title: 4T1 cells_Rep1

description: Copy number variation data

source_name: Mouse mammary tumor-derived cell line 4T1

value: BALB/c

value: Spontaneous mammary tumor


title: 86397_M430-2_7_ILEUM_MGI_GENE-4

status: Public on Jun 15 2016

type: RNA

city: Cincinnati

first: Jing

last: Chen

state: OH

address: 3333 Burnet Ave

country: USA

institute: CCHMC

hyb_protocol: The biotinylated cRNA was prepared and hybridized to the Mouse 430A_2.0 GeneChip in accordance with Affymetrix protocols.

scan_protocol: GeneChips were scanned by the Affymetrix GeneChip Scanner.

data_processing: Microarray data was preprocessed using RMA implemented in R with BrainArray custom CDF.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Normal Diet_ILEUM

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

growth_protocol: Nine-week-old male, ob/ob (B6.V-Lepob/J), and ob lean control (Lepob, heterozygote from the colony) mice were purchased from Jackson Lab (Bar Harbor, Main) and acclimatized to a constant temperature and humidity (72°F and 50% relative humidity with a 12 h light and dark cycle from 05:00 h to 17:00 h) and had free access to food (LabDiet 5K20, LabDiet, St. Louis, MO) and water.  At the age of twelve weeks, all animals were fasted for four hours in the morning and euthanized at 1pm under isoflurane anathesia. Nine-week-old male, C57BL/6J mice were purchased from Jackson Lab (Bar Harbor, Main) and acclimatized to a constant temperature and humidity (72°F and 50% relative humidity with a 12 h light and dark cycle from 05:00 h to 17:00 h) for one week with free access to food (LabDiet 5001, LabDiet, St. Louis, MO) and water.  After acclimation, half of the mice (n=6) were kept on the regular chow diet (LabDiet 5001) and half of them (n=6) were switched to TD93075 (Harlan Teklad, Madison, Wisconsin), a high-fat diet with 54.8%Kcal from fat for four weeks. At the end of the study, all animals were fasted for four hours in the morning and euthanized at 1pm under isoflurane anesthesia.

extract_protocol: Gastrointestinal tissues (whole stomach and about 1cm of intestinal samples from the middle of each part of the intestine) were collected.  Finally a 1cm3 segment of the inferior right lobe of the liver was taken. Segments were immediately snap frozen in liquid nitrogen and stored at -80°C for subsequent RNA extraction.  RNA extraction was performed using the RNeasy Mini kit (Qiagen Inc, Valencia, Calif). Total RNA yield and purity was estimated by UV spectroscopy (Nanodrop ND-1000 Spectrophotometer; Nanodrop Technologies, Wilmington, DE, USA) and RNA quality was assessed on an Agilent 2100 Bioanalyzer.  Subsequently mRNA expression analysis was carried out.

tag: group

value: Normal Diet

tag: genotype

tag: tissue

value: ILEUM

tag: animal


title: P35 Cm 205 3

city: Farmington

first: Jeffrey

last: Chuang

state: CT

address: 263 Farmington Avenue

department: Computational Biology

institute: The Jackson Laboratory for Genomic Medicine

hyb_protocol: 2.3µg of biotin-labeled and fragmented cDNA was then hybridized onto GeneChip® Mouse Gene 1.0 ST Arrays (Affymetrix) for 16 hours at 45°C.  Post-hybridization staining and washing were performed according to manufacturer’s protocols using the Fludics Station 450 instrument (Affymetrix)

scan_protocol: The arrays were scanned with a GeneChipTM Scanner 3000 laser confocal slide scanner.

data_processing: Average signal intensities for each probe set were calculated using Expression Console software (Version 1.1, Affymetrix) using the average (RMA) method  Fs, a modified F-statistic incorporating shrinkage estimates of variance components from within the R/maanova package was used to determine differentially expressed genes by one pairwise comparisons   Permutations analysis was used to calculate the levels of statistical significance of pairwise comparisons and these were adjusted for multiple testing using the false discovery rate, q-value method   Differentially expressed genes are declared at an FDR q-value threshold of 0.05

source_name: cerebellum

label_protocol: Following reverse transcription with random primers-T7 primers (Affymetrix, Santa Clara, Ca), double stranded cDNA was synthesized with the GeneChip® WT cDNA Synthesis and Amplification Kit (Affymetrix, Santa Clara, Ca).  In an in vitro trancription (IVT) reaction with T7 RNA polymerase, the cDNA was linearly amplified to generate cRNA.  In the second cycle of cDNA synthesis, random primers are used to generate single stranded DNA in the sense orientation.  Incorporation of dUTP in the cDNA synthesis step allows for the fragmentation of the cDNA strand utilizing uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) that specifically recognizes the dUTP and allows for breakage at these residues. Labeling occurs by terminal deoxynucleotidyl transferase (TdT) where biotin is added by a Affymetrix Labeling Reagent.

extract_protocol: The cerebellum and hippocampus were collected from B6J and B6J-nmf205-/- mice at 3 weeks and 5 weeks of age. Total RNA was isolated by TRIzolPlus(TM) methods according to the manufacturer’s protocols, and quality was assessed using an Agilent 2100 Bioanalyzer instrument and RNA 6000 Nano LabChip assay (Agilent Technologies, Palo Alto, CA).

tag: strain

tag: age


title: 2508 cells_Rep1

type: genomic

city: Bethesda

first: Maxwell

last: Lee

state: MD

address: Building 37, Room 5120

department: CCR

institute: National Cancer Institute, NIH

description: Copy number variation data

hyb_protocol: Samples were hybridized to the arrays at 50oC for 16-18 hours

scan_protocol: Washing and staining of the hydridized array was performed using the Affymetrix 450 fluidics station, and arrays were scanned using the Affymetrix GeneChip 3000 7G Plus scanner

data_processing:
Array images and intensity data were collected using the Affymetrix GEneChip Command Console (AGCC) Software.  Array data were analyzed using the R package MouseDivGeno.  Data from normal tissue of matched mouse strains were used as references to identify regions of copy number gain or loss.
The 27 mouse tumor cell lines were assayed by the Mouse Diversity Genotyping array, a Affymetrix mouse genotyping array similar to human SNP 6.0. The array were analyzed by using the R package MouseDivGeno.  Copy number analysis was performed using data from normal DNA of matched mouse strains as references for copy number inference. Reference set can be downloaded from http://cgd.jax.org/datasets/diversityarray/CELfiles.shtml.

label: Biotin

molecule: genomic DNA

source_name: Mouse mammary tumor-derived cell line 2508

label_protocol: The Affymetrix SNP 6.0 protocol was used.  gDNA was subjected to spearate restriction enzyme digestions using Sty1 and Nsp.  For each digest reaction (2/sample) restriction products were ligated to a common adaptor and amplifed by PCR.  The amplified reaction products for each sample were pooled, purified and then fragmented.  Fragmented PCR amplicons were end-labeled using terminal deoxynucleotidyl transferase with the Biotin-labled GeneChip DNA Labeling Reagent.

growth_protocol: Cells were cultured in their recommended growth media using standard procedures

extract_protocol: RNA-free DNA was prepared from the cell lines using the Gentra Puregene Cell Kit (Qiagen) according to manufacturer's protocol and resuspended in low EDTA TE buffer.  DNA quantity was assessed using PicoGreen fluorometry and integrity was assessed by agarose gel electrophoresis.  Qualified gDNA samples were normalized to 50ng/ul.

tag: cell line

tag: mouse strain

value: FVB/N

tag: cell line origin

value: Genetically engineered mouse mammary tumor

tag: malignancy status

value: Malignant

tag: metastatic ability

value: Not tested


title: 86398_M430-2_7_A.COLON_MGI_GENE-4

source_name: Normal Diet_A.COLON


title: P35 Cm 205 1


title: Plasma cfRNA from healthy subject2

city: Jerusalem

first: Vardit

last: Moshayoff

address: Hadassaah Medical Center, Ein Kerem

country: Israel

institute: BioMarCare technology

hyb_protocol: the use of the GeneChip® Hybridization, Wash and Stain Kit (catalog no. 900720, Affymetrix) and the GeneChip human 1.0 ST Arrays (catalog no. 901085, Affymetrix). Hybridization cocktail was prepared by mixing the following materials: 25 microliter of fragmented, biotin-labeled and amplified cDNA, 1.9 microliter control oligonucleotide B2 (3 nM), 5.5 microliter of 20X Eukaryotic hybridization controls (bioB, bioC, bioD, cre), 55 microliter 2X Hybridization Buffer, 11 microliter 100% DMSO, 11.6 microliter water. The procedure was performed according to manufacturer instructions.

scan_protocol: Arrays were scanned on the Affymetrix GeneChip Scanner 3000 7G

data_processing: Raw CEL files were imported into Partek Genomics Suite and preprocessed using RMA background correction, quantile normalization and log2 transformation. No probe summarization to probeset was performed.

organism: Homo sapiens

source_name: Plasma cfRNA from healthy subject

label_protocol: For gene expression profiling using Affymetrix expression microarray, cDNA was synthesized using the Ovation PicoSL WTA System (catalog no. 3312, Nugen), according to kit's protocol. Subsequently, the cDNA was purified with MiniElute Reaction Cleanup kit (catalog no. 28204, Qiagen), according to kit protocol. Next, fragmentation and biotin labeling of the cDNA was done by Encore biotin module (catalog no. 4200, Nugen). The extent of fragmentation was monitored using Bioanalyzer 2100 Pico chip (Agilnet) using 1 µl of the reaction volume.

growth_protocol: not applicable

extract_protocol: Plasma total RNA was purified from 3.2ml of plasma mixed with 11.2 TRIzol reagent, with addition of 15 microgram of linear acrylamide. 200 μl of chloroform were added per each 1 ml of Trizol and mixed vigorously. After incubated for 10 minutes at room temperature, the mixture was centrifuged for 15 minutes at 14000 rpm at 4°C. The aqueous phase was transferred to a new tube and mixed vigorously with equal volume of chloroform, incubated for 3 minutes at room temperature and centrifuged for 15 minutes at 14,000 rpm at 4°C. Following the centrifugation, the upper phase was transferred to a new tube and mix thoroughly with a total of 2.8 ml of RLT plus buffer RNeasy mini kit (catalog no. 74104, Qiagen). This mixture was passed through the kit's gDNA eliminator mini spin column as described by the manufacture protocol. The flow-through was collected in a new tube, and 1.5 times volume of 100% EtOH was added. The solution was well mixed and incubated at -20°C for over-night. Next, 700 ml of the mixture was loaded on an RNeasy spin column and micro-centrifuged at 23°C, 14,000 RPM, for 30 seconds and flow-through was saved. The rest of the thawed solution was passed through the same RNeasy spin column, as described above.RNA purification process was completed by following the RNeasy mini kit protocol. The RNA-loaded RNeasy spin column were washed with 700 ml of RW1 buffer, centrifuged at 23°C 14,000 RPM for 30 seconds and flow through discarded. Additional two washes of spin column were done with 500 ml of RPE buffer. Finally, RNA was eluted in 35 ml of RNase-free water.

treatment_protocol: Subject were classified as being either healthy, having adavnaced adenoma or cancer according to colonoscopy result or biopsy results.

tag: subject status/id

value: healthy subject2

tag: gender

value: Female

tag: age (yrs)

tag: colonoscopy result

value: normal

tag: molecule subtype

value: human plasma circulating free RNA


title: 86395_M430-2_7_DUODENUM_MGI_GENE-4

source_name: Normal Diet_DUODENUM

value: DUODENUM


title: P35 Cm WT 3

value: wild type


title: LCL5_control_21days

city: Bonn

first: Julia

middle: Carolin

last: Stingl

address: Kurt-Georg-Kiesinger Allee 3

department: Research

country: Germany

institute: Federal Institute for Drugs and Medical Devices

hyb_protocol: 600ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 0.025ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 0.025ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner using one color scan setting .

data_processing: The scanned images were analyzed with Feature Extraction Software 10 (Agilent) using default parameters (protocol GE1_1100 and Grid: 039494_D_F_20120411) to obtain background subtracted and spatially detrended Processed Signal intensities.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Germany).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: LCLs were grown in RPMI medium supplemented with 15% heat-inactivated fetal bovine serum, antibiotics (100 µg/ml penicillin, 100 µg/ml streptomycin) and a final concentration of 4 mM L-glutamine. Medium exchanging was done every second day.

extract_protocol: RNA was extracted using the NucleoSpin® RNA Kit (Macherey-Nagel, Germany) according to the manufacturer instructions. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, USA).

treatment_protocol: LCLs were treated with 0.5µg/ml fluoxetine (dissolved in DMSO) for 21 days. MOCK treated control cultures were grown in parallel.

