the RMA function, performing background correction, quantile normalization and probe set summary. MAS 5.0 detection calls and P-values were obtained by the mas5calls function included in the affy package. The processed data provided here were further analysed using the limma package. Since the quality of arrays varied, array quality weights were obtained and used in the linear model fit. Probe sets were mapped to Entrez genes using the celegans.db package. When we used absolute intensities or relative expression values for individual genes, these were obtained from the linear model fit. In the case of multiple probe sets mapping to the same gene, values were summarized by the arithmetic mean (on the log2 scale).

source_name: GFP+ cells, wild-type embryos

label_protocol: According to Affymetrix protocol (one-cycle target labeling)

growth_protocol: C. elegans strains were cultured using standard methods (Brenner, 1974) at 20º C.

extract_protocol: mRNA was extracted from 500,000 cells by using the Absolutely RNA microprep kit (Stratagene), yielding ~15 ng mRNA, which was subsequently amplified.

treatment_protocol: Germline transformations were carried out as described in (Mello and Fire 1995). pmir-124::GFP (5ng/ul) was coinjected with pEM27 (plin-15 rescue) into lin-15 (n765) worms. Extrachromosomal transgenes [pmir-124::GFP + lin-15(+)] were integrated by X-ray irradiation and subsequently outcrossed twice into N2 background. Embryos were obtained from synchronised populations of worms and dissociated as previously described (Bacaj et al. 2008; Christensen et al. 2002; Fox et al. 2005). Briefly, 500,000 gravid adults (grown at 20º C in 5 x 15 cm plates) were lysed in hypochlorite solution to release embryos. Embryos were washed in egg buffer containing 118 mM NaCl, 48 mM KCl, 2 mM CaCl2, 2 mM MgCl2 and 25 mM HEPES (pH7.3), and subsequently treated with Chitinase 1 u/ml (Sigma C-7809) for 45 mins to digest egg shells. Embryo pellets were washed in egg buffer and incubated in Trypsin (GIBCO) for 20 mins prior to pipetting several times to facilitate cell dissociation. Dissociated cells were purified by passage through 5 μm filters (Durapore) using a 10 ml syringe and resuspended in L-15 medium (GIBCO) supplemented with 10% FBS (HYCLONE), 50 U/ml penicillin and 50 μg/ml streptomycin, plus sucrose for osmolarity. Embryonic cells were plated on poly-L-Lysine (0.01%, Sigma) coated culture dishes at 10^7 cells/ml and cultured for 24 hours. Sorting experiments were carried out as previously described in (Bacaj et al. 2008) with the following modifications. A BD FACSAriaII (BD Biosciences) equipped with a 50 mw 488 nm laser was used to sort 500,000 cells for each sample directly into extraction buffer (Absolutely RNA microprep kit, Stratagene).

tag: celltype

value: GFP+


title: MT_GFPm_rep3

description: GFP- cells from mir-124 mutant embryos

source_name: GFP- cells, mir-124 mutant embryos

value: GFP-


title: piwi n4357 n4358 rep3


title: piwi n4357 n4358 rep1


title: piwi n4503 nDf57 rep3


title: WT_GFPm_rep3

description: GFP- cells from wild-type embryos

source_name: GFP- cells, wild-type embyros


title: N2 rep2

description: wild-type young adult


title: N2 rep1

description: wild-type young adult


title: MT_GFPp_rep3

description: GFP+ cells from mir-124 mutant embryos

source_name: GFP+ cells, mir-124 mutant embryos


title: WT_GFPm_rep2

description: GFP- cells from wild-type embryos


title: WT_GFPp_rep2

description: GFP+ cells from wild-type embryos


title: MT_GFPp_rep2

description: GFP+ cells from mir-124 mutant embryos


title: WT_GFPm_rep1

description: GFP- cells from wild-type embryos


title: WT_GFPp_rep1

description: GFP+ cells from wild-type embryos


title: MT_GFPm_rep2

description: GFP- cells from mir-124 mutant embryos


title: MT_GFPp_rep1

description: GFP+ cells from mir-124 mutant embryos


title: Ges_15d_2

status: Public on Sep 30 2009

type: other

hyb_protocol: To obtain expression profiles for 318 miRNAs, four distinct sets of bead-coupled oligonucleotide probes were created, and each sample was hybridized to all four bead sets. Samples were hybridized to probes in solution overnight at 50°C, including two water-only blanks and three bead blanks containing water instead of the labelled sample for use as a background control. After washing off unbound sample, the sample-bead solution hybrids were incubated with streptavidin-phycoerythrin at 50°C for 10 min to detect sample-bound biotin moieties.

scan_protocol: Median fluorescence intensity (MFI) values were measured on a Luminex 100IS machine using StarStation software (ACS, Sheffield, UK).

data_processing: MFI values smaller than 1 were set equal to 1 and all values were transformed by taking logs (base 2). To filter out probes for absent miRNAs, each probe was required to exceed 6 on the log2 scale in all replicate samples for one or more time points. The criterion was satisfied by 118 probes, corresponding to 102 unique miRNAs. Technical sample effects were estimated by mean relative levels of two spike-in controls as indicated under platform column 'USAGE' (one measurement per bead set and control, eight measurements in total) and each sample was normalised by subtracting the estimated technical effect. Four probes replicated within and between bead sets were summarized by their mean expression profiles.

