title: D10MGT2

status: Public on Oct 25 2017

city: WAUWATOSA

first: ZIQING

last: LIU

state: WI

address: 8701 W Watertown Plank Rd, BSB 5320

department: Biology

institute: Medical College of Wisconsin

description: Gene expression of D10 control CF transduced with MGT

hyb_protocol: Standard Agilent Protocol

scan_protocol: Standard Agilent Protocol

data_processing: The microarray data were processed using the limma package from Bioconductor (Ritchie et al., 2015). Raw data were first background corrected and normalized using “normexp” and “quantile” methods, respectively. Next, control probes and low intensity probes were filtered out using the 1.1 multiplier of 95% quantile for negative controls as a cutoff. Lastly, replicated probes for each gene were averaged to obtain gene expression estimation for subsequent analyses.

label_protocol: Standard Agilent Protocol

growth_protocol: iCMs were generated by infecting CFs with retroviruses expressing a polycistronic Mef2c, Gata4 and Tbx5 transgene (Wang et al., J. Vis. Exp. 2015).

extract_protocol: Total RNA was isolated with TRIzol (Invitrogen) and purified using RNeasy mini kit (QIAGEN) according to the manufacturer’s instruction.

treatment_protocol: Cells were lysed using TRIzol.

tag: time point

value: control CF transduced with MGT

value: aMHC-GFP


title: Pcan3H1

status: Public on Oct 26 2017

type: RNA

city: Göttingen

first: Victor

last: Chano

address: Buesgenweg 2

department: Forest Genetics and Forest Tree Breeding

country: Germany

institute: University of Göttingen

description: Pc16 CH0 (Cy5) vs Pc16 H0 (Cy3)

hyb_protocol: Probes were mixed and hybridized to a 60K custom microarray (Agilent Technologies) for 17 hours at 65ºC in Gex Hybridization Buffer HI-RPM in a hybridization oven. Arrays were washed according to the manufacturer’s instructions, dried by centrifugation.

scan_protocol: Arrays were scanned at 3 mm resolution on Agilent DNA Microarrays Scanner (G2565BA, Agilent Technologies) and the images were analyzed with Feature Extraction software (Agilent Technologies).

data_processing: For local background correction and normalization, the methods normexp and loess in LIMMA were used, respectively (Smyth and Speed 2003).

molecule: total RNA

organism: Pinus canariensis

source_name: Traumatic xylem formed in wound margins

label_protocol: The Low Input Quick Amp Labeling Kit, Two-Color generates fluorescent cRNA (complimentary RNA) with 200 ng of total RNA  for two-color processing. The method uses T7 RNA Polymerase Blend (red cap), which simultaneously amplifies target material and incorporates Cyanine 3-CTP or Cyanine 5-CTP.

growth_protocol: Pines were grown in greenhouse, using 650 ml conical containers with 3:1 (v/v) peat:vermiculite. After the first year, trees were transferred to soil in experimental garden at UPM facilities, and grown under environmental conditions. At the moment of the beginning of this experiment, trees were 5 years old, approximately 2 m high and 7-10 cm diameter at the base.

extract_protocol: Total RNA was isolated from differentiating xylem samples stored at -80ºC, using the CTAB-LiCl precipitation method (Chang et al. 1993), and purified with the RNeasy Plant Mini Kit (Qiagen, CA, USA). Quantity of total RNA for each sample was measured with Nanodrop model ND-1000 (Thermo Scientific, MA, USA), and RNA quality was checked using the Experion Bioanalyzer (Bio-Rad, CA, USA).

tag: tissue

value: Traumatic xylem

tag: Stage

source_name: Cambial cells differentiating to xylem in remote parts of the plant

value: Xylem (control)


title: D10lacZ2

country: USA

description: Gene expression of D10 control CF transduced with lacZ

organism: Mus musculus

tag: strain

tag: cell type

value: control CF transduced with lacZ

tag: genotype


title: CRHR1-/- KO;AAV-flex GFP 5

city: Houston

first: Benjamin

middle: R

last: Arenkiel

state: Texas

address: 1250 Moursund St, 11th floor, Ste 1150.01

department: Molecular and Human Genetics

institute: Baylor College of Medicine

description: Gene expression in mouse olfactory bulbs with CRHR1 knocked out of mouse genome, including olfactory granule cells.

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 600 ng Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65 ¡C) to Agilent Whole Mouse Genome Oligo Microarrays 8x60K using Agilent's recommended hybridization chamber and oven. Finally, the microarrays were washed once with the Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 (37 °C) for 1 min.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent's Microarray Scanner System (Agilent Technologies).

data_processing: The Agilent Feature Extraction Software v.9.1was used to read out and process the microarray image files. The software determines feature intensities (including background subtraction), rejects outliers and calculates statistical confidences.

source_name: Olfactory bulb

label_protocol: For the linear T7-based amplification step, 100 ng of each total RNA sample was used. To produce Cyanine-3 (Cy3)-labeled cRNA, the RNA samples were amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer's protocol. Yields of cRNA and the dye-incorporation rate were measured with the ND-1000 Spectrophotometer (NanoDrop Technologies).

extract_protocol: Total bulb RNA was isolated by TRIzol reagent (Ambion, Invitrogen) according to manufacturer's protocol and treated with DNaseI (Promega).

treatment_protocol: The three animal groups in this experiment were CRHR1-/- mice injected with control AAV-flex-EGFP (CRHR1-/-;AAV-flex-EGFP = low CRH signaling group), CRHR1-Cre;AAV-flex-GFP (pseudo-wild type CRH signaling group), and CRHR1-Cre;AAV-flex-(CA)CRHR1 (high CRH signaling group) (n = 5 per group). All animals were males aged 6-8 weeks old. Animals were injected with 500 nL of virus (titer  5x10^10 particles/l) and sacrificed for total bulb RNA extraction 2 weeks post-injection.

tag: age

value: 6-8 week old

tag: gender

value: Male

value: Olfactory bulb infected with AAV-FLEX-GFP


title: D7lacZ2

description: Gene expression of D7 control CF transduced with lacZ


title: D7MGT1

description: Gene expression of D7 control CF transduced with MGT


title: D14lacZ1

description: Gene expression of D14 control CF transduced with lacZ


title: D14lacZ2


title: Pcan1H1

description: Pc13 CH0 (Cy3) vs Pc13 H0 (Cy5)


title: D7MGT2


title: D10MGT1


title: D14MGT1

description: Gene expression of D14 control CF transduced with MGT


title: D10lacZ1


title: D14MGT2


title: D5MGT1

description: Gene expression of D5 control CF transduced with MGT


title: D7lacZ1


title: D5MGT2


title: podocytes treated with DMSO as control, biological rep3

city: Boston

first: Abbe

middle: Rose

last: Clark

state: Massachusetts

address: 4 Blackfan Circle, HIM 534

institute: Harvard, Brigham and Women's Hospital

description:
podocytes cultured in vitro
control_A3

hyb_protocol: As performed by UTSW core facility

scan_protocol: As performed by UTSW core facility

data_processing: Data were processed using ‘affy’ package in R. Background correction, normalization and expression calculation was performed with the rma function using default parameters.

label: biotin

source_name: podocytes cultured in vitro

label_protocol: As performed by UTSW core facility

growth_protocol: Podocytes were differentiated at 37 C for 11 days prior to treatment

extract_protocol: Total RNA extraction performed as in Sieber et al., 2013

treatment_protocol: 2.5µM thapsigargin in the presence or absence of 10µM forskolin for 16 hours

value: podocyte


title: D5lacZ2

description: Gene expression of D5 control CF transduced with lacZ


title: injected with PBS, fish 3, 2 weeks

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol for 4x44k microarrays

scan_protocol: Arrays were scanned with GenePix 4100A DNA microarray scanner at a resolution of 5 microns

data_processing: Images were processed with GenePix Pro 6.0. After removal of flagged spots lowess normalization was performed

organism: Salmo salar

source_name: muscle

label_protocol: Amplified and labeled  with Low Input Quick Amp Labeling Kit (Agilent).

growth_protocol: Atlantic salmon (Salmo salar L.) presmolts (30–40 g) of the strain Aquagen standard were kept in 300 L tanks supplied with fresh water at 10 °C and were fed commercial dry food

extract_protocol: Total RNA was extracted using the RNeasy® Mini Kit (Qiagen)

treatment_protocol: Presmolt salmon were injected intramuscularly (i.m.) approximately 1 cm below the dorsal fin with 15 μg plasmids in 50 μl sterile phosphate-buffered saline (PBS) at pH7.4 or with PBS only. Fish groups included non-treated fish, fish injected with PBS, pcDNA3.3, pIFNa and pHE. Muscle at the injection site was sampled at one week (W1) and two weeks (W2) after injection and used for RNA isolation.

value: muscle

value: Aquagen

source_name: Pooled muscle of PBS injected fish


title: injected with PBS, fish 1, 2 weeks


title: D3lacZ2

description: Gene expression of D3 control CF transduced with lacZ


title: D3MGT2

description: Gene expression of D3 control CF transduced with MGT


title: D3lacZ1


title: D3MGT1


title: D5lacZ1


title: injected with PBS, fish 4, 2 weeks


title: injected with PBS, fish 2, 2 weeks


title: D0CF2

description: Gene expression of D0 CF

value: CF


title: CRHR-Cre;AAV-flex GFP 3

description: Gene expression in mouse olfactory bulbs with CRHR1+ olfactory granule cells expressing a control, Cre-dependent EGFP.


title: injected with pIFNa, fish 4, 2 weeks


title: injected with pHE, fish 2, 2 weeks


title: D0CF1

description: Gene expression of D0 CF


title: injected with pIFNa, fish 3, 2 weeks


title: injected with pHE, fish 4, 2 weeks


title: injected with pIFNa, fish 1, 2 weeks


title: injected with pHE, fish 1, 2 weeks


title: injected with control plasmid pcDNA3.3, fish 4, 2 weeks


title: uninjected control, fish 1, 2 weeks


title: uninjected control, fish 4, 2 weeks


title: uninjected control, fish 3, 2 weeks


title: injected with PBS, fish 2, 1 week


title: injected with PBS, fish 1, 1 week


title: injected with pHE, fish 3, 2 weeks


title: injected with pIFNa, fish 2, 1 week


title: injected with PBS, fish 4, 1 week


title: uninjected control, fish 4, 1 week


title: injected with control plasmid pcDNA3.3, fish 2, 2 weeks


title: uninjected control, fish 2, 1 week


title: injected with pHE, fish 4, 1 week


title: injected with pHE, fish 1, 1 week


title: injected with pIFNa, fish 1, 1 week


title: uninjected control, fish 2, 2 weeks


title: injected with pHE, fish 2, 1 week


title: injected with pIFNa, fish 3, 1 week


title: injected with control plasmid pcDNA3.3, fish 1, 2 weeks


title: injected with control plasmid pcDNA3.3, fish 3, 2 weeks


title: injected with control plasmid pcDNA3.3, fish 2, 1 week


title: injected with control plasmid pcDNA3.3, fish 4, 1 week


title: injected with PBS, fish 3, 1 week


title: uninjected control, fish 1, 1 week


title: injected with pIFNa, fish 4, 1 week


title: injected with pHE, fish 3, 1 week


title: uninjected control, fish 3, 1 week


title: injected with control plasmid pcDNA3.3, fish 1, 1 week


title: injected with control plasmid pcDNA3.3, fish 3, 1 week


title: Patient 101 2nd vaccination

city: Frankfurt am Main

first: Franziska

last: Matthäus

address: Ruth-Moufang-Str. 1

department: Frankfurt Institute for Advance Studies (FIAS)

institute: Goethe University of Frankfurt

hyb_protocol: Standard Illumina hybridization protocol

data_processing: quantil normalizations, a cut-off at 20 intensity values and a p-value of ≤0.01 with respect to the expression level.