tag: disease state

value: depressive disorder

tag: treatment

value: control

tag: clinical treatment outcome

value: responder


title: P35 Cm WT 2

tag: genotype


title: LCL6_control_21days


title: LCL4_fluoxetine_21days

value: fluoxetine


title: Plasma cfRNA from healthy subject1

value: healthy subject1


title: LCL3_fluoxetine_21days

value: non-responder


title: 86394_M430-2_7_STOMACH_MGI_GENE-4

source_name: Normal Diet_STOMACH

tag: group

value: Normal Diet

tag: tissue

value: STOMACH

tag: animal


title: P35 Cm WT 1

tag: strain

tag: age


title: 86393_M430-2_6_D.COLON_MGI_GENE-4

source_name: Normal Diet_D.COLON


title: LCL3_control_21days

tag: cell line


title: P22 Hp 205 2

source_name: hippocampus


title: LCL4_control_21days


title: 86392_M430-2_6_A.COLON_MGI_GENE-4


title: P22 Hp 205 3


title: P22 Hp 205 1


title: 86386_M430-2_3_A.COLON_MGI_GENE-4


title: 86389_M430-2_6_DUODENUM_MGI_GENE-4


title: 86391_M430-2_6_ILEUM_MGI_GENE-4

value: ILEUM


title: 86385_M430-2_3_ILEUM_MGI_GENE-4


title: 86383_M430-2_3_DUODENUM_MGI_GENE-4


title: P22 Hp WT 1


title: 86388_M430-2_6_STOMACH_MGI_GENE-4


title: P22 Cm 205 1


title: P22 Hp WT 3


title: 86387_M430-2_3_D.COLON_MGI_GENE-4


title: LCL2_fluoxetine_21days


title: P22 Cm WT 3


title: P22 Hp WT 2


title: LCL1_control_21days


title: LCL1_fluoxetine_21days


title: 86382_M430-2_3_STOMACH_MGI_GENE-4


title: P22 Cm 205 3


title: P22 Cm WT 2


title: LCL2_control_21days


title: P22 Cm 205 2


title: 86379_M430-2_2_ILEUM_MGI_GENE-4


title: 86261_26_ILEUM_MGI_GENE-3

source_name: ob control_ILEUM

value: ob control

value: ob lean control (Lepob, heterozygote from the colony)


title: Stable MDA-MB-231 cell line established by the integration of shRNA targeting to ELK3, Biological repeat 2

city: SungNam

first: Jae

middle: Yong

address: 335, Pangyo-ro

country: South Korea

institute: Cha Unniversity

description:
Stable MDA-MB-231 cell line established by the integration of shRNA targeting to ELK3, (RHS4531-EG2004, Dharmacon), Biological repeat 2
mammary gland/breast; derived from metastatic site: pleural effusion, female
gene expression data from ELK3 knocked down MDA-MB-231 cell line

hyb_protocol: The fragmented cRNA was hybridized to the Affymetrix GeneChip Human PrimeView Array for 16 hr at 45°C in a Hybridization Oven.

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: Raw data were extracted automatically in Affymetrix data extraction protocol using the software provided by Affymetrix GeneChip® Command Console® Software (AGCC). After importing CEL files, the data were summarized and normalized with robust multi-average (RMA) method implemented in Affymetrix® Expression Console™ Software (EC).

source_name: MDA-MB-231 breast cancer cell line

label_protocol: The Affymetrix 3’IVT Expression array process was executed according to the manufacturer's protocol  (GeneChip 3’IVT Plus Reagent Kit).

growth_protocol: Cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.Biotin-labeled, amplified RNA (aRNA) was synthesized from 100 ng total RNA using the 3′IVT Plus reagent Kit. A 12μg labeled cRNA was fragmented by heat and ion-mediated hydrolysis at 94°C for 35 min.

treatment_protocol: Total RNA was extracted from stable ELK3 knocked down MDA-MB-231.

tag: genotype/variation

value: stable ELK3 knockdown


title: NODULE CONTROL/VHb_M2_BEAN

city: Cuernavaca

first: Mario

last: Ramírez

state: Morelos

address: Avenida Universidad S/N

department: Functional Genomics of Eukaryotes

country: Mexico

institute: Centro de Ciencias Genomicas-UNAM

hyb_protocol: Prehybridization was performed by incubating the arrays with prehybridization solution (6X SSPE, 0.05% Tween-20, 20mM EDTA, 5x Denhardt's solution, 100 ng/µl Salmon Sperm DNA, 0.05% SDS) for 30 minutes at 45 °C. 4 µg of labeled aRNA were fragmented by incubation with 5 µl of Fragmentation Solution (200mM Tris Acetate pH 8.1, 500 mM KOAc, 150 mM MgOAc) for 20 min at 95 °C.  -  Hybridization was performed at 45°C for 16 hours in hybridization solution (6X SSPE, 0.05% Tween-20, 20mM EDTA, 25% Diformamide, 100 ng/µl Salmon Sperm DNA, 0.04% SDS).    Hybridization washings were performed as the following:  - wash with 6X SSPET wash solution (6X SSPE, 0.05% Tween-20).  - wash with 3X SSPET wash solution (3X SSPE, 0.05% Tween-20).  - wash with 0.5X SSPET wash solution (0.5X SSPE, 0.05% Tween-20).  - wash with PBST wash solution (2X PBS, 0.1% Tween-20).  - 2 washes with 2X PBS

scan_protocol: After hybridization and washing, the microarray was dipped in imaging solution, covered with LifterSlip™, and then scanned using a GenePix 4000B microarray scanner (Axon, Toronto, CA) and the accompanying acquisition software (CombiMatrix Microarray Imager Software). Multiple scanning at different PMT was provided for each hybridization.

data_processing:
The raw intensities data were first processed using the CombiMatrix Microarray Imager software. This program allows the visual inspection of the entire microarray slide and is used to check the quality of each spot and, if needed, to perform possible corrections (i.e. dust or scratches on the surface). Intensity data were then exported into the Feature and Probe format of CombiMatrix, where the actual raw intensity per probe and per spot is stored.
Data were loaded into R and analyzed using the Limma package (Smyth 2004). The median value of each spot on the array was considered and the probes were filtered to remove quality and factory controls. Within-array probe replicates were defined as technical replicates, by calculating the mean intensity across the different probes. The probe intensity values of each biological condition were then normalized using the quantile function of Limma.

organism: Phaseolus vulgaris

source_name: NODULES

label_protocol: Total RNA (1μg) was used as a template to synthesize antisense RNA (aRNA) with Cy5-ULS using the RNA Amplification and Labelling Kit from CombiMatrix (ampULSe Cat. no. GEA-022; Kreatech Biotechnology, Amsterdam, The Netherlands) according to manufacturer's instructions.

growth_protocol: Phaseolus vulgaris cv. Negro Jamapa 81surface-sterilized seeds were germinated at 30 °C over sterile, wet filter paper in darkness for 3 days. Germinated seedlings were planted in pots with vermiculite and inoculated with 1 ml of saturated Rhizobium etli liquid culture. The R. etli strains used in this study were the wild type CE3 strain and CE3 bearing the stable plasmid pMR4 (Ramírez et al. 1999) containing the Vitreoscilla sp. vhb gene, hereby denominated CE3/Vhb. The expression of Vhb, driven by its native promoter, in the CE3/Vhb strain was demonstrated (Ramírez et al. 1999) Pots were watered 3 d per week with N-free Summerfield plant nutrient solution (Summerfield et al. 1977). Plants were grown under controlled environmental conditions (26-28°C, 70% humidity, 16-h photoperiod) for 18 days.

extract_protocol: Total RNA was isolated from 18 dpi PQ treated and control bean nodules using Trizol reagent (Life Technologies, Carlsbad, California. USA) according to manufacturer's instructions.

treatment_protocol: For oxidative stress conditions, at 16 days post-inoculation (dpi) plants were watered with 1 mM 1,1 '-Dimethyl-4, 4'-bipyridinium dichloride hydrate, the herbicide Paraquat (PQ), for 48 hours. Mature nodules from stressed PQ  and control plants were harvested at 18 dpi, immediately frozen in liquid nitrogen and stored at –80°C until used.

tag: cultivar

value: Negro Jamapa 81

value: Nodules

value: Control


title: NODULE CONTROL_M1_BEAN


title: 86263_26_D.COLON_MGI_GENE-3

source_name: ob control_D.COLON


title: 86381_M430-2_2_D.COLON_MGI_GENE-4


title: 86262_26_A.COLON_MGI_GENE-3

source_name: ob control_A.COLON


title: P22 Cm WT 1


title: 86380_M430-2_2_A.COLON_MGI_GENE-4


title: 86375_M430-2_1_D.COLON_MGI_GENE-4


title: NODULE STRESSED/VHb_M4_BEAN

value: Oxidative stress


title: 86259_26_DUODENUM_MGI_GENE-3

source_name: ob control_DUODENUM

value: DUODENUM


title: 86374_M430-2_1_A.COLON_MGI_GENE-4


title: Stable MDA-MB-231 cell line established by the integration of control shRNA, Biological repeat 1

description:
Stable MDA-MB-231 cell line established by the integration of control shRNA, (RHS4080, Dharmacon), Biological repeat 1
mammary gland/breast; derived from metastatic site: pleural effusion, female
gene expression data from control MDA-MB-231 cell line


title: NODULE STRESSED_M3_BEAN


title: 86370_M430-2_1_STOMACH_MGI_GENE-4


title: 86260_26_JEJUNUM_MGI_GENE-3

source_name: ob control_JEJUNUM

value: JEJUNUM


title: 86376_M430-2_2_STOMACH_MGI_GENE-4


title: Stable MDA-MB-231 cell line established by the integration of shRNA targeting to ELK3, Biological repeat 1

description:
Stable MDA-MB-231 cell line established by the integration of shRNA targeting to ELK3, (RHS4531-EG2004, Dharmacon), Biological repeat 1
mammary gland/breast; derived from metastatic site: pleural effusion, female
gene expression data from ELK3 knocked down MDA-MB-231 cell line


title: Stable MDA-MB-231 cell line established by the integration of control shRNA, Biological repeat 2

description:
Stable MDA-MB-231 cell line established by the integration of control shRNA, (RHS4080, Dharmacon), Biological repeat 2
mammary gland/breast; derived from metastatic site: pleural effusion, female
gene expression data from control MDA-MB-231 cell line

value: control


title: 86257_25_D.COLON_MGI_GENE-3


title: 86373_M430-2_1_ILEUM_MGI_GENE-4


title: 86258_26_STOMACH_MGI_GENE-3

source_name: ob control_STOMACH


title: 86254_25_JEJUNUM_MGI_GENE-3


title: Trigeminal ganglion_Stomatitis_5

city: Inashiki-gun

first: Kiyoshi

last: Terawaki

state: Ibaraki

address: 3586 Yoshiwara, Ami-machi

country: Japan

institute: Tsumura & Co.

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Rat GE 8x60K Microarray (G4858A#28279) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028279_D_F_20131202) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Rattus norvegicus

source_name: Trigeminal ganglion, Stomatitis, 5

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low RNA Input Quick Amplification Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was purified with an RNeasy Mini Kit (Qiagen) following the manufacturer's protocol.

treatment_protocol: Trigeminal ganglion tissues from control or acetic acid-induced oral ulcerative mucositis model rats were collected. Control rats received only anesthesia without any treatment. In oral ulcerative mucositis model, rats were anesthetized and treated with acetic acid. A piece of filter paper was soaked in 50% acetic acid diluted with water and placed in the labial fornix region of the inferior incisors of rats for 30 sec. On day 2 after acetic acid treatment, oral ulcerative mucositis was obvious and trigeminal ganglion tissues in two groups were collected.

value: Wistar rat

value: trigeminal ganglion

value: male

value: day 2 after acetic acid treatment


title: 86255_25_ILEUM_MGI_GENE-3


title: Trigeminal ganglion_Stomatitis_4

source_name: Trigeminal ganglion, Stomatitis, 4


title: 86256_25_A.COLON_MGI_GENE-3


title: Trigeminal ganglion_Stomatitis_2

source_name: Trigeminal ganglion, Stomatitis, 2


title: 86253_25_DUODENUM_MGI_GENE-3


title: 86252_25_STOMACH_MGI_GENE-3


title: Blood - Cord-17

city: Oviedo

first: Agustin

middle: F

last: Fernandez

email: affernandez@hca.es, agusff@gmail.com

state: Asturias

address: Avenida de Roma s/n

department: IUOPA

country: Spain

institute: Oviedo University-HUCA

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

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

data_processing:
R-bioconductor/minfi
The beta values were obtained before raw data normalization; we used Subset-quantile Within Array Normalization (SWAN)(available in the minfi Bioconductor package)
the non_normalized.txt contains unmethylated and methylated signal intensities.