molecule: other

source_name: whole mammary gland, gestational day 15, animal 2

label_protocol: For each sample, small RNAs (18–26 nucleotides) were recovered from 5 ug total RNA through denaturing polyacrylamide gel purification, after spiking in three synthetic pre-labelling control RNAs to account for target preparation efficiency. Small RNAs were adaptor-ligated sequentially on the 3’-end and 5’-end using T4 RNA ligase (Fermentas, Burlington, ONT, Canada). After reverse-transcription using adaptor-specific primers, products were PCR-amplified using a biotinylated 5’-primer.

growth_protocol: Six- to ten-week old female C57Bl/6 mice were obtained from Charles River Laboratories (Margate, UK) and either culled for virgin mammary glands or mated at 10 weeks of age. For involution time points females were force weaned at 10 days of lactation. Pups were culled at the specified age for juvenile time points. Mammary glands of the following six key developmental stages, including 16 time points, were harvested: juvenile (12, 15, 19, and 25 days of age), puberty (6 weeks of age), mature virgin (10 weeks of age), gestation (gestational day 5, 10, and 15), lactation (5 days post partum), early involution (12, 24, 48 hours after weaning), and late involution (4, 5 and 6 days after weaning).

extract_protocol: Frozen tissue samples were homogenized in Trizol reagent (Invitrogen, Carlsbad, CA, USA) with a polytron tissue homogenizer, using a whole mammary gland per sample for juvenile, virgin, and gestational time points, and equally sized partial glands for lactation and involution time points. After pre-spinning homogenized samples at 10,000 rpm at 4°C for 10 minutes to remove fat and cell debris, total RNA was extracted from the supernatant according to the manufacturer’s protocol (Invitrogen, Carlsbad, CA, USA), modified by washing the final RNA pellet in 80% ethanol. RNA quantity and integrity were confirmed with a NanoDrop spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) and Agilent 2100 bioanalyser (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Tissue was always collected at the same time of day to account for circadian effects. One complete inguinal gland was removed following excision of the intra-mammary lymph node and immediately frozen in liquid nitrogen.

