title: 84317/CO399 LEC Stroma+SP2/Biological LEC Stromal replicate 2

city: Nottingham

first: Patrick

middle: Jason

last: Tighe

state: Nottinghamshire

address: University Hospital

department: School of Molecular Medical Sciences

country: United Kingdom

institute: The University of Nottingham

description: The Standard Probe (SP) was prepared by combining 500 ng of extracted RNA from corneal and conjunctival epithelium and ethanol precipitating it to a concentration of 1µg/10µl.  The Standard probe RNA was amplified with 2 rounds using Ambion Aminoallyl Message Amp II kit. 1.o ul of 1:5000 dilution of spike was added to RNA sample during amplification.

hyb_protocol: Firstly hybrid probe were prepared by mixing equal amount (500ng) of Cy5 & Cy3 labelled probes in a 0.5 ml tube, 2 µl of Cot I DNA and 2 µl Poly A was added to the mix (to reduce non specific hybridization).  The aliquote was then ethanol precipitated to 1-2 µl.  The pellet was rehydrated with 2µl of nuclease free pure water. Standard protocol for slide hybridization (Tecan HS 4800) was followed.  It consisted of Buffer and probe preparation which included heating the Hybrid probes to 95ºc for two minutes followed by pulse centrifugation, the microarray slides were treated by Pre-Hybridization Blocking treatment of the microarray slides.  Following which the Hybridization station was primed with first buffer and the blocked microarray slides were placed in the station.  The hybridization programme was started followed by probe insertion. Standard Protocol for hybridization is briefly described: Standard Protocol  * Buffer one to six as previously stated.  Step 1: Wash, 42oC, Buffer 6, Wash 30 sec, Soak 5 Sec, 5 Runs.  Step 2: Wash, 50oC, Buffer 1, Wash 1 min, Soak 15 min, 1 Run.    Step 3: Probe Injection, 50oC.  Step 4: Hybridization, 50oC, Low Agitation, 16 hours.  Step 5. Wash, 40oC, Buffer 2, Wash 1 min, Soak 1 min, 4 Run.  Step 6. Wash, 40oC, Buffer 3, Wash 1 min, Soak 1 min, 2 Run.  Step 7. Wash, 40oC, Buffer 4, Wash 1 min, Soak 30 sec, 2 Run.  Step 8. Wash, 23oC, Buffer 5, Wash 1 min, Soak 30 sec, 2 Run.  Step 9. Slide Drying, 23oC, 2 min, Final Manifold Cleaning Yes, Buffer 6. Composition of Buffer 1-6 is as follows:  2L of Buffer One: 5xSSC 0.2%SDS - 2x (250ml SSC, 20ml SDS, 730ml Water) * 2L of Buffer Two: 2xSSC 0.1%SDS - 2x(100ml SSC. 10ml SDS, 890ml Water)  * 2L of Buffer Three: 1xSSC 0.1%SDS - 2x(50ml SSC, 10ml SDS 940ml Water) * 2L of Buffer Four: 0.1xSSC 0.2%SDS - 2x(5ml SSC, 20mlSDS 975ml Water)   * 2L of Buffer Five: 0.1xSSC - 2x(5ml SSC, 995ml Water)  * 2L of Buffer Six: Ultra pure water.

scan_protocol: Microarray slides were scanned with Agilent BA scanner at 10 µm resolution with 635 and 532 lasers at 100% power. TIFF images were imported into Genepix Pro v6.01 (Axon Instruments) aligned and analyzed for feature quantification

data_processing: GPR files were uploaded to a local version of BASE 1.2.17 (source code at Lund University Sweden).  All data in the set were filtered to 1: remove landing-lights and scorecard control probes  2:remove any  features  which were flagged as bad or missing  by Genepix Pro.  3: Dual channel filtering to remove any features  where the percentage of foreground pixels below the background +2SD was <50%.  Both fluorecent channels were then used  to normalise red/green ration (635/352nm ratio) by the method of Lowess.  Data was exported to JExpress Pro, v2.7 (Molmin AS) and all samples, as log2 ratio values, were mean  normalised and filtered to remove any genes where the Standard deviation across the dataset was less than 0.5

source_name: SC-CO399 LEC Stroma

label_protocol: 10µg of 2nd round amplified RNA (Channel 1 samples) were labelled with Cy5 dye and the Standard Probe (Channel 2 sample) with Cy3 dye.  These Cy dyes were single use Amersham cy dye post-labeling kit supplied with Ambion Amino Allyl  MessageAmp II kit.  The manufacturer's protocol for labelling was followed.

growth_protocol: Corneoscleral button with conjunctiva was dissected from freshly obtained cadaver eyes.  The corneoscleral button was further dissected radially into eight segments and embedded in OCT medium in aluminium foil cups. These segments were snap frozen in  isopentane prechilled in Liquid Nitrogen and stored at -80ºc till further use.

extract_protocol: Total RNA extraction from LCM samples was performed with Qiagen Rneasy Microkit, following manufacturer's protocol. Reference samples were processed using the Qiagen Rneasy minikit.  For the reference samples only, equal RNA quantities from both cornea and conjunctiva were mixed together and ethanol precipitated prior to use in the labelling procedure.

treatment_protocol: The frozen tissue blocks were cryosectioned and taken on glass slides.  The serial sections (unstained wet preparations) were observed under the light microscope to study the epithelial histology. Sections with good histology and those showing beginning of the Limbal Epithelial Crypt (LEC) were further taken on PALM slides for Laser microdissection (LMD).  The sections on PALM slides were briefly fixed in 70% prechilled ethanol, followed by air drying.  The slides were stored in suitable containers at -80ºc till further use. All these procedures were performed under RNASE and DNASE free conditions.  Prior to LMD the slides were stored at 4ºc.  The sections on PALM slides were then covered with 0.1% Toludine Blue for 5-10 seconds.  The slides were then washed twice in DEPC treated water for 5 seconds and air dried.  The slides are now ready for Laser Microdissection, the slide is placed on the rotating stage of the microscope and the section image is viewed on the computer screen attached to the microscope. The area of interest is brought to focus and outlined with computer graphic drawing tool.  The cap of special collection tube is brought into place over the area of interest by an automated holding device.  On activating the RoboLPC function of the Laser microdissector, the laser is activated and cuts the tissue and the membrane coating the slide which underlies the tissue along the outline.  At the end of the cut a burst of energy is generated which catapults the tissue into the collection tube cap.  As the cap is coated with special adhesive the catapulted tissue sections stick to the inside of the cap.  On collection of sufficent tissue area 100µl of RLT Buffer activated with 1µl of β-mercaptoethanol was added to the collection tube and sealed with paraffin and thoroughly vortexed upside down.  The tubes were stored at -80ºc till further RNA extraction was performed. Reference samples were prepared by mechanical scraping of conjunctival and corneal epithelium from fresh cadaver eye and cells were lysed in RLT buffer as per manufacturers protocol.

tag: donor age (years)

tag: donor sex

value: Male

tag: eye orientation

value: Left Eye

tag: time between donor death and sample collection

value: 24 Hours

tag: tissue type

value: Limbal Epithelial Crypt Stroma

tag: laser microdissected area (µm2)

tag: rna conc (pg/µl)

tag: 2nd round amplified rna conc (ng/µl )

tag: labelled extract conc (ng/µl )

tag: frequency of incorporation of cy5 dye (foi)

tag: labelled extract concentration

tag: frequency of incorporation of cy5 dye

tag: donor type

value: Human cadaver eye

value: Left eye

value: 12 hours

value: Corneal and conjunctival epithelium

tag: rna concentration

value: Corneal epithelium (2.22 µg), Conjunctival epithelium (8.98 µg)


title: 84543/CO404 LEC Stroma+SP2/Biological LEC Stromal replicate 3

status: Public on Mar 24 2010

type: RNA

molecule: total RNA

organism: Homo sapiens

source_name: SC-CO404 LEC Stroma

value: Female

value: Right Eye

value: 48 Hours


title: 84316/CO418 LEC Stroma+SP1/Biological LEC Stromal replicate 4

source_name: SC-CO418 LEC Stroma


title: 84550/CO418 Conjunctiva+SP2/Biological Conjunctival replicate 3

source_name: SC-CO418 Conjunctiva

value: Conjunctival epithelium


title: OCT8

city: Birmingham

first: Molly

middle: Bray

last: Bray

state: AL

address: 720 20th Street S

department: Genetics

country: USA

institute: Univ of Alabama at Birmingham

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
OCT8

hyb_protocol: A total of 0.75 micrograms of biotin-labeled cRNA was applied to a BeadChip and allowed to hybridize overnight at 55°C for approximately 18 hours, followed by washing and staining with streptavidin-Cy3 prior to visualization.

scan_protocol: BeadChips were visualized using the BeadStation scanner, which uses a dual-laser confocal scanner with 0.8 µm resolution to determine fluorescence values for each bead on the chip.

data_processing: After scanning the probe arrays, the resulting images were analyzed using the BeadStudio software (V3, Illumina, Inc., San Diego, CA), which calculates the mean fluorescence signal across all replicates of each gene/transcript, along with a probability that the mean signal for each gene/transcript on the chip is greater than background (i.e., detection p-value).  Both non-normalized and normalized (qspline) data were generated for each tissue type.

organism: Rattus norvegicus

source_name: Cardiomyocytes, octonoeic acid

label_protocol: Total RNA was converted to cDNA by reverse transcription using Superscript II reverse transcriptase and T7-(dT)24 primers, followed by second-strand synthesis to generate double-stranded cDNA.

extract_protocol: RNA was extracted from all tissues using a standard protocol and Tri-reagent.

treatment_protocol: Isolated, cultured adult rat cardiomyocytes were challenged with 1% BSA (control) or 0.4 mM octanoate, palmitate, stearate, oleate, or linoleate conjugated to 1% BSA for 24 h, after which RNA was isolated and utilized for gene expression analysis.

tag: strain

value: Wistar

tag: gender

value: male

tag: developmental stage

value: adult

tag: genotype

value: wildtype

tag: cell type

value: cardiomyocytes

tag: treatment

value: exposed to 1%BSA + octonoeic acid


title: OLE3

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
OLE3

source_name: Cardiomyocytes, oleic acid

value: exposed to 1%BSA + oleic acid


title: OCT7

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
OCT7


title: 84318/CO399 Conjunctiva+SP2/Biological conjunctival replicate 1

source_name: SC-CO399 Conjunctiva

tag: donor age (years)

tag: donor sex

value: Male

tag: eye orientation

value: Left Eye

tag: time between donor death and sample collection

value: 24 Hours


title: 84410/CO398 LEC Stroma+SP1/Biological LEC Stromal replicate 1

source_name: SC-CO398 LEC Stroma

tag: tissue type

value: Limbal Epithelial Crypt Stroma

tag: laser microdissected area (µm2)

tag: rna conc (pg/µl)

tag: 2nd round amplified rna conc (ng/µl )

value: Human cadaver eye

value: Left eye

value: 12 hours


title: 84571/CO404 Conjunctiva+SP1/Biological Conjunctival replicate 2

source_name: SC-CO404 Conjunctiva

value: Female

value: Right Eye

tag: labelled extract conc (ng/µl )

tag: frequency of incorporation of cy5 dye (foi)

tag: labelled extract concentration

tag: frequency of incorporation of cy5 dye

value: Corneal and conjunctival epithelium

value: Corneal epithelium (2.22 µg), Conjunctival epithelium (8.98 µg)


title: 84315/CO418 LEC+SP1/Biological LEC replicate 4

source_name: SC-CO418 LEC

value: Limbal Epithelial Crypts

tag: donor type

tag: rna concentration


title: 84542/CO404 LEC+SP2/Biological LEC replicate 3

source_name: SC-CO404 LEC

value: 48 Hours


title: 84313/CO418 Limbus+SP2/Biological Limbus replicate 4

source_name: SC-CO418 Limbus

value: Limbal Epithelium


title: OCT3

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
OCT3

tag: strain

value: Wistar

tag: gender

value: male

tag: developmental stage

value: adult

tag: genotype

value: wildtype

value: cardiomyocytes


title: OCT6

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
OCT6

tag: cell type

tag: treatment

value: exposed to 1%BSA + octonoeic acid


title: OCT4

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
OCT4


title: 84320/CO399 LEC+SP2/Biological LEC replicate 2

source_name: SC-CO399 LEC

tag: donor age (years)

