title: Tg2576 hippocampus + LXR agonist TO901317, biological rep 10


title: P45 D-4

status: Public on Aug 01 2017

type: RNA

city: Trondheim

first: Lene

middle: Christin

last: Olsen

address: Erling Skjalgsons gt. 1

department: Medical Faculty

country: Norway

institute: Norwegian University of Science and Technology - NTNU

description: miRNA expression in entorhinal cortex deep layers at postnatal age P45

hyb_protocol: The Cy3-labeled miRNA samples were hybridized for 20hrs  at  55°C onto separate Rat miRNA Microarrays, Release 15.0 (Agilent Technologies, AMADID 029200, 8x15K format). The microarrays were then washed with increasing stringency using Gene Expression Wash Buffers (Agilent Technologies) followed by drying  with  acetonitrile  (SIGMA)

scan_protocol: Fluorescent signal intensities were detected with  Scan Control A.8.4.1  Software (Agilent Technologies) on the Agilent DNA Microarray Scanner

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) to obtain QC stats of Feature Outliers, Background and Non-Uniformity.  The additive error was below 12 for all samples, and the Hyb Spike-In signal was above the recommended threshold of 2.50 for all arrays.
The raw values were processed using the AgiMicroRna Bioconductor package, filtering according to the quality flag (filterMicroRna function with settings wellaboveNEG = FALSE, limIsGeneDetected = 50, limNEG = 25), and normalizing using the quantile method.

molecule: total RNA

organism: Rattus norvegicus

source_name: Medial entorhinal cortex, deep layers, P45, replicate 4

label_protocol: 100 ng of total RNA from each sample was spiked with MicroRNA Spike-In Kit (Agilent Technologies), treated with calf intestinal phosphatase, and labeled with Cy3 using the miRNA Complete Labeling and Hyb Kit according to the manufacturer's recommendations.

extract_protocol: Total RNA was extracted using Ambion's RNAqueous®-Micro kit, following the manufacturer's recommendations except for an extra 1 minute incubation with wash buffer, and the ethanol added for precipitation was increased to 1.25x lysis buffer volume to include small RNAs. RNA was eluted with 2x10μl RNAqueous Elution Buffer. The RNA in four samples  (RS-198_20, RS-198_25, RS-198_27, RS-198_28) was extracted using Ambion's mirVana kit according to the manufacturer's recommendations and eluted in 2x50 µl mirVana Elution Buffer.  The amount of RNA in all samples was analyzed on the Nano Drop, and the quality of the RNA on the BioAnalyzer Nano Chip

treatment_protocol: Long Evans rats were deeply anesthetized and sacrificed by guillotine. The brain was immediately placed in oxygenated ACSF, sliced on a microtome (400μm) and placed in RNAlater. Layer slices were then dissected under a microscope.

tag: age

tag: layer

value: Deep

tag: strain

value: Long Evans


title: Tg2576 hippocampus + LXR agonist TO901317, biological rep 4

city: Cambridge

first: Andrew

last: Hill

state: MA

address: 300 Technology Square

department: Research Business Technology

country: USA

institute: Pfizer

description: Gene expression data from transgenic mouse Tg2576 hippocampus treated 7d with LXR agonist TO901317

hyb_protocol: Ten micrograms of cRNA was fragmented and hybridized to the MOE430 2.0 array (Affymetrix, Santa Clara, CA).

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

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

label: Biotin

organism: Mus musculus

source_name: Mus musculus hippocampus Tg2576, TO901317 treated

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 2ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Tg2576 mice express hAPP with the Swedish familial AD mutation (Lys-670-Asn; Met-671-Leu) under the control of the prion promoter 28 , and were maintained on a SJL × C57BL/6J genetic background.

extract_protocol: The hippocampus was dissected and immediately placed in RNAlater solution. Total RNA was isolated using a FastPrep Homogenizer and Isolation System (Thermo Fisher Scientific, Waltham, MA) and further purified using RNeasy spin columns (Qiagen, CA), with on-column DNase I digestion (RNase-free DNAse Set; Qiagen, CA).  RNA quantity and quality were assessed using the Agilent Technologies (Palo Alto, CA) Bioanalyzer and the NanoDrop ND-1000 spectrophotometer (Wilmington, DE).

treatment_protocol: Five-month-old heterozygous male Tg2576 mice (n=11-12 group) treated with vehicle or 50 mg/kg/d TO901317 for 5 days and age-matched, vehicle-dosed, wild-type littermate controls were anesthetized using isoflurane, saline perfused and the brains removed.

value: SJL × C57BL/6J

tag: genotype/variation

tag: treatment

value: LXR agonist TO901317


title: P45 II-3

description: miRNA expression in entorhinal cortex layer II at postnatal age P45

source_name: Medial entorhinal cortex, layer II, P45, replicate 3

value: II


title: P45 D-3

source_name: Medial entorhinal cortex, deep layers, P45, replicate 3


title: Tg2576 hippocampus + LXR agonist TO901317, biological rep 3


title: P45 D-1

source_name: Medial entorhinal cortex, deep layers, P45, replicate 1


title: P45 II-1

source_name: Medial entorhinal cortex, layer II, P45, replicate 1


title: Tg2576 hippocampus + LXR agonist TO901317, biological rep 2


title: P23 D-3

description: miRNA expression in entorhinal cortex deep layers at postnatal age P23

source_name: Medial entorhinal cortex, deep layers, P23, replicate 3


title: Tg2576 hippocampus + LXR agonist TO901317, biological rep 5


title: Tg2576 hippocampus, biological rep 10

description: Gene expression data from transgenic mouse Tg2576 hippocampus

source_name: Mus musculus hippocampus Tg2576

value: Vehicle


title: Tg2576 hippocampus, biological rep 11


title: Tg2576 hippocampus, biological rep 9


title: P23 D-2

source_name: Medial entorhinal cortex, deep layers, P23, replicate 2


title: P23 II-3

description: miRNA expression in entorhinal cortex layer II at postnatal age P23

source_name: Medial entorhinal cortex, layer II, P23, replicate 3


title: Tg2576 hippocampus + LXR agonist TO901317, biological rep 1


title: P45 II-4

source_name: Medial entorhinal cortex, layer II, P45, replicate 4


title: shTMS1AS-2, biological rep2

city: chengdu

first: Tao

last: Liu

address: 24th,yihuan road

country: China

institute: Sichuan University

description: Gene expression data from SKBR3 cells infected with shTMS1AS-2

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. 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 hybridization data were analyzed using Affymetrix GeneChip Command Console Software (AGCC), which uses statistical criteria to generate a ‘present’ or ‘absent’ call for genes represented by each probe set on the array. Afterwards, genes with ‘absent’ scores were filtered out and the remaining genes were analyzed.

label: biotin

organism: Homo sapiens

source_name: SKBR3 cells infected with shTMS1AS-2

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: SKBR3 cells were cultured in RPMI-1640 with 10% fetal bovine serum

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

treatment_protocol: SKBR3 cells were infected with shNC, shTMS1AS or shTMS1.

tag: cells

value: breast cancer cells


title: P23 D-1

source_name: Medial entorhinal cortex, deep layers, P23, replicate 1


title: CaPO4 treatment 3

city: Beijing

first: Qinghua

last: Cui

address: 38 Xueyuan Road

institute: Peking University

hyb_protocol: The labeled cRNAs were hybridized onto the Mouse LncRNA Array v2.0 (8 x 60K, Arraystar).

scan_protocol: After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v12.0 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 1 out of 6 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.

source_name: mouse abdominal aorta

label_protocol: The sample preparation and microarray hybridization were performed based on the manufacturer’s standard protocols with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method.

extract_protocol: Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

tag: tissue

value: aorta

tag: Sex

value: Male


title: ps_8_d2_2

city: Ramat-Gan

first: Hiba

last: Waldman Ben-Asher

address: Ramat-Gan

department: Life-Sciences

country: Israel

institute: Bar-Ilan University

hyb_protocol: Equal amounts of labeled RNA were then hybridized on the chip using the Gene Expression hybridization kit (Agilent Technologies) and processed as described previously in detail (Stern et al., 2009, PMID: 19218552).

scan_protocol: Scanned on an Agilent G2565BA microarray scanner

data_processing: The data from all arrays were first subjected to Normexp-Background correctionand LOESS within-array normalization using the Bioconductor Limma package. The rest of the analysis was performed in Partek® Genomics Suite software, version 6.6 Copyright © 2012 Partek Inc., St. Louis, MO, USA.The log expression ratios that were produced during the normalization step were analyzed.

organism: Trypanosoma brucei

source_name: Total RNA was isolated from cells carrying the SEC63 silencing construct before silencing

label_protocol: Total RNA was labeled using the Amino Allyl MessageAmp II aRNA kit (Ambion).

growth_protocol: Procyclic forms of T. brucei strain 29-13, which carries integrated genes for T7 polymerase and the tetracycline repressor were grown in SDM-79 supplemented with 10% fetal calf serum in the presence of 50 lg ml21 hygromycin B and 15 lg ml21 G418

extract_protocol: RNA quality was determined using the Eukaryote Total RNA Nano 6000 assay kit (Agilent Technologies) on the Agilent Technologies 2100 Bioanalyzer. To generate the fluorescently labeled cRNA, total RNA was labeled using the Ambion Amino Allyl MessageAmp II aRNA kit (Ambion).

tag: name

value: uninduced cells 8

source_name: Total RNA was isolated from cells carrying the SEC63 silencing construct 2 days post-induction

value: silenced cells day 2_2


title: P23 II-1

source_name: Medial entorhinal cortex, layer II, P23, replicate 1


title: Tg2576 hippocampus, biological rep 7


title: P9 D-4

description: miRNA expression in entorhinal cortex deep layers at postnatal age P9

source_name: Medial entorhinal cortex, deep layers, P9, replicate 4


title: P23 II-2

source_name: Medial entorhinal cortex, layer II, P23, replicate 2


title: Tg2576 hippocampus, biological rep 8


title: P9 II-5

description: miRNA expression in entorhinal cortex layer II at postnatal age P9

source_name: Medial entorhinal cortex, layer II, P9, replicate 5


title: Tg2576 hippocampus, biological rep 6


title: LV-GFP infused rat, biological replicate 2

city: Albuquerque

first: Nora

last: Perrone-Bizzozero

state: NM

address: 1 University of New Mexico MSC08 4740

department: Neurosciences

institute: University of New Mexico

description: Gene expression data from control LV-GFP rat

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. Also, we used RMA for normalization of the signal.

source_name: Rat nucleus accumbens

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions polling both nuclie accumbens of each animal.

