title: GROUND BRIC A PDFU-3 333 ARG1 KO Rep2

city: Gainesville

first: Robert

middle: J.

last: Ferl

state: Florida

address: 1301 Fifield Hall PO Box 110690

department: Horticultural Sciences

institute: University of Florida

hyb_protocol: Amplified and labeled cDNA (5 µg/sample) was fragmented and hybridized with rotation onto Affymetrix GeneChip Arabidopsis ATH1 Genome Arrays for 16h at 45°C. Arrays were washed on a Fluidics Station 450 (Affymetrix) with the Hybridization Wash and Stain Kit (Affymetrix) and the Washing Procedure FS450_0004.

scan_protocol: scan was performed using Affymetrix GeneChip Scanner 3000 7G

data_processing: The MAS5 data was generated by using the Affymetrix Expression Console software using default analysis settings and global scaling as normalization method.

source_name: ARG1 KO_ground_control_solid media plates; BRIC-17; OES chamber: BRIC-A PDFU-3

label_protocol: cDNA was synthesized using Ovation Pico WTA System (NuGEN Technologies Inc.) and cDNA was labeled using Encore Biotin Module (NuGEN Technologies Inc.)

growth_protocol: General biology operations   Two Arabidopsis thaliana Col-0 cell culture lines were used: Wild Type (WT) and ARG1 KO SALK_024542C line (ARG1 T-DNA insertion knockout), all cell cultures derived from hypocotyls. Tissue culture cells were plated on 60mm round, nutrient agar Petri plates cultured in a horizontal position until turnover and installation into the BRIC hardware.  All of the sub-culturing on the plates was conducted in the laboratory of the PIs and the University of Florida.  Plates were planted in a laminar flow hood and stored in sterile Biotransfer Boxes (BT). Plates with cells were kept in the dark and at ambient temperature.  Preparation of specialized plates and biology  Petri plates.   Because of their configuration within the BRIC flight hardware, sterility was maintained on all surfaces (interior and exterior) of the Petri plates. The media in the plates for BRIC had to be 5mm deep or less to accommodate the biology and the PDFU cover hardware. For a 60mm dish, this calculates out to 6.7 mLs. After pouring, the plates are allowed to solidify, and then transferred to a sterile Biotransporter (to maintain sterility of external surface) until planting.  Preparation of cell culture plates.  The liquid media from a sterile cell suspension was decanted, and the cells were washed once with fresh liquid media, and then decanted again. A sterile scoop was used to place about 1 gram of cells in the surface on the plate and disperse evenly across the surface. The cover was replaced, but not taped, and transferred to a sterile BT.  The BT was wrapped in black cloth and stored at room temperature. The same day plates were transported by car to the Kennedy Space Center, NASA for the same night (3:00 AM) Turn Over. The ground control plates were turned over 48 hours later.   BRIC Spaceflight Hardware  The hardware for this experiment was the NASA BRIC-LED (Biological Research In a Canister – Light Emitting Diode). The LED component of the hardware was disabled and all biology was held in the dark for the duration of the experiment. The BRIC-LED canisters hold six 60 mm diameter Petri plates in small sub-compartments called PDFUs (Petri Dish Fixation Units). The PDFUs allow an externally activated fixation step without manipulating the samples. We were allocated 10 PDFUs: 5 in BRIC A and 5 in BRIC B. The 2 replicate plates of WT cultured cells and the 3 replicate plates of ARG1 KO were distributed among the BRIC A canister. The 2 replicate plates of WT cultured cells were distributed among the BRIC B canister. One of the PDFU slots in each BRIC was used to hold a HOBO™ data logger to record temperature. The HOBO temperature data collection begins immediately after the biology is sealed in the BRICs, 24 hours before launch.   An additional set of Petri plates within BRIC hardware, identical to that launched for Spaceflight, was prepared for the Ground Control. The Ground Control was housed in the OES (Orbital Environmental Simulator) chamber in the Spaceflight Life Sciences Laboratory (SLSL) at Kennedy Space Center (KSC). The Ground Control was initiated with a precise 24 hour delay to enable the OES environment to be programmed with the environmental profile taken from telemetry of the Space Shuttle. Nominally, the Ground Control BRIC hardware and samples experienced the same external environment profile as the hardware and samples on the Space Shuttle. Environmental parameters that are controlled on the OES and made identical to flight are cabin temperature, humidity and CO2 concentration.

extract_protocol: Total cellular RNA was extracted using RNeasy Mini Kit (QIAGEN)

treatment_protocol: The BRIC-17 experiment was turned over to payload engineers in the SLSL at KSC 48 hours before the scheduled launch time. The payload launched on Dragon cargo spacecraft, SpaceX CRS-2 on March 1st, 2013, at 10:10 EST, and achieved orbit approximately twelve minutes later. Dragon berthed to the ISS on the March 3rd, 2013. The biology was in orbit 10 days before being fixed on orbit with RNAlater. The Dragon unmanned spacecraft unberthed the ISS and splashed into Pacific on the March 26th and the biology was returned to the Kennedy Space Center and handed to the PIs at SLSL on the April the 2nd.

tag: flight status

value: ground control

tag: cultivar

tag: genotype

value: ARG1 KO

tag: material type

value: Tissue culture cells

tag: tissue source

value: derived from hypocotyls of SALK_024542C plants (ARG1 T-DNA insertion knockout plants)

value: 14 days old

tag: biosource type

value: RNAlater fixed_sample


title: Epithelial ovarian carcinoma tissue, primary [PL70T]

status: Public on Sep 01 2017

type: RNA

city: Prague 10

first: Pavel

last: Soucek

address: Srobarova 48

country: Czech Republic

institute: National Institute of Public Health

description:
PL70T
Primary tumor

data_processing:
Raw data were processed by REST2009 software (Pfaffl et al. Nucleic Acids Res. 2000, 30, e36).
Mean expression of reference genes (PPIA, UBC, and YWHAZ) was used for normalization.

label: FAM

molecule: total RNA

organism: Homo sapiens

source_name: Primary EOC tumor

label_protocol: cDNA was synthesized using 0.5 µg of total RNA by help of RevertAidTM First Strand cDNA Synthesis Kit (MBI Fermentas, Vilnius, Lithuania) with random hexamer primers according to manufacturer´s protocol and stored at -20 °C. cDNA was preamplified using 5x PerfeCTa PreAmp SuperMix (Quanta Biosciences, Beverly, MA). qPCR was performed in ViiA7 Real-Time PCR System (Life Technologies, Carlsbad, CA) with 45 cycles at 95 °C for 15 seconds and 60 °C for 60 seconds.

extract_protocol: Total RNA was isolated from frozen tissues using AllPrep DNA/RNA/Protein Mini Kit (Qiagen, Hildesheim, Germany) according to manufacturer's protocol.

tag: tissue

value: Primary EOC tumor

tag: age at diagnosis

tag: Stage

tag: grade

tag: histological type

value: high grade serous carcinoma

tag: progression, recurrence or death

value: no

tag: progression-free survival [months]

tag: first-line chemotherapy

value: administered


title: GROUND BRIC A PDFU-4 334 ARG1 KO

country: USA

label: biotin

organism: Arabidopsis thaliana

source_name: ARG1 KO_ground_control_solid media plates; BRIC-17; OES chamber: BRIC-A PDFU-4

tag: age


title: FLIGHT BRIC A PDFU-5 327 ARG1 KO

source_name: ARG1 KO_space_flown_solid media plates; BRIC-17; Dragon,ISS; BRIC-A PDFU-5

value: space flown

value: RNAlater in-flight fixed_sample


title: GROUND BRIC A PDFU-3 333 ARG1 KO Rep1


title: Epithelial ovarian carcinoma tissue, primary [PL66T]

description:
PL66T
Primary tumor


title: Epithelial ovarian carcinoma tissue, primary [PL69T]

description:
PL69T
Primary tumor


title: GROUND BRIC A PDFU-5 336 ARG1 KO

source_name: ARG1 KO_ground_control_solid media plates; BRIC-17; OES chamber: BRIC-A PDFU-5


title: Epithelial ovarian carcinoma tissue, primary [PL62T]

description:
PL62T
Primary tumor

tag: drug resistance status

value: sensitive


title: Epithelial ovarian carcinoma tissue, primary [PL72T]

description:
PL72T
Primary tumor


title: FLIGHT BRIC A PDFU-4 326 ARG1 KO

source_name: ARG1 KO_space_flown_solid media plates; BRIC-17; Dragon,ISS; BRIC-A PDFU-4


title: Epithelial ovarian carcinoma tissue, primary [PL59T]

description:
PL59T
Primary tumor

value: yes

value: intermediate


title: FLIGHT BRIC A PDFU-3 305 ARG1 KO Rep1

source_name: ARG1 KO_space_flown_solid media plates; BRIC-17; Dragon,ISS; BRIC-A PDFU-3


title: FLIGHT BRIC A PDFU-3 305 ARG1 KO Rep2


title: Epithelial ovarian carcinoma tissue, primary [PL58T]

description:
PL58T
Primary tumor

value: other than high grade serous carcinoma


title: Epithelial ovarian carcinoma tissue, primary [PL56T]

description:
PL56T
Primary tumor


title: Epithelial ovarian carcinoma tissue, primary [PL53T]

description:
PL53T
Primary tumor

value: not administered


title: Epithelial ovarian carcinoma tissue, primary [PL52T]

description:
PL52T
Primary tumor


title: Epithelial ovarian carcinoma tissue, primary [PL55T]

description:
PL55T
Primary tumor


title: Epithelial ovarian carcinoma tissue, primary [PL57T]

description:
PL57T
Primary tumor


title: Epithelial ovarian carcinoma tissue, primary [PL51T]

description:
PL51T
Primary tumor


title: Epithelial ovarian carcinoma tissue, primary [PL47T]

description:
PL47T
Primary tumor


title: Lung_epithelial_cells_PLY_rep.3

city: Jena

first: S.

last: Lambeck

address: Erlanger Allee 101

country: Germany

institute: JUH

description: Mm AT II cells, PLY

hyb_protocol: Standard hybridization protocol for BeadArray Reader 500 X from Illumina® (San Diego, CA, USA)

scan_protocol: Standard Illumina scan protocol

data_processing: Robust spline normalization (rsn) and detection filtering via lumi package within Bioconductor and R

organism: Mus musculus

source_name: AT II cells, PLY

label_protocol: Biotinylated probes were prepared from 500 ng of total RNA, using the TargetAmp™-Nano Labeling Kit for Illumina® Expression BeadChip®.

extract_protocol: Total RNA was extracted from purified type II alveolar epithelial cells of AdTGF-b1+PLY versus AdTGF-b1+PdB treated mice using the RNeasy minikit (Qiagen, Germany).

treatment_protocol: Replication-deficient adenoviral vectors carrying the gene for active TGF-b1 (AdTGF-b1) were prepared. Mice received AdTGFb-1 for 14 days, and then received daily intratracheal instillations for three consecutive days of either cytotoxic PLY, or its non-cytotoxic derivative, PdB to investigate its effect on lung fibrosis perpetuation

tag: strain

tag: gender

value: female

value: 8 to 12 weeks

tag: cell type

value: alveolar type II cells

tag: treatment

value: PLY


title: Lung_epithelial_cells_PLY_rep.4

description: Mm AT II cells, PLY


title: Epithelial ovarian carcinoma tissue, primary [PL3T]

description:
PL3T
Primary tumor

value: resistant


title: Lung_epithelial_cells_PdB_rep.2

description: Mm AT II cells, PdB

source_name: AT II cells, PdB

value: PdB


title: Epithelial ovarian carcinoma tissue, primary [PL37T]

description:
PL37T
Primary tumor

value: Primary EOC tumor


title: Lung_epithelial_cells_PLY_rep.1

description: Mm AT II cells, PLY


title: Epithelial ovarian carcinoma tissue, primary [PL41T]

description:
PL41T
Primary tumor

value: high grade serous carcinoma


title: Lung_epithelial_cells_PdB_rep.3

description: Mm AT II cells, PdB


title: Epithelial ovarian carcinoma tissue, primary [PL45T]

description:
PL45T
Primary tumor

value: no


title: Epithelial ovarian carcinoma tissue, primary [PL35T]

description:
PL35T
Primary tumor

value: administered


title: Epithelial ovarian carcinoma tissue, primary [PL34T]

description:
PL34T
Primary tumor


title: Campylobacter jejuni strain 81116 suspended in Fraquil, biological replicate 3

type: mixed

city: St-Anne-de-Bellevue

first: Sebastien

last: Faucher

state: QC

address: 21,111 Lakeshore

department: Natural Resource Sciences

country: Canada

institute: McGill University

hyb_protocol: Hybridization was performed as previously described (Li, 2015, BMC Genomics).