tag: donor sex

value: Male

tag: eye orientation

value: Left Eye

tag: time between donor death and sample collection

value: 24 Hours


title: OCT5

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
OCT5


title: 84409/CO399 Limbus+SP1/Biological Limbus replicate 2

source_name: SC-CO399 Limbus

tag: tissue type

tag: laser microdissected area (µm2)

tag: rna conc (pg/µl)

tag: 2nd round amplified rna conc (ng/µl )

value: Human cadaver eye

value: Left eye

value: 12 hours


title: 84412/CO404 Limbus+SP1/Biological Limbus replicate 3

source_name: SC-CO404 Limbus

value: Female

value: Right Eye

tag: labelled extract conc (ng/µl )

tag: frequency of incorporation of cy5 dye (foi)

tag: labelled extract concentration

tag: frequency of incorporation of cy5 dye

value: Corneal and conjunctival epithelium


title: 84403/CO398 Limbus+SP1/Biological Limbus replicate 1

source_name: SC-CO398 Limbus

tag: donor type

tag: rna concentration

value: Corneal epithelium (2.22 µg), Conjunctival epithelium (8.98 µg)


title: OCT2

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
OCT2

tag: strain

tag: gender

tag: developmental stage

tag: genotype


title: 84549/CO399 Cornea+SP1/Biological cornea replicate 2

source_name: SC-CO399 Cornea

tag: donor age (years)

tag: donor sex

value: Corneal Epithelium


title: 84390/CO398 Cornea+SP1/Biological cornea replicate 1

source_name: SC-CO398 Cornea

tag: eye orientation

tag: time between donor death and sample collection


title: 84411/CO398 LEC+SP1/Biological LEC replicate 1

source_name: SC-CO398 LEC

tag: tissue type

value: Limbal Epithelial Crypts

tag: laser microdissected area (µm2)


title: OCT1

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
OCT1

value: Wistar

value: male

tag: cell type

tag: treatment


title: LIN7

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
LIN7

source_name: Cardiomyocytes, linoleic acid

value: adult

value: wildtype

value: exposed to 1%BSA + linoleic acid


title: LIN3

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
LIN3

value: cardiomyocytes


title: CONTROL6

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
CONTROL6

source_name: Cardiomyocytes, control

value: exposed to 1%BSA


title: LIN6

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
LIN6


title: LIN5

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
LIN5


title: LIN4

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
LIN4


title: 84544/CO418 Cornea+SP1/Biological cornea replicate 3

source_name: SC-CO418 Cornea

value: Male

value: 24 Hours

tag: rna conc (pg/µl)

tag: 2nd round amplified rna conc (ng/µl )

tag: labelled extract conc (ng/µl )

tag: frequency of incorporation of cy5 dye (foi)


title: LIN1

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
LIN1


title: CONTROL4

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
CONTROL4


title: Animal 40

description:
Approximately 46,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
40

hyb_protocol: A total of 1.5 micrograms of biotin-labeled cRNA was applied to a BeadChip and allowed to hybridize overnight at 55°C for approximately 18 hours, followed by washing and staining with streptavidin-Cy3 prior to visualization.

organism: Mus musculus

source_name: Heart, WT, normal diet

treatment_protocol: Heart tissue was collected at ZT 18 after 16 weeks of high fat or normal diet in transgenic (CCM) and wildtype animals.

value: FVB/N

tag: tissue

value: heart

tag: diet

value: normal diet

tag: time

value: ZT 18


title: CONTROL7

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
CONTROL7

tag: strain

tag: gender

tag: developmental stage


title: CONTROL3

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
CONTROL3

tag: genotype


title: LIN2

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
LIN2


title: CONTROL5

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
CONTROL5


title: Animal 22

description:
Approximately 46,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
22


title: Animal 13

description:
Approximately 46,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
13


title: CONTROL2

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
CONTROL2


title: Animal 37

description:
Approximately 46,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
37

source_name: Heart, WT, high fat diet

value: high fat diet


title: Animal 14

description:
Approximately 46,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
14


title: CONTROL1

description:
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
CONTROL1


title: Animal 21

description:
Approximately 46,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
21


title: Animal 29

description:
Approximately 46,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
29


title: Animal 33

description:
Approximately 46,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
33

source_name: Heart, CCM, normal diet

value: CCM transgenic


title: Animal 15

description:
Approximately 46,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
15


title: Animal 16

description:
Approximately 46,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
16


title: Animal 17

description:
Approximately 46,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
17


title: Animal 12

description:
Approximately 46,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
12

source_name: Heart, CCM, high fat diet


title: Animal 32

description:
Approximately 46,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
32


title: Animal 25

description:
Approximately 46,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
25


title: Animal 11

description:
Approximately 46,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
11


title: Animal 19

description:
Approximately 46,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
19


title: Animal 18

description:
Approximately 46,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
18


title: Animal 38

description:
Approximately 46,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
38


title: Animal 4

description:
Approximately 46,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
4


title: HUVEC_p5SRNAP_TNF_30min

status: Public on Mar 23 2010

type: genomic

city: Komaba

first: Shuichi

last: Tsutsumi

country: Japan

institute: The University of Tokyo

description: Gene expression data of HUVEC cells afterTNF-alpha stimulation.

hyb_protocol: Following fragmentation, 5.5 microg of cDNA were hybridized for 16 hr at 45C on NimbleExpress Array. Chips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-PackardGeneArray Scanner G3000A7G.

data_processing: The data were analyzed with Affymetrix -GeneChipR Operating Software (GCOS) using Affymetrix default analysis settings.

label: biotin

molecule: genomic DNA

source_name: Huvec cells treated by TNFalpha

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 2 microg cRNA

growth_protocol: Before stimulation, HUVECs were serum-starved in EBM-2 (Clonetics) containing 0.5% FBS for 18 h.

extract_protocol: Cells were crosslinked with paraformaldehyde and sonicted, then immunoprecipitated with antibody for p5SRNAP(H14) and DNA was prepared

treatment_protocol: HUVECs were treated with/without 10 ng/ml TNF alpha(Peprotec) and samples collected 30 min after stimulation

value: HUVEC

tag: antibody:


title: HUVEC_p5SRNAP_TNF_60min

treatment_protocol: HUVECs were treated with/without 10 ng/ml TNF alpha(Peprotec) and samples collected 60 min after stimulation

tag: antibody

value: for p5SRNAP(H14)


title: HUVEC_CTCF_TNF_60min

extract_protocol: Cells were crosslinked with paraformaldehyde and sonicted, then immunoprecipitated with antibody for CTCF and DNA was prepared

value: for CTCF


title: DN3 rep4 (4459290113_F)

city: Frederick

first: Jack

last: Chen

state: MD

address: SAIC-Frederick Miller Dr

institute: NIH

description: replicate 4

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with dChip

source_name: mice lymphocytes

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

growth_protocol: After 4-hydroxytamoxifen (OHT) treatment, DN3 thymocytes from Bcl11bCKO/CKO and Bcl11bCKO/+ were sorted by FACS and co-cultured with OP9-DL1 in T cell culture media (3,000 cells per well in 24-well plates) with 100 ng/ml huIL-2, respectively. Every three days, cells were collected by vigorous pipetting, filtered through cell strainers and transferred to new tissue culture plates pre-seeded with fresh OP9-DL1 stromal cells. Fourteen days after OHT treatment, cells were collected for RNA extraction. For ex vivo expansion, splenic ITNK cells were enriched using the NK Isolation Kit (Miltenyi) and cultured for 6-9 days at 1 x 106 cells/ml in RPMI 1640 medium containing 10% FCS/50 µM 2-mercaptoethanol/2.0 mM L-glutamine and 1000 U/ml hIL-2 (Chiron).

extract_protocol: RNA from primary cells was extracted using the RNAqueous-Micro RNA isolation kit according to the manufacture protocol (Ambion). Briefly, cells were counted and pelleted by centrifuge at 4,000 G for 5 min. Remove supernatant thoroughly by aspiration. Resuspend cell pellet by vortexing vigorously in at least 100 ul Lysis Solution. Then 50 ul of 100% ethanol was added and mixed with lysate thoroughly. Next load the lysate/ethanol mixture onto a Micro Filter Cartridge Assembly and centrifuge for 10 sec at 16,000 G. Then wash the filter with 180 ul of Wash Solution 1 once and 180 ul of Wash Solution 2/3 twice. Discard the flow-through and centrifuge the filter for 1 min at 16,000 G. Elute the RNA into a Micro Elution Tube with 2X5 ul preheated Elution Solution. To eliminate contaminated DNA from extracted RNA, 1/10th volume of 10X DNase I Buffer and 1 ul of DNase I were added into the RNA sample and mixed gently but thoroughly. After incubation at 20 min at 370C, the DNase reaction was mixed with 2 ul DNase Inactivation Reagent and left at room temperature for 2 min. Finally, pellet the DNase Inactivation Reagent and transfer the RNA to a fresh tube. For RT-PCR or qRT-PCR experiments, RNA quality and quantity was verified using a Nanodrop ND-100 Spectrophotometer (Thermo Scientific). For gene expression array experiments, RNA quality and quantity was determined using 2100 Bioanalyzer platform (Aglient Technologies).

treatment_protocol: Thymocytes or splenocytes from Cre-ERT2; Bcl11bflox/flox mice were cultured in T cell medium with 1 μM 4-OHT (Sigma) at 370 C for 48 hrs. After this time, cells were washed and resuspended with fresh media.  T cell media: RPMI-1640, 10% FCS, 1% penicillin/streptomycin, 2 mM L-glutamine, 5 ng/ml muFlt-3-L, 5 ng/ml huIL-7.

value: DN3 (parental T cells)


title: DN3 rep3 (4459290113_E)

description: replicate 3


title: HUVEC_INPUT_TNF_60min

extract_protocol: Cells were crosslinked with paraformaldehyde and sonicted, then immunoprecipitated without antibody and DNA was prepared

treatment_protocol: HUVECs were treated with/without 10 ng/ml TNF alpha(Peprotec) and samples collected  60 min after stimulation


title: HUVEC_INPUT_TNF_00min

treatment_protocol: HUVECs were treated with/without 10 ng/ml TNF alpha(Peprotec) and samples collected  0 min after stimulation


title: HUVEC_RAD21_TNF_60min

extract_protocol: Cells were crosslinked with paraformaldehyde and sonicted, then immunoprecipitated with antibody for RAD21 and DNA was prepared

value: for RAD21


title: HUVEC_CTCF_TNF_00min


title: HUVEC_INPUT_TNF_30min

treatment_protocol: HUVECs were treated with/without 10 ng/ml TNF alpha(Peprotec) and samples collected  30 min after stimulation


title: HUVEC_p5SRNAP_TNF_00min

treatment_protocol: HUVECs were treated with/without 10 ng/ml TNF alpha(Peprotec) and samples collected 0 min after stimulation


title: HUVEC_RAD21_TNF_00min


title: HUVEC_H3K36me3_TNF_00min

extract_protocol: Cells were crosslinked with paraformaldehyde and sonicted, then immunoprecipitated using anti H3K36me3 antibody and DNA was prepared


title: HUVEC_H3K4me3_TNF_00min

extract_protocol: Cells were crosslinked with paraformaldehyde and sonicted, then immunoprecipitated using anti H3K4me3 antibody and DNA was prepared

treatment_protocol: HUVECs were treated with/without 10 ng/ml TNF alpha (Peprotec) and samples collected 0 min after stimulation


title: ITNK rep4 (4459290113_B)

description: replicate 4

value: ITNK (DN3-derived T-to-NK cells)


title: DN3 rep1 (4459290113_C)

description: replicate 1


title: ITNK rep3 (4459290113_A)

description: replicate 3


title: ITNK rep2 (4459290092_F)

description: replicate 2


title: ITNK rep1 (4459290092_E)

description: replicate 1


title: DN3 rep2 (4459290113_D)

description: replicate 2


title: LAK rep2 (4459290092_B)

description: replicate 2

value: LAK (IL-2-expanded NK cells)


title: LAK rep4 (4459290092_D)

description: replicate 4


title: fibroblast_pertussis toxin (PTX) -treated rep3

city: Kawasaki

first: Shihori

last: Tanabe

state: Kanagawa

address: 3-25-26, Tonomachi, Kawasaki-ku

department: Division of Risk Assessment

institute: National Institute of Health Sciences

description: Gene expression data of rat fibroblast treated with water or PTX.

hyb_protocol: Following fragmentation, 10 microgram of cRNA were hybridized for 16-24 hr at 45C on GeneChip Rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChip array was scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed using GCOS Affymetrix standard analysis settings and global scaling as normalization methods. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: Rat cardiac fibroblast primary culture

label_protocol: Biotinylated cRNA were prepared using One-cycle Affymetrix protocol from 1 microgram total RNA.