treatment_protocol: Control rats were infused bilaterally with 2.0 ul of LV-GFP viral particles (8.28 x 10^8 IUF/mL) into nucleus accumbens and miR-495 OE rats were infused with 2.0 ul LV-miR-495 (1.39 x10^9 IU/ml). Viral contructs were from System Biosciences

value: control

tag: lentivirus

value: LV-GFP


title: P9 D-5

source_name: Medial entorhinal cortex, deep layers, P9, replicate 5


title: P9 D-3

source_name: Medial entorhinal cortex, deep layers, P9, replicate 3


title: P9 II-4

source_name: Medial entorhinal cortex, layer II, P9, replicate 4


title: d2_1_ps_7

value: silenced cells day 2_1

value: uninduced cells 7


title: Tg2576 hippocampus, biological rep 3

source_name: Mus musculus hippocampus Tg2576


title: d3_4_ps_6

source_name: Total RNA was isolated from cells carrying the SEC63 silencing construct 3 days post-induction

value: silenced cells day 3_4

value: uninduced cells 6


title: LMS patient 3

city: Stanford

first: Joanna

last: Przybyl

address: 300 Pasteur Drive

department: Department of Pathology

institute: Stanford University

hyb_protocol: Gene expression analysis was performed using SurePrint G3 Human GE 8x60K microarrays (G4851A) according to the one-color microarray-based expression analysis protocol (Agilent Technologies, SantaClara, CA, USA).

scan_protocol: The microarray slides were scanned using the Agilent G2565A DNA Microarray Scanner (Agilent Technologies, Santa Clara, CA, USA).

data_processing: Image analysis was done using the Feature Extraction V10.10.1.1 software (Agilent Technologies, SantaClara, CA, USA). Expression values from different probes mapped to the same transcript were collapsed using avereps function from limma package. For the exploratory analysis, raw signal values were normalized to median equal 0 and log2 transformed. Principal component analysis (PCA) was performed using prcomp function (“stats” R package, version 3.0.2). Unsupervised hierarchical clustering was performed using Euclidean distance and complete linkage rule on genes with standard deviation (SD) > 1 (function hclust in “stats” R package, version 3.0.2). Differential expression analysis was performed using significance analysis of microarrays (SAM) on quantile-normalized expression values filtered for SD >100 and log2 transformed (with seed value 1234567 and adjusted p-value cut-off 0.05).

source_name: LMS patient

label_protocol: Total RNA (25ng) was reverse transcribed into cDNA by incorporating a T7 oligo-dT promoter primer prior to the generation of fluorescent cRNA using an Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies, Santa Clara, CA, USA).

extract_protocol: Total RNA were extracted from 25 frozen tumor specimens using the miRNeasy Mini Kit (Qiagen) with optional DNase treatment using RNase-free DNase Set (Qiagen). RNA quality was checked using the Bio-Rad Experion system (Bio-Rad Laboratories).

tag: subject status

value: highly malignant undifferentiated uterine sarcomas (UUS)

tag: gender

value: Female

value: Uterus

tag: tissue type

value: Recurrent tumor

tag: tumor type

value: leiomyosarcoma


title: LMS patient 2

value: Primary tumor


title: ps_5_d3_3

value: uninduced cells 5

value: silenced cells day 3_3


title: LMS patient 4


title: Tg2576 hippocampus, biological rep 5

value: SJL × C57BL/6J

value: Vehicle


title: LMS patient 1


title: Tg2576 hippocampus, biological rep 4


title: Tg2576 hippocampus, biological rep 2


title: P9 II-3

source_name: Medial entorhinal cortex, layer II, P9, replicate 3

value: II

value: Long Evans


title: Tg2576 hippocampus, biological rep 1


title: Wild type hippocampus, biological rep 9

description: Gene expression data from wild type mouse hippocampus

source_name: Mus musculus hippocampus wildtype

value: Wildtype


title: Wild type hippocampus, biological rep 10


title: UUS patient 8

source_name: UUS patient

value: undifferentiated uterine sarcoma


title: UUS patient 7


title: Wild type hippocampus, biological rep 8


title: P9 D-2

source_name: Medial entorhinal cortex, deep layers, P9, replicate 2

value: Deep


title: P9 D-1

source_name: Medial entorhinal cortex, deep layers, P9, replicate 1


title: P2 D-4

description: miRNA expression in entorhinal cortex deep layers at postnatal age P2

source_name: Medial entorhinal cortex, deep layers, P2, replicate 4


title: Wild type hippocampus, biological rep 7


title: P9 II-1

source_name: Medial entorhinal cortex, layer II, P9, replicate 1


title: Wild type hippocampus, biological rep 6


title: P9 II-2

source_name: Medial entorhinal cortex, layer II, P9, replicate 2


title: Wild type hippocampus, biological rep 4


title: UUS patient 1


title: UUS patient 6


title: WT vs ΔlancRNA Stat2

city: Cork

first: Denise

middle: B

last: Lynch

state: Not Applicable

address: College Road

department: APC Microbiome Institute

country: Ireland

institute: University College Dublin

description:
WT vs ΔlancRNA in stationnary growth phase Replicate 2
Biological replicate 2 of 2

hyb_protocol: Labeled cDNA was hybridized using the Agilent Gene Expression hybridization kit (part number 5188-5242) as described in the Agilent Two-Color Microarray-Based Gene Expression Analysis v4.0 manual (G4140-90050)

scan_protocol: Slides were scanned using an Agilent Microarray Scanner System (G2505B) with Agilent scan control software version 7.0 for the 44k microarray at a resolution of 5 microns. Agilent feature extraction software version 9.1 was used to process the image file from the scanner

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction.

organism: Ligilactobacillus salivarius UCC118

source_name: wild-type pure culture

label_protocol: Reverse Transcription on 7 µg RNA and labelling on 500 ng cDNA

growth_protocol: MRS broth, 37°C, 5% CO2

extract_protocol: Total RNA, Rneasy kit (Qiagen) following manufacturer's instructions + DNA digestion (Turbo Dnase, Ambion) following manufacturer's instructions

tag: genotype

value: wild-type

tag: growth

value: Exponential

source_name: ΔlancRNA mutant pure culture

value: ΔlancRNA


title: UUS patient 3

value: highly malignant undifferentiated uterine sarcomas (UUS)

value: Female


title: P2 II-4

description: miRNA expression in entorhinal cortex layer II at postnatal age P2

source_name: Medial entorhinal cortex, layer II, P2, replicate 4


title: P2 D-3

source_name: Medial entorhinal cortex, deep layers, P2, replicate 3


title: UUS patient 4

value: Uterus


title: Wild type hippocampus, biological rep 2


title: WT vs ΔlancRNA ΔHTH Stat1

description:
WT vs ΔlancRNA ΔHTH in stationnary growth phase Replicate 1
Biological replicate 1 of 2

value: Stationnary

source_name: ΔlancRNA ΔHTH mutant pure culture

value: ΔlancRNA ΔHTH


title: WT vs ΔlancRNA Stat1

description:
WT vs ΔlancRNA in stationnary growth phase Replicate 1
Biological replicate 1 of 2


title: WT vs ΔlancRNA ΔHTH Expo2

description:
WT vs ΔlancRNA ΔHTH in exponential growth phase Replicate 2
Biological replicate 2 of 2


title: WT vs ΔlancRNA ΔHTH Stat2

description:
WT vs ΔlancRNA ΔHTH in stationnary growth phase Replicate 2
Biological replicate 2 of 2


title: UUS patient 5

value: Recurrent tumor


title: WT vs ΔlancRNA ΔHTH Expo1

description:
WT vs ΔlancRNA ΔHTH in exponential growth phase Replicate 1
Biological replicate 1 of 2


title: Wild type hippocampus, biological rep 3


title: Wild type hippocampus, biological rep 1


title: Medial entorhinal cortex 2

description: Control to compare technologies

data_processing:
The ViiA7 Software v1.2 (Applied Biosystems) was used for instrument and raw data control as well as calculation of Ct values (Automatic settings).
The Bioconductor package HTqPCR was used to analyze the raw data. We used the setCategory function to set Ct boundaries between 10 and 32. The data was normalized using the deltaCt function, and the filterCt function was used to remove undetermined and unreliable values. Differential expression was determined using the limmaCt function
Fold Change worksheet reports test/control (i.e., DiO+ and DiO-) ratios.

label: FAM

source_name: Dissected medial entorhinal cortex

label_protocol: The RNA samples were preamplified with the TaqMan®  PreAmp  Master  Mix  together  with  the Megaplex™  PreAmp  Primers,  Rodent  Pool  Set  v3.0. Reverse transcription was performed using TaqMan  ®  MicroRNA Reverse Transcription Kit. The products of the reverse transcription were diluted 1:1 with TaqMan  ®  Universal PCR Master Mix before analysis on the TaqMan® Array. Due to the low concentration of the sorted samples, 2.5 ul was used for preamplification, and 3 ul of the preamplified products were used for reverse transcription.   Rodent MicroRNA A Card Set v3.0 according to the manufacturer's recommendations.

extract_protocol: RNA was purified from the FACS sorted cell populations using the RNAqueous Micro kit from Ambion. The mirVana kit from Ambion was used to extract RNA from the tissue pieces. The concentration was measured by NanoDrop ND-1000, and the quality by BioAnalyzer 2100 using RNA 6000 Nano and Pico chips from Agilent.

treatment_protocol: The fluorescent dye DiO was iontophoretically injected bilaterally into the dentate gyrus of Long Evans pups aged P2. The pups were sacrificed at postnatal ages P4/P5 by decapitation, followed by dissection and enzymatic and mechanical dissociation of the medial entorhinal cortex. Fluorescent cells were separated from non-fluorescent cells using FACS. For the tissue samples, Long Evans rats aged P23 sacrificed by decapitation, and the medial entorhinal cortex was dissected and placed in RNAlater.

tag: replicate

value: B

tag: fluorescence

tag: cell type

value: TIssue


title: Wild type hippocampus, biological rep 5

tag: strain

value: SJL × C57BL/6J

value: Vehicle


title: Medial entorhinal cortex 1

description: Control to compare technologies

value: A

value: Tissue


title: UUS patient 2

value: Primary tumor

value: undifferentiated uterine sarcoma


title: WT vs ΔlancRNA Expo2

description:
WT vs ΔlancRNA in exponential growth phase Replicate 2
Biological replicate 2 of 2

value: wild-type


title: Medial entorhinal non-stellate cells 5

description: Labeled

source_name: FACS sorted unlabeled medial entorhinal cells

value: DiO negative

value: Other


title: WT vs ΔlancRNA Expo1

description:
WT vs ΔlancRNA in exponential growth phase Replicate 1
Biological replicate 1 of 2

value: Exponential

value: ΔlancRNA


title: Medial entorhinal non-stellate cells 3

description: Labeled


title: ESS low-grade patient 11

source_name: ESS low-grade patient

value: low-grade endometrial stromal sarcomas (ESS) patient

value: Female

value: Uterus

value: low-grade endometrial stromal sarcoma


title: P2 II-1

source_name: Medial entorhinal cortex, layer II, P2, replicate 1

tag: age

tag: layer

value: II

value: Long Evans


title: P2 D-2

source_name: Medial entorhinal cortex, deep layers, P2, replicate 2

value: Deep


title: ESS low-grade patient 10


title: P2 D-1

source_name: Medial entorhinal cortex, deep layers, P2, replicate 1


title: Met-48H +24h -5

city: Rennes

first: Aurelie

last: LE CAM

address: Campus de Beaulieu

department: PHASE

country: France

institute: INRA

description: Cultured cells  in methionine supplemented DMEM during 24h after a 48h methionine restriction period

hyb_protocol: RNA was hybridized to the slides with Spike-In at 55C, 20rpm for 20 h. Slides were washed.