value: whole mammary gland

tag: developmental time point

value: gestational day 15

value: gestation


title: Ges_15d_3

source_name: whole mammary gland, gestational day 15, animal 3


title: Inv_5d_1A_2

source_name: whole mammary gland, 5 days after weaning, animal 1

value: 5 days after weaning

value: late involution


title: Ges_10d_3

source_name: whole mammary gland, gestational day 10, animal 3

value: gestational day 10


title: Inv_48h_5

source_name: whole mammary gland, 48 hours after weaning, animal 5

value: 48 hours after weaning

value: early involution


title: Lac_5d_1B

source_name: whole mammary gland, day 5 post partum, animal 1

value: day 5 post partum

value: lactation


title: Inv_24h_4

source_name: whole mammary gland, 24 hours after weaning, animal 4

value: 24 hours after weaning


title: Inv_24h_3

source_name: whole mammary gland, 24 hours after weaning, animal 3


title: Inv_6d_1A

source_name: whole mammary gland, 6 days after weaning, animal 1

value: 6 days after weaning


title: Ges_15d_1

source_name: whole mammary gland, gestational day 15, animal 1


title: Ges_10d_2

source_name: whole mammary gland, gestational day 10, animal 2


title: Inv_4d_A

source_name: whole mammary gland, 4 days after weaning, animal 1

value: 4 days after weaning


title: Ges_10d_1

source_name: whole mammary gland, gestational day 10, animal 1


title: Inv_5d_1B


title: Inv_4d_B


title: Inv_48h_1

source_name: whole mammary gland, 48 hours after weaning, animal 1


title: Inv_12h_

source_name: whole mammary gland, 12 hours after weaning, animal 1

value: 12 hours after weaning


title: Inv_6d_1B


title: Ges_5d_2

source_name: whole mammary gland, gestational day 5, animal 2

value: gestational day 5


title: Inv_5d_1A_1


title: Ges_5d_1

source_name: whole mammary gland, gestational day 5, animal 1


title: Ges_5d_3

source_name: whole mammary gland, gestational day 5, animal 3


title: Age_10wk_3

source_name: whole mammary gland, 10 weeks of age, animal 3

value: 10 weeks of age

value: mature virgin


title: MT_GFPm_rep1

description: GFP- cells from mir-124 mutant embryos

source_name: GFP- cells, mir-124 mutant embryos

value: GFP-


title: Age_10wk_1

source_name: whole mammary gland, 10 weeks of age, animal 1

value: whole mammary gland


title: Age_6wk_3

source_name: whole mammary gland, 6 weeks of age, animal 3

value: 6 weeks of age

value: puberty


title: Age_25d_1

source_name: whole mammary gland, 25 days of age, animal 1

value: 25 days of age

value: juvenile


title: Age_6wk_2

source_name: whole mammary gland, 6 weeks of age, animal 2


title: Age_25d_2

source_name: whole mammary gland, 25 days of age, animal 2


title: Age_19d_1_1

source_name: whole mammary gland, 19 days of age, animal 1

value: 19 days of age


title: Age_15d_3

source_name: whole mammary gland, 15 days of age, animal 3

value: 15 days of age


title: Age_19d_1_2


title: Age_12d_1A

source_name: whole mammary gland, 12 days of age, animal 1

value: 12 days of age


title: Age_19d_3

source_name: whole mammary gland, 19 days of age, animal 3


title: Age_19d_2

source_name: whole mammary gland, 19 days of age, animal 2


title: Age_15d_2

source_name: whole mammary gland, 15 days of age, animal 2


title: Age_15d_1_2

source_name: whole mammary gland, 15 days of age, animal 1


title: Age_12d_1B


title: Age_6wk_1

source_name: whole mammary gland, 6 weeks of age, animal 1


title: Age_15d_3_2

hyb_protocol: Labelled samples were hybridized to BeadChips overnight (18 hours) at 55°C and stringency washes were performed according to the manufacturer’s protocol.

scan_protocol: Data were acquired using Illumina BeadArray Reader and BeadScan software (Illumina Inc., San Diego, CA, USA).

data_processing: Data were processed and summarized in the Illumina BeadStudio software. Analyses of the background corrected probe level data were performed using the beadarray Bioconductor package. Data were transformed by taking logs (base 2) and quantile normalised.

label_protocol: For each sample, 200 ng of total RNA were labelled using the Illumina TotalPrep RNA  Amplification Kit according to the manufacturer’s instructions (Applied Biosystems, Foster City, CA, USA).

growth_protocol: Six- to ten-week old female C57Bl/6 mice were obtained from Charles River Laboratories (Margate, UK) and either culled for virgin mammary glands or mated at 10 weeks of age. For involution time points females were force weaned at 10 days of lactation. Pups were culled at the specified age for juvenile time points. Mammary glands of the following six key developmental stages, including 17 time points, were harvested: juvenile (12, 15, 19, and 25 days of age), puberty (6 weeks of age), mature virgin (8, 10 weeks of age), gestation (gestational day 5, 10, and 15), lactation (5, 10 days post partum), early involution (24, 48 hours after weaning), and late involution (4, 5 and 6 days after weaning).