growth_protocol: Cells were cultured on 6 well plates in CO2 incubator at 37C.

extract_protocol: Total RNA isolation was performed using silica-gel-based membrane according to manufacturer's protocol.

treatment_protocol: Cells were treated with water or PTX and lysed with Buffer RLT (QIAGEN).

value: SD

tag: age

value: 1-2 Days

value: ventricle


title: fibroblast_pertussis toxin (PTX) -treated rep2

value: Sprague-Dawley


title: Llactis_genomicDNA_5

city: Belfast

first: Guillermo

last: López-Campos

state: Northern Ireland

address: 97 Lisburn road

department: Centre for Experimental Medicine

institute: Queen's University of Belfast

description: Experiment purpose is identifying spots with positive signal

hyb_protocol: Labelled samples were mixed in 45 µl EGT hybridization solution (Eurogentec, Serain, Belgium) and denatured at 65ºC for 2 min. The hybridization mixture was then loaded onto a microarray slide, covered with a coverslip and incubated at 38ºC overnight

scan_protocol: Scanning was perfomed using a Scanarray HT microarray scanner (Perkin-Elmer). Scanned images were quantified using Imagene 6.0 software.

data_processing: VALUE was obtained as the background corrected data using the following formula "VALUE=SIGNAL_RAW-(BKD_RAW-2*(BKDstd)"

organism: Lactococcus lactis subsp. lactis

source_name: L. lactis cell culture

label_protocol: Each DNA aliquot was fragmented by sonication to obtain fragments from 400 to 1000bp. Fragmented DNA was mixed with 5 µl 10X NEBlot labelling buffer containing random sequence octamer oligonucleotides (New England Biolabs, Ipswich, MA, USA) and water to a final volume of 43.5 µl. This mixture was denatured by heating to 95ºC for 5 min and then cooled down for 5 min at 4ºC. After this denaturing step, the remaining components of the labelling reaction were added: 5 µl of 10 X dNTP labelling mix (1.2 mM each dATP, dGTP and dCTP in 10 mM Tris pH 8.0, 1 mM EDTA), 1.5 µL of 1 mM Cy3-dUTP or Cy5-dUTP and 1.5 µl of 10 U/µl Klenow fragment (Fermentas Life Sciences, Glen Burnie, MD, USA). The labelling reactions were incubated overnight at 37ºC and then stopped by adding 2.5 µL of 0.5 M EDTA

growth_protocol: Grown statically at 37ºC in BHI broth. Cells were grown until the late-exponential phase of growth (OD600~1.5–2)

extract_protocol: DNA isolation and purification using the DNeasy Blood and Tissue kit (Qiagen, Hilden, Germany) according to the manufacturer’s specifications


title: fibroblast_pertussis toxin (PTX) -treated rep1


title: Spneumoniae_genomicDNA_6

organism: Streptococcus pneumoniae

source_name: S. pneumoniae cell culture

growth_protocol: Grown statically at 37ºC in Todd Hewitt broth. Cells were grown until the late-exponential phase of growth (OD600~1.5–2)


title: LAK rep3 (4459290092_C)

description: replicate 3


title: LAK rep1 (4459290092_A)

description: replicate 1


title: fibroblast_control rep2


title: Spneumoniae_genomicDNA_5


title: Lgarvieae_genomicDNA_4

organism: Lactococcus garvieae

source_name: L. garvieae cell culture


title: fibroblast_control rep1


title: Adult C. elegans strain GE-31 exposed to 1000 mg/L Fluoranthene, replicate 5

city: Cardiff

first: Peter

last: Kille

address: Park Place

department: Cardiff School of Biosciences

institute: Cardiff University

description:
Adult C. elegans strain GE-31 exposed to 1000 mg/L Fluoranthene replicate 5.
Ce_Fa1CF_WL1000_05AD

hyb_protocol: Hybridisations used 20pmol of each Cy5 and Cy3 labelled cDNA. Hybridisation was completed in a humidity chamber at 42°C overnight (24 hr). Slides were separated in 1x SSC, 0.2% SDS at room temperature and washed in the same buffer for 10 min at 55°C. They were subsequently washed twice in 0.1x SSC, 1% SDS at 55°C prior to a final room-temperature rinse in 0.1x SSC.

scan_protocol: Scanning was performed with a ScanArrayTM Express HT Microarray Scanner (Perkin Elmer, MA, USA) at the appropriate wavelength for each channel, i.e. at 550nm for Cy3 and at 650nm for Cy5.

data_processing: Data was imported into Limma with edwards background subtraction and normalised using a within array per pin-Lowess and a between array scaled normalisation. Normalised data was imported into GeneSpring where it was expressed as a ratio of the median expression of the relevant experimental control samples.

organism: Caenorhabditis elegans

source_name: adult whole body, 1000mg/L fluoranthene

label_protocol: For hybridisation, sample and universal mRNA was purified from 15µg total RNA using Qiagen columns. RNAs were indirectly labelled with fluorescent dyes, Cy3 and Cy5 and reverse transcribed using Moloney Murine Leukaemia Virus reverse transcriptase (ABgene, Surrey, UK). Cy3 and Cy5 labelled cDNA was purified using the CyScribe™ GFX Purification Kit (Amersham Biosciences, Buckinghamshire, UK). cDNA labelling quality was assessed by scanning 1µl of sample run on a slide gel under a green (560 BP filter) and red (675BP filter) laser on a GENETAC™ LS IV scanner (Genomic Solutions, Huntingdon, UK).

growth_protocol: Experiments were conducted with C. elegans strain GE-31, a temperature-sensitive mutant that is wild-type below 25°C, but displays an embryonic lethal phenotype above 25°C. This means that eggs are laid at temperatures above 25C, but ultimately fail to hatch. This mutant strain was used for this study because it meant that by conducting the experiment at 25C, a cohort could be reared throughout the full life-span without the population (and thus the sample for transcriptional profiling) becoming infiltrated by hatched and growing juveniles.

extract_protocol: Sample RNA was collected using the tri-reagent protocol, cleaned up using the RNeasy Mini kit (Qiagen, Crawley, UK) and quantified spectroscopically.

treatment_protocol: C. elegans strain GE31 nematodes were cultured on nematode growth medium (NGM) agar plates at 15C and fed on a bacterial lawn of E. coli OP50. Initially a stage-synchronised population was obtained by bleaching. Aliquots of extracted eggs were then transferred to a series NGM plates dosed to the test concentrations and previously inoculated with OP50. Dosing of the NGM agar was conducted using analytical grade fluoranthene (Fisher Chemicals, Loughborough, UK) with the stock solutions being prepared in dimethyl sulfoxide (DMSO) . Stock solutions were added to NGM cooled to 55C to give concentrations of: FA - 0, 100, 250, 500, 1000  mg/L. Eggs transferred to the dosed plates were incubated at 15°C to hatch and worms grown to adult for each treatment. Each exposed population was then synchronised again by bleaching and eggs hatched to produce a cohort of juveniles derived from mothers exposed for the full life-time for each exposure concentration. The generation exposed, age synchronised worms were initially grown on appropriately dosed 90 mm diameter NGM agar plates. At L2/L3 stage, 48 individuals were transferred from the large plates to appropriately dosed wells held in separate wells of a 12 well multi-compartment plate. From then on, each individual worm was transferred daily to a fresh appropriately dosed well. At each transfer, worm survival was checked and the number lain eggs counted. Every 6 hours throughout the exposure, growth of 10 random individual worms per treatment was recorded by photographing worms using a Nikon Coolpix 4500 digital camera. Size was measured using image Pro Express software (Media Cybernetics, Marlow, UK) and volumetric length (cubic root of body volume) calculated. The approximately 1000 worms remaining on the large dosed NGM agar plates were kept under parallel conditions to monitor individuals and periodically check to ensure they developed simultaneously. At transition to L4 and 12 hours after onset of egg production, these worms were collected by washing off NGM plates in M9 buffer and collected by centrifugation. The worm pellets collected from this sampling was immediately frozen in liquid nitrogen and stored at -80°C for use in transcriptional profiling.

value: whole organism

value: fluoranthene

tag: nominal dose (mg/l)

tag: replicate number

value: adult

source_name: Common Reference

tag: sample type

value: reference


title: fibroblast_control rep3


title: Lgarvieae_genomicDNA_2


title: Adult C. elegans strain GE-31 exposed to 1000 mg/L Fluoranthene, replicate 4

description:
Adult C. elegans strain GE-31 exposed to 1000 mg/L Fluoranthene replicate 4.
Ce_Fa1CF_WL1000_04AD

tag: treatment


title: Lgarvieae_genomicDNA_1


title: Spneumoniae_genomicDNA_4


title: Llactis_genomicDNA_6


title: Replication timing of BG01 NPC, replicate 1

city: Tallahassee

first: Tyrone

last: Ryba

state: FL

address: 319 Stadium Dr.

department: Biological Science

institute: Florida State University

description: submitted as of 1/20/10

hyb_protocol: Standard NimbleGen protocol (www.nimblegen.com/products/lit/index.html). Briefly, Cy3 and Cy5 labeled DNA samples (34 ug each) were co-hybridized to Nimblegen CGH arrays containing one oligonucleotide probe every 1.1 kb across the human genome.

scan_protocol: GenePix 4000B scanner (Molecular Devices) and GenePix software were used per NimbleGen's standard protocol (www.nimblegen.com/products/lit/index.html).

data_processing: NimbleScan software was used to obtain .pair raw data per manufacturer's instructions. Raw early/late data (i.e. from .pair files) from two independent biological replicates in which early and late replicating DNA were labeled reciprocally were loess-normalized to remove signal intensity-dependent bias, scaled to a reference data set to have the same median absolute deviation and averaged (limma package, R/Bioconductor).The mean early/late ratios were used to generate a smoothed profile (i.e. processed data) using local polynomial smoothing (loess, 300-kb span) for each chromosome using basic functions in the statistical language R. Processed data sets can be graphically displayed (and are also downloadable) on our web site (http://www.replicationdomain.org). Further details can be found in Hiratani et al [PLoS Biology (2008) 6: e245].

source_name: Early-replicating DNA of BG01 NPC

label_protocol: Standard NimbleGen protocol (www.nimblegen.com/products/lit/index.html). Briefly, randomly-amplified BrdU-immunoprecipitated DNA samples (1 ug each) were Cy3- or Cy5-labeled by Klenow reaction using end-labeled Cy3- or Cy5-random 9-mers.

extract_protocol: Replication timing data were obtained by hybridizing early and late replication intermediates to NimbleGen oligonucleotide arrays, as described in Hiratani et al [PLoS Biology (2008) 6: e245]. Briefly, replication intermediates are prepared from cells that are first pulse-labeled with BrdU and then sorted into early (1st half of S) and late (2nd half of S) stages of S-phase by flow cytometry, followed by anti-BrdU immunoprecipitation of the BrdU-substituted (nascent) replication intermediates that were synthesized either early or late during S-phase. Samples were labeled after unbiased amplification of recovered DNA by whole-genome amplification (WGA; Sigma, GenomePlex). Further details can be found in Hiratani et al [PLoS Biology (2008) 6: e245].

tag: cell line

tag: cell type

value: NPC

source_name: Late-replicating DNA of BG01 NPC


title: Adult C. elegans strain GE-31 exposed to 1000 mg/L Fluoranthene, replicate 3

description:
Adult C. elegans strain GE-31 exposed to 1000 mg/L Fluoranthene replicate 3.
Ce_Fa1CF_WL1000_03AD


title: Adult C. elegans strain GE-31 exposed to 1000 mg/L Fluoranthene, replicate 2

description:
Adult C. elegans strain GE-31 exposed to 1000 mg/L Fluoranthene replicate 2.
Ce_Fa1CF_WL1000_02AD


title: Adult C. elegans strain GE-31 exposed to 1000 mg/L Fluoranthene, replicate 1

description:
Adult C. elegans strain GE-31 exposed to 1000 mg/L Fluoranthene replicate 1.
Ce_Fa1CF_WL1000_01AD


title: Replication timing of C0202 lymphoblastoid, replicate 2

description: submitted as of 1/20/10

source_name: Early-replicating DNA of lymphoblastoid

value: Lymphoblastoid

source_name: Late-replicating DNA of lymphoblastoid


title: Spneumoniae_genomicDNA_3


title: Spneumoniae_genomicDNA_2


title: Replication timing of C0202 lymphoblastoid, replicate 1

description: submitted as of 1/20/10


title: Replication timing of iPS5, replicate 1

description: submitted as of 1/20/10

source_name: Early-replicating DNA of iPS5

value: iPSC (induced pluripotent stem cells)

source_name: Late-replicating DNA of iPS5


title: Spneumoniae_genomicDNA_1


title: melanoma patient 33

city: Homburg

first: Andreas

last: Keller

address: Building 60

country: Germany

institute: Saarland University

hyb_protocol: according to manufacturers instruction (febit biomed)

scan_protocol: Wizard software on standard Microsoft Windows Workstation PC

data_processing:
Technical replicates: using this platform we can determine the number of spots for each miRNA and we choose 7. The platform output (raw data) is the averaged intensity. The raw data of the machine then consist of the value of the miRNA.
Summarizing of technical replica by median and quantile normalization. Following BG correction, negative values were corrected to 1.