scan_protocol: Scanning and image acquisition was performed on a InnoScan 710 using the mapix software. Spot intensity an local background was measured.

data_processing: Data were processed with the mapix software. Values from each channel were background substracted and the % contribution of each sopts to the total fluorsecence in each channel was calculated. Then the ratio Ch1/Ch2 was calculated. We used gDNA (Ch2) for data normalization accross slides, as described in Talaat, 2002, NAR.

label: Alexa Fluor 647

organism: Campylobacter jejuni subsp. jejuni 81116

source_name: Fraquil

label_protocol: RNA: 15 ug of Total RNA was labeled with amino-allyl dUTP during reverse transcriptase and subsequently coupled with the succinimidyl ester fluorescent dye AlexaFluor 647 (Ch1) as previously described (Faucher, 2013, Methods. Mol. Biol.). Genomic DNA: 5 ug of genomic DNA was labeled with amino-allyl dUTP with klenow fragment and random hexamer as previously described (Faucher, 2013, Methods. Mol. Biol.). Subsequently, the resulting DNA was coupled to the succinimidyl ester fluorescent dye AlexaFluor 546 (Ch2).

growth_protocol: Brucella broth at OD600 of 1 for 4h at 4°C

extract_protocol: RNA: TRIzol reagent (Invitrogen), reverse-transcribed into cDNA. Genomic DNA: Wizard gDNA extraction kit (Promega).

treatment_protocol: Exposition to defined freswater (Fraquil: 0,004% CaCl2, 0,004% MgSO4, 0,001% NaHCO3, 0,0002% K2HPO4, 0,004% NaNO3, 10 nM FeCl3, 1 nM CuSO4, 0.22 nM (NH4)6Mo7O24, 2.5 nM CoCl2, 23 nM MnCl2, 4 nM ZnSO4) at OD600 of 1, for 4h at 4°C.

tag: growth condition

value: Fraquil, OD600 of 1, 4h at 4°C

label: Alexa Fluor 546

molecule: genomic DNA

source_name: genomic DNA, reference channel

value: TSA-Blood plate at 42 °C for 2 days


title: Lung_epithelial_cells_PLY_rep.2

description: Mm AT II cells, PLY


title: Campylobacter jejuni strain 81116 suspended in Fraquil, biological replicate 2


title: Campylobacter jejuni strain 81116 suspended in Brucella broth, biological replicate 3

source_name: Brucella broth, control

value: Brucella broth, OD600 of 1, 4h at 4°C


title: Not infected WT C57BL/6 mice

city: Toronto

first: Tiago

last: Medina

address: 101 College Street

institute: University Health Network

description: Control

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://sabiosciences.com/pcrarraydataanalysis.php
For the normalization it uses the average of five housekeeping genes: Actb, B2m, Gapdh, Gusb, Hsp90ab1
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Fold Change worksheet reports test/control (i.e., C57Bl6 infected versus IL27Ebi3 knockout mice) ratios.

label: SYBR Green

source_name: Heart

label_protocol: PCR array was performed using qPCR assay according to RT²ProfilerPCRArrayTM kit of Mouse Innate Immune Responses & Adaptive (PAMM 052Z - Qiagen) on the ABI StepOnePlusTM equipment. Reverse transcription was performed from 500 ng total RNA using the High-Capacity RNA-to-cDNA kit (Thermo Fisher Scientific). Quantitative real-time PCR were performed (Applied Biosystems) with 1 cycle at 95oC for 10 minutes and 40 cycles at 95oC for 15 seconds and 60oC for 60 seconds.

extract_protocol: Hearts were removed and digested with a cocktail of liberase TL (Roche) for 1h at 37°C. Total RNA was extracted using RNeasy Mini Kit followed by DNase I treatment.

treatment_protocol: WT and Ebi3 deficient mice were intraperitoneally infected or not with 1,000 forms of trypomastigotes of T. cruzi Y strain for 7 days

tag: genotype

value: WT

tag: agent

value: control

tag: time

value: 7 days


title: Campylobacter jejuni strain 81116 suspended in Fraquil, biological replicate 1


title: Lung_epithelial_cells_PdB_rep.1

description: Mm AT II cells, PdB


title: Not infected Ebi3 deficient mice

description: Control

value: Ebi3 deficient


title: Epithelial ovarian carcinoma tissue, primary [PL33T]

description:
PL33T
Primary tumor

tag: tissue

tag: age at diagnosis

value: yes

value: not administered


title: WT C57BL/6 mice 7 days after T cruzi infection

description: Test

value: Trypanosoma cruzi


title: Ebi3 deficient mice 7 days after T cruzi infection

description: Test


title: Campylobacter jejuni strain 81116 suspended in Brucella broth, biological replicate 2


title: Campylobacter jejuni strain 81116 suspended in Brucella broth, biological replicate 1


title: Epithelial ovarian carcinoma tissue, primary [PL2T]

description:
PL2T
Primary tumor

tag: Stage

tag: grade

value: intermediate


title: Epithelial ovarian carcinoma tissue, primary [PL30T]

description:
PL30T
Primary tumor

tag: histological type

value: other than high grade serous carcinoma

tag: progression, recurrence or death

value: sensitive


title: Epithelial ovarian carcinoma tissue, primary [PL31T]

description:
PL31T
Primary tumor

value: Primary EOC tumor

tag: progression-free survival [months]

tag: first-line chemotherapy

value: resistant


title: Campylobacter jejuni strain 81-176 suspended in Fraquil, biological replicate 3

organism: Campylobacter jejuni subsp. jejuni 81-176


title: Campylobacter jejuni strain 81-176 suspended in Fraquil, biological replicate 2


title: Epithelial ovarian carcinoma tissue, primary [PL29T]

description:
PL29T
Primary tumor

tag: drug resistance status


title: Epithelial ovarian carcinoma tissue, primary [PL27T]

description:
PL27T
Primary tumor

value: high grade serous carcinoma

value: no


title: Campylobacter jejuni strain 81-176 suspended in Fraquil, biological replicate 1

value: Fraquil, OD600 of 1, 4h at 4°C


title: Epithelial ovarian carcinoma tissue, primary [PL25T]

description:
PL25T
Primary tumor

value: administered


title: Epithelial ovarian carcinoma tissue, primary [PL32T]

description:
PL32T
Primary tumor


title: Campylobacter jejuni strain 81-176 suspended in Brucella broth, biological replicate 3

value: Brucella broth, OD600 of 1, 4h at 4°C

value: TSA-Blood plate at 42 °C for 2 days


title: Epithelial ovarian carcinoma tissue, primary [PL20T]

description:
PL20T
Primary tumor


title: Epithelial ovarian carcinoma tissue, primary [PL23T]

description:
PL23T
Primary tumor


title: Epithelial ovarian carcinoma tissue, primary [PL24T]

description:
PL24T
Primary tumor


title: Epithelial ovarian carcinoma tissue, primary [PL19T]

description:
PL19T
Primary tumor


title: Campylobacter jejuni strain 81-176 suspended in Brucella broth, biological replicate 1


title: Campylobacter jejuni strain 81-176 suspended in Brucella broth, biological replicate 2


title: Epithelial ovarian carcinoma tissue, primary [PL18T]

description:
PL18T
Primary tumor


title: Epithelial ovarian carcinoma tissue, primary [PL17T]

description:
PL17T
Primary tumor


title: Epithelial ovarian carcinoma tissue, primary [PL16T]

description:
PL16T
Primary tumor


title: Limb MEF-1

city: Tsukuba

first: Naoto

last: Ninomiya

state: Ibaraki

address: 1-1-1 Higashi

department: Biotechnology Research Institute for Drug Discovery

country: Japan

institute: National Institute of Advanced Industrial Science and Technology

hyb_protocol: 1.65 μg of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 μl containing 25x Agilent fragmentation buffer and 10x Agilent gene expression blocking agent following the manufacturers protocols. To stop fragmentation reaction, 2x Hi-RPM hybridization buffer was added, and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4112F) for 18 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), 1 minute with 37°C GE Wash buffer 2 (Agilent), 30 sec with Acetonitrile (Wako), and then dried immediately.

scan_protocol: Slides were scanned immediately after wash and dried on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10 μm, Dye channel is set to Green).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5 (Agilent) using default parameters (protocol: GE1_1105_Oct12, and Grid: 014868_D_F_20131202) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: E13.5 mouse limb fibroblasts

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 600 ng RNA using the One-Color Quick amp labeling kit (Qiagen) following the manufacturer's instructions, followed by RNeasy column purification (Qiagen). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: MEFs and MDF were cultured in DMEM supplemented with 12% FBS and 100U/ml penicillin/streptomycin. iLung cells were cultured in DMEM supplemented with 12% FBS and 100U/ml penicillin/streptomycin for 7 days. On day 7, the medium was changed to Advanced RPMI 1460 supplemented with 0.2% FBS and L-glutamine, and cultured for 10 days.

extract_protocol: Total RNA was prepared using RNeasy Mini kit (Qiagen) following the manufacturer's instructions. The protocol of RNeasy Mini kit includes DNase digestion. Extracted RNA was qualified using a NanoDrop ND-1000 Spectrophotometer.

treatment_protocol: iLung cells were generated by retroviral transduction of transcription factors.

tag: strain

value: ICR

value: Embryonic fibroblasts


title: eye_day14

city: Fuchu-shi

first: Tsuyoshi

last: Shimmura

state: Tokyo

address: 3-8-1 Harumi-cho

institute: Tokyo University of Agriculture and Technology

description:
13_eye_day14_1
14_eye_day14_2
Gene expression on days 14 after transfer from SL to LD.

hyb_protocol: Labeled cRNA was purified with RNeasy mini spin columns (QIAGEN) and hybridized using the Gene Expression Hybridization Kit (Agilent Technologies).

scan_protocol: After washing with Gene Expression Wash Buffer (Agilent Technologies), the slide glass was scanned on a Microarray Scanner (Agilent Technologies).

data_processing: Microarray data were analyzed using the GeneSpring software (Agilent Technologies).

organism: Oryzias latipes

source_name: Eye, LD, day 14, replicate 1

label_protocol: cDNA synthesis and cRNA labeling reactions were performed with the Low Input Quick Amp Labeling Kit (Agilent Technologies).

growth_protocol: Medaka fish (Oryzias latipes) were obtained from a local dealer and kept outdoor.

extract_protocol: Total RNA was prepared from three fish (n=2) to duplicate our observations on two arrays using RNeasy tissue kit (QIAGEN).

treatment_protocol: Both eyes were collected from six animals at 16 hours after light onset (zeitgeber time: ZT16) on days 0, 1, 2, 3, 5, 7, and 14 after transfer from SL to LD conditions.

value: Eye

tag: gender

value: female

tag: protocol

value: transfer from SL to LD

value: day 14


title: eye_day7

description:
11_eye_day7_1
12_eye_day7_2
Gene expression on days 7 after transfer from SL to LD.

source_name: Eye, LD, day 7, replicate 1

value: day 7


title: eye_day5

description:
09_eye_day5_1
10_eye_day5_2
Gene expression on days 5 after transfer from SL to LD.

source_name: Eye, LD, day 5, replicate 1

value: day 5


title: Epithelial ovarian carcinoma tissue, primary [PL11T]

description:
PL11T
Primary tumor

value: other than high grade serous carcinoma

value: yes


title: eye_day2

description:
05_eye_day2_1
06_eye_day2_2
Gene expression on days 2 after transfer from SL to LD.

source_name: Eye, LD, day 2, replicate 1

value: day 2


title: eye_day1

description:
03_eye_day1_1
04_eye_day1_2
Gene expression on day 1 after transfer from SL to LD.