label: Cy3, Cy5

source_name: umbilical cord blood_at birth

label_protocol: Standard Illumina labelling protocol

growth_protocol: FROZEN

extract_protocol: Genomic DNA was extracted  with the RealPure kit (REALPURE, REAL, DURVIZ, Ref: RBMEG01) and was quantified with the Nanodrop-2000C Spectrophotometer. A DNA quality check was performed with Quant-iT PicoGreen dsDNA reagent.

treatment_protocol: Umbilical cord and peripheral blood were collected in EDTA-tubes, centrifuged to yield plasma, stored at -80ºC and thawed before use.

tag: subject id

value: at birth

value: Umbilical cord blood


title: Trigeminal ganglion_Stomatitis_3

source_name: Trigeminal ganglion, Stomatitis, 3

tag: gender


title: Trigeminal ganglion_Control_3

source_name: Trigeminal ganglion, Control, 3

value: day 2 after control treatment


title: Trigeminal ganglion_Stomatitis_1

source_name: Trigeminal ganglion, Stomatitis, 1


title: Trigeminal ganglion_Control_5

source_name: Trigeminal ganglion, Control, 5


title: 86251_24_D.COLON_MGI_GENE-3

value: ob control


title: 86250_24_A.COLON_MGI_GENE-3

value: ob lean control (Lepob, heterozygote from the colony)


title: Trigeminal ganglion_Control_2

source_name: Trigeminal ganglion, Control, 2


title: Trigeminal ganglion_Control_4

source_name: Trigeminal ganglion, Control, 4


title: Blood - Cord-10

value: female


title: 86249_24_ILEUM_MGI_GENE-3

source_name: ob control_ILEUM

value: ILEUM


title: Blood - Cord-14


title: Trigeminal ganglion_Control_1

source_name: Trigeminal ganglion, Control, 1


title: Blood - Cord-9


title: Blood - Cord-13


title: Blood - Cord-15


title: Blood - Cord-11


title: 86248_24_JEJUNUM_MGI_GENE-3


title: 86245_23_D.COLON_MGI_GENE-3

source_name: ob control_D.COLON


title: D39 MOI 0.5 16h 2

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

institute: Justus-Liebig University Giessen

hyb_protocol: Hybridization was performed at 65°C over-night in an in-situ hybridization oven with slides mounted in Agilent hybridization chambers. Slides were rotated with 2 rpm.

scan_protocol: Slides were scanned using the InnoScan 900 scanner (Innopsys, Carbonne France) and analyzed with GenePix software V5.2 (MDS).

data_processing: Raw data was further processed using R (http://www.R-project.org)

source_name: donor blood human

label_protocol: Purified total RNA was amplified and Cy-labeled using the dual-color QuickAmp kit (Agilent Technologies, Palo Alto, CA) following the kit instructions.

growth_protocol: Human monocytes which were isolated from donor buffy coats obtained from the German Red Cross were differentiated into macrophages with 1 % human AB serum for 5-7 days. Prior to that,  PBMCs were isolated by density-gradient centrifugation using Pancoll (PAN Biotech GmbH). Then, monocytes were isolated with α-CD14 magnetic microbeads(Miltenyi Biotec).

extract_protocol: Total RNA extracted using Isol-RNA lysis reagent (5 PRIME) following manufacturer's instructions

treatment_protocol: BDMs were left untreated or exposed to S. pneumoniae strain D39 for 16 hours

value: exposed to MOI 0.5 Streptococcus pneumoniae for 16 hours

value: day 7


title: Blood - Cord-8


title: 86246_24_STOMACH_MGI_GENE-3

value: STOMACH


title: D39 MOI 0.1 16h 3

value: exposed to MOI 0.1 Streptococcus pneumoniae for 16 hours


title: 86244_23_A.COLON_MGI_GENE-3

source_name: ob control_A.COLON


title: Blood - Cord-16


title: 86243_23_ILEUM_MGI_GENE-3


title: Blood - Cord-3


title: Blood - Cord-1


title: uninfected 2

value: Blood derived macrophages

value: untreated


title: Blood - Cord-2


title: Blood - Year5-15

source_name: peripheral blood_5 year-old

value: 5 years

value: Peripheral blood


title: D39 MOI 0.5 16h 1


title: Blood - Year5-16


title: Blood - Cord-4


title: 86241_23_DUODENUM_MGI_GENE-3

source_name: ob control_DUODENUM

value: DUODENUM


title: Blood - Cord-5


title: Blood - Year5-14


title: 86240_23_STOMACH_MGI_GENE-3

source_name: ob control_STOMACH


title: 86247_24_DUODENUM_MGI_GENE-3


title: Blood - Year5-17

value: male


title: uninfected 3


title: Blood - Cord-7

value: at birth


title: 86238_22_A.COLON_MGI_GENE-3


title: 86237_22_ILEUM_MGI_GENE-3


title: 86234_22_STOMACH_MGI_GENE-3


title: Blood - Year5-11


title: 86231_21_ILEUM_MGI_GENE-3


title: Blood - Year5-7


title: Blood - Year5-8


title: D39 MOI 0.1 16h 2


title: Blood - Year5-10


title: 86233_21_D.COLON_MGI_GENE-3


title: 86232_21_A.COLON_MGI_GENE-3


title: 86226_9_A.COLON_MGI_GENE-3

value: ob/ob

value: ob/ob (B6.V-Lepob/J)


title: 86239_22_D.COLON_MGI_GENE-3

value: ob control


title: 86229_21_DUODENUM_MGI_GENE-3

value: ob lean control (Lepob, heterozygote from the colony)


title: 86228_21_STOMACH_MGI_GENE-3


title: Blood - Year5-9

value: female


title: 86221_8_D.COLON_MGI_GENE-3


title: Blood - Year5-13


title: 86220_8_A.COLON_MGI_GENE-3


title: 86217_8_DUODENUM_MGI_GENE-3


title: 86227_9_D.COLON_MGI_GENE-3


title: 86225_9_ILEUM_MGI_GENE-3

value: ILEUM


title: 86216_8_STOMACH_MGI_GENE-3


title: 3000Hz, biological rep2

city: Gyeongsan

first: Ritesh

last: Ghosh

address: 280 Daehak-Ro

department: School of Biotechnology

institute: Yeungnam University

description: Gene expression data from Arabidopsis rosette after 3000Hz treatment at 80 db

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip® arabidopsis ATH1 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Genechip Array scanner 3000 7G (Affymetrix).

data_processing: Expression data were generated by Affymetrix Expression Console software version1.1. For the normalization, RMA (Robust Multi-Average) algorithm implemented in Affymetrix Expression Console software was used. To reduce noise for the significance analysis, probe sets that were not present by the MAS5 detection call in over 50% of the samples in at least one sample group were filtered out.

organism: Arabidopsis thaliana

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

growth_protocol: Arabidopsis thaliana ecotypes Columbia (Col-0) plants were grown under continuous light (~150±10 µmol m-2 s-1) at 22C in  growth room. Seeds were stratified in cold (4C) and dark for 2 days.

extract_protocol: Total RNA was extracted with the RNeasy Plant Mini kit (Qiagen) according to the manufacturer’s instruction.

treatment_protocol: 20 days old Arabidopsis plants were transferred to noiseless chamber and subjected to different frequency (250Hz, 500Hz, 1000Hz, 2000Hz, and 3000Hz) of sound wave at 80 dB for 1 hour. Control sample was kept in the same noisless chamber without sound for 1 hr.

value: rossette

value: 20 days


title: Blood - Year5-4


title: 86212_6_JEJUNUM_MGI_GENE-3

value: JEJUNUM


title: 86213_6_ILEUM_MGI_GENE-3


title: 3000Hz, biological rep1

source_name: Arabidopsis rosette after 3000Hz treatment at 80 db


title: Blood - Year5-5


title: 86214_6_A.COLON_MGI_GENE-3


title: 86215_6_D.COLON_MGI_GENE-3


title: 2000Hz, biological rep3

description: Gene expression data from Arabidopsis rosette after 2000Hz treatment at 80 db


title: Blood - Year5-3


title: Blood - Year5-2


title: 86209_5_D.COLON_MGI_GENE-3


title: 86210_6_STOMACH_MGI_GENE-3

value: STOMACH


title: 1000Hz, biological rep3

description: Gene expression data from Arabidopsis rosette after 1000Hz treatment at 80 db


title: 86211_6_DUODENUM_MGI_GENE-3


title: 1000Hz, biological rep2

source_name: Arabidopsis rosette after 1000Hz treatment at 80 db


title: 86207_5_ILEUM_MGI_GENE-3


title: 86242_23_JEJUNUM_MGI_GENE-3

source_name: ob control_JEJUNUM


title: 2000Hz, biological rep1

source_name: Arabidopsis rosette after 2000Hz treatment at 80 db


title: 1000Hz, biological rep1


title: 30m/10a-3

city: Beijing

first: Mengjing

last: Xia

address: No.5 Yiheyuan Road

country: China

institute: Peking University

description: GeoChip data for refuse sample with landfill depth and age of 30m/10a, replicate 3

hyb_protocol: DNA was dried in a SpeedVac (ThermoSavant, Milford, MA, USA) at 45 ℃ for 45 min. All hybridizations were carried out with 40% formamide at 42 ℃ for 16 h on a MAUI hybridization station (BioMicro, Salt Lake City, UT, USA).

scan_protocol: After hybridization, GeoChip microarrays were scanned by a NimbleGen MS200 scanner (Roche, Madison, WI, USA) using a laser power and photomultiplier tube gain of 100% and 75%, respectively.

data_processing: Microarray data was extracted and preprocessed as described previously (He et al 2010, Tu et al 2014). A spot was considered positive if the signal-to-noise ratio was at least 2.0 and detected in at least two replicates. The remaining probe data was log transformed and normalized by dividing the probe signal intensity by the average of all positive probes on the array.

organism: Bacteria

source_name: Refuse microbes in a sanitary landfill in Beijing, China

label_protocol: DNA samples were labeled with the fluorescent dye Cy-3 using random primers and purified with the QIA quick purification kit (Qiagen, Valencia, CA, USA)

growth_protocol: Three core samples with intervals of 20 m were obtained through 140 mm-diameter dry boring over a depth of 0-33m without water addition. Five subsamples were collected from each core at depths of 6, 12, 18, 24 and 30 m and placed into sealed plastic bags and stored at -80℃ prior to analysis.

extract_protocol: DNA was extracted using a freeze-grind method (Zhou et al 1996).

treatment_protocol: Before DNA extraction, refuse samples were processed as described previously (Staley et al 2012). 50g of refuse samples were homogenized with 250 mL chilled 23.7 mM phosphate buffer at pH 6.73 (31.87 g Na2HPO4•7H2O L-1 and 16.1 g KH2PO4 L-1) with a shaker. The mixture was strained (75 μm) and the filtrate was centrifuged at 3220g for 5min to collect pellets. The centrifuge tubes were rinsed with sterile deionized water and recentrifuged to collect any residual cells. The final pellets were then lyophilized with a vacuum freeze drier until ready for DNA extraction.