source_name: RNA from blood

label_protocol: MPEA, microfluidic primer extension assay Biotin labeling

extract_protocol: Blood of patients and volunteers without known disease was extracted in PAXgene Blood RNA tubes (BD, Franklin Lakes, New Jersey USA). For each blood donor, 5 ml of peripheral blood were obtained. The content of blood sampling tubes of each patient and healthy donor was centrifuged at 5000 g for 10 min at room temperature. The supernatant was discarded while the pellet was resuspended in 10 ml RNase free water by vortex. The suspension is again centrifuged at 5000 g for 10 min at RT. Subsequently, the total RNA including the miRNA was isolated using the miRNeasy kit (Qiagen GmbH, Hilden). Therefore the pellet was resuspended in 700 μl QIAzol lysis reagent and incubated for 5 min at RT. Then, 140 μl chloroform were added, vortexed for 15 sec, and incubated for 2-3 min at RT. This was followed by a centrifugation at 14000 rpm and 4°C for 15 min. The upper, watery phase was removed and 1,5 times of its volume added in 100% ethanol (ca. 900 μl). Each 700 μl of this mixture were placed on a column and centrifuged at 13000 rpm at RT for 15 sec. After the mixture had completely passed the column, 700 μl of Buffer RWT were added to each column, and again centrifuged at 13000 rpm at RT for 15 sec. Following this, 500 μl Buffer RPL were added to the column and centrifuged at 13000 rpm at RT for 15 sec. After this, another 500 μl Buffer RPL were added to the column and centrifuged at 13000 rpm at RT for 2 min. The column was then centrifuged at 13000 rpm and RT for 1 min to dry it. The following was the elution step with 40 μl RNase free water, centrifuging at 13000 rpm at RT for 1 min. The eluted RNA was stored at -70°C.

treatment_protocol: stored at -20 degree

tag: disease state

value: melanoma patient


title: melanoma patient 35


title: Replication timing of BG02 ESC, replicate 1

description: submitted as of 1/20/10

source_name: Early-replicating DNA of BG02 ESC

value: ESC

source_name: Late-replicating DNA of BG02 ESC


title: Lgarvieae_genomicDNA_3


title: melanoma patient 32


title: Replication timing of iPS4, replicate 2

description: submitted as of 1/20/10

source_name: Early-replicating DNA of iPS4

source_name: Late-replicating DNA of iPS4


title: melanoma patient 31


title: Replication timing of H9 ESC

description: submitted as of 1/20/10

source_name: Early-replicating DNA of H9 ESC

source_name: Late-replicating DNA of H9 ESC


title: melanoma patient 30


title: melanoma patient 34


title: Replication timing of BG01 NPC, replicate 2

description: submitted as of 1/20/10


title: Replication timing of iPS4, replicate 1

description: submitted as of 1/20/10


title: Replication timing of BG02 ESC, replicate 2

description: submitted as of 1/20/10


title: Adult C. elegans strain GE-31 exposed to 500 mg/L Fluoranthene, replicate 4

description:
Adult C. elegans strain GE-31 exposed to 500 mg/L Fluoranthene replicate 4.
Ce_Fa1CF_WL0500_04AD

source_name: adult whole body, 500mg/L fluoranthene

tag: tissue


title: Adult C. elegans strain GE-31 exposed to 500 mg/L Fluoranthene, replicate 3

description:
Adult C. elegans strain GE-31 exposed to 500 mg/L Fluoranthene replicate 3.
Ce_Fa1CF_WL0500_03AD


title: Adult C. elegans strain GE-31 exposed to 500 mg/L Fluoranthene, replicate 2

description:
Adult C. elegans strain GE-31 exposed to 500 mg/L Fluoranthene replicate 2.
Ce_Fa1CF_WL0500_02AD


title: Adult C. elegans strain GE-31 exposed to 500 mg/L Fluoranthene, replicate 5

description:
Adult C. elegans strain GE-31 exposed to 500 mg/L Fluoranthene replicate 5.
Ce_Fa1CF_WL0500_05AD


title: melanoma patient 29


title: Adult C. elegans strain GE-31 exposed to 250 mg/L Fluoranthene, replicate 5

description:
Adult C. elegans strain GE-31 exposed to 250 mg/L Fluoranthene replicate 5.
Ce_Fa1CF_WL0250_05AD

source_name: adult whole body, 250mg/L fluoranthene


title: Adult C. elegans strain GE-31 exposed to 250 mg/L Fluoranthene, replicate 3

description:
Adult C. elegans strain GE-31 exposed to 250 mg/L Fluoranthene replicate 3.
Ce_Fa1CF_WL0250_03AD


title: Adult C. elegans strain GE-31 exposed to 250 mg/L Fluoranthene, replicate 2

description:
Adult C. elegans strain GE-31 exposed to 250 mg/L Fluoranthene replicate 2.
Ce_Fa1CF_WL0250_02AD


title: Adult C. elegans strain GE-31 exposed to 250 mg/L Fluoranthene, replicate 4

description:
Adult C. elegans strain GE-31 exposed to 250 mg/L Fluoranthene replicate 4.
Ce_Fa1CF_WL0250_04AD


title: Adult C. elegans strain GE-31 exposed to 500 mg/L Fluoranthene, replicate 1

description:
Adult C. elegans strain GE-31 exposed to 500 mg/L Fluoranthene replicate 1.
Ce_Fa1CF_WL0500_01AD


title: Replication timing of H7 ESC

description: submitted as of 1/20/10

source_name: Early-replicating DNA of H7 ESC

source_name: Late-replicating DNA of H7 ESC


title: melanoma patient 27


title: melanoma patient 23


title: melanoma patient 25


title: melanoma patient 28


title: melanoma patient 24


title: melanoma patient 22


title: melanoma patient 26


title: melanoma patient 21


title: Replication timing of BG01 ESC

description: submitted as of 1/20/10

source_name: Early-replicating DNA of BG01 ESC

source_name: Late-replicating DNA of BG01 ESC


title: melanoma patient 20


title: melanoma patient 18


title: Adult C. elegans strain GE-31 exposed to 100 mg/L Fluoranthene, replicate 4

description:
Adult C. elegans strain GE-31 exposed to 100 mg/L Fluoranthene replicate 4.
Ce_Fa1CF_WL0100_04AD

source_name: adult whole body, 100mg/L fluoranthene

source_name: Common Reference


title: Adult C. elegans strain GE-31 exposed to 100 mg/L Fluoranthene, replicate 2

description:
Adult C. elegans strain GE-31 exposed to 100 mg/L Fluoranthene replicate 2.
Ce_Fa1CF_WL0100_02AD


title: Adult C. elegans strain GE-31 control, replicate 8b

description:
Adult C. elegans strain GE-31 control replicate 8
Ce_Fa1CF_WL0000_08AD

source_name: adult whole body, control


title: Adult C. elegans strain GE-31 control, replicate 7b

description:
Adult C. elegans strain GE-31 control replicate 7
Ce_Fa1CF_WL0000_07AD


title: Adult C. elegans strain GE-31 exposed to 100 mg/L Fluoranthene, replicate 3

description:
Adult C. elegans strain GE-31 exposed to 100 mg/L Fluoranthene replicate 3.
Ce_Fa1CF_WL0100_03AD


title: Adult C. elegans strain GE-31 control, replicate 5c

description:
Adult C. elegans strain GE-31 control replicate 5.
Ce_Fa1CF_WL0000_05AD


title: melanoma patient 17


title: Adult C. elegans strain GE-31 exposed to 100 mg/L Fluoranthene, replicate 1

description:
Adult C. elegans strain GE-31 exposed to 100 mg/L Fluoranthene replicate 1.
Ce_Fa1CF_WL0100_01AD


title: Adult C. elegans strain GE-31 control, replicate 4c

description:
Adult C. elegans strain GE-31 control replicate 4.
Ce_Fa1CF_WL0000_04AD


title: Replication timing of iPS5, replicate 2

description: submitted as of 1/20/10

source_name: Early-replicating DNA of iPS5

source_name: Late-replicating DNA of iPS5


title: Adult C. elegans strain GE-31 control, replicate 3b

description:
Adult C. elegans strain GE-31 control replicate 3.
Ce_Fa1CF_WL0000_03AD


title: melanoma patient 19

source_name: RNA from blood


title: CD93-ko contralateral hemisphere after 30min MCAo and 72h of reperfusion

city: Berlin

first: Denise

last: Harhausen

address: Chariteplatz 1

department: Experimental Neurology

institute: Charite University Berlin

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: mouse brain

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up according to standard protocol.

tag: genotype/variation

value: CD93 knockout

value: 10 weeks

value: brain


title: wild-type contralateral hemisphere after 30min MCAo and 72h of reperfusion

value: wild-type


title: melanoma patient 16


title: Adult C. elegans strain GE-31 control, replicate 6b

description:
Adult C. elegans strain GE-31 control replicate 6
Ce_Fa1CF_WL0000_06AD


title: wild-type ipsilateral hemisphere after 30min MCAo and 72h of reperfusion


title: Adult C. elegans strain GE-31 control, replicate 2b

description:
Adult C. elegans strain GE-31 control replicate 2.
Ce_Fa1CF_WL0000_02AD


title: CD93-ko ipsilateral hemisphere after 30min MCAo and 72h of reperfusion


title: Adult C. elegans strain GE-31 exposed to 60 mg/L Cadmium, replicate 4

description:
Adult C. elegans strain GE-31 exposed to 60 mg/L Cadmium replicate 4.
Ce_Cd1CF_WL0060_04AD_2UG

source_name: adult whole body, 60mg/L Cd

treatment_protocol: C. elegans strain GE-31 nematodes were cultured on nematode growth medium (NGM) agar plates at 15C and fed on a bacterial lawn of E. coli OP50. Initially a stage-synchronised population was obtained by bleaching. Aliquots of extracted eggs were then transferred to a series of NGM plates dosed to the test concentrations and previously inoculated with OP50. Dosing of the NGM agar was conducted using analytical grade cadmium chloride (Sigma Chemicals, Poole, UK). Stock solutions were added to NGM cooled to 55C to give concentrations of: Cd - 0, 10, 20, 40, 60 mg/L. Eggs transferred to the dosed plates were incubated at 15°C to hatch and worms grown to adult for each treatment. Each exposed population was then synchronised again by bleaching and eggs hatched to produce a cohort of juveniles derived from mothers exposed for the full life-time for each exposure concentration. The generation exposed, age synchronised worms were initially grown on appropriately dosed 90 mm diameter NGM agar plates. At L2/L3 stage, 48 individuals were transferred from the large plates to appropriately dosed wells held in separate wells of a 12 well multi-compartment plate. From then on, each individual worm was transferred daily to a fresh appropriately dosed well. At each transfer, worm survival was checked and the number lain eggs counted. Every 6 hours throughout the exposure, growth of 10 random individual worms per treatment was recorded by photographing worms using a Nikon Coolpix 4500 digital camera. Size was measured using image Pro Express software (Media Cybernetics, Marlow, UK) and volumetric length (cubic root of body volume) calculated. The approximately 1000 worms remaining on the large dosed NGM agar plates were kept under parallel conditions to monitor individuals and periodically check to ensure they developed simultaneously. At transition to L4 and 12 hours after onset of egg production, these worms were collected by washing off NGM plates in M9 buffer and collected by centrifugation. The worm pellets collected from this sampling was immediately frozen in liquid nitrogen and stored at -80°C for use in transcriptional profiling.