source_name: Eye, LD, day 1, replicate 1

value: day 1


title: eye_day0

description:
01_eye_day0_1
02_eye_day0_2
Gene expression under SL condition

source_name: Eye, SL (day 0), replicate 1

value: SL condition

value: day 0


title: Copper 96h control replicate 4

status: Public on Aug 31 2017

city: Aachen

first: Laura

last: Sonnack

address: Forckenbeckstr. 6

institute: Fraunhofer IME

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes and hybridized overnight for 17 h at 65°C

scan_protocol: Slides were scanned immediately after washing on Agilent Microarray Scanner (Agilent Technologies) using one color scan setting for 4x44k array slides

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1-v5_95_Feb07 and QC Metric Set GE_QCMT_Jan09) During this step the background was subtracted and outliers detected and flagged.

organism: Danio rerio

source_name: Copper 96h control replicate 4

label_protocol: The samples were processed following the Agilent´s One-Color Microarray-Based Gene Expression Analysis Protocol (Low Input Quick Amp Labeling, Version 6.6, September 2012). The starting amount of all samples was 100 ng of total RNA.

growth_protocol: Zebrafish embryo toxicity test followig DIN EN ISO 15088; After harvest of the eggs, the embryos were quickly transferred to the wells (one embryo/well) of the plates and incubated for 48 h and 96 h at 26 ± 1°C with a 14-h photoperiod

extract_protocol: Total RNA was extracted from the frozen, pooled embryos by the Trizol-Method and homogenization with motor-driven plastic micro pistils. Subsequently, RNA was cleaned-up using RNeasy Mini Spin Columns (QIAGEN, Hilden, Germany) according to the manufacturers' protocols. For all RNA samples, the absorbance ratio 260/280 was above 2.0 and 260/230 above 1.8 while the RNA integrity number was above 8.7

treatment_protocol: All metal test solutions were prepared in ISO-standard water (prepared according to OECD guideline 203, Annex 2) diluted 1:5

tag: developmental stage

value: 96hpf embryos


title: eye_day3

description:
07_eye_day3_1
08_eye_day3_2
Gene expression on days 3 after transfer from SL to LD.

source_name: Eye, LD, day 3, replicate 1

value: day 3


title: Copper 96h control replicate 3

source_name: Copper 96h control replicate 3


title: Copper 96h control replicate 2

source_name: Copper 96h control replicate 2


title: Copper 96h control replicate 1

source_name: Copper 96h control replicate 1


title: Cobalt 96h control replicate 4

source_name: Cobalt 96h control replicate 4


title: Copper 48h control replicate 2

source_name: Copper 48h control replicate 2

value: 48hpf embryos


title: Copper 48h control replicate 1

source_name: Copper 48h control replicate 1


title: Cobalt 96h control replicate 1

source_name: Cobalt 96h control replicate 1


title: Copper 48h control replicate 3

source_name: Copper 48h control replicate 3


title: Cobalt 96h control replicate 2

source_name: Cobalt 96h control replicate 2


title: Cobalt 48h control replicate 1

source_name: Cobalt 48h control replicate 1


title: Cobalt 96h control replicate 3

source_name: Cobalt 96h control replicate 3


title: 1154337-CNV-IM1

type: genomic

city: Daejeon

first: Hee-jin

last: Kim

address: 125 Gwahak-ro, Yuseong-gu

country: South Korea

institute: KRIBB

description: MDA-DNA from intestinal metaplasia cells

hyb_protocol: Each array according to the manufacturer`s instruction

data_processing: Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using Genotypeing Console software. Circular Binary segmentation was applied using DNAcopy package for R Bioconductor on raw data.

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Standard DNA preparation protocol using Qiagen's DNA prep kit

tag: cell type

value: intestinal metaplasia cell


title: Cadmium 96h control replicate 2

source_name: Cadmium 96h control replicate 2


title: Cadmium 96h control replicate 4

source_name: Cadmium 96h control replicate 4


title: Cobalt 48h control replicate 2

source_name: Cobalt 48h control replicate 2


title: Cadmium 48h control replicate 2

source_name: Cadmium 48h control replicate 2


title: Cadmium 96h control replicate 1

source_name: Cadmium 96h control replicate 1


title: Cadmium 96h control replicate 3

source_name: Cadmium 96h control replicate 3


title: Cadmium 48h control replicate 1

source_name: Cadmium 48h control replicate 1


title: 1154337-CNV-GM1

description: MDA-DNA from gastric normal mucosa cells

scan_protocol: Each array according to the manufacturer`s instruction

value: gastric mucosa cell


title: Cadmium 48h control replicate 3

source_name: Cadmium 48h control replicate 3


title: 1154337-CNV-GC2

description: MDA-DNA from gastric cancer cells

source_name: MDA-DNA from gastric cancer cells

value: gastric cancer cell


title: AG04110_miR

status: Public on Aug 23 2017

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

description: primary human fibroblasts

hyb_protocol: The standard hybridization protocol was used as recommended by a custom miRNA microarray chip (OSU-CCC version 4.0).

scan_protocol: GeneChips were scanned using the Axon 4000B Scanner through the Laboratory of Molecular Technology (NCI-Frederick).

data_processing: Genepix (version Pro 6.0.1.00)

source_name: primary fibroblast cells

label_protocol: total RNA (5 micro-g) was converted to biotin-labeled complementary DNA, hybridized onto the chips, and processed by direct detection of the biotin-containing transcripts by streptavidin-Alexa 647 conjugate through a core facility in the Laboratory of Molecular Technology (NCI-Frederick) according to the manufacturer's instructions.

extract_protocol: Total RNA samples from fibroblasts were isolated using Qiagen’s miRNAeasy Mini Kit (Qiagen, Valencia, CA). RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA), and only samples of high quality, defined by distinct 28S and 18S rRNA bands together with a RIN (RNA integrity number) > 7, were used for further analyses.

value: primary fibroblast

tag: age

value: F


title: AG12797_miR

description: primary human fibroblasts

value: M


title: AG00780_miR

description: primary human fibroblasts


title: 1154337-CNV-GM2

source_name: MDA-DNA from gastric normal mucosa cells


title: AG03141_miR

description: primary human fibroblasts


title: No Reaction [LRI_TP 006]

city: Vellore

first: Sundeep

middle: Chaitanya

last: Vedithi

state: Tamil Nadu

address: Karigiri

department: Molecular Biology

country: India

institute: Schieffelin Institute of Health Research and Leprosy Center

description: RNA from Skin Biopsies

hyb_protocol: 600ng of labeled cRNA sample were fragmented at 60°C and hybridized on to a Genotypic designed M leprae Gene Expression  2x400k Array (AMADID: 074058). Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65° C for 16 hours.

scan_protocol: Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D).

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the quantile normalization method .Gene based analysis was performed.

organism: Mycobacterium leprae

source_name: No Reaction_Skin Biopsy

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

extract_protocol: RNA extraction was perforemd by using Qiagen Rneasy mini kit with Dnase Treatment.

treatment_protocol: Excisional Skin Biopsy Specimen was taken from the site of active skin lesion or from the area of maximum sensory loss from leprosy cases in Type 2 Reactions (Erythema Nodosum Leprosum) and cases without any reactions (Controls).

tag: subject status

value: Leprosy case without reaction

value: Lesional Skin Biopsy


title: AG05229_miR

description: primary human fibroblasts


title: AG06300

description: primary fibroblast cells

hyb_protocol: The standard hybridization protocol was used as recommended by Affymterix.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000 through the Laboratory of Molecular Technology (NCI-Frederick).

data_processing: Affymetrix Expression Console Software , RMA normalization, log2

label_protocol: For microarray hybridization, RNA was processed for hybridization to Affymetrix Human Exon 1.0 ST Array through a core facility in the Laboratory of Molecular Technology (NCI-Frederick) according to the manufacturer's instructions.

extract_protocol: RNA was isolated from primary fibroblast cultures when 75 percent confluent. Cells were washed in 1X PBS, scrapped off plates and collected as pellets that were stored at -80 C. Total RNA was isolated using TRIZOL reagent, following the manufacturer’s protocol (Invitrogen).


title: Type 2 Reaction [LRI_TP 004_TR1]

description: RNA from Skin Biopsies

source_name: Type 2 Reaction_Skin Biopsy

value: Leprosy case in Type 2 reaction


title: 1154337-CNV-IM2

source_name: MDA-DNA from intestinal metaplasia cells


title: AG03141

description: primary fibroblast cells


title: AG06300_miR

description: primary human fibroblasts


title: WRN_miR_11

description: 82-6 primary human fibroblasts, PMID 11978740

hyb_protocol: The standard hybridization protocol was used as recommended by  the Nanostring nCounter Human miRNA Expression Assay Kit (Nanostring, Seattle, WA).

data_processing: Genepix (version Pro 6.0.1.00). nCounter RCC files were imported into nSolver (Nanostring), quality control-verified and normalized to the geometric mean of the top 100 expressed miRNAs.^SAMPLE = GSM1535466

source_name: 82-6 primary fibroblast cells

label_protocol: For microarray hybridization, RNA was processed for hybridization as recommended by  the Nanostring nCounter Human miRNA Expression Assay Kit (Nanostring, Seattle, WA) through a core facility in the Laboratory of Molecular Technology (NCI-Frederick) according to the manufacturer's instructions.

tag: group

value: WRN


title: AG00780

description: primary fibroblast cells

tag: tissue


title: AG12797

description: primary fibroblast cells


title: WRN_miR_12

data_processing: Genepix (version Pro 6.0.1.00). nCounter RCC files were imported into nSolver (Nanostring), quality control-verified and normalized to the geometric mean of the top 100 expressed miRNAs.


title: WRN_12

description: primary fibroblast cells, PMID 11978740


title: G797 ATAC-seq

status: Public on Jul 21 2017

type: SRA

first: Paul

last: Guilhamon

state: ON

address: 686 Bay Street

institute: SickKids

description: Raw file: G797_P9_SF_AT_2_TAGGCATG_L003_R1.fastq.gz

library_source: genomic

data_processing:
Libraries were sequenced with 50 bp single-end reads which  were mapped to hg19 using bowtie2. Reads were filtered to remove duplicates, unmapped or poor quality (Q <30)reads, mitochondrial reads, chrY reads, and those overlapping the ENCODE blacklist
Following alignment, open chromatin regions/peaks were called using MACS2. Default parameters were used except for  the following: --keep-dup all  -B --nomodel --SPMR -q 0.05 --slocal 6250 --llocal 6250
The signal intensity featured in the bedgraph files was calculated as the fold enrichment of the signal per million reads in a sample over a modelled local background using the bedgraphcmp function in MACS2.
Genome_build: hg19
Supplementary_files_format_and_content: [peak] called peaks using MACS2, with settings described above
Supplementary_files_format_and_content: [bedgraph] signal file produced with MACS2 as described above

growth_protocol: cells were cultured adherently under neural stem cell conditions

extract_protocol: Libraries were contructed as described in Buenrostro et al, Nature Methods, (2013)

value: glioblastoma

tag: ascl1 status

value: LO


title: WRN_11

description: primary fibroblast cells, PMID 11978740


title: Cobalt 48h control replicate 3

source_name: Cobalt 48h control replicate 3


title: WRN_10

description: primary fibroblast cells, PMID 11978740


title: Type 2 Reaction [LRI_TP 001_TR1]

description: RNA from Skin Biopsies


title: No Reaction [LRI_TP 005_TR1]

description: RNA from Skin Biopsies


title: G729 ATAC-seq

description:
Raw file: G729_P9_SF_AT_1_AGGCAGAA_L001_R1.fastq.gz
Raw file: G729_P9_SF_AT_2_TAGGCATG_L001_R1.fastq.gz


title: No Reaction [LRI_TP 005_TR2]

description: RNA from Skin Biopsies


title: AG05229

description: primary fibroblast cells


title: G411 ATAC-seq

description:
Raw file: G411_P11_SF_AT_1_AGGCAGAA_L003_R1.fastq.gz
Raw file: G411_P11_SF_AT_2_TAGGCATG_L003_R1.fastq.gz


title: No Reaction [LRI_TP 007]

description: RNA from Skin Biopsies


title: Type 2 Reaction [LRI_TP 004_TR2]

description: RNA from Skin Biopsies


title: G571 ATAC-seq

description: Raw file: G571_P11_SF_AT_1_TAGGCATG_L003_R1.fastq.gz


title: G754 ATAC-seq

description:
Raw file: G754_P10_SF_AT_1_GGACTCCT_L001_R1.fastq.gz
Raw file: G754_P10_SF_AT_2_AGGCAGAA_L006_R1.fastq.gz

value: HI


title: 1154337-CNV-GC1

description: MDA-DNA from gastric cancer cells


title: Type 2 Reaction [LRI_TP 001_TR2]

description: RNA from Skin Biopsies


title: G702 ATAC-seq

description: Raw file: G702_P11_SF_AT_1_GGACTCCT_L004_R1.fastq.gz


title: G549 ATAC-seq

description: Raw file: G549_P8_SF_AT_1_AGGCAGAA_L008_R1.fastq.gz


title: G719 ATAC-seq

description:
Raw file: G719_P11_SF_AT_1_TAGGCATG_L004_R1.fastq.gz
Raw file: G719_P11_SF_AT_2_GGACTCCT_L004_R1.fastq.gz


title: G489 ATAC-seq

description: Raw file: G489_P14_SF_AT_1_AGGCAGAA_L003_R1.fastq.gz


title: G799 ATAC-seq

description: Raw file: G799_P11_SF_AT_1_TAGGCATG_L004_R1.fastq.gz


title: TO_123_13June08

status: Public on Jul 18 2017

description: blood cells

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000 through the University of Washington Functional Genomics & Proteomics Facility Core Laboratory in the Center for Ecogenetics and Environmental Health (http://depts.washington.edu/ceeh/members/core-services.html).