scan_protocol: Microarrays were scanned using an Agilent DNA Microarray Scanner (Agilent Technologies). Signal intensities were quantified using Feature Extraction software (Agilent v10.7.3.1). Data was processed using GeneSpring software (Agilent v.11.5.0) using GmedianSignal values. Data were normalized using the quantile method.

data_processing: Data was processed using GeneSpring software (Agilent v.11.5.0). Data were normalized using the quantile method and logged.

organism: Oncorhynchus mykiss

source_name: cultured cells

label_protocol: The miRNA array (Gene expression Omnibus [GEO] platform GPL21776) was done according to Jaunchich et al, 2013. The Briefly 200ng of total RNA from cells was collected and dephosphorylated for 30min at 37C, denatured with dimethyl sulfoxide for 7 min at 100C. The RNA was labeled by terminal ligation of cyanine3-pCp using T4 ligase for 2h at 16C. Purification was performed using Micro Bio-Spin columns to get rid of spare cyanine3-pCp.

growth_protocol: All experiments were carried out on rainbow trout, Oncorhynchus mykiss (Walbaum). Fish 5-10 g were maintained in 12 °C recirculating water under artificial light-darkness conditions to mimic natural photoperiod. Chemical parameters were monitored routinely and oxygen levels always remained above 98 % saturation.

extract_protocol: Cells were collected using Tri reagent (Sigma), and total RNA was extracted according to the manufacturer’s instructions

treatment_protocol: Satellite cells were extracted from the white muscle of trout (5 - 10 g), as previously reported (Gabillard et al., 2010; Froehlich et al., 2014). Brieﬂy, after several enzymatic digestion and cell filtration steps, the cells were seeded at a density of 160,000 cells/cm2 and left for 40 min. The first three days, the cells were cultured in DMEM (Dulbecco’s Modiﬁed Eagle’s Medium) supplemented with 10% of the fetal calf serum (FCS). Afterward the medium was replaced by methionine-depleted DMEM  supplemented with 2% FCS supplemented or not by  100µM of methionine. For kinetic analysis of differentiation, cells were cultured in F10 medium (Nutrient mixture Ham’s F10) supplemented with 10% of FCS for 3 days to stimulate cell proliferation, and then 3 days in DMEM supplemented with 2% of FCS to stimulate differentiation.

tag: treatment


title: P2 II-2

source_name: Medial entorhinal cortex, layer II, P2, replicate 2


title: Medial entorhinal non-stellate cells 2

description: Unlabeled


title: ESS low-grade patient 9

tag: tissue


title: Met-48H +24h -6


title: Met-48H +24h -3


title: Wild type hippocampus, biological rep 11

source_name: Mus musculus hippocampus wildtype

value: SJL × C57BL/6J

tag: genotype/variation

value: Wildtype

value: Vehicle


title: Medial entorhinal non-stellate cells 1

description: Unlabeled


title: ESS low-grade patient 7

value: Primary tumor


title: ESS low-grade patient 6


title: Medial entorhinal non-stellate cells 4

description: Unlabeled


title: P2 II-3

source_name: Medial entorhinal cortex, layer II, P2, replicate 3


title: Met-48H +24h -4


title: Met-48H +24h -2


title: Medial entorhinal stellate cells 5

description: Labeled

source_name: FACS sorted retrogradely labeled stellate neurons

value: DiO positive

value: Stellate


title: Met+72H -6

description: Cultured Cells in methionine supplemented DMEM during 72h


title: Medial entorhinal stellate cells 4

description: Labeled


title: ESS low-grade patient 4

value: Recurrent tumor


title: Medial entorhinal stellate cells 3

description: Labeled


title: Met+72H -4


title: ESS low-grade patient 8


title: Met+72H -5


title: ESS low-grade patient 5


title: ESS low-grade patient 2


title: ps4_d3_2

source_name: Total RNA was isolated from cells carrying the SEC63 silencing construct before silencing

tag: name

value: uninduced cells 4

source_name: Total RNA was isolated from cells carrying the SEC63 silencing construct 3 days post-induction

value: silenced cells day 3_2


title: Medial entorhinal stellate cells 2

description: Labeled


title: d3_1_ps_3

value: silenced cells day 3_1

value: uninduced cells 3


title: ESS high-grade patient 4

source_name: ESS high-grade patient

value: high-grade endometrial stromal sarcomas (ESS) patient

value: Female

value: high-grade endometrial stromal sarcoma


title: d1_2_ps_2

source_name: Total RNA was isolated from cells carrying the SEC63 silencing construct 1 day post-induction

value: silenced cells day 1_2

value: uninduced cells 2


title: ESS high-grade patient 2

value: Uterus


title: ESS high-grade patient 3


title: Met+72H -2


title: Met-72H -6

description: Cultured Cells in methionine depleted DMEM during 72h


title: ps_1_d1_1

value: uninduced cells 1

value: silenced cells day 1_1


title: Met-72H -2


title: ESS high-grade patient 1


title: Medial entorhinal stellate cells 1

description: Labeled


title: heart_Old_mf_35_(Mouse430_2)

status: Public on Jul 31 2017

city: Cologne

first: Agapios

last: Sachinidis

state: NRW

address: Robert-Kochstr. 39

department: Institute of Neurophysiology

country: Germany

institute: University of Cologne

description: Sample name: Old_mf_vivo

hyb_protocol: 12.5µg of fragmented aRNA was hybridized to the Mouse Genome 430 2.0 microarrays in the Genechip Hybridisation Oven-645 (Affymetrix, United Kingdom) for 16 h at 45º C.

scan_protocol: Arrays were washed and stained with phycoerythrin with Fluidics Station 450 and scanned using the Gene-Chip Scanner 3000 7G (Affymetrix, United Kingdom) according to the manufacturer's instructions

data_processing: The quality control (QC) matrices were confirmed with expression console software (Affymertix, USA) and Partek genomics suite version 6.6 (Partek Inc.St.Louis,USA). QC passed CEL files were further analyzed using Partek genomics suite version 6.6. All CEL files were RMA background corrected, quantile normalized and all probe sets were summarized using median polish algorithm.

source_name: heart

label_protocol: 100ng total RNA was used for aRNA amplification with GeneChip® 3’ IVT Express Kit (Affymetrix, United Kingdom) according to the manufacturer’s instructions. After 16 h of biotinylated in vitro transcription, aRNA was purified using magnetic beads and 15µg of purified aRNA was fragmented with fragmentation buffer

extract_protocol: Total RNA from the mice liver tissues was isolated using Trizol reagent (Invitrogen) and purified with the RNeasy Plus kit from Qiagen

value: OF1 (Oncins France 1)

value: heart

tag: developmental stage

value: old

value: mixed males and females


title: heart_mRNA_19,5 m_28_(Mouse430_2)

description: Sample name: 19.5_m_vivo

value: embryonic stage E19.5

value: male


title: heart_mRNA_18,5m f_26_(Mouse430_2)

description: Sample name: 18.5_m_f_vivo

value: embryonic stage E18.5


title: heart_Adult_f_33_(Mouse430_2)

description: Sample name: Adult_f_vivo

value: adult

value: female


title: heart_Old_f_36_(Mouse430_2)

description: Sample name: Old_f_vivo


title: heart_mRNA_17,5 f_24_(Mouse430_2)

description: Sample name: 17.5_f_vivo

value: embryonic stage E17.5


title: heart_Adult_mf_32_(Mouse430_2)

description: Sample name: Adult_mf_vivo


title: 16,5 mf _20_(Mouse430_2)

description: Sample name: 16.5_mf_vivo

value: embryonic stage E16.5


title: heart_mRNA_17,5 m_22_(Mouse430_2)

description: Sample name: 17.5_m_vivo


title: heart_mRNA_18,5 m_25_(Mouse430_2)

description: Sample name: 18.5_m_vivo


title: heart_mRNA_19,5 mf_29_(Mouse430_2)

description: Sample name: 19.5_mf_vivo


title: heart_mRNA_19,5 f_30_(Mouse430_2)

description: Sample name: 19.5_f_vivo


title: heart_mRNA_18,5 f_27_(Mouse430_2)

description: Sample name: 18.5_f_vivo


title: 15,5 mf_17_(Mouse430_2)

description: Sample name: 15.5_mf_vivo

value: embryonic stage E15.5


title: 16,5 m _19_(Mouse430_2)

description: Sample name: 16.5_m_vivo


title: heart_Adult_m_31_(Mouse430_2)

description: Sample name: Adult_m_vivo


title: heart_mRNA_17,5m f_23_(Mouse430_2)

description: Sample name: 17.5_m_f_vivo


title: Met-72H -5


title: heart_Old_m_34_(Mouse430_2)

description: Sample name: Old_m_vivo


title: 13,5 f_12_(Mouse430_2)

description: Sample name: 13.5_f_vivo

value: embryonic stage E13.5


title: 12,5 m_7_(Mouse430_2)

description: Sample name: 12.5_m_vivo

value: embryonic stage E12.5


title: 15,5 f_18_(Mouse430_2)

description: Sample name: 15.5_f_vivo


title: 13,5 m_10_(Mouse430_2)

description: Sample name: 13.5_m_vivo


title: 15,5 m_16_(Mouse430_2)

description: Sample name: 15.5_m_vivo


title: heart_mRNA_16,5 f_21_(Mouse430_2)

description: Sample name: 16.5_f_vivo


title: 14,5 f_15_(Mouse430_2)

description: Sample name: 14.5_f_vivo

value: embryonic stage E14.5


title: 14,5 m_13_(Mouse430_2)

description: Sample name: 14.5_m_vivo


title: 14,5 mf_14_(Mouse430_2)

description: Sample name: 14.5_mf_vivo


title: old m -34_(miRNA-3_0)

description: Sample name: Old_m_vivo

hyb_protocol: After incubation, the arrays were washed and stained in the fluidics station 450 using fluidics script FS450_0002

scan_protocol: Arrays were scanned using an Affymetrix Gene-Chip Scanner-3000-7G

data_processing: The quality control (QC) matrices were confirmed with expression console software (Affymertix, USA). QC passed CEL files were further analyzed using the Bioconductor package limma . All CEL files were RMA background corrected, quantile normalized and all probe sets were summarized using median polish algorithm.

