title: nelso-00262: 15447-15419 #1905 GBM 133B 22603

value: LEFT TEMPORAL LOBE


title: nelso-00262: 6947-6919 #1681 GBM 133b 6-28-02

status: Public on Jun 14 2016

type: RNA

city: Rockville

first: Mervi

last: Heiskanen

state: MD

address: 9609 Medical Center Drive, 1W378

department: CBIIT

country: USA

institute: NCI

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

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Brain

tag: ^sample

tag: diseasestate

value: Glioblastoma

tag: Sex

value: male

tag: age

tag: celltype

value: Glia

tag: organismpart

value: Brain

tag: tumorgrading

value: Grade 4

tag: histology

value: GBM

tag: diseaselocation

value: LEFT THALAMIC


title: DB_iPTB_4

type: SRA

city: Columbus

first: William

middle: Edward

last: Ackerman IV

state: Ohio

address: N521 Doan Hall, 410 West 10th Avenue

department: Obstetrics and Gynecology

institute: The Ohio State University

library_source: transcriptomic

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

source_name: Basal plate decidual basalis, placenta

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

tag: tissue

value: placenta

tag: tissue compartment

value: Basal plate decidual basalis

tag: gestational age

value: 32 weeks gestation

tag: fetal gender

value: Male fetus

tag: diagnosis

value: preterm birth


title: nelso-00262: 15453-15422 #2158 GBM 133B 22603

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

value: female

value: RIGHT TEMPORAL LOBE


title: nelso-00262: 7192-7184#671astro133b62602

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

value: ASTRO III 671

value: astrocytomas

value: Grade 3

value: AA

value: RIGHT FRONTAL LOBE


title: nelso-00262: 15457-15425 #2079 GBM 133B 22603

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

value: Glioblastoma

value: male

value: Glia

value: RIGHT TEMPORAL PARIETAL LOB


title: DB_iPTB_3

value: 30.6 weeks gestation


title: DB_iPTB_2

value: placenta

value: 33 weeks gestation

value: Female fetus


title: nelso-00262: 10736-10730 #1667 GBM 133B 82702

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

value: Brain

value: Grade 4

value: GBM

value: RIGHT FRONTAL PARIETAL


title: DB_iPTB_5

value: Basal plate decidual basalis

value: 32.7 weeks gestation

value: preterm birth


title: DB_iPTB_1

value: 29.9 weeks gestation

value: Male fetus


title: DB_Term_3

value: 39.3 weeks gestation

value: normal


title: nelso-00262: 14628-14596 oligoIII #840 133B

value: OLIGO III 840

value: Oligodendroglial Tumor

value: female

value: Glia

value: Grade 3

value: AO

value: LEFT FRONTAL LOBE


title: nelso-00262: 7217-7211#744oligo133b62602

value: OLIGO III 744

value: male

value: Brain


title: VT_Term_1

source_name: Villous trophoblast, placenta

value: placenta

value: Villous trophoblast

value: 39.1 weeks gestation

value: Female fetus


title: nelso-00262: 15435-15411 #746 GBM 133B 22603

value: GBM 746

value: Glioblastoma

value: Grade 4

value: GBM


title: Endometrial-epithelial-cells_1016_secretory_modified

city: Setagaya

first: Kazuhiko

last: Nakabayashi

state: Tokyo

department: Department of Maternal-Fetal Biology

country: Japan

institute: National Research Institute for Child Health and Development

hyb_protocol: Hybridization and washing were performed in accordance with the instructions of the manufacturer. The resultant cRNAs were fragmented at 60oC for 30 min in dark, 600 ng of which were hybridized on the microarray at 65oC for 17 h. After washing, slides were scanned with the Agilent microarray scanner G2505C.

scan_protocol: Feature extraction software (version 10.7.3.1) was used to calculate signal intensities from the scanned images.

data_processing: Raw intensity data were imported into the Subio Platform software (https://www.subio.jp/), and normalized (75th percentile global normalization).

source_name: Human endometrial epithelial cells isolated by the modified protocol from the endometrium of the donor EM1016 in the secretory phase

label_protocol: Total RNAs (5 ng each) were amplified using Ovation Pico WTA System V2 (NuGen), and labelled with Cy3 using the Low Input QuickAmp Labeling Kit (Agilent).