data_processing: Affymetrix Expression Console, RMA normalization log2

organism: Vulpes lagopus

source_name: blood cells

label_protocol: For microarray hybridization, RNA was processed for hybridization to Affymetrix Canine Genome 2.0 Array through a core facility in the Functional Genomics Laboratory in the Center for Ecogenetics and Environmental Health at the University of Washington according to the manufacturer's instructions.

extract_protocol: All blood samples destined for molecular analyses were collected in PAXgene (Qiagen) RNA tubes and stored on ice in the field until they were placed in -20°C or -80°C freezers.  RNA was extracted using PaxGene Blood miRNA Kit (Qiagen) and quantity and integrity determined using an Agilent 2100 Bioanalyzer (Agilent Technologies) or a NanoDrop ND-1000 Spectrophotometer (Thermo Fisher Scientific).

value: blood


title: TO_1B_13June08

description: blood cells


title: TO_144_13June08

description: blood cells


title: TO_Canine_control_13June08

description: blood cells


title: TO_143_13June08

description: blood cells


title: TO_133_13June08

description: blood cells


title: TO_121_13June08

description: blood cells


title: TO_132_13June08

description: blood cells


title: TO_124_13June08

description: blood cells


title: Pancreatic islets from BPA (100 μg/kg/d)-treated mice isolated at postnatal day 30_2

status: Public on Jun 01 2017

city: Barcelona

first: Joan Marc

last: Servitja

state: Catalonia

address: Rosselló, 153

country: Spain

institute: IDIBAPS

hyb_protocol: Following fragmentation, cRNA was hybridized to Genechip Mouse 430 2.0 Affymetrix arrays, washed and stained according to the standard Affymetrix protocol.

scan_protocol: GeneChips were scanned according to the standard Affymetrix protocol (Affymetrix Genechip Command Console program 3.0.0.1214, scanner GCS 3000-7G)

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

source_name: Pancreatic islets from one BPA (100 μg/kg/d)-treated mice isolated at postnatal day 30

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol through two cycles of cDNA synthesis (150 ng starting total RNA).

growth_protocol: Islets from control, BPA10 and BPA100 mice were isolated at postnatal day 30

extract_protocol: RNA was extracted with the Rneasy mini kit from Qiagen

treatment_protocol: Offspring was treated with vehicle (control) or BPA at the doses of 10 or 100 ug/kg/day from day 9 to 16 of gestation. Islets were isolated at postnatal day 30

value: Islets of Langerhans

tag: genotype

value: wild-type

value: male


title: Pancreatic islets from BPA (10 μg/kg/d)-treated mice isolated at postnatal day 30_2

source_name: Pancreatic islets from two BPA (10 μg/kg/d)-treated mice isolated at postnatal day 30


title: Pancreatic islets from vehicle-treated mice isolated at postnatal day 30_1

source_name: Pancreatic islets from five vehicle-treated mice isolated at postnatal day 30


title: Pancreatic islets from BPA (100 μg/kg/d)-treated mice isolated at postnatal day 30_1


title: Pancreatic islets from BPA (10 μg/kg/d)-treated mice isolated at postnatal day 30_1

source_name: Pancreatic islets from one BPA (10 μg/kg/d)-treated mice isolated at postnatal day 30


title: Pancreatic islets from vehicle-treated mice isolated at postnatal day 30_2

source_name: Pancreatic islets from one vehicle-treated mice isolated at postnatal day 30


title: TO_125_13June08

description: blood cells


title: TO_122_13June08

description: blood cells


title: Sorted mesenchymal hGBM36 specimen, WNT5A- tech Rep 2

status: Public on Mar 07 2017

city: S. Giovanni Rotondo (FG)

first: Tommaso

last: Mazza

address: Viale Cappuccini, 1

department: Bioinformatics

country: Italy

institute: IRCCS Casa Sollievo della Sofferenza

description: Wnt5A- cell sorted population of the mesenchymal GBM#36 specimen

hyb_protocol: Each sample, fragmented and labeled, has been hybridized on Human Transcriptome Array 2.0 by using the Affymetrix GeneChip Hybridization Oven 645, according to the manufacturer's instructions

scan_protocol: Each arrays were scanned using the Affymetrix GeneChip Scanner 3000 7G while the array image was acquired using Affymetrix GeneChip® Command Console Software 4.1.2.

data_processing:
Expression data analysis was performed using R and the Partek Genomics Suite package ver. 6.6. Background correction was performed by RMA. Probeset signals were normalized by quantile normalization and summarized by the median polish method. The file normalized_data_all_na35.hg19.txt.gz (available on the series record) contains normalized data for all analyzed probe sets including all controls. Sample data tables do not include all control probe sets. The file Additonal_Probeset_information.txt contains information on probe sets with hg.0 designation in HTA-2_0.na35.hg19.transcript.csv but revised to hg.1 in the normalized data. Data for these probe sets are available only in the file normalized_data_all_na35.hg19.txt.
probe group file: HTA-2_0.r3.pgf
meta-probeset file: HTA-2_0.na35.hg19.transcript.csv

source_name: GBM#36, WNT5A- sorted

label_protocol: As per manufacturer by using the WT Plus Reagent Kit (Affymetrix, Santa Clara, CA). Briefly, on 100 ng of total RNA, a random priming method was used to generate cDNA from all RNA transcripts present in a sample. The cDNA was fragmented and labeled with biotin using terminal deoxynucleotidyl transferase (TdT)

extract_protocol: Total RNA was isolated using the Qiagen RNeasy kit (Qiagen), including DNase I treatment before the final elution to eliminate any DNA contamination, following the manufacturer’s directions.

value: brain


title: Sorted mesenchymal hGBM36 specimen, WNT5A- tech Rep 1


title: Sorted mesenchymal hGBM36 specimen, WNT5A+ tech Rep 2

description: Wnt5A+ cell sorted population of the mesenchymal GBM#36 specimen

source_name: GBM#36, WNT5A+ sorted


title: Unsorted mesenchymal hGBM36 specimen, tech Rep 2

description: Unsorted cell population of the mesenchymal GBM#36 specimen

source_name: GBM#36, unsorted


title: Sorted mesenchymal hGBM36 specimen, WNT5A+ tech Rep 1


title: Unsorted mesenchymal hGBM36 specimen, tech Rep 1


title: Unsorted mesenchymal hGBM23 specimen, tech Rep 1

description: Unsorted cell population of the mesenchymal GBM23 specimen

source_name: GBM#23, unsorted


title: Unsorted mesenchymal hGBM23 specimen, tech Rep 2


title: RNAseq-lncRNAs_5

status: Public on Jan 30 2017

city: Montreal

first: Daniel

last: Sinnett

state: Quebec

address: 3175 Cote-Sainte-Catherine

institute: CHU Sainte-Justine

library_source: transcriptomic

data_processing:
AB SOLID data:  Primary alignment with Lifescope software version 2.1
Mark duplicate with PICARD version 1.107
SplitNCigar with GATK version 3.2-2
Read counts using HTSeq version 0.6.1p1
Genome_build: hg19
Supplementary_files_format_and_content: Reads counts based on Ensembl GRCH37 version 75 + lncRNAs from Casero D, Sandoval S, Seet CS, Scholes J, Zhu Y, Ha VL, Luong A, Parekh C, Crooks GM. 2015. Long non-coding RNA profiling of human lymphoid progenitor cells reveals transcriptional divergence of B cell and T cell lineages. Nat Immunol 16(12): 1282-1291.

source_name: Tumoral biospecimen

extract_protocol:
see Baccichet A, Qualman SK, Sinnett D. Allelic loss in childhood acute lymphoblastic leukemia. Leuk Res. 1997;21(9):817-23.
Total RNA was extracted from bone marrow samples at diagnosis using the mirVana Isolation kit (Ambion) according to the manufacturer’s protocol. Following a DNAse I treatment, total or mature RNA samples were quantified by NanoDrop ND1000 (Thermo-Fisher Scientific) and RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent). Ribosomal ribonucleic acid (rRNA) were depleted using the Invitrogen RiboMinus Eukaryote kit (Life Technologies). cDNA libraries were prepared using the SOLiD Total RNA-seq kit (diagnosis samples) based on manufacturer’s protocol and sequenced on the Life Technologies SOLiD 5500 System.

value: Bone marrow

tag: age diagnosis (month)

tag: Sex


title: RNAseq-lncRNAs_6


title: RNAseq-lncRNAs_42


title: RNAseq-lncRNAs_44


title: RNAseq-lncRNAs_51


title: RNAseq-lncRNAs_35


title: RNAseq-lncRNAs_32


title: RNAseq-lncRNAs_13


title: RNAseq-lncRNAs_52


title: Sorted mesenchymal hGBM23 specimen, WNT5A- tech Rep 2

description: Wnt5A- cell sorted population of the mesenchymal GBM23 specimen

source_name: GBM#23, WNT5A- sorted


title: Sorted mesenchymal hGBM23 specimen, WNT5A+ tech Rep 2

description: Wnt5A+ cell sorted population of the mesenchymal GBM23 specimen

source_name: GBM#23, WNT5A+ sorted


title: RNAseq-lncRNAs_41


title: Sorted mesenchymal hGBM23 specimen, WNT5A- tech Rep 1


title: RNAseq-lncRNAs_10


title: G705 ATAC-seq

description: Raw file: G705_P9_SF_AT_1_AGGCAGAA_L003_R1.fastq.gz


title: AG04110

description: primary fibroblast cells

source_name: primary fibroblast cells


title: CON03_4_mucosa

status: Public on Dec 19 2016

city: Aalborg

first: Julie

middle: Støve

last: Bødker

address: Sdr. Skovvej 15

department: Department of Heamatology

country: Denmark

institute: Aalborg University Hospital

hyb_protocol: As described in the user guide, appendix A, of the The Encore™Biotin Module  (NuGEN)

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G. CEL-files generated using AGCC

data_processing:
The CEL-files produced by the Affymetrix Expression Console were preprocessed and summarized to gene level using the RMA algorithm with the Bioconductor package affy using custom CDF-files [Dai M et al. Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data http://dx.doi.org/10.1093/nar/gni179]
Probe set data extracted from custom CDF (HuEx-1_0-st-v2)
Probe set data extracted from custom CDF (HuEx-1_0-st-v2)

label: Biotin

label_protocol: The samples were prepared for hybridization to Affymetrix GeneChip Human Exon 1.0 ST Arrays using Affymetrix GeneChip WT Terminal Labeling and Controls Kit (P/N 901524)

growth_protocol: not applicable

extract_protocol: The frozen samples of the oral mucosa/nunonuclear cells were homogenized using TRIzolR Reagent (InvitrogenTM) and total RNA was isolated using the mirVanaTM miRNA Isolation Kit (AmbionR/InvitrogenTM) (Life Technologies Corporation). RNA amplification was performed using the “AmbionR WT Expression Kit” (Applied BiosystemsR) starting with 100 ng total RNA and a TP Basic Thermocycler real time PCR instrument (BiometraR). Amplificatio System (NuGEN Technologies, Inc., San Carlos, CA)

treatment_protocol: Consecutive homo sapiens buccal mucosa  and peripheral blood secured from 10 patients with multiple myeloma imediately before (day0), two days after (day2) and 21 days (day21) after high dose melphalan treatment (200mg/m2), and buccal mucosa and peripheral blood 10 healthy homo sapiens individuals. Mononuclear cells were isolated from the blood.