label_protocol: 700 ng total RNA was used as the starting material, and the Affymetrix FlashTag Biotin HSR RNA Labelling kit was used for miRNA ligation (Affymetrix, United Kingdom) according to the manufacturer’s instructions. The labeled samples were  hybridized to the Affymetrix miRNA 3.0 arrays for 16 h at 48 °C in an Affymetrix hybridization oven 645

extract_protocol: Total RNA from the mice heart tissues was isolated using Trizol reagent (Invitrogen) and purified with the RNeasy Plus kit from Qiagen


title: 12,5 mf_8_(Mouse430_2)

description: Sample name: 12.5_mf_vivo


title: 13,5 mf_11_(Mouse430_2)

description: Sample name: 13.5_mf_vivo


title: 18.5mf-26_(miRNA-3_0)

description: Sample name: 18.5_m_f_vivo


title: 19.5m-28_(miRNA-3_0)

description: Sample name: 19.5_m_vivo


title: old f -36_(miRNA-3_0)

description: Sample name: Old_f_vivo


title: 12,5 f _9_(Mouse430_2)

description: Sample name: 12.5_f_vivo


title: 19.5mf-29_(miRNA-3_0)

description: Sample name: 19.5_mf_vivo


title: 19.5f-30_(miRNA-3_0)

description: Sample name: 19.5_f_vivo


title: adult f-33_(miRNA-3_0)

description: Sample name: Adult_f_vivo


title: adult m-31_(miRNA-3_0)

description: Sample name: Adult_m_vivo


title: 18.5f-27_(miRNA-3_0)

description: Sample name: 18.5_f_vivo


title: 11,5 mf_5_(Mouse430_2)

description: Sample name: 11.5_mf2_vivo

value: embryonic stage E11.5


title: 18.5m-25_(miRNA-3_0)

description: Sample name: 18.5_m_vivo


title: 10,5 mf_2_(Mouse430_2)

description: Sample name: 10.5_mf2_vivo

value: embryonic stage E10.5


title: 10,5 mf_3_(Mouse430_2)

description: Sample name: 10.5_mf3_vivo

value: OF1 (Oncins France 1)


title: 17.5 mf-23_(miRNA-3_0)

description: Sample name: 17.5_m_f_vivo

value: heart


title: 11,5 mf_6_(Mouse430_2)

description: Sample name: 11.5_mf3_vivo


title: 11,5 mf_4_(Mouse430_2)

description: Sample name: 11.5_mf1_vivo


title: 10,5 mf_1_(Mouse430_2)

description: Sample name: 10.5_mf1_vivo


title: 17.5 m-22_(miRNA-3_0)

description: Sample name: 17.5_m_vivo


title: 16.5mf_20_(miRNA-3_0)

description: Sample name: 16.5_mf_vivo


title: 16.5 m-19_(miRNA-3_0)

description: Sample name: 16.5_m_vivo


title: 17.5 f-24_(miRNA-3_0)

description: Sample name: 17.5_f_vivo


title: 15.5 mf-17_(miRNA-3_0)

description: Sample name: 15.5_mf_vivo


title: 15.5 f- 18_(miRNA-3_0)

description: Sample name: 15.5_f_vivo


title: adult mf-32_(miRNA-3_0)

description: Sample name: Adult_mf_vivo


title: 14.5 mf-14_(miRNA-3_0)

description: Sample name: 14.5_mf_vivo


title: 14.5 f- 15_(miRNA-3_0)

description: Sample name: 14.5_f_vivo


title: 16.5f-21_(miRNA-3_0)

description: Sample name: 16.5_f_vivo


title: 15.5 m- 16_(miRNA-3_0)

description: Sample name: 15.5_m_vivo


title: 14.5 m-13_(miRNA-3_0)

description: Sample name: 14.5_m_vivo


title: 13.5 m-10_(miRNA-3_0)

description: Sample name: 13.5_m_vivo


title: 13.5 f-12_(miRNA-3_0)

description: Sample name: 13.5_f_vivo


title: 13.5 mf-11_(miRNA-3_0)

description: Sample name: 13.5_mf_vivo


title: 11.5 mf-6_(miRNA-3_0)

description: Sample name: 11.5_mf3_vivo


title: 12.5 m- 7_(miRNA-3_0)

description: Sample name: 12.5_m_vivo


title: 11.5 mf-5_(miRNA-3_0)

description: Sample name: 11.5_mf2_vivo


title: 11.5 mf-4_(miRNA-3_0)

description: Sample name: 11.5_mf1_vivo


title: 10.5 mf-1_(miRNA-3_0)

description: Sample name: 10.5_mf1_vivo


title: 10.5 mf-3_(miRNA-3_0)

description: Sample name: 10.5_mf3_vivo


title: 10.5 mf-2_(miRNA-3_0)

description: Sample name: 10.5_mf2_vivo


title: P11/12  Muller glia (MG)_data set2 normalized

status: Public on Feb 11 2017

city: New York

first: Stefanie

middle: G

last: Wohl

state: NY

address: 33w 42nd Street

department: Biological and Vision Sciences

institute: SUNY Optometry

description:
P11+
pooled from 32 P11 retinas

hyb_protocol: The miRtagged mature miRNA was then hybridized to a probe pair (reporter probe and capture probe) in the standard nCounter gene expression array workflow.

scan_protocol: 200 ng of total RNA per sample (33 ng/μ l, n = 20 mice for adult MG, n = 16 mice for P11 MG, n = 13 mice for cell culture, pooled samples) was submitted for NanoString analysis, performed at the Fred Hutchinson Cancer Center in Seattle, WA, USA.

data_processing:
[1] Values from adult MG, adult neurons, P11 MG and P11 neurons were normalized against 4 housekeeping genes (β -actin, GAPDH, Rpl19, and B2m), 8 negative controls, and 6 positive controls that were run simultaneously with the samples.
[2] Values from adult MG, P11 MG and cultured MG for 8 DIV or 14 DIV were normalized against 4 housekeeping genes (β -actin, GAPDH, Rpl19, and B2m), 8 negative controls, and 6 positive controls that were run simultaneously with the samples.

Two samples, adult MG and P11/12 MG, were used in both data sets and normalized differently. Therefore the normalized data for these samples in dataset 1 is different from that in data set 2 and represented with a unique GSM (adult MG data set 1: GSM2482296 and adult MG data set 2: GSM2482308; P11/12 MG data set 1: GSM2482298 and P11/12 MG data set 2: GSM2482309). The raw data for these samples are identical.

source_name: mouse retina

label_protocol: NanoString nCounter® was used for miRNA expression analysis. DNA sequences called miRtags were ligated to the mature miRNAs through complementary oligonucleotides with sequence-specific binding (bridges). All excess tags and ridges were removed, resulting in sequence-specific tagging of mature miRNAs.

growth_protocol: cell culture: Müller glia were dissociated from a total of 20 postnatal day (P) 11/12 mice and grown in Neurobasal medium supplemented with N-2, tetracycline-free 10% fetal bovine serum (FBS, Clontech), and epidermal growth factor (EGF, R&D Systems, 100 ng/mL) as described previously. After 6 days in vitro (DIV), cells were passaged and two day later either used for the 8 DIV sample or kept for another week in normal medium.

extract_protocol: The sorts of 40 retinas and of 2 independent primary cultures were pooled for the RNA-purification. RNA was extracted and purified with a miRNeasy Micro Kit in accordance with manufacturer’s instructions (Qiagen). For miRNA RT-qPCR, DNA stem-loop RT primers were used to produce cDNA for specific miRNAs64,65

treatment_protocol: tamoxifen for cre activation: Tamoxifen (Sigma) was administered intraperitoneally at 75 mg/kg in corn oil at P9 + 10 for the P11 analysis and for two consecutive days at ages P > 21 for the adult assay.

tag: condition

value: FACS-sorted


title: 8DIV Muller glia (MG)_data set2 normalized

description:
MD8div
pooled from 20 P11 retinas - split experiment

data_processing:
[1] Values from adult MG, adult neurons, P11 MG and P11 neurons were normalized against 4 housekeeping genes (β -actin, GAPDH, Rpl19, and B2m), 8 negative controls, and 6 positive controls that were run simultaneously with the samples.

[2] Values from adult MG, P11 MG and cultured MG for 8 DIV or 14 DIV were normalized against 4 housekeeping genes (β -actin, GAPDH, Rpl19, and B2m), 8 negative controls, and 6 positive controls that were run simultaneously with the samples.!Sample_data_processing = Two samples, adult MG and P11/12 MG, were used in both data sets and normalized differently. Therefore the normalized data for these samples in dataset 1 is different from that in data set 2 and represented with a unique GSM (adult MG data set 1: GSM2482296 and adult MG data set 2: GSM2482308; P11/12 MG data set 1: GSM2482298 and P11/12 MG data set 2: GSM2482309). The raw data for these samples are identical.

value: cultured


title: 14DIV Muller glia (MG)_data set2 normalized

description:
MG14div
pooled from 20 P11 retinas - split experiment

value: P11 + 8div


title: adult Muller glia (MG)_data set2 normalized

description:
A+
pooled from 40 adult retinas


title: P11/12 neurons_data set1 normalized

description:
P11-
pooled from 32 P11 retinas


title: P11/12  Muller glia (MG)_data set1 normalized

description:
P11+
pooled from 32 P11 retinas


title: 12.5 mf- 8_(miRNA-3_0)

description: Sample name: 12.5_mf_vivo

tag: gender

value: mixed males and females


title: 12.5 f- 9_(miRNA-3_0)

description: Sample name: 12.5_f_vivo


title: adult neurons_data set1 normalized

description:
A-
pooled from 40 adult retinas


title: adult Muller glia (MG)_data set1 normalized

description:
A+
pooled from 40 adult retinas


title: mesenterial adipose tissue_newborn rat_maternal vitamin D deficient diet_rep 1

status: Public on Dec 31 2016

city: Halle

first: Alexandra

last: Schutkowski

address: von Danckelmann Platz 2

institute: MLU Halle-Wittenberg

hyb_protocol: Following fragmentation, biotinylated cDNA was hybridized on GeneChip Rat Genome 230 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The data were analyzed using the MAS5 algorithm with Affymetrix Expression Console

source_name: mesenterial adipose_newborn rat_maternal vit. D deficient diet

label_protocol: Biotinylated cDNA was prepared according to the standard Affymetrix protocol

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

value: Sprague-Dawley

value: newborn

value: wildtype

tag: dams fed on

value: vitamin D deficient diet (0 IU vitamin D/kg diet)

value: mesenterial adipose tissue


title: mesenterial adipose tissue_newborn rat_maternal vitamin D adequate diet_rep 1

description: adaequat 10

source_name: mesenterial adipose_newborn rat_maternal vit. D adequate diet

value: vitamin D adequate (1,000 IU vitamin D/kg diet)


title: mesenterial adipose tissue_newborn rat_maternal vitamin D deficient diet_rep 3


title: mesenterial adipose tissue_newborn rat_maternal vitamin D adequate diet_rep 2

description: adaequat 11


title: mesenterial adipose tissue_newborn rat_maternal vitamin D deficient diet_rep 2


title: sorted cell fraction 226

status: Public on Dec 02 2016

city: Toronto

first: Stanley

last: Ng

state: Ontario

address: 160 College Street

country: Canada

institute: Univerity of Toronto

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Scanned on a BeadArray™ Reader using BeadScan software (v3.2).