growth_protocol: Isolation and culture of human endometrial cells by the conventional protocol:  Endometrial tissues were minced into pieces of less than 1 mm in DMEM containing 50 U/ml penicillin, 50 mg/ml streptomycin and 10% fetal bovine serum (FBS, Hyclone, Logan, USA). Minced tissues were incubated with 200 µg/ml collagenase NB4 (SERVA, Heidelberg, Germany) for 2 h at 37˚C with agitation. The dispersed endometrial tissue fragments/cells were separated into two fractions by filtration using the nylon mesh of 440 μm diameter pores (Costar, #3480), the residual tissue fragments and the filtrate. This first filtrate fraction was further separated into two fractions by filtration using the nylon mesh of 40 μm diameter pores (FALCON, #0556), the residual cell clumps and the second filtrate. The residual cell clumps, which are considered to be the pieces of glandular epithelia, were seeded onto a collagen I-coated 6cm tissue culture dish (CORNING, #345501) with MF-start medium (TOYOBO, #TMMFS-001) as the EMEC fraction. The dispersed cells in the second filtrate were collected by centrifugation, and seeded onto a collagen I-coated 6cm tissue culture dish with MF-start medium as the EMSC fraction. The EMEC outgrowths were trypsinized, collected, and counted for their cell numbers, at 5 days after seeding. The EMSCs were expanded through four serial passages to > 1.0 x 10^7 cells.    Isolation of human endometrial cells by the modified protocol:  First, the mincing of endometrial tissues and collagenase treatment were conducted in the same way as in the conventional protocol. Then, the dispersed endometrial tissue fragments/cell clumps were separated into two fractions by filtration using the nylon mesh of 40-µm diameter pores: the residual tissue fragments/cell clumps and the filtrate corresponding to the SC fraction in the conventional protocol. The cells in the SC fraction were collected by centrifugation (200 xg for 5 min), resuspended in 1 to 2  ml of MF-start medium, and kept at room temperature until seeding on tissue culture dishes. The residual tissue fragments and cell clumps were collected into a new 50 ml tube using 3 to 5 ml of Accumax (Innovative Cell Technologies, Inc.), which is a solution of proteolytic and collagenolytic enzymes, added to an equal volume of 0.25% Trypsin/EDTA (GIBCO, 25200-056) and then incubated for 10 min at room temperature with continuous pipetting (or mild agitation). The resultant cell suspension was added with 30 ml of DMEM containing 10% FBS (HyClone, SH30070) to inhibit proteolytic and collagenolytic activity in the enzymes. After filtration using a nylon mesh with 40 μm diameter pores, the cells in the filtrate were collected by centrifugation (200 xg for 5 min), resuspended in MF-start medium, and combined with the SC fraction cells. After the ratio of viable cells was determined by a trypan blue absorption assay using a portion of cells, the cells were seeded onto 10 cm collagen I-coated culture dishes (approximately 1 x 10^6 cells / dish), and maintained at 37°C in a humidified environment with 5% CO2 in air. After 48–96 h, the adherent cells were dissociated by TrypLE Express Enzyme (GIBCO, 12604-013), collected, and subjected to immunostaining followed by FACS.

extract_protocol: Total RNA was extracted using Allprep micro kit (Qiagen).

value: endometrium

tag: cell type

value: epithelial cell

tag: gender


title: DB_IAI_5

value: Basal plate decidual basalis

value: 25.6 weeks gestation

value: preterm birth


title: Endometrial-epithelial-cells_0808a_proliferative_modified

source_name: Human endometrial epithelial cells isolated by the modified protocol from the endometrium of the donor EM0808a in the proliferative phase

value: female


title: Endometrial-epithelial-cells_0808b_proliferative_conventional

source_name: Human endometrial epithelial cells isolated by the conventional protocol from the endometrium of the donor EM0808b in the proliferative phase


title: DB_IAI_4

value: 31.4 weeks gestation


title: DB_IAI_3

value: 25.4 weeks gestation


title: Endometrial-epithelial-cells_0808b_proliferative_modified

source_name: Human endometrial epithelial cells isolated by the modified protocol from the endometrium of the donor EM0808b in the proliferative phase


title: nelso-00262: 6927-6909 #2166 GBM 133b 6-28-02

value: Glia

value: Brain

value: LEFT FRONTAL LOBE


title: Endometrial-epithelial-cells_1018_proliferative_modified

source_name: Human endometrial epithelial cells isolated by the modified protocol from the endometrium of the donor EM1018 in the proliferative phase


