title: untreated control of Overexpression 1

source_name: untreated control of Overexpression 1


title: SIRPα-KO splenic red pulp macrophage

status: Public on Nov 22 2016

type: RNA

city: Nanjing

first: Zhen

last: Zhou

state: Jiangsu

address: 22th,Hankou Road

department: School of Lifesciences

country: China

institute: Nanjing University

hyb_protocol: Hybridization was  performed using Agilent SureHyb (Agilent Technologies).

scan_protocol: Slides were scanned with an AgilentDNA Microarray Scanner, and the images were processed by Feature Extraction software 11.0.0.1 (Agilent Technologies) with background correction to prepare the raw data output files.

data_processing: Normalization was carried out using GeneSpring GX 12.1 software (Agilent Technologies).

molecule: total RNA

organism: Mus musculus

source_name: Splenic red pulp macrophages isolated from 5 SIRPα-KO mice

label_protocol: Labeled cRNA was synthesized using the Quick Amp Labeling kit (Agilent Technologies).

extract_protocol: RNA was isolated from freshly isolated macrophages using TRIzol Reagent (Invitrogen, Life technology) according to the manufacturer’s instructions. Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both α- and β-globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Mouse spleens were harvested and minced in digestion mix (1mg/mL collagenase D (Roche Molecular Products), 20 µg/mL DNase I (Roche Molecular Products), 2% FCS in HEPES-buffered RPMI-1640), followed by passing through nylon meshes. The splenocytes were collected followed by lysis of RBC. Spleen red pulp macrophages were defined as F4/80+CD11blow cells and purified by FACS sorting (1, 2).   1. Davies, L. C., S. J. Jenkins, J. E. Allen, and P. R. Taylor. 2013. Tissue-resident macrophages. Nat Immunol 14: 986-995.  2. Wang, C., X. Yu, Q. Cao, Y. Wang, G. Zheng, T. K. Tan, H. Zhao, Y. Zhao, Y. Wang, and D. C. Harris. 2013. Characterization of murine macrophages from bone marrow, spleen and peritoneum. BMC Immunology 14: 1-10.

tag: genotype/variation

value: SIRP{alpha}-KO

tag: tissue

value: spleen

tag: cell type

value: red pulp macrophage


title: C3, biological rep2

city: SuZhou

first: Tao

last: Chen

state: JiangSu

address: 199 Ren-Ai-rd

institute: Soochow University

description: miRNA expression data from control liver

hyb_protocol: The labeled RNAs were hybridized onto Affymetrix miRNA 3.0 array.

scan_protocol: The arrays were scanned by the Affymetrix Scanner 3000 (Affymetrix).

data_processing: Affymetrix GeneChip Conmand Console software (version4.0, Affymetrix) was used to analyze array images to get raw data and then offered RMA normalization. Next, Genesrping software (version 12.5; Agilent Technologies) was used to proceed the following data analysis. Probes that at least 100% of the values in any 1 out of 2 conditions have flags in P were chosen for further data analysis. Differentially expressed miRNAs were then identified through fold change as well as P value calculated using t-test.

label: biotin

source_name: liver from mice exposed to vehicle control

label_protocol: Total RNA were tailed with Poly A and then labeled with Biotin.

growth_protocol: B6C3F1 male mice were housed with a 12h light and 12h dark cycle at 22+/-2 °C temperature.

extract_protocol: Total RNA were purified using AllPrep DNA/RNA Mini Kit (Tiangen, Beijing, China). Turbo DNA-freeTM kit (Life Technologies, Shanghai, China) was used to remove genomic DNA contamination in purified RNA samples.

treatment_protocol: Adult B6C3F1 male mice were oral administrated with either corn oil or TCE for five days. Form each mouse, liver was excised rapidly, frozen in liquid nitrogen, and stored at -80oC.

tag: strain

value: liver

tag: age

value: 7 week


title: siAF control of Knockdown 1

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

country: Germany

institute: RWTH Aachen University

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Arrays were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: CEL files were processed using the Affymetrix Power Tools (APT) Software Package. Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003).

organism: Homo sapiens

source_name: siAF control of Knockdown 1

label_protocol: Standard Illumina labelling protocol

growth_protocol: Cells were cultured in DMEM low glucose medium (PAA) supplemented with 2mM L-glutamine, 100U/ml penicillin/streptomycin, 5,000U/ml heparin and 10% human platelet lysate (HPL) in a humidified atmosphere at 5% CO2. Cells were seeded at a densitiy of 5000/cm2 and passaged at 80% confluency.

extract_protocol: Total RNA was extracted using NucleoSpin miRNA kit (Macherey-Nagel, Düren, Germany) acording to manufacturers instruction

treatment_protocol: For siRNA mediated knockdown MSCs were seeded at a density of 5000/cm². At 80% confluence medium was changed and transfection of 10µM siRNA was performed with 3% HiPerfect transfection reagent (Qiagen, Hilden, Germany) dissolved in serum free DMEM. After 48h total RNA was isolated or medium change occurred in the case of differentiation assays. ANRIL siRNA (si04378563; Qiagen) and HOTAIR siRNA (5'-GAACGGGAGUACAGAGAGA-3'; MWG, Huntsville, USA) were used for knockdown. For control we used the AllStars Neg. siRNA (AF 488, Qiagen, Hilden, Germany), which has no human target sequence and carries an AlexaFluor488 molecule. Overexpression experiments were performed according to permission of the district council Düsseldorf, Germany (Az. 53.02.01-K-1.118/12). The plasmids lzrs-HOTAIR and lzrs-GFP were purchased from Addgene (Cambridge, USA; #26110 and #21961, respectively). Plasmids were transduced into E.coli plasmid-DNA isolation was realized with the NucleoBond Xtra Maxi Prep (Macherey-Nagel, Düren, Germany) according to manufacturer´s instructions. Next amphotrophic Phoenix cells were treated with a suspension of 50% HOTAIR-plasmid, 10% gagPol-plasmid and 40% env-plasmid bubble-resuspended in 2xHBS and Calciumchloride. Efficiency of transfection was surveyed after 24h in the GFP transfected cell subset (Figure S1) and medium was changed. 72h hours after transfection supernatants with viruses were harvested and transferred onto non-confluent MSCs at passage 4.

tag: treatment

value: ANRIL siRNA (si04378563; Qiagen) transfection

value: Mesenchymal stromal cell


title: HOTAIR knockdown 2

source_name: HOTAIR knockdown 2

value: HOTAIR siRNA (5'-GAACGGGAGUACAGAGAGA-3' transfection


title: HOTAIR overexpression 3

source_name: HOTAIR overexpression 3

value: lzrs-HOTAIR plasmid transduced


title: HSC_WT_Adult_16453

city: St Louis

first: Jeffery

last: Magee

state: Missouri

address: 660 S Euclid Ave.

department: Internal Medicine - Cardiovascular Division

country: USA

institute: Washington University School of Medicine

description: Gene expression in HSCs

hyb_protocol: The balanced aRNAs were suspended in Agilent 2X Gene Expression buffer (55ul), Agilent 10X Blocking agent (11ul), and Kreablock (6ul).  The hybridization solutions were applied to Agilent Mouse v2 4x44K microarrays (G4846A-026655).  Hybridization was carried out at 65C for 20 hours.  Washing procedures were carried out according to Agilent gene expression protocols.

scan_protocol: Slides were scanned on an Agilent C-class Microarray scanner to detect Cy5 fluorescence, according to manufacturer's specifications.

data_processing: Gridding and analysis of images was performed using Feature Extraction (v11.5.1.1, Agilent Technologies).

source_name: Bone marrow

label_protocol: RNA samples were amplified using SIGMA WTA2 RNA amplification system. Amplified cDNAs were chemically labeled with Kreatech ULS RNA labeling kit (Kreatech Diagnostics).  Per reaction, 3ug of each RNA (+water=16ul) was mixed with Kreatech 10x labeling buffer (2ul) and Kreatech cy5/DY-ULS (2ul).  The reactions were incubated at 85C for 15 minutes in the dark and placed on ice for 3 minutes.  Labeled cDNA was purified with Qiagen PCR purification columns according to manufacturer’s protocol.  cDNAs were quantitated on a Nanodrop spectrophotometer. Detailed protocol can be found at http://www.kreatech.com/fileadmin/user_upload/Documenten/PDF/12_man_EA-021-022-023__D0.6.pdf

growth_protocol: HSCs and HPCs harvested directly from mouse by flow cytometry

extract_protocol: RNA was prepared using the Qiagen RNAeasy micro plus columns

treatment_protocol: No treatments.  Cells were harvested directly from mice by flow cytometry

tag: developmental stage

value: Adult

tag: genotype

value: wildtype

value: HSC


title: SK-1C LC128 Tregs B

city: London

first: Shahram

last: Kordasti

state: London

address: Rayne Institute, 123 Coldharbour Lane

country: United Kingdom

institute: King's College London

description: RMA expression value derived from Expression Console software; core-exon analysis

hyb_protocol: Biotinylated cDNA was applied and hybridised to Human Gene 2.0 ST arrays (Affymetrix) following NuGEN's guidelines.

scan_protocol: Arrays were processed using the Hybridisation Wash Stain kit and scanned following manufacturer's guidelines (Affymetrix).

data_processing: CEL files were processed in Expression Console to generate normalised, summarised and background-corrected data (CHP files), and further analysed for differential gene expression using gene set enrichment analysis (GSEA) as described before.

source_name: Healthy donor 128

label_protocol: Total RNA (8ng) was amplified and biotin labelled using the Ovation Pico WTA V2 and Encore Biotin Module kits (NuGEN).

growth_protocol: PBMCs from healthy donors were isolated by gradient media and further sorted based on CD4,CD25,CD127,CCR4,CD45RO and CD95 expression

extract_protocol: RNA was purified from Trizol lysates following manufacturer's protocols (Invitrogen), followed by RNeasy MinElute cleanup (Qiagen).

value: healthy donor peripheral blood

tag: sub-population

value: Tregs B


title: SK-1A LC128 Tcon

value: T conventional


title: Oryza sativa OsNPR1 overexpression,biological replicate 1

city: Shanghai

first: Zuhua

last: He

state: Shanghai

address: 300 Fenglin Road

department: shanghai institute of plant physiology and ecology

institute: Chinese Academy of Science

description: Gene expression data from the uppermost internodes in rice at heading stage

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: The data were analyzed with Affymetrix GeneChip® Operating Software (GCOS, Version 1.4) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label: Biotin

organism: Oryza sativa

source_name: G316,the uppermost two internodes

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol with GeneChip IVT Labeling Kit and Genechip Sample Cleanup Module (Affymetrix)

growth_protocol: the rice plants grow  in the paddy filed for about 100 days.

extract_protocol: Total RNA was extracted from the two uppermost internodes using the Trizol method (Invitrogen) and purified with RNeasy MiniKit (Qiagen). cDNA was synthesized and purified with one-cycle cDNA Synthesis Kit (Affymetrix) and GeneChip Sample Cleanup Module (Affymetrix), respectively.

treatment_protocol: no treatment

value: the uppermost internodes at heading stage


title: Oryza sativa OsNPR1 overexpression,biological replicate 2


title: Oryza sativa Taipei 309,biological replicate 3

source_name: Taipei309,the uppermost two internodes


title: siAF control of Knockdown 3

source_name: siAF control of Knockdown 3


title: Oryza sativa OsNPR1 overexpression,biological replicate 3


title: umbilical cord tissue-3

city: Seoul

first: Seong-Oh

last: Kim

address: 250 Seongsanno, Seodaemun-gu

department: Pediatric dentistry

country: South Korea

institute: Yonsei University College of Dentistry

hyb_protocol: Following fragmentation, fragmented cDNA were hybridized for 16 hr at 45C on Affymetrix GeneChip® Human Gene 1.0 ST Array. The GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The Robust Multiarray Average (RMA) algorithm implemented in Affymetrix Expression Console software (version1.3.1) was used to normalize the raw data. Highly expressed genes that showed over 2-fold difference between the signal values of control and test samples were selected for further study.

source_name: umbilical cord tissue

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 300  ng total RNA (GeneChip® WT Terminal Labeling and Controls Kit P/N 901525 1, Affymetrix).

growth_protocol: Umbilical cord tissues were obtained from three newborns.

extract_protocol: Umbilical cord tissues were homogenized using a homogenizer. And total RNA was extracted from umbilical cord tissues using the RNeasy Fibrous Mini kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Umbilical cord tissues were sliced at a thickness of 10-14 um using cryostat. And then the umbilical cord immediately submerged in a buffer RLT, the component of the RNeasy Fibrous Mini kit.