organism: Homo sapiens

source_name: blood

label_protocol: Human Sentrix HumanRef-6 Expression Beadchips (Illumina, USA) that entail six arrays per chip (48,803 genes and gene variants derived from RefSeq), hybridized overnight with biotinylated cDNAs, washed, blocked and fluorescence-labeled using streptavidin-Cy3. Data were obtained and analyzed by the Illumina® Beadarray Reader system, Illumina® BeadStudio Application software and R+ Bioconductor software.

extract_protocol: RNA was isolated from 10 mL of patient blood, using the LeukoLOCKTM total RNA Isolation System (Ambion, Inc., USA), according to manufacturer’s instructions. The quantity of RNA was assessed using the NanoDrop ΝD-1000A spectrophotometer (Thermo Scientific, USA) and RNA quality was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, USA).

treatment_protocol: Patients were vaccinated intradermally either with 1 mL of TRIMEL/DCs mixed with aluminum hydroxide (500 μg; J.T. Baker, USA), denoted by rDC+Al(OH), or with TRIMEL/DCs mixed with Keyhole limpet haemocyanin (KLH; 100 μg; Calbiochem, USA), denoted rDC+KLH, in the leg or arm closest to intact lymph nodes. The vaccination protocol consisted of four doses injected on days 0, 10, 30, and 50. One month after the end of therapy, patients were assessed for in vivo DTH reactions to the TRIMEL cell lysate, subcutaneously injecting 200 μL of TRIMEL (2 mg/mL) and 100 μL of control antigens KLH (1 mg/mL) or MULTITEST cell-mediated immunity (CMI; Pasteur-Mérieux, France) in saline solutions.

value: Blood

value: M

tag: ajcc stage

value: IV

tag: primary tumor localization

value: Dorsal/Right Leg

tag: metastasis

tag: additional treatment

value: Surgery

tag: dth response

tag: overall survivel (months)

tag: type of vaccination

value: information lost


title: Patient 101 post-vaccination

scan_protocol: Standard Illumina hybridization protocol


title: Patient 101 1st vaccination


title: Patient 101 4th vaccination


title: Patient 101 3rd vaccination


title: Patient 98 1st vaccination

value: Right Hand

value: NT

value: rDC+Al(OH)


title: Patient 96 post-vaccination

value: IIIA

value: Dorsal


title: Patient 96 5th vaccination


title: injected with pIFNa, fish 2, 2 weeks


title: Patient 93 4th vaccination

value: F

value: Uveal melanoma

value: rDC+KLH


title: Patient 96 pre-vaccination


title: Patient 96 1st vaccination


title: Patient 94 3rd vaccination

value: Head/Neck


title: Patient 94 4th vaccination


title: Patient 98 2nd vaccination


title: Patient 93 pre-vaccination


title: Patient 94 2nd vaccination


title: Patient 93 2nd vaccination


title: Patient 93 post-vaccination


title: Patient 94 post-vaccination


title: Patient 93 3rd vaccination


title: Patient 91 4th vaccination

value: Scalp

value: Surgery, RT


title: Patient 93 1st vaccination

value: Blood


title: genomic DNA from placental sample 74

type: genomic

city: Chapel Hill

first: Rebecca

middle: Catherine

last: Fry

address: 1213 MHRC

department: Environmental Sciences and Engineering

institute: UNC-Chapel Hill

description: normal placental sample

hyb_protocol: bisulphite converted DNA was  hybridised to Illumina  Human Methylation450 Beadchip using standard Illumina protocol

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

data_processing: wateRmelon package (version 1.11.0) in R (version 3.2.3)

molecule: genomic DNA

source_name: placental sample 74

label_protocol: Zymo Research EZ DNA methylation kit

extract_protocol: genomic DNA and RNA sequences were extracted from placental tissue using Qiagen AllPrep DNA/RNA/miRNA Universal Kit according to standard instructions

tag: bacteria present

value: placenta

tag: fetal sex

value: female

tag: maternal race

value: White

tag: antibiotic use

value: yes

tag: vaginal infection

value: no

tag: uti

tag: c-section


title: Patient 91 2nd vaccination

tag: tissue

value: M

value: IV


title: genomic DNA from placental sample 83

description: normal placental sample

source_name: placental sample 83

value: male

value: Non-white


title: genomic DNA from placental sample 70

description: normal placental sample

source_name: placental sample 70


title: genomic DNA from placental sample 84

description: normal placental sample

source_name: placental sample 84


title: Patient 91 pre-vaccination

value: rDC+Al(OH)


title: Patient 91 1st vaccination


title: Patient 91 3rd vaccination


title: genomic DNA from placental sample 81

description: normal placental sample

source_name: placental sample 81


title: genomic DNA from placental sample 82

description: normal placental sample

source_name: placental sample 82


title: genomic DNA from placental sample 75

description: normal placental sample

source_name: placental sample 75

value: Peptostreptococcus, U. urealyticum, Actinomyces, Corneybacterium


title: Patient 89 2nd vaccination

value: Right Foot

value: NT


title: genomic DNA from placental sample 71

description: normal placental sample

source_name: placental sample 71

value: Staphlococcus sp., S. aureus


title: genomic DNA from placental sample 79

description: normal placental sample

source_name: placental sample 79


title: genomic DNA from placental sample 72

description: normal placental sample

source_name: placental sample 72


title: genomic DNA from placental sample 76

description: normal placental sample

source_name: placental sample 76


title: genomic DNA from placental sample 69

description: normal placental sample

source_name: placental sample 69

value: Lactobacillus


title: genomic DNA from placental sample 78

description: normal placental sample

source_name: placental sample 78


title: Patient 89 1st vaccination

value: Surgery, RT

value: rDC+KLH


title: genomic DNA from placental sample 77

description: normal placental sample

source_name: placental sample 77

value: placenta


title: genomic DNA from placental sample 80

description: normal placental sample

source_name: placental sample 80

value: female


title: genomic DNA from placental sample 73

description: normal placental sample

source_name: placental sample 73

value: White

value: not specified


title: genomic DNA from placental sample 66

description: normal placental sample

source_name: placental sample 66

value: no

value: yes


title: genomic DNA from placental sample 64

description: normal placental sample

source_name: placental sample 64


title: genomic DNA from placental sample 65

description: normal placental sample

source_name: placental sample 65

value: E. coli


title: Patient 87 2nd vaccination

source_name: blood

value: Blood

value: M

value: IV

value: Right Hand


title: Patient 87 1st vaccination


title: genomic DNA from placental sample 68

description: normal placental sample

source_name: placental sample 68

value: Peptostreptococcus

value: male

value: Non-white


title: genomic DNA from placental sample 67

description: normal placental sample

source_name: placental sample 67

value: Staphlococcus sp., S. aureus, Alpha Strep, Strep Group D


title: Patient 84 4th vaccination

value: IIIC

value: Right Foot

value: Surgery


title: Patient 87 pre-vaccination

value: Surgery, RT

value: NT

value: rDC+KLH


title: Patient 84 3rd vaccination


title: Patient 89 pre-vaccination


title: Patient 84 2nd vaccination


title: Patient 84 post-vaccination


title: genomic DNA from placental sample 58

description: normal placental sample

source_name: placental sample 58

value: placenta

value: White

value: not specified


title: Patient 83 post-vaccination

value: Blood


title: genomic DNA from placental sample 57

description: normal placental sample

source_name: placental sample 57

value: female

value: yes

value: no


title: Patient 80 post-vaccination

value: M

value: IV

value: Palate


title: Patient 83 4th vaccination

value: Right Hand


title: Patient 83 pre-vaccination

value: IIIC


title: genomic DNA from placental sample 60

description: normal placental sample

source_name: placental sample 60

value: Actinomyces

value: male

value: Non-white


title: Patient 83 1st vaccination

value: Surgery


title: genomic DNA from placental sample 61

description: normal placental sample

source_name: placental sample 61


title: genomic DNA from placental sample 56

description: normal placental sample

source_name: placental sample 56

value: Propionibacterium


title: genomic DNA from placental sample 62

description: normal placental sample

source_name: placental sample 62

value: Lactobacillus

value: placenta


title: Patient 83 2nd vaccination

value: rDC+KLH


title: genomic DNA from placental sample 54

description: normal placental sample

source_name: placental sample 54

value: White


title: Patient 83 3rd vaccination

value: Blood


title: Patient 80 pre-vaccination

value: Surgery, RT


title: genomic DNA from placental sample 63

description: normal placental sample

source_name: placental sample 63

value: female

value: no

value: yes


title: genomic DNA from placental sample 52

description: normal placental sample

source_name: placental sample 52


title: Patient 79 4th vaccination

value: F

value: IV

value: Left flank


title: genomic DNA from placental sample 55

description: normal placental sample

source_name: placental sample 55


title: genomic DNA from placental sample 53

description: normal placental sample

source_name: placental sample 53


title: Patient 79 pre-vaccination


title: genomic DNA from placental sample 48

description: normal placental sample

source_name: placental sample 48


title: genomic DNA from placental sample 51

description: normal placental sample

source_name: placental sample 51


title: Patient 79 post-vaccination


title: genomic DNA from placental sample 47

description: normal placental sample

source_name: placental sample 47


title: genomic DNA from placental sample 59

description: normal placental sample

source_name: placental sample 59

value: Mycoplasma


title: genomic DNA from placental sample 44

description: normal placental sample

source_name: placental sample 44

value: male


title: genomic DNA from placental sample 50

description: normal placental sample

source_name: placental sample 50

value: Peptostreptococcus, P. bivia, Staphlococcus sp., Corneybacterium, S. aureus, Strep Group B

value: Non-white


title: genomic DNA from placental sample 45

description: normal placental sample

source_name: placental sample 45


title: genomic DNA from placental sample 46

description: normal placental sample

source_name: placental sample 46


title: genomic DNA from placental sample 49

description: normal placental sample

source_name: placental sample 49


title: genomic DNA from placental sample 42

description: normal placental sample

source_name: placental sample 42


title: genomic DNA from placental sample 29

description: normal placental sample

source_name: placental sample 29


title: genomic DNA from placental sample 37

description: normal placental sample

source_name: placental sample 37

value: not specified


title: genomic DNA from placental sample 35

description: normal placental sample

source_name: placental sample 35

value: U. urealyticum


title: genomic DNA from placental sample 43

description: normal placental sample

source_name: placental sample 43

value: Alpha strep, Mycoplasma, Strep Group B

value: placenta


title: genomic DNA from placental sample 30

description: normal placental sample

source_name: placental sample 30


title: genomic DNA from placental sample 25

description: normal placental sample

source_name: placental sample 25

value: Staphlococcus sp., S. aureus, Actinomyces


title: genomic DNA from placental sample 33

description: normal placental sample

source_name: placental sample 33

value: Staphlococcus sp., S. aureus

value: White


title: genomic DNA from placental sample 26

description: normal placental sample

source_name: placental sample 26


title: genomic DNA from placental sample 36

description: normal placental sample

source_name: placental sample 36

value: P. bivia, U. urealyticum


title: genomic DNA from placental sample 41

description: normal placental sample

source_name: placental sample 41

value: no


title: genomic DNA from placental sample 39

description: normal placental sample

source_name: placental sample 39

value: yes


title: genomic DNA from placental sample 31

description: normal placental sample

source_name: placental sample 31

value: Propionibacterium, Mycoplasma, U. urealyticum


title: genomic DNA from placental sample 16

description: normal placental sample

source_name: placental sample 16

value: Propionibacterium


title: genomic DNA from placental sample 17

description: normal placental sample

source_name: placental sample 17

value: Staphlococcus sp., S. aureus, G. vaginalis, Strep Group D


title: genomic DNA from placental sample 20

description: normal placental sample

source_name: placental sample 20


title: genomic DNA from placental sample 27

description: normal placental sample

source_name: placental sample 27

value: Alpha strep


title: genomic DNA from placental sample 24

description: normal placental sample

source_name: placental sample 24

value: Mycoplasma

value: male


title: genomic DNA from placental sample 32

description: normal placental sample

source_name: placental sample 32

value: Non-white


title: genomic DNA from placental sample 22

description: normal placental sample

source_name: placental sample 22


title: genomic DNA from placental sample 15

description: normal placental sample

source_name: placental sample 15

value: female


title: genomic DNA from placental sample 34

description: normal placental sample

source_name: placental sample 34


title: genomic DNA from placental sample 18

description: normal placental sample

source_name: placental sample 18


title: genomic DNA from placental sample 21

description: normal placental sample

source_name: placental sample 21


title: genomic DNA from placental sample 19

description: normal placental sample

source_name: placental sample 19


title: genomic DNA from placental sample 40

description: normal placental sample

source_name: placental sample 40


title: genomic DNA from placental sample 28

description: normal placental sample

source_name: placental sample 28


title: genomic DNA from placental sample 23

description: normal placental sample

source_name: placental sample 23


title: genomic DNA from placental sample 14

description: normal placental sample

source_name: placental sample 14


title: genomic DNA from placental sample 11

description: normal placental sample

source_name: placental sample 11


title: 231_shSREBP1

status: Public on Oct 24 2017

city: Jinan

first: Qifeng

last: Yang

state: Shandong

address: Wenhua West Road No.44

department: Department of Breast Surgery

country: China

institute: Qilu Hospital

description: Stable knockdown of SREBP1 in MDA-MB-231 by transfection with pLKO.1-shSREBP vector

hyb_protocol: Following labeling, 5.5 ug of cDNA were hybridized for 16 hr at 45℃ on GeneChip Affymetrix Human Transcriptome Array 2.0 in GeneChip® Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