tag: mucositis grade

tag: person id

value: oral buccal mucosa


title: CON06_4_blood

value: blood mononuclear cells


title: CON03_4_blood


title: CON07_4_blood


title: PTC_19

status: Public on Nov 01 2016

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

institute: IRCCS Ospedale San Raffaele

hyb_protocol: Standard Agilent hybridization protocol

scan_protocol: Standard Agilent scanning protocol with Agilent SureScan microarray scanner (G2505C).

data_processing: Scanned images were processed with Agilent Feature Extraction v10.7 with default parameters to obtain raw data. Raw data were imported in R and processed using the AgiMicroRna package. microRNA-level processed signals were obtained using the RMA algorithm with quantile normalization.

source_name: papillary thyroid carcinoma

label_protocol: Total RNA from each sample was labeled according to the manufacturers recommendations.

extract_protocol: RNA was extracted from snap-frozen tissues with QIAzol reagent (Qiagen), followed by clean-up with RNeasy mini kit (Qiagen) according to the protocol provided by the manufacturer.

value: thyroid

tag: disease state

value: papillary thyroid carcinoma

tag: histological type

value: Tall-Cell


title: NT_4

source_name: normal thyroid

value: normal thyroid


title: NT_5


title: PTC_18

value: Classical


title: NT_1


title: NT_2


title: NT_3


title: WRN_miR_10

description: 82-6 primary human fibroblasts, PMID 11978740

data_processing: Genepix (version Pro 6.0.1.00). nCounter RCC files were imported into nSolver (Nanostring), quality control-verified and normalized to the geometric mean of the top 100 expressed miRNAs.^SAMPLE = GSM1535465

source_name: 82-6 primary fibroblast cells

value: primary fibroblast

tag: strain

value: WRN


title: CON01_4_blood


title: CON11_4_blood


title: CON10_4_blood


title: CON11_4_mucosa


title: CON07_4_mucosa


title: CON08_4_mucosa


title: CON04_4_blood


title: CON05_4_mucosa


title: CON06_4_mucosa


title: CON10_4_mucosa


title: CON04_4_mucosa


title: PTC_17

value: Follicular


title: CON01_4_mucosa


title: Sorted mesenchymal hGBM23 specimen, WNT5A+ tech Rep 1

value: glioblastoma


title: PTC_15


title: PTC_13


title: PTC_12


title: PTC_11


title: PTC_10


title: PTC_8


title: PTC_9

value: Other


title: PTC_3


title: PTC_6


title: PTC_7


title: PTC_2


title: PTC_1


title: PTC_16


title: PTC_14


title: PTC_5


title: PTC_4


title: CON08_4_blood


title: CON05_4_blood


title: ACC 4h_rep3

status: Public on Oct 01 2016

city: WINSTON SALEM

first: Gloria

middle: Kressin

last: Muday

state: North Carolina

address: 1834 Wake Forest Road

department: Biology

institute: Wake Forest University

description:
ACC4_3
gene expression data from 6 day old arabidopsis roots

hyb_protocol: Following fragmentation, 20 ug of labeled cRNA was hybridized for 16 hr at 45 degrees C on the Affymetrix GeneChips. GeneChips were washed and stained using the GeneChip 450 Fluidics Station according to standard Affymetrix operating procedures

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G system according to the standard Affymetrix protocol

data_processing: Raw data were normalized using systematic variation normalization, and the log2 of the signal intensity is reported.

source_name: 6 day old roots placed on ACC medium for 4 hours

label_protocol: Approximately 5ug of purified total RNA was processed to produce biotinylated cRNA targets followed by streptavidin-phycoerythrin fluorescent staining according to the standard Affymetrix 3’-IVT labeling protocol

growth_protocol: 6 days of growth in 100 umol/m2sec2 continuous cool white light on a nylon screen (03-100/32; Sefar Filtration) pressed tightly against 1xMS 1% sucrose media (pH 5.6)

extract_protocol: Root samples were ground in liquid nitrogen and the RNA was extracted using the Qiagen Plant RNeasy kit.  The RNA was then precipitated from the eluate with isopropanol

treatment_protocol: Nylon mesh with seedlings was transferred to a fresh control media or media containing 1 uM ACC at time 0

tag: agent

value: ACC medium

tag: time

value: 4 hours

value: seedling

value: 6 days old

value: root


title: TO_134_13June08

description: blood cells

source_name: blood cells

value: blood


title: ACC 12h_rep3

description:
ACC12_3
gene expression data from 6 day old arabidopsis roots

source_name: 6 day old roots placed on ACC medium for 12 hours

value: 12 hours

tag: developmental stage


title: ACC 24h_rep3

description:
ACC24_3
gene expression data from 6 day old arabidopsis roots

source_name: 6 day old roots placed on ACC medium for 24 hours

value: 24 hours


title: ACC 0h_rep3

description:
ACC0.0_3
gene expression data from 6 day old arabidopsis roots

source_name: 6 day old roots placed on ACC medium for < 5 minutes

value: <5 minutes


title: ACC 8h_rep2

description:
ACC8_2
gene expression data from 6 day old arabidopsis roots

source_name: 6 day old roots placed on ACC medium for 8 hours

value: 8 hours


title: ACC 12h_rep2

description:
ACC12_2
gene expression data from 6 day old arabidopsis roots


title: ACC 24h_rep2

description:
ACC24_2
gene expression data from 6 day old arabidopsis roots


title: ACC .5h_rep2

description:
ACC0.5_2
gene expression data from 6 day old arabidopsis roots

source_name: 6 day old roots placed on ACC medium for 30 minutes

value: 30 minutes


title: ACC 2h_rep2

description:
ACC2_2
gene expression data from 6 day old arabidopsis roots

source_name: 6 day old roots placed on ACC medium for 2 hours

value: 2 hours


title: ACC 8h_rep3

description:
ACC8_3
gene expression data from 6 day old arabidopsis roots


title: ACC 4h_rep1

description:
ACC4_1
gene expression data from 6 day old arabidopsis roots


title: ACC 24h_rep1

description:
ACC24_1
gene expression data from 6 day old arabidopsis roots


title: ACC 8h_rep1

description:
ACC8_1
gene expression data from 6 day old arabidopsis roots


title: ACC .5h_rep1

description:
ACC0.5_1
gene expression data from 6 day old arabidopsis roots


title: ACC 1h_rep1

description:
ACC1_1
gene expression data from 6 day old arabidopsis roots

source_name: 6 day old roots placed on ACC medium for 1 hour

value: 1 hour


title: ACC 12h_rep1

description:
ACC12_1
gene expression data from 6 day old arabidopsis roots


title: ACC 0h_rep1

description:
ACC0.0_1
gene expression data from 6 day old arabidopsis roots


title: ACC 4h_rep2

description:
ACC4_2
gene expression data from 6 day old arabidopsis roots


title: ACC 2h_rep3

description:
ACC2_3
gene expression data from 6 day old arabidopsis roots


title: ACC .5h_rep3

description:
ACC0.5_3
gene expression data from 6 day old arabidopsis roots


title: ACC 2h_rep1

description:
ACC2_1
gene expression data from 6 day old arabidopsis roots


title: ACC 0h_rep2

description:
ACC0.0_2
gene expression data from 6 day old arabidopsis roots


title: PB_CD56low_rep2

status: Public on May 13 2016

city: Saint Louis

first: Eugene

middle: M

last: Oltz

state: Missouri

address: 660 Euclid Ave, Campus Box 8118

department: Pathology & Immumonolgy

institute: Washington University in St Louis

description: Gene expression data

hyb_protocol: Products were hybridized to Affymetrix Human Gene 1.0 ST arrays according to the manufacturer’s protocol

data_processing: Gene expression levels were determined using the Affymetrix Expression Console software (v1.2.0.20) with gene-level RMA analysis and default settings

source_name: Peripheral blood

label_protocol: Purified RNA was amplified using Nugen Ovation Pico SL or Ovation Pico kits and labeled using Nugen Encore Biotin kit.

extract_protocol: RNA was purified using Qiagen RNeasy Kits according to the manufacturer’s protocol.

tag: cell type

value: NK

tag: markers


title: AMAP2

status: Public on Mar 29 2016

description: TAMH cells

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000 through the University of Washington Functional Genomics Laboratory in the Center for Ecogenetics and Environmental Health (http://depts.washington.edu/ceeh/ServiceCores/FC1/FC1.html).

source_name: TAMH cells

label_protocol: For microarray hybridization, RNA was processed for hybridization to Affymetrix Mouse Gene 430A_2 Array through a core facility in the Functional Genomics Laboratory in the Center for Ecogenetics and Environmental Health at the University of Washington according to the manufacturer's instructions.

extract_protocol: RNA was isolated from TAMH cells dosed with 2 mM APAP, 2 mM AMAP or control culture media for 2, 6 or 24 hours.  For each treatment, cells were grown to confluence in two 150 mm2 tissue culture dishes and dosed.  At the end of each treatment, cells were harvested using a rubber scraper and collected by centrifugation.  Following an ice-cold DPBS wash step, Trizol reagent was added.  Once vortexed, the cell suspension was passed through a 22G needle multiple times to ensure complete cell lysis.  Following the addition of a chloroform solution and a centrifugation step, the aqueous phase of the sample mixture was isolated and dissolved in 70% ethanol.  The resulting mixture was loaded onto a Qiagen RNeasy column, Valencia, CA, and purified total RNAs were eluted according to the manufacturer’s protocol.

value: TAMH

value: liver


title: APAP6

description: TAMH cells


title: APAP24

description: TAMH cells


title: AMAP6

description: TAMH cells


title: APAP2

description: TAMH cells


title: AMAP24

description: TAMH cells


title: PB_CD56low_rep1

description: Gene expression data


title: PB_CD56low_rep4

description: Gene expression data


title: CONTROL2

description: TAMH cells


title: CONTROL24

description: TAMH cells


title: CONTROL6

description: TAMH cells


title: c.9.Gills

status: Public on Mar 22 2016

hyb_protocol: The standard hybridization protocol was used as recommended by Agilent

scan_protocol: Arrays were scanned using an Agilent DNA microarray scanner through the University of Washington Functional Genomics Laboratory in the Center for Ecogenetics and Environmental Health (http://depts.washington.edu/ceeh/ServiceCores/FC1/FC1.html).

data_processing: Expression level data from the Agilent Microarray Scanner and Feature Extraction Software were normalized using a multiple-loess algorithm (Sasik et al., 2004).

organism: Oncorhynchus kisutch

label_protocol: The standard labeling protocol was used as recommended by Agilent

extract_protocol: The gill, liver and olfactory tissues were dissected for subsequent RNA isolation. Total RNA was isolated using the RNeasy Mini Kit (Qiagen Inc, Valencia, CA) according to the vendor's protocol and stored at -80C.

treatment_protocol: Fish were transferred and sequentially acclimated to hypersaline water up to concentrations of <0.5 (control), 8 (low), 16 (medium), and 32 ppth (high) saline concentrations, with an increase of 4 ppth every two days (CrystalSea Marine Mix, Marine Enterprises International, Baltimore, MA) in 24 L tanks.