value: umbilical cord tissue


title: Oryza sativa Taipei 309,biological replicate 1


title: untreated control of Overexpression 2

source_name: untreated control of Overexpression 2

value: lzrs-GFP plasmid transduced


title: WT splenic red pulp macrophage

source_name: Splenic red pulp macrophages isolated from 5 WT mice

value: WT

value: spleen


title: Oryza sativa Taipei 309,biological replicate 2

source_name: Taipei309,the uppermos twot internodes


title: umbilical cord tissue-2


title: umbilical cord tissue-1


title: SK-2A LC133 Tcon

source_name: Healthy donor 133


title: Adult tooth pulp tissue-3

source_name: adult tooth pulp

growth_protocol: The PDL samples were obtained from healthy persons (n=10;from 2 males and 3 females, aged 11-19 years) and the pulp samples were obtained from healthy matured permanent premolar extracted for orthodontic reasons from healthy persons (n=24; from 6 males and 6 females, aged 18-25 years).

extract_protocol: The PDL and the pulp tissues were homogenized using a homogenizer. The Rneasy Fibrous mini kit(Qiagen) was then used to extract total RNA from the PDL and pulp tissues, according to the manufacturer's instructions

treatment_protocol: Extracted teeth were immediately frozen and stored in liguid nitrogen. The PDL tissues were obtained carefully using sterile curetes from the middle-third. Teeth were subsequently crushed with a bolt cutter and pulp tissues were carefully obtained using a sterile tweezers.

value: adult tooth pulp


title: Gene expression MV4-11R cell line rep2

city: Heidelberg

first: Christian

last: Rohde

address: Im Neuenheimer Feld 410

institute: Heidelberg University

hyb_protocol: Arrays were hybridized and washed according to the manufacturer's specifications (Affymetrix Inc., Santa Clara, CA, USA)

scan_protocol: The arrays were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Expression data was normalized, background corrected and summarized using the RMA algorithm implemented in the Affymetrix Expression Console software Build 1.3.1.187.

label_protocol: The samples were labeled according to the Affymetrix GeneChip WT Terminal Labeling protocol (Affymetrix UK Ltd., High Wycombe, UK).

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (QIAgen Hilden). RNA quality was approved using the Agilent RNA 6000 Nano Kit (Agilent Technologies).

tag: cell line

value: Acute Myeloid Leukemia (AML) cell line

tag: drug resistance

value: yes

tag: ezh2 expression

value: low


title: Cx43/45 flox EB 1

city: Würzburg

first: Philipp

last: Wörsdörfer

state: Bavaria

address: Koellikerstr. 6

department: Institute of Anatomy and Cell Biology

institute: University of Würzburg

description: Replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: embryoid bodies (approx. 300 single EBs, pooled)

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

growth_protocol: Embryonic stem cells were cultured in ES cell culture medium (DMEM, 15% FCS, 1mM sodium pyruvate, 2mM L-glutamine, 1% non-essential amino acids, 0.1 mM 2-mercaptoethanol and 1000 U/ml mouse Leukemia inhibitory factor (mLIF)) on a MEF feeder layer. Hanging drop cultures were prepared with 2000 cells per drop in embryoid body (EB) differentiation medium (DMEM, 15% FCS, 1mM sodium pyruvate, 2mM L-glutamine, 1% non-essential amino acids, 0.1 mM 2-mercaptoethanol). Drops were hung on the lid of PBS containing petri dishes (day 0). After 2 days EBs were transferred into 10 cm bacteriological petri dishes and cultured in 10 ml EB differentiation medium. Medium was changed every other day. EBs were harvested at day6.

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: ES cells were trypsinized to obtain a single cell solution. Cells were pelleted using centrifugation. Cell pellet was washed in PBS and frozen at -80°C. EBs were collected, washed with PBS and pelleted by centrifugation. Samples were frozen at -80°C.

tag: es cell line

value: male, mus musculus, C57BL/6

tag: tisuse

value: embryoid body


title: Cx43/45 flox EB 3

description: Replicate 3


title: Adult tooth pulp tissue-1


title: Cx43/45 del ESC 1

description: Replicate 1

source_name: embryonic stem cells (cell pellet, 1 well of a 6-well plate)

value: male, mus musculus, C57BL/6, lacZ under control of Cx43 promotor, eGFP under control of Cx45 promotor, Cx43 Exon3 deleted, Cx45 Exon3 deleted

value: embryonic stem cell


title: Gene expression MV4-11R cell line rep1


title: Gene expression MV4-11 cell line rep1

value: no

value: high


title: Cx43/45 del EB 3

description: Replicate 3


title: Gene expression MV4-11 cell line rep2


title: Cx43/45 del EB 1

description: Replicate 1


title: Cx43/45 del EB 4

description: Replicate 4


title: Adult tooth PDL tissue-3

source_name: adult tooth PDL

value: adult tooth PDL


title: Cx43/45 flox ESC 1

description: Replicate 1


title: Cx43/45 del ESC 2

description: Replicate 2


title: Cx43/45 del EB 2

description: Replicate 2


title: Cx43/45 flox EB 2

description: Replicate 2


title: Adult tooth pulp tissue-2


title: Lung C57Bl/6 IFNa4 treated rep4

first: Stefania

last: Crotta

address: The Ridgeway

department: IR

institute: The Crick- Mill Hill Laboratories

description:
Gene expression data from lung cells
Sample14

hyb_protocol: 1.5µg of sample hybridised using standard illumina Protocol (55ºC High Stringency wash 100%EtOHFix Illumina BlockBuffer Block Cy3Streptavidin Staining)

scan_protocol: Scanner : Illumina iScan. DataAcquisition software:Illumina iScan Control Software-V3. Intensity .idat files for use in downstream analysis software Genome Studio

data_processing: The data were normalised using 75th percentile normalisation in GeneSpring 11.5. Non-normalised values have only had background subtraction.

source_name: Lung C57Bl/6 IFNa4 treated rep4

label_protocol: Ambion Illumina Total Prep 96RNAAmplification Kit

extract_protocol: Lung samples were homogenized in 10 volumes of TRI Reagent and then processed using the RiboPure kit (Ambion) according to manufacturer's instructions

treatment_protocol: IFNa4, IFNl2 or Vehcile Control treated lungs from C57BL/6 mice taken at 18hr post treatment (intranasal). Whole lungs collected and processed for expression profiling

value: lung


title: Lung C57Bl/6 IFNl2 treated rep4

description:
Gene expression data from lung cells
Sample9

source_name: Lung C57Bl/6 IFNl2 treated rep4


title: Lung C57Bl/6 IFNa4 treated rep2

description:
Gene expression data from lung cells
Sample12

source_name: Lung C57Bl/6 IFNa4 treated rep2


title: Lung C57Bl/6 IFNl2 treated rep5

description:
Gene expression data from lung cells
Sample10

source_name: Lung C57Bl/6 IFNl2 treated rep5


title: Lung C57Bl/6 IFNa4 treated rep3

description:
Gene expression data from lung cells
Sample13

source_name: Lung C57Bl/6 IFNa4 treated rep3


title: Lung C57Bl/6 IFNa4 treated rep1

description:
Gene expression data from lung cells
Sample11

source_name: Lung C57Bl/6 IFNa4 treated rep1


title: Cx43/45 flox ESC 2

description: Replicate 2


title: Lung C57Bl/6 IFNl2 treated rep3

description:
Gene expression data from lung cells
Sample8

source_name: Lung C57Bl/6 IFNl2 treated rep3


title: Lung C57Bl/6 Vehicle Control treated rep4

description:
Gene expression data from lung cells
Sample4


title: Lung C57Bl/6 IFNl2 treated rep2

description:
Gene expression data from lung cells
Sample7

source_name: Lung C57Bl/6 IFNl2 treated rep2


title: Lung C57Bl/6 IFNl2 treated rep1

description:
Gene expression data from lung cells
Sample6

source_name: Lung C57Bl/6 IFNl2 treated rep1


title: Lung C57Bl/6 IFNa4 treated rep5

description:
Gene expression data from lung cells
Sample15

source_name: Lung C57Bl/6 IFNa4 treated rep5


title: Lung C57Bl/6 Vehicle Control treated rep2

description:
Gene expression data from lung cells
Sample2


title: Lung C57Bl/6 Vehicle Control treated rep3

description:
Gene expression data from lung cells
Sample3


title: mouse_colon tumor_single gene KO_rep2

city: Hiroshima City

first: MASASHI

last: MIGUCHI

state: Please Select

address: 3-2-1 Kasumi Minami-Ku

country: Japan

institute: Hiroshima University

description: APC DD #390_130125_(MoGene-1_0-st-v1)

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip mouse ST Array. GeneChips were washed and stained in the hybridization cocktail mix.

scan_protocol: The arrays were scanned using a GeneArray scanner (Affymetrix), and gene expression data were analyzed using GeneSpring GX software ver. 11 (Agilent Technology, Santa Clara, CA, USA).

data_processing: The robust multichip analysis (RMA) algorithm was used for normalization to remove artifactual differences between arrays, and cut-off values were set at less than 20% to eliminate poorly reproducible entities between chips.

source_name: Tumors in CDX2P-G19Cre;Apcflox/flox mice at 3 weeks of age

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5.5 ug single-stranded cDNA (UserGuide GeneChip WT PLUS Reagent Kit, Affymetrix).

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

value: APC DD

value: colon tumor


title: mouse_colon tumor_double gene KO_rep3

description: APC-TGFbeta2R DD #65_130125_(MoGene-1_0-st-v1)

source_name: Tumors in CDX2P-G19Cre;Apcflox/flox;Tgfbr2flox/flox mice at 3 weeks of age

value: APC-TGFbeta2R DD


title: mouse_colon tumor_single gene KO_rep3

description: APC DD #13_130125_(MoGene-1_0-st-v1)


title: mouse_colon tumor_double gene KO_rep1

description: APC-TGFbeta2R DD #3995_130125_(MoGene-1_0-st-v1)


title: mouse_colon tumor_single gene KO_rep1

description: APC DD #3776_130125_(MoGene-1_0-st-v1)


title: mouse_colon tumor_double gene KO_rep2

description: APC-TGFbeta2R DD #391_130125_(MoGene-1_0-st-v1)


title: Ctrl_EC + E2 replicate 3

city: Boston

first: Gavin

middle: R.

last: Schnitzler

state: MA

address: 800 Washington St. Box 80

department: Molecular Cardiology Research Institute

institute: Tufts Medical Center

data_processing: The data were normalised using quantile normalisation using the lumiN command in the lumi package in R

source_name: Eahy926 cells stably transfected with empty vector

label_protocol: Total RNA samples hybridized to Illumina BeadChips are prepared using the Illumina TotalPrep RNA Amplification kit from Applied Biosystems/Ambion, catalog # AMIL1791 (library preparation & array hybridization was performed by the Yale Center for Genome Analysis).

growth_protocol: EAhy926 cells (a human umbilical vein endothelial cell hybrid, kind gift of C.J. Edgell, University of North Carolina at Chapel Hill), that do not express ERalpha, were transfected with pCMV3-ERalpha plasmid (ERa-EC cells) or control backbone vector pCDNA 3.1 (Invitrogen, Ctrl-EC cells) using PolyFect transfection reagent (Qiagen). After 24 hours the cells were placed in selective media with 5 microgram/ml puromycin (Sigma) for 2 to 3 weeks. Eight to ten single colonies were selected and maintained in the presence of 2 microgram/ml puromycin.  ERa expression was confirmed by western blot.

extract_protocol: Total RNA was purified with the RNeasy mini kit (Qiagen)

treatment_protocol: EAhy926 stable cells were grown in 6-well plates to 80% confluence, switched to serum free medium for 24 hours, and then treated with 10 nM E2 or ethanol vehicle for 16 hours.

tag: transfectant

value: empty vector

value: 10nM E2


title: ERa_EC + E2 replicate 1

source_name: Eahy926 cells stably transfected with human ERalpha expression vector

value: ERalpha expression vector


title: ERa_EC + E2 replicate 2


title: Ctrl_EC + Veh replicate 2

value: ethanol vehicle


title: Ctrl_EC + Veh replicate 3


title: ERa_EC + Veh replicate 1

growth_protocol: EAhy926 cells (a human umbilical vein endothelial cell hybrid, kind gift of C.J. Edgell, University of North Carolina at Chapel Hill), that do not express ERalpha, were transfected with pCMV3-ERalpha plasmid (ERa-EC cells) or control backbone vector pCDNA 3.1 (Invitrogen, Ctrl-EC cells) using PolyFect transfection reagent (Qiagen). After 24 hours the cells were placed in selective media with 5 microgramg/ml puromycin (Sigma) for 2 to 3 weeks. Eight to ten single colonies were selected and maintained in the presence of 2 microgram/ml puromycin.  ERa expression was confirmed by western blot.


title: ERa_EC + Veh replicate 3


title: Ctrl_EC + E2 replicate 2


title: Arabidopsis Col-0, treatment with BrvC, 48 h, biological rep1

city: Olomouc

first: Ondrej

last: Plihal

address: Slechtitelu 27

country: Czech Republic

institute: CRH, Palacky University

description: Gene expression data from brevicompanine-treated Arabidopsis leaves

hyb_protocol: Biotin-tagged cDNA was subsequently used for hybridization with the Arabidopsis Gene 1.0 ST Array (Affymetrix, Inc., Santa Clara, CA). GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned on the Affymetrix GC Scanner 3000 7G.

data_processing: The data were analyzed with R/Bioconductor oligo package with default settings and RMA normalization method. All statistical analyses were performed by methods in limma package, moderated t-test and Benjamini-Hochberg correction were applied.