data_processing: The data were normalized with variance stabilization and quantile normalization using the lumi (v2.16.0) package in R (v3.1.0).

source_name: Human acute myeloid leukemia cells

label_protocol: Biotin.

extract_protocol: RNA was extracted from sorted cells with RNeasy kit or Trizol reagent.

treatment_protocol: T-cell depleted mononuclear cells from primary acute myeloid leukemia patients were thawed and flow-sorted according to expression of CD34 and CD38.

tag: cd34/cd38 expression

tag: lsc content

value: LSC+


title: sorted cell fraction 221


title: sorted cell fraction 223


title: sorted cell fraction 215


title: sorted cell fraction 227


title: sorted cell fraction 222

value: LSC-


title: sorted cell fraction 225


title: mesenterial adipose tissue_newborn rat_maternal vitamin D adequate diet_rep 3

description: adaequat 12


title: sorted cell fraction 216


title: sorted cell fraction 220


title: sorted cell fraction 219


title: sorted cell fraction 218


title: sorted cell fraction 214


title: sorted cell fraction 213


title: sorted cell fraction 210


title: sorted cell fraction 211


title: sorted cell fraction 209


title: sorted cell fraction 207


title: sorted cell fraction 208


title: sorted cell fraction 217


title: sorted cell fraction 206


title: sorted cell fraction 212


title: sorted cell fraction 201


title: sorted cell fraction 205


title: sorted cell fraction 197


title: sorted cell fraction 196


title: sorted cell fraction 204


title: sorted cell fraction 203


title: sorted cell fraction 194


title: sorted cell fraction 202


title: sorted cell fraction 188


title: sorted cell fraction 186


title: sorted cell fraction 199


title: sorted cell fraction 184


title: sorted cell fraction 187


title: sorted cell fraction 198


title: sorted cell fraction 193


title: sorted cell fraction 189


title: sorted cell fraction 200


title: sorted cell fraction 183


title: sorted cell fraction 195


title: sorted cell fraction 180


title: sorted cell fraction 191


title: sorted cell fraction 182


title: sorted cell fraction 190


title: sorted cell fraction 185


title: old mf -35_(miRNA-3_0)

description: Sample name: Old_mf_vivo

value: old


title: sorted cell fraction 179


title: sorted cell fraction 181


title: sorted cell fraction 178


title: sorted cell fraction 174


title: sorted cell fraction 176


title: sorted cell fraction 170


title: sorted cell fraction 163


title: sorted cell fraction 167


title: sorted cell fraction 164


title: sorted cell fraction 168


title: sorted cell fraction 175


title: sorted cell fraction 173


title: sorted cell fraction 172


title: sorted cell fraction 155


title: sorted cell fraction 162


title: sorted cell fraction 156


title: sorted cell fraction 165


title: sorted cell fraction 158


title: sorted cell fraction 159


title: sorted cell fraction 169


title: sorted cell fraction 171


title: sorted cell fraction 166


title: sorted cell fraction 157


title: sorted cell fraction 160


title: sorted cell fraction 153


title: sorted cell fraction 150


title: sorted cell fraction 152


title: sorted cell fraction 151


title: sorted cell fraction 154


title: sorted cell fraction 177


title: sorted cell fraction 143


title: sorted cell fraction 148


title: sorted cell fraction 142


title: sorted cell fraction 224


title: sorted cell fraction 147


title: sorted cell fraction 138


title: sorted cell fraction 144


title: sorted cell fraction 149


title: sorted cell fraction 139


title: sorted cell fraction 130


title: sorted cell fraction 146


title: sorted cell fraction 134


title: sorted cell fraction 132


title: sorted cell fraction 140


title: sorted cell fraction 133


title: sorted cell fraction 145


title: sorted cell fraction 124


title: sorted cell fraction 141


title: sorted cell fraction 136


title: sorted cell fraction 126


title: sorted cell fraction 127


title: sorted cell fraction 131


title: sorted cell fraction 125


title: sorted cell fraction 129


title: sorted cell fraction 135


title: sorted cell fraction 137


title: sorted cell fraction 128


title: sorted cell fraction 123


title: sorted cell fraction 115


title: sorted cell fraction 192


title: sorted cell fraction 116


title: sorted cell fraction 110


title: sorted cell fraction 119


title: sorted cell fraction 121


title: sorted cell fraction 118


title: sorted cell fraction 113


title: sorted cell fraction 111


title: sorted cell fraction 117


title: sorted cell fraction 114


title: sorted cell fraction 108


title: sorted cell fraction 106


title: sorted cell fraction 99


title: sorted cell fraction 120


title: sorted cell fraction 100


title: sorted cell fraction 105


title: sorted cell fraction 102


title: sorted cell fraction 101


title: sorted cell fraction 98


title: sorted cell fraction 109


title: sorted cell fraction 103


title: sorted cell fraction 104


title: sorted cell fraction 107


title: sorted cell fraction 112


title: sorted cell fraction 97


title: sorted cell fraction 96


title: sorted cell fraction 161


title: sorted cell fraction 122


title: sorted cell fraction 95


title: sorted cell fraction 92


title: sorted cell fraction 85


title: sorted cell fraction 93


title: sorted cell fraction 94


title: sorted cell fraction 88


title: sorted cell fraction 87


title: sorted cell fraction 91


title: sorted cell fraction 89


title: sorted cell fraction 86


title: sorted cell fraction 90


title: sorted cell fraction 81


title: sorted cell fraction 83


title: sorted cell fraction 82


title: sorted cell fraction 84


title: sorted cell fraction 78


title: sorted cell fraction 79


title: sorted cell fraction 80


title: sorted cell fraction 77


title: sorted cell fraction 75


title: sorted cell fraction 74


title: sorted cell fraction 69


title: sorted cell fraction 76


title: sorted cell fraction 71


title: sorted cell fraction 73


title: sorted cell fraction 68


title: sorted cell fraction 72


title: sorted cell fraction 70


title: sorted cell fraction 66


title: sorted cell fraction 67


title: sorted cell fraction 61


title: sorted cell fraction 65


title: sorted cell fraction 55


title: sorted cell fraction 51


title: sorted cell fraction 58


title: sorted cell fraction 52


title: sorted cell fraction 50


title: sorted cell fraction 56


title: sorted cell fraction 54


title: sorted cell fraction 44


title: sorted cell fraction 41


title: sorted cell fraction 49


title: sorted cell fraction 42


title: sorted cell fraction 40


title: sorted cell fraction 39


title: sorted cell fraction 45


title: sorted cell fraction 59


title: sorted cell fraction 57


title: sorted cell fraction 38


title: sorted cell fraction 60


title: sorted cell fraction 36


title: sorted cell fraction 46


title: sorted cell fraction 47


title: sorted cell fraction 64


title: sorted cell fraction 43


title: sorted cell fraction 62


title: sorted cell fraction 48


title: sorted cell fraction 37


title: sorted cell fraction 34


title: sorted cell fraction 29


title: sorted cell fraction 30


title: sorted cell fraction 32


title: sorted cell fraction 28


title: sorted cell fraction 33


title: sorted cell fraction 35


title: sorted cell fraction 26


title: sorted cell fraction 25


title: sorted cell fraction 31


title: sorted cell fraction 23


title: sorted cell fraction 24


title: sorted cell fraction 22


title: sorted cell fraction 17


title: sorted cell fraction 20


title: sorted cell fraction 12


title: sorted cell fraction 15


title: sorted cell fraction 27


title: sorted cell fraction 9


title: sorted cell fraction 16


title: sorted cell fraction 13


title: sorted cell fraction 7


title: sorted cell fraction 21


title: sorted cell fraction 18


title: sorted cell fraction 63


title: sorted cell fraction 11


title: sorted cell fraction 14


title: sorted cell fraction 4


title: sorted cell fraction 8


title: sorted cell fraction 10


title: sorted cell fraction 6


title: sorted cell fraction 5


title: sorted cell fraction 3


title: sorted cell fraction 19


title: sorted cell fraction 1


title: Liver, AIN 93W (control) diet, age 28 months, replicate 1

status: Public on Aug 09 2016

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Mouse Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.36.1)

label_protocol: One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT expression kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands).

growth_protocol: Mice arrived at the age of 7 weeks and received AIN-93G for 2 weeks acclimatization period. At the age of 9 weeks, dietary intervention was started and the diets were maintained until sacrifice time points at the age of 6, 12, 24 and 28 months.

extract_protocol: Total RNA was isolated using RNeasy micro kit from Qiagen. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Prior to sacrifice each mouse was first fasted for 4 hours after which they received an intragastric gavage of 400ul of 0.5% carboxymethyl cellulose, then fasted again for another 6 hours. The animals in CR diet group were fed with half of the portion they normally received 15 min before the first fasting. During the sacrifice, after sedation with a mixture of isoflurane (1.5%), nitrous oxide (70%) and oxygen (30%), liver tissue was snap-frozen and stored at -80C until further analysis.

tag: strain/background

value: male

value: 28 months

value: AIN-93W (control)

tag: nafld status

value: NAFLD (IHTG >5%)


title: Liver, calorie restriction (30%), age 28 months, replicate 3

value: caloric restriction, 30% (CR)

value: no NAFLD


title: Liver, medium fat diet (25% energy), age 28 months, replicate 2

value: medium fat (25energy%) (MF)


title: Liver, calorie restriction (30%), age 28 months, replicate 2


title: Wild-type BMDM infected with influenza A virus PR8, rep 2

status: Public on Aug 11 2016

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

hyb_protocol: Five micrograms of cDNA was hybridized for 16h at 45C on a Mouse Gene 2.0 ST GeneChip array

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

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using Partek Genomics Suite software v6.5

source_name: Wild-type BMDM_influenza A virus PR8

label_protocol: Sense target cDNA was prepared from 100ng of total RNA using the Ambion® WT Expression Kit (Life Technologies P/N 4411973). cDNA was fragmented and biotin-labeled using the Affymetrix® GeneChip® WT Terminal Labeling Kit (Affymetrix P/N 900671)

growth_protocol: Primary BMDMs were grown for 5–6 days in DMEM (Gibco) supplemented with 1% non-essential amino acids (Gibco), 10% FBS (Atlanta Biologicals), 30% medium conditioned by L929 mouse fibroblasts, and 1% penicillin and streptomycin (Sigma).

extract_protocol: Total RNA was extracted using the Qiagen Rneasy protocol according to the manufacturer's recommended methods

treatment_protocol: BMDMs in antibiotic–free medium were seeded onto 12-well plates at a density of 1 × 106 cells per well, followed by incubation overnight. Cells were then infected with influenza A virus PR8 (MOI, 25) and cultured for an additional 9 hours before extracting total RNA.