value: cadmium


title: CD93-ko untreated


title: melanoma patient 14


title: melanoma patient 13


title: Adult C. elegans strain GE-31 exposed to 60 mg/L Cadmium, replicate 5

description:
Adult C. elegans strain GE-31 exposed to 60 mg/L Cadmium replicate 5.
Ce_Cd1CF_WL0060_05AD_2UG


title: Adult C. elegans strain GE-31 exposed to 60 mg/L Cadmium, replicate 3

description:
Adult C. elegans strain GE-31 exposed to 60 mg/L Cadmium replicate 3.
Ce_Cd1CF_WL0060_03AD_2UG


title: melanoma patient 15


title: wild-type untreated


title: Adult C. elegans strain GE-31 exposed to 60 mg/L Cadmium, replicate 2

description:
Adult C. elegans strain GE-31 exposed to 60 mg/L Cadmium replicate 2.
Ce_Cd1CF_WL0060_02AD_2UG


title: wild-type contralateral hemisphere after 60min MCAo and 48h of reperfusion


title: CD93-ko contralateral hemisphere after 60min MCAo and 48h of reperfusion


title: Denuded metaphase II oocytes, biological rep3

city: Bonn

first: Alemu

last: Regassa

state: NRW

address: Endenicher allee 15

department: Animal breeding and husbandry

institute: University of Bonn

description:
Gene expression data from oocytes matured without their companion CCs.
OODMII3
18G_6

hyb_protocol: The biotin-labeled cRNA was fragmented. Following this, a hybridization cocktail consisting of fragmented and labeled cRNA, control oligonucleotide B2 (3nM), 20X eukaryotic hybridization controls (bioB, bioC, bioD, cre), 2X hybridization mix, DMSO and RNAse free water were mixed to a final volume of 200 µl and heated to 99°C for 5 followed by warming at 45°C for 5 min. The samples were then hybridized to GeneChip® Bovine Genome Array for 16 h at 45°C in hybridization oven.

scan_protocol: The arrays were washed and stained using Fluidics Station 450/250 and scanned using the GeneChip® scanner 3000 integrated with Affymetrix® Microarray Suite software as recommended in GeneChip® expression wash, stain and scan user manual (P/N 702731).

data_processing: The microarray data normalization and background correction was performed using guanine cytosine robust multi-array analysis (gcrma) . The quality of the arrays after hybridization was evaluated by assessing the absent and present calls of the control probesets. Differentially expressed genes were generated using linear models for microarray data analysis (LIMMA) and under R software, (www.r-project.org) and bioconductor packages (www.bioconductor.org).

organism: Bos taurus

source_name: Oocytes denuded at GV stage and matured without it

label_protocol: RNA amplification was perfomed using MEGAscript® T7 Kit (Ambion, Inc., Austin, TX, USA) according to GeneChip® expression analysis technical manual (P/N 702232). The cRNA was biotin labeled using the GeneChip® IVT Labeling Kit (Affymetrix, Inc., Santa Clara, CA, USA) according to GeneChip® expression analysis technical manual (P/N 702232).

extract_protocol: Total RNA was extracted from three pools of each oocyte and CC sample using Picopure total RNA isolation kit (Qiagen).

value: cumulus-denuded oocytes

value: metaphase II (MII)


title: wild-type ipsilateral hemisphere after 60min MCAo and 48h of reperfusion


title: CD93-ko ipsilateral hemisphere after 60min MCAo and 48h of reperfusion


title: Adult C. elegans strain GE-31 exposed to 60 mg/L Cadmium, replicate 1

description:
Adult C. elegans strain GE-31 exposed to 60 mg/L Cadmium replicate 1.
Ce_Cd1CF_WL0060_01AD_2UG


title: melanoma patient 12


title: Metaphase II CCs, biological rep3

description:
Gene expression data from CCs matured with their ooplasm.
CCMII3
15G_5

source_name: CCs matured with their enclosed ooplasm

value: cumulus cells


title: Denuded metaphase II oocytes, biological rep1

description:
Gene expression data from oocytes matured without their companion CCs.
OODMII1
16G_6


title: Metaphase II CCs, biological rep2

description:
Gene expression data from CCs matured with their ooplasm.
CCMII2
14G_5


title: melanoma patient 11


title: Adult C. elegans strain GE-31 exposed to 40 mg/L Cadmium, replicate 5

description:
Adult C. elegans strain GE-31 exposed to 40 mg/L Cadmium replicate 5.
Ce_Cd1CF_WL0040_05AD_2UG

source_name: adult whole body, 40mg/L Cd

value: whole organism


title: melanoma patient 10


title: Metaphase II CCs, biological rep1

description:
Gene expression data from CCs matured with their ooplasm.
CCMII1
13G_5


title: Metaphase II oocytes, biological rep3

description:
Gene expression data from oocytes matured with their companion CCs.
OOMII3
12G_4

source_name: Oocytes matured with their companion CCs

value: oocytes


title: melanoma patient 9


title: melanoma patient 8


title: Metaphase II oocytes, biological rep1

description:
Gene expression data from oocytes matured with their companion CCs.
OOMII1
10G_4


title: Metaphase II oocytes, biological rep2

description:
Gene expression data from oocytes matured with their companion CCs.
OOMII2
11G_4


title: melanoma patient 7


title: Adult C. elegans strain GE-31 exposed to 40 mg/L Cadmium, replicate 4

description:
Adult C. elegans strain GE-31 exposed to 40 mg/L Cadmium replicate 4.
Ce_Cd1CF_WL0040_04AD_2UG

value: adult


title: Adult C. elegans strain GE-31 exposed to 250 mg/L Fluoranthene, replicate 1

description:
Adult C. elegans strain GE-31 exposed to 250 mg/L Fluoranthene replicate 1.
Ce_Fa1CF_WL0250_01AD

source_name: adult whole body, 250mg/L fluoranthene

value: fluoranthene

value: reference


title: Oocytectomised complexes (CCs without ooplasm), biological rep 3

description:
Gene expression data from MII CCs of which ooplasm was removed at GV stage.
OOXMII3
9G_3

source_name: Matured CCs from which the ooplasm was microsurgically removed at GV stage

value: cumulus cells without ooplasm


title: Denuded metaphase II oocytes, biological rep2

description:
Gene expression data from oocytes matured without their companion CCs.
OODMII2
17G_6


title: melanoma patient 6


title: GV stage CCs, biological rep2

description:
Gene expression data from CCs at GV stage.
IMCC2
5G_2

source_name: CCs removed off GV stage oocytes

value: germinal vesicle (GV) stage


title: Adult C. elegans strain GE-31 exposed to 40 mg/L Cadmium, replicate 3

description:
Adult C. elegans strain GE-31 exposed to 40 mg/L Cadmium replicate 3.
Ce_Cd1CF_WL0040_03AD_2UG


title: Oocytectomised complexes (CCs without ooplasm), biological rep 1

description:
Gene expression data from MII CCs of which ooplasm was removed at GV stage.
OOXMII1
7G_3


title: melanoma patient 4

value: melanoma patient


title: Adult C. elegans strain GE-31 exposed to 40 mg/L Cadmium, replicate 2

description:
Adult C. elegans strain GE-31 exposed to 40 mg/L Cadmium replicate 2.
Ce_Cd1CF_WL0040_02AD_2UG


title: GV stage CCs, biological rep3

description:
Gene expression data from CCs at GV stage.
IMCC3
6G_2


title: Adult C. elegans strain GE-31 exposed to 20 mg/L Cadmium, replicate 3

description:
Adult C. elegans strain GE-31 exposed to 20 mg/L Cadmium replicate 3.
Ce_Cd1CF_WL0020_03AD_2UG

source_name: adult whole body, 20mg/L Cd


title: Adult C. elegans strain GE-31 exposed to 40 mg/L Cadmium, replicate 1

description:
Adult C. elegans strain GE-31 exposed to 40 mg/L Cadmium replicate 1.
Ce_Cd1CF_WL0040_01AD_2UG


title: melanoma patient 5


title: Denuded GV stage oocytes, biological rep3

description:
Gene expression data from oocytes at GV stage.
IMOO3
3G_1

source_name: Oocytes denuded at GV stage


title: Denuded GV stage oocytes, biological rep1

description:
Gene expression data from oocytes at GV stage.
IMOO1
1G_1


title: melanoma patient 2


title: melanoma patient 3


title: Oocytectomised complexes (CCs without ooplasm), biological rep 2

description:
Gene expression data from MII CCs of which ooplasm was removed at GV stage.
OOXMII2
8G_3


title: Adult C. elegans strain GE-31 exposed to 20 mg/L Cadmium, replicate 4

description:
Adult C. elegans strain GE-31 exposed to 20 mg/L Cadmium replicate 4.
Ce_Cd1CF_WL0020_04AD_2UG


title: Denuded GV stage oocytes, biological rep2

description:
Gene expression data from oocytes at GV stage.
IMOO2
2G_1


title: Adult C. elegans strain GE-31 exposed to 20 mg/L Cadmium, replicate 2

description:
Adult C. elegans strain GE-31 exposed to 20 mg/L Cadmium replicate 2.
Ce_Cd1CF_WL0020_02AD_2UG


title: GV stage CCs, biological rep1

description:
Gene expression data from CCs at GV stage.
IMCC1
4G_2


title: melanoma patient 1


title: normal sample 22

value: normal control


title: normal sample 21


title: Adult C. elegans strain GE-31 exposed to 20 mg/L Cadmium, replicate 1

description:
Adult C. elegans strain GE-31 exposed to 20 mg/L Cadmium replicate 1.
Ce_Cd1CF_WL0020_01AD_2UG


title: Adult C. elegans strain GE-31 exposed to 10 mg/L Cadmium, replicate 1

description:
Adult C. elegans strain GE-31 exposed to 10 mg/L Cadmium replicate 1.
Ce_Cd1CF_WL0010_01AD_3UG

source_name: adult whole body, 10mg/L Cd


title: normal sample 20


title: Adult C. elegans strain GE-31 exposed to 10 mg/L Cadmium, replicate 4

description:
Adult C. elegans strain GE-31 exposed to 10 mg/L Cadmium replicate 4.
Ce_Cd1CF_WL0010_04AD_3UG

source_name: Common Reference


title: Adult C. elegans strain GE-31 exposed to 10 mg/L Cadmium, replicate 3

description:
Adult C. elegans strain GE-31 exposed to 10 mg/L Cadmium replicate 3.
Ce_Cd1CF_WL0010_03AD_3UG


title: normal sample 19


title: Adult C. elegans strain GE-31 exposed to 10 mg/L Cadmium, replicate 2

description:
Adult C. elegans strain GE-31 exposed to 10 mg/L Cadmium replicate 2.
Ce_Cd1CF_WL0010_02AD_3UG


title: normal sample 18


title: Adult C. elegans strain GE-31 control, replicate 5b

description:
Adult C. elegans strain GE-31 control replicate 5.
Ce_Cd1CF_WL0000_05AD_3UG

source_name: adult whole body, control


title: normal sample 17


title: Adult C. elegans strain GE-31 control, replicate 4b

description:
Adult C. elegans strain GE-31 control replicate 4.
Ce_Cd1CF_WL0000_04AD_3UG


title: patient 4 (CF4) vs 5 normal controls

city: Beaumont

first: Irene

last: Oglesby

address: ERC, beaumont Hospital

department: Medicine

country: Ireland

institute: Royal College of Surgeons in Ireland

description:
RNA (30 ng)  was reverse transcribed with the Megaplex primer pool allowing simultaneous reverse transcription of 430 miRNAs and 36 endogenous controls in one RT pool
Raw data files available on the series record.  'card A 1_5 sdm-Result Data.txt' and 'card B 1_5 sdm-Result Data.txt' correspond to CF Patient data

Non-CF control patient characteristics are as follows:

patient 6 - C11; RAW DATA FILES: card B 3_5_6_7_11  sdm-Result Data.txt and card A 3_5_6_7_11  sdm-Result Data.txt; SEX: Female; AGE: 20

patient 7 - C3; RAW DATA FILES: card B 3_5_6_7_11  sdm-Result Data.txt and card A 3_5_6_7_11  sdm-Result Data.txt; SEX: Male; AGE: 57

patient 8 - C5; RAW DATA FILES: card B 3_5_6_7_11  sdm-Result Data.txt and card A 3_5_6_7_11  sdm-Result Data.txt; SEX: Female; AGE: 73

patient 9 - C6; RAW DATA FILES: card B 3_5_6_7_11  sdm-Result Data.txt and card A 3_5_6_7_11  sdm-Result Data.txt; SEX: Female; AGE: 60

patient 10 - C7; RAW DATA FILES: card B 3_5_6_7_11  sdm-Result Data.txt and card A 3_5_6_7_11  sdm-Result Data.txt; SEX: Female; AGE: 45

data_processing:
CF patient data was normalized to set of 5 normal patient contols.
Mean normalisation was carried out by subtracting the mean sample Ct from the individual miRNA Ct values, Ref : Mestdagh, P., P. Van Vlierberghe, A. De Weer, D. Muth, F. Westermann, F. Speleman, and J. Vandesompele. 2009. A novel and universal method for microRNA RT-qPCR data normalization. Genome Biol 10:R64.
Relative quantification of gene expression was determined using the comparative cycle threshold method (2(-ddCt)) as previously described Ref : Livak, K. J., and T. D. Schmittgen. 2001. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 25:402-408. . In the case of the non-CF samples, the mean Ct value was calculated for each individual miRNA, and this was used to calculate the dCt for the calibrator sample.