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

data_processing: Expression data were generated by Affymetrix Expression Console software and normalized by the RMA(Robust Multi-chip Average ) method.

source_name: 231 cells, stably transfected with pLKO.1-shSREBP vector

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA by using GeneChip® WT PLUS Reagent Kit

growth_protocol: MDA-MB-231 cells were cultured in DMEM/high glucose supplemented with 10% FBS and streptomycin and penicillin.

extract_protocol: Total RNA was extracted and purified using miRNeasy Mini Kit and RNase-Free Dnase Set.

treatment_protocol: MDA-MB-231  cells were stably knocked down of SREBP1 and the control cells

tag: cell line

tag: genotype

value: SREBP1 KD


title: genomic DNA from placental sample 13

description: normal placental sample

source_name: placental sample 13


title: 231_shNC

description: MDA-MB-231 stably transfected with pLKO.1 vector

source_name: 231 cells, stably transfected with pLKO.1 vector

value: control


title: genomic DNA from placental sample 4

description: normal placental sample

source_name: placental sample 4

value: placenta


title: genomic DNA from placental sample 5

description: normal placental sample

source_name: placental sample 5


title: genomic DNA from placental sample 38

description: normal placental sample

source_name: placental sample 38

value: G. vaginalis


title: genomic DNA from placental sample 3

description: normal placental sample

source_name: placental sample 3


title: genomic DNA from placental sample 9

description: normal placental sample

source_name: placental sample 9


title: genomic DNA from placental sample 8

description: normal placental sample

source_name: placental sample 8


title: genomic DNA from placental sample 10

description: normal placental sample

source_name: placental sample 10


title: genomic DNA from placental sample 2

description: normal placental sample

source_name: placental sample 2

value: Lactobacillus, Mycoplasma


title: genomic DNA from placental sample 7

description: normal placental sample

source_name: placental sample 7

value: Staphlococcus sp., S. aureus

value: White


title: genomic DNA from placental sample 1

description: normal placental sample

source_name: placental sample 1

value: P. bivia, Mycoplasma, Actinomyces, Corneybacterium

value: no


title: LB-1

city: Burlington

first: Matthew

middle: J

last: Wargo

state: VT

address: 95 Carrigan Dr

department: Department of Microbiology and Molecular Genetics

institute: University of Vermont

hyb_protocol: Following fragmentation, 2.4 ug of cRNA were hybridized on the Pseudomonas aeruginosa PAO1 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix 7G Scanner.

data_processing: Probe intensities were first generated using the Expression Console program (Affymetrix). Probe-level intensities were background-corrected, normalized, and summarized, and Robust Multichip Average (RMA) statistics were calculated for each probe set and sample as is implemented in Transcriptome Analysis Console v2.0 (Affymetrix).

organism: Pseudomonas aeruginosa

source_name: dilute LB Lennox

label_protocol: Biotinylated cDNA was prepared from 50 ng of whole RNA using the NuGen Ovation Pico system and the Encore Biotin Module according to manufacturer's instructions.

growth_protocol: Cells were pregrown overnight in 1/2R2B at 30C, washed, and resuspended in filtered and heat-treated inducing condition in the top chamber of a transwell, while non-sterile inducing condition was placed in the bottom chamber. Cells were incubated with no shaking at 22C for 3 h.

extract_protocol: RNA was prepared using a Qiagen RNeasy kit following the manufacturer’s protocol with the following changes. Prior to extraction, cell pellets were resuspended in 200 µL of TE supplemented with 3 mg/mL lysozyme and incubated at room temperature for 20 minutes. An on-column DNase I treatment was performed before the RNA was eluted in RNase-free water. Samples were then treated a second time with RNase-free DNase I (NEB) and incubated for 1 hour at 37 ºC before a second round of RNeasy column purification was performed.

treatment_protocol: Following induction, cells were gathered by scraping the filter and walls of the upper chamber and removing all of the upper chamber media and added to 1000 µL of RNA Protect Bacterial Reagent (Qiagen). After 5 minutes, the protected cells were collected by centrifugation and the supernatant decanted before the pellets were frozen at -80 °C.

tag: strain

value: wildtype

tag: condition

value: dilute LB Lennox


title: Pond Water-1

source_name: Pond Water

value: Pond Water


title: LB-2


title: 1/2R2B-1

source_name: dilute R2B

value: dilute R2B


title: 1/2R2B-2


title: genomic DNA from placental sample 12

description: normal placental sample

source_name: placental sample 12

value: Propionibacterium

value: yes


title: Tap Water-3

source_name: Tap Water

value: Tap Water


title: Tap Water-1


title: Pond Water-2


title: Tap Water-2


title: TIS21-knockout fetal liver

city: Suwon-si

first: In Kyoung

last: Lim

state: Gyeonggi Do

address: Song-Jae Gwan, rm309,  Ajou univ.,  Woncheon-dong, Yeongtong-gu

department: Biochemistry and Molecular Biology

country: South Korea

institute: Ajou University School of Medicine

description: several fetus were pooled

hyb_protocol: The Cy3-labeled amplified RNAs (aRNAs) were re-suspended in 50 μL of hybridization solution (Agilent technologies, CA). After, labeled aRNAs were placed on Agilent SurePrint G3 Mouse GE 8 X 60K array (Agilent technologies, CA) and covered by a Gasket 8-plex slide (Agilent technologies, CA). The slides were hybridized for 17h at 65℃ oven. The hybridized slides were washed in 2X SSC, 0.1% SDS for 2 min, 1X SSC for 3 min, and then 0.2X SSC for 2 min at room temperature. The slides were centrifuged at 3000 rpm for 20 sec to dry.

scan_protocol: The arrays were analyzed using an Agilent scanner with associated software. Gene expression levels were calculated with Feature Extraction v10.7.3.1 (Agilent technologies, CA).

data_processing: The data were processed based on quantile normalization method using the GeneSpring GX 12.6 (Agilent technologies, CA). This normalization method aims to make the distribution of intensities for each array in a set of arrays the same. The normalized, and log transformed intensity values were then analyzed using GeneSpring GX 12.6 (Agilent technologies, CA).

source_name: KO Fetal

label_protocol: Each total RNA sample (200 ng) was labeled and amplified using Low Input Quick Amp labeling kit (Agilent technologies, CA).

growth_protocol: 10 week old adult male TIS21WT and TIS21KO mouse liver, and from fetal livers of embryonic day 13.5 from both strains

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: To minimize variation and to synchronize metabolic status, both TIS21-WT and TIS21-KO adult mice were fasted for 20h (from 17:00pm to next day 13:00 pm), and liver from fetuses conceived within a womb (n>3) were pooled.

tag: gender

value: pooled male and female

tag: age

value: Embryonic day 13.5

value: liver


title: genomic DNA from placental sample 6

description: normal placental sample

source_name: placental sample 6

value: placenta

value: male


title: TIS21-wild type fetal liver

description: several fetus were pooled

source_name: WT Fetal

value: TIS21-wild type


title: TIS21-knockout adult male mouse liver (duplicate)

description: 20 hour fasted

source_name: KO Ad

value: Male

value: 10 week old

tag: treatment

value: fasted for 20hr


title: 3W+Dox

city: Toronto

first: Li

last: Guo

address: 101 College Street

country: Canada

institute: University Health Network

description: Isolated Club cells were cultured in doxcycline contained medium for 3 weeks

hyb_protocol: GeneChip® Fluidics Script FS450_0002

scan_protocol: Scanned on Affymetrix GeneChip Scanner 3000

data_processing: Affymetrix CEL files were imported and processed using RMA in R version 3.0.2 with the affy package. We used an alternative CDF probset description file from Brainarray at the University of Michigan (Nucleic Acid Research 33 (20), e175; http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp): mogene20stmmentrezgcdf_17.1.0

source_name: Cultured cells

label_protocol: RNA was prepared using the Ambion WT kit

growth_protocol: Cells were cultured at 5% CO2, 37°C

extract_protocol: Total RNA was extracted using RNeasy kit (Qiagen)

treatment_protocol: Doxycycline was added to the culture medium for 3 weeks and removed after

value: Lung

tag: developmental stage

value: Adult

tag: cell type

value: Club-iPL cells (3w+Dox)


title: Day0

source_name: Freshly isolated Club cells

value: Freshly isolated Club cells


title: PFC HFD mice, biological replicate 3

city: Zurich

first: Juliet

last: Richetto

address: Winterthurerstrasse 260

department: Institute for Pharmacology and Toxicology

country: Switzerland

institute: University of Zurich - Vetsuisse

description: Gene epression data in HFD offspring

hyb_protocol: The labeled sample was then hybridized to the miRNA 4.1 array strips (Affymetrix) that show a comprehensive coverage as they are designed to interrogate all miRNA sequences in miRBase Release 20, for a total of 1255 mouse mature miRNAs.

scan_protocol: GeneChips were scanned using theGeneAtlas Platform following the manufacturers' instructions.

data_processing: Affymetrix CEL files were imported into Partek Genomics Suite version 6.6 for data visualization and statistical testing. Quality control assessment was performed using Partek Genomic Suite 6.6. All samples passed the criteria for hybridization controls, labelling controls and 3’/5’ Metrics. Background correction was conducted using Robust Multi-strip Average (RMA) (Irizarry et al, 2003) to remove noise from auto fluorescence. After background correction, normalization was conducted using Quantiles normalization (Bolstad et al, 2003) to normalize the distribution of probe intensities among different microarray chips. Subsequently, a summarization step was conducted using a linear median polish algorithm (Tukey, 1977) to integrate probe intensities in order to compute the expression levels for each gene transcript. Upon data upload, and after the selection of the species (mus musculus), statistical analyses to compare animals exposed or not to HFD were performed using the Robust MultiChip Average ANOVA statistical test to assess treatment effects. Differential miRNA expression was assessed by applying a p-value filter (for attribute) of p<0.05 to the ANOVA results.

source_name: C57BL/6 mouse Prefrontal Cortex - brain tissue - HFD

label_protocol: We performed whole genome microRNA analysis using the Flash Tag Biotin HSR RNA Labeling kit (Affymetrix, Italy), according to the manufacturer’s protocol. Briefly, 2 μl of polyA were added to 500 ng total RNA (containing low molecular weight RNA), allowing appropriate monitoring of the efficiency of labeling and hybridization procedures. Addition of the Tag Ligation Mix allowed the ligation of the biotinylated signal molecule to the target miRNA sample.