title: DB_IAI_1

value: placenta

value: 26 weeks gestation


title: Endometrial-stromal-cells_1018_proliferative_modified

source_name: Human endometrial stromal cells isolated by the modified protocol from the endometrium of the donor EM1018 in the proliferative phase

value: stromal cell


title: Endometrial-stromal-cells_1016_secretory_modified

source_name: Human endometrial stromal cells isolated by the modified protocol from the endometrium of the donor EM1016 in the secretory phase


title: Endometrial-stromal-cells_1008_proliferative_conventional

source_name: Human endometrial stromal cells isolated by the conventional protocol from the endometrium of the donor EM1008 in the proliferative phase


title: nelso-00262: 8913-8900#650 oligo 133b 8502

value: OLIGO III 650

value: Oligodendroglial Tumor

value: Grade 3

value: AO


title: nelso-00262: 14610-14587 GBM #2017 133B

value: Glioblastoma

value: male

value: Grade 4

value: GBM

value: LEFT TEMPORAL LOBE


title: Endometrial-stromal-cells_0206_proliferative_conventional

source_name: Human endometrial stromal cells isolated by the conventional protocol from the endometrium of the donor EM0206 in the proliferative phase

value: endometrium

value: stromal cells

value: female


title: DB_IAI_2

value: Basal plate decidual basalis

value: 27.1 weeks gestation

value: Female fetus

value: preterm birth


title: Endometrial-epithelial-cells_0808a_proliferative_conventional

source_name: Human endometrial epithelial cells isolated by the conventional protocol from the endometrium of the donor EM0808a in the proliferative phase

value: epithelial cell


title: Endometrial-stromal-cells_0625_secretory_conventional

source_name: Human endometrial stromal cells isolated by the conventional protocol from the endometrium of the donor EM0625 in the secretory phase

value: stromal cell


title: Peritoneal_Macrophages_3

status: Public on Jun 12 2016

city: Boston

first: Laura

middle: M

last: Cox

state: MA

address: 77 Avenue Louis Pasteur

department: Neurology

institute: Brigham and Women's Hospital

hyb_protocol: Hydridized according to the manufacturer's protocol. http://www.nanostring.com/media/pdf/MAN_nCounter_Gene_Expression_Assay.pdf

scan_protocol: Scanned according to the manufacturer's protocol. http://www.nanostring.com/media/pdf/MAN_nCounter_Gene_Expression_Assay.pdf

data_processing: nSolver software, background and internal control standardization

label: nanostring oligonucleotide probe

organism: Mus musculus

source_name: peritoneal macrophages

label_protocol: Labeled according to the manufacturer's protocol. http://www.nanostring.com/media/pdf/MAN_nCounter_Gene_Expression_Assay.pdf

extract_protocol: Qiagen miRNeasy Mini Kit Cat#217004

value: peritoneum

value: macrophages

tag: mouse strain


title: Peritoneal_Macrophages_2


title: Splenic_DC_3

source_name: splenic dendritic cells

value: spleen

value: dendritic cells


title: Peritoneal_Macrophages_1


title: Sciatic nerve P25_mutant_biological replicate 3

status: Public on Jun 13 2016

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

description: gene expression data of mice with Sip1-deficient Schwann cells compared to controls

hyb_protocol: Affymetrix Hybridization Oven 645, Affymetrix Wash and stain Kit, Gene Chip Fluidics Station45 , Wash Protocol  MoGene-1.0.st-V1 universal FS 450-0007

scan_protocol: Affymetrix Gene Chip Scanner AGCC Scan control

data_processing: CEL files were processed with R/BioConductor using the 'affy' and 'limma' packages. Candidates for differential gene expression were identified using empirical bayes fit with a minimum fold-change of log2(2) and p-value<=0.05.

source_name: sciatic nerve isolated at P25

label_protocol: Ambion WT Expession Kit ,  Affymetrix Gene Chip WT Terminal Labeling and Hybridization User Manual(PN702880)

growth_protocol: Sciatic nerves of 3 mutant mice and 3 corresponding controls were isolated at the age of 25 days.