tag: strain background

value: wild type

value: bone marrow derived macrophages

tag: infected with

value: influenza A virus PR8 for 9 hrs


title: Liver, medium fat diet (25% energy), age 28 months, replicate 7


title: sorted cell fraction 2


title: Liver, AIN 93W (control) diet, age 28 months, replicate 4


title: Liver, medium fat diet (25% energy), age 28 months, replicate 4


title: Ifnar1-/- BMDM infected with influenza A virus PR8, rep 2

source_name: Ifnar1-/- BMDM_influenza A virus PR8

value: Ifnar1-/- mouse backcrossed to the C57BL/6 background

tag: cell type


title: sorted cell fraction 53


title: Liver, calorie restriction (30%), age 28 months, replicate 5

tag: age


title: Liver, medium fat diet (25% energy), age 28 months, replicate 6


title: Liver, AIN 93W (control) diet, age 28 months, replicate 6


title: Liver, AIN 93W (control) diet, age 28 months, replicate 3


title: Liver, medium fat diet (25% energy), age 28 months, replicate 3


title: Liver, medium fat diet (25% energy), age 28 months, replicate 5


title: Wild-type BMDM infected with influenza A virus PR8, rep 1


title: Liver, calorie restriction (30%), age 28 months, replicate 4


title: Liver, calorie restriction (30%), age 28 months, replicate 1


title: Ifnar1-/- BMDM infected with influenza A virus PR8, rep 1


title: Liver, AIN 93W (control) diet, age 28 months, replicate 5


title: Liver, AIN 93W (control) diet, age 28 months, replicate 2


title: Liver, medium fat diet (25% energy), age 28 months, replicate 1


title: Liver, AIN 93W (control) diet, age 28 months, replicate 8


title: Cpt2KO Interscapular Brown Adipose Tissue, injected with 10mg/kg CL316243 3hrs prior to dissection, biological rep3

status: Public on Feb 04 2016

city: Baltimore

first: Michael

middle: J.

last: Wolfgang

state: MD

address: 855 N Wolfe Street

department: Institute for Basic Biomedical Sciences

institute: The Johns Hopkins University School of Medicine

hyb_protocol: 17hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual.

scan_protocol: Using Affymetrix' GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual.

data_processing:
Affymetrix CEL files were extracted and their data normalized with the Partek GS 6.6 platform. Partek's Extended Meta-Probeset set was used with RMA normalization to create quantile-normalized log2 transcript signal values, which were used in subsequent ANOVA analyses.
Probe group file: MoEx-1_0-st-v1.r2.pgf
Meta-probeset file: MoEx-1_0-st-v1.na32.mm9.probeset_extended.mps

source_name: Cpt2KO interscapular brown adipose tissue, CL316243

label_protocol: The Ambion Expression WT kit was used as described in the manufacturer's manual.

growth_protocol: Mouse interscapular brown adipose tissue dissected from 12-week-old mice.

extract_protocol: Adiponectin-Cre; Cpt2f/f and Cpt2f/f (control) mice were identified by PCR genotyping and confirmed by qRT-PCR analysis of mRNA extracted from interscapular brown adipose tissue. All samples were prepared using Trizol followed by RNeasy cleanup (Qiagen).

treatment_protocol: All mice were acclimatized for 2 weeks at 30 degrees Celsius. Mice were injected with either saline or 10mg/kg CL316243 and interscapular brown adipose tissue collected 3hrs later.

value: Cpt2 knockout (adiponectin-Cre;Cpt2f/f)

value: 12 weeks

tag: Sex

value: female

value: interscapular brown adipose tissue

tag: ambient temperature

value: 2 weeks of prior incubation at 30 degrees Celsius

tag: stimulation

value: intraperitoneal injection of 10mg/kg CL316243 (3hrs)


title: Adult Human Input

status: Public on May 18 2015

type: SRA

city: Minneapolis

first: Micah

last: Gearhart

state: MN

address: 6-160 Jackson Hall, 321 Church St.

department: Genetics, Cell Biology and Development

institute: University of Minnesota

description: clinical sample: raw data not submitted to GEO due to patient privacy concerns

library_source: genomic

data_processing:
Reads were trimmed with Trimmomatic Version 0.32, parameters: ILLUMINACLIP:TruSeq3-SE.fa (or -PE.fa):2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:5 MINLEN:25
Trimmed reads were mapped to the mm9 or hg19 genomes with bwa mem version 0.7.10-r789.
Mapped reads were indexed and sorted with samtools 0.1.18.
Peaks were called with MACS2 (MACS2.1.0.20140616)
Genome_build: mm9 or hg19

molecule: genomic DNA

source_name: Adult Human Testis

extract_protocol:
Testis samples were fixed with formaldehyde.
The ChIP libraries were made from the input and the material immuniprecipitated with the Dmrt1 antibody described in PMID 11040213.   Chromatin fragments were blunted with Lucigen DNA terminator enyme mix (Lucigen# 40035).  Blunted fragments were adenylated with Exo- Klenow (NEB #MO2125).  Illumina adapters (Illumina #100521) were diluted 1:50 and ligated to adenylated fragments with T4 ligase (NEB #NEB M0202T).  Products were amplified with 18 rounds of PCR using Phusion Polymerase (NEB M0530s) using barcoded oligonucleotides.  DNA fragments between 150 and 250 were purified by agarose gel electrophoresis. ChIP-Exo libraries were prepared as described in PMID: 22153082.

value: adult

tag: tissue

value: Testes

tag: antibody

value: none (input)


title: Adult Human ChIP

tag: developmental stage

value: dmrt1 Antibody (PMID:11040213)


title: Cpt2KO Interscapular Brown Adipose Tissue, injected with 10mg/kg CL316243 3hrs prior to dissection, biological rep1

tag: genotype/variation


title: Cpt2KO Interscapular Brown Adipose Tissue, injected with 10mg/kg CL316243 3hrs prior to dissection, biological rep2


title: Cpt2KO Interscapular Brown Adipose Tissue, injected with saline 3hrs prior to dissection, biological rep3

source_name: Cpt2KO interscapular brown adipose tissue, saline

value: intraperitoneal injection of saline (3hrs)


title: MeDIP_parental_rep1

status: Public on Dec 03 2014

city: Heidelberg

first: Lukas

last: Chavez

address: Im Neuenheimer Feld 280

institute: German Cancer Research Center (DKFZ)

data_processing:
MeDIP and Input reads derived from parental v6.5 mESC and Tet2 kd mESC and mapped against mm9 as previously described [Pastor et al. Nature 2011, PMID 21552279] by discarding all reads that map to multiple positions in the genome. The obtained mapping results (b ed files) were converted to bam files using the bedToBam function of bedtools. Mapping results from replicates were pooled. Reads that map to the same genomic position were replaced by one representative.
In order to identify genome wide differentially hydroxymethylated regions (DHMRs) in parental v6.5 compared to Tet1, or Tet2 kd, respectively, we calculated library size normalized differential coverage of the CMS-IP data at genome wide 300 bp windows by employing a developmental version (v1.9.10) of the Bioconductor package MEDIPS (extend=200, uniq=F, window_size=300, BSgenome=BSgenome.Mmusculus.UCSC.mm9, diff.method = edgeR, p.vale = 1e-5), and adjacent significant windows with the same direction of 5hmC change were merged.
Genome_build: mm9
Supplementary_files_format_and_content: BED files with mapped read alignments available on the sample records due to absence of available raw data files. Result tables contain counts, rpkm, log2FC, and p-values at genome wide 300 bp windows as returned by the MEDIPS software for Tet2 kd mESC vs. V6.5mESC

source_name: parental V6.5 mES cells

growth_protocol: Mouse embryonic stem cells were cultured in Knockout D-MEM with 15% ES-qualified FBS (Gemini Bio-products), 2 mM L-glutamine with 0.1 mM 2-mercaptoethanol, 0.1 mM nonessential amino acids, 50 units/ml penicillin/streptomycin and 1000 U/ml ESGRO® (LIF; Chemicon).

extract_protocol:
not provided
libraries were prepared followed by the instruction provied by illumina Truseq DNA library preperation kit

treatment_protocol: Cells stably depleted of Tet1 and Tet2 were obtained by electroporating V6.5 mESC with pSUPER-puro-Tet1shRNA or pSUPER-puro-Tet2shRNA (320V, 250F). Cells were selected by 1.5 ug/ml puromycin for 7-10 days on puromycin-resistant mitomycine C-inactivated SNL76/7-4 feeder cells. Individual clones were picked and propagated in the absence of puromycin if the passage number was less than 10, or maintained in 1 ug/ml puromycin if the passage number was longer than 10. Tet1 and Tet2 mRNA expression in individual clones was evaluated by qPCR.

tag: knockdown

tag: dna enrichment

value: MeDIP

tag: biological replicate

tag: cell line

value: mES


title: WT Interscapular Brown Adipose Tissue, injected with 10mg/kg CL316243 3hrs prior to dissection, biological rep1

source_name: WT interscapular brown adipose tissue, CL316243

tag: strain/background

value: wild-type control (Cpt2f/f)


title: WT Interscapular Brown Adipose Tissue, injected with 10mg/kg CL316243 3hrs prior to dissection, biological rep2


title: MeDIP_Tet2kd_rep1

source_name: Tet2kd mES cells

value: Tet2 kd


title: MeDIP_parental_Input_rep1

value: none, input


title: Cpt2KO Interscapular Brown Adipose Tissue, injected with saline 3hrs prior to dissection, biological rep2


title: BM CD34+ cells from Healthy Donor 9 (GEP)

status: Public on Oct 01 2014

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Life Sciences

country: Italy

institute: Centre for Regenerative Medicine

description: Bone Marrow CD34+ cells from healthy donor

hyb_protocol: Regarding GEP, fragmented cRNA was hybridized for 16 hr at 45C on Affymetrix HG-U219 array strips in GeneAtlas Hybridization Station. GeneChips were washed and stained using GeneAtlas Hybridization, Wash, and Stain Kit for 3’IVT Arrays, according to the standard protocol supplied by Affymetrix (GeneAtlas 3’ IVT Express Kit, P/N 702833 Rev. 4). As for miEP, tagged RNA was hybridized to the Affymetrix Genechip miRNA array 2.0 using manufacturer's recommendations (FlashTag™ Biotin HSR RNA Labeling Kit, P/N 703095 Rev. 1). The miRNA arrays were washed and stained by GeneChip Hybridization, Wash and Stain Kit (Affymetrix) with Fluidic Station 450 using fluidic script FS450_003.

scan_protocol: Affymetrix HG-U219 array strips were finally scanned using GeneAtlas Scanner.  Affymetrix Genechip miRNA arrays 2.0 were scanned using the Affymetrix GCS3000 7G Scanner.

data_processing: Gene expression data were imported into Partek Genomics Suite 6.6 (Partek, St Louis, Mo) as CEL files using default parameters. Raw data were preprocessed, including background correction, normalization, and summarization using robust multiarray average (RMA) analysis.