extract_protocol:
The brains from adult offspring (12 weeks) were rapidly extracted from the skull (within < 20 s) and placed on an ice-chilled plate. This was followed by preparing 1-mm coronal brain sections using razorblade cuts and subsequent micro-dissection of the brain areas of interest. We dissected  We dissected the medial prefrontal cortex (mPFC, including anterior cingulate, prelimbic and dorsal parts of the infralimbic cortices; bregma: +2.3 to +1.3 mm) . Brain specimens were collected in 96-well microtiter plates kept on dry ice and allowed to freeze before storage at −80°C until further use. Total RNA was isolated using the Qiagen miRNeasy Mini kit (Qiagen, Italy) according to the manufacturer’s instructions, and quantified by spectrophotometric analysis. Genome-wide gene expression analyses were performed using Affymetrix microarray assays (Affymetrix miRNA-4.1 Array Strips on GeneAtlas platform), following the 3’IVT one cycle labelling.
Total DNA and RNA were isolated using the Qiagen AllPrep DNA and RNA Mini kit following the manufacturers' instructions

treatment_protocol: C57BL/6N male where exposed to HFD or Low fat diet (LFD) for 8 weeks starting from PND28. (HFD:consisting of 60% of calories from fat; LFD 10% of calories from fat ). We then performed genome wide miRNA expression analyses, validations, behavioral analyses.

value: Frozen brain tissue

value: 12 weeks

tag: diet

value: HFD


title: PFC HFD mice, biological replicate 2

description: Gene epression data in HFD offspring


title: PFC LFD mice, biological replicate 3

description: Gene epression data in control (LFD) offspring

source_name: C57BL/6 mouse Prefrontal Cortex - brain tissue - CONTROL

value: LFD


title: PFC LFD mice, biological replicate 6


title: PFC LFD mice, biological replicate 4


title: TIS21-wild type adult male mouse liver (duplicate)

description: 20 hour fasted

source_name: WT Ad


title: PFC LFD mice, biological replicate 2


title: TIS21-wild type fetal liver (duplicate)

description: several fetus were pooled

value: pooled male and female


title: TIS21-wild type adult male mouse liver

description: 20 hour fasted


title: TIS21-knockout fetal liver (duplicate)

description: several fetus were pooled

value: Embryonic day 13.5


title: TIS21-knockout adult male mouse liver

description: 20 hour fasted

value: liver


title: PFC LFD mice, biological replicate 1


title: iPS

value: Club-iPS cells


title: PFC HFD mice, biological replicate 5

description: Gene epression data in HFD offspring


title: PFC HFD mice, biological replicate 6

description: Gene epression data in HFD offspring


title: PFC LFD mice, biological replicate 5


title: PFC HFD mice, biological replicate 4

description: Gene epression data in HFD offspring


title: 3W+Dox+2W-Dox

description: 3-week induced cells with subsequent 2-week culture in Dox-free media

value: Club-iPL cells with subsequent 2-week culture in Dox-free media (3w+Dox+2w-Dox)


title: PFC HFD mice, biological replicate 1

description: Gene epression data in HFD offspring


title: Genomic DNA from nasal epithelial cells [sample22]

status: Public on Oct 23 2017

city: Davis

first: Hong

last: Ji

state: CA

address: County Rd 98 & Hutchison Drive

institute: University of California Davis

description:
Nasal epithelial cells obtained by nasal brushing
sample22

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450 Beadchip using standard Illumina protocol

data_processing: RnBeads

label: Cy5 and Cy3

source_name: Nasal epithelial cells

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted using Qiagen Allprep micro kit according to manufacturer’s  instructions.

tag: diagnosis

value: asthma

value: nasal epithelium

value: MALE

tag: race

value: black

tag: length of stay

value: LONG

tag: time


title: Genomic DNA from nasal epithelial cells [sample32]

description:
Nasal epithelial cells obtained by nasal brushing
sample32

value: FEMALE


title: Genomic DNA from nasal epithelial cells [sample21]

description:
Nasal epithelial cells obtained by nasal brushing
sample21


title: Genomic DNA from nasal epithelial cells [sample20]

description:
Nasal epithelial cells obtained by nasal brushing
sample20


title: Genomic DNA from nasal epithelial cells [sample40]

description:
Nasal epithelial cells obtained by nasal brushing
sample40

value: non-black


title: Genomic DNA from nasal epithelial cells [sample24]

description:
Nasal epithelial cells obtained by nasal brushing
sample24

value: SHORT


title: Genomic DNA from nasal epithelial cells [sample36]

description:
Nasal epithelial cells obtained by nasal brushing
sample36


title: Genomic DNA from nasal epithelial cells [sample15]

description:
Nasal epithelial cells obtained by nasal brushing
sample15


title: Genomic DNA from nasal epithelial cells [sample38]

description:
Nasal epithelial cells obtained by nasal brushing
sample38


title: Genomic DNA from nasal epithelial cells [sample26]

description:
Nasal epithelial cells obtained by nasal brushing
sample26


title: Genomic DNA from nasal epithelial cells [sample27]

description:
Nasal epithelial cells obtained by nasal brushing
sample27


title: Genomic DNA from nasal epithelial cells [sample30]

description:
Nasal epithelial cells obtained by nasal brushing
sample30


title: Genomic DNA from nasal epithelial cells [sample28]

description:
Nasal epithelial cells obtained by nasal brushing
sample28


title: Genomic DNA from nasal epithelial cells [sample29]

description:
Nasal epithelial cells obtained by nasal brushing
sample29


title: Genomic DNA from nasal epithelial cells [sample19]

description:
Nasal epithelial cells obtained by nasal brushing
sample19


title: Genomic DNA from nasal epithelial cells [sample16]

description:
Nasal epithelial cells obtained by nasal brushing
sample16


title: Genomic DNA from nasal epithelial cells [sample23]

description:
Nasal epithelial cells obtained by nasal brushing
sample23


title: Genomic DNA from nasal epithelial cells [sample37]

description:
Nasal epithelial cells obtained by nasal brushing
sample37


title: Genomic DNA from nasal epithelial cells [sample18]

description:
Nasal epithelial cells obtained by nasal brushing
sample18


title: Genomic DNA from nasal epithelial cells [sample25]

description:
Nasal epithelial cells obtained by nasal brushing
sample25


title: Genomic DNA from nasal epithelial cells [sample33]

description:
Nasal epithelial cells obtained by nasal brushing
sample33


title: Genomic DNA from nasal epithelial cells [sample14]

description:
Nasal epithelial cells obtained by nasal brushing
sample14


title: Genomic DNA from nasal epithelial cells [sample31]

description:
Nasal epithelial cells obtained by nasal brushing
sample31


title: Genomic DNA from nasal epithelial cells [sample34]

description:
Nasal epithelial cells obtained by nasal brushing
sample34


title: Genomic DNA from nasal epithelial cells [sample35]

description:
Nasal epithelial cells obtained by nasal brushing
sample35


title: Genomic DNA from nasal epithelial cells [sample39]

description:
Nasal epithelial cells obtained by nasal brushing
sample39


title: Genomic DNA from nasal epithelial cells [sample12]

description:
Nasal epithelial cells obtained by nasal brushing
sample12


title: Genomic DNA from nasal epithelial cells [sample11]

description:
Nasal epithelial cells obtained by nasal brushing
sample11


title: Genomic DNA from nasal epithelial cells [sample13]

description:
Nasal epithelial cells obtained by nasal brushing
sample13


title: Genomic DNA from nasal epithelial cells [sample17]

description:
Nasal epithelial cells obtained by nasal brushing
sample17


title: DP Control1

city: Wuhan

first: Mi

last: Zhou

address: Jiefang Ave

institute: Tongji Hospital, Tongji Medical College,Huazhong University of Science and Technology

hyb_protocol: Following fragmentation, 12.5 μg of fragmented cRNA were hybridized for 16 hr at 45℃ on GeneChip Affymetrix Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000

data_processing: The data were analyzed with Microarray Suite version 3.0 (MAS 3.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: double positive thymocytes from MBD2 wild-type mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 7 μg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The percentage of GFP+ cells in the PB of the recipient mice was determined every 5 days from day 10 after the transplantation. When the proportion of GFP+> 50% of the PB WBCs (P1), The GFP+ BM cells were sorted using flow cytometry for subsequent microarray analysis. The double positive CD4+CD8+ thymocytes from steady-state mice were sorted using flow cytometry for subsequent microarray analysis.

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

treatment_protocol: Mice GFP+ BM leukemia cells or CD4+CD8+ thymocytes were rinsed with PBS with 0,7% NaCl, 0,04% triton-X100 and placed on ice in the Trizol solution (GibcoBRL).

value: CD4+CD8+ thymocytes

value: MBD2 wild type


title: DP MBD2-/-2

source_name: double positive thymocytes from MBD2 Deletion mice

value: MBD2 deletion


title: T-ALL Control3

source_name: leukemia cells from MBD2 wild-type T-ALL mice

value: GFP+ BM leukemia cells


title: DP Control2


title: T-ALL Control2


title: DP MBD2-/-3


title: Gene expression comparison of Hic-5 clone pCMV-Hic-5 vs control A2780s clone

status: Public on Oct 22 2017

city: Quebec

first: Dimcho

last: Bachvarov

state: Quebec

address: 9, rue McMahon

institute: CHU-Q, Centre de recherche-HDQ

description:
Cy3 label sample being the reference
log ratio clone  clone C - pCMV-Hic-5

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers.

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing:
Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.
Normalized log10 ratio (Cy3/Cy5) representing test/reference for samples C - clone sh-S1, C - clone sh-S2 and C -pCMV-Hic-5; normalized log10 ratio (Cy5/Cy3) representing test/reference for samples  clone sh-S1, clone sh-S2 – C and clone pCMV-Hic-5 - C.

source_name: control (mock-transfected) A2780s clone

label_protocol: Fluorescently labeled cRNA targets were generated from 0.5 µg of total RNA in each reaction using the Fluorescent Linear Amplification Kit (Agilent) and 10.0 mM Cyanine 3- or 5-labeled CTP (PerkinElmer, Boston, MA), following the user’s manual. Labeled cRNAs were purified using the RNeasy Mini Kit (Qiagen) and applied to the Agilent Whole Human Genome microarrays, containing ~ 44,000 genes.

growth_protocol: SKOV3 and A2780s cells were maintained in Roswell Park Memorial Institute (RPMI) 1640 (HyClone Europe Ltd, Cramlington, UK) supplemented with 10% heat-inactivated fetal calf serum, 2 mM l-glutamine, 1 mM sodium pyruvate, 100 units/ml penicillin and 100 μg/ml streptomycin (all reagents were from HyClone Europe). Cells were grown as adherent cells in a humidified atmosphere at 37°C in 5% CO2.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions. The quality of all RNA samples was examined by capillary electrophoresis using the Agilent 2100 Bioanalyzer.