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

value: sciatic nerve

value: 25 days

tag: genotype

value: DhhCre::Sip1 flox/flox


title: WT biological replicate #3

city: Stanford

first: Marten

middle: CG

last: Winge

state: CA

address: 269 Campus Drive

department: Dermatology

institute: Stanford University

hyb_protocol: A total of 1500 ng of cRNA was hybridized for each array using standard Illumina protocols with streptavidin-Cy3 for detection.

scan_protocol: Slides were scanned on an Illumina Beadstation and analyzed using BeadStudio (Illumina, Inc).

data_processing: Samples were log-transformed and quantile normalized using Partek GS 6.6

source_name: Wholeskin WT pup D7

label_protocol: Each RNA sample was amplified using the Ambion Illumina RNA amplification kit with biotin UTP labeling. T7 oligo(dT) primer was used to generate single stranded cDNA,  followed by  second strand synthesis to generate double-stranded cRNA, which is then column purified. In vitro transcription was performed to synthesize biotin-labeled cRNA using T7 RNA polymerase. The cRNA was then column purified and measured.

extract_protocol: RNA was extracted using a Qiagen RNA miniprep kit. RNA concentration was determined with spectrophotometric analysis; purity analyzed with 260:280 absorbance ratios; RNA quality and integrity were assessed and ensured using Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA) and RNA 6000 NanoAssay.

tag: strain

value: CBA/CaJ

value: Whole skin

tag: genotype/variation

value: wild type


title: WT biological replicate #2

tag: age


title: Splenic_DC_2


title: Rac1 biological replicate #3

source_name: Wholeskin Rac1 pup D7

value: overexpressing epidermal specific (K14) activated mutant (V12) Rac1


title: Rac1 biological replicate #2


title: Splenic_DC_1


title: WT biological replicate #1


title: Rac1 biological replicate #1


title: Sciatic nerve P25_mutant_biological replicate 1


title: DKO BMDMs-LPS 3h

city: New York

first: Yingli

last: Shang

state: NY

address: 535E 70th Street

institute: Hospital for Special Surgery

description: Gene expression data from BMDMs

hyb_protocol: Fragmented aRNAs (10 ug per sample) were processed for hybridization to GeneChip Mouse Genome 430 2.0 according to the manufacturer's instruction (Affymetrix).

scan_protocol: GeneChips were scanned using Hewlett-Packard Gene Array Scanner G2500A.

data_processing: Genespring v11.0 (Agilent) was used to analyze the microarray data (Algorithm: ExpressionStat 5.0) and 2 fold indcution was set as cut-off.

source_name: primary macrophages

label_protocol: aRNA for microarray were amplified by using a MessageAMP Premier RNA Amplification Kit according to the manufacturer's protocol (Ambion)

growth_protocol: Bone marrows cells from WT and DKO mice were cultured for 5 days in DMEM supplemented with 10% FBS and 10% L929 cell supernatant as conditioned medium providing macrophage colony stimulating factor to generate BMDMs

extract_protocol: Total RNA were extracted with an RNeasy Mini kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: WT and DKO BMDMs were left untreated or exposed to 2 ng/ml cell culture grade LPS (Escherichia coli 0111:B4, Sigma) for 3 hours.

tag: strain background

value: Hes1 and Hey1 double knockout (DKO)

value: Bone marrow-derived macrophages (BMDMs)

tag: treated with

value: LPS for 3 hrs


title: Sciatic nerve P25_control_biological replicate 2

value: Sip1 flox/flox


title: Sciatic nerve P25_control_biological replicate 3


title: WT BMDMs-UT

description: Gene expression data from BMDMs

value: none (untreated control)