tag: different landfill depths and ages


title: 500Hz, biological rep3

description: Gene expression data from Arabidopsis rosette after 500Hz treatment at 80 db


title: 86208_5_A.COLON_MGI_GENE-3


title: 2000Hz, biological rep2


title: 86206_5_JEJUNUM_MGI_GENE-3


title: 3000Hz, biological rep3


title: D39 MOI 0.1 16h 1

value: Blood derived macrophages

value: exposed to MOI 0.1 Streptococcus pneumoniae for 16 hours

value: day 7


title: 30m/10a-2

description: GeoChip data for refuse sample with landfill depth and age of 30m/10a, replicate 2


title: Blood - Year5-1

value: 5 years

value: Peripheral blood


title: 500Hz, biological rep1

source_name: Arabidopsis rosette after 500Hz treatment at 80 db


title: 500Hz, biological rep2


title: 86203_4_D.COLON_MGI_GENE-3


title: uninfected 1

value: untreated


title: 30m/10a-1

description: GeoChip data for refuse sample with landfill depth and age of 30m/10a, replicate 1


title: 86219_8_ILEUM_MGI_GENE-3


title: 24m/8a-3

description: GeoChip data for refuse sample with landfill depth and age of 24m/8a, replicate 3


title: 250Hz, biological rep3

description: Gene expression data from Arabidopsis rosette after 250Hz treatment at 80 db


title: 24m/8a-2

description: GeoChip data for refuse sample with landfill depth and age of 24m/8a, replicate 2


title: 86205_5_DUODENUM_MGI_GENE-3

value: DUODENUM


title: 86204_5_STOMACH_MGI_GENE-3

value: ob/ob


title: 24m/8a-1

description: GeoChip data for refuse sample with landfill depth and age of 24m/8a, replicate 1


title: 86201_4_ILEUM_MGI_GENE-3

value: ob/ob (B6.V-Lepob/J)


title: 86202_4_A.COLON_MGI_GENE-3


title: 86200_4_JEJUNUM_MGI_GENE-3


title: 250Hz, biological rep2

source_name: Arabidopsis rosette after 250Hz treatment at 80 db


title: 250Hz, biological rep1


title: 18m/6a-3

description: GeoChip data for refuse sample with landfill depth and age of 18m/6a, replicate 3


title: 18m/6a-1

description: GeoChip data for refuse sample with landfill depth and age of 18m/6a, replicate 1


title: 86199_4_DUODENUM_MGI_GENE-3


title: 18m/6a-2

description: GeoChip data for refuse sample with landfill depth and age of 18m/6a, replicate 2


title: 86198_4_STOMACH_MGI_GENE-3


title: control, biological rep3

description: Gene expression data from Arabidopsis rosette without sound treatment


title: 12m/4a-3

description: GeoChip data for refuse sample with landfill depth and age of 12m/4a, replicate 3


title: control, biological rep1

source_name: Arabidopsis rosette without sound treatment


title: DG-8052 vs. WT-8052 at 24h replicate 2

city: Wooster

first: Yan

last: Zhang

address: 1680 Madison Avenue

department: Animal Sciences

institute: The Ohio State University

description: Biological replicate 2 of 3.  degenerated strain vs wild type strain, 24h culture cells

hyb_protocol: The labelled DNA was dissolved into hybridization buffer (2×GEx Hyb buffer (HI-RPM), Agilent In Situ Hybridization Kit; 25% formamide) at 45°C overnight. After hybridization, the slides were washed in 0.2% SDS and 2× SSC at 42°C for 5min, and then in 0.2× SSC at room temperature for 5min. Finally the slides were dried for microarray scan.

scan_protocol: Scanned on an Agilent G2565CA scanner

data_processing: Quantile normalized,background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.

organism: Clostridium beijerinckii NCIMB 8052

source_name: collected the whole fermentation cells, 24h

label_protocol: The Crystal Core® cDNA amplified RNA labelling kit (CapitalBio, Beijing, China) were used as the protocol. One µg of total RNA were primed with 1 µl of 100 µM T7 Oligo (dT) DNA primer at 70°C for 10 min to get the 1st strand cDNA, and then transcribed into cRNA at 37°C for 4 h in the presence of T7 enzyme Mix. Two µg of cRNA were reversed transcribed into cDNA at 25°C for 10min followed by  37°C for 1.5 h in the presence of 1.5 µl CbcScript II RTase (CapitalBio) with 4µl Random Primer. For each 1 µg of cDNA,100 µM each dATP, dTTP, dGTP, with 25 µM dCTP Cy3-label (Cy5-label) were used for labeling by 4µl Random Primer and1.2 µl Klenow Fragment .

growth_protocol: WT-8052 and DG-8052 cells were grown at P2 medium in anaerobic chamber at 35 °C.

extract_protocol: Total cellular RNA was extracted from homogenized cells using RiboPureTM RNA Purification Kit, bacteria (Ambion®, Life Technologies, Inc., US) according to the manufacturer’s instructions.

value: degenerated strain

value: wild type


title: DG-8052 vs. WT-8052 at 24h replicate 3

description: Biological replicate 3 of 3.  degenerated strain vs wild type strain, 24h culture cells


title: 12m/4a-2

description: GeoChip data for refuse sample with landfill depth and age of 12m/4a, replicate 2


title: control, biological rep2


title: 86195_1_ILEUM_MGI_GENE-3


title: 6m/2a-3

description: GeoChip data for refuse sample with landfill depth and age of 6m/2a, replicate 3


title: 86196_1_A.COLON_MGI_GENE-3


title: DG-8052 vs. WT-8052 at 12h replicate 2

description: Biological replicate 2 of 3. wild type strain vs degenerated strain, 12h culture cells

source_name: collected the whole fermentation cells, 12h


title: DG-8052 vs. WT-8052 at 12h replicate 3

description: Biological replicate 3 of 3. wild type strain vs degenerated strain, 12h culture cells


title: DG-8052 vs. WT-8052 at 12h replicate 1

description: Biological replicate 1 of 3. wild type strain vs degenerated strain, 12h culture cells


title: 6m/2a-2

description: GeoChip data for refuse sample with landfill depth and age of 6m/2a, replicate 2


title: 86193_1_DUODENUM_MGI_GENE-3


title: 6m/2a-1

description: GeoChip data for refuse sample with landfill depth and age of 6m/2a, replicate 1


title: DG-8052 vs. WT-8052 at 24h replicate 1

description: Biological replicate 1 of 3.  degenerated strain vs wild type strain, 24h culture cells


title: 86222_9_STOMACH_MGI_GENE-3


title: 12m/4a-1

description: GeoChip data for refuse sample with landfill depth and age of 12m/4a, replicate 1


title: 86192_1_STOMACH_MGI_GENE-3


title: 86197_1_D.COLON_MGI_GENE-3


title: LSK cells Abi-1 WT, biological rep1

status: Public on Jun 14 2016

city: Providence

first: Patrycja

middle: M

last: Dubielecka

state: RI

address: One Hoppin street

department: Medicine/Hem-Onc

institute: Rhode Island Hospital and Warren Alpert Medical School at Brown University

description: LSK-enriched population of hematopoietic progenitor cells isolated via sorting from the whole bone marrow of Abi-1 WT mouse

hyb_protocol: After purification, a 5.5 μg sscDNA sample was fragmented, and a 3.22 μg sample was end-labeled and hybridized to mouse Gene ST arrays overnight at 45°C, 60 rpm. The wash/stain reaction was carried out on a FS450 Fluidics Station using Fluidics protocol FS450-0001.

scan_protocol: The arrays were scanned on an Affymetrix 3000 7G gene scanner.

data_processing:
Partek Genomics Suite version 6.6 software was used for quality control analysis and determination of differentially expressed genes. Data were analyzed using ANOVA with repeated measures analysis. Changes of 1.5 fold above or below baseline with FDR corrected p-values of ≤0.05 were considered significant.
MTA-1_0.r3.pgf
MTA-1_0.r3.Psrs.mps

source_name: LSK cells from bone marrow, Abi-1 WT

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

growth_protocol: 8-9 weeks old Abi1(fl/fl);Tg (Mx1- cre(-)) or Abi1(fl/fl);Tg (Mx1-cre(+)) mice were subjected to polyinosinic:polycytidylic acid [poly(I:C)]-induced activation (3 injections, each on every other day within the one week period) of the Cre recombinase under control of the Mx1 promoter to obtain animals with an  Abi1(fl/fl);Tg (Mx1-cre(-)) (Abi-1 WT) or Abi1(-/-);Tg (Mx1-cre(+)) (Abi-1 KO) genotype. Recombination and Abi-1 gene inactivation was confirmed in the bone marrow of 12-14 weeks old mice. LSK cells were obtained from the bone marrow samples, in which the recombination was confirmed by PCR.

extract_protocol: To isolate LSKs flushing method was used. For sorting LSKs or for frequency analysis, lineage-depleted bone marrow cells were stained with BUV395 Streptavidin, APC CD117/c-Kit (2B8), and PE.Cy7 Ly-6A/E/Sca-1 (D7) (BD Pharmingen, San Diego,CA). Total mRNA from LSK cells was purified using a PureLink RNA Mini Kit from Ambion/Life Technologies (Grand Island, NY). The Affymetrix WT Pico Expression Kit (Affymetrix, INC., Louisville, KY) was used according to the manufacturer’s instructions. The quality of the input RNA was assessed using an Agilent Bioanalyzer Picochip. Preamplification was performed on 5 ng total RNA followed by the initial reverse transcription reaction. The cDNA was converted to dsDNA, which was then amplified and converted in an in vitro transcription reaction, yielding between 25 and 75 μg purified cRNA. A 20 μg sample of cRNA was converted to 2nd cycle cDNA.

treatment_protocol: LSK cells were sorted and frozen.

value: 12-14 weeks old

value: bone marrow

value: Abi-1 WT


title: LSK cells Abi-1 WT, biological rep4


title: ECV304_IL1β_1h_rep2

city: Milano

first: Gualtiero

middle: Ivanoe

last: Colombo

address: Via Carlo Parea, 4

country: Italy

institute: Centro Cardiologico Monzino IRCCS

description: Confluent cells

hyb_protocol: 11 µg of of labeled sense DNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Human Gene 1.0 ST arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned on an Affymetrix 7G Scanner.

data_processing: Data were extracted using the Affymetrix Expression Console software. Background correction, log2 transformation, quantile normalization, and median polish probeset summarization was performed using the Robust Multi-array Average (RMA) method implemented in the RMAExpress software v1.0.5.

source_name: ECV304 endothelial cell line, IL-1β stimulated, 1 hour

label_protocol: 100 ng of total RNA were amplified and labeled according to the Whole-Transcript Sense Target Labeling Protocol by Affymetrix, without ribosomal RNA reduction.

growth_protocol: Human ECV304 endothelial cells (ECACC No. 92091712) were seeded at × 105/well in 6-well tissue-culture treated plates and grown to confluence in M199 complete medium supplemented with 10% FBS. Cells were serum starved (1% FBS) to synchronize the mitotic phase 24 h before treatment.

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

treatment_protocol: Confluent cells were then incubated for 1, 3, and 6 h with recombinant IL-1β 100 IU/ml in the presence of Aminaphtone 6 μg/ml or an equal volume of medium alone.

tag: phenotype

value: Cells exhibit both endothelial and epithelial characteristics


title: ECV304_AMNA_6h_rep3

description: Confluent cells

source_name: ECV304 endothelial cell line, IL-1β stimulated and Aminaphtone treated, 6 hour


title: ECV304_IL1β_3h_rep3

description: Confluent cells

source_name: ECV304 endothelial cell line, IL-1β stimulated, 3 hour


title: LSK cells Abi-1 WT, biological rep3


title: ECV304_AMNA_1h_rep3

description: Confluent cells

source_name: ECV304 endothelial cell line, IL-1β stimulated and Aminaphtone treated, 1 hour


title: ECV304_AMNA_6h_rep2

description: Confluent cells


title: ECV304_IL1β_1h_rep3

description: Confluent cells


title: LSK cells Abi-1 KO, biological rep2

description: LSK-enriched population of hematopoietic progenitor cells isolated via sorting from the whole bone marrow of Abi-1 KO mouse

source_name: LSK cells from bone marrow, Abi-1 KO

value: Abi-1 KO


title: ECV304_AMNA_3h_rep2

description: Confluent cells

source_name: ECV304 endothelial cell line, IL-1β stimulated and Aminaphtone treated, 3 hour


title: ECV304_IL1β_6h_rep2

description: Confluent cells

source_name: ECV304 endothelial cell line, IL-1β stimulated, 6 hour


title: ECV304_AMNA_3h_rep3

description: Confluent cells


title: ECV304_IL1β_3h_rep2

description: Confluent cells


title: LSK cells Abi-1 WT, biological rep5


title: LSK cells Abi-1 KO, biological rep3


title: ECV304_IL1β_6h_rep3

description: Confluent cells


title: ECV304_AMNA_6h_rep1

description: Confluent cells


title: LSK cells Abi-1 KO, biological rep4


title: ECV304_AMNA_1h_rep2

description: Confluent cells


title: ECV304_IL1β_6h_rep1

description: Confluent cells


title: ECV304_AMNA_1h_rep1

description: Confluent cells


title: LSK cells Abi-1 WT, biological rep2


title: ECV304_AMNA_3h_rep1

description: Confluent cells


title: ECV304_IL1β_3h_rep1

description: Confluent cells


title: MyD88 KO CD8 T cells + TLR2 ligand, Replicate 3

city: New Orleans

first: Jovanny

last: Zabaleta

state: LA

address: 1700 Tulane Ave

department: Interdisciplinary Oncology

institute: LSUHSC

description: SAMPLE 12

hyb_protocol: Hybridization using standard hybridization protocols from Illumina for 14h at 58°C

scan_protocol: Standard Illumina protocols for MouseWG-6_v2 chips from Illumina using the Illumina BeadArray Reader

data_processing: Background signal was removed using the Detection P value algorithm. Signals were normalized using the cubic spline algorithm. Differential expression was determined using the Illumina Custom Algorithm. Ratios were determined as the fraction between the treatments and the Control group

source_name: MyD88 ko CD8 T cells + TLR2 ligand

label_protocol: cRNA was labeled with the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin, TX),

growth_protocol: Cells were cultured in RPMI 1640 with FBS, isolated and expanded in vitro before being injected into mice where the accumulation in different organs was determined by flow cytometry

extract_protocol: Total RNA was extracted with TriZol

treatment_protocol: pmel T cells were stimulated with MyD88–/– splenocytes pulsed with 10ng/ml of mouse gp-100 peptide (EGSRNQDWL; GenScript Corp) at 37°C in 7% CO2 at 1:5 T cell:APC ratio while WT (C57BL/6) CD8+T cells were stimulated with plate bound anti-CD3ε (BD pmel T cells were stimulated with MyD88–/– splenocytes pulsed with 10ng/ml of mouse gp-100 peptide (EGSRNQDWL; GenScript Corp) at 37°C in 7% CO2 at 1:5 T cell:APC ratio while WT (C57BL/6) CD8+T cells were stimulated with plate bound anti-CD3ε (BD Biosciences) at 0.5µg/ml with or without the TLR1-TLR2 agonist, Pam3CSK4 (1.5µg/ml) (Invivogen). After being transfer to the mice the cells were re-stimulated by vaccinating mice (s.c, subcutaneous injection) with 100µg of hgp100 peptide admixed in IFA and 10µg CpG-ODN on day 20 after T cell transfer.