treatment_protocol: Two Hic-5 shRNAs cloned into the pLKO.1-puro vector (targeting the Hic-5 mRNA sequences 5′-CAGTTCAACATCACAGATGAA-3′ and 5′-CGGTTGCTTCAGGAACTTAAT-3’)   were retrieved from the Sigma Mission TRC human 1.5 shRNA library (clone numbers TRCN0000020100 and TRCN0000281350). Viral supernatants were generated by transfecting 293T cells with the shRNA constructs and the packaging vectors psPAX2 and pMD2.G (Addgene, Cambridge, MA). The high-titer lentiviral supernatants in the presence of 8 mg/ml polybrene were used to infect SKOV3 cells. Two days later, infected cells were treated with puromycin (0,5 mg/ml) for the selection of stably-transduced clones. The pLKO.1-puro vector encoding a scramble sequence not matching any mammalian sequence was used for the generation of mock-transduced (control) clones. Stable clones with inhibited Hic-5 expression were evaluated and validated by quantitative RT-PCR and Western blot. For Hic-5 ectopic expression, the human Hic-5 gene cloned in the pCMV6 entry eukaryotic expression vector (pCMV-Hic-5) was purchased from OriGene Technologies, Inc. (Rockville, MD). Transfection with ExGen 500 (Fermentas Canada Inc., Burlington ON) was carried out according to the manufacturer’s guidelines. Stably transfected clones were selected by adding neomycin (500 µg/ml) and further cultivation for about 2 weeks.  Stable clones with inhibited Hic-5 expression were evaluated and validated by quantitative RT-PCR and Western blot. Cells were also mock-transfected with the empty pCMV6 vector, and stably transfected clones were isolated as controls.

value: ovarian adenocarcinoma  cell line

tag: genotype/variation

value: control (mock-transfected)clone

source_name: pCMV-Hic-5 - overexpressing A2780s clone

value: pCMV-Hic-5 - overexpressing clone


title: DP MBD2-/-1


title: Gene expression comparison of Hic-5 knockdown clone sh-S1 vs control SKOV3 clone - dye-swap replica

description:
Cy5 label sample being the reference
log ratio clone sh-S1 – C

source_name: shRNA-Hic-5 knockdown SKOV3 clone sh-S1

value: shRNA-Hic-5 knockdown  clone sh-S1

source_name: control (mock-transfected) SKOV3 clone

value: control (mock-transfected) clone


title: T-ALL MBD2-/-3

source_name: leukemia cells from MBD2 Deletion T-ALL mice


title: DP Control3


title: Gene expression comparison of Hic-5 knockdown clone sh-S2 vs control SKOV3 clone - dye-swap replica

description:
Cy5 label sample being the reference
log ratio clone sh-S2 – C

source_name: shRNA-Hic-5 knockdown SKOV3 clone sh-S2

value: shRNA-Hic-5 knockdown clone sh-S2


title: Gene expression comparison of Hic-5 knockdown clone sh-S1 vs control SKOV3 clone

description:
Cy3 label sample being the reference
log ratio C – clone sh-S1

value: shRNA-Hic-5 knockdown clone sh-S1


title: Genomic DNA from nasal epithelial cells [sample8]

description:
Nasal epithelial cells obtained by nasal brushing
sample8

value: asthma

value: nasal epithelium

value: MALE


title: Gene expression comparison of Hic-5 clone pCMV-Hic-5 vs control A2780s clone - dye-swap replica

description:
Cy5 label sample being the reference
log ratio clone  clone pCMV-Hic-5 - C

value: pCMV-Hic-5 -overexpressing clone

value: control (mock-transfected) A2780s clone


title: T-ALL MBD2-/-2


title: T-ALL MBD2-/-1


title: T-ALL Control1


title: Genomic DNA from nasal epithelial cells [sample9]

description:
Nasal epithelial cells obtained by nasal brushing
sample9

value: black

value: SHORT


title: Genomic DNA from nasal epithelial cells [sample6]

description:
Nasal epithelial cells obtained by nasal brushing
sample6


title: Genomic DNA from nasal epithelial cells [sample7]

description:
Nasal epithelial cells obtained by nasal brushing
sample7


title: Genomic DNA from nasal epithelial cells [sample10]

description:
Nasal epithelial cells obtained by nasal brushing
sample10


title: Gene expression comparison of Hic-5 knockdown clone sh-S2 vs control SKOV3 clone

description:
Cy3 label sample being the reference
log ratio C – clone sh-S2


title: monocytes_CVD_rep31

status: Public on Oct 21 2017

city: Amsterdam

first: Perry

middle: D

last: Moerland

address: Meibergdreef 9

department: Epidemiology and Data Science

country: Netherlands

institute: Amsterdam UMC

hyb_protocol: Labeled samples were hybridized on 14 Human 8x15k miRNA microarrays based on Sanger miRBase release 19.0 containing 866 human and 89 human viral miRNAs (G4470C, Agilent Technologies) at 55°C and 20 rpm for 20 hours.

scan_protocol: After washing, the arrays were scanned using the Agilent DNA microarray scanner (G2565CA, Agilent Technologies). Data were extracted with Feature Extraction software (v10.7.3.1, Agilent Technologies) with the miRNA_107_Sep09 protocol for miRNA microarrays.

data_processing: A two-step normalization approach was taken. In the first step, we corrected for systematic technical effects in the raw probe-level data as extracted via the Agilent Feature Extraction software. For this purpose, we fitted a linear mixed-effects model with coefficients for two technical effects (slide and slide position, that is, upper or lower half of a slide), and patient status using the R/MAANOVA package. Residuals after correcting for the two technical effects were further pre-processed and summarized using a modified version of the robust multi-array average (RMA) method with background correction, as implemented in the AgiMicroRna R package. Quality control was performed using the arrayQualityMetrics R package. Based on arrayQualityMetrics outlier detection and visual inspection of heatmaps, MA-plots, and intensity distributions, seven arrays were excluded from further analysis. Data from the 105 remaining arrays (36 CVD (+2 technical replicates), 40 control without medication (+2 technical replicates) and 25 control after medication) were renormalized using the two-stage procedure described above. Only non-control miRNAs detected on at least one array according to Agilent Feature Extraction software were included in the further analysis.

source_name: monocytes,CVD

label_protocol: The integrity of total RNA including miRNAs from monocytes was investigated with the BioAnalyzer (Agilent Technologies, Santa Clara, California) using the RNA 6000 Pico kit (Agilent Technologies) and Small RNA kit (Agilent Technologies) according to the manufacturer’s instructions. 100 ng of total RNA including miRNAs was dried down in a Centrivap concentrator (Labconco, Kansas City) and dissolved in 2 µl RNase-free water. Sample labeling with Cy3 was performed as described in the miRNA microarray System with miRNA Complete Labeling and Hyb Kit manual version 2.2 (Agilent Technologies) with the inclusion of spike-ins and the optional desalting step with spin columns (Micro Bio-Spin 6, Bio-Rad).

extract_protocol: Monocyte RNA was isolated using the mirVana PARIS kit (Ambion), according to the manufacturer’s protocol.

treatment_protocol: Circulating monocytes were isolated from peripheral blood samples. Non-fasting venous blood was drawn in CTAD tubes (Becton Dickinson, Alphen aan de Rijn, the Netherlands) and centrifuged for 20 minutes at 163 g at 20°C within 30 minutes after blood collection and processed over a similar timeframe. The buffy coat was collected and monocytes were positively selected with CD14+ Dynal beads (Invitrogen, Dynal Biotech, Oslo, Norway) according to the manufacturer’s instructions. Monocytes were incubated in RNAlater® (Ambion, Thermofisher Scientific, Waltham, Massachusetts, USA) for 45 minutes. Subsequently, ice-cold phosphate buffered saline (PBS) was added in a 1:1 volume ratio and the samples were centrifuged for one minute at 5000 g, after which monocytes were obtained and snap-frozen in liquid nitrogen.

value: blood

tag: Sex

value: male

value: monocyte

value: CVD

tag: bmi


title: monocytes_CTRL_without_medication_rep42

tag: tissue


title: monocytes_CVD_rep29

description:
3574_1_4
technical replicate of sample 3574_1_1


title: M7_shSREBP1

hyb_protocol: Following labeling, 5.5 ug of cDNA were hybridized for 16 hr at 45℃ on GeneChip Human Transcriptome Array 2.0 in GeneChip® Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

growth_protocol: MCF-7 cells were cultured in DMEM/high glucose supplemented with 10% FBS and streptomycin and penicillin.

treatment_protocol: MCF-7 cells were stably knocked down of SREBP1 and the control cells

tag: cell line

value: breast cancer cells

value: stablely transfected with pLKO.1-shSREBP vector


title: monocytes_CVD_rep36


title: monocytes_CTRL_without_medication_rep39


title: Genomic DNA from nasal epithelial cells [sample4]

description:
Nasal epithelial cells obtained by nasal brushing
sample4


title: M7_shNC

value: stablely transfected with pLKO.1 vector


title: monocytes_CTRL_without_medication_rep37


title: monocytes_CTRL_without_medication_rep41


title: monocytes_CVD_rep35


title: Genomic DNA from nasal epithelial cells [sample3]

description:
Nasal epithelial cells obtained by nasal brushing
sample3


title: monocytes_CVD_rep33


title: monocytes_CVD_rep34


title: Genomic DNA from nasal epithelial cells [sample2]

description:
Nasal epithelial cells obtained by nasal brushing
sample2


title: Genomic DNA from nasal epithelial cells [sample1]

description:
Nasal epithelial cells obtained by nasal brushing
sample1


title: Genomic DNA from nasal epithelial cells [sample5]

description:
Nasal epithelial cells obtained by nasal brushing
sample5


title: monocytes_CTRL_without_medication_rep40


title: monocytes_CVD_rep32


title: monocytes_CTRL_without_medication_rep38


title: monocytes_CTRL_after_medication_rep25


title: monocytes_CVD_rep28


title: monocytes_CTRL_without_medication_rep31


title: monocytes_CVD_rep24


title: monocytes_CTRL_without_medication_rep36

value: smoker


title: monocytes_CVD_rep27


title: monocytes_CVD_rep26


title: monocytes_CVD_rep23


title: monocytes_CTRL_without_medication_rep32


title: monocytes_CVD_rep21


title: monocytes_CVD_rep22


title: monocytes_CVD_rep25


title: monocytes_CTRL_without_medication_rep34


title: monocytes_CTRL_without_medication_rep30


title: monocytes_CTRL_without_medication_rep33


title: monocytes_CTRL_after_medication_rep23


title: monocytes_CTRL_after_medication_rep24


title: monocytes_CTRL_without_medication_rep35


title: monocytes_CTRL_without_medication_rep28


title: monocytes_CTRL_without_medication_rep29


title: monocytes_CTRL_after_medication_rep22


title: monocytes_CVD_rep20


title: monocytes_CTRL_without_medication_rep27

description:
3332_2_2
technical replicate of sample 3332_1_1


title: monocytes_CTRL_without_medication_rep26


title: monocytes_CVD_rep37


title: monocytes_CVD_rep19


title: monocytes_CVD_rep17


title: monocytes_CTRL_without_medication_rep24


title: monocytes_CTRL_without_medication_rep23


title: monocytes_CVD_rep15


title: monocytes_CTRL_after_medication_rep20


title: monocytes_CTRL_after_medication_rep21


title: monocytes_CVD_rep18


title: monocytes_CVD_rep16


title: monocytes_CTRL_without_medication_rep25


title: monocytes_CVD_rep12


title: monocytes_CVD_rep11


title: monocytes_CTRL_after_medication_rep17


title: monocytes_CVD_rep13


title: monocytes_CVD_rep30


title: monocytes_CTRL_without_medication_rep22


title: monocytes_CTRL_without_medication_rep21


title: monocytes_CTRL_without_medication_rep20


title: monocytes_CTRL_after_medication_rep15


title: monocytes_CTRL_without_medication_rep18


title: monocytes_CVD_rep9


title: monocytes_CTRL_after_medication_rep16


title: monocytes_CTRL_without_medication_rep19


title: monocytes_CTRL_after_medication_rep18


title: monocytes_CVD_rep14


title: monocytes_CVD_rep10


title: monocytes_CVD_rep8


title: monocytes_CTRL_without_medication_rep17


title: monocytes_CTRL_after_medication_rep19


title: monocytes_CTRL_after_medication_rep14


title: CSC_Kras_rep2

city: Baltimore

first: Hariharan

last: Easwaran

state: Maryland

address: 1650 Orleans St #544, Baltimore, MD 21205

department: SOM Onc Cancer Biology

institute: Johns Hopkins Medicine

hyb_protocol: Agilent human GE 4x 44K v2 microarrays (Agilent design ID 026652, part number G4845A) were used, which contain 41,000 unique probes targeting 27,958 Entrez gene RNAs. 825 ng of each Cyanine-labeled samples was used for hybridization at 65ºC for 17 hours in a hybridization oven with rotation. After hybridization, microarrays are washed and dried according to Agilent microarray processing protocol in a walk-in ozone-controlled enclosure

scan_protocol: Microarrays were scanned using an Agilent G2505C Scanner controlled by Agilent Scan Control 7.0 software. Data were extracted with Agilent Feature Extraction 9.5.3.1 software.