value: gills

value: juvenile

tag: body weight


title: PB_CD56low_rep3

description: Gene expression data


title: ACC 1h_rep2

description:
ACC1_2
gene expression data from 6 day old arabidopsis roots

value: ACC medium

tag: age


title: c.7.Liver

tag: tissue


title: c.3.Liver


title: L.7.Liver


title: M.10.Rosettes

value: olfactory rosettes


title: L.5.Gills


title: H.9.Rosettes


title: H.7.Rosettes


title: H.7.Gills


title: L.7.Gills


title: L.2.Liver


title: c.9.Liver


title: M.10.Gills


title: H.8.Rosettes


title: M.4.Gills


title: M.9.Rosettes


title: L.2.Rosettes


title: c.6.Gills


title: L.2.Gills


title: L.6.Rosettes


title: H.9.Liver


title: M.4.Rosettes


title: L.6.Gills


title: H.8.Liver


title: M.3.Rosettes


title: M.4.Liver


title: H.10.Rosettes


title: c.7.Gills


title: c.6.Liver


title: H.7.Liver


title: L.5.Liver


title: c.7.Rosettes


title: M.3.Gills


title: M.10.Liver


title: L.5.Rosettes


title: c.3.Gills


title: c.6.Rosettes


title: H.8.Gills


title: H.10.Gills


title: L.7.Rosettes


title: c.3.Rosettes


title: L.6.Liver


title: M.3.Liver


title: c.9.Rosettes


title: H.10.Liver


title: M.9.Liver


title: M.9.Gills


title: H.9.Gills


title: Epo_Y_3F_9

status: Public on Dec 11 2015

data_processing: Affymetrix Expression Console, core RMA normalization log2

source_name: hippocampus cells

label_protocol: For microarray hybridization, RNA was processed for hybridization to Affymetrix Mouse Exon 1.0 ST Arrays through a core facility in the Functional Genomics Laboratory in the Center for Ecogenetics and Environmental Health at the University of Washington according to the manufacturer's instructions.

extract_protocol: After removal, the brain was placed in a grid submerged in iced 100 mM phosphate buffered saline (PBS). A 3 mm coronal slice was removed using the mammillary bodies as a posterior landmark. The right hippocampus (ipsilateral to carotid artery ligation) was isolated, and total RNA was purified following manufactures’ directions (Cartagen Molecular Systems, San Carlos, CA), and stored at -70?C. The quality of the total RNA and cRNA were evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies Inc. Palo Alto, CA). RNA yields were quantified by measuring the absorbance of a 1:50 dilution of the samples with an UV spectrophotometer at 260nm and 280nm. Only total RNA and subsequent cRNA samples with appropriate size distribution and an A260:A280 ratio of 1.8 – 2.1 were used for analysis. The manufacturer’s protocols for the GeneChip platform by Affymetrix (Santa Clara, CA) were used. These methods include the synthesis of first- and second-strand cDNAs, the purification of double-stranded cDNA, the synthesis of cRNA by in vitro transcription (IVT), the recovery and quantitation of biotin-labeled cRNA, the fragmentation of this cRNA and subsequent hybridization to the microarray slide, post-hybridization washings, and the detection of the hybridized cRNAs using a streptavidin-coupled fluorescent dye.

value: BALB-c

value: 10 days

tag: mouse status

value: brain-injured

tag: treated with

value: high-dose recombinant erythropoietin

value: hippocampus


title: Sham_Y_3F_11

value: sham-injured


title: Sham_N_3G_2


title: Sham_Y_3E_10


title: Sham_N_3F_5


title: Epo_Y_3D_3


title: Epo_N_3F_1


title: Sham_N_3D_21


title: Sham_N_3D_26


title: Epo_N_3D_32


title: Sham_N_3E_14


title: Sham_Y_3D_33


title: Epo_N_3D_30


title: Epo_N_3D_13


title: Epo_N_3A_5


title: Sham_Y_3A_3


title: Epo_N_3D_15


title: Epo_Y_3D_17


title: Sham_Y_3C_1


title: Epo_Y_3D_24


title: Sham_N_3B_11


title: Sham_Y_3D_14


title: t0.miR.17

status: Public on Oct 05 2015

description: Hippocampal brain

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000 through the University of Washington Functional Genomics Laboratory CHDD Genomics Core Laboratory.

data_processing: Bioconductor software, RMA normalization log2

source_name: Hippocampal brain_untreated control

label_protocol: For microarray hybridization, RNA was processed for hybridization to Affymetrix microRNA 2.0 Arrays through a core facility in the CHDD Genomics Core Laboratory at the University of Washington according to the manufacturer's instructions.

extract_protocol: RNA extraction was performed by the CHDD Genomics Core Laboratory followed by the manufacturer’s protocols using the GeneChip platform by Affymetrix.

tag: gender

value: male

value: postnatal day 9 (P9)

value: Hippocampal brain

value: 0 mg/kg morphine (untreated control)


title: t2.miR.3

description: Hippocampal brain

source_name: Hippocampal brain_MS2

value: 2 mg/kg morphine + stress (MS2)


title: t0.miR.18

description: Hippocampal brain


title: t2.miR.4

description: Hippocampal brain


title: t2.miR.6

description: Hippocampal brain


title: t5.miR.14

description: Hippocampal brain

source_name: Hippocampal brain_MS5

value: 5 mg/kg morphine + stress (MS5)


title: t5.miR.12

description: Hippocampal brain


title: t0.miR.16

description: Hippocampal brain


title: Epo_Y_3A_15


title: Epo_Y_3A_1


title: saline_M05267

status: Public on Aug 05 2015

organism: Macaca nemestrina

source_name: fetal lung tissue

label_protocol: For microarray hybridization, RNA was processed for hybridization to Affymetrix Rhesus Macaque Genome Arrays through a core facility in the Functional Genomics Laboratory in the Center for Ecogenetics and Environmental Health at the University of Washington according to the manufacturer's instructions.

value: fetal lung


title: saline_5109


title: saline_M99183


title: gbs_M02217


title: saline_5081


title: gbs_5096


title: gbs_K94129


title: gbs_L99192


title: t0.16

description: Hippocampal brain

hyb_protocol: The standard hybridization protocol was used as recommended by Agilent.

scan_protocol: Arrays were scanned using the Axon scanner.

data_processing: Bioconductor Software , RMA normalization, log2

label_protocol: For microarray hybridization, RNA was processed for hybridization to Agilent Technologies Arraythrough a core facility in the Functional Genomics Laboratory CHDD Genomics Core Laboratory at the University of Washington according to the manufacturer's instructions.

extract_protocol: RNA extraction was performed by the CHDD Genomics Core Laboratory followed by the manufacturer’s protocols using the Agilent 8x60K arrays.


title: t2.3

description: Hippocampal brain


title: t5.9

description: Hippocampal brain


title: t5.13

description: Hippocampal brain


title: t5.14

description: Hippocampal brain


title: 13732473_2007

status: Public on Aug 03 2015

description: Using sets of wild-type C57BL/6J mice, we established primary cortical neuron cultures from P0 littermates, and cultured these neurons (n = 3 / set) in CM or NLM for 4 hrs.

hyb_protocol: Hybridizations were performed using Exiqon's protocol.

scan_protocol: Arrays were scanned using the Axon 4000B Scanner through the Functional Genomics Laboratory (UW).

data_processing: Genepix (version Pro 6.0.1.00)

source_name: primary cortical neurons

label_protocol: RNA was 3' end labeled with Hy3 following the Exiqon miRCURY LNA Labeling Kit protocol.

extract_protocol: Total RNA extracted using miRNeasy kit (Qiagen) following manufacturer's instructions.

tag: treatment

value: NLM (nutrient limited media)

value: primary cortical neurons

label_protocol: RNA was 3' end labeled with Hy5 following the Exiqon miRCURY LNA Labeling Kit protocol.

value: CM (complete media)


title: 13732474_2007


title: 13732475_2007


title: t2.4

description: Hippocampal brain


title: t2.1

description: Hippocampal brain


title: t5.12

description: Hippocampal brain


title: 13732485_2007


title: t0.17

description: Hippocampal brain


title: t0.19

description: Hippocampal brain


title: t0.18

description: Hippocampal brain


title: t0.15

description: Hippocampal brain


title: t5.8

description: Hippocampal brain


title: t2.5

description: Hippocampal brain


title: t2.7

description: Hippocampal brain


title: gbs_A03159


title: saline_4105


title: 13732480_2007


title: 13732481_2007


title: mouse_heart20_young

status: Public on Jul 03 2015

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000.

data_processing: Bioconductor GCRMA normalization log2

source_name: heart

label_protocol: Total RNA (2 ug) was labeled and hybridized to the Affymetrix GeneChip Mouse Genome 430 2.0 Arrays and hybridized according to manufacurer’s instructions.

extract_protocol: Cardiac ventricle total RNA from 10 young (4-6 month) and 10 old (25-28 month) mice was prepared and hybridized to Affymetrix™GeneChip® MOE430 2.0 arrays. Total RNA was prepared from frozen tissues using the Qiagen RNeasy kit following homogenization in Trizol (Invitrogen). Genomic DNA was prepared using the Qiagen Dneasy kit.

treatment_protocol: 10 young (4-6 month) and 10 old (25-28 month) C57BL/6J male mice were multiply housed in ventilated cages in a specific pathogen free barrier facility at the University of Washington on a 12/12-h light/dark cycle. All animal procedures were approved by the University of Washington Animal Care and Use Committee.


title: mouse_heart17_young

description: C57BL/6J male mice were multiply housed in ventilated cages in a specific pathogen free barrier facility at the University of Washington on a 12/12-h light/dark cycle. All animal procedures were approved by the University of Washington Animal Care and Use Committee.


title: mouse_heart18_young

tag: C57BL/6J male mice were multiply housed in ventilated cages in a specific pathogen free barrier facility at the University of Washington on a 12/12-h light/dark cycle.


title: mouse_heart15_young


title: mouse_heart12_young


title: mouse_heart2_old


title: mouse_heart19_young


title: mouse_heart1_old


title: mouse_heart9_old


title: mouse_heart8_old


title: mouse_heart7_old


title: mouse_heart4_old


title: mouse_heart16_young


title: mouse_heart14_young


title: mouse_heart10_old


title: mouse_heart6_old


title: mouse_heart11_young


title: mouse_heart3_old


title: mouse_heart5_old


title: mouse_heart13_young


title: SJMLL024-SOM-METHYLATION

status: Public on Mar 24 2015

city: Memphis

first: Steven

last: Paugh

state: TN

address: 262 Danny Thomas Place

department: Pharmaceutical Sciences Department

institute: St. Jude Children's Research Hospital

description: DNA methylation data

hyb_protocol: Illuminia HumanMethylation27

scan_protocol: Illuminia HumanMethylation27

data_processing: Average Beta

label: Cy3 and Cy5

source_name: Leukemia cells

label_protocol: Illuminia HumanMethylation27

extract_protocol: Qiagen

tag: source

value: Primary Sample


title: SJETV085-SOM-METHYLATION

description: DNA methylation data


title: SJPHALL010-SOM-METHYLATION

description: DNA methylation data


title: SJETV021-SOM-METHYLATION

description: DNA methylation data


title: SJETV084-SOM-METHYLATION

description: DNA methylation data


title: SJETV095-SOM-METHYLATION

description: DNA methylation data


title: SJMLL004-SOM-METHYLATION

description: DNA methylation data


title: SJHYPER091-SOM-METHYLATION

description: DNA methylation data


title: t5.miR.9

description: Hippocampal brain


title: SJDOWN014-SOM-METHYLATION

description: DNA methylation data


title: SJHYPER121-SOM-METHYLATION

description: DNA methylation data


title: SJHYPER116-SOM-METHYLATION

description: DNA methylation data


title: SJE2A035-SOM-METHYLATION

description: DNA methylation data


title: SJBALL117-SOM-METHYLATION

description: DNA methylation data


title: SJHYPER119-SOM-METHYLATION

description: DNA methylation data


title: SJERG015-SOM-METHYLATION

description: DNA methylation data


title: SJBALL197-SOM-METHYLATION

description: DNA methylation data


title: SJMLL032-SOM-METHYLATION

description: DNA methylation data


title: SJHYPER106-SOM-METHYLATION

description: DNA methylation data


title: SJHYPER150-SOM-METHYLATION

description: DNA methylation data


title: mSalineControl_M05267

status: Public on Nov 18 2014

tag: subject

value: pregnant monkeys at 118-125 days gestation

tag: sample group

value: choriodecidual inoculation of saline

tag: time point

value: 7 days after saline inoculation

value: amniotic epithelium


title: SJBALL092-SOM-METHYLATION

description: DNA methylation data


title: SJETV111-SOM-METHYLATION

description: DNA methylation data


title: SJHYPER137-SOM-METHYLATION

description: DNA methylation data


title: mSalineControl_05109


title: mSalineControl_M99183


title: BLM_9

status: Public on Jun 12 2014

description: primary fibroblast cells

data_processing: Affymetrix Expression Console Software , RMA normalization, log2

source_name: primary fibroblast cells

label_protocol: For microarray hybridization, RNA was processed for hybridization to Affymetrix Human Exon 1.0 ST Array through a core facility in the Laboratory of Molecular Technology (NCI-Frederick) according to the manufacturer's instructions.