tag: beadchip

tag: array

value: F


title: Age_25d_3

source_name: whole mammary gland, 25 days of age, animal 3


title: Lac_10d_2

source_name: whole mammary gland, day 10 post partum, animal 2

value: day 10 post partum

value: lactation

value: B


title: Lac_10d_1A

source_name: whole mammary gland, day 10 post partum, animal 1

value: A


title: Inv_24h_3

source_name: whole mammary gland, 24 hours after weaning, animal 3

value: 24 hours after weaning

value: early involution

value: E


title: Inv_24h_2

source_name: whole mammary gland, 24 hours after weaning, animal 2

value: D


title: Lac_5d_2

source_name: whole mammary gland, day 5 post partum, animal 2

value: whole mammary gland

value: day 5 post partum


title: Ges_15d_2

source_name: whole mammary gland, gestational day 15, animal 2

value: gestational day 15

value: gestation


title: Ges_15d_1

source_name: whole mammary gland, gestational day 15, animal 1


title: Ges_15d_3_2

source_name: whole mammary gland, gestational day 15, animal 3

value: C


title: Age_6wk_3_2

source_name: whole mammary gland, 6 weeks of age, animal 3

value: 6 weeks of age

value: puberty


title: Lac_5d_1B

source_name: whole mammary gland, day 5 post partum, animal 1


title: Inv_24h_1A

source_name: whole mammary gland, 24 hours after weaning, animal 1


title: Age_15d_1_1

value: 15 days of age

value: juvenile


title: Ges_10d_3

source_name: whole mammary gland, gestational day 10, animal 3

value: gestational day 10

value: F


title: Ges_10d_2

source_name: whole mammary gland, gestational day 10, animal 2


title: Ges_10d_1

source_name: whole mammary gland, gestational day 10, animal 1


title: Ges_5d_2

source_name: whole mammary gland, gestational day 5, animal 2

value: gestational day 5

value: B


title: Ges_5d_3

source_name: whole mammary gland, gestational day 5, animal 3


title: Inv_48h_3_2

source_name: whole mammary gland, 48 hours after weaning, animal 3

value: 48 hours after weaning


title: Age_10wk_3

source_name: whole mammary gland, 10 weeks of age, animal 3

value: 10 weeks of age

value: mature virgin


title: Age_8wk_1

source_name: whole mammary gland, 8 weeks of age, animal 1

value: 8 weeks of age

value: D


title: Inv_48h_4

source_name: whole mammary gland, 48 hours after weaning, animal 4

value: whole mammary gland

value: early involution


title: Age_12d_1A

source_name: whole mammary gland, 12 days of age, animal 1

value: 12 days of age


title: Age_12d_1B

value: E


title: Ges_5d_1

source_name: whole mammary gland, gestational day 5, animal 1

value: gestation

value: A


title: Age_8wk_2

source_name: whole mammary gland, 8 weeks of age, animal 2

value: puberty


title: Age_10wk_1

source_name: whole mammary gland, 10 weeks of age, animal 1


title: Ges_15d_3_1

source_name: whole mammary gland, gestational day 15, animal 3

value: gestational day 15


title: Inv_5d_1A

source_name: whole mammary gland, 5 days after weaning, animal 1

value: 5 days after weaning

value: late involution


title: Inv_48h_1

source_name: whole mammary gland, 48 hours after weaning, animal 1


title: Inv_4d_B

source_name: whole mammary gland, 4 days after weaning, animal 1

value: 4 days after weaning


title: Age_6wk_3_1

source_name: whole mammary gland, 6 weeks of age, animal 3

value: 6 weeks of age

value: F


title: Inv_6d_1A

source_name: whole mammary gland, 6 days after weaning, animal 1

value: 6 days after weaning

value: C


title: Inv_4d_A


title: Age_19d_3

source_name: whole mammary gland, 19 days of age, animal 3

value: 19 days of age

value: juvenile


title: Inv_6d_2

source_name: whole mammary gland, 6 days after weaning, animal 2

value: whole mammary gland

value: D


title: Age_10wk_2

source_name: whole mammary gland, 10 weeks of age, animal 2

value: 10 weeks of age

value: mature virgin

value: B


title: Inv_5d_2

source_name: whole mammary gland, 5 days after weaning, animal 2


title: Age_15d_2

source_name: whole mammary gland, 15 days of age, animal 2

value: 15 days of age


title: Age_6wk_2

source_name: whole mammary gland, 6 weeks of age, animal 2

value: puberty

value: E


title: Age_19d_2

source_name: whole mammary gland, 19 days of age, animal 2


title: Age_15d_1

source_name: whole mammary gland, 15 days of age, animal 1

value: A


title: Age_15d_3_1

source_name: whole mammary gland, 15 days of age, animal 3


title: Age_6wk_1

source_name: whole mammary gland, 6 weeks of age, animal 1


title: Inv_48h_3_1

source_name: whole mammary gland, 48 hours after weaning, animal 3

value: 48 hours after weaning

value: early involution


title: Age_25d_3

source_name: whole mammary gland, 25 days of age, animal 3

value: 25 days of age


title: 2079

status: Public on Oct 09 2007

description: Primary breast tumour

hyb_protocol: 15ul sample and 33ul of the bead pool were incubated overnight at 50ºC and washed after 16 hours

scan_protocol: Median fluorescence intensity values were measured on a Luminex 100 machine

data_processing: Raw values smaller than 1 were set equal to 1. After log2 transformation probes were filtered by requiring each probe to exceed 6 in at least one sample. Systematic probe effects between plates were removed by subtracting differences between the probe median for the samples on a given plate and the probe median for all samples on both plates. Unused probes were removed and replicate probes were summarized by their mean expression profile. Two alternative between-sample normalizations were used: 1) Median centering (VALUE) The sample median was subtracted for each sample. Replicate samples were summarized by their mean expression profile. 2) Control-based normalization (CTRL_BASED_NORM) Control probes used for normalization as indicated in 'USAGE' were median centred. Sample effects were estimated by taking the mean over eight control measurements per sample. Normalization was performed by subtracting the estimated effect for each sample. Replicate samples were summarized by their mean expression profile.

label: Biotin

source_name: Nottingham City Hospital Tumour Bank

label_protocol: Indirect PCR-based labelling method: Linkers were ligated to the 3' and 5' end of miRNAs, cDNA was synthesized using superscript Reverse Transcriptase, cDNA was labelled (Biotin) and amplified by PCR

extract_protocol: Standard Trizol extraction protocol, modified by washing the final RNA pellet with 80% EtOH

tag: Plate = 2; Grade = 3; Stage = 3; Vascular Invasion = 2; NPI = 6.5; ER status = Negative; Molecular subtype = Normal-like


title: 2214

description: Primary breast tumour

tag: Plate = 2; Grade = 2; Stage = 1; Vascular Invasion = 2; NPI = 3.3; ER status = Positive; Molecular subtype = Luminal A


title: 2105

description: Primary breast tumour

tag: Plate = 2; Grade = 2; Stage = 1; Vascular Invasion = 1; NPI = 3.3; ER status = Positive; Molecular subtype = Luminal B


title: 2347

description: Primary breast tumour

tag: Plate = 2; Grade = 2; Stage = 1; Vascular Invasion = 2; NPI = 3.22; ER status = Positive; Molecular subtype = unknown


title: 2113

description: Primary breast tumour

tag: Plate = 2; Grade = 2; Stage = 1; Vascular Invasion = 2; NPI = 3.22; ER status = Positive; Molecular subtype = Luminal A


title: HCC1569

description: Breast cancer cell line

source_name: University of Cambridge

tag: Plate = 2


title: 2125

description: Primary breast tumour

tag: Plate = 2; Grade = 3; Stage = 1; Vascular Invasion = 1; NPI = 4.7; ER status = Negative; Molecular subtype = Luminal B


title: 2433

description: Primary breast tumour

tag: Plate = 2; Grade = 2; Stage = 2; Vascular Invasion = 1; NPI = 4.4; ER status = Positive; Molecular subtype = Luminal B