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana Col-0 leaves

label_protocol: Double-stranded cDNA was prepared and amplified using the WT expression kit (Ambion, Life Technologies Ltd, UK). The resulting cDNA was then fragmented by the combined action of uracil DNA glycosylase and apurinic/apyrimidinic endonuclease 1 with the WT terminal labeling kit (Affymetrix, Inc., Santa Clara, CA) to yield biotin-tagged cDNA.

growth_protocol: The plants were grown in soil for 4 weeks in growth chamber at a day/night cycle of 16/8 h at 21/19 °C, respectively, after which leaves of similar size and chlorophyll content were cut and immediately treated with BrvC.

extract_protocol: Total RNA was isolated from Arabidopsis leaves using the RNAqueous total RNA isolation kit (Ambion, Life Technologies Ltd, UK) according to the manufacturer's recommendations. In addition, samples were treated with DNase I to remove contaminant genomic DNA.

treatment_protocol: 10-15 detached leaves were immersed in 1 x MS medium supplemented with 50 µM BrvC; this amount represented one sample. Three biological replicates were performed for each brevicompanine treatment and the control group. Control samples were treated with 0.05% DMSO in MS medium. After incubation for 6 h or 48 h in the dark, detached leaves were frozen in liquid nitrogen and used for RNA isolation.

value: leaf

tag: ecotype


title: Arabidopsis Col-0, treatment with BrvC, 48 h, biological rep2


title: ERa_EC + Veh replicate 2


title: Arabidopsis Col-0, control treatment, biological rep3


title: Arabidopsis Col-0, treatment with BrvC, 6 h, biological rep3


title: ERa_EC + E2 replicate 3


title: Ctrl_EC + E2 replicate 1

growth_protocol: EAhy926 cells (a human umbilical vein endothelial cell hybrid, kind gift of C.J. Edgell, University of North Carolina at Chapel Hill), that do not express ERalpha, were transfected with pCMV3-ERalpha plasmid (ERa-EC cells) or control backbone vector pCDNA 3.1 (Invitrogen, Ctrl-EC cells) using PolyFect transfection reagent (Qiagen). After 24 hours the cells were placed in selective media with 5 microgram/ml puromycin (Sigma) for 2 to 3 weeks. Eight to ten single colonies were selected and maintained in the presence of 2  microgram/ml puromycin.  ERa expression was confirmed by western blot.


title: Arabidopsis Col-0, control treatment, biological rep1


title: Arabidopsis Col-0, control treatment, biological rep2


title: Arabidopsis Col-0, treatment with BrvC, 48 h, biological rep3


title: Ctrl_Ecs + Veh replicate 1


title: Lung C57Bl/6 Vehicle Control treated rep1

description:
Gene expression data from lung cells
Sample1


title: Arabidopsis Col-0, treatment with BrvC, 6 h, biological rep2


title: VenousPlasma_rep3

city: Beijing

first: Yuan

address: 38 Xueyuan Rd, Haidian District

department: Department of Biomedical Informatics and Department of Physiology and Pathophysiology, School of Basic Medical Sciences

institute: Peking University

description: MiRNA expression in venous plasma

hyb_protocol: The microarray hybridization was performed following the standard Agilent pipeline.

scan_protocol: Slides were scanned using Agilent Microarray Scanner.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze the acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies).

organism: Rattus norvegicus

source_name: Venous Plasma, replicate 3

label_protocol: High quality miRNAs were Cy3 labeled using miRNA Complete Labeling and Hyb Kit (Agilent, USA) according to the manufacturer's guidelines.

growth_protocol: Male 10-week-old SD rats (280-300 g) were provided by the Animal Department, Health Science Center, Peking University. All the animals were housed in standard cages in a temperature- and humidity-controlled environment, on a 12-h light/dark cycle, with free access to water. All animal care and experimental protocols complied with the Declaration of Helsinki, Animal Management Rules of the Ministry of Health of the People’s Republic of China and the guide for the Care and Use of the Laboratory Animals of Peking University. The protocol was approved by the Peking University Animal Ethics Committee.

extract_protocol: Total 3mL of arterial or venous blood was collected from abdominal aorta or postcava respectively. And then blood was transferred into an anti-coagulation tube (EDTA, prepared with DEPC water) containing RNAase inhibitor. Plasma was obtained by centrifugation at 1600 g for 10 min, and the supernatant was centrifuged at 16000 g for 5 min at 4℃. Then the plasma was filtered through a 0.22-μm filter (MILLEXGV; Millipore). RNA was extracted using the miRNeasy Serum/Plasma kit (Qiagen; Valencia, CA)

treatment_protocol: No specific treament was applied before the extraction of blood samples.

value: venous plasma

value: Sprague-Dawley

tag: gender

value: male

value: 10 weeks

tag: rat number


title: VenousPlasma_rep1

description: MiRNA expression in venous plasma

source_name: Venous Plasma, replicate 1

tag: tissue


title: ArterialPlasma_rep3

description: MiRNA expression in arterial plasma

source_name: Arterial Plasma, replicate 3

value: arterial plasma


title: ArterialPlasma_rep2

description: MiRNA expression in arterial plasma

source_name: Arterial Plasma, replicate 2


title: VenousPlasma_rep2

description: MiRNA expression in venous plasma

source_name: Venous Plasma, replicate 2


title: Arabidopsis Col-0, treatment with BrvC, 6 h, biological rep1


title: ArterialPlasma_rep1

description: MiRNA expression in arterial plasma

source_name: Arterial Plasma, replicate 1


title: CIC_HUS_301_78706

status: Public on Nov 21 2016

type: genomic

city: Salamanca

first: María

last: Abáigar

state: Salamanca

address: Campus Miguel de Unamuno

country: Spain

institute: Centro de Investigación del Cáncer

hyb_protocol: 20 µg of each labeled test and the corresponding sex-matched reference DNA were mixed and co-hybridized to the NimbleGen aCGH slide overnight at 42°C. After hybridization, slides were washed following the manufacturer's instructions (Roche NimbleGen) (http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf).

scan_protocol: Slides were scanned with a NimbleGen MS 200 Microarray Scanner (Roche NimbleGen), set at 532 nm and 635 nm, with a 2-µm resolution, to produce images in TIFF format according to the manufacturer's instructions (Roche NimbleGen) (http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf).

data_processing: Raw data were extracted from the scanned images and analyzed using the segMNT algorithm from NimbleScan software (version2.6; Roche NimbleGen) (http://www.nimblegen.com/downloads/support/NimbleScan_v2p6_UsersGuide.pdf). SignalMap (version1.9; Roche NimbleGen) was used for visual examination of the resulting data (http://www.nimblegen.com/products/lit/05434564001_NG_SignalMap_UGuide_v1p9p1.pdf).

molecule: genomic DNA

source_name: Genomic DNA reference sample

label_protocol: Test sample and it's corresponding reference sample are labeled in parallel. 500 ng of each genomic DNA test sample was labeled with Cy3 using a Cy3-random nonamer, whereas 500 ng of each genomic DNA reference sample was labeled with Cy5 using a Cy5-random nonamer, according to the manufacturer's instructions (Roche NimbleGen) (http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf <http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf>)

extract_protocol: Genomic DNA (gDNA) was isolated from methanol-acetic-acid stored bone marrow samples after cytogenetic analysis. The pellet cells from cytogenetics were washed twice with PBS 1x, and then isolated using the QIAamp DNA Mini Kit (Qiagen) according to the manufacturer’s standard protocol. gDNA concentration and quality were determined spectrophotometrically (ND-1000; NanoDrop Technologies) by calculating the 260/280 and A260/230 ratios. gDNA integrity was evaluated by electrophoresis on 1% agarose gels.

tag: reference source info

value: Human Genomic DNA:Male (Promega; Madison, WI, USA)

source_name: DNA of sample 301 with an hematological malignancy

value: bone marow

value: Male

tag: who 2008 classification

value: RARS


title: CIC_HUS_289_79994

value: Human Genomic DNA:Female (Promega; Madison, WI, USA)

source_name: DNA of sample 289 with an hematological malignancy

value: Female

tag: age

value: RCMD


title: siAF control of Knockdown 1

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Standard Infinium HD Methylation Assay protocol

data_processing: Data pre-processing of DNA methylation arrays was performed with BeadStudio Methylation Module. Differentially methylated CpGs were identified using the minfi package. Preprocessing included quality control, removal of low quality samples (cutoff of 10.5), and quantile normalization.