label: FAM

source_name: Cystic Fibrosis

label_protocol: standard Taqman Assay

extract_protocol: Total RNA was extracted using TriReagent according to manufacturer's protocol.

tag: disease status

value: Cystic Fibrosis

tag: sex

value: Female


title: normal sample 15


title: patient 5 (CF5) vs 5 normal controls

value: Male


title: normal sample 16


title: Adult C. elegans strain GE-31 control, replicate 1

description:
Adult C. elegans strain GE-31 control replicate 1.
Ce_Cd1CF_WL0000_01AD_3UG

tag: strain


title: patient 2 (CF2) vs 5 normal controls


title: Adult C. elegans strain GE-31 control, replicate 3

description:
Adult C. elegans strain GE-31 control replicate 3.
Ce_Cd1CF_WL0000_03AD_3UG

tag: developmental stage


title: Tumour Sample 4 (sl84.Ic3)

city: new delhi

first: Thoudam

middle: Regina

last: Devi

state: delhi

address: Safdarjung hospital campus

department: Safdarjung Hospital Campus

country: India

institute: Institute of Pathology

description:
The objective of my study was to identify the genes differentially expressed in gastric adenocarcinoma associated with prevalent risk factor such as tobacco use (Meiziol, Tuibur etc) in high-risk Indian population. The Tumor tissue and matched normal tissue distant to the tumor were collected during endoscopy in RNA later, Snap-frozen in liquid nitrogen and stored at -70°C until processed. Data of clinicopathologic parameters were obtained from patients’ clinical report, operative notes and pathologic report. Institutional Human ethics committee approved the study
MEIZIOL is a local cigarette made from vaihlo (Nicotiana dadacum) tobacco. The tobacco content of each meiziol is about 0.8 to 1 g. The length of each meiziol is 6 to 7 cm.
TUIBUR is a unique tobacco smoke–infused water used in Mizoram and is locally known as tuibur. This product is made locally by passing smoke, generated by burning tobacco, through water until the preparation turns cognac in color and has a pungent smell.

hyb_protocol: 10.0 µg of the labeled aRNA in 100 µl of Ocimum's Hyb buffer was denatured at 95°C for 3 mins and was used for hybridization with the Human 40 K A chip and printed at Ocimum Biosolutions, Hyderabad. Hybridization was performed at 50°C for two hrs on Tecan HS 4800 automated Hyb station. Hybridized chips were scanned using Affymetrix 428TMarray scanner at three different PMT gains (40, 50, 60).

scan_protocol: Scanner Used: AFFYMETRIX,428 Array. Define scan area: Always set size Y to 0. Use array finder to define the size height (1mm on the array finder » 1mm on the OciChip). Height means the distance from the top of the slide to the end of the spotted array (plus safe distance of 2 mm).Set scan settings: The PMT gain settings of the multiple scanning have to be increased with the same distance (usually a distance of 10 between the settings is used). Set the range of the increasing PMT gain setting to achieve both to avoid saturation of the strongest spots at lowest value and to receive reliable signals from the weak spots at the highest PMT gain setting. Scanning was performed at 40, 50 and 60 PMT gain for the hybridized chips.

data_processing:
The data obtained through image processing showed positively skewed
distribution for each array. In order to have across array comparison, the data was normalized using log2 transformation.It is evident that the transformation could normalize the data for each array; however, mean intensity level across arrays was different. Also, the scatter for each array was found varying. To overcome this, median centering and median absolute deviation (MAD) scaling was performed on each array

source_name: Ocimum

label_protocol: Five  microgram of total RNA was used for amplification using Express Art® mRNA amplification Kit Message by linear transcription based RNA amplification system to produce cRNA. Briefly, mRNA is  reverse transcribed followed by second strand synthesis priming with a oligo (dT) primer bearing T7 promoter in a thermal cycler  using the conditions described in the manual. The resulting cDNA was then purified and was then transcribed with T7 RNA polymerase to generate multiple copies of aminoallyl antisense RNA (aRNA) at 37°C for 16 hrs. aRNA is then labelled with Cy3TM post-labelling reactive dye pack (GE Healthcare, UK) at room temperature and unincorporated Cy3 molecules were removed by purification process.

extract_protocol: Isolation Kit: RNeasy mini Kit (Qiagen). RNA concentration was evaluated by measuring taking an absorbance at 260 and 280 nm using a NanoDrop (NanoDrop, USA) and RNA quality was evaluated by electrophoretic analysis with Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA). Total RNA that met the quality standards was released for probe generation.

tag: patient id

value: M

tag: meiziol

value: yes

tag: tuibur

tag: betal nut

tag: smoking

tag: alcohol

tag: site of cancer

value: Antrum

tag: histopathology

value: Adenocarcinoma


title: normal sample 14

source_name: RNA from blood


title: Adult C. elegans strain GE-31 control, replicate 2

description:
Adult C. elegans strain GE-31 control replicate 2.
Ce_Cd1CF_WL0000_02AD_3UG

tag: treatment

value: cadmium

tag: nominal dose (mg/l)

tag: replicate number

tag: sample type


title: normal sample 12

tag: disease state


title: normal sample 13


title: Tumour Sample 2 (sl74.IC3)

tag: age


title: patient 3 (CF3) vs 5 normal controls

tag: disease status

tag: sex


title: Adult C. elegans strain GE-31 exposed to 150 mg/L Atrazine, replicate 2

description:
Adult C. elegans strain GE-31 exposed to 150 mg/L Atrazine replicate 2.
Ce_Az1CF_WL0150_02AD_2UG

source_name: adult whole body, 150mg/L AZ

treatment_protocol: C. elegans strain GE-31 nematodes were cultured on nematode growth medium (NGM) agar plates at 15C and fed on a bacterial lawn of E. coli OP50. Initially a stage-synchronised population was obtained by bleaching. Aliquots of extracted eggs were then transferred to a series of NGM plates dosed to the test concentrations and previously inoculated with OP50. Dosing of the NGM agar was conducted using analytical grade atrazine (Sigma, UK) with stock solutions prepared in ethanol. Stock solutions were added to NGM cooled to 55C to give concentrations of: Atrazine - 0, 5, 25, 75, 150 mg/L. Eggs transferred to the dosed plates were incubated at 15°C to hatch and worms grown to adult for each treatment. Each exposed population was then synchronised again by bleaching and eggs hatched to produce a cohort of juveniles derived from mothers exposed for the full life-time for each exposure concentration. The generation exposed, age synchronised worms were initially grown on appropriately dosed 90 mm diameter NGM agar plates. At L2/L3 stage, 48 individuals were transferred from the large plates to appropriately dosed wells held in separate wells of a 12 well multi-compartment plate. From then on, each individual worm was transferred daily to a fresh appropriately dosed well. At each transfer, worm survival was checked and the number lain eggs counted. Every 6 hours throughout the exposure, growth of 10 random individual worms per treatment was recorded by photographing worms using a Nikon Coolpix 4500 digital camera. Size was measured using image Pro Express software (Media Cybernetics, Marlow, UK) and volumetric length (cubic root of body volume) calculated. The approximately 1000 worms remaining on the large dosed NGM agar plates were kept under parallel conditions to monitor individuals and periodically check to ensure they developed simultaneously. At transition to L4 and 12 hours after onset of egg production, these worms were collected by washing off NGM plates in M9 buffer and collected by centrifugation. The worm pellets collected from this sampling was immediately frozen in liquid nitrogen and stored at -80°C for use in transcriptional profiling.

tag: strain

tag: tissue

value: whole organism

value: atrazine

tag: developmental stage


title: patient 1 (CF1) vs 5 normal controls


title: Lgarvieae_genomicDNA_12

description: Experiment purpose is identifying spots with positive signal

source_name: Lactococcus garvieae


title: Tumour Sample 3 (sl81.Ic3)

tag: patient id

tag: meiziol

tag: tuibur


title: Tumour Sample 1 (sl69.Ic3)

tag: betal nut

tag: smoking

tag: alcohol


title: Adult C. elegans strain GE-31 exposed to 150 mg/L Atrazine, replicate 5

description:
Adult C. elegans strain GE-31 exposed to 150 mg/L Atrazine replicate 5.
Ce_Az1CF_WL0150_05AD_2UG

tag: treatment

value: adult


title: Adult C. elegans strain GE-31 exposed to 150 mg/L Atrazine, replicate 4

description:
Adult C. elegans strain GE-31 exposed to 150 mg/L Atrazine replicate 4.
Ce_Az1CF_WL0150_04AD_2UG

tag: nominal dose (mg/l)


title: Llactis_genomicDNA_12

source_name: L. lactis cell culture


title: Tumour Sample 5 (sl85.Ic)

tag: site of cancer

tag: histopathology


title: Normal Sample_2 (sl65.IC3)

tag: disease state

value: Normal


title: Normal Sample 1 (sl83.Ic3)


title: Adult C. elegans strain GE-31 exposed to 150 mg/L Atrazine, replicate 1

description:
Adult C. elegans strain GE-31 exposed to 150 mg/L Atrazine replicate 1.
Ce_Az1CF_WL0150_01AD_2UG

tag: replicate number

tag: sample type

value: reference


title: Adult C. elegans strain GE-31 exposed to 150 mg/L Atrazine, replicate 3

description:
Adult C. elegans strain GE-31 exposed to 150 mg/L Atrazine replicate 3.
Ce_Az1CF_WL0150_03AD_2UG


title: Lgarvieae_genomic_DNA_11

source_name: L. garvieae cell culture


title: Adult C. elegans strain GE-31 exposed to 75 mg/L Atrazine, replicate 5

description:
Adult C. elegans strain GE-31 exposed to 75 mg/L Atrazine replicate 5.
Ce_Az1CF_WL0075_05AD_2UG

source_name: adult whole body, 75mg/L AZ


title: Lgarvieae_genomicDNA_10


title: normal sample 8


title: Llactis_genomic_DNA_11


title: normal sample 10


title: normal sample 11


title: normal sample 7


title: normal sample 6


title: normal sample 9


title: normal sample 5


title: normal sample 4


title: Lgarvieae_genomicDNA_9


title: Lgarvieae_genomicDNA_8


title: Llactis_genomicDNA_10


title: Adult C. elegans strain GE-31 exposed to 75 mg/L Atrazine, replicate 2

description:
Adult C. elegans strain GE-31 exposed to 75 mg/L Atrazine replicate 2.
Ce_Az1CF_WL0075_02AD_2UG


title: Llactis_genomicDNA_9


title: Lgarvieae_genomicDNA_7


title: normal sample 2


title: Adult C. elegans strain GE-31 exposed to 25 mg/L Atrazine, replicate 3

description:
Adult C. elegans strain GE-31 exposed to 25 mg/L Atrazine replicate 3.
Ce_Az1CF_WL0025_03AD_2UG

source_name: adult whole body, 25mg/L AZ


title: normal sample 3


title: Adult C. elegans strain GE-31 exposed to 25 mg/L Atrazine, replicate 2

description:
Adult C. elegans strain GE-31 exposed to 25 mg/L Atrazine replicate 2.
Ce_Az1CF_WL0025_02AD_2UG


title: Adult C. elegans strain GE-31 exposed to 25 mg/L Atrazine, replicate 5

description:
Adult C. elegans strain GE-31 exposed to 25 mg/L Atrazine replicate 5.
Ce_Az1CF_WL0025_05AD_2UG


title: Adult C. elegans strain GE-31 exposed to 75 mg/L Atrazine, replicate 1

description:
Adult C. elegans strain GE-31 exposed to 75 mg/L Atrazine replicate 1.
Ce_Az1CF_WL0075_01AD_2UG