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

source_name: Human bronchial epithelial cells_rep2

label_protocol: Sample amplification and labeling procedures were carried out by using Quick RNA Amplification and Labeling Kit (Cat# 5190-0447, Agilent Technologies) with minor modifications. Briefly, 400 ng total RNA was reverse-transcribed into cDNA by MMLV-RT using oligo dT primers (Cat# RA300A-2, System Bioscience) that incorporate T7 promoter sequence. The cDNA is then used as a template for in vitro transcription in the presence of T7 RNA polymerase and Cyanine-labeled CTP (Perkin Elmer). The labeled cRNA is purified using RNeasy mini kit (Qiagen). RNA spike-in controls (Agilent Technologies) are added to RNA samples before amplification and labeling according to manufacturer’s protocol.

growth_protocol: Cells were maintained in keratinocyte serum-free medium (KSFM; Life Technologies Inc.) media containing 50mg/mL of bovine pituitary extract (BPE; Life Technologies Inc.) and 5 ng/mL of EGF (Life Technologies Inc.)

extract_protocol: RNA was extracted and purified using using the RNeasy Mini kit (Qiagen) and processed for hybridization on an Human Gene Expression v2 4x44K Microarray chip.

treatment_protocol: cells were treated with 10 ug/ml CSC or DMSO (con cells) for upto 15 months. 15 month control and CSC exposed cells were then infected with empty vector (EV) or KRASV12 and change in gene expression in CSC cells compared to the respective controls was

value: cigarette smoke condensate (CSC)

tag: treatment time

value: 15 months

source_name: HBEC control cells with KRASV12

value: 15 months with KRASV12

value: lung epithelial


title: monocytes_CTRL_without_medication_rep14

tag: condition


title: monocytes_CTRL_after_medication_rep13


title: monocytes_CTRL_after_medication_rep11


title: CSC_EV_rep1

source_name: Human bronchial epithelial cells_rep1

source_name: HBEC control cells with EV

value: 15 months with EV


title: monocytes_CTRL_without_medication_rep16


title: monocytes_CTRL_after_medication_rep12


title: monocytes_CTRL_without_medication_rep12


title: monocytes_CTRL_without_medication_rep15


title: monocytes_CTRL_without_medication_rep11

description:
3332_1_4
technical replicate of sample 3379_2_3


title: monocytes_CTRL_without_medication_rep13


title: monocytes_CTRL_without_medication_rep10


title: CSC_10 months_rep2

value: 10 months

source_name: HBEC control cells at 10 months


title: CSC_EV_rep2


title: CSC_15 months_rep1

source_name: HBEC control cells at 15 months


title: CSC_15 months_rep2


title: CSC_6 months_rep2

value: 6 months

source_name: HBEC control cells at 6 months


title: CSC_10 months_rep1


title: monocytes_CVD_rep38


title: CSC_1 month_rep2

value: 1 month

source_name: HBEC control cells at 1 month


title: monocytes_CTRL_after_medication_rep10


title: CSC_1 month_rep1


title: monocytes_CTRL_after_medication_rep9


title: CSC_Kras_rep1


title: monocytes_CTRL_after_medication_rep8


title: CSC_6 months_rep1


title: monocytes_CTRL_after_medication_rep7


title: monocytes_CVD_rep7


title: monocytes_CTRL_after_medication_rep5


title: monocytes_CTRL_without_medication_rep9


title: Rep2_T3

description: gene expression in xenograft obtained from 15m CSC treated cells expressing KRASV12

hyb_protocol: Agilent human GE 4x 44K v2 microarrays (Agilent design ID 026652, part number G4845A) were used, which contain 41,000 unique probes targeting 27,958 Entrez gene RNAs. 825 ng of each Cyanine-labeled samples was used for hybridization at 65ºC for 17 hours in a hybridization oven with rotation. After hybridization, microarrays are washed and dried according to Agilent microarray processing protocol in a walk-in ozone-controlled enclosure.

source_name: xenograft from CSC treated HBEC cells with KRASV12_rep2

growth_protocol: Cells were maintained in keratinocyte serum-free medium (KSFM; Life Technologies Inc.) media containing 50mg/mL of bovine pituitary extract (BPE; Life Technologies Inc.) and 5 ng/mL of EGF (Life Technologies Inc.). Xenografts were grown in NSG mice

treatment_protocol: CSC treated cells were infected with KRASV12 expressing lentiviral constructs. Stable cells expressing KRAS were injected in NSG mice. Tumors ontained from CSC cells + KRAS were used for RNA extraction and gene expression studies. Gene expression in Control cells at the same time point and expressing KRASV12 was used for comparison in final analysis.

value: xenograft

value: CSC


title: Rep2_T2


title: CSC_3 months_rep2

value: 3 months

source_name: HBEC control cells at 3 months


title: monocytes_CTRL_after_medication_rep6

value: blood

value: male

value: monocyte


title: monocytes_CVD_rep6

value: CVD


title: Rep1_C+KRAS

description: gene expression in 15 month control cells expressing KRASV12

source_name: 15month control HBEC cells with KRASV12_rep1

value: control epithelial cells

value: Control


title: CSC_3 months_rep1

value: cigarette smoke condensate (CSC)


title: Rep2_T4


title: Rep1_T3

source_name: xenograft from CSC treated HBEC cells with KRASV12_rep1


title: CSC_10days_rep2

value: day 10

source_name: HBEC control cells at 10 days


title: Rep2_T1


title: Rep1_T1


title: monocytes_CTRL_after_medication_rep4


title: monocytes_CTRL_without_medication_rep4


title: monocytes_CTRL_after_medication_rep2


title: monocytes_CVD_rep5


title: monocytes_CTRL_without_medication_rep7


title: monocytes_CVD_rep4


title: monocytes_CTRL_without_medication_rep6


title: monocytes_CTRL_after_medication_rep1


title: monocytes_CTRL_without_medication_rep5


title: monocytes_CVD_rep3


title: monocytes_CTRL_without_medication_rep1


title: CSC_10days_rep1


title: Rep2_C+KRAS

source_name: 15month control HBEC cells with KRASV12_rep2


title: Rep1_T2


title: monocytes_CTRL_without_medication_rep3


title: monocytes_CTRL_without_medication_rep2


title: monocytes_CVD_rep2

description:
3332_1_3
technical replicate of sample 3386_2_2


title: monocytes_CTRL_after_medication_rep3


title: ctl adult 4 week, biological rep2

city: Binghamton

first: Laura

middle: Palanker

last: Musselman

state: New York

address: 4400 Vestal Parkway East

department: Biological Sciences

institute: Binghamton University

hyb_protocol: Following fragmentation, cRNA were hybridized on GeneChip Drosophila 2.0 arrays. GeneChips were washed and stained according to the recommended protocol.

scan_protocol: GeneChips were scanned using a scanner.

data_processing: dChip (2006 version) was used to extract probeset intensites and to normalize using the precise match/mismatch algorithm.

organism: Drosophila melanogaster

source_name: Drosophila adult males aged 31-33 days after 4 weeks of control feeding

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol using 5 ug total RNA/biological replicate.

growth_protocol: See Musselman et al, 2011 (PMID 21719444) for diets. Adult Canton-S genotype flies were aged in single-sex vials until sacrifice.

extract_protocol: Tripure extraction of total RNA was performed followed by RNeasy column to clean the total RNA.

treatment_protocol: Flies were anesthetized with CO2, then homogenized on ice in the Tripure solution using a fresh RNAse-free pellet pestle for each biological replicate.

tag: strain

value: Canton-S

tag: developemental stage

value: young adult (3-5 days)

tag: fed with

value: control diet for 4 weeks

tag: age at sacrifice

value: 31-33 days old


title: HS adult 4 week, biological rep2

source_name: Drosophila adult males aged 31-33 days after 4 weeks of high-sugar feeding

value: high-sugar diet for 4 weeks


title: HS adult 2 day, biological rep3

source_name: Drosophila adult males aged 5-7 days after 2 days high-sugar feeding

value: high-sugar diet for 2 days

value: 5-7 days old


title: monocytes_CVD_rep1

source_name: monocytes,CVD

tag: cell type

tag: age


title: HS adult 2 day, biological rep2


title: HS adult 2 day, biological rep1


title: HS adult 4 week, biological rep1


title: HS adult 4 week, biological rep3


title: ctl adult 4 week, biological rep3


title: genomic DNA from xenograft with 15month CSC cells + KRASV12_rep2_T4

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

data_processing:
BeadStudio software v3.2
SWAN_Normalization Beta values

label: cy3, cy5

extract_protocol: genomic DNA was extracted and purified using Qiagen DNA blood mini kit (Qiagen, CA) according to standard instructions

treatment_protocol: cells were treated with 10 ug/ml CSC or DMSO (con cells)

tag: cell or tissue type

value: tumor xenograft with 15month CSC cells

value: expressing mutant KRAS (KRASV12)


title: genomic DNA from xenograft with 15month CSC cells + KRASV12_rep1_T3


title: genomic DNA from CSC cells at 15 month + EV_rep2

description: rep2_CSC + EV

source_name: CSC cells at 15 month + EV

value: human bronchial epithelial cells (HBEC)

value: expressing empty vector (EV)

tag: treated with

value: cigarette smoke condensate (CSC) over a period of 15 months

tag: time point

value: at 15 month


title: ctl adult 2 day, biological rep3

source_name: Drosophila adult males aged 5-7 days after 2 days control feeding

value: male

value: control diet for 2 days


title: genomic DNA from CSC cells at 15 month + KRASV12_rep2

description: rep2_CSC + KRASV12

source_name: CSC cells at 15 month + KRASV12


title: genomic DNA from xenograft with 15month CSC cells + KRASV12_rep2_T2


title: monocytes_CTRL_without_medication_rep8

value: blood

value: monocyte


title: genomic DNA from xenograft with 15month CSC cells + KRASV12_rep1_T2


title: ctl adult 2 day, biological rep2

value: Canton-S


title: ctl adult 4 week, biological rep1

value: young adult (3-5 days)


title: ctl adult 2 day, biological rep1


title: genomic DNA from xenograft with 15month CSC cells + KRASV12_rep2_T3


title: Ovarian cancer_EC-9

city: Daejeon

first: Kyunghee

last: Noh

address: 125 gahakro

institute: KRIBB

description: Fresh tissue samples (5 normal ovaries, 7 wound tissues, and 10 epithelial high-grade, stage III or IV invasive serous ovarian cancers) were obtained from patients undergoing primary surgical exploration after approval from the Institutional Review Board. Positive selection was done with CD146 and vWF immunobeads, and the beas linked to secondary antibody were form Dynal biotech.

hyb_protocol: 15.0-μg aliquot of labeled product was fragmented by heat and ion-mediated hydrolysis at 94°C for 35 min in 24 μL of H2O and 6 μL of 5× Fragmentation Buffer (Affymetrix). The fragmented cRNA was hybridized for 16 h at 45°C in a Hybridization Oven 640 to a U133 plus 2.0 oligonucleotide array (Affymetrix).

scan_protocol: The arrays were then scanned using a confocal laser GeneChip Scanner 3000 and GeneChip Operating Software (Affymetrix).

data_processing: Global normalization at a target value of 500 was applied to all 15 arrays under consideration using GeneChip Operating Software (Affymetrix).