extract_protocol: RNA was isolated from primary fibroblast cultures when 75 percent confluent. Cells were washed in 1X PBS, scrapped off plates and collected as pellets that were stored at -80 C. Total RNA was isolated using TRIZOL reagent, following the manufacturer’s protocol (Invitrogen).

value: primary fibroblast

tag: strain

tag: group

value: BLM


title: SJE2A025-SOM-METHYLATION

description: DNA methylation data


title: SJMLL033-SOM-METHYLATION

description: DNA methylation data


title: BLM_7

description: primary fibroblast cells


title: mGBS_L99192

source_name: amniotic epithelium tissue_GBS inoculated

value: choriodecidual Group B Streptococcus (GBS) inoculation

value: 4 days after GBS inoculation


title: mGBS_05096


title: mGBS_M02217


title: mSalineControl_05081


title: mGBS_K94129


title: BLM_8

description: primary fibroblast cells


title: mGBS_A03159


title: BLM_4

description: primary fibroblast cells

value: NS


title: GM16891

description: primary fibroblast cells

tag: cell line

tag: blm mutation

value: homozygous (Q645X missen mutation of BLM protein)

tag: clinical features

value: Bloom syndrome

value: Male


title: BLM_2

description: primary fibroblast cells

tag: cell type

value: control


title: GM16882

description: primary fibroblast cells

value: compound heterozygous (3261delT and 2281delT of RECQL3 gene)

tag: age

value: Female


title: GM16883

description: primary fibroblast cells

value: compound heterozygous ([2015A>G] and [IVS5-2A>G] of RECQL3 gene)


title: GM16859

description: primary fibroblast cells

value: homozygous (6-bp del/7-bp ins] at nucleotide 2,281 of RECQL3 gene)


title: GM16881

description: primary fibroblast cells

value: homozyguous (2293delC of RECQL3 gene)


title: BLM_3

description: primary fibroblast cells


title: GM03498

description: primary fibroblast cells

value: compound heterozygous (2281delT and 3233delT of RECQL3 gene)


title: GM07532

description: primary fibroblast cells

value: Wildtype

value: Not clinically affected


title: GM05289

description: primary fibroblast cells

value: primary fibroblast

value: homozygous (1544insA of RECQL3 gene)


title: GM08398

description: primary fibroblast cells


title: GM02674

description: primary fibroblast cells


title: BLM_1

description: primary fibroblast cells


title: GM02520

description: primary fibroblast cells

value: compound hererozygous (2293delC and  deletion of exon 15 resulting in a frameshift )


title: GM02548

description: primary fibroblast cells

value: compound hererozygous (1544insA and  T2328C transition of the RECQL3 gene)


title: GM16886

description: primary fibroblast cells

value: Q700X missen mutation in BLM protein


title: GM03402

description: primary fibroblast cells

value: homozygous (2281delT of RECQL3 gene)


title: GM08402

description: primary fibroblast cells


title: GM02085

description: primary fibroblast cells

value: homozygous (6-bp del/7-bp insertion at nucleotide 2281 of REQL3 gene)

value: Bloom syndrome


title: GM03377

description: primary fibroblast cells

value: Male


title: GM04260

description: primary fibroblast cells


title: GM02932

description: primary fibroblast cells


title: SJE2A030-SOM-METHYLATION

description: DNA methylation data

value: Primary Sample


title: GM01651

description: primary fibroblast cells

value: Female


title: GM01492

description: primary fibroblast cells

value: homozygous (2281delT of RECQL3) and T>G transversion resulting a transcated p53 protein


title: GM01948

description: primary fibroblast cells


title: GM00730

description: primary fibroblast cells


title: GM00969

description: primary fibroblast cells


title: GM00497

description: primary fibroblast cells


title: GM16890_miR

description: primary human fibroblasts

label_protocol: total RNA (5 micro-g) was converted to biotin-labeled complementary DNA, hybridized onto the chips, and processed by direct detection of the biotin-containing transcripts by streptavidin-Alexa 647 conjugate through a core facility in the Laboratory of Molecular Technology (NCI-Frederick) according to the manufacturer's instructions.

extract_protocol: Total RNA samples from fibroblasts were isolated using Qiagen’s miRNAeasy Mini Kit (Qiagen, Valencia, CA). RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA), and only samples of high quality, defined by distinct 28S and 18S rRNA bands together with a RIN (RNA integrity number) > 7, were used for further analyses.

value: F


title: GM16882_miR

description: primary human fibroblasts

value: compound hererozygous (2293delC and deletion of exon 15 resulting in a frameshift )


title: GM16891_miR

description: primary human fibroblasts

value: M


title: GM16883_miR

description: primary human fibroblasts

value: compound hererozygous (1544insA and T2328C transition of the RECQL3 gene)


title: GM16886_miR

description: primary human fibroblasts

value: Wildtype

value: Not clinically affected


title: GM16881_miR

description: primary human fibroblasts

value: primary fibroblast


title: GM16859_miR

description: primary human fibroblasts


title: GM03377_miR

description: primary human fibroblasts

value: homozyguous (2293delC of RECQL3 gene)


title: GM05289_miR

description: primary human fibroblasts


title: GM03402_miR

description: primary human fibroblasts


title: GM03651_miR

description: primary human fibroblasts

value: compound heterozygous (3261delT and 2281delT of RECQL3 gene


title: GM03498_miR

description: primary human fibroblasts


title: GM04260_miR

description: primary human fibroblasts

value: compound heterozygous ([2015A>G] and [IVS5-2A>G] of RECQL3 gene)


title: GM00408

description: primary fibroblast cells


title: GM02548_miR

description: primary human fibroblasts


title: GM02674_miR

description: primary human fibroblasts

value: homozygous (6-bp del/7-bp ins] at nucleotide 2,281 of RECQL3 gene)


title: GM02932_miR

description: primary human fibroblasts


title: GM02185_miR

description: primary human fibroblasts


title: GM08398_miR

description: primary human fibroblasts

value: homozygous (Q645X missen mutation of BLM protein)


title: GM01651_miR

description: primary human fibroblasts

value: homozygous (1544insA of RECQL3 gene)

value: Bloom syndrome


title: GM01948_miR

description: primary human fibroblasts


title: GM07532_miR

description: primary human fibroblasts

value: Q700X missen mutation in BLM protein


title: GM01492_miR

description: primary human fibroblasts


title: GM02085_miR

description: primary human fibroblasts


title: BLM_miR_9

description: 82-6 primary human fibroblasts

data_processing: Genepix (version Pro 6.0.1.00). nCounter RCC files were imported into nSolver (Nanostring), quality control-verified and normalized to the geometric mean of the top 100 expressed miRNAs.

source_name: 82-6 primary fibroblast cells

label_protocol: For microarray hybridization, RNA was processed for hybridization as recommended by  the Nanostring nCounter Human miRNA Expression Assay Kit (Nanostring, Seattle, WA) through a core facility in the Laboratory of Molecular Technology (NCI-Frederick) according to the manufacturer's instructions.

value: BLM


title: BLM_miR_8

description: 82-6 primary human fibroblasts


title: BLM_miR_7

description: 82-6 primary human fibroblasts


title: GM00408_miR

description: primary human fibroblasts


title: GM00969_miR

description: primary human fibroblasts


title: GM02520_miR

description: primary human fibroblasts


title: BLM_miR_6

description: 82-6 primary human fibroblasts

value: NS


title: BLM_miR_4

description: 82-6 primary human fibroblasts


title: BLM_miR_1

description: 82-6 primary human fibroblasts


title: BLM_miR_3

description: 82-6 primary human fibroblasts


title: GM00497_miR

description: primary human fibroblasts

value: homozygous (2281delT of RECQL3 gene)


title: BLM_miR_5

description: 82-6 primary human fibroblasts


title: GM00730_miR

description: primary human fibroblasts

value: F


title: BLM_miR_2

description: 82-6 primary human fibroblasts


title: GM00499_miR

description: primary human fibroblasts

value: compound heterozygous (2281delT and 3233delT of RECQL3 gene

value: M


title: GM00811_miR

description: primary human fibroblasts

value: Wildtype


title: BLM_6

description: primary fibroblast cells


title: Wt-7

status: Public on May 12 2014

data_processing: Bioconductor software, GCRMA normalization log2

source_name: stromal cells, wildtype

label_protocol: For microarray hybridization, RNA was processed for hybridization to Affymetrix Mouse Gene 1.0 ST Array through a core facility in the Functional Genomics Laboratory in the Center for Ecogenetics and Environmental Health at the University of Washington according to the manufacturer's instructions.

extract_protocol: Total hepatic RNA was extracted with TriZol reagent (Invitrogen) according to a standard protocol. Mouse livers were fixed in 10% neutral buffered formalin or Methacarnoy (60% methanol, 30% chloroform and 10% acetic acid: v/v/v) overnight, and analyzed using standard histological techniques. IHC was performed using antibodies specific for BrdU (anti-mouse Dako, Carpinteria, CA), CD34 (anti-rat CD34, Cedar Lanes), vWF (Dako, A0082), anti-active caspase 3 (Cell Signaling), anti-PDGFRalpha (R&D AF1062) and, anti-PDGFRalpha (Cell Signaling).  Detection of the primary antibody was carried out using the appropriate biotinylated secondary antibody (Vectastain, Burlingame, CA) and the peroxidase DAB kit (Ventana, Tucson, AZ).  Nuclear incorporation of BrdU into liver cells was used to measure cell proliferation using the mouse on mouse (M.O.M.) kit (Vectastain) to detect NPCs and hepatocytes, and the number of mitotic figures were evaluated.

tag: strain/background

tag: genotype

value: wildtype

tag: tissue

value: liver

value: stromal cells


title: medCu4_pid_1117

status: Public on Apr 30 2014

description: olfactory rosettes

data_processing: Affymetrix Expression Console, RMA normalization log2

source_name: olfactory rosettes

label_protocol: For microarray hybridization, RNA was processed for hybridization to Affymetrix miRNA-2_0 Arrays through a core facility in the Functional Genomics Laboratory in the Center for Ecogenetics and Environmental Health at the University of Washington according to the manufacturer's instructions.

value: AB

value: olfactory rosettes, olfactory bulbs, and telencephalons

value: 16 ppb Cu


title: medCu1_pid_1117

description: olfactory rosettes


title: lowCu_pid_1039

description: olfactory rosettes

value: 6.3 ppb Cu


title: highCu4_pid_1117

description: olfactory rosettes

value: 40 ppb Cu


title: lowCu5_pid_1117

description: olfactory rosettes


title: control5_pid_1117

description: olfactory rosettes

value: control


title: control_pid_1039

description: olfactory rosettes


title: highCu_pid_1039

description: olfactory rosettes


title: highCu2_pid_1117

description: olfactory rosettes


title: Wt-9


title: control4_pid_1117

description: olfactory rosettes


title: Wt-6


title: Tg-3

source_name: stromal cells, Pdgf-c transgenic

value: Pdgf-c transgenic


title: Tg-5


title: Wt-5


title: Wt-2


title: mSalineControl_04105

value: pregnant monkeys at 118-125 days gestation

value: choriodecidual inoculation of saline

value: 7 days after saline inoculation

value: amniotic epithelium


title: Wt-8


title: Wt-4


title: Tg-2


title: Tg-7


title: Tg-6


title: Wt-1


title: lowCu4_pid_1117

description: olfactory rosettes


title: Tg-4


title: Tg-1


title: BLM_5

description: primary fibroblast cells

value: primary fibroblast

value: NS


title: Wt-3


title: gd19_3_small_int

status: Public on Oct 08 2013

hyb_protocol: The standard hybridization protocol was used as recommended by Affymetrix.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000 through the University of Washington Functional Genomics Laboratory in the Center for Ecogenetics and Environmental Health (http://depts.washington.edu/ceeh/).

data_processing: Bioconductor software, log2 RMA normalization.