title: Liver_Kuppfer_Cell_2

source_name: kuppfer cells

value: liver

value: kuppfer cells


title: Liver_Kuppfer_Cell_1


title: Liver_Kuppfer_Cell_3


title: mille-00271: 46A25_U133A

status: Public on Jun 11 2016

source_name: breast cancer

value: breast cancer


title: Liver_DC_3

source_name: liver dendritic cells


title: mille-00271: 71A50_U133A


title: WT BMDMs-LPS 3h

description: Gene expression data from BMDMs


title: mille-00271: 297C26_U133A


title: mille-00271: 49A07_U133A


title: mille-00271: 48A46_U133A


title: mille-00271: 224C93_U133A


title: mille-00271: 188B13_U133A


title: Sciatic nerve P25_control_biological replicate 1


title: mille-00271: 35C29_U133A


title: mille-00271: 146B39_U133A


title: mille-00271: 9B52_U133A


title: Liver_DC_1


title: Liver_DC_2


title: mille-00271: 257C87_U133A


title: mille-00271: 249C42_U133A


title: mille-00271: 231C80_U133A


title: mille-00271: 54A09_U133A


title: mille-00271: 86A40_U133A


title: Sciatic nerve P25_mutant_biological replicate 2


title: mille-00271: 174B41_U133A


title: mille-00271: 113B11_U133A


title: mille-00271: 39C24_U133A


title: mille-00271: 162B98_U133A


title: mille-00271: 182B43_U133A


title: mille-00271: 58A50_U133A


title: mille-00271: 112B55_U133A


title: mille-00271: 122B81_U133A


title: mille-00271: 226C06_U133A


title: mille-00271: 47A87_U133A


title: mille-00271: 101B88_U133A


title: mille-00271: 102B06_U133A


title: mille-00271: 180B38_U133A


title: mille-00271: 181B70_U133A


title: mille-00271: 38C94_U133A


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title: mille-00271: 44A53_U133A


title: mille-00271: 163B27_U133A


title: mille-00271: 89A64_U133A


title: mille-00271: 90A63_U133A


title: mille-00271: 193B72_U133A


title: DKO BMDMs-UT

description: Gene expression data from BMDMs


title: mille-00271: 271C71_U133A


title: mille-00271: 296C95_U133A


title: mille-00271: 223C51_U133A


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title: mille-00271: 307C50_U133A


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title: mille-00271: 114B68_U133A


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title: mille-00271: 8B87_U133A


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title: mille-00271: 176B74_U133A


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title: mille-00271: 256C45_U133A


title: mille-00271: 304C89_U133A


title: mille-00271: 238C87_U133A


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title: mille-00271: 275C70_U133A


title: mille-00271: 185B44_U133A


title: mille-00271: 241C01_U133A


title: mille-00271: 255C06_U133A


title: mille-00271: 237C56_U133A


title: nelso-00262: 14618-14591 GBM #938 133B

source_name: Brain

tag: ^sample

value: GBM 938

tag: diseasestate

value: Glioblastoma

tag: Sex

value: male

tag: celltype

value: Glia

tag: organismpart

value: Brain

tag: tumorgrading

value: Grade 4

value: GBM

value: LEFT FRONTAL LOBE


title: mille-00271: 131B79_U133A


title: mille-00271: 217C79_U133A


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title: mille-00271: 84A44_U133A


title: mille-00271: 248C91_U133A


title: mille-00271: 36C17_U133A


title: mille-00271: 143B81_U133A


title: mille-00271: 316C65_U133A


title: mille-00271: 191B79_U133A


title: mille-00271: 207C08_U133A


title: mille-00271: 243C70_U133A


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title: mille-00271: 216C61_U133A


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title: mille-00271: 233C91_U133A


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title: mille-00271: 294C04_U133A


title: mille-00271: 21C28_U133A


title: mille-00271: 173B43_U133A


title: mille-00271: 128B48_U133A


title: mille-00271: 104B91_U133A


title: mille-00271: 151B84_U133A


title: mille-00271: 272C88_U133A


title: mille-00271: 158B84_U133A


title: mille-00271: 313A87_U133A


title: mille-00271: 140B91_U133A


title: mille-00271: 65A68_U133A


title: mille-00271: 179B28_U133A


title: mille-00271: 168B51_U133A


title: mille-00271: 138B34_U133A


title: mille-00271: 253C20_U133A


title: mille-00271: 262C85_U133A


title: mille-00271: 246C75_U133A


title: mille-00271: 208C06_U133A


title: mille-00271: 13B79_U133A


title: mille-00271: 189B83_U133A


title: mille-00271: 227C50_U133A


title: mille-00271: 178B74_U133A


title: mille-00271: 314B55_U133A


title: mille-00271: 168B51_U133B


title: mille-00271: 166B79_U133A


title: mille-00271: 269C68_U133A


title: mille-00271: 77A50_U133A


title: 4TO7 cells stably expressing TM4SF1, biological rep1 of 3

first: Jeffrey

last: Zhao

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

description: gene expression data from 4TO7 cells stably transduced with retroviral vectors encoding TM4SF1 (pBabepuro-TM4SF1)

hyb_protocol: Following fragmentation, cRNA were hybridized for Illumina GX mouse ref8 Array. Slides were washed and stained in the Illumina instrument.

scan_protocol: Slides were scanned using Illumina iScanner

data_processing: The data were analyzed with GenomeStudio using Illumina default analysis settings