tag: cell type

value: CD8+ T lymphocytes

tag: agent

value: TLR1-TLR2 agonist, Pam3CSK4


title: LSK cells Abi-1 KO, biological rep1


title: MyD88 KO CD8 T cells + TLR2 ligand, Replicate 2

description: SAMPLE 11


title: MyD88 KO CD8 T cells + TLR2 ligand, Replicate 1

description: SAMPLE 10


title: pmel CD8 T cells + TLR2 ligand, Replicate 2

description: SAMPLE 5

source_name: pmel CD8 T cells + TLR2 ligand

value: pmel


title: MyD88 KO CD8 T cells, Replicate 1

description: SAMPLE 7

source_name: MyD88 KO CD8 T cells


title: Hippocampus_WT_Ibu_rep5

city: Stanford

first: Katrin

last: Andreasson

state: CA

address: 1201 Welch Road, MSLS P210

department: Neurology and Neurological Sciences

institute: Stanford University

hyb_protocol: Performed by the Stanford University PAN facility using the GeneChip Hybridization protocol from Affymetrix (P/N 702731)

scan_protocol: Performed by the Stanford University PAN facility using a GCS 3000 Scanner and Gene Chip Command Console software

data_processing: The data were analyzed using Partek Genomics Suite version 6.5, using RMA default settings.

source_name: Hippocampus from 6 month old C57BL/6J mice

label_protocol: Performed by the Stanford University PAN facility using the GeneChip Whole Transcript Sense Target Labeling Assay from Affymetrix (P/N 701880)

growth_protocol: This study was conducted in accordance with NIH guidelines, and protocols were approved by the Institutional Animal Care and Use Committee at Stanford University. All mice were housed in an environment controlled for lighting (12h light/dark cycle), temperature, and humidity, with food and water available ad libitum.

extract_protocol: Total RNA was isolated using Trizol followed by Qiagen RNeasy kit extraction according to the manufacturer's instructions.

treatment_protocol: Mouse chow containing ibuprofen (375 ppm) was formulated in ProLab RMH 3000 rodent chow by TestDiet (Purina Feed, Richmond, IN). APP-PS1 mice and their wild-type littermates were randomly assigned to treatment groups receiving ibuprofen-containing chow or the identical chow formulation without ibuprofen (Control) ad libitum from 3 to 6 months of age.

value: hippocampus

value: 6 months-old

value: wild-type

tag: treatment

value: chow with 375ppm ibuprofen from 3 to 6 months


title: Hippocampus_WT_Con_rep4

value: chow without additive


title: Hippocampus_WT_Con_rep3


title: pmel CD8 T cells, Replicate 1

description: SAMPLE 1

source_name: pmel CD8 T cells


title: Hippocampus_WT_Ibu_rep3


title: pmel CD8 T cells + TLR2 ligand, Replicate 1

description: SAMPLE 4


title: Hippocampus_WT_Ibu_rep4


title: pmel CD8 T cells + TLR2 ligand, Replicate 3

description: SAMPLE 6


title: MyD88 KO CD8 T cells, Replicate 2

description: SAMPLE 8


title: Hippocampus_WT_Con_rep2


title: pmel CD8 T cells, Replicate 2

description: SAMPLE 2


title: MyD88 KO CD8 T cells, Replicate 3

description: SAMPLE 9


title: nelso-00262: 4784-4768 #1423 GBM 133A 4-24-02

city: Rockville

first: Mervi

last: Heiskanen

address: 9609 Medical Center Drive, 1W378

department: CBIIT

institute: NCI

hyb_protocol: See mage-tab files linked to series entry for additional details

source_name: Brain

tag: ^sample

tag: diseasestate

value: Glioblastoma

tag: Sex

value: female

tag: celltype

value: Glia

tag: organismpart

value: Brain

tag: tumorgrading

value: Grade 4

tag: histology

value: GBM

tag: diseaselocation

value: LEFT FRONTAL TEMPORAL


title: Hippocampus_WT_Ibu_rep1

tag: tissue

tag: age

tag: strain

tag: genotype


title: Hippocampus_WT_Con_rep1


title: nelso-00262: 6944-6918 #1675 GBM 133A 6-26-02

scan_protocol: See mage-tab files linked to series entry for additional details

value: male


title: Hippocampus_WT_Ibu_rep2


title: Hippocampus_APPS_Ibu_rep1


title: Hippocampus_APPS_Ibu_rep2


title: Hippocampus_APPS_Ibu_rep4


title: Hippocampus_APPS_Con_rep4


title: Hippocampus_APPS_Con_rep2


title: Hippocampus_APPS_Ibu_rep5


title: Hippocampus_APPS_Con_rep5


title: Hippocampus_APPS_Con_rep1


title: nelso-00262: 7096-7088#1704astro133a62502

data_processing: See mage-tab files linked to series entry for additional details

value: ASTRO III 1704

value: astrocytomas

value: Grade 3

value: AA

value: RIGHT CEREBELLUM


title: nelso-00262: 10434-10425 #799 mix oligoastro III 133A 8-22-02

label_protocol: See mage-tab files linked to series entry for additional details

value: MIXED III 799

value: Glioma

value: AO

value: RIGHT FRONTAL LOBE


title: nelso-00262: 8920-8904#613oligo133a72502

extract_protocol: See mage-tab files linked to series entry for additional details