label: Cy3, Cy5

source_name: siAF control of Knockdown 1

extract_protocol: Total DNA was isolated by standard procedures

tag: treatment

value: ANRIL siRNA (si04378563; Qiagen) transfection

tag: cell type

value: Mesenchymal stromal cell


title: siAF control of Knockdown 3

source_name: siAF control of Knockdown 3


title: CIC_HUS_286_79442

source_name: DNA of sample 286 with an hematological malignancy

value: RCUD


title: CIC_HUS_296_81332

source_name: DNA of sample 296 with an hematological malignancy


title: CIC_HUS_297_80775

source_name: DNA of sample 297 with an hematological malignancy


title: CIC_HUS_290_80023

source_name: DNA of sample 290 with an hematological malignancy


title: CIC_HUS_298_76414

source_name: DNA of sample 298 with an hematological malignancy


title: CIC_HUS_293_82683

source_name: DNA of sample 293 with an hematological malignancy


title: CIC_HUS_288_79931

source_name: DNA of sample 288 with an hematological malignancy


title: untreated control of Overexpression 1

source_name: untreated control of Overexpression 1

value: lzrs-GFP plasmid transduced


title: CIC_HUS_292_81733

source_name: DNA of sample 292 with an hematological malignancy


title: siAF control of Knockdown 2

source_name: siAF control of Knockdown 2


title: CIC_HUS_287_79885

source_name: DNA of sample 287 with an hematological malignancy


title: CIC_HUS_294_80147

source_name: DNA of sample 294 with an hematological malignancy


title: CIC_HUS_299_78250

source_name: Genomic DNA reference sample

source_name: DNA of sample 299 with an hematological malignancy


title: CIC_HUS_295_81094

source_name: DNA of sample 295 with an hematological malignancy


title: HOTAIR knockdown 3

source_name: HOTAIR knockdown 3

value: HOTAIR siRNA (5'-GAACGGGAGUACAGAGAGA-3' transfection


title: HOTAIR knockdown 1

source_name: HOTAIR knockdown 1


title: CIC_HUS_300_77808

source_name: DNA of sample 300 with an hematological malignancy


title: CIC_HUS_291_80119

source_name: DNA of sample 291 with an hematological malignancy


title: Lung C57Bl/6 Vehicle Control treated rep5

description:
Gene expression data from lung cells
Sample5

tag: genotype

value: lung


title: HOTAIR knockdown 2

source_name: HOTAIR knockdown 2


title: HOTAIR overexpression 3

source_name: HOTAIR overexpression 3

value: lzrs-HOTAIR plasmid transduced


title: untreated control of Overexpression 2

source_name: untreated control of Overexpression 2


title: HOTAIR overexpression 2

source_name: HOTAIR overexpression 2


title: CIC_HUS_284_78813

source_name: DNA of sample 284 with an hematological malignancy


title: untreated control of Overexpression 3

source_name: untreated control of Overexpression 3


title: HOTAIR overexpression 1

source_name: HOTAIR overexpression 1


title: CIC_HUS_283_75742

source_name: DNA of sample 283 with an hematological malignancy


title: CIC_HUS_280_75412

source_name: DNA of sample 280 with an hematological malignancy


title: CIC_HUS_276_71623

source_name: DNA of sample 276 with an hematological malignancy


title: CIC_HUS_278_71575

source_name: Genomic DNA reference sample

source_name: DNA of sample 278 with an hematological malignancy


title: CIC_HUS_281_74272

source_name: DNA of sample 281 with an hematological malignancy


title: CIC_HUS_266_76898

source_name: DNA of sample 266 with an hematological malignancy


title: CIC_HUS_271_67438

source_name: DNA of sample 271 with an hematological malignancy


title: CIC_HUS_282_75669

source_name: DNA of sample 282 with an hematological malignancy


title: CIC_HUS_277_69055

source_name: DNA of sample 277 with an hematological malignancy


title: CIC_HUS_269_77773

source_name: DNA of sample 269 with an hematological malignancy


title: CIC_HUS_264_76971

source_name: DNA of sample 264 with an hematological malignancy


title: CIC_HUS_275_72397

source_name: DNA of sample 275 with an hematological malignancy


title: CIC_HUS_268_76474

source_name: DNA of sample 268 with an hematological malignancy


title: CIC_HUS_272_72373

source_name: DNA of sample 272 with an hematological malignancy


title: CIC_HUS_267_77708

source_name: DNA of sample 267 with an hematological malignancy


title: CIC_HUS_263_76477

source_name: DNA of sample 263 with an hematological malignancy


title: CIC_HUS_274_72542

source_name: DNA of sample 274 with an hematological malignancy


title: CIC_HUS_273_67120

source_name: DNA of sample 273 with an hematological malignancy


title: CIC_HUS_261_76228

source_name: DNA of sample 261 with an hematological malignancy


title: CIC_HUS_260_79164

source_name: Genomic DNA reference sample

source_name: DNA of sample 260 with an hematological malignancy


title: CIC_HUS_270_77765

source_name: DNA of sample 270 with an hematological malignancy


title: CIC_HUS_259_79860

source_name: DNA of sample 259 with an hematological malignancy


title: CIC_HUS_262_76587

source_name: DNA of sample 262 with an hematological malignancy


title: CIC_HUS_256_79737

source_name: DNA of sample 256 with an hematological malignancy


title: CIC_HUS_255_79901

source_name: DNA of sample 255 with an hematological malignancy


title: CIC_HUS_257_78823

source_name: DNA of sample 257 with an hematological malignancy


title: CIC_HUS_285_79205

source_name: DNA of sample 285 with an hematological malignancy


title: CIC_HUS_254_78820

source_name: DNA of sample 254 with an hematological malignancy


title: CIC_HUS_253_78832

source_name: DNA of sample 253 with an hematological malignancy


title: CIC_HUS_258_78790

source_name: DNA of sample 258 with an hematological malignancy


title: CIC_HUS_251_78126

source_name: DNA of sample 251 with an hematological malignancy


title: CIC_HUS_247_77129

source_name: DNA of sample 247 with an hematological malignancy


title: CIC_HUS_250_78623

source_name: DNA of sample 250 with an hematological malignancy


title: CIC_HUS_249_77455

source_name: DNA of sample 249 with an hematological malignancy


title: CIC_HUS_246_75743

source_name: DNA of sample 246 with an hematological malignancy


title: CIC_HUS_243_75963

source_name: Genomic DNA reference sample

source_name: DNA of sample 243 with an hematological malignancy

value: MDS-U


title: CIC_HUS_241_74956

source_name: DNA of sample 241 with an hematological malignancy


title: CIC_HUS_248_77340

source_name: DNA of sample 248 with an hematological malignancy


title: CIC_HUS_245_76454

source_name: DNA of sample 245 with an hematological malignancy


title: CIC_HUS_244_76157

source_name: DNA of sample 244 with an hematological malignancy


title: CIC_HUS_236_74757

source_name: DNA of sample 236 with an hematological malignancy


title: CIC_HUS_240_75350

source_name: DNA of sample 240 with an hematological malignancy


title: CIC_HUS_232_64195

source_name: DNA of sample 232 with an hematological malignancy


title: CIC_HUS_239_75701

source_name: DNA of sample 239 with an hematological malignancy


title: CIC_HUS_237_75599

source_name: DNA of sample 237 with an hematological malignancy


title: CIC_HUS_235_71015

source_name: DNA of sample 235 with an hematological malignancy


title: CIC_HUS_242_75019

source_name: DNA of sample 242 with an hematological malignancy


title: CIC_HUS_265_77080

source_name: DNA of sample 265 with an hematological malignancy


title: CIC_HUS_227_77776

source_name: DNA of sample 227 with an hematological malignancy


title: CIC_HUS_233_66869

source_name: DNA of sample 233 with an hematological malignancy

value: RARS-T


title: CIC_HUS_225_77317

source_name: DNA of sample 225 with an hematological malignancy


title: CIC_HUS_230_53392

source_name: Genomic DNA reference sample

source_name: DNA of sample 230 with an hematological malignancy


title: CIC_HUS_229_53179

source_name: DNA of sample 229 with an hematological malignancy


title: CIC_HUS_221_75409

source_name: DNA of sample 221 with an hematological malignancy


title: CIC_HUS_228_79181

source_name: DNA of sample 228 with an hematological malignancy


title: CIC_HUS_231_53689

source_name: DNA of sample 231 with an hematological malignancy


title: CIC_HUS_220_75273

source_name: DNA of sample 220 with an hematological malignancy


title: CIC_HUS_224_80367

source_name: DNA of sample 224 with an hematological malignancy

value: MDS del(5q)


title: CIC_HUS_238_75457

value: Human Genomic DNA:Male (Promega; Madison, WI, USA)

source_name: DNA of sample 238 with an hematological malignancy


title: CIC_HUS_226_71799

source_name: DNA of sample 226 with an hematological malignancy

value: bone marow


title: CIC_HUS_222_80025

source_name: DNA of sample 222 with an hematological malignancy

value: Male


title: CIC_HUS_234_69458

source_name: DNA of sample 234 with an hematological malignancy


title: CIC_HUS_223_80055

source_name: DNA of sample 223 with an hematological malignancy


title: CIC_HUS_217_79895

source_name: DNA of sample 217 with an hematological malignancy


title: CIC_HUS_219_74971

source_name: DNA of sample 219 with an hematological malignancy


title: CIC_HUS_218_75589

source_name: DNA of sample 218 with an hematological malignancy


title: CIC_HUS_214_76936

source_name: DNA of sample 214 with an hematological malignancy


title: CIC_HUS_215_78912

source_name: Genomic DNA reference sample

source_name: DNA of sample 215 with an hematological malignancy


title: CIC_HUS_279_69575

source_name: DNA of sample 279 with an hematological malignancy

value: RARS


title: CIC_HUS_252_78860

source_name: DNA of sample 252 with an hematological malignancy


title: CIC_HUS_209_76518

source_name: DNA of sample 209 with an hematological malignancy


title: CIC_HUS_201_54110

source_name: DNA of sample 201 with an hematological malignancy


title: CIC_HUS_211_77305

source_name: DNA of sample 211 with an hematological malignancy


title: CIC_HUS_200_61857

source_name: DNA of sample 200 with an hematological malignancy


title: CIC_HUS_202_61948

source_name: DNA of sample 202 with an hematological malignancy


title: CIC_HUS_216_79227

source_name: DNA of sample 216 with an hematological malignancy


title: L. Garvieae 8831, 13C rep2

city: Madrid

first: Mónica

last: Aguado-Urda

address: Avda. Puerta de Hierro s/n

department: Animal Health

institute: Complutense University of Madrid

description: Biological replicate 2 of 3. L. Garvieae str.8831 grown at 13 degrees celsius

hyb_protocol: Hybridization protocol followed was that suggested by Agilent´s according to the Two-color microarray-based prokaryote analysis protocol

scan_protocol: Image acquisition and scanning was done following Agilent's instruction and protocols (GE2_107_Sep09) on an Agilent G2565AA scanner.

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS Normalization was done using BRB Array Express software

organism: Lactococcus garvieae 8831

source_name: L. Garvieae 8831, 13C

label_protocol: A total of 5 ug of total RNA of each sample replicate was reverse transcripted and labeled by using the FairPlay III labeling kit (Agilent ) and according to the two color microarray-based prokaryote analysis protocol provided by the manufacturer except for the following: purification of the dye-coupled cDNA was performed by using QIAquick PCR purification kit (Qiagen). The yield and the specific activity of each labelling reaction were determined in a NanoDrop 1000 spectrophotometer.

growth_protocol: L. garvieae strains 8831 and 2881 were grown aerobically in MRS broth at 13 ºC and 29 ºC and harvested at the mid-log phase (OD600 ~ 0.9) for RNA extraction.

extract_protocol: Total RNA from L. garvieae strains 8831 and 21881 was isolated from three independent biological replicates by using RNeasy protect bacteria mini kit (Qiagen) according to the manufacturer’s protocol. The quality and concentration of RNA was determined by using the RNA 6000 NanoKit on the Bioanalyzer 2100 (Agilent). Only high- quality RNA samples (RIN > 9) were used for labeling and hybridization.

tag: temperature

value: 13 degrees Celsius

organism:
Lactococcus garvieae 8831
Lactococcus garvieae 21881

source_name: Reference control

tag: reference

value: Equimolar mixture of 21881 & 8831 strains at 29C


title: CIC_HUS_203_64267

source_name: DNA of sample 203 with an hematological malignancy


title: CIC_HUS_205_76826

value: Human Genomic DNA:Female (Promega; Madison, WI, USA)

source_name: DNA of sample 205 with an hematological malignancy

value: Female


title: CIC_HUS_206_79434

source_name: DNA of sample 206 with an hematological malignancy

value: RCMD


title: CIC_HUS_199_55566

source_name: DNA of sample 199 with an hematological malignancy


title: CIC_HUS_207_77015

source_name: DNA of sample 207 with an hematological malignancy


title: CIC_HUS_193_65403

source_name: Genomic DNA reference sample

source_name: DNA of sample 193 with an hematological malignancy


title: L. Garvieae 8831, 13C rep3

description: Biological replicate 3 of 3. L. Garvieae str.8831 grown at 13 degrees celsius


title: CIC_HUS_212_76301

source_name: DNA of sample 212 with an hematological malignancy


title: CIC_HUS_195_71831

source_name: DNA of sample 195 with an hematological malignancy


title: CIC_HUS_196_67048

source_name: DNA of sample 196 with an hematological malignancy


title: CIC_HUS_197_69137

source_name: DNA of sample 197 with an hematological malignancy


title: CIC_HUS_192_74088

source_name: DNA of sample 192 with an hematological malignancy


title: CIC_HUS_213_76806

source_name: DNA of sample 213 with an hematological malignancy


title: CIC_HUS_204_56847

source_name: DNA of sample 204 with an hematological malignancy


title: CIC_HUS_198_62420

source_name: DNA of sample 198 with an hematological malignancy


title: CIC_HUS_208_76200

source_name: DNA of sample 208 with an hematological malignancy


title: HEK293T_siTCERG1_exp4

city: Granada

first: Carles

last: Suñé Negre

address: Avenida del conocimiento S/N

department: Molecular Biology

institute: Instituto Parasitología y Biomedicina López-Neyra

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials according to manufacturer's indications. Fluidics Station 450

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using EASANA from GenoSplice technology. GC background correction were applied to probe intensities (core), gene level expression were summarized from the corrected intensities and then quantile normalized. The exon-level normalized data are available in the sample tables. Gene-level normalized data are available on the series record.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: HEK293T cells HEK293T cells were grown in Dulbecco’s modified Eagle’s medium (Sigma) supplemented with 10% fetal bovine serum (Invitrogen), L-glutamine at 4 mM (Invitrogen), and penicillin/streptomycin to 100 units and 100  g per ml, respectively (Invitrogen).