source_name: Endotehlial cell from epithelial high-grade stage III invasive serous ovarian cancer

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

tag: gender

value: female

value: Human ovarian cancer


title: genomic DNA from xenograft with 15month CSC cells + KRASV12_rep2_T1

tag: genotype/variation


title: Ovarian cancer_EC-8


title: genomic DNA from xenograft with 15month CSC cells + KRASV12_rep1_T1


title: genomic DNA from control cells at 15 month + KRASV12_rep2

description: rep2_Con + KRASV12

source_name: control cells at 15 month + KRASV12

value: none (control)


title: genomic DNA from control cells at 15 month_rep2

description: rep2_Con 15M

source_name: control cells at 15 month


title: genomic DNA from control cells at 15 month + KRASV12_rep1

description: rep1_Con + KRASV12


title: genomic DNA from control cells at 15 month + EV_rep1

description: rep1_Con + EV

source_name: control cells at 15 month + EV


title: genomic DNA from CSC treated cells at 15 month_rep2

description: rep2_CSC 15M

source_name: CSC treated cells at 15 month


title: Ovarian cancer_EC-7


title: genomic DNA from CSC cells at 15 month + EV_rep1

description: rep1_CSC + EV


title: Ovarian cancer_EC-10


title: Ovarian cancer_EC-6


title: Ovarian cancer_EC-4


title: genomic DNA from control cells at 15 month + EV_rep2

description: rep2_Con + EV


title: genomic DNA from CSC cells at 15 month + KRASV12_rep1

description: rep1_CSC + KRASV12


title: Ovarian cancer_EC-3


title: Ovarian cancer_EC-5


title: genomic DNA from CSC treated cells at 10 month_rep2

description: rep2_CSC 10M

source_name: CSC treated cells at 10 month

value: at 10 month


title: Wound_EC-7

source_name: Endothelial cell from wound tissue after surgery

value: Human abdominal region of surgery


title: Ovarian cancer_EC-1


title: Ovarian cancer_EC-2


title: genomic DNA from control cells at 10 month_rep2

description: rep2_Con 10M

source_name: control cells at 10 month


title: genomic DNA from CSC treated cells at 1 month_rep2

description: rep2_CSC 1M

source_name: CSC treated cells at 1 month

value: at 1 month


title: Wound_EC-3


title: Wound_EC-6


title: genomic DNA from CSC treated cells at 6 month_rep2

description: rep2_CSC 6M

source_name: CSC treated cells at 6 month

value: at 6 month


title: genomic DNA from control cells at 1 month_rep2

description: rep2_Con 1M

source_name: control cells at 1 month

value: human bronchial epithelial cells (HBEC)


title: Wound_EC-5


title: Wound_EC-4


title: Normal ovary_EC-3

source_name: Endothelial cell from normal ovary tissue

value: Human ovary


title: genomic DNA from control cells at 6 month_rep2

description: rep2_Con 6M

source_name: control cells at 6 month


title: Normal ovary_EC-4


title: Normal ovary_EC-5


title: Wound_EC-1


title: Wound_EC-2


title: genomic DNA from CSC treated cells at 10 month_rep1

description: rep1_CSC 10M

value: cigarette smoke condensate (CSC) over a period of 15 months


title: DMSO control-2

city: Chengdu

first: Baowen

last: Qi

state: Sichuan

address: No.1 Chengluo Road

institute: Chengdu University

description: high expression of Aurora-A and PLK-1

hyb_protocol: Hybridization 98℃，10min → 45℃，3min → 45℃.

scan_protocol: GeneChip Scanner 3000

data_processing: The data were analyzed with rma using Affymetrix default analysis settings and global scaling as normalization method.

label: Biotin

source_name: DMSO control, HCT-116 cells

label_protocol: IVT

extract_protocol: Trizol

treatment_protocol: 10uM drug treat 48h

value: HCT-116 cells

tag: agent

value: control


title: Normal ovary_EC-1


title: genomic DNA from CSC treated cells at 15 month_rep1

description: rep1_CSC 15M

value: at 15 month


title: AAPK-3

description: high expression of Aurora-A and PLK-1

source_name: AAPK, HCT-116 cells

value: AAPK


title: DMSO control-1

description: high expression of Aurora-A and PLK-1


title: AAPK-1

description: high expression of Aurora-A and PLK-1


title: Normal ovary_EC-2


title: AAPK-2

description: high expression of Aurora-A and PLK-1


title: WT

status: Public on Oct 20 2017

city: Mishima

first: Kousuke

last: Mouri

address: Yata 1111

country: Japan

institute: National Institute of Genetics

description: gene expression data from wildtype autopod

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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.
affymetrix-algorithm-name = ExpressionStat
affymetrix-algorithm-version = 5.0
program-name = Expression Console
program-id = 1.4.1.46

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Natural mate, E13.5

extract_protocol: RNeasy (QIAGEN) was used to isolate total RNA.

treatment_protocol: ID2 and ID3 from hind limb were dissected in cold PBS.

value: B6; wild type

tag: Stage

value: hind limb, interdigit


title: genomic DNA from control cells at 15 month_rep1

description: rep1_Con 15M


title: Hm

description: gene expression data from mutant autopod

source_name: Hammer toe (homo)

value: Hammer toe (homo)

tag: tissue


title: TED 1

city: Portland

first: James

last: Rosenbaum

state: OR

address: 3181 SW Sam Jackson Park Road

department: Casey Eye Institute

institute: Oregon Health & Science University

description: Gene expression data from formalin-fixed, paraffin-embedded tissues

hyb_protocol: Biotin-labeled cDNA targets were hybridized with a GeneChip Human Genome U133 Plus 2.0 array (Affymetrix, Santa Clara, CA) according to standard Affymetrix protocol. Following hybridization, arrays were washed and stained with streptavidin-phycoerythrin.

scan_protocol: Arrays scanned using the GeneChip Scanner 3000 7G system (Affymetrix) and Affymetrix GeneChip Command Console (AGCC) v. 3.1.1

data_processing: Initial quality control analysis was performed using Affymetrix Expression Console v. 1.1 software. Affymetrix CEL files preprocessed by the Robust Multi-array Analysis algorithm for R for expression analysis

source_name: TED, lacrimal gland

label_protocol: Approximately 20 to 50 ng of RNA were amplified and labeled with the SensationPlus FFPE Amplification and 3’ IVT Labeling kit (Affymetrix, Santa Clara, CA).

extract_protocol: After deparaffinization, total RNA was extracted from tissue sections with the miRNeasy FFPE kit (Qiagen, Valencia, CA).

treatment_protocol: Specimens were formalin-fixed and paraffin embedded as soon as possible after surgery

value: Female

tag: diagnosis

value: TED

value: lacrimal gland


title: DMSO control-3

description: high expression of Aurora-A and PLK-1

tag: cell line


title: TED 3

value: Male


title: TED 4


title: TED 2


title: genomic DNA from CSC treated cells at 6 month_rep1

description: rep1_CSC 6M


title: Sarcoidosis 32

source_name: Sarcoidosis, lacrimal gland

value: Sarcoidosis


title: Sarcoidosis 31


title: Sarcoidosis 30  block D


title: genomic DNA from control cells at 10 month_rep1

description: rep1_Con 10M

value: none (control)

value: at 10 month


title: NSOI 27

source_name: NSOI, lacrimal gland

value: NSOI


title: Sarcoidosis 33


title: Sarcoidosis 30  block A


title: NSOI 23


title: genomic DNA from control cells at 6 month_rep1

description: rep1_Con 6M

value: human bronchial epithelial cells (HBEC)

value: at 6 month


title: Sarcoidosis 34


title: Sarcoidosis 29


title: NSOI 5


title: NSOI 3


title: NSOI 25


title: NSOI 9


title: Sarcoidosis 28


title: genomic DNA from CSC treated cells at 1 month_rep1

description: rep1_CSC 1M

value: cigarette smoke condensate (CSC) over a period of 15 months

value: at 1 month


title: NSOI 4


title: genomic DNA from control cells at 1 month_rep1

description: rep1_Con 1M


title: NSOI 1


title: NSOI 6


title: NSOI 22


title: NSOI 7


title: NSOI 8


title: NSOI 2


title: NSOI 16


title: NSOI 20


title: NSOI 15


title: NSOI 24


title: NSOI 17


title: NSOI 21


title: NSOI 14


title: NSOI 13


title: Normal 2

source_name: Normal, lacrimal gland

value: Normal


title: NSOI 26


title: NSOI 18


title: Normal 1


title: Normal 6


title: NSOI 19


title: NSOI 11


title: NSOI 10


title: Normal 4


title: NSOI 12


title: Normal 5


title: GPA 3

source_name: GPA, lacrimal gland

value: GPA


title: Normal 7


title: GPA 2


title: RNAP2_Smarca4_WT

type: SRA

city: Houston

first: H. Courtney

last: Hodges

state: TX

address: 1 Baylor Plaza, BCM 229

department: Department of Molecular & Cellular Biology

institute: Baylor College of Medicine

description: anti-RNAP2 ChIP in mES cells expressing WT Smarca4V5.

library_source: genomic

data_processing:
Basecalls performed using Illumina CASAVA version 1.8.2.
Reads were aligned to the mm9 genome assembly using bowtie version 2.1.0, requiring mapping qualities > 10. Duplicate reads were discarded.
Peaks were called by comparing ChIP and input samples using MACS 2.1.1 with default settings.
Peaks with less than 30 reads per million were discarded to ensure high-quality peak calls.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: bigWig files were generated by extending all read fragments to 200 bp, then calculating the basepair coverage for each replicate using Bedtools, normalizing by the total number of reads within called peaks. For samples with multiple replicates, values in the bigWig files represent coverage calculated in this way averaged across both replicates using bwtool.

source_name: Mouse embryonic stem cells, Smarca4_WT, RNAP2 ChIP

growth_protocol: Cells are grown in DMEM media supplemented with 15% FBS and LIF.

extract_protocol:
Lysates were obtained from sonicated nuclei crosslinked with formaldehyde, and protein-DNA complexes were isolated by immunoprecipitation.
All libraries were barcoded and prepared for sequencing using standard Illumina protocols.

treatment_protocol: Wild-type and heterozygous Smarca4 mutant cells received no treatment.

tag: strain/background

value: Embryonic stem cells

tag: passage

tag: chip antibody

value: Mouse anti-RNAP2

tag: chip antibody vendor

value: Covance

tag: chip antibody cat. #

tag: chip antibody lot/batch #

value: n/a (monoclonal)


title: H3K27ac_Smarca4_G784E

description: anti-H3K27ac ChIP in mES cells expressing G784E Smarca4V5.

source_name: Mouse embryonic stem cells, Smarca4_G784E, H3K27ac ChIP

tag: cell type

value: Rabbit anti-H3K27ac

value: Abcam


title: H3K27ac_Smarca4_WT

description: anti-H3K27ac ChIP in mES cells expressing WT Smarca4V5.

source_name: Mouse embryonic stem cells, Smarca4_WT, H3K27ac ChIP


title: H3K4me1_Smarca4_WT

description: anti-H3K4me1 ChIP in mES cells expressing WT Smarca4V5.

source_name: Mouse embryonic stem cells, Smarca4_WT, H3K4me1 ChIP

value: Rabbit anti-H3K4me1


title: Normal 3

value: Female

value: lacrimal gland


title: H3K4me1_Smarca4_G784E

description: anti-H3K4me1 ChIP in mES cells expressing G784E Smarca4V5.

source_name: Mouse embryonic stem cells, Smarca4_G784E, H3K4me1 ChIP


title: ExVivoSVF_adipose tissue_miRNA_Control_rep2

city: Stockholm

first: Carina

last: Fischer

address: Nobels väg 16

country: Sweden

institute: Karolinska Institute

description: microRNA expression after 3d of control treatment (PBS, Phosphate buffered salt solution)

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US)in hybridization Oven(Cat#G2545A, Agilent technologies, Santa Clara, CA, US)at 55℃，20rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US).

scan_protocol: The chip results were scanned using the Agilent Microarray Scanner (Cat # G2565BA, Agilent technologies, Santa Clara, CA, US) with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) , PMT 100%, 5% were finally normalized using Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US) using Quantile.

data_processing: Normalization and analysis for differentially expressed genes were performed using robust multi-array analysis and significance analysis of microarrays (SAM) via R statistical software packages “oligo” and “samr”.