value: OLIGO III 613

value: Oligodendroglial Tumor

value: LEFT FRONTAL LOBE


title: Hippocampus_APPS_Con_rep3

value: hippocampus

value: 6 months-old

value: chow without additive


title: Hippocampus_APPS_Ibu_rep3

value: chow with 375ppm ibuprofen from 3 to 6 months


title: nelso-00262: 6928-6910 #636 GBM 133A 6-26-02

value: GBM 636

value: Glioblastoma

value: female

value: Glia

value: Brain

value: Grade 4

value: GBM

value: RIGHT TEMPORAL LOBE


title: nelso-00262: 10442-10429 #713 mix oligoastro III 133A 8-22-02

value: MIXED III 713

value: Glioma

value: Grade 3

value: AM


title: nelso-00262: 4774-4763 #706 GBM 133A 4-24-02

value: GBM 706

value: male

value: RIGHT FRONTAL TEMPORAL


title: nelso-00262: 6940-6916 #1521 GBM 133A 6-26-02

value: LEFT FRONTAL TEMPORAL


title: nelso-00262: 14633-14599 GBM #1463 133A


title: nelso-00262: 15454-15424 #1902 GBM 133A 22403

value: RIGHT FRONTAL LOBE


title: nelso-00262: 14625-14595 GBM #782 133A

value: GBM 782

value: LEFT TEMPORAL LOBE


title: pmel CD8 T cells, Replicate 3

description: SAMPLE 3

tag: genotype/variation

value: pmel

value: CD8+ T lymphocytes


title: nelso-00262: 8949-8941#587astro133a72402

value: ASTRO III 587

value: astrocytomas

value: female

value: Glia

value: Brain

value: AA

value: LEFT FRONTAL LOBE


title: nelso-00262: 6930-6911 #697 GBM 133A 6-26-02

value: GBM 697

value: Glioblastoma

value: Grade 4

value: GBM


title: nelso-00262: 6932-6912 #1038 GBM 133A 6-26-02


title: nelso-00262: 14639-14602 GBM #996 133A

value: GBM 996

value: male


title: nelso-00262: 7098-7090#672astro133a62502

value: ASTRO III 672

value: Grade 3

value: LEFT PARIETAL LOBE


title: nelso-00262: 10430-10423 #615 mix oligoastro III 133A 8-22-02

value: MIXED III 615

value: Glioma


title: nelso-00262: 10432-10424 #912 mix oligoastro III 133A 8-22-02

value: MIXED III 912

value: AM


title: nelso-00262: 4378-4377#660gbm133a41802

value: GBM 660

value: Glia


title: nelso-00262: 14623-14594 GBM #2068 133A

value: female

value: Brain


title: nelso-00262: 15428-15408 #1342 GBM 133A 22403

value: RIGHT TEMPORAL LOBE


title: nelso-00262: 15426-15407 #1511 GBM 133A 22403

value: Glioblastoma

value: RIGHT FRONTAL TEMPORAL


title: nelso-00262: 6950-6921 #1798 GBM 133A 6-26-02

value: Grade 4

value: GBM

value: LEFT FRONTAL LOBE


title: nelso-00262: 15450-15421 #2015 GBM 133A 22403

value: male

value: RIGHT FRONTAL LOBE


title: nelso-00262: 7111-7105#1804oligo133a62502

value: OLIGO III 1804

value: Oligodendroglial Tumor

value: Grade 3

value: AO


title: nelso-00262: 14621-14593 GBM #2067 133A


title: nelso-00262: 6924-6908 #839 GBM 133A 6-26-02

value: GBM 839


title: nelso-00262: 14611-14588 GBM #2028 133A


title: nelso-00262: 14635-14600 GBM #2029 133A


title: nelso-00262: 4782-4767 #1354 GBM 133A 4-24-02


title: nelso-00262: 7110-7104#975oligo133a62502

value: OLIGO III 975

value: RIGHT PARIETAL LOBE


title: nelso-00262: 4368-4367#597gbm133a41802

value: GBM 597

value: Glia


title: nelso-00262: 15440-15415 #749 GBM 133A 22403

value: GBM 749

value: Brain


title: nelso-00262: 14641-14603 oligoIII #112 133A

value: OLIGO III 744.1


title: nelso-00262: 15444-15418 #1900 GBM 133A 22403

value: Glioblastoma

value: female

value: Grade 4

value: RIGHT TEMPORAL PARIETAL LOB


title: nelso-00262: 14619-14592 oligoIII #975 133A

value: OLIGO III 975.1


title: nelso-00262: 4780-4766 #985 GBM 133A 4-24-02

value: GBM 995

value: GBM

value: RIGHT FRONTAL TEMPORAL


title: nelso-00262: 4778-4765 #976 GBM 133A 4-24-02

value: GBM 976

value: LEFT FRONTAL LOBE


title: nelso-00262: 7097-7089#1723astro133a62502

value: ASTRO III 1723

value: astrocytomas

value: Grade 3

value: AA


title: nelso-00262: 6922-6907 #824 GBM 133A 6-26-02

value: GBM 824

value: Glia

value: RIGHT TEMPORAL LOBE


title: nelso-00262: 6936-6914 #1478 GBM 133A 6-26-02

value: Glioblastoma

value: male

value: Brain


title: nelso-00262: 6934-6913 #1414 GBM 133A 6-26-02

value: female

value: Grade 4

value: RIGHT PARIETAL OCCIPITAL


title: nelso-00262: 15662-15649 #2098 GBM 133A 22603 Repeat

value: GBM

value: LEFT TEMPORAL LOBE


title: nelso-00262: 6938-6915 #1516 GBM 133A 6-26-02


title: nelso-00262: 4388-4387#1469gbm133a41802

value: LEFT FRONTAL TEMPORAL


title: nelso-00262: 10436-10426 #886 mix oligoastro III 133A 8-22-02

value: MIXED III 886

value: Glioma

value: AM


title: nelso-00262: 8947-8940#747astro133a72402

value: ASTRO III 747

value: astrocytomas

value: Grade 3

value: LEFT FRONTAL LOBE


title: nelso-00262: 4770-4761 #585 GBM 133A 4-24-02

value: GBM 585

value: Glia

value: LEFT TEMPORAL PARIETAL LOB


title: nelso-00262: 15432-15410 #932 GBM 133A 22403

value: GBM 932

value: Glioblastoma

value: Brain

value: RIGHT FRONTAL LOBE


title: nelso-00262: 4772-4762 #604 GBM 133A 4-24-02

value: GBM 604

value: male

value: Grade 4

value: GBM

value: LEFT PARIETAL OCCIPITAL


title: nelso-00262: 7093-7085#659astro133a62502

value: ASTRO III 659

value: female

value: AA


title: nelso-00262: 15438-15414 #1022 GBM 133A 22403


title: nelso-00262: 15430-15409 #1032 GBM 133A 22403

value: RIGHT TEMPORAL PARIETAL LOB


title: nelso-00262: 15442-15417 #712 GBM 133A 22403

value: GBM 712


title: nelso-00262: 15448-15420 #2013 GBM 133A 22403

value: RIGHT ANTERIOR TEMPORAL LOBE


title: nelso-00262: 4786-4769 #1495 GBM 133A 4-24-02

value: Glia

value: RIGHT FRONTAL TEMPORAL


title: nelso-00262: 10219-10218 #1656 GBM 133A 8-13-02


title: nelso-00262: 7114-7108#742oligo133a62502

value: OLIGO III 742

value: Oligodendroglial Tumor

value: Grade 3

value: AO

value: LEFT FRONTAL LOBE


title: nelso-00262: 14629-14597 GBM #1043 133A

value: Glioblastoma

value: Brain

value: LEFT FRONTAL TEMPORAL


title: nelso-00262: 10440-10428 #664 mix oligoastro III 133A 8-22-02

value: MIXED III 664

value: Glioma

value: AM


title: ECV304_IL1β_1h_rep1

description: Confluent cells

tag: cell line

tag: phenotype

value: Cells exhibit both endothelial and epithelial characteristics


title: nelso-00262: 14605-14585 GBM #1334 133A

value: female

value: Grade 4

value: GBM


title: nelso-00262: 14631-14598 GBM #1398 133A

value: Glia


title: nelso-00262: 14627-14596 oligoIII #840 133A

value: OLIGO III 840


title: nelso-00262: 6948-6920 #1745 GBM 133A 6-26-02

value: RIGHT FRONTAL PARIETAL


title: nelso-00262: 6946-6919 #1681 GBM 133A 6-26-02

value: male

value: LEFT THALAMIC


title: nelso-00262: 7095-7087#1425astro133a62502

value: ASTRO III 1425

value: astrocytomas

value: Grade 3

value: AA

value: LEFT TEMPORAL LOBE


title: nelso-00262: 4776-4764 #931 GBM 133A 4-24-02

value: GBM 931

value: Glioblastoma

value: Brain

value: RIGHT FRONTAL LOBE


title: nelso-00262: 8928-8908#1433oligo133a72402

value: OLIGO III 1433

value: Oligodendroglial Tumor

value: AO


title: nelso-00262: 15456-15425 #2079 GBM 133A 22403

value: Glia

value: Grade 4

value: GBM

value: RIGHT TEMPORAL PARIETAL LOB


title: nelso-00262: 7113-7107#695oligo133a62502

value: OLIGO III 695

value: female

value: LEFT PARIETAL LOBE


title: nelso-00262: 14643-14604 GBM #1028 133A

value: RIGHT PARIETAL LOBE


title: nelso-00262: 10438-10427 #1721 mix oligoastro III 133A 8-22-02

value: MIXED III 1721

value: Glioma

value: Grade 3

value: AA


title: nelso-00262: 15446-15419 #1905 GBM 133A 22403

value: Glioblastoma

value: male

value: Brain

value: LEFT TEMPORAL LOBE


title: nelso-00262: 15434-15411 #746 GBM 133A 22403

value: GBM 746

value: LEFT FRONTAL LOBE


title: nelso-00262: 15479-15471 #1544 GBM 133A 22603

value: Glia

value: Grade 4

value: LEFT FRONTAL TEMPORAL


title: Normal skin tissue 1

city: Wuhan

first: Guozheng

last: Xu

state: Hubei

address: 627 Wuluo Street

department: Department of Neurosurgery

institute: Wuhan General Hospital of Guangzhou Military Command of Chinese PLA

description: Gene expression in normal skin tissue

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human lncRNA（4*180K）for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: Earlobe piercing

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

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556 ) following the manufacturer's instructions

value: 21 years old

tag: gender

value: Female

tag: history of keloid

value: 10 months


title: nelso-00262: 14607-14586 GBM #1406 133A

tag: ^sample

value: GBM


title: CESCs cultured in osteogenic induction medium under normoxia

city: Chongqing

first: Yuan

last: Yao

address: 83 Xinqiao Street, District of Shapingba

institute: Xinqiao Hospital, Third Military Medical University

description: Gene expression data from osteogenic differentiated CESCs under normoxia

hyb_protocol: After fragmentation, 5 ug cDNA were hybridized for 16hr at 45C in 60rpm of spanning on Human Transcriptome Array 2.0. The microarray was washed and stained using Affymetrix GeneChip Command Console (AGCC) software

scan_protocol: The microarray was scanned using AGCC software.

data_processing: We used Expression Console software to pre-treat .CEL files through Robust Multichip Analysis (RMA) algorithm (3), including background correction, probeset signal integration, quantile normalization. After pretreatment, the obtained chp files were analyzed by Transcriptome Analysis Console software to identify differentially expressed genes (DEGs) and alternatively spliced genes (ASGs).

source_name: Osteogenic differentiated CESCs under normoxia

label_protocol: Fragmented single-stranded DNA was labeled using DNA labeling reagent according to standard Affymetrix protocol.

growth_protocol: CESCs were isolated from the human cartilage endplate and cultured at 37C and 5% CO2 condition. The cells within 3 passages were used in this study.

treatment_protocol: CESCs were cultured in the osteogenic induction medium for 21 days under hypoxia and normoxia respectively.

tag: cell type

value: Osteogenic differentiated CESCs


title: nelso-00262: 15452-15422 #2158 GBM 133A 22403

tag: diseasestate

tag: Sex

value: female

value: RIGHT TEMPORAL LOBE


title: Normal skin tissue 2

description: Gene expression in normal skin tissue

value: 34 years old

value: 14 months


title: CESCs cultured in osteogenic induction medium under hypoxia

description: Gene expression data from osteogenic differentiated CESCs under hypoxia

source_name: Osteogenic differentiated CESCs under hypoxia


title: Earlobe keloid tissue 1

description: Gene expression in earlobe keloid tissue


title: Earlobe keloid tissue 2


title: Earlobe keloid tissue 3

value: 24 years old

value: 17 months


title: nelso-00262: 14609-14587 GBM #2017 133A

value: Glioblastoma

value: male

tag: celltype

tag: organismpart

value: Brain

value: LEFT TEMPORAL LOBE


title: nelso-00262: 7099-7091#671astro133a62502

value: ASTRO III 671

value: astrocytomas

value: Glia

tag: tumorgrading

value: Grade 3

tag: histology

value: AA

value: RIGHT FRONTAL LOBE


title: nelso-00262: 10735-10730 #1667 GBM 133A 82702 Repeat

value: Grade 4

value: GBM

tag: diseaselocation

value: RIGHT FRONTAL PARIETAL


title: nelso-00262: 7115-7109#744oligo133a62502

value: OLIGO III 744

value: Oligodendroglial Tumor

tag: age

value: AO

value: LEFT FRONTAL LOBE


title: nelso-00262: 6926-6909 #2166 GBM 133A 6-26-02

value: Glioblastoma

value: female


title: Control newborn skin epidermis replicate 2

city: Beer Sheva

first: Idan

last: Cohen

address: David Ben Gurion Blvd 1

department: Microbiology, Immunology and Genetics

institute: Ben-Gurion University

description: Biological replicate 2 of 4. Newborn skin epidermis, Control.

hyb_protocol: 300ng of labeled sample was fragmented and hybridized against 300ng of labeled Universal Mouse Reference RNA on SurePrint G3 Mouse GE 8X60K microarrays (Agilent) for 17 hours at 65°C in a rotating hybridization oven (Agilent). Following hybridization, microarrays were washed with GE wash buffer 1 (Agilent) for 1 min at room temperature and with GE wash buffer 2 (Agilent) at 37°C for 1 min.

scan_protocol: SureScan Microarray Scanner (Agilent Technologies).

data_processing: The scanned images were analyzed with Agilent Feature Extraction v.12.0.1.1 Software (protocol GE2_1200_Jun14) and analyzed using GeneSpring software v13.0 software (Agilent Technologies).

source_name: P0 skin epidermis, control

label_protocol: RNA samples (100ng of total RNA ) were amplified and labeled using the Low Input Quick Amp Labeling Kit (Agilent Technologies, USA).

growth_protocol: Newborn back-skins were incubated in 1.26U/ml dispase (Invitrogen) for 4-5 hours at 4°C. The epidermis was gently peeled off from the dermis, and washed twice with phosphate-buffered saline.  Epidermal cells were dissociated by treatment in 0.25% trypsin (Cellgro Mediatech) for 10, dissociated keratinocytes were washed twice with phosphate-buffered saline

extract_protocol: Total RNA was purified with the RNeasy ® Plus mini Kit (QIAGEN)

treatment_protocol: No treatment

tag: strain

value: P0 Newborn

tag: tissue

value: Epidermis

value: CTL

source_name: Universal Mouse Reference RNA (Agilent Technologies)

tag: sample type

value: Universal Mouse Reference RNA


title: Control newborn skin epidermis replicate 4

description: Biological replicate 4 of 4. Newborn skin epidermis, Control.

tag: genotype/variation


title: nelso-00262: 8912-8900#650oligo133a72502

value: OLIGO III 650

value: Glia

value: Brain


title: Control newborn skin epidermis replicate 3

description: Biological replicate 3 of 4. Newborn skin epidermis, Control.


title: Control newborn skin epidermis replicate 1

description: Biological replicate 1 of 4. Newborn skin epidermis, Control.


title: Eed conditional KO skin epidermis replicate 4

description: Biological replicate 4 of 4. Newborn skin epidermis, Eed conditional KO.

source_name: P0 skin epidermis, Eed conditional KO

value: Eed cKO


title: Normal skin tissue 3

description: Gene expression in normal skin tissue

value: 24 years old

value: Female

value: 17 months


title: nelso-00262: 14617-14591 GBM #938 133A

value: GBM 938

value: male

value: Grade 4

value: GBM


title: nelso-00262: 4785-4768 #1423 GBM 133B 4-29-02

value: Glioblastoma

value: LEFT FRONTAL TEMPORAL


title: nelso-00262: 8921-8904#613 oligo 133b 8502

value: OLIGO III 613

value: Oligodendroglial Tumor

value: female

value: Grade 3

value: AO

value: LEFT FRONTAL LOBE


title: nelso-00262: 10435-10425 #799 mix oligoastro III 133B 8-23-02

value: MIXED III 799

value: Glioma

value: Glia

value: Brain

value: RIGHT FRONTAL LOBE


title: nelso-00262: 7189-7181#1704astro133b62602

value: ASTRO III 1704

value: astrocytomas

value: AA

value: RIGHT CEREBELLUM


title: nelso-00262: 6945-6918 #1675 GBM 133b 6-28-02

value: Glioblastoma

value: male

value: Grade 4

value: GBM


title: nelso-00262: 6929-6910 #636 GBM 133b 6-28-02

value: GBM 636

value: female

value: RIGHT TEMPORAL LOBE


title: nelso-00262: 10443-10429 #713 mix oligoastro III 133B 8-23-02

value: MIXED III 713

value: Grade 3

value: AM

value: LEFT FRONTAL LOBE


title: nelso-00262: 6941-6916 #1521 GBM 133b 6-28-02

value: Glia

value: Brain

value: LEFT FRONTAL TEMPORAL


title: nelso-00262: 4775-4763 #706 GBM 133B 4-29-02

value: GBM 706

value: RIGHT FRONTAL TEMPORAL


title: Eed conditional KO skin epidermis replicate 3

description: Biological replicate 3 of 4. Newborn skin epidermis, Eed conditional KO.

value: P0 Newborn

value: Epidermis

value: Eed cKO

value: Universal Mouse Reference RNA


title: knockout Th9 cells

city: SHANGHAI

first: Guangwei

last: Liu

state: SHANGHAI

address: DONGANROAD 130

department: Immunity

institute: Fudan University

description: Gene expression after 5 day induction with TH9-inducing codition

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, genes that at least 1 out of 2 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes with statistical significance between the two groups were identified through Volcano Plot filtering. Differentially expressed genes between the two samples were identified through Fold Change filtering. Hierarchical Clustering was performed using the R scripts. GO analysis and Pathway analysis were performed in the standard enrichment computation method.