title: Adult C. elegans strain GE-31 exposed to 25 mg/L Atrazine, replicate 4

description:
Adult C. elegans strain GE-31 exposed to 25 mg/L Atrazine replicate 4.
Ce_Az1CF_WL0025_04AD_2UG


title: Llactis_genomicDNA_4


title: Adult C. elegans strain GE-31 exposed to 25 mg/L Atrazine, replicate 1

description:
Adult C. elegans strain GE-31 exposed to 25 mg/L Atrazine replicate 1.
Ce_Az1CF_WL0025_01AD_2UG


title: normal sample 1


title: Llactis_genomicDNA_3


title: Llactis_genomicDNA_2


title: Lgarvieae_genomicDNA_6


title: Lgarvieae_genomicDNA_5


title: Llactis_genomicDNA_1


title: Adult C. elegans strain GE-31 exposed to 5 mg/L Atrazine, replicate 5

description:
Adult C. elegans strain GE-31 exposed to 5 mg/L Atrazine replicate 5.
Ce_Az1CF_WL0005_05AD_2UG

source_name: adult whole body, 5mg/L AZ


title: Adult C. elegans strain GE-31 exposed to 5 mg/L Atrazine, replicate 3

description:
Adult C. elegans strain GE-31 exposed to 5 mg/L Atrazine replicate 3.
Ce_Az1CF_WL0005_03AD_2UG


title: Adult C. elegans strain GE-31 exposed to 5 mg/L Atrazine, replicate 4

description:
Adult C. elegans strain GE-31 exposed to 5 mg/L Atrazine replicate 4.
Ce_Az1CF_WL0005_04AD_2UG


title: Adult C. elegans strain GE-31 exposed to 5 mg/L Atrazine, replicate 1

description:
Adult C. elegans strain GE-31 exposed to 5 mg/L Atrazine replicate 1.
Ce_Az1CF_WL0005_01AD_2UG


title: Tumor 3, replicate 2

city: Worcester

first: Matthew

middle: J

last: Simmons

state: MA

address: 364 Plantation St

department: Cancer Biology

institute: UMASS Medical School

description: Gene expression data from spleen-derived tumor cells from FL5.12 Bfl-1DC/p53DD-injected mouse 3

hyb_protocol: Following fragmentation, cRNA were hybridized to Affymetrix Mouse Genome 430A_2.0 chip. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed using the Affymetrix ‘Netaffex’ software by Microarray Suite version 5.0 (MAS 5.0).

label: Biotin

source_name: Spleen-derived tumor cells from FL5.12 Bfl-1DC/p53DD-injected mouse

label_protocol: Samples were processed using the One-Cycle cDNA Synthesis Kit and labeled with the IVT Labeling Kit with biotin according to the standard Affymetrix protocol from 5ug of total RNA  (Expression Analysis Technical Manual, 2005, Affymetrix).

growth_protocol: Cells were maintained in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS), 20mM HEPES, 2mM L-glutamine, penicillin (100 U/ml) and streptomycin (100 µg/ml), supplemented with 10% supernatant from confluent WEHI-3B cell cultures, as a source of IL-3. Cells were maintained at 37°C in an atmosphere of 5% CO2.

extract_protocol: Microarrays were performed with RNA extracted with RNAzolTM (Tel-Test) followed by purification using RNeasy Mini Kit (Qiagen), according to the manufacturer's protocol.

treatment_protocol: No treatment

value: splenic tumor


title: Tumor 2, replicate 2

description: Gene expression data from spleen-derived tumor cells from FL5.12 Bfl-1DC/p53DD-injected mouse 2


title: Llactis_genomicDNA_8

description: Experiment purpose is identifying spots with positive signal


title: Adult C. elegans strain GE-31 control, replicate 8

description:
Adult C. elegans strain GE-31 control replicate 8.
Ce_Az1CF_WL0000_08AD_2UG


title: Spneumoniae_genomicDNA_8

source_name: S. pneumoniae cell culture


title: Adult C. elegans strain GE-31 exposed to 5 mg/L Atrazine, replicate 2

description:
Adult C. elegans strain GE-31 exposed to 5 mg/L Atrazine replicate 2.
Ce_Az1CF_WL0005_02AD_2UG


title: Tumor 3, replicate 1


title: Adult C. elegans strain GE-31 control, replicate 7

description:
Adult C. elegans strain GE-31 control replicate 7.
Ce_Az1CF_WL0000_07AD_2UG


title: Adult C. elegans strain GE-31 control, replicate 5

description:
Adult C. elegans strain GE-31 control replicate 5.
Ce_Az1CF_WL0000_05AD_2UG


title: Tumor 1, replicate 1

description: Gene expression data from spleen-derived tumor cells from FL5.12 Bfl-1DC/p53DD-injected mouse 1


title: Spneumoniae_genomic_DNA_7


title: Tumor 1, replicate 2


title: Tumor 2, replicate 1


title: Adult C. elegans strain GE-31 control, replicate 4

description:
Adult C. elegans strain GE-31 control replicate 4.
Ce_Az1CF_WL0000_04AD_2UG


title: garcia.30487

status: Public on Mar 22 2010

city: Ottawa

first: Andrew

last: Williams

state: ON

address: 50 Columbine

country: Canada

institute: Health Canada

description:
Stratagene, La Jolla, CA, USA
garcia scan
raw data files: ArrayNumber_PMT_ScanID_Dye.txt, PMT is % of maximum power

hyb_protocol: Agilent Mouse G4121A Microarrays (containing approximately 22,000 probes) were hybridized with 5 µg Cy3-labelled Universal Mouse Reference RNA (Stratagene, CA, USA). Arrays were incubated overnight at 60 ºC in Agilent hybridization solution and washed according to manufacturer’s instructions.

scan_protocol: Arrays were scanned using a ScanArray Express (Perkin-Elmer Life Sciences, Woodbridge, ON, Canada), and data were acquired with ImaGene 5.5 (BioDiscovery, CA, USA).

data_processing: The median signal intensities were normalized by cyclic lowess.

source_name: universal mouse reference total RNA (Catalog #740100; Stratagene, La Jolla, CA, USA)

label_protocol: Individual 2.5 µg aliquots of RNA from each sample were amplified and labelled using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent).

extract_protocol:
purchased from Stratagene
Unknown: Material was purchased as total RNA (universal mouse reference total RNA (Stratagene, CA, USA))

value: Total RNA derived from 11 mouse cell lines

tag: id

tag: set

value: Hybridization Block 6


title: khondoker2Scan.30487

description:
Stratagene, La Jolla, CA, USA
khondoker2Scan
raw data files: ArrayNumber_PMT_ScanID_Dye.txt, PMT is % of maximum power


title: Parental cell line, replicate 1

description: Gene expression data from stably transfected FL5.12 pro-B-cells expressing Bfl-1DC and p53DD

source_name: Stably transfected FL5.12 pro-B-cells expressing Bfl-1DC and p53DD

value: parental FL5.12 pro-B-cells


title: Parental cell line, replicate 2


title: Adult C. elegans strain GE-31 control, replicate 6

description:
Adult C. elegans strain GE-31 control replicate 6.
Ce_Az1CF_WL0000_06AD_2UG

tag: strain

tag: tissue


title: lyng.30487

description:
Stratagene, La Jolla, CA, USA
lyng scan
raw data files: ArrayNumber_PMT_ScanID_Dye.txt, PMT is % of maximum power


title: Llactis_genomic_DNA_7


title: khondoker3Scan.30487

description:
Stratagene, La Jolla, CA, USA
khondoker3Scan
raw data files: ArrayNumber_PMT_ScanID_Dye.txt, PMT is % of maximum power


title: lyng.30486


title: khondoker2Scan.30485

value: Hybridization Block 5


title: medium.30487

description:
Stratagene, La Jolla, CA, USA
medium scan
raw data files: ArrayNumber_PMT_ScanID_Dye.txt, PMT is % of maximum power


title: high.30485

description:
Stratagene, La Jolla, CA, USA
high scan
raw data files: ArrayNumber_PMT_ScanID_Dye.txt, PMT is % of maximum power


title: garcia.30486


title: high.30486


title: khondoker2Scan.30486


title: khondoker3Scan.30486


title: low.30487

description:
Stratagene, La Jolla, CA, USA
low scan
raw data files: ArrayNumber_PMT_ScanID_Dye.txt, PMT is % of maximum power


title: medium.30486


title: khondoker3Scan.30485


title: low.30486


title: lyng.30485


title: garcia.30485


title: medium.30485


title: khondoker2Scan.30484


title: khondoker3Scan.30484


title: low.30485


title: garcia.30484


title: medium.30484


title: high.30484


title: low.30484


title: lyng.30484


title: garcia.30483

value: Hybridization Block 4


title: khondoker3Scan.30483


title: medium.30483


title: high.30483


title: khondoker2Scan.30483


title: lyng.30464

value: Hybridization Block 7


title: khondoker3Scan.30463

value: Hybridization Block 1


title: khondoker3Scan.30464


title: khondoker2Scan.30464


title: garcia.30464


title: medium.30464


title: garcia.30463


title: high.30464


title: low.30464


title: high.30463


title: lyng.30463


title: khondoker2Scan.30463


title: khondoker2Scan.30462


title: lyng.30462


title: medium.30463


title: low.30483


title: low.30463


title: medium.30462


title: garcia.30461


title: high.30461


title: high.30462


title: khondoker3Scan.30461


title: khondoker2Scan.30461


title: low.30461


title: low.30462


title: medium.30461


title: high.30460


title: lyng.30460


title: garcia.30460


title: khondoker3Scan.30460


title: khondoker2Scan.30460


title: low.30460


title: khondoker3Scan.30462


title: medium.30460


title: lyng.30483


title: high.30487


title: garcia.30459


title: khondoker3Scan.30459


title: garcia.30462


title: CD138_selected_plasma_cells_presentation_MM258

city: Sutton

first: Brian

middle: A

last: Walker

address: 15 Cotswold Road

department: Haemato-Oncology Research Unit

institute: The Institute of Cancer Research

description: pre-treatment bone marrow plasma cells selected for CD138+ using microbeads and magnet-assisted cell sorting (MACS; Miltenyi Biotech, Bergisch Gladbach, Germany), according to the manufacturer's instructions.

hyb_protocol: Affymetrix Fluidics Station Protocol: Hybridization-EukGE-WS2v5_450, 15ug of fragmented cRNA were hybridised to U133 Plus 2.0 arrays using the standard Affymetrix conditions for 16 hours at 45C.

scan_protocol: Genechips were scanned on an Affymetrix GeneChip 3000 7G/4 color early acces scanner and processed using GCOS 1.4.0.

data_processing: The data were analyzed with dChip (April 2007 build) using default analysis settings for normalization and summarization methods.

source_name: pre-treatment bone marrow

label_protocol: 100 ng of RNA was used in the Affymetrix 2-cycle IVT reaction and cRNA was labelled with biointylated rUTP during the second IVT reaction as per Affymetrix protocol.

extract_protocol: Sample was CD138 positively selected using MACS beads and stored in RLT, extracted using Qiagen AllPrep DNA/RNA mini kit as per manufacturer's protocol.