source_name: CTR Bone Marrow CD34+ Cells

label_protocol: Gene expression profiling (GEP) and miRNA expression profiling (miEP) were performed on the same RNA preparation. As regards GEP, biotinylated cRNA were prepared according to the standard GeneAtlas 3’IVT Express Kit protocol from 100ng of  total RNA (P/N 702833 Rev. 4, Affymetrix). Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) was used to evaluate the cRNA sample concentration.As for miEP, total RNA (100ng for samples) were labeled using the FlashTag® Biotin HSR kit (Affymetrix).

growth_protocol: CD34+ cells were purified from 30–50 ml of PB collected from PMF patients, from 150 ml of PB from G-CSF untreated healthy donors, or from 5 ml of BM aspirates, all obtained in preservative free heparin.  Mononuclear cells were separated over a Ficoll-Paque gradient (Lympholyte; Cederlane Labs) and processed through two sequential steps of immunomagnetic CD34  selection (Miltenyi Biotec, Bergisch Gladbach,Germany,http://www.miltenyibiotec.com). Purity of the isolated CD34+ cell population was evaluated by flow cytometry after labeling with PE-HPCA2 anti-CD34 monoclonal antibody (BD Biosciences) and was always > 95%.

extract_protocol: CD34+ cells were purified from Peripheral Blood of PMF patients and immediately  lysed in 700uL of QIAZOL Buffer (Qiagen, Valencia, CA, USA). Total RNA from CD34+ cells was extracted using miRNeasy Mini Kit (Qiagen, Valencia, CA, USA) in accordance with the manufacturer’s recommendations for Purification of Total RNA, Including Small RNAs, from Animal Cells. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit; Agilent Technologies, Waldbrunn, Germany) were used to determine the concentration and purity/integrity of RNA samples using Agilent 2100 Bioanalyzer. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) was used to evaluate the RNA sample concentration, and 260/280 and 260/230 nm ratios were considered to verify the purity of total RNA.

tag: supplier

value: Vannucchi

value: CTR

tag: disease

value: BM CTR

value: neg

value: BM


title: WT Interscapular Brown Adipose Tissue, injected with saline 3hrs prior to dissection, biological rep3

source_name: WT interscapular brown adipose tissue, saline

value: 12 weeks

value: female

value: interscapular brown adipose tissue

value: 2 weeks of prior incubation at 30 degrees Celsius


title: WT Interscapular Brown Adipose Tissue, injected with saline 3hrs prior to dissection, biological rep2


title: Cpt2KO Interscapular Brown Adipose Tissue, injected with saline 3hrs prior to dissection, biological rep1

value: Cpt2 knockout (adiponectin-Cre;Cpt2f/f)


title: WT Interscapular Brown Adipose Tissue, injected with 10mg/kg CL316243 3hrs prior to dissection, biological rep3

value: intraperitoneal injection of 10mg/kg CL316243 (3hrs)


title: BM CD34+ cells from Healthy Donor 13 (GEP)


title: BM CD34+ cells from Healthy Donor 12 (GEP)


title: BM CD34+ cells from Healthy Donor 2 (GEP)


title: BM CD34+ cells from Healthy Donor 5 (GEP)


title: BM CD34+ cells from Healthy Donor 8 (GEP)


title: BM CD34+ cells from Healthy Donor 11 (GEP)


title: BM CD34+ cells from Healthy Donor 3 (GEP)


title: BM CD34+ cells from Healthy Donor 15 (GEP)

value: Cazzola


title: BM CD34+ cells from Healthy Donor 6 (GEP)


title: BM CD34+ cells from Healthy Donor 4 (GEP)


title: WT Interscapular Brown Adipose Tissue, injected with saline 3hrs prior to dissection, biological rep1

value: intraperitoneal injection of saline (3hrs)


title: BM CD34+ cells from Healthy Donor 14 (GEP)


title: BM CD34+ cells from Healthy Donor 7 (GEP)


title: BM CD34+ cells from Healthy Donor 10 (GEP)


title: BM CD34+ cells from Healthy Donor 8 (miEP)


title: BM CD34+ cells from Healthy Donor 2 (miEP)


title: BM CD34+ cells from Healthy Donor 9 (miEP)


title: BM CD34+ cells from Healthy Donor 7 (miEP)


title: BM CD34+ cells from Healthy Donor 15 (miEP)


title: BM CD34+ cells from Healthy Donor 14 (miEP)


title: Liver, AIN 93W (control) diet, age 28 months, replicate 7

tag: gender

value: male

value: 28 months

value: AIN-93W (control)

tag: nafld status

value: NAFLD (IHTG >5%)


title: BM CD34+ cells from Healthy Donor 6 (miEP)

value: Vannucchi

tag: cell type


title: BM CD34+ cells from Healthy Donor 5 (miEP)

value: CTR


title: BM CD34+ cells from Healthy Donor 4 (miEP)

value: BM CTR


title: BM CD34+ cells from Healthy Donor 12 (miEP)

value: neg


title: BM CD34+ cells from Healthy Donor 3 (miEP)

value: BM


title: BM CD34+ cells from Healthy Donor 1 (GEP)


title: BM CD34+ cells from Healthy Donor 13 (miEP)


title: MeDIP_Tet2kd_rep2

value: Tet2 kd

value: MeDIP

value: mES


title: BM CD34+ cells from Healthy Donor 10 (miEP)


title: BM CD34+ cells from Healthy Donor 1 (miEP)


title: BM CD34+ cells from Healthy Donor 11 (miEP)


title: Tissue_model_Epi_200_0Gy_16h_rep2

status: Public on Aug 31 2011

first: Alexandre

last: Mezentsev

address: 630 west 168th Street, VC 15-204

department: Dermatology

institute: Columbia University

description: Gene expression in 0 Gy-proton irradiated tissue model, 4h postirradiation

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 250 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan setting with eXtended dynamic range, Scan area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR Lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1.3.1 (Agilent) using default parameters (protocol GE1-v1_91_1 and Grid: 014850_D_20070207) to obtain background subtracted and spatially detrended green Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers or Features not Positive and significant were excluded.

source_name: human foreskin

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer’s instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Samples were supplied on ice with overnight delivery and were cultured 24 h prior irradiation and 1 or 16 h prior harvesting, postirradiation. Growth medium, NMM-100, was kindly supplied by the manufacturer. Medium was changed every 24h.

extract_protocol: Total RNA was isolated with RNaqueous Kit (Applied Biosystems), tested for spectral characteristics (NanoDrop, Thermo Scientific) and electrophoretically (Bioanalyser 2100, Agilent).

treatment_protocol: Tissues were irradiated with 0 and 0.5Gy of alpha particles

tag: sample type

value: epidermis model

tag: treatment

value: 0Gy 16h


title: Tissue_model_Epi_200_0Gy_16h_rep1


title: Tissue_model_Epi_200_0.5Gy_1h_rep1


title: Tissue_model_Epi_200_0.5Gy_16h_rep2

description: Gene expression in 0.1 Gy-proton irradiated tissue model, 4h postirradiation


title: Tissue_model_Epi_200_0Gy_16h_rep3


title: Tissue_model_Epi_200_0.5Gy_1h_rep2


title: Tissue_model_Epi_200_0.5Gy_16h_rep1


title: Bcell-H3K4me3-Kdo2-1h-ChIP-Seq

status: Public on Jan 01 2011

city: La Jolla

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

description: Chromatin IP against H3K4me3 in immature B cells treated with Kdo2 for 1h

data_processing:
Alignment: Reads were truncated to 25 bp (ChIP-Seq) or 32 bp (RNA, GRO-Seq) and aligned to the mouse mm8 genome (NCBI Build 36) using eland. Only reads that mapped to a single, unique position were used for downstream analysis.
Data analysis was performed using HOMER, a software suite for ChIP-Seq analysis and created in part to support this study (http://biowhat.ucsd.edu/homer/). Each ChIP-Seq experiment was normalized to a total of 10^7 uniquely mapped tags by adjusting the number of tags at each position in the genome to the correct fractional amount given the total tags mapped. UCSC Genome Browser bedGraph files were created by calculating ChIP-Fragment pileups given a fragment size of ~150 bp.
bedGraph files were replaced Sept 01, 2010 and have been re-formatted for use with the updated UCSC Genome Browser.

source_name: resting splenic B cells

growth_protocol: Splenic B cells were isolated by magnetic depletion of CD43- and CD11b-expressing cells (Miltenyi, Bergisch Gladbach, Germany).

extract_protocol: For ChIP-Seq, lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, ChIP DNA was PCR-amplified with Illumina primers for 12-16 cycles and library fragments of 200-300 bp (ChIP) (insert plus adaptor and PCR primer sequences) were isolated from a 2% agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer or Genome Analyzer II following the manufacturer's protocols.

value: resting splenic B cells

tag: chip antibody

value: Kdo2 Lipid A for 1 hour

tag: transgenes

tag: genetic background


title: Tissue_model_Epi_200_0.5Gy_16h_rep3

tag: tissue


title: Tissue_model_Epi_200_0Gy_1h_rep3

value: 0Gy 1h


title: PUER-CEBPb-1h-ChIP-Seq

status: Public on May 27 2010

description: Chromatin IP against C/EBPb in PUER cells after 1h Tamoxifen treatment

data_processing:
Alignment: Reads were truncated to 25 bp and aligned to the mouse mm8 genome (NCBI Build 36) using eland. Only reads that mapped to a single, unique position were used for downstream analysis.
Peak Identification: Peaks were identified using custom software (HOMER, available at http://biowhat.ucsd.edu/homer/). For transcription factors, peaks were found by identifying 200 bp regions with tag density exceeding a threshold set at a 0.1% false discovery rate (determined by tag randomization). Only peaks with >4x normalized tag density relative to control sequencing and >4x normlaized tag density to the sourrounding 10kb of region were considered for analysis.

source_name: PUER cells

growth_protocol: PUER cells were propagated in 10 % FCS/Iscove's Modified Dulbecco's Medium (IMDM) supplemented with 100 U/ml penicillin/streptomycin, 1 µg/ml puromycin, 2 mM L-glutamine and 5 ng/ml recombinant mIL-4. The PU.1-ER fusion protein was activated by adding 4-hydroxy-tamoxifen at a final concentration of 100 nM to the media.

extract_protocol: Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody. Alternatively, DNA was phenol/chloroform-extracted from MNase-treated nuclei, and 134-154 bp long fragments were extractred from a 2% agarose gel. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, ChIP DNA was PCR-amplified with Illumina primers for 12-16 cycles and library fragments of 200-300 bp (ChIP) (insert plus adaptor and PCR primer sequences) were isolated from a 2% agarose gel. For MNase-Seq, size-selected mononucleosome-derived DNA fragments were ligated to modified adapters that incorporate both the adapter sequence as well as the primer landing sites for the flow cell-conjugated primers. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer or Genome Analyzer II following the manufacturer's protocols.