extract_protocol: Total RNA from four independent experiments was isolated from HEK293T cells with TRIzol (Invitrogen) and then purified with RNeasy columns (QIAGEN). Total RNA was then sended to CABIMER's for quality analysis and subsequent labeling, hybridization and scanning

treatment_protocol: HEK293T cells were grown to approximately 50% confluence and transfected using Lipofectamine 2000 reagent (Invitrogen) according to the manufacturer’s protocols with 60 nM (final concentration) of either one of the following siRNA duplexes: siEGFP, 5’-CUACAACAGCCACAACGE-3’ or siTCERG1, 5’-GGAGUUGCACAAGAUAGUU-3’ {Pearson, 2008 #921}. The cells were harvested 72 h after transfection.

tag: cell line


title: CIC_HUS_194_73512

source_name: DNA of sample 194 with an hematological malignancy


title: CIC_HUS_191_70606

source_name: DNA of sample 191 with an hematological malignancy


title: HEK293T_siTCERG1_exp2


title: CIC_HUS_188_54384

source_name: DNA of sample 188 with an hematological malignancy


title: CIC_HUS_187_66240

source_name: DNA of sample 187 with an hematological malignancy


title: CIC_HUS_185_67752

source_name: DNA of sample 185 with an hematological malignancy


title: CIC_HUS_190_60096

source_name: DNA of sample 190 with an hematological malignancy


title: HEK293T_siTCERG1_exp3


title: CIC_HUS_189_45867

source_name: Genomic DNA reference sample

source_name: DNA of sample 189 with an hematological malignancy


title: CIC_HUS_175_44979

source_name: DNA of sample 175 with an hematological malignancy


title: CIC_HUS_176_44221

source_name: DNA of sample 176 with an hematological malignancy


title: CIC_HUS_172_69948

source_name: DNA of sample 172 with an hematological malignancy


title: L. Garvieae 8831, 13C rep1

description: Biological replicate 1 of 3. L. Garvieae str.8831 grown at 13 degrees celsius

source_name: L. Garvieae 8831, 13C

source_name: Reference control


title: CIC_HUS_183_46103

source_name: DNA of sample 183 with an hematological malignancy


title: CIC_HUS_210_77927

source_name: DNA of sample 210 with an hematological malignancy


title: CIC_HUS_171_69630

source_name: DNA of sample 171 with an hematological malignancy


title: HEK293T_siEGFP_exp2


title: CIC_HUS_177_45900

source_name: DNA of sample 177 with an hematological malignancy


title: HEK293T_siEGFP_exp3


title: CIC_HUS_180_44252

source_name: DNA of sample 180 with an hematological malignancy


title: CIC_HUS_181_46294

source_name: DNA of sample 181 with an hematological malignancy


title: CIC_HUS_173_47095

source_name: DNA of sample 173 with an hematological malignancy


title: CIC_HUS_170_69382

source_name: DNA of sample 170 with an hematological malignancy


title: HEK293T_siEGFP_exp1


title: CIC_HUS_182_45888

source_name: DNA of sample 182 with an hematological malignancy


title: CIC_HUS_174_46240

source_name: DNA of sample 174 with an hematological malignancy


title: CIC_HUS_184_45282

source_name: Genomic DNA reference sample

source_name: DNA of sample 184 with an hematological malignancy


title: CIC_HUS_179_44524

source_name: DNA of sample 179 with an hematological malignancy


title: CIC_HUS_178_46135

source_name: DNA of sample 178 with an hematological malignancy


title: non-cancerous, FFPE, Patient 6, renal biopsy

type: SRA

city: Bergen

last: Strauss

address: Haukeland Universitetssykehus Laboratoriebygget, 7. etg. Heis øst

country: Norway

institute: University of Bergen

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version 1.8.2
Assembly of reads and alignment of the contigs to the Human genome assembly GRCh38 was guided by Tophat and Bowtie
logcpm (counts per million) were calculated using EdgeR (R bioconductor)
features with logcpm>=15 in at least 8 samples were considered further
Genome_build: GRCh38 (hg19)
Supplementary_files_format_and_content: Eikrem_counts.txt, Eikrem_logcpm_filtered.txt
Genome_build: GRCh38 (hg19)
Supplementary_files_format_and_content: Eikrem_counts.txt was generated by assembling the raw count data into a single matrix using Cufflinks
Supplementary_files_format_and_content: Eikrem_logcpm_filtered.txt was generated by keeping the count data features with logcpm>=15 in at least 8 samples

molecule: polyA RNA

source_name: renal biopsy

extract_protocol:
Total RNA was extracted with miRNeasy FFPE kit (Qiagen, Germany).
Sequencing libraries were generated using TruSeq RNA Access library kit (Illumina, Inc., San Diego, CA, USA) according to the manufacturer`s protocol.

value: kidney

tag: individual

value: patient 65

tag: disease state

value: non-cancerous

tag: storage

value: FFPE


title: CIC_HUS_186_67404

source_name: DNA of sample 186 with an hematological malignancy


title: cancerous, FFPE, Patient 65, renal biopsy

value: ccRCC (clear cell renal cell carcinoma)


title: cancerous, FFPE, Patient 64, renal biopsy

value: patient 64


title: HEK293T_siTCERG1_exp1


title: non-cancerous, FFPE, Patient 64, renal biopsy


title: CIC_HUS_167_48676

source_name: DNA of sample 167 with an hematological malignancy


title: CIC_HUS_164_48463

source_name: DNA of sample 164 with an hematological malignancy


title: CIC_HUS_166_73600

source_name: DNA of sample 166 with an hematological malignancy


title: cancerous, FFPE, Patient 63b, renal biopsy

value: patient 63b


title: CIC_HUS_168_47614

source_name: DNA of sample 168 with an hematological malignancy

value: MDS-U


title: non-cancerous, FFPE, Patient 63b, renal biopsy


title: CIC_HUS_169_49801

source_name: DNA of sample 169 with an hematological malignancy

value: MDS del(5q)


title: non-cancerous, FFPE, Patient 63a, renal biopsy

value: patient 63a


title: CIC_HUS_165_48225

source_name: DNA of sample 165 with an hematological malignancy

value: bone marow


title: cancerous, FFPE, Patient 59, renal biopsy

value: patient 59


title: cancerous, FFPE, Patient 63a, renal biopsy


title: non-cancerous, FFPE, Patient 59, renal biopsy


title: cancerous, FFPE, Patient 57, renal biopsy

value: patient 57


title: CIC_HUS_163_48502

source_name: DNA of sample 163 with an hematological malignancy


title: non-cancerous, FFPE, Patient 57, renal biopsy


title: CIC_HUS_153_52223

value: Human Genomic DNA:Male (Promega; Madison, WI, USA)

source_name: DNA of sample 153 with an hematological malignancy

value: Male


title: CIC_HUS_155_63275

source_name: DNA of sample 155 with an hematological malignancy


title: CIC_HUS_160_40324

source_name: DNA of sample 160 with an hematological malignancy


title: cancerous, FFPE, Patient 55, renal biopsy

value: patient 55


title: CIC_HUS_158_73022

value: Human Genomic DNA:Female (Promega; Madison, WI, USA)

source_name: DNA of sample 158 with an hematological malignancy

value: Female

value: RCMD


title: CIC_HUS_156_60361

source_name: Genomic DNA reference sample

source_name: DNA of sample 156 with an hematological malignancy


title: non-cancerous, FFPE, Patient 55, renal biopsy

value: kidney

value: non-cancerous


title: CIC_HUS_159_72365

source_name: DNA of sample 159 with an hematological malignancy


title: CIC_HUS_157_66535

source_name: DNA of sample 157 with an hematological malignancy


title: CIC_HUS_154_61104

source_name: DNA of sample 154 with an hematological malignancy


title: CIC_HUS_151_60820

source_name: DNA of sample 151 with an hematological malignancy

value: RARS-T


title: CIC_HUS_152_61172

source_name: DNA of sample 152 with an hematological malignancy


title: CIC_HUS_148_71728

source_name: DNA of sample 148 with an hematological malignancy


title: CIC_HUS_150_59457001

source_name: DNA of sample 150 with an hematological malignancy


title: CIC_HUS_149_65819

source_name: DNA of sample 149 with an hematological malignancy


title: CIC_HUS_147_62140

source_name: DNA of sample 147 with an hematological malignancy


title: CIC_HUS_142_69737

source_name: DNA of sample 142 with an hematological malignancy


title: CIC_HUS_145_67299

source_name: DNA of sample 145 with an hematological malignancy


title: CIC_HUS_146_61070

source_name: DNA of sample 146 with an hematological malignancy


title: CIC_HUS_144_60342

source_name: DNA of sample 144 with an hematological malignancy


title: cancerous, FFPE, Patient 53, renal biopsy

source_name: renal biopsy

value: patient 53

value: ccRCC (clear cell renal cell carcinoma)

value: FFPE


title: cancerous, FFPE, Patient 50, renal biopsy

value: patient 50


title: CIC_HUS_162_73635

source_name: DNA of sample 162 with an hematological malignancy


title: CIC_HUS_140_71033

source_name: Genomic DNA reference sample

source_name: DNA of sample 140 with an hematological malignancy


title: non-cancerous, FFPE, Patient 50, renal biopsy


title: CIC_HUS_141_71195

source_name: DNA of sample 141 with an hematological malignancy

value: RCUD


title: cancerous, FFPE, Patient 46, renal biopsy

value: patient 46


title: CIC_HUS_139_70949

source_name: DNA of sample 139 with an hematological malignancy

value: bone marow


title: CIC_HUS_138_70576

source_name: DNA of sample 138 with an hematological malignancy


title: non-cancerous, FFPE, Patient 53, renal biopsy


title: non-cancerous, FFPE, Patient 46, renal biopsy


title: CIC_HUS_137_67708

source_name: DNA of sample 137 with an hematological malignancy


title: cancerous, FFPE, Patient 39, renal biopsy

value: patient 39


title: non-cancerous, FFPE, Patient 39, renal biopsy


title: CIC_HUS_136_67572

value: Human Genomic DNA:Male (Promega; Madison, WI, USA)

source_name: DNA of sample 136 with an hematological malignancy


title: CIC_HUS_134_71521

source_name: DNA of sample 134 with an hematological malignancy


title: CIC_HUS_161_72297

source_name: DNA of sample 161 with an hematological malignancy

value: Male


title: CIC_HUS_132_73861

source_name: DNA of sample 132 with an hematological malignancy


title: CIC_HUS_135_67091

source_name: DNA of sample 135 with an hematological malignancy


title: CIC_HUS_133_74014

source_name: DNA of sample 133 with an hematological malignancy


title: non-cancerous, FFPE, Patient 44, renal biopsy

value: patient 44


title: CIC_HUS_129_71829

source_name: DNA of sample 129 with an hematological malignancy


title: CIC_HUS_128_72926

source_name: DNA of sample 128 with an hematological malignancy


title: cancerous, FFPE, Patient 44, renal biopsy


title: CIC_HUS_127_71875

value: Human Genomic DNA:Female (Promega; Madison, WI, USA)