value: myeloma cells

tag: extraction

value: AllPrep

tag: storage

value: RLT


title: CD138_selected_plasma_cells_presentation_MM255


title: high.30459


title: CD138_selected_plasma_cells_presentation_MM257


title: khondoker2Scan.30459


title: CD138_selected_plasma_cells_presentation_MM256


title: low.30459


title: medium.30459


title: CD138_selected_plasma_cells_presentation_MM253


title: lyng.30459


title: CD138_selected_plasma_cells_presentation_MM252


title: khondoker3Scan.30446


title: CD138_selected_plasma_cells_presentation_MM251


title: khondoker2Scan.30446


title: CD138_selected_plasma_cells_presentation_MM250


title: garcia.30446


title: CD138_selected_plasma_cells_presentation_MM249


title: CD138_selected_plasma_cells_presentation_MM248


title: high.30446


title: CD138_selected_plasma_cells_presentation_MM247


title: lyng.30446


title: low.30446


title: CD138_selected_plasma_cells_presentation_MM246


title: CD138_selected_plasma_cells_presentation_MM254


title: khondoker2Scan.30445


title: khondoker3Scan.30445


title: garcia.30445


title: CD138_selected_plasma_cells_presentation_MM245


title: CD138_selected_plasma_cells_presentation_MM244


title: CD138_selected_plasma_cells_presentation_MM243


title: CD138_selected_plasma_cells_presentation_MM242


title: medium.30446


title: CD138_selected_plasma_cells_presentation_MM238


title: high.30445


title: lyng.30445


title: low.30445


title: medium.30445


title: CD138_selected_plasma_cells_presentation_MM240


title: khondoker3Scan.30444


title: CD138_selected_plasma_cells_presentation_MM239


title: lyng.30444


title: CD138_selected_plasma_cells_presentation_MM241


title: khondoker2Scan.30444


title: CD138_selected_plasma_cells_presentation_MM236


title: garcia.30444


title: CD138_selected_plasma_cells_presentation_MM234


title: CD138_selected_plasma_cells_presentation_MM235


title: CD138_selected_plasma_cells_presentation_MM233


title: high.30444


title: lyng.30461


title: khondoker3Scan.30428

value: Hybridization Block 3


title: garcia.30428


title: khondoker2Scan.30428


title: high.30428


title: medium.30444


title: CD138_selected_plasma_cells_presentation_MM232


title: lyng.30428


title: CD138_selected_plasma_cells_presentation_MM229


title: CD138_selected_plasma_cells_presentation_MM230


title: CD138_selected_plasma_cells_presentation_MM231


title: CD138_selected_plasma_cells_presentation_MM226


title: CD138_selected_plasma_cells_presentation_MM228


title: low.30444


title: CD138_selected_plasma_cells_presentation_MM227


title: CD138_selected_plasma_cells_presentation_MM237


title: low.30428


title: khondoker2Scan.30427

value: Hybridization Block 2


title: CD138_selected_plasma_cells_presentation_MM222


title: CD138_selected_plasma_cells_presentation_MM223


title: CD138_selected_plasma_cells_presentation_MM225


title: CD138_selected_plasma_cells_presentation_MM221


title: medium.30428


title: CD138_selected_plasma_cells_presentation_MM224


title: khondoker3Scan.30427


title: CD138_selected_plasma_cells_presentation_MM220


title: high.30427


title: garcia.30423


title: low.30427


title: khondoker3Scan.30423


title: lyng.30427


title: medium.30427


title: CD138_selected_plasma_cells_presentation_MM219


title: CD138_selected_plasma_cells_presentation_MM217


title: lyng.30423


title: khondoker2Scan.30423


title: CD138_selected_plasma_cells_presentation_MM214


title: CD138_selected_plasma_cells_presentation_MM218


title: CD138_selected_plasma_cells_presentation_MM215


title: CD138_selected_plasma_cells_presentation_MM216


title: CD138_selected_plasma_cells_presentation_MM211


title: CD138_selected_plasma_cells_presentation_MM212


title: medium.30423


title: low.30423


title: high.30423


title: khondoker3Scan.30422


title: khondoker2Scan.30422


title: CD138_selected_plasma_cells_presentation_MM210


title: CD138_selected_plasma_cells_presentation_MM207


title: CD138_selected_plasma_cells_presentation_MM206


title: CD138_selected_plasma_cells_presentation_MM208


title: CD138_selected_plasma_cells_presentation_MM209


title: garcia.30427


title: lyng.30422


title: garcia.30422


title: low.30422


title: medium.30422


title: khondoker3Scan.30421


title: CD138_selected_plasma_cells_presentation_MM204


title: high.30422


title: CD138_selected_plasma_cells_presentation_MM203


title: CD138_selected_plasma_cells_presentation_MM198


title: CD138_selected_plasma_cells_presentation_MM199


title: lyng.30421


title: CD138_selected_plasma_cells_presentation_MM200


title: high.30421


title: CD138_selected_plasma_cells_presentation_MM201


title: garcia.30421


title: CD138_selected_plasma_cells_presentation_MM205


title: CD138_selected_plasma_cells_presentation_MM202


title: CD138_selected_plasma_cells_presentation_MM196

extract_protocol: Sample was CD138 positively selected using MACS beads and stored in Trizol, RNA was isolated using Trizol and the Invitrogen Micro-to-Midi total RNA purification kit as per manufacturer's instructions.

value: Trizol


title: medium.30421


title: CD138_selected_plasma_cells_presentation_MM195


title: CD138_selected_plasma_cells_presentation_MM192


title: khondoker2Scan.30421


title: medium.30420


title: CD138_selected_plasma_cells_presentation_MM193


title: low.30421


title: CD138_selected_plasma_cells_presentation_MM182


title: lyng.30420


title: high.30420


title: low.30420


title: CD138_selected_plasma_cells_presentation_MM186


title: khondoker3Scan.30420


title: CD138_selected_plasma_cells_presentation_MM185


title: khondoker3Scan.30241


title: CD138_selected_plasma_cells_presentation_MM189


title: khondoker2Scan.30420


title: CD138_selected_plasma_cells_presentation_MM197


title: CD138_selected_plasma_cells_presentation_MM190


title: low.30241


title: medium.30241


title: CD138_selected_plasma_cells_presentation_MM183


title: khondoker3Scan.30240


title: CD138_selected_plasma_cells_presentation_MM187


title: CD138_selected_plasma_cells_presentation_MM180


title: CD138_selected_plasma_cells_presentation_MM184


title: lyng.30241


title: high.30241


title: CD138_selected_plasma_cells_presentation_MM191


title: CD138_selected_plasma_cells_presentation_MM179


title: garcia.30241


title: khondoker2Scan.30240


title: CD138_selected_plasma_cells_presentation_MM181


title: CD138_selected_plasma_cells_presentation_MM178


title: CD138_selected_plasma_cells_presentation_MM176


title: CD138_selected_plasma_cells_presentation_MM177


title: high.30240


title: khondoker2Scan.30241


title: medium.30240


title: garcia.30240


title: CD138_selected_plasma_cells_presentation_MM174


title: garcia.30420


title: CD138_selected_plasma_cells_presentation_MM175


title: CD138_selected_plasma_cells_presentation_MM173


title: low.30240


title: lyng.30239


title: lyng.30238


title: khondoker3Scan.30239


title: medium.30239


title: khondoker3Scan.30238


title: khondoker2Scan.30239


title: CD138_selected_plasma_cells_presentation_MM166


title: garcia.30239


title: CD138_selected_plasma_cells_presentation_MM172


title: CD138_selected_plasma_cells_presentation_MM162


title: CD138_selected_plasma_cells_presentation_MM169


title: CD138_selected_plasma_cells_presentation_MM168


title: high.30238


title: CD138_selected_plasma_cells_presentation_MM160


title: low.30239


title: high.30239


title: garcia.30238


title: CD138_selected_plasma_cells_presentation_MM170


title: khondoker2Scan.30238


title: CD138_selected_plasma_cells_presentation_MM164


title: CD138_selected_plasma_cells_presentation_MM161


title: CD138_selected_plasma_cells_presentation_MM165


title: CD138_selected_plasma_cells_presentation_MM158


title: lyng.30240


title: CD138_selected_plasma_cells_presentation_MM157


title: CD138_selected_plasma_cells_presentation_MM171


title: medium.30238


title: CD138_selected_plasma_cells_presentation_MM159


title: khondoker2Scan.30237


title: khondoker3Scan.30237


title: garcia.30237


title: lyng.30237


title: medium.30237


title: CD138_selected_plasma_cells_presentation_MM153


title: CD138_selected_plasma_cells_presentation_MM151


title: low.30238


title: CD138_selected_plasma_cells_presentation_MM154


title: CD138_selected_plasma_cells_presentation_MM152


title: CD138_selected_plasma_cells_presentation_MM150


title: CD138_selected_plasma_cells_presentation_MM155


title: high.30237


title: CD138_selected_plasma_cells_presentation_MM156


title: CD138_selected_plasma_cells_presentation_MM149


title: khondoker3Scan.30178


title: khondoker2Scan.30178


title: CD138_selected_plasma_cells_presentation_MM146


title: CD138_selected_plasma_cells_presentation_MM148


title: garcia.30178


title: lyng.30178


title: CD138_selected_plasma_cells_presentation_MM147


title: low.30237


title: CD138_selected_plasma_cells_presentation_MM145


title: CD138_selected_plasma_cells_presentation_MM143


title: khondoker3Scan.30177


title: CD138_selected_plasma_cells_presentation_MM142


title: high.30178


title: low.30178


title: garcia.30177


title: lyng.30177


title: CD138_selected_plasma_cells_presentation_MM144


title: CD138_selected_plasma_cells_presentation_MM141


title: high.30177


title: CD138_selected_plasma_cells_presentation_MM140


title: CD138_selected_plasma_cells_presentation_MM138


title: khondoker2Scan.30177


title: medium.30178


title: CD138_selected_plasma_cells_presentation_MM137


title: medium.30177


title: low.30177


title: khondoker3Scan.30176


title: CD138_selected_plasma_cells_presentation_MM134


title: CD138_selected_plasma_cells_presentation_MM133

extract_protocol: Sample was CD138 positively selected using MACS beads and stored in RLT, extracted using Qiagen RNA/DNA kit and nucleic acids extracted as per manufacturer's protocol.

value: RNA/DNA kit


title: CD138_selected_plasma_cells_presentation_MM135


title: CD138_selected_plasma_cells_presentation_MM136


title: khondoker2Scan.30176


title: high.30176


title: medium.30176


title: lyng.30176


title: garcia.30176


title: CD138_selected_plasma_cells_presentation_MM132


title: CD138_selected_plasma_cells_presentation_MM130


title: low.30176


title: khondoker3Scan.30175


title: CD138_selected_plasma_cells_presentation_MM124


title: garcia.30175


title: lyng.30175


title: CD138_selected_plasma_cells_presentation_MM126


title: high.30175


title: CD138_selected_plasma_cells_presentation_MM123


title: low.30175


title: medium.30175


title: CD138_selected_plasma_cells_presentation_MM121


title: khondoker2Scan.30175


title: CD138_selected_plasma_cells_presentation_MM120


title: CD138_selected_plasma_cells_presentation_MM139


title: CD138_selected_plasma_cells_presentation_MM127


title: khondoker2Scan.30174


title: CD138_selected_plasma_cells_presentation_MM128


title: CD138_selected_plasma_cells_presentation_MM122


title: CD138_selected_plasma_cells_presentation_MM125


title: CD138_selected_plasma_cells_presentation_MM119


title: khondoker3Scan.30174


title: CD138_selected_plasma_cells_presentation_MM118


title: CD138_selected_plasma_cells_presentation_MM117


title: lyng.30174


title: garcia.30174


title: CD138_selected_plasma_cells_presentation_MM115


title: high.30174


title: khondoker2Scan.30173


title: CD138_selected_plasma_cells_presentation_MM110


title: high.30173


title: lyng.30173


title: khondoker3Scan.30173


title: low.30173


title: CD138_selected_plasma_cells_presentation_MM113


title: low.30174


title: khondoker3Scan.30172


title: CD138_selected_plasma_cells_presentation_MM114


title: CD138_selected_plasma_cells_presentation_MM104


title: garcia.30173


title: khondoker2Scan.30172


title: CD138_selected_plasma_cells_presentation_MM111


title: CD138_selected_plasma_cells_presentation_MM103


title: garcia.30172


title: CD138_selected_plasma_cells_presentation_MM102


title: CD138_selected_plasma_cells_presentation_MM105


title: medium.30173


title: CD138_selected_plasma_cells_presentation_MM112


title: CD138_selected_plasma_cells_presentation_MM109


title: CD138_selected_plasma_cells_presentation_MM106


title: CD138_selected_plasma_cells_presentation_MM108


title: CD138_selected_plasma_cells_presentation_MM107


title: lyng.30172


title: CD138_selected_plasma_cells_presentation_MM129


title: khondoker3Scan.30028


title: khondoker2Scan.30029


title: medium.30172


title: CD138_selected_plasma_cells_presentation_MM100


title: garcia.30029


title: CD138_selected_plasma_cells_presentation_MM099


title: medium.30029


title: khondoker2Scan.30028


title: lyng.30028


title: CD138_selected_plasma_cells_presentation_MM096


title: CD138_selected_plasma_cells_presentation_MM086


title: lyng.30029


title: garcia.30028


title: CD138_selected_plasma_cells_presentation_MM093


title: CD138_selected_plasma_cells_presentation_MM092


title: CD138_selected_plasma_cells_presentation_MM089


title: CD138_selected_plasma_cells_presentation_MM090


title: CD138_selected_plasma_cells_presentation_MM094


title: CD138_selected_plasma_cells_presentation_MM087


title: CD138_selected_plasma_cells_presentation_MM091


title: khondoker3Scan.30029


title: medium.30174


title: CD138_selected_plasma_cells_presentation_MM098


title: CD138_selected_plasma_cells_presentation_MM088


title: high.30172