source_name: Peripheral CD4+T lymph cells

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). Briefly, total RNA from each sample was linearly amplified and labeled with Cy3-UTP. The Labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: Lymphocytes were isolated from the spleen and lymph nodes of mice and sorted on a FACSAria II (Becton Dickinson). The sorted naïve T cells (CD4+TCR+CD62Lhi CD44lo) from WT or SIRT1flox/flox-CD4-Cre mice were used for in vitro culture. T cells were activated with 2 ug/ml anti-CD3 (2C11; Bio X Cell), 2 ug/ml anti-CD28 (37.51; Bio X Cell) and 100 U/ml human IL-2. For TH9 cell differentiation, cultures were supplemented with 10 ng/ml IL-4 (R&D system), 2 ng/ml TGFβ1 (R&D system). After 5-6 d culture, differentiated T cells were collected and for microarray assay.

tag: genotype

value: spleen and lymph node


title: wild-type Th9 cells

value: wild-type


title: Npl3 IP 25°C

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

hyb_protocol: Affymetrix Hybridization Oven 645, Affymetrix Wash and stain Kit, Gene Chip Fluidics Station 450, Wash Protocol Yeast 2

scan_protocol: Affymetrix Gene Chip Scanner AGCC Scan control

data_processing: CEL files were processed with R/BioConductor using the 'affy' package.

organism: Saccharomyces cerevisiae

source_name: HKY157 Cell lysate, Npl3 IP 25°C

label_protocol: 3' IVT Expess Kit,  Affymetrix Gene Chip WT Terminal Labeling and Hybridization User Manual(PN702880)

growth_protocol: Yeast cells were grown at 25°C in YPD full medium to log phase. Cells were splitted into two parts and collected by centrifugation. Pellets were resuspended in 50mL YPD medium and incubated either at 25°C or 42°C in a petri dish for 30 min.  After subsequent UV cross-linking cells were harvested and further porcessed by RNA Co Immunoprecipitation (IP).

extract_protocol: Eluates were purified via trizol-chloroform (Ambion® RNA by Life technologies™) extraction.

treatment_protocol: RNA Co-IP: cell pellets were washed in 1 ml RIP buffer (50 mM Tris-HCl, pH 7.5, 150 mM NaCl, 0,2 % (v/v) Triton X-100, 2 mM DTT, 10 U RiboLockTM RNase Inhibitor (Thermo Scientific)). One volume of the pellet was mixed with 1.5 volumes of RIP buffer, containing EDTA-free Protease inhibitor cocktail (Roche) and one volume of glass beads. Cells were lysed by vigorous mixing for 30 sec at 4 m/s using the FastPrep®-24 machine (MP Biomedicals).Co-immunoprecipitation experiments were performed at 4°C for 4h by incubating the lysates with Protein G sepharose beads (Amersham Biosciences) bound to monoclonal c-myc (9E10) antibody (Santa Cruz) and GFP-Trap beads (Chromotek). Afterwards beads were washed five times with RIP buffer.


title: No tag control 42°C

source_name: HKY36/381 Cell lysate, No tag control 42°C


title: Mex67 IP 25°C

source_name: HKY1266 Cell lysate, Mex67 IP 25°C


title: Eed conditional KO skin epidermis replicate 1

description: Biological replicate 1 of 4. Newborn skin epidermis, Eed conditional KO.


title: Mex67 IP 42°C

source_name: HKY1266 Cell lysate, Mex67 IP 42°C


title: nelso-00262: 15429-15408 #1342 GBM 133B 22603

value: Glioblastoma

value: male

value: Grade 4

value: GBM


title: Npl3 IP 42°C

source_name: HKY157 Cell lysate, Npl3 IP 42°C


title: Eed conditional KO skin epidermis replicate 2

description: Biological replicate 2 of 4. Newborn skin epidermis, Eed conditional KO.


title: PCC6803_WT_+NH4_0h_iron depletion_2

city: Freiburg

first: Jens

last: Georg

address: Schänzlestr. 1

institute: University of Freiburg

description: WT

hyb_protocol: The labelled RNA was fragmented and hybridized as described by the manufacturer's instructions for Agilent one color microarrays with 1.65 µg of labeled RNA

scan_protocol: Arrays were scanned on the Agilent Technologies Scanner G2505C US90900275, using Agilent Feature Extraction Software 10.7.3.1 and the protocols GE1_107_Sep09  for Cy3 labelled arrays

data_processing: Raw data were processed with the R package Limma. Normexp background substraction with an offset of 50 and cyclicloess normalization was aplied to median signal intensities.

organism: Synechocystis sp. PCC 6803

source_name: PCC6803_WT_+NH4_0h_iron depletion

label_protocol: The RNA was labeled directly, without cDNA synthesis in 2 µg aliquots with the Kreatech “ULS labeling kit for Agilent gene expression arrays” with Cy3 according to the manufacturers protocol.

growth_protocol: The previously described FtsH3down (originally termed SynFtsH3reg (Boehm et al., 2012)), FtsH2-less (ΔFtsH2) (Komenda et al., 2006), FtsH1down (Krynicka et al., 2014) strains as well as the wild type strain used for the control were derived from the non-motile glucose-tolerant Synechocystis sp. PCC 6803 strain obtained from the laboratory of Wim Vermaas. FtsH3down and its respective control (WT) were cultivated photoautotrophically in the presence of ammonium ions as described in Boehm (2012). To deplete iron, cells were transferred to iron depleted medium (residual concentration of iron about 5 µM) supplemented 10 μM deferoxamin B (DFB), an iron chelator, at an irradiance of 40 µmol photons m-2 s-1 of white light (Krynicka et al., 2014).

extract_protocol: WT and FtsH3down cultures were harvested by rapid filtration on hydrophilic polyethersulfone filters (Pall Supor 800 Filter, 0.8 mm). The filter covered with cells was immediately immersed in 1 ml of PGTX solution (Pinto et al., 2009) and frozen in liquid nitrogen.

treatment_protocol: To deplete iron, cells were transferred to iron depleted medium (residual concentration of iron about 5 µM) supplemented 10 μM deferoxamin B (DFB), an iron chelator for 24h.

value: WT


title: PCC6803_WT_+NH4_24h_iron depletion_2

source_name: PCC6803_WT_+NH44h_iron depletion


title: No tag control IP 25°C

source_name: HKY36/381 Cell lysate, No tag control IP 25°C


title: nelso-00262: 14626-14595 GBM #782 133B repeat

value: GBM 782

value: female

value: LEFT TEMPORAL LOBE


title: nelso-00262: 6931-6911 #697 GBM 133b 6-28-02

value: GBM 697

value: Glia

value: Brain

value: RIGHT FRONTAL LOBE


title: nelso-00262: 6933-6912 #1038 GBM 133b 6-28-02


title: PCC6803_WT_+NH4_24h_iron depletion_1


title: PCC6803_FtsHdown_+NH4_0h_iron depletion_2

source_name: PCC6803_FtsHdown_+NH4_0h_iron depletion


title: PCC6803_FtsHdown_+NH4_24h_iron depletion_2

source_name: PCC6803_FtsHdown_+NH44h_iron depletion


title: PCC6803_FtsHdown_+NH4_24h_iron depletion_1


title: PCC6803_FtsHdown_+NH4_0h_iron depletion_1


title: PCC6803_WT_+NH4_0h_iron depletion_1

description: WT


title: nelso-00262: 7191-7183#672astro133b62602

source_name: Brain

value: ASTRO III 672

value: astrocytomas

value: Grade 3

value: AA

value: LEFT PARIETAL LOBE


title: nelso-00262: 14640-14602 GBM #996 133B

value: GBM 996

value: Glioblastoma

value: LEFT FRONTAL LOBE


title: nelso-00262: 10433-10424 #912 mix oligoastro III 133B 8-23-02

value: MIXED III 912

value: Glioma

value: AM


title: nelso-00262: 10431-10423 #615 mix oligoastro III 133B 8-23-02

value: MIXED III 615

value: female


title: nelso-00262: 14624-14594 GBM #2068 133B

value: Grade 4

value: GBM


title: nelso-00262: 4408-4407#660 gbm 133b 41902

value: GBM 660

value: male

value: Glia

value: Brain


title: nelso-00262: 6951-6921 #1798 GBM 133b 6-28-02


title: nelso-00262: 14622-14593 GBM #2067 133B


title: nelso-00262: 8950-8941#587astro133b73102

value: ASTRO III 587

value: astrocytomas

value: Grade 3


title: nelso-00262: 15451-15421 #2015 GBM 133B 22603

value: RIGHT FRONTAL LOBE


title: nelso-00262: 15427-15407 #1511 GBM 133B 22603

value: Glioblastoma

value: RIGHT FRONTAL TEMPORAL


title: nelso-00262: 7213-7207#1804oligo133b62602

value: OLIGO III 1804

value: Oligodendroglial Tumor

value: AO

value: LEFT FRONTAL LOBE


title: nelso-00262: 15455-15424 #1902 GBM 133B 22603

value: female


title: nelso-00262: 4783-4767 #1354 GBM 133B 4-29-02

value: Grade 4


title: VT_Term_5_miRNA

type: SRA

city: Columbus

first: William

middle: Edward

last: Ackerman IV

state: Ohio

address: N521 Doan Hall, 410 West 10th Avenue

department: Obstetrics and Gynecology

library_source: transcriptomic

data_processing:
Adapter sequences from the small-RNA-Seq libraries were removed using Cutadapt version 1.4.1.
Trimmed reads were mapped to the miRBase 21 database and tabulated using miRExpress version 2.0.
Genome_build: miRBase 21
Supplementary_files_format_and_content: Tab-delimited text file of raw (non-normalized) read counts for miRNAs.

source_name: Villous trophoblast, placenta

extract_protocol:
Individual paired placental specimens (basal plate decidua basalis and villous trophoblast biopsies) were flash frozen in liquid nitrogen in the Operating Room and stored at -80°C for RNA studies. Total RNA was isolated using TRIzol reagent (Life Technologies, Grand Island, NY, USA) per the manufacturer's recommendations. Total RNA integrity was initially assessed by agarose gel electrophoresis with ethidium bromide labeling in the presence of Protector RNase Inhibitor (Roche) to visualize intact 28S and 18S rRNA bands. The RNA was further purified using an RNA Clean-Up and Concentration Kit (Norgen Biotek, Thorold, Ontario, Canada) prior to sequencing.
Small RNA-Seq libraries were generated using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs, Ipswich, MA), according to the manufacturer's protocols. In brief, 300 ng total RNA (as determined by the Qubit RNA assay, Life Technologies) with an RNA Quality Score > 7 (as determined by the LabChip GX Microfluidics Electrophoresis system, PerkinElmer, Waltham, MA) was used to prepare sequencing libraries. The small RNAs were targeted with modified Illumina-compatible 3’ and 5' adaptors and a reverse transcription primer. Next, first strand synthesis was achieved using Protoscript II Reverse Transcriptase (New England Biolabs), followed by 15 cycles of PCR amplification. The small RNA-Seq libraries were then assessed for relative amounts of micro RNAs (miRNAs) and piwi-interacting RNAs (piRNAs) migrating between 140 to 160 bp using the LabChip GX DNA assay (PerkinElmer). DNA concentrations were assessed using the Qubit fluorometer. Information from the LabChip and Qubit assays allowed pooling of samples prior to size selection using the Pippin Prep system (Sage Science, Beverly, MA). The profile of the combined size-selected libraries was ascertained using the LabChip GX DNA assay. Each pooled library was then sequenced together with other samples tagged with compatible barcodes within a single channel of an Illumina single-read 50 bp flow cell, using the Illumina HiSeq 2500 platform.