source_name: DNA of sample 127 with an hematological malignancy


title: CIC_HUS_130_72149

source_name: DNA of sample 130 with an hematological malignancy

value: Female


title: CIC_HUS_126_69918

source_name: DNA of sample 126 with an hematological malignancy

value: RCMD


title: CIC_HUS_131_72755

source_name: Genomic DNA reference sample

source_name: DNA of sample 131 with an hematological malignancy


title: CIC_HUS_125_69369

source_name: DNA of sample 125 with an hematological malignancy


title: HEK293T_siEGFP_exp4


title: CIC_HUS_124_70955

source_name: DNA of sample 124 with an hematological malignancy


title: CIC_HUS_123_70875

source_name: DNA of sample 123 with an hematological malignancy


title: CIC_HUS_119_69998

source_name: DNA of sample 119 with an hematological malignancy


title: CIC_HUS_120_71375

source_name: DNA of sample 120 with an hematological malignancy


title: CIC_HUS_117_67782

source_name: DNA of sample 117 with an hematological malignancy


title: CIC_HUS_122_67847

source_name: DNA of sample 122 with an hematological malignancy


title: CIC_HUS_121_73019

source_name: DNA of sample 121 with an hematological malignancy


title: CIC_HUS_118_68874

source_name: DNA of sample 118 with an hematological malignancy


title: CIC_HUS_116_67657

source_name: DNA of sample 116 with an hematological malignancy


title: CIC_HUS_114_74245

source_name: DNA of sample 114 with an hematological malignancy


title: CIC_HUS_110_74397

source_name: DNA of sample 110 with an hematological malignancy


title: CIC_HUS_115_74283

source_name: DNA of sample 115 with an hematological malignancy


title: CIC_HUS_112_74599

source_name: DNA of sample 112 with an hematological malignancy


title: CIC_HUS_105_72191

source_name: DNA of sample 105 with an hematological malignancy


title: CIC_HUS_103_71342

source_name: Genomic DNA reference sample

source_name: DNA of sample 103 with an hematological malignancy


title: CIC_HUS_104_71596

source_name: DNA of sample 104 with an hematological malignancy


title: CIC_HUS_108_72819

source_name: DNA of sample 108 with an hematological malignancy


title: CIC_HUS_101_71869

source_name: DNA of sample 101 with an hematological malignancy


title: CIC_HUS_091_69809

source_name: DNA of sample 091 with an hematological malignancy


title: CIC_HUS_143_72586

source_name: DNA of sample 143 with an hematological malignancy


title: CIC_HUS_102_72381

source_name: DNA of sample 102 with an hematological malignancy


title: CIC_HUS_113_71231

source_name: DNA of sample 113 with an hematological malignancy


title: CIC_HUS_090_70598

source_name: DNA of sample 090 with an hematological malignancy

value: MDS-U


title: CIC_HUS_096_70805

source_name: DNA of sample 096 with an hematological malignancy


title: CIC_HUS_111_74369

source_name: DNA of sample 111 with an hematological malignancy


title: CIC_HUS_094_70595

source_name: DNA of sample 094 with an hematological malignancy


title: CIC_HUS_100_73030

source_name: DNA of sample 100 with an hematological malignancy


title: CIC_HUS_099_72458

source_name: DNA of sample 099 with an hematological malignancy


title: CIC_HUS_092_70008

source_name: DNA of sample 092 with an hematological malignancy


title: CIC_HUS_109_73056

source_name: DNA of sample 109 with an hematological malignancy


title: CIC_HUS_093_69994

source_name: Genomic DNA reference sample

source_name: DNA of sample 093 with an hematological malignancy


title: CIC_HUS_106_71754

source_name: DNA of sample 106 with an hematological malignancy


title: CIC_HUS_098_69144

source_name: DNA of sample 098 with an hematological malignancy


title: CIC_HUS_107_72322

source_name: DNA of sample 107 with an hematological malignancy


title: CIC_HUS_087_69015

source_name: DNA of sample 087 with an hematological malignancy


title: CIC_HUS_086_70572

source_name: DNA of sample 086 with an hematological malignancy


title: LATE TUMOR 2

city: NEW DELHI

first: SUNITA

last: SAXENA

state: NEW DELHI

address: NIP,ICMR,SAFADRJUNG HOSPITAL CAMPUS,NEW DELHI

department: TUMOUR BIOLOGY

country: India

institute: NATIONAL INSTITUTE OF PATHOLOGY

description: LATE TUMOR

data_processing: The data were normalised using LIMMA on R base Bioconductor package

label: BIOTIN

source_name: HUMAN BREAST

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: sample type

value: LATE TUMOR


title: CIC_HUS_097_67475

source_name: DNA of sample 097 with an hematological malignancy


title: CIC_HUS_082_65570

source_name: DNA of sample 082 with an hematological malignancy


title: CIC_HUS_084_69731

source_name: DNA of sample 084 with an hematological malignancy


title: CIC_HUS_095_67401

source_name: DNA of sample 095 with an hematological malignancy


title: LATE TUMOR 3

description: LATE TUMOR


title: Ebf1(-/-)::Ebf1-H240A-Rep1

city: Freiburg

first: Senthilkumar

last: Ramamoorthy

address: Stübeweg 51

department: Cellular & Molecular Immunology

institute: Max Planck Institute of Immunobiology and Epigenetics

description: Gene expression after pmys-EBF1H240A_rep1-IRES-GFP transduction

hyb_protocol: 1,65 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 55µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Microarray 4x44K (14868) 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 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan Resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 014868_D_F_20131202) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Ebf1−/− c-Kit+ fetal liver cells, pmys-EBF1-H240A-IRES-GFP,Replicate1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Quick Amp Labeling Kit (One-Color) and RNA Spike-In Kit, according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Single cell suspensions of freshly isolated Ebf1−/− fetal liver cells were stained with biotinylated c-Kit and c-Kit positive cells were enriched on an AutoMACS separator and subsequently plated on OP9 feeder cells in OptiMEM medium, supplemented with 4% FCS, 1% PSG, 50 μM β-mercaptoethanol, 5 ng/ml interleukin 7 (IL-7), 10 ng/ml Flt3 ligand (Flt3L) and 10 ng/ml stem cell factor (SCF).

extract_protocol: The total RNA was extracted using RNeasy Mini Kit according to the protocol recommended by the manufacturer.

treatment_protocol: The cells were transduced with pMys-IRES-GFP (vector), pMys-EBF1wt-IRES-GFP or pMys-EBF1-H240A-IRES-GFP retroviruses. 36h after transduction, GFP+ cells were sorted and RNA was prepared.

value: fetal liver

tag: cell marker

value: c-Kit+

tag: background strain

tag: transductant


title: CIC_HUS_085_68212

source_name: DNA of sample 085 with an hematological malignancy

tag: tissue

tag: gender


title: CIC_HUS_088_69287

tag: reference source info

source_name: DNA of sample 088 with an hematological malignancy

tag: who 2008 classification


title: CIC_HUS_081_67172

source_name: DNA of sample 081 with an hematological malignancy

tag: age


title: LATE TUMOR 4

description: LATE TUMOR


title: LATE NORMAL 3

description: LATE NORMAL

value: LATE NORMAL


title: CIC_HUS_080_70727

source_name: DNA of sample 080 with an hematological malignancy


title: Ebf1(-/-)::Ebf1-H240A-Rep3

description: Gene expression after pmys-EBF1-H240A_rep3-IRES-GFP transduction

source_name: Ebf1−/− c-Kit+ fetal liver cells, pmys-EBF1-H240A-IRES-GFP,Replicate3


title: LATE NORMAL 4

description: LATE NORMAL


title: EARLY NORMAL 4

description: EARLY NORMAL

value: EARLY NORMAL


title: EARLY TUMOR 1

description: EARLY TUMOR

value: EARLY TUMOR


title: LATE TUMOR 1

description: LATE TUMOR


title: Ebf1(-/-)::Ebf1wt-Rep2

description: Gene expression after pmys-EBF1wt-IRES-GFP transduction

source_name: Ebf1−/− c-Kit+ fetal liver cells, pmys-EBF1wt-IRES-GFP,Replicate2


title: LATE NORMAL 5

description: LATE NORMAL


title: CIC_HUS_083_69990

source_name: Genomic DNA reference sample

source_name: DNA of sample 083 with an hematological malignancy


title: CIC_HUS_089_70248

source_name: DNA of sample 089 with an hematological malignancy


title: EARLY NORMAL 2

description: EARLY NORMAL


title: Ebf1(-/-)::Ebf1wt-Rep1

source_name: Ebf1−/− c-Kit+ fetal liver cells, pmys-EBF1wt-IRES-GFP,Replicate1


title: Ebf1(-/-)::Ebf1wt-Rep3

source_name: Ebf1−/− c-Kit+ fetal liver cells, pmys-EBF1wt-IRES-GFP,Replicate3


title: LATE TUMOR 15

description: LATE TUMOR

source_name: HUMAN BREAST


title: LATE TUMOR 16

description: LATE TUMOR


title: LATE NORMAL 1

description: LATE NORMAL


title: LATE TUMOR 17

description: LATE TUMOR


title: EARLY TUMOR 10

description: EARLY TUMOR


title: EARLY NORMAL 3

description: EARLY NORMAL


title: Ebf1(-/-)::Empty-Rep2

description: Gene expression after pmys-Empty-IRES-GFP transduction

source_name: Ebf1−/− c-Kit+ fetal liver cells, pmys-Empty-IRES-GFP,Replicate2

value: Empty


title: LATE TUMOR 14

description: LATE TUMOR


title: EARLY TUMOR 11

description: EARLY TUMOR


title: LATE TUMOR 11

description: LATE TUMOR


title: LATE TUMOR 13

description: LATE TUMOR


title: EtOH fed 8 weeks plus multi-binge 1

city: Rockville

first: Ming-Jiang

last: Xu

state: MD

address: 5625 Fishers LN, 2S12

department: NIAAA

institute: NIH

description:
E8w+MB1
E8MB1.txt:cy5ByCy3Signal(normalized)

hyb_protocol: Blocking buffer and Hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, 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 G2565AA scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software version 11.5.1.1. Agilent Feature Extraction Software was used for background subtraction and LOWESS normalization.

source_name: Mouse liver with EtOH diet for 8 weeks plus EtOH binge (5 g/kg) twice per week

label_protocol: cDNA was generated with SuperScript® Indirect cDNA Labeling Core kit (Invitrogen) and labeled with Cy3/Cy5-mono reactive dye pack (GE healthcare), and the labeled cDNA was purified with Qiagen kit (#28004)

extract_protocol: Total RNA extracted using Trizol from liver and purified with QIAGEN kit (#74104) following manufacturer's instructions.

treatment_protocol: Collected tissues from fresh liver

tag: strain

value: male

tag: diet group

value: EtOH diet for 8 wks plus EtOH binge (5 g/kg) twice per wk

value: Liver

source_name: Ambion Mouse Assorted Total RNA

value: liver

value: reference RNA


title: EARLY TUMOR 12

description: EARLY TUMOR


title: EtOH fed 8 weeks plus multi-binge 3

description:
E8w+MB3
E8MB3.txt:cy5ByCy3Signal(normalized)


title: EtOH fed 8 weeks plus binge 5

description:
E8w+1B5
E8w1B5.txt:cy5ByCy3Signal(normalized)

source_name: Mouse liver with EtOH diet for 8 weeks plus EtOH binge (5 g/kg)

value: EtOH diet for 8 wks plus EtOH binge (5 g/kg)


title: EtOH fed 8 weeks plus multi-binge 4

description:
E8w+MB4
E8MB4.txt:cy5ByCy3Signal(normalized)


title: EtOH fed 10 days plus binge 3

description:
E10d1B3
E10d1B3.txt:cy5ByCy3Signal(normalized)

source_name: Mouse liver with EtOH diet for 10 days plus EtOH binge (5 g/kg)


title: EtOH fed 8 weeks plus binge 3

description:
E8w+1B3
E8w1B3.txt:cy5ByCy3Signal(normalized)


title: EARLY NORMAL 1

description: EARLY NORMAL


title: LATE TUMOR 12

description: LATE TUMOR


title: LATE NORMAL 2

description: LATE NORMAL


title: EtOH fed 8 weeks plus binge 2

description:
E8w+1B2
E8w1B2.txt:cy5ByCy3Signal(normalized)


title: EtOH fed 8 weeks plus multi-binge 2

description:
E8w+MB2
E8MB2.txt:cy5ByCy3Signal(normalized)


title: EtOH fed 8 weeks plus binge 4

description:
E8w+1B4
E8w1B4.txt:cy5ByCy3Signal(normalized)


title: EtOH fed 10 days plus binge 2

description:
E10d1B2
E10d1B2.txt:cy5ByCy3Signal(normalized)

value: EtOH diet for 10 days plus EtOH binge (5 g/kg)


title: EtOH fed 8 weeks plus binge 1

description:
E8w+1B1
E8w1B1.txt:cy5ByCy3Signal(normalized)


title: Ebf1(-/-)::Empty-Rep1

source_name: Ebf1−/− c-Kit+ fetal liver cells, pmys-Empty-IRES-GFP,Replicate1

tag: genotype


title: Ebf1(-/-)::Ebf1-H240A-Rep2

description: Gene expression after pmys-EBF1H240A_rep2-IRES-GFP transduction

source_name: Ebf1−/− c-Kit+ fetal liver cells, pmys-EBF1-H240A-IRES-GFP,Replicate2


title: EtOH fed 10 days plus binge 1

description:
E10d1B1
E10d1B1.txt:cy5ByCy3Signal(normalized)


title: LATE TUMOR 10

description: LATE TUMOR


title: LATE TUMOR 6

description: LATE TUMOR


title: EARLY TUMOR 9

description: EARLY TUMOR


title: EtOH fed 8 weeks 3

description:
E8w3
E8w3.txt:cy5ByCy3Signal(normalized)

source_name: Mouse liver with EtOH diet for 8 weeks

value: EtOH diet for 8 wks


title: EtOH fed 8 weeks 5

description:
E8w5
E8w5.txt:cy5ByCy3Signal(normalized)