treatment_protocol: Tamoxifen, 1h

value: PUER cells

value: C/EBPb (sc-150)

value: Tamoxifen, 1h

tag: strain

tag: genotype/variation

value: C/EBPb (Vendor:Santa Cruz, cat# sc-150, lot# D0808)


title: PUER-PU.1-6h-ChIP-Seq

description: Chromatin IP against PU.1 in PUER cells after 6h Tamoxifen treatment

treatment_protocol: Tamoxifen, 6h

value: Tamoxifen, 6h

value: PU.1 (Vendor:Santa Cruz, cat# sc-352, lot# F1808)


title: PUER-PU.1-0h-ChIP-Seq

description: Chromatin IP against PU.1 in PUER cells after 0h Tamoxifen treatment

growth_protocol: PUER cells were propagated in 10 % FCS/Iscove's Modified Dulbecco's Medium (IMDM) supplemented with 100 U/ml penicillin/streptomycin, 1 µg/ml puromycin, 2 mM L-glutamine and 5 ng/ml recombinant mIL-4.


title: PUER-CEBPb-6h-ChIP-Seq

description: Chromatin IP against C/EBPb in PUER cells after 6h Tamoxifen treatment


title: BMDM-H3K4me3-Kdo2-1h-ChIP-Seq

description: Chromatin IP against H3K4me3 in BMDM treated with Kdo2 for 1h

source_name: bone marrow-derived macrophages

growth_protocol: Bone marrow was harvested and washed once with PBS, seeded/cultured in DMEM containing 20 % FCS, 30 % L-cell conditioned media (as source of macrophage colony stimulating factor, M-CSF), and 100 U/ml penicillin/streptomycin in non-tissue culture-treated petri dishes. After 6-8 days of culture, non-adherent cells were washed off with room temperature PBS and macrophages were obtained as a homogeneous population of adherent cells which were scraped and subsequently seeded onto tissue culture-treated petri dishes overnight in RPMI 1640 containing 10% FCS, 100 U/ml penicillin/streptomycin, and 10ng/ml M-CSF.

value: macrophage


title: PUER-PU.1-1h-ChIP-Seq

description: Chromatin IP against PU.1 in PUER cells after 1h Tamoxifen treatment


title: PUER-CEBPb-24h-ChIP-Seq

description: Chromatin IP against C/EBPb in PUER cells after 24h Tamoxifen treatment

treatment_protocol: Tamoxifen, 24h

value: Tamoxifen, 24h


title: ThioMac-H3ac-ChIP-Seq

description: Chromatin IP against H3ac

growth_protocol: Peritoneal macrophages were harvested by peritoneal lavage with 10 ml ice-cold PBS 3 days after peritoneal injection of 3 ml thioglycollate broth. Peritoneal cells were washed once with PBS, and seeded in 10% fetal calf serum (FCS)/DMEM containing 100 U/ml penicillin/streptomycin in tissue culture-treated petri dishes overnight. Non-adherent cells were washed off with room temperature PBS.

value: H3ac (Millipore 06-599 LOT 25233)


title: PUER-CEBPb-0h-ChIP-Seq

description: Chromatin IP against C/EBPb in PUER cells after 0h Tamoxifen treatment


title: PUER-PU.1-24h-ChIP-Seq

description: Chromatin IP against PU.1 in PUER cells after 24h Tamoxifen treatment


title: PHF8_HeLa_G1_S_ChIPSeq

status: Public on Sep 01 2010

last: Rosenfeld

state: CA

address: 9500 Gilman Drive

department: School of Medicine

institute: HHMI/UCSD

description: ChIP against PHF8

data_processing: The image analysis and base calling were performed by using Illumina's Genome Analysis pipeline. The sequencing reads were aligned to the human genome UCSC build hg18 by using BOWTIE alignment. Both uniquely aligned reads and the sequencing reads that align to repetitive regions were kept for downstream analysis (if a read aligns to multiple genome locations, only one location is arbitrarily chosen).

source_name: HeLa cells

growth_protocol: HeLa cells were cultured in DMEM medium with 10% FBS.

extract_protocol: the libraries were constructed following Illumina's Chip-Seq. Sample prep kit. Briefly, Chip DNA was end-blunted and added with an "A" base so the adaptors from Illumina with a “T” can ligate on the ends. Then 200-400 bp fragments are gel isolated and then purified.  18 cycles of PCR was done to amplify the library.

treatment_protocol: HeLa cells were either unsynchronized or synchronized by double thymidine block protocol to obtain G1 and G1/S phases cells or by colcemid to obtain M phase cells

value: HeLa cells

tag: antibody

tag: antibody catalog

tag: antibody manufacturer

value: Abcam


title: PHF8_HeLa_G1_ChIPSeq

description: ChIP against PHF8

tag: cell line


title: Tissue_model_Epi_200_0.5Gy_1h_rep3


title: EBFKO-PU.1-ChIP-Seq

description: Chromatin IP against PU.1 in EBF-/- pre-pro-B cells

source_name: EBF-/- pre-pro-B cell

growth_protocol: E2A-/-and EBF-/- pre-pro-B cells were cultured on S17 stromal cells in the presence of IL7 (10 ng/ml), SCF (10 ng/ml), and FLT3 ligand (10 ng/ml) in Iscove’s Dulbecco’s medium and in the presence of 10% FCS, 200 U/ml penicillin, 200 mg/ml streptomycin and 4 mM L-glutamine.

value: pre-pro-B cell

value: EBF-/-


title: E2AKO-PU.1-ChIP-Seq

description: Chromatin IP against PU.1 in E2A-/- pre-pro-B cells

source_name: E2A-/- pre-pro-B cell


title: RAG1KO-E2A-ChIP-Seq

status: Public on Jun 13 2010

description: Chromatin IP against E2A in RAG1-/- pro-B cells

source_name: RAG1-/- pro-B cell

growth_protocol: Pro-B cells were isolated from femoral bone marrow of Rag1 knockout mice by positive enrichment of B220+ cells using magnetic separation (Miltenyi) and expanded for 10 d in Opti-MEM medium containing 10% FCS, 2x penicillin/streptomycin/glutamine, and 50 µM ß-mercaptoethanol supplemented with IL-7 and SCF.

extract_protocol: Lysates were clarified from sonicated cells or nuclei and protein-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, ChIP DNA was PCR-amplified with Illumina primers for 12-18 cycles and library fragments (ChIP) (insert plus adaptor and PCR primer sequences) were size selected from a 2% agarose gel or a 8% polyacrylamide gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer I or Genome Analyzer II following the manufacturer's protocols.

value: pro-B cell


title: Bcell-input-ChIP-Seq

description: Mock IP in immature B cells

value: resting splenic B cells

value: none (input)


title: Bcell-H3K4me3-ChIP-Seq

description: Chromatin IP against H3K4me3 in immature B cells

value: H3K4me3 (Vendor:Abcam, cat# ab8580, lot# 122342)


title: Tissue_model_Epi_200_0Gy_1h_rep1

value: epidermis model

value: 0Gy 1h


title: Tissue_model_Epi_200_0Gy_1h_rep2


title: ThioMac-input-ChIP-Seq

description: Mock IP in ThioMac


title: ThioMac-CEBPa-ChIP-Seq

description: Chromatin IP against C/EBPa in ThioMac

value: C/EBPa (sc-61)

value: C/EBPa (Vendor:Santa Cruz, cat# sc-61, lot# D0108)


title: ThioMac-H3K4me3-ChIP-Seq

description: Chromatin IP against H3K4me3 in ThioMac


title: Bcell-PU.1-ChIP-Seq

description: Chromatin IP against PU.1 in immature B cells


title: Bcell-Oct2-ChIP-Seq

description: Chromatin IP against Oct-2 in immature B cells

value: Oct2 (Vendor:Santa Cruz, cat# sc-233)


title: ThioMac-CEBPb-ChIP-Seq

description: Chromatin IP against C/EBPb in ThioMac

value: C/EBPb (sc-150)

value: C/EBPb (Vendor:Santa Cruz, cat# sc-150, lot# D0808)


title: ThioMac-PU.1-ChIP-Seq

description: Chromatin IP against PU.1 in ThioMac

value: macrophage

value: PU.1 (Vendor:Santa Cruz, cat# sc-352, lot# F1808)


title: PU.1.LPS_2h

status: Public on Mar 05 2010

city: Vienna

first: Iros

last: Barozzi

address: Borschkegasse 8a

country: Austria

institute: Medical University Vienna

description: Chromatin IP against PU.1 2hrs post treatment

data_processing:
Alignment: sequence reads were mapped to the mouse mm9 genome using ELAND (Illumina pipeline version 1.3). All reads that maps uniquely to the genome with two or fewer mismatches were kept.
Peaks: analyses were performed using MACS (PMID: 18798982) with a bandwith of 150bp and a p-value threshold of 10^-5. p300 and H3K4me1 ChIPs were normalized against input DNA. PU.1 ChIPs were normalized against a theoric distribution of the same number of tags.

source_name: Primary bone marrow-derived macrophages (BMDM) from Fvb mice

growth_protocol: Bone marrow cells isolated from female Fvb mice were plated in 10 cm plates in 5ml of BM-medium (high glucose DMEM supplemented with 20% low endotoxin fetal bovine serum, 30% L929-conditioned medium, 1% glutamine, 1%, Pen/Strep, 0.5% Sodium Pyruvate, 0.1% β-mercaptoethanol). Cultures were fed with 2.5 ml of fresh medium every two days.

extract_protocol: ChIP lysates were generated from 2x10^8 cells. Cells were fixed in 1% formaldehyde for 10min.  Lysate was immunoprecipitated with 10ug of antibody. Antibodies were pre-bound overnight to 100ul of G protein-coupled paramagnetic beads in PBS/BSA 0.5%. Beads were then added to lysates (the preclearing step was omitted) and incubation was let to proceed overnight. Beads were washed 6 times in a modified RIPA buffer (50mM Hepes pH 7.6, 500mM LiCl, 1mM EDTA, 1% NP-40, 0.7% Na-deoxycholate) and once in TE containing 50mM NaCl. DNA was eluted in TE containing 2% SDS and crosslinks reversed by incubation overnight at 65ºC. DNA was then purified by Qiaquick columns (Qiagen) and quantified using PicoGreen (Invitrogen). ChIP DNA was prepared for Solexa 2G sequencing using a standard protocol consisting in blunting, addition of dA overhangs, ligation of Illumina adapters, selection on gel and PCR. A mixture of T4 DNA polymerase, DNA polymerase I and T4 kinase was used according to manufacturer’s instruction.

treatment_protocol: Macrophages were stimulated with lipopolysaccharide (LPS, 10 ng/ml)

value: BMDM cells (7th day of differentiation)

value: Santa Cruz

tag: antibody catalog number

value: LPS (10 ng/ml) for 2hrs


title: Input_DNA

description: Control Input DNA

value: No treatment


title: p300.UT

description: Chromatin IP against p300


title: p300.LPS_2h

description: Chromatin IP against p300 2hrs post treatment


title: PU.1.UT

description: Chromatin IP against PU.1


title: H3K4me1.UT

description: Chromatin IP against H3K4me1

value: Abcam