title: Age_25d_2

source_name: whole mammary gland, 25 days of age, animal 2

tag: developmental stage


title: Age_25d_1

source_name: whole mammary gland, 25 days of age, animal 1


title: SKBR7

description: Breast cancer cell line


title: N_BRST_5

description: Normal breast sample


title: 2498

description: Primary breast tumour

tag: Plate = 2; Grade = 2; Stage = 2; Vascular Invasion = 1; NPI = 4.4; ER status = Positive; Molecular subtype = Luminal A


title: 2444

description: Primary breast tumour

tag: Plate = 2; Grade = 3; Stage = 1; Vascular Invasion = 1; NPI = 4.3; ER status = Negative; Molecular subtype = unknown


title: HCC1500

description: Breast cancer cell line


title: HS578T

description: Breast cancer cell line


title: 2474

description: Primary breast tumour

tag: Plate = 2; Grade = 2; Stage = 1; Vascular Invasion = 1; NPI = 3.5; ER status = Positive; Molecular subtype = unknown


title: HCC1395

description: Breast cancer cell line


title: 2075

description: Primary breast tumour

tag: Plate = 2; Grade = 1; Stage = 2; Vascular Invasion = 3; NPI = 3.44; ER status = Positive; Molecular subtype = unknown


title: 2504

description: Primary breast tumour

tag: Plate = 2; Grade = 2; Stage = 1; Vascular Invasion = 1; NPI = 3.18; ER status = Positive; Molecular subtype = Luminal B


title: 2084

description: Primary breast tumour

tag: Plate = 2; Grade = 3; Stage = 1; Vascular Invasion = unknown; NPI = 4.4; ER status = Negative; Molecular subtype = unknown


title: HCC1954

description: Breast cancer cell line


title: Idenitfication of differentially expressed genes in Runx1-/- primitive erythroid

status: Public on Feb 02 2008

hyb_protocol: 17 hour incubation following Agilent protocols using 750ng of both Cy3 and Cy5 labeled material, In Situ Hybridization Kit reagents and control probes followed by a 10 minute room temperature wash in 6X SSC,0.005% tritonX-102 and 5 minutes at 4 degrees C in 0.1X SSC, 0.005% Triton X-102. The arrays were dried in a Nitrogen stream and scanned.

scan_protocol: The scanning was performed with an Agilent Technologies Microarray Scanner (Agilent Technologies).

data_processing: The log ratio of the red over green processed signals is calculated.

source_name: WT

label_protocol: Total RNA was labeled using a Low Input Fluorescent Linear Amplification kit (Agilent) following the manufacturer’s instruction.

extract_protocol: Total RNA from E10.5 wild type yolk sacs was extracted using RNeasy kit (Qiagen), and three samples were mixed equally. The quality of the isolated RNA was determined using an Agilent 2100 Bioanalyzer (Agilent Technologies).

tag: tissue:yolk sac

extract_protocol: Total RNA from E10.5 runx1-/- yolk sacs was extracted using RNeasy kit (Qiagen), and three samples were mixed equally. The quality of the isolated RNA was determined using an Agilent 2100 Bioanalyzer (Agilent Technologies).


title: 2345

description: Primary breast tumour

tag: Plate = 2; Grade = 2; Stage = 1; Vascular Invasion = 2; NPI = 3.4; ER status = Positive; Molecular subtype = unknown


title: 2374

description: Primary breast tumour

tag: Plate = 2; Grade = 2; Stage = 2; Vascular Invasion = 2; NPI = 4.34; ER status = Positive; Molecular subtype = unknown


title: MDA134

description: Breast cancer cell line


title: 2159

description: Primary breast tumour

tag: Plate = 2; Grade = 1; Stage = 1; Vascular Invasion = 1; NPI = 2.2; ER status = Positive; Molecular subtype = unknown


title: 2096

description: Primary breast tumour

tag: Plate = 2; Grade = 2; Stage = 1; Vascular Invasion = 1; NPI = 3.36; ER status = Positive; Molecular subtype = unknown


title: Age_19d_1

source_name: whole mammary gland, 19 days of age, animal 1

tag: tissue

tag: developmental time point

tag: beadchip

tag: array


title: 2179

description: Primary breast tumour

tag: Plate = 2; Grade = 2; Stage = 3; Vascular Invasion = 1; NPI = 5.4; ER status = Positive; Molecular subtype = Normal-like


title: 2483

description: Primary breast tumour

tag: Plate = 2; Grade = 1; Stage = 1; Vascular Invasion = 2; NPI = 2.38; ER status = Positive; Molecular subtype = unknown


title: 2077

description: Primary breast tumour

tag: Plate = 2; Grade = 1; Stage = 1; Vascular Invasion = 2; NPI = 2.24; ER status = Positive; Molecular subtype = Luminal A


title: 2166

description: Primary breast tumour

tag: Plate = 2; Grade = 3; Stage = 1; Vascular Invasion = unknown; NPI = 4.02; ER status = Negative; Molecular subtype = Basal-like


title: 2390

description: Primary breast tumour

tag: Plate = 2; Grade = 2; Stage = 3; Vascular Invasion = 1; NPI = 5.34; ER status = Positive; Molecular subtype = unknown