title: EtOH fed 8 weeks 1

description:
E8w1
E8w1.txt:cy5ByCy3Signal(normalized)


title: Pair fed 8 weeks 4

description:
P8w4
P8w4.txt:cy5ByCy3Signal(normalized)

source_name: Mouse liver with pair fed for 8 weeks

value: pair fed for 8 wks


title: Pair fed 8 weeks 2

description:
P8w2
P8w2.txt:cy5ByCy3Signal(normalized)


title: Pair fed 10 days 1

description:
P10d1
P10d1.txt:cy5ByCy3Signal(normalized)

source_name: Mouse liver with pair fed for 10 days

value: pair fed for 10 days


title: EtOH fed 8 weeks 2

description:
E8w2
E8w2.txt:cy5ByCy3Signal(normalized)


title: LATE TUMOR 7

description: LATE TUMOR

value: LATE TUMOR


title: Pair fed 8 weeks 1

description:
P8w1
P8w1.txt:cy5ByCy3Signal(normalized)


title: LATE TUMOR 8

description: LATE TUMOR


title: Pair fed 10 days 2

description:
P10d2
P10d2.txt:cy5ByCy3Signal(normalized)


title: EARLY TUMOR 4

description: EARLY TUMOR


title: EARLY TUMOR 7

description: EARLY TUMOR


title: EARLY TUMOR 5

description: EARLY TUMOR


title: Pair fed 8 weeks 3

description:
P8w3
P8w3.txt:cy5ByCy3Signal(normalized)


title: Pair fed 10 days 3

description:
P10d3
P10d3.txt:cy5ByCy3Signal(normalized)


title: LATE TUMOR 5

description: LATE TUMOR


title: EtOH fed 8 weeks 4

description:
E8w4
E8w4.txt:cy5ByCy3Signal(normalized)


title: EARLY TUMOR 6

description: EARLY TUMOR


title: EARLY TUMOR 2

description: EARLY TUMOR


title: EARLY TUMOR 8

description: EARLY TUMOR


title: Steap 48h interleukin 12

first: Claus

middle: Juergen

last: Scholz

address: Josef-Schneider-Str. 2

department: Core Unit SysMed

institute: University Hospital Würzburg

hyb_protocol: 130µl hybridization mix prepared from labeled cRNA fragments was hybridized for 16h at 45°C and 60 rpm to GeneChip PrimeView arrays. Microarrays were washed and stained in the Affymetrix Fluidics Station 450 using script FS450_0002.

scan_protocol: Microarrays were scanned using a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Data were preprocessed in the R v3.2.1 environment with Bioconductor packages affy and vsn; VSN normalization and RMA probeset summary were performed with the vsnrma command using default parameter settings.

source_name: Steap cells, 48h interleukin 12-treated

label_protocol: 100ng of total RNA were amplified and labeled with the IVT PLUS Kit (Affymetrix); all steps were performed according to the manufacturers' protocols.

growth_protocol: As previously published (Ho YW et al., 2006; PMID: 16469329).

extract_protocol: RNA extraction with the mirVana miRNA Isolation Kit Thermo Fisher Scientific acc. to manufacturers' protocoll.

treatment_protocol: Cells were or were not treated with 12ng/ml IL12 at timepoint 12h and 48h

value: Steap

tag: treatment

value: interleukin 12

tag: treatment duration


title: Steap 12h control

source_name: Steap cells, 12h control-treated

tag: cell line

value: control


title: LATE TUMOR 9

description: LATE TUMOR


title: Steap 48h control

source_name: Steap cells, 48h control-treated


description:
expression profile of B-Raf-inhibited INA-6 cells, replicate 4
B_Raf.2R

hyb_protocol: 200µl hybridization mix prepared from labeled cRNA fragments was hybridized for 16h at 45°C to GeneChip Human Genome U133 Plus 2.0 arrays. Microarrays were washed and stained in the Affymetrix Fluidics Station 450 using script FS450_0001.

data_processing: Data were preprocessed in the R v3.0.1 environment with Bioconductor packages affy and vsn; VSN normalization and RMA probeset summary were performed with the vsnrma command using default parameter settings.

source_name: SB590885-treated INA-6 cells

label_protocol: 100ng of total RNA were amplified and labeled with the IVT Express Kit (Affymetrix); all steps were performed according to the manufacturers' protocols.

growth_protocol: INA-6 cells were cultured in RPMI1640 supplemented with 10% fetal calf serum, 1% Penicillin/Streptomycin at 37°C and 5% CO2 and 2 ng/ml interleukin-6.

extract_protocol: Total RNA extraction was performed with the RNeasy Mini Kit (50) from QIAGEN according to the manufacturer's instructions.

treatment_protocol: 3 x 10^5 INA-6 cells were either treated with DMSO as a solvent control, the MEK inhibitor PD-325901 or the Raf inhibitor SB-590885.

value: myeloma cell line INA-6

tag: agent

tag: inhibition

value: B-Raf


title: Steap 12h interleukin 12

source_name: Steap cells, 12h interleukin 12-treated


title: Prame 48h control

source_name: Prame cells, 48h control-treated

value: Prame


title: INA-6 control, replicate 4

description:
expression profile of INA-6 control, replicate 4
control.2R

source_name: DMSO-treated INA-6 cells

value: DMSO

value: no


title: MEK1-inhibited INA-6 cells, replicate 3

description:
expression profile of MEK1-inhibited INA-6 cells, replicate 3
MEK.1R

source_name: PD325901-treated INA-6 cells

value: MEK


title: EARLY TUMOR 3

description: EARLY TUMOR

source_name: HUMAN BREAST

tag: sample type

value: EARLY TUMOR


description:
expression profile of B-Raf-inhibited INA-6 cells, replicate 3
B_Raf.1R


title: MEK1-inhibited INA-6 cells, replicate 2

description:
expression profile of MEK1-inhibited INA-6 cells, replicate 2
MEK.2


title: Prame 12h interleukin 12

source_name: Prame cells, 12h interleukin 12-treated


title: MEK1-inhibited INA-6 cells, replicate 4

description:
expression profile of MEK1-inhibited INA-6 cells, replicate 4
MEK.2R


title: Prame 12h control

source_name: Prame cells, 12h control-treated


title: INA-6 control, replicate 2

description:
expression profile of INA-6 control, replicate 2
control.2


description:
expression profile of B-Raf-inhibited INA-6 cells, replicate 1
B_Raf.1


title: INA-6 control, replicate 3

description:
expression profile of INA-6 control, replicate 3
control.1R


title: Prame 48h interleukin 12

source_name: Prame cells, 48h interleukin 12-treated


title: INA-6 control, replicate 1

description:
expression profile of INA-6 control, replicate 1
control.1


title: Cecal tissue_FFdiet_rep2

city: Ann Arbor

first: Eric

middle: Charles

last: Martens

state: MI

address: 1150 West Medical Center Drive

department: Dept. of Microbiology and Immunology

institute: University of Michigan Medical School

hyb_protocol: Following labeling procedure, 2.76 ug of cDNA were hybridized at 48C on Mouse Gene ST 2.1 strips, and were washed and stained using the Affymetrix Gene Atlas system (software version 1.0.4.267)

scan_protocol: Arrays were scanned using the Affymetrix Gene Atlas system (software version 1.0.4.267)

data_processing: Expression values for each gene were calculated using robust multi-array average (RMA) method

source_name: cecal tissue, Fiber free diet

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix Plus WT kit protocol (GeneChip® WT Plus Reagent Kit Manual P/N 703174 Rev. 2) from 400 ng total RNA

growth_protocol: Mice were fed either a diet rich in fiber (control) or a diet lacking fiber (experimental condition)

extract_protocol: Bead beating and Trizol extraction

value: Swiss webster

tag: diet

value: fiber-free diet

value: cecum


title: Cecal tissue_FRdiet_rep3

source_name: cecal tissue, Fiber rich diet

value: fiber-rich diet


description:
expression profile of B-Raf-inhibited INA-6 cells, replicate 2
B_Raf.2


title: Cecal tissue_FFdiet_rep1


title: Cecal tissue_FFdiet_rep3


title: U937 Empty Vector, 24 hr incubation

city: Houston

first: Lalitha

last: Nagarajan

state: TX

address: 6767 Bertner

department: Genetics

institute: Unviersity of Texas MD Anderson Cancer Center

description: Gene expression data from 5X10^4/ml U937-Vec cells after 24 hours incubation in RPMI+10% FBS

hyb_protocol: The  biotin-labeled nucleotides in the final product (15 ug) were fragmented before undergoing an overnight  hybridization to Affymetrix Genechip microarrays (HG U133 Plus 2.0).  After the 16-18 hr hybridization at 45C with 60 rpm rotation in a GeneChip Hybridization Oven 640, the Genechips were washed and stained using a GeneChip Fluidics Station 400 where the arrays were stained with strepavidin-phycoerythrin conjugate

scan_protocol: The plate was scanned using Affymetrix GeneChip Scanner 3000 with 7G upgrade.

data_processing: Array raw data (CEL) were generated using Affymetrix GCOS software (Mas5 algorithm).  Data was further processed using dChip software platform (build date 2009), following the Perfect Model-only approach.  Data was normalized with HL003-Vec as the baseline array.

source_name: U937 cells containing empty expression vector, grown for 24 hours before harvest

label_protocol: The samples (100 ng total RNA input) were amplified and biotinylated using Affymetrix Two-Cycle IVT labeling protocol following manufacturer’s specifications.

growth_protocol: Stably transfected cells were grown from 5x10^4/mL concentration for 24 hours in 90%RPMI 10% FBS Medium before being harvested.

extract_protocol: Extraction of Total RNA was performed by QIAGEN Rneasy Miniprep kit following manufacturer's instructions

tag: vector

value: empty expression vector

tag: disease

value: histiocytic lymphoma

value: male


title: Cecal tissue_FRdiet_rep2

tag: tissue


title: Cecal tissue_FRdiet_rep4


title: Cecal tissue_FRdiet_rep1


title: CIC_HUS_079_58506

source_name: Genomic DNA reference sample

value: Human Genomic DNA:Male (Promega; Madison, WI, USA)

source_name: DNA of sample 079 with an hematological malignancy

value: bone marow

tag: gender

value: Male


title: U937 MIXL1 Expression Vector, 24 hr incubation

description: Gene expression data from 5X10^4/ml U937-MIXL1 cells after 24 hours incubation in RPMI+10% FBS

source_name: U937 cells containing MIXL1 enforced expression vector, grown for 24 hours before harvest

value: MIXL1 enforced expression vector


title: CIC_HUS_078_65271

tag: reference source info

source_name: DNA of sample 078 with an hematological malignancy

value: RCMD


title: CIC_HUS_077_65843

source_name: DNA of sample 077 with an hematological malignancy

tag: who 2008 classification


title: MEK1-inhibited INA-6 cells, replicate 1

description:
expression profile of MEK1-inhibited INA-6 cells, replicate 1
MEK.1

value: myeloma cell line INA-6


title: CIC_HUS_071_63749

value: Human Genomic DNA:Female (Promega; Madison, WI, USA)

source_name: DNA of sample 071 with an hematological malignancy

value: Female

tag: age


title: CIC_HUS_066_52088

value: Human Genomic DNA (Promega; Madison, WI, USA)

source_name: DNA of sample 066 with an hematological malignancy


title: CIC_HUS_067_52740

source_name: DNA of sample 067 with an hematological malignancy


title: CIC_HUS_072_56094

source_name: DNA of sample 072 with an hematological malignancy


title: CIC_HUS_073_56812

source_name: DNA of sample 073 with an hematological malignancy

value: MDS del(5q)


title: CIC_HUS_068_52830

source_name: DNA of sample 068 with an hematological malignancy


title: CIC_HUS_064_51735

source_name: DNA of sample 064 with an hematological malignancy


title: CIC_HUS_075_58858

source_name: DNA of sample 075 with an hematological malignancy


title: HUVEC_Ctl_12h_rep1

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

institute: University of Lübeck

description:
cell line from endothelium of veins from the umbilical cord
8123460102

data_processing: All arrays were normalized together using the quantile normalization algorithm without background subtraction using Illumina's BeadStudio Data Analysis Software.

source_name: HUVEC, Ctl, 12h, rep1

growth_protocol: Human umbilical vein endothelial cells (HUVEC #C12253) were purchased from Promocell (Heidelberg, Germany) and cultured according to the manufacturer’s instruction in endothelial  growth medium-2 (Promocell #C22111).  For the purpose of synchronizing, cells were cultured over night in endothelial basal medium (EBM) without growth factors and serum.