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US)followed the manufacturer’s instructions, labeling section.

growth_protocol: C57/BL6 mice were kept at room temperature with access to water and standard diet. Cellular fractions containing primary adipocytes and SVF cells were isolated from eight-week-old C57BL/6 female mice by a standard collagenase-based digestion method. Briefly, freshly isolated adipose tissues were minced and digested at 37 °C in digestion medium (0.2% collagenase II, 5% FBS in DMEM) for 30 min with shaking. Mature adipocyte fractions and stromal vascular fractions were separated by incubation on ice for 10 min, followed by centrifugation at 300 g for 10 min. The adipocyte fraction was removed and the SVF was filtered through a 100-µm mesh, followed by washing twice with PBS and filtering through a 40-µm mesh. SVFs were directly used for microRNA isolation.

extract_protocol: A QIAzol-Chloroform based protocol was used for the extraction of RNA from tissue samples. Briefly, QIAzol lysis reagent (Qiagen) was added to SVFs. The samples were incubated on ice for 10 min before adding chloroform followed by centrifugation at 7000 g for 20 min. RNA-containing supernatants were mixed with 100% ethanol and subsequently applied to RNA extraction columns provided in the miRNeasy Mini Kit Cat # 217004, Qiagen). To extract RNA, manufacturer’s instructions were followed.

treatment_protocol: Mice were treated subcutenously for 3 days with 1mg/kg CL 316243 disodium salt dissolved in PBS or PBS as control.

value: adipose tissue stromal vascular fraction

tag: strain

value: female

tag: age


title: ExVivoSVF_adipose tissue_miRNA_3dCL_rep2

description: microRNA expression after 3d of CL-316,243 treatment


title: ExVivoSVF_adipose tissue_miRNA_3dCL_rep1


title: ExVivoSVF_adipose tissue_miRNA_Control_rep1


title: Input_Smarca4_G784E

description: Input sample for mES cells expressing G784E Smarca4V5.

source_name: Mouse embryonic stem cells, Smarca4_G784E, input


title: HIV- CD28- resting, biological rep3

city: San Francisco

first: Philip Ansumana

last: Hull

address: 1650 Owens Street

department: GIVI

institute: Gladstone Insitute of Virology and Immunology

description: Gene expression data from HIV- CD28- resting CD8+ T cells

hyb_protocol: Following fragmentation, 1000 ng of cRNA were hybridized for 16 hr at 45C on GeneChip Homo sapiens Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing:
Command Console
rma-gene-default

source_name: Homo sapiens HIV- CD28- resting CD8+ T cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 600ng or 1000ng total RNA in 6ul or 10ul respectively (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: CD8+ T cells were negatively selected and enriched from human peripheral blood and sorted for CD28+ and CD28- subsets.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Samples were Turbo™ Dnase treated  (Applied Biosystems)

treatment_protocol: Sorted T cells were cultured in complete RPMI o/n at 37C. T cells were spun down, washed once in PBS and lyzed in the Trizol solution (GibcoBRL).

value: peripheral blood

value: primary CD8+ T cells

tag: cell subset

value: 53 years


title: HIV- CD28+ resting, biological rep1

description: Gene expression data from HIV- CD28+ resting CD8+ T cells

source_name: Homo sapiens HIV- CD28+ resting CD8+ T cells

value: 59 years


title: HIV- CD28+ resting, biological rep3


title: HIV- CD28+ resting, biological rep2

value: 62 years


title: HIV- CD28- resting, biological rep1


title: HIV- CD28- resting, biological rep2


title: WT_Kb-OVA+_CD8+_T_CELLS_REP3

city: Paris

first: Luigia

last: Pace

address: 26 rue d'Ulm

country: France

institute: Institut Curie

description: Wild-type, activated CD8 T cells, biological rep3

hyb_protocol: Labelled DNA was hybrized on the Affymetrix Mouse Gene 2.1 ST processed on an Affymetrix GeneTitan device.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Microarray data were carried out with R (version 3.1.0) using packages from the Bioconductor. Raw data CEL files were used and the quality control analysis was performed using ArrayQualityMetrics package. The raw data were preprocessed using the RMA (Robust Multi-array Average) method available in oligo package. Gene expression levels were analyzed on a base-2 logarithmic scale.

source_name: wild-type

label_protocol: For each condition, RNA was employed to synthetize cDNA according to the standard Affymetrix protocol.Affymetrix GeneTitan device.

growth_protocol: Naïve littermate and Suv39h1-KO CD8+ T cells, and day 7 post-infection Kb-OVA+ CD8+ T cells (from Listeria .m-OVA infected mice), were isolated by flowcytometry

extract_protocol: RNA was extracted using Rneasy Micro Kit (QUIGEN) according to the manufacturer protocol. A column DNAse treatment was included (QUIGEN).

tag: genotype

value: wild-type

value: activated CD8 T cells


title: KO_Kb-OVA+_CD8+_T_CELLS_REP1

description: Suv39h1 -/-, activated CD8 T cells, biological rep1


title: Input_Smarca4_WT

description: Input sample for mES cells expressing WT Smarca4V5.

source_name: Mouse embryonic stem cells, Smarca4_WT, input

value: Embryonic stem cells


title: KO_Kb-OVA+_CD8+_T_CELLS_REP3

description: Suv39h1 -/-, activated CD8 T cells, biological rep3


title: KO_NAIVE_CD8+_T_CELLS_REP1, TECH2

description: Suv39h1 -/-, naive CD8 T cells, biological rep1, technical 2

value: naive CD8 T cells


title: GPA 1

tag: gender

value: GPA


title: WT_NAIVE_CD8+_T_CELLS_REP3

description: Wild-type, naive CD8 T cells, biological rep3


title: WT_Kb-OVA+_CD8+_T_CELLS_REP2

description: Wild-type, activated CD8 T cells, biological rep2


title: WT_NAIVE_CD8+_T_CELLS_REP2

description: Wild-type, naive CD8 T cells, biological rep2


title: WT_Kb-OVA+_CD8+_T_CELLS_REP1

description: Wild-type, activated CD8 T cells, biological rep1


title: KO_NAIVE_CD8+_T_CELLS_REP3

description: Suv39h1 -/-, naive CD8 T cells, biological rep3


title: WT_NAIVE_CD8+_T_CELLS_REP1, TECH2

description: Wild-type, naive CD8 T cells, biological rep1, technical 2


title: KO_NAIVE_CD8+_T_CELLS_REP2

description: Suv39h1 -/-, naive CD8 T cells, biological rep2


title: KO_Kb-OVA+_CD8+_T_CELLS_REP2

description: Suv39h1 -/-, activated CD8 T cells, biological rep2


title: WT_NAIVE_CD8+_T_CELLS_REP1, TECH1

description: Wild-type, naive CD8 T cells, biological rep1, technical 1


title: hetero_Ahsg_2

status: Public on Oct 19 2017

city: Aachen

first: Bernd

last: Denecke

state: NRW

address: Pauwelsstrasse 30

department: IZKF Aachen

institute: RWTH Aachen University

hyb_protocol: Samples were hybridized using Affymetrix haybridization kit materials according to the manufacturers instructions: hybridization 45°C for 16 hours at 60 rpm; Fluidics Station Program FS_450_0001

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

data_processing: Raw image data were analysed with Affymetrix® Expression Console™ Software (Affymetrix, USA), and gene expression intensities were normalized and summarized with SST robust multiarray average algorithm (Affymetrix): SST-RMA. Further analyses was performed using the Transcriptome Analysis Console (TAC) Software of Affymetrix.

source_name: growth plate cartilage from heterozygous mouse

label_protocol: Fragmented, biotinylated cDNAs were prepared from 150 ng total RNA using  the Affymetrix WT plus reagent kit according to the manufacturers instructions.

extract_protocol: From each mouse, the right femur was directly frozen in OCT in isopentane cooled with dry ice. Cryo-section preparation was performed under nuclease-free conditions to maintain RNA integrity. Sections of 14 µm were mounted on PEN-membrane slides (Zeiss). Slides were fixed with 95 % ethanol for 2 min, dehydrated with 100 % ethanol for 1 min, air dried at room temperature for 5 min and stored at  80 °C for up to 48 h until further processing. Laser capture microdissection (LCM) was performed using a Zeiss P.A.L.M. micro laser system. For each sample, approx. 40 frozen sections were prepared and processed. Per section, the entire growth plate (resting zone, proliferative zone and hypertrophic zone) was isolated and captured in an adhesive cap (Zeiss). The isolated tissue was suspended in 50 µl extraction buffer (PicoPure RNA Isolation Kit, Thermo Fisher Scientific), incubated at 42 °C for 20 min and stored at  80 °C until RNA isolation, which was carried out according to the manufacturer’s protocol.

value: growth plate cartilage

value: 13 days postnatal

tag: Sex

value: male

tag: genetic background

value: Ahsg+/-


title: hetero_Ahsg_3

tag: tissue


title: ko_Ahsg_3

source_name: growth plate cartilage from knockout mouse

value: Ahsg-/-


title: ko_Ahsg_1


title: wt_Ahsg_3

source_name: growth plate cartilage from wildtype mouse

value: Ahsg+/+


title: ko_Ahsg_2


title: KO_NAIVE_CD8+_T_CELLS_REP1, TECH1

description: Suv39h1 -/-, naive CD8 T cells, biological rep1, technical 1


title: hetero_Ahsg_1


title: wt_Ahsg_2


title: wt_Ahsg_1


title: sample not used due to quality control

city: Aurora

first: Robert

middle: C

last: Roach

state: CO

address: Campus Box F-524, 12469 E. 17th Place

department: Department of Pulmonology

institute: University of Colorado

hyb_protocol: Genome-wide methylation was assessed using Illumina's Infinium HumanMethylation450 BeadChip

scan_protocol: Illumina HiScan was used with control software version 3.2.26.

data_processing: Data were normalized with the SWAN algorithm as implemented in the R/Bioconductor minfi package.

label: Cy5, Cy3

source_name: NA, PBMC

label_protocol: gDNA was quantitated with the NanoDrop spectrophotometer, bisulfite converted using the Zymo EZ DNA Methylation Kit, and labeled according to Illumina protocols.

growth_protocol: not applicable

extract_protocol: Peripheral blood samples were collected from an antecubital vein prior to exercise on the first, seventh, and sixteenth days of initial altitude exposure (ALT1, ALT7, and ALT16) and on the re-exposure days (POST7 and POST21), and placed into a BD Vacutainer Cell Preparation Tube containing sodium citrate and Ficoll Hypaque density fluid. PBMC (peripheral blood mononuclear cell) pellets were stored at -80C until analysis.  gDNA was purified using the Qiagen QIAEX II Kit.

treatment_protocol: exposure to altitude

value: PBMC


title: altitude exposure at post21, biological rep 007

source_name: post21, PBMC

tag: time point

tag: subject

value: M

tag: height (in.)

tag: weight (kg.)


title: altitude exposure at post21, biological rep 001


title: altitude exposure at post7, biological rep 022

source_name: post7, PBMC


title: altitude exposure at post21, biological rep 002


title: altitude exposure at post21, biological rep 005

value: F


title: altitude exposure at post7, biological rep 020


title: altitude exposure at post7, biological rep 023


title: altitude exposure at post7, biological rep 014


title: altitude exposure at post7, biological rep 021


title: altitude exposure at post7, biological rep 015


title: altitude exposure at post7, biological rep 018