title: 2091

description: Primary breast tumour

tag: Plate = 2; Grade = 2; Stage = 1; Vascular Invasion = 1; NPI = 3.3; ER status = Negative; Molecular subtype = HER2+


title: 2078

description: Primary breast tumour

tag: Plate = 2; Grade = 1; Stage = 1; Vascular Invasion = 2; NPI = 2.3; ER status = Positive; Molecular subtype = Luminal A


title: 2378

description: Primary breast tumour

tag: Plate = 2; Grade = 2; Stage = 1; Vascular Invasion = 2; NPI = 3.2; ER status = Positive; Molecular subtype = unknown


title: ZR7530

description: Breast cancer cell line

tag: Plate = 2


title: MDA453

description: Breast cancer cell line


title: 2230

description: Primary breast tumour

tag: Plate = 2; Grade = 1; Stage = 1; Vascular Invasion = 2; NPI = 2.4; ER status = Positive; Molecular subtype = Luminal A


title: 2348

description: Primary breast tumour

tag: Plate = 2; Grade = 3; Stage = 3; Vascular Invasion = 3; NPI = 6.46; ER status = Positive; Molecular subtype = Basal-like


title: 2372

description: Primary breast tumour

tag: Plate = 2; Grade = 2; Stage = 2; Vascular Invasion = 2; NPI = 4.42; ER status = Positive; Molecular subtype = Luminal A


title: 2219

description: Primary breast tumour

tag: Plate = 2; Grade = 3; Stage = 1; Vascular Invasion = 1; NPI = 4.48; ER status = Negative; Molecular subtype = Basal-like


title: 2086

description: Primary breast tumour

tag: Plate = 2; Grade = 3; Stage = 1; Vascular Invasion = 1; NPI = 4.5; ER status = Negative; Molecular subtype = Basal-like


title: MDA157

description: Breast cancer cell line


title: 2156

description: Primary breast tumour

tag: Plate = 2; Grade = 3; Stage = 1; Vascular Invasion = 2; NPI = 4.44; ER status = Positive; Molecular subtype = Luminal B


title: 2081

description: Primary breast tumour

tag: Plate = 2; Grade = 3; Stage = 2; Vascular Invasion = 2; NPI = 5.24; ER status = Positive; Molecular subtype = unknown


title: 2461

description: Primary breast tumour


title: 2153

description: Primary breast tumour

tag: Plate = 2; Grade = 3; Stage = 1; Vascular Invasion = 1; NPI = 4.3; ER status = Negative; Molecular subtype = Basal-like


title: 2149

description: Primary breast tumour

tag: Plate = 2; Grade = 3; Stage = 1; Vascular Invasion = 1; NPI = 4.24; ER status = Negative; Molecular subtype = unknown


title: 2416

description: Primary breast tumour

tag: Plate = 2; Grade = 3; Stage = 1; Vascular Invasion = 1; NPI = 4.5; ER status = Negative; Molecular subtype = unknown


title: 2177

description: Primary breast tumour

tag: Plate = 2; Grade = 3; Stage = 1; Vascular Invasion = 1; NPI = 4.44; ER status = Positive; Molecular subtype = unknown


title: 2438

description: Primary breast tumour

tag: Plate = 2; Grade = 3; Stage = 1; Vascular Invasion = 1; NPI = 4.4; ER status = Negative; Molecular subtype = HER2+


title: GI101

description: Breast cancer cell line


title: MDA175

description: Breast cancer cell line


title: MDA468

description: Breast cancer cell line


title: 2196

description: Primary breast tumour

tag: Plate = 2; Grade = 3; Stage = 2; Vascular Invasion = 1; NPI = 5.36; ER status = Negative; Molecular subtype = Basal-like


title: 2211

description: Primary breast tumour

tag: Plate = 1,2,2; Grade = 3; Stage = 2; Vascular Invasion = 3; NPI = 5.74; ER status = Negative; Molecular subtype = unknown


title: 2425

description: Primary breast tumour

tag: Plate = 1; Grade = 2; Stage = 1; Vascular Invasion = 2; NPI = 3.2; ER status = Positive; Molecular subtype = Luminal A


title: 2421

description: Primary breast tumour

tag: Plate = 1; Grade = 1; Stage = 2; Vascular Invasion = 3; NPI = 3.4; ER status = Positive; Molecular subtype = unknown


title: 2453

description: Primary breast tumour

tag: Plate = 1; Grade = 2; Stage = 1; Vascular Invasion = 1; NPI = 3.18; ER status = Positive; Molecular subtype = unknown


title: 2386

description: Primary breast tumour

tag: Plate = 1; Grade = 2; Stage = 1; Vascular Invasion = 2; NPI = 3.26; ER status = Positive; Molecular subtype = Normal-like


title: 2083

description: Primary breast tumour

tag: Plate = 1,2; Grade = 2; Stage = 2; Vascular Invasion = 1; NPI = 4.3; ER status = Negative; Molecular subtype = Basal-like


title: 2111

description: Primary breast tumour

tag: Plate = 1,2,2; Grade = 1; Stage = 3; Vascular Invasion = 2; NPI = 4.24; ER status = Positive; Molecular subtype = unknown