extract_protocol: RNA was extracted with the QIAGEN RNeasy Plus Mini Kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: S100A6 knockdown (KD) was achieved transfecting cells with siRNA against human S100A6 (Sigma 01_00139273) using the Lipofectamine RNAiMAX reagent (Invitrogen) 48 hours prior to measuring. Transfectiing the cells with a scrambled siRNA vector was used as control. To stimulate proliferation EGM-2 was supplemented with 50ng/ml VEGF (R&D systems).

value: umbilical cord

value: HUVEC

tag: time point

tag: stimulus

value: VEGF-A (50ng/ml)

tag: sirna knockdown

value: Control


title: CIC_HUS_074_60800

source_name: DNA of sample 074 with an hematological malignancy


title: CIC_HUS_061_52985

source_name: DNA of sample 061 with an hematological malignancy


title: HUVEC_Ctl_8h_rep1

source_name: HUVEC, Ctl, 8h, rep1


title: HUVEC_Ctl_1h_rep2

source_name: HUVEC, Ctl, 1h, rep2


title: CIC_HUS_062_52504

source_name: Genomic DNA reference sample

source_name: DNA of sample 062 with an hematological malignancy

value: MDS-U


title: HUVEC_Ctl_1h_rep1

source_name: HUVEC, Ctl, 1h, rep1


title: CIC_HUS_065_51827

source_name: DNA of sample 065 with an hematological malignancy


title: CIC_HUS_057_52937

source_name: DNA of sample 057 with an hematological malignancy


title: CIC_HUS_070_55775

source_name: DNA of sample 070 with an hematological malignancy


title: HUVEC_Ctl_12h_rep2

source_name: HUVEC, Ctl, 12h, rep2


title: CIC_HUS_056_52272

source_name: DNA of sample 056 with an hematological malignancy


title: CIC_HUS_069_53874

source_name: DNA of sample 069 with an hematological malignancy


title: CIC_HUS_063_53335

source_name: DNA of sample 063 with an hematological malignancy

value: RCUD


title: HUVEC_Ctl_24h_rep1

source_name: HUVEC, Ctl, 24h, rep1


title: HUVEC_Ctl_4h_rep1

source_name: HUVEC, Ctl, 4h, rep1


title: CIC_HUS_059_54540

source_name: DNA of sample 059 with an hematological malignancy


title: CIC_HUS_076_58231

source_name: DNA of sample 076 with an hematological malignancy


title: CIC_HUS_058_52462

source_name: DNA of sample 058 with an hematological malignancy


title: CIC_HUS_060_52368

source_name: DNA of sample 060 with an hematological malignancy


title: HUVEC_Ctl_0h_rep2

source_name: HUVEC, Ctl, 0h, rep2


title: CIC_HUS_055_52761

source_name: Genomic DNA reference sample

source_name: DNA of sample 055 with an hematological malignancy


title: HUVEC_Ctl_0h_rep1

source_name: HUVEC, Ctl, 0h, rep1


title: CIC_HUS_054_53093

source_name: DNA of sample 054 with an hematological malignancy


title: HUVEC_KD_12h_rep1

description:
cell line from endothelium of veins from the umbilical cord
8123460096

source_name: HUVEC, KD, 12h, rep1


title: CIC_HUS_052_54736

source_name: DNA of sample 052 with an hematological malignancy


title: HUVEC_KD_8h_rep1

source_name: HUVEC, KD ,8h, rep1


title: CIC_HUS_049_56548

source_name: DNA of sample 049 with an hematological malignancy


title: CIC_HUS_053_52069

source_name: DNA of sample 053 with an hematological malignancy


title: CIC_HUS_051_53585

source_name: DNA of sample 051 with an hematological malignancy


title: HUVEC_KD_12h_rep2

source_name: HUVEC, KD, 12h, rep2


title: HUVEC_KD_2h_rep1

source_name: HUVEC, KD, 2h, rep1


title: HUVEC_KD_6h_rep1

source_name: HUVEC, KD, 6h ,rep1


title: HUVEC_KD_4h_rep1

source_name: HUVEC, KD, 4h, rep1


title: HUVEC_KD_8h_rep2

source_name: HUVEC ,KD, 8h, rep2


title: CIC_HUS_047_60967

source_name: DNA of sample 047 with an hematological malignancy


title: CIC_HUS_050_65448

source_name: DNA of sample 050 with an hematological malignancy


title: HUVEC_KD_18h_rep1

source_name: HUVEC, KD, 18h, rep1


title: HUVEC_KD_24h_rep1

source_name: HUVEC, KD, 24h, rep1


title: HUVEC_KD_1h_rep1

source_name: HUVEC, KD, 1h, rep1


title: HUVEC_KD_0h_rep3

source_name: HUVEC, KD, 0h, rep3


title: CIC_HUS_046_61038

source_name: Genomic DNA reference sample

source_name: DNA of sample 046 with an hematological malignancy


title: HUVEC_KD_1h_rep2

source_name: HUVEC, KD, 1h, rep2


title: CIC_HUS_044_61292

source_name: DNA of sample 044 with an hematological malignancy


title: CIC_HUS_045_61536

source_name: DNA of sample 045 with an hematological malignancy


title: HUVEC_Ctl_0h_rep3

source_name: HUVEC, Ctl, 0h, rep3


title: CIC_HUS_048_57727

source_name: DNA of sample 048 with an hematological malignancy


title: CIC_HUS_043_61539

source_name: DNA of sample 043 with an hematological malignancy


title: HUVEC_KD_0h_rep1

source_name: HUVEC, KD, 0h, rep1


title: CIC_HUS_042_63728

source_name: DNA of sample 042 with an hematological malignancy


title: HUVEC_KD_0h_rep2

source_name: HUVEC, KD, 0h, rep2


title: CIC_HUS_041_62800

source_name: DNA of sample 041 with an hematological malignancy


title: 76_04111

city: Lexington

first: Tim

last: McClintock

state: KY

address: 780 Rose St.

department: Physiology

institute: University of Kentucky

description: mRNA abundance data

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Mouse GeneChip 1.0 ST arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using an Affymetrix GCS3000 7G Scanner

data_processing: The data were analyzed with Affymetrix Gene Expression Console sofware using default analysis settings and global scaling as normalization method.

source_name: P26 olfactory mucosa, 123Cre:Lhx2(fl/fl):Emx2(fl/fl)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: 123Cre:Lhx2(fl/+):Emx2(fl/+) and Lhx2(fl/fl:)Emx2(fl/fl) mice were bred in standard laboratory conditions

extract_protocol: Olfactory mucosa were dissected and total RNA isolated using TriReagent.

treatment_protocol: MIce of the desired genotypes were raised to 26 days postnatal.

value: olfactory mucosa

tag: background strain

value: mixed 129 x C57BL/6J

tag: genotype

tag: phenotype

value: Knockout


title: CIC_HUS_039_58152

source_name: DNA of sample 039 with an hematological malignancy

value: bone marow


title: A7_08281

description: mRNA abundance data

source_name: P1 olfactory mucosa, 123Cre:Emx2(fl/fl)

growth_protocol: 123Cre:Emx2(fl/+) and Emx2(fl/fl) mice were bred in standard laboratory conditions

treatment_protocol: MIce of the desired genotypes were raised to 1 day postnatal.

tag: developmental stage


title: A4_08281

description: mRNA abundance data

source_name: P1 olfactory mucosa, Emx2(fl/fl)

value: control littermate


title: 35_041113

description: mRNA abundance data

source_name: P26 olfactory mucosa, Lhx2(fl/+):Emx2(fl/+)


title: A5_082812

description: mRNA abundance data


title: A2_08281

description: mRNA abundance data


title: 34_041113

description: mRNA abundance data


title: 33_041113

description: mRNA abundance data

source_name: P26 olfactory mucosa, 123Cre:Lhx2(fl/+):Emx2(fl/+)


title: 79_041113

description: mRNA abundance data


title: 78_041113

description: mRNA abundance data

source_name: P26 olfactory mucosa, 123Cre:Lhx2(+/+):Emx2(fl/+)


title: A8_082812

description: mRNA abundance data


title: CIC_HUS_030_57207

source_name: Genomic DNA reference sample

source_name: DNA of sample 030 with an hematological malignancy

value: RCMD


title: CIC_HUS_037_57682

source_name: DNA of sample 037 with an hematological malignancy


title: CIC_HUS_035_63141

source_name: DNA of sample 035 with an hematological malignancy

value: Male


title: A6_082812

description: mRNA abundance data

source_name: P1 olfactory mucosa, 123Cre:Emx2(fl/+)


title: CIC_HUS_029_57113

source_name: DNA of sample 029 with an hematological malignancy


title: CIC_HUS_034_58580

source_name: DNA of sample 034 with an hematological malignancy


title: CIC_HUS_027_64541

source_name: DNA of sample 027 with an hematological malignancy


title: 91_041113

description: mRNA abundance data


title: CIC_HUS_032_57552

source_name: DNA of sample 032 with an hematological malignancy


title: CIC_HUS_025_62876

source_name: DNA of sample 025 with an hematological malignancy


title: CIC_HUS_040_62694

source_name: DNA of sample 040 with an hematological malignancy


title: CIC_HUS_038_57869

source_name: DNA of sample 038 with an hematological malignancy


title: CIC_HUS_033_60109

source_name: DNA of sample 033 with an hematological malignancy


title: CIC_HUS_026_64188

source_name: DNA of sample 026 with an hematological malignancy


title: A1_082812

description: mRNA abundance data


title: CIC_HUS_036_64981

source_name: DNA of sample 036 with an hematological malignancy


title: CIC_HUS_031_57412

source_name: DNA of sample 031 with an hematological malignancy


title: A4_020212

description: mRNA abundance data

source_name: P3 olfactory mucosa, 123Cre:Lhx2(fl/fl)

growth_protocol: 123Cre:Lhx2(fl/+) and Lhx2(fl/fl) mice were bred in standard laboratory conditions

treatment_protocol: MIce of the desired genotypes were raised to 3 days postnatal.


title: CIC_HUS_028_57098

source_name: Genomic DNA reference sample

source_name: DNA of sample 028 with an hematological malignancy


title: A3_020212

description: mRNA abundance data


title: A1_020212

description: mRNA abundance data

source_name: P3 olfactory mucosa, 123Cre:Lhx2(fl/+)


title: A8_020212

description: mRNA abundance data


title: A3_082812

description: mRNA abundance data

source_name: P1 olfactory mucosa, 123Cre:Emx2(fl/fl)


title: CIC_HUS_022_58302

source_name: DNA of sample 022 with an hematological malignancy


title: B15_02021

description: mRNA abundance data

source_name: P3 olfactory mucosa, Lhx2(fl/+)


title: B10_020212

description: mRNA abundance data


title: CIC_HUS_021_62376

source_name: DNA of sample 021 with an hematological malignancy


title: OE20

description: mRNA abundance data

source_name: P1 olfactory mucosa, OmpCre:Emx2(fl/+)

growth_protocol: OmpCre:Emx2(fl/+) and Emx2(fl/fl) mice were bred in standard laboratory conditions


title: OE23

description: mRNA abundance data

source_name: P1 olfactory mucosa, OmpCre:Emx2(fl/fl)


title: CIC_HUS_024_60950

source_name: DNA of sample 024 with an hematological malignancy


title: CIC_HUS_023_59613

source_name: DNA of sample 023 with an hematological malignancy


title: CIC_HUS_015_59008

source_name: DNA of sample 015 with an hematological malignancy


title: OE19

description: mRNA abundance data


title: OE17

description: mRNA abundance data


title: OE22

description: mRNA abundance data


title: CIC_HUS_018_61355

source_name: DNA of sample 018 with an hematological malignancy


title: CIC_HUS_013_61987

source_name: DNA of sample 013 with an hematological malignancy


title: OE15

description: mRNA abundance data


title: CIC_HUS_012_59609

source_name: DNA of sample 012 with an hematological malignancy


title: CIC_HUS_017_59592

source_name: DNA of sample 017 with an hematological malignancy


title: CIC_HUS_011_59548

source_name: DNA of sample 011 with an hematological malignancy


title: A6_020212

description: mRNA abundance data


title: CIC_HUS_010_59731

source_name: Genomic DNA reference sample

source_name: DNA of sample 010 with an hematological malignancy