value: placenta

tag: tissue compartment

value: Villous trophoblast

tag: gestational age

value: 38.7 weeks gestation

tag: fetal gender

value: Male fetus

tag: diagnosis

value: normal


title: VT_Term_4_miRNA

value: 39.1 weeks gestation


title: nelso-00262: 14612-14588 GBM #2028 133B

tag: ^sample

tag: diseasestate

value: Glia

value: Brain

value: GBM


title: nelso-00262: 6925-6908 #839 GBM 133b 6-28-02

value: GBM 839

value: Glioblastoma

tag: Sex

value: male

tag: celltype

value: RIGHT TEMPORAL LOBE


title: VT_iPTB_4_miRNA

value: 32 weeks gestation

value: preterm birth


title: VT_Term_2_miRNA

value: Female fetus


title: VT_Term_1_miRNA


title: VT_iPTB_2_miRNA

value: 33 weeks gestation


title: nelso-00262: 15441-15415 #749 GBM 133B 22603

value: GBM 749

tag: organismpart

tag: tumorgrading

value: Grade 4

value: RIGHT PARIETAL LOBE


title: nelso-00262: 14636-14600 GBM #2029 133B

value: female

tag: histology

tag: diseaselocation

value: LEFT FRONTAL LOBE


title: nelso-00262: 7212-7206#975oligo133b62602

value: OLIGO III 975

value: Oligodendroglial Tumor

tag: age

value: Grade 3

value: AO


title: VT_iPTB_5_miRNA

tag: tissue

value: placenta

value: Villous trophoblast

value: 32.7 weeks gestation


title: VT_iPTB_1_miRNA

value: 29.9 weeks gestation

value: Male fetus


title: VT_iPTB_3_miRNA

value: 30.6 weeks gestation

value: preterm birth


title: VT_IAI_5_miRNA

value: 25.6 weeks gestation

value: Female fetus


title: nelso-00262: 4398-4397#597 gbm 133b 41902

value: GBM 597

value: Glioblastoma

value: male

value: Glia

value: Brain

value: Grade 4

value: GBM


title: nelso-00262: 14634-14599 GBM #1463 133B

value: RIGHT TEMPORAL LOBE


title: VT_IAI_4_miRNA

value: placenta

value: 31.4 weeks gestation


title: VT_IAI_3_miRNA

value: Villous trophoblast

value: 25.4 weeks gestation


title: nelso-00262: 4779-4765 #976 GBM 133B 4-29-02

value: GBM 976

value: female

value: LEFT FRONTAL LOBE


title: VT_Term_3_miRNA

value: 39.3 weeks gestation

value: Male fetus

value: normal


title: DB_Term_5_miRNA

source_name: Basal plate decidual basalis, placenta

value: Basal plate decidual basalis

value: 38.7 weeks gestation


title: nelso-00262: 4781-4766 #985 GBM 133B 4-29-02

value: GBM 995

value: Glioblastoma

value: Glia

value: RIGHT FRONTAL TEMPORAL


title: nelso-00262: 7190-7182#1723astro133b62602

value: ASTRO III 1723

value: astrocytomas

value: Brain

value: Grade 3

value: AA


title: VT_IAI_1_miRNA

value: placenta

value: Villous trophoblast

value: 26 weeks gestation

value: Female fetus

value: preterm birth


title: DB_Term_4_miRNA

value: 39.1 weeks gestation

value: Male fetus

value: normal


title: nelso-00262: 6923-6907 #824 GBM 133b 6-28-02

value: GBM 824

value: female

value: Grade 4

value: GBM

value: RIGHT TEMPORAL LOBE


title: nelso-00262: 15445-15418 #1900 GBM 133B 22603

value: Glioblastoma

value: Glia

value: RIGHT TEMPORAL PARIETAL LOB


title: nelso-00262: 6937-6914 #1478 GBM 133b 6-28-02

value: male

value: Brain

value: LEFT FRONTAL LOBE


title: nelso-00262: 4773-4762 #604 GBM 133B 4-29-02

value: GBM 604

value: LEFT PARIETAL OCCIPITAL


title: DB_Term_1_miRNA

value: placenta

value: Basal plate decidual basalis

value: Female fetus


title: DB_iPTB_4_miRNA

value: 32 weeks gestation

value: Male fetus

value: preterm birth


title: nelso-00262: 14620-14592 oligoIII #975 2nd 133B

value: OLIGO III 975.1

value: Oligodendroglial Tumor

value: female

value: Grade 3

value: AO

value: RIGHT PARIETAL LOBE


title: DB_iPTB_5_miRNA

value: 32.7 weeks gestation


title: nelso-00262: 6939-6915 #1516 GBM 133b 6-28-02

value: Glioblastoma

value: Glia

value: Brain

value: Grade 4

value: GBM


title: nelso-00262: 8948-8940#747astro133b73102

value: ASTRO III 747

value: astrocytomas

value: AA

value: LEFT FRONTAL LOBE


title: nelso-00262: 15663-15649 #2098 GBM 133B 22603

value: male

value: LEFT TEMPORAL LOBE


title: DB_Term_2_miRNA

value: placenta

value: Basal plate decidual basalis

value: 39.1 weeks gestation

value: Female fetus

value: normal


title: nelso-00262: 14642-14603 oligoIII #112 133B

value: OLIGO III 744.1

value: Oligodendroglial Tumor

value: Grade 3

value: AO


title: nelso-00262: 15439-15414 #1022 GBM 133B 22603

value: Glioblastoma

value: Glia

value: Brain

value: Grade 4


title: VT_IAI_2_miRNA

value: Villous trophoblast

value: 27.1 weeks gestation

value: preterm birth


title: nelso-00262: 4418-4417#1469 gbm 133b 41902

value: male

value: GBM

value: LEFT FRONTAL TEMPORAL


title: nelso-00262: 15431-15409 #1032 GBM 133B 22603

value: female

value: RIGHT TEMPORAL PARIETAL LOB


title: DB_iPTB_2_miRNA

value: placenta

value: Basal plate decidual basalis

value: 33 weeks gestation

value: Female fetus


title: DB_iPTB_1_miRNA

value: 29.9 weeks gestation

value: Male fetus


title: nelso-00262: 15443-15417 #712 GBM 133B 22603

value: GBM 712

value: Glioblastoma

value: Glia

value: RIGHT FRONTAL LOBE


title: DB_IAI_4_miRNA

value: 31.4 weeks gestation


title: DB_IAI_3_miRNA

value: 25.4 weeks gestation

value: preterm birth


title: nelso-00262: 4771-4761 #585 GBM 133B 4-29-02

value: GBM 585

value: Brain

value: Grade 4

value: GBM

value: LEFT TEMPORAL PARIETAL LOB


title: DB_Term_3_miRNA

value: placenta

value: Basal plate decidual basalis

value: 39.3 weeks gestation

value: normal


title: nelso-00262: 7186-7178#659astro133b62602

value: ASTRO III 659

value: astrocytomas

value: female

value: Grade 3

value: AA

value: LEFT FRONTAL LOBE


title: DB_IAI_1_miRNA

value: 26 weeks gestation

value: Female fetus


title: DB_IAI_2_miRNA

value: 27.1 weeks gestation

value: preterm birth


title: VT_Term_5

data_processing:
Long RNA reads were subjected to low quality read and adapter trimming using Trim Galore version 0.3.2.
Long RNA reads were mapped to the University of California Santa Cruz hg38 human genome assembly using TopHat2 version 2.0.11.
Raw read counts were generated using HTseq version 0.5.3p3 with the hg38_UCSC_alt.gtf file.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text file of raw (non-normalized) read counts.

extract_protocol:
Individual paired placental specimens (basal plate decidua basalis and villous trophoblast biopsies) were flash frozen in liquid nitrogen in the Operating Room and stored at -80°C for RNA studies. Total RNA was isolated using TRIzol reagent (Life Technologies, Grand Island, NY, USA) per the manufacturer's recommendations. Total RNA integrity was initially assessed by agarose gel electrophoresis with ethidium bromide labeling in the presence of Protector RNase Inhibitor (Roche) to visualize intact 28S and 18S rRNA bands. The RNA was further purified using an RNA Clean-Up and Concentration Kit (Norgen Biotek, Thorold, Ontario, Canada) prior to sequencing.
Long total RNA-Seq libraries were constructed using the TruSeq Stranded Total RNA Sample Prep Kit with Ribo-Zero Gold (Illumina, San Diego, CA). The Ribo-Zero kit was utilized to remove contaminating ribosomal RNA and mitochondrial RNA while retaining both coding and non-coding long RNAs in the subsequent libraries. A Qubit 2.0 fluorometer (Life Technologies) and BioAnalyzer 2100 system (Agilent, Santa Clara, CA) were used to select transcripts of appropriate mass and insert size. The Illumina HiSeq 2500 system and HiSeq version 3 sequencing reagents were used to generate 50 bp single-end reads. Automated clonal amplification was accomplished using the cBOT system (Illumina) using Illumina HiSeq version 3 cluster generation reagents to achieve a target density of approximately 800,000/mm^2 in a single flow cell channel. Image analysis, base calling, and error estimation was performed using Illumina Analysis Pipeline in HiSeq Control Software version 2.2.38.

value: Villous trophoblast

value: 38.7 weeks gestation

value: Male fetus


title: nelso-00262: 6935-6913 #1414 GBM 133b 6-28-02

value: Glioblastoma

value: Glia

value: Brain

value: Grade 4

value: GBM

value: RIGHT PARIETAL OCCIPITAL


title: DB_iPTB_3_miRNA

value: placenta

value: Basal plate decidual basalis

value: 30.6 weeks gestation


title: VT_Term_4

value: 39.1 weeks gestation

value: normal


title: nelso-00262: 7216-7210#742oligo133b62602

value: OLIGO III 742

value: Oligodendroglial Tumor

value: male

value: Grade 3

value: AO

value: LEFT FRONTAL LOBE


title: nelso-00262: 4787-4769 #1495 GBM 133B 4-29-02

value: Glioblastoma

value: female

value: RIGHT FRONTAL TEMPORAL


title: nelso-00262: 14630-14597 GBM #1043 133B

value: Glia

value: Brain

value: Grade 4

value: LEFT FRONTAL TEMPORAL


title: nelso-00262: 10441-10428 #664 mix oligoastro III 133B 8-23-02

value: MIXED III 664

value: Glioma

value: AM


title: DB_IAI_5_miRNA

value: placenta

value: Basal plate decidual basalis

value: 25.6 weeks gestation

value: Female fetus

value: preterm birth


title: nelso-00262: 10437-10426 #886 mix oligoastro III 133B 8-23-02

value: MIXED III 886

value: male

value: Grade 3

value: RIGHT TEMPORAL LOBE


title: VT_Term_3

value: Villous trophoblast

value: 39.3 weeks gestation

value: Male fetus

value: normal


title: VT_iPTB_4

value: 32 weeks gestation


title: VT_iPTB_5

value: 32.7 weeks gestation


title: VT_Term_2

value: 39.1 weeks gestation


title: nelso-00262: 15449-15420 #2013 GBM 133B 22603

value: Glioblastoma

value: female

value: Glia

value: Brain

value: Grade 4

value: GBM

value: RIGHT ANTERIOR TEMPORAL LOBE


title: nelso-00262: 4777-4764 #931 GBM 133B 4-29-02

value: GBM 931

value: RIGHT FRONTAL LOBE


title: VT_iPTB_3

value: placenta

value: 30.6 weeks gestation

value: preterm birth


title: nelso-00262: 15433-15410 #932 GBM 133B 22603

value: GBM 932


title: VT_iPTB_2

value: Villous trophoblast

value: 33 weeks gestation

value: Female fetus


title: nelso-00262: 14608-14586 GBM #1406 133B

value: male

value: LEFT FRONTAL LOBE


title: nelso-00262: 14632-14598 GBM #1398 133B

value: Glioblastoma

value: female

value: LEFT FRONTAL TEMPORAL


title: VT_iPTB_1

value: 29.9 weeks gestation

value: Male fetus


title: VT_IAI_5

value: 25.6 weeks gestation


title: nelso-00262: 14606-14585 GBM #1334 133B

value: Glia

value: Brain

value: Grade 4

value: GBM


title: nelso-00262: 6949-6920 #1745 GBM 133b 6-28-02

value: RIGHT FRONTAL PARIETAL


title: VT_IAI_3

value: placenta

value: 25.4 weeks gestation

value: preterm birth


title: VT_IAI_4

value: Villous trophoblast

value: 31.4 weeks gestation

value: Female fetus


title: nelso-00262: 10220-10218 #1656 GBM 133 B 8-16-02

value: Glioblastoma

value: male

value: RIGHT FRONTAL LOBE


title: VT_IAI_2

value: 27.1 weeks gestation


title: nelso-00262: 7188-7180#1425astro133b62602

value: ASTRO III 1425

value: astrocytomas

value: Grade 3

value: AA

value: LEFT TEMPORAL LOBE


title: VT_IAI_1

value: 26 weeks gestation


title: nelso-00262: 7215-7209#695oligo133b62602

value: OLIGO III 695

value: Oligodendroglial Tumor

value: female

value: Glia

value: Brain

value: AO

value: LEFT PARIETAL LOBE


title: DB_Term_5

value: placenta

value: Basal plate decidual basalis

value: 38.7 weeks gestation

value: Male fetus

value: normal


title: DB_Term_4

value: 39.1 weeks gestation


title: DB_Term_2

value: Female fetus


title: nelso-00262: 10439-10427 #1721 mix oligoastro III 133B 8-23-02

value: MIXED III 1721

value: Glioma

value: Grade 3

value: AA

value: RIGHT FRONTAL LOBE


title: nelso-00262: 15480-15471 #1544 GBM 133B 22603

value: Glioblastoma

value: female

value: Grade 4

value: GBM

value: LEFT FRONTAL TEMPORAL


title: DB_Term_1

value: placenta


title: nelso-00262: 8929-8908#1433oligo133b73102

value: OLIGO III 1433

value: Oligodendroglial Tumor

value: male

value: Glia

value: Brain

value: AO


title: nelso-00262: 14644-14604 GBM #1028 133B

value: RIGHT PARIETAL LOBE