title: 2222

description: Primary breast tumour

tag: Plate = 1; Grade = 3; Stage = 2; Vascular Invasion = 2; NPI = 5.68; ER status = Negative; Molecular subtype = HER2+


title: 2312

description: Primary breast tumour

tag: Plate = 2; Grade = 1; Stage = 2; Vascular Invasion = 1; NPI = 3.6; ER status = Positive; Molecular subtype = unknown


title: 2405

description: Primary breast tumour

tag: Plate = 1; Grade = 2; Stage = 2; Vascular Invasion = 3; NPI = 4.5; ER status = Positive; Molecular subtype = unknown


title: 2375

description: Primary breast tumour

tag: Plate = 1,2; Grade = 2; Stage = 2; Vascular Invasion = 1; NPI = 4.28; ER status = Positive; Molecular subtype = unknown


title: 2460

description: Primary breast tumour

tag: Plate = 1; Grade = 3; Stage = 2; Vascular Invasion = 1; NPI = 5.5; ER status = Positive; Molecular subtype = unknown


title: N_BRST_4

description: Normal breast sample


title: HCC1187

description: Breast cancer cell line

tag: Plate = 1


title: 2134

description: Primary breast tumour

tag: Plate = 1; Grade = 2; Stage = 1; Vascular Invasion = 1; NPI = 3.3; ER status = Negative; Molecular subtype = unknown


title: 2456

description: Primary breast tumour

tag: Plate = 1; Grade = 3; Stage = 1; Vascular Invasion = 1; NPI = 4.3; ER status = Positive; Molecular subtype = unknown


title: 2228

description: Primary breast tumour

tag: Plate = 1; Grade = 3; Stage = 1; Vascular Invasion = 2; NPI = 4.34; ER status = Positive; Molecular subtype = Luminal B


title: 2227

description: Primary breast tumour

tag: Plate = 1; Grade = 3; Stage = 3; Vascular Invasion = 1; NPI = 6.5; ER status = Negative; Molecular subtype = Basal-like


title: 2229

description: Primary breast tumour

tag: Plate = 1; Grade = 3; Stage = 1; Vascular Invasion = 1; NPI = 4.6; ER status = Negative; Molecular subtype = Basal-like


title: 2167

description: Primary breast tumour

tag: Plate = 1; Grade = 2; Stage = 1; Vascular Invasion = 3; NPI = 3.2; ER status = Positive; Molecular subtype = Normal-like


title: 2162

description: Primary breast tumour

tag: Plate = 1; Grade = 2; Stage = 1; Vascular Invasion = 2; NPI = 3.3; ER status = Positive; Molecular subtype = unknown


title: 2446

description: Primary breast tumour

tag: Plate = 1; Grade = 3; Stage = 2; Vascular Invasion = 2; NPI = 5.5; ER status = Positive; Molecular subtype = unknown


title: 2225

description: Primary breast tumour

tag: Plate = 1; Grade = 1; Stage = 1; Vascular Invasion = 1; NPI = 2.3; ER status = Positive; Molecular subtype = Luminal A


title: 2082

description: Primary breast tumour

tag: Plate = 1; Grade = 2; Stage = 2; Vascular Invasion = 2; NPI = 4.34; ER status = Positive; Molecular subtype = unknown


title: 2098

description: Primary breast tumour

tag: Plate = 1; Grade = 1; Stage = 1; Vascular Invasion = 2; NPI = 2.32; ER status = Positive; Molecular subtype = unknown


title: 2209

description: Primary breast tumour

tag: Plate = 1; Grade = 3; Stage = 1; Vascular Invasion = 2; NPI = 4.6; ER status = Negative; Molecular subtype = Basal-like


title: 2200

description: Primary breast tumour

tag: Plate = 1; Grade = 2; Stage = 3; Vascular Invasion = 1; NPI = 5.48; ER status = Positive; Molecular subtype = Luminal A


title: 2334

description: Primary breast tumour

tag: Plate = 1; Grade = 3; Stage = 2; Vascular Invasion = 1; NPI = 5.4; ER status = Positive; Molecular subtype = Luminal B


title: OCUBF

description: Breast cancer cell line


title: 2327

description: Primary breast tumour

tag: Plate = 1; Grade = 3; Stage = 1; Vascular Invasion = 2; NPI = 4.4; ER status = Negative; Molecular subtype = Basal-like


title: N_BRST_3

description: Normal breast sample


title: 2176

description: Primary breast tumour

tag: Plate = 1,1,2; Grade = 2; Stage = 2; Vascular Invasion = 2; NPI = 4.6; ER status = Negative; Molecular subtype = unknown


title: 2133

description: Primary breast tumour

tag: Plate = 1; Grade = 1; Stage = 1; Vascular Invasion = 2; NPI = 2.5; ER status = Positive; Molecular subtype = Normal-like


title: 2138

description: Primary breast tumour

tag: Plate = 1,1,2; Grade = 3; Stage = 1; Vascular Invasion = 1; NPI = 4.5; ER status = Positive; Molecular subtype = unknown


title: 2100

description: Primary breast tumour

tag: Plate = 1; Grade = 3; Stage = 2; Vascular Invasion = 2; NPI = 5.6; ER status = Negative; Molecular subtype = Basal-like