source_name: gestational day 19, small intestine

label_protocol: For microarray hybridization, RNA was processed for hybridization to Affymetrix Mouse Gene 1.0 ST Arrays through a core facility in the Functional Genomics Laboratory in the Center for Ecogenetics and Environmental Health at the University of Washington according to the manufacturer's instructions.

extract_protocol: RNA extraction was performed by the CEEH Genomics Core Laboratory followed by the manufacturer’s protocols using the GeneChip platform by Affymetrix.

value: maternal small intestine

tag: gestational day


title: gd15_4_small_int

source_name: gestational day 15, small intestine


title: gd0_1_small_int

source_name: gestational day 0, small intestine


title: gd0_5_small_int


title: gd15_1_small_int


title: gd19_3_placenta

source_name: gestational day 19, placenta

value: placenta


title: gd19_1_small_int


title: gd0_2_small_int


title: gd10_3_small_int

source_name: gestational day 10, small intestine


title: gd7_5_5_small_int

source_name: gestational day 7.5, small intestine


title: gd19_5_placenta


title: gd15_5_small_int


title: gd19_2_placenta


title: gd7_5_2_small_int


title: gd19_2_small_int


title: gd19_6_small_int


title: gd10_1_small_int


title: gd7_5_3_small_int


title: gd0_4_small_int


title: gd7_5_4_small_int


title: gd19_4_placenta_2


title: gd15_3_small_int_2


title: gd10_6_small_int


title: gd19_4_small_int


title: gd7_5_6_small_int


title: gd15_2_small_int


title: gd0_6_small_int


title: gd10_4_small_int


title: gd10_2_small_int


title: gd15_3_placenta

source_name: gestational day 15, placenta


title: gd15_5_placenta


title: gd10_6_liver

source_name: gestational day 10, liver

value: maternal liver


title: gd15_2_liver

source_name: gestational day 15, liver


title: gd19_3_liver

source_name: gestational day 19, liver


title: gd10_3_placenta

source_name: gestational day 10, placenta


title: gd15_1_liver


title: gd19_1_liver


title: gd15_5_liver_2


title: gd10_5_liver


title: gd10_5_placenta


title: gd7_5_6_liver

source_name: gestational day 7.5, liver


title: gd7_5_3_liver


title: gd19_6_liver


title: gd7_5_2_liver


title: gd15_4_liver


title: gd10_4_liver


title: gd15_3_liver


title: gd10_4_placenta_2


title: gd15_4_placenta


title: gd19_1_placenta


title: gd10_2_placenta_2


title: gd19_2_liver_2


title: gd15_2_placenta


title: gd15_1_placenta


title: gd7_5_4_liver


title: gd19_4_liver


title: gd7_5_1_liver


title: gd10_1_placenta


title: gd10_2_liver


title: gd0_6_liver

source_name: gestational day 0, liver


title: gd10_3_liver


title: medCu_pid_1039

description: olfactory rosettes

tag: treatment


title: gd0_1_liver


title: gd0_2_liver_2


title: gd7_5_4_kidney

source_name: gestational day 7.5, kidney

value: maternal kidney


title: gd0_3_liver


title: gd7_5_2_kidney


title: gd7_5_3_kidney


title: gd10_1_kidney

source_name: gestational day 10, kidney


title: gd10_4_kidney


title: gd7_5_6_kidney


title: gd0_5_liver


title: gd19_1_kidney

source_name: gestational day 19, kidney


title: gd10_6_kidney


title: gd15_3_kidney

source_name: gestational day 15, kidney


title: gd15_4_kidney


title: gd0_5_kidney

source_name: gestational day 0, kidney


title: gd19_6_kidney_3


title: gd19_5_kidney


title: gd15_2_kidney


title: gd19_3_kidney


title: gd10_5_kidney


title: gd15_5_kidney


title: gd10_3_kidney


title: gd19_4_kidney


title: gd0_2_kidney


title: gd0_6_kidney


title: gd15_1_kidney


title: gd0_1_kidney


title: gd0_3_kidney


title: gd7_5_1_kidney


title: MPI-850_tissue

status: Public on Sep 25 2013

city: Regensburg

first: Christian

middle: W

last: Kohler

state: Bavaria

address: Am BioPark 9

department: Institute of Functional Genomics

institute: University of Regensburg

hyb_protocol: Affymetrix hybridization was carried on U133A GeneChips according to the manufacturer's recommendations. In brief, 15 microgram of Biotin-labelled and fragmented cRNA were mixed with 20x GeneChip Eukaryotic Hybridization Control (Affymetrix) and supplemented with B2 control oligonucletide, salmon sperm DNA, acetylated bovine serum albumin and hybridization buffer and water making up a total volume of 300 microliter

scan_protocol: After hybridization of night (16 hours, 45° C) the hybridization mixture was removed from the GeneChip and washing and staining of the GeneChips was performed in a fluidics station (Affymetrix). The detection of the Biotin-labeled cRNA was mediated by a streptavidin-phycoerythrin complex. The measurement of the fluorescence intensity was carried out in an Agilent scanner (GA2500)

data_processing: Probe level normalization was done using the calibration and variance stabilization method by Huber et al. (Bioinformatics 2002, PMID: 12169536). Probe-set summarization was performed using the median polish method on the normalised data (Irizarry et al. Nucleic Acids Research 2003, PMID: 12582260)

source_name: tumor

label_protocol: For Affymetrix GeneChip hybridization, 5 microgram of total RNA was employed to generate a double-stranded cDNA with the help of the INVITROGEN Superscript kit. After removal of small molecular components (Affymetrix Clean-up Module), Biotin-labelled cRNA was synthesized by application of the ENZO Labeling kit (T7 RNA polymerase). The concentration of the produced cRNA was determined photometrically (NanoDrop) and the size range of the labelled products was evaluated by BioAnalyzer (Agilent) measurement before and after fragmentation

extract_protocol: RNA was isolated using RNeasy Mini Kit (QIAGEN) and the concentration was determined photometrically (NanoDrop). The quality of the RNA was assessed based on the presence of the tht 18S and 28S tRNA by analysis of an aliquot in the Agilent BioAnalyzer (Agilent)

value: diffuse large B-Cell lymphoma

tag: dlbcl molecular subtype

value: germinal center B-cell-like (GCB)

tag: molecular diagnosis

value: intermediate


title: MPI-852_tissue


title: MPI-873_tissue

value: non-mBL


title: H2_SS8_01Nov07

status: Public on Aug 30 2013

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000 through the University of Washington Functional Genomics Laboratory in the Center for Ecogenetics and Environmental Health.

data_processing: Bioconductor, RMA normalization, log2.

source_name: hippocampus, SSS

label_protocol: RNA was processed for hybridization to Affymetrix Mouse Gene 1.0 ST Arrays through a core facility in the Functional Genomics Laboratory in the Center for Ecogenetics and Environmental Health at the University of Washington according to the manufacturer's instructions.

tag: gender

value: male

value: postnatal day 9

value: right hippocampus

value: severe stress + saline vehicle


title: H3_SS9_01Nov07

source_name: hippocampus, SSM

value: severe stress + morphine


title: H3_SS11_01Nov07

source_name: hippocampus, MSM

value: mild stress + morphine


title: H5_SS11_01Nov07

source_name: hippocampus, MSS

value: mild stress + saline vehicle


title: H5_SS9_01Nov07


title: H3_SS12_01Nov07

source_name: hippocampus, CC


title: H12_SS10_01Nov07


title: H6_SS11_01Nov07


title: H4_SS11_01Nov07


title: H2_SS12_01Nov07


title: H1_SS12_01Nov07


title: H2_SS11_01Nov07


title: H1_SS8_01Nov07


title: CC133

status: Public on Jun 30 2013

city: Changsha

first: Chao

last: Chen

state: Hunan

address: 110 Xiangya Road

department: State Key Lab of Medical Genetics

country: China

institute: Central South University

description:
human brain tissue
4437568030_F

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

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

data_processing:
BeadStudio software
Matrix signal intensities value definition: Unmethylated and methylated signal intensities [linked as supplementary file on Series record]

label: Cy5 and Cy3

source_name: cerebellum

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from Stanley human brain samples using Qiagen DNeasy Kit according to standard instructions

value: cerebellum

tag: batch

tag: pmi

tag: disease state

value: Schiz.


title: H1_SS11_01Nov07


title: CC125

description:
human brain tissue
4437568030_C

value: Unaffected control


title: H11_SS10_01Nov07


title: CC100

description:
human brain tissue
4437568030_G


title: CC144

description:
human brain tissue
4437568030_J


title: CC420

description:
human brain tissue
4437568030_H

value: BP


title: CC135_rep

description:
human brain tissue
4437568030_A


title: CC404_rep

description:
human brain tissue
4437568030_B


title: CC143

description:
human brain tissue
4437568030_E


title: CC116

description:
human brain tissue
4437568030_K


title: CC421

description:
human brain tissue
4437568030_D


title: CC136

description:
human brain tissue
4437568030_I


title: CC124

description:
human brain tissue
4437568030_L


title: CC110

description:
human brain tissue
4437568029_K


title: CC96

description:
human brain tissue
4437568029_L


title: CC108

description:
human brain tissue
4437568029_G


title: CC414

description:
human brain tissue
4437568028_I


title: CC128

description:
human brain tissue
4437568029_E


title: CC135

description:
human brain tissue
4437568029_I


title: CC97

description:
human brain tissue
4437568028_J


title: CC418

description:
human brain tissue
4437568029_F


title: CC416

description:
human brain tissue
4437568028_L


title: CC129

description:
human brain tissue
4437568029_J


title: CC134

description:
human brain tissue
4437568029_C


title: CC416_rep

description:
human brain tissue
4437568029_A


title: CC415

description:
human brain tissue
4437568028_K


title: CC413

description:
human brain tissue
4437568028_H


title: CC109

description:
human brain tissue
4437568029_D


title: CC419

description:
human brain tissue
4437568029_H


title: CC417

description:
human brain tissue
4437568029_B


title: CC90

description:
human brain tissue
4437568028_G


title: CC85

description:
human brain tissue
4437568028_E


title: CC91

description:
human brain tissue
4437568028_D


title: CC411

description:
human brain tissue
4437568024_G

value: Dep.


title: CC142

description:
human brain tissue
4437568028_F


title: CC103

description:
human brain tissue
4437568024_J


title: CC76

description:
human brain tissue
4437568024_F


title: CC89

description:
human brain tissue
4437568024_H


title: CC88

description:
human brain tissue
4437568024_L


title: CC76_rep

description:
human brain tissue
4437568028_A


title: CC93

description:
human brain tissue
4437568028_C


title: CC412

description:
human brain tissue
4437568024_I


title: CC86

description:
human brain tissue
4437568024_K


title: CC94

description:
human brain tissue
4437568028_B


title: CC71

description:
human brain tissue
4437568024_E


title: CC81

description:
human brain tissue
4437568012_K


title: CC59

description:
human brain tissue
4437568012_G


title: CC79_rep

description:
human brain tissue
4437568024_A


title: CC79

description:
human brain tissue
4437568012_I


title: CC92

description:
human brain tissue
4437568024_B


title: CC87

description:
human brain tissue
4437568024_C


title: CC95

description:
human brain tissue
4437568012_E


title: CC65

description:
human brain tissue
4437568012_B


title: CC80

description:
human brain tissue
4437568012_C


title: CC73

description:
human brain tissue
4437568006_K


title: CC410

description:
human brain tissue
4437568012_J


title: CC84

description:
human brain tissue
4437568012_H


title: CC82

description:
human brain tissue
4437568012_L


title: CC69

description:
human brain tissue
4437568012_F


title: CC105

description:
human brain tissue
4437568006_L


title: CC105_rep

description:
human brain tissue
4437568012_A


title: CC102

description:
human brain tissue
4437568024_D


title: CC58

description:
human brain tissue
4437568006_G


title: CC83

description:
human brain tissue
4437568012_D


title: CC72

description:
human brain tissue
4437568006_I


title: CC57

description:
human brain tissue
4437568006_F


title: CC78

description:
human brain tissue
4437568006_E


title: CC75

description:
human brain tissue
4437568006_J


title: CC127

description:
human brain tissue
4437568006_D


title: CC106_rep

description:
human brain tissue
4437568005_L


title: CC68

description:
human brain tissue
4437568005_K


title: CC409

description:
human brain tissue
4437568005_F


title: CC137

description:
human brain tissue
4437568006_H