title: 2174

description: Primary breast tumour

tag: Plate = 1; Grade = 2; Stage = 1; Vascular Invasion = 3; NPI = 3.34; ER status = Positive; Molecular subtype = Luminal A


title: 2076

description: Primary breast tumour

tag: Plate = 1; Grade = 1; Stage = 1; Vascular Invasion = 1; NPI = 2.42; ER status = Positive; Molecular subtype = Luminal A


title: 2171

description: Primary breast tumour

tag: Plate = 1,1,2; Grade = 3; Stage = 1; Vascular Invasion = 1; NPI = 4.36; ER status = Positive; Molecular subtype = unknown


title: 2218

description: Primary breast tumour

tag: Plate = 1; Grade = 2; Stage = 2; Vascular Invasion = 2; NPI = 4.34; ER status = Negative; Molecular subtype = HER2+


title: 2237

description: Primary breast tumour

tag: Plate = 1; Grade = 2; Stage = 1; Vascular Invasion = 2; NPI = 3.3; ER status = Negative; Molecular subtype = unknown


title: 2104

description: Primary breast tumour

tag: Plate = 1; Grade = 1; Stage = 1; Vascular Invasion = unknown; NPI = 2.3; ER status = Positive; Molecular subtype = Normal-like


title: N_BRST_2

description: Normal breast sample


title: 2233

description: Primary breast tumour

tag: Plate = 1; Grade = 1; Stage = 1; Vascular Invasion = 2; NPI = 2.4; ER status = Negative; Molecular subtype = unknown


title: 2210

description: Primary breast tumour

tag: Plate = 1; Grade = 3; Stage = 1; Vascular Invasion = 2; NPI = 4.4; ER status = Positive; Molecular subtype = unknown


title: 2236

description: Primary breast tumour

tag: Plate = 1; Grade = 1; Stage = 2; Vascular Invasion = 2; NPI = 3.5; ER status = Positive; Molecular subtype = Luminal A


title: 2160

description: Primary breast tumour

tag: Plate = 1; Grade = 3; Stage = 2; Vascular Invasion = 2; NPI = 5.26; ER status = Negative; Molecular subtype = unknown


title: 2157

description: Primary breast tumour

tag: Plate = 1; Grade = 2; Stage = 3; Vascular Invasion = 2; NPI = 5.38; ER status = Positive; Molecular subtype = Luminal A


title: 2152

description: Primary breast tumour

tag: Plate = 1; Grade = 3; Stage = 1; Vascular Invasion = 2; NPI = 4.56; ER status = Positive; Molecular subtype = Luminal B


title: 2254

description: Primary breast tumour

tag: Plate = 1; Grade = 1; Stage = 1; Vascular Invasion = 2; NPI = 2.3; ER status = Positive; Molecular subtype = unknown


title: SUM52

description: Breast cancer cell line

tag: Plate = 1


title: VP229

description: Breast cancer cell line


title: 2231

description: Primary breast tumour

tag: Plate = 1; Grade = 3; Stage = 1; Vascular Invasion = 3; NPI = 4.34; ER status = Positive; Molecular subtype = HER2+


title: HCC1806

description: Breast cancer cell line


title: 2268

description: Primary breast tumour

tag: Plate = 1; Grade = 3; Stage = 1; Vascular Invasion = 2; NPI = 4.34; ER status = Negative; Molecular subtype = unknown


title: IBEP1

description: Breast cancer cell line


title: N_BRST_1

description: Normal breast sample


title: HCC1419

description: Breast cancer cell line


title: HCC1937

description: Breast cancer cell line


title: 2462

description: Primary breast tumour

tag: Plate = 1; Grade = 3; Stage = 1; Vascular Invasion = 2; NPI = 4.7; ER status = Negative; Molecular subtype = Basal-like


title: 2187

description: Primary breast tumour

tag: Plate = 1; Grade = 1; Stage = 1; Vascular Invasion = 2; NPI = 2.3; ER status = Negative; Molecular subtype = Basal-like


title: 2199

description: Primary breast tumour

tag: Plate = 1,2; Grade = 3; Stage = 2; Vascular Invasion = 1; NPI = 5.4; ER status = Positive; Molecular subtype = Luminal B


title: 2172

description: Primary breast tumour

tag: Plate = 1; Grade = 2; Stage = 1; Vascular Invasion = 2; NPI = 3.44; ER status = Positive; Molecular subtype = Luminal A


title: 2204

description: Primary breast tumour

tag: Plate = 1; Grade = 1; Stage = 1; Vascular Invasion = 2; NPI = 2.44; ER status = Negative; Molecular subtype = unknown


title: 2185

description: Primary breast tumour

tag: Plate = 1; Grade = 3; Stage = 3; Vascular Invasion = 1; NPI = 6.36; ER status = Negative; Molecular subtype = Basal-like


title: 2180

description: Primary breast tumour

tag: Plate = 1; Grade = 2; Stage = 1; Vascular Invasion = 1; NPI = 3.44; ER status = Positive; Molecular subtype = unknown


title: 2136

description: Primary breast tumour

tag: Plate = 1; Grade = 1; Stage = 1; Vascular Invasion = 1; NPI = 2.3; ER status = Positive; Molecular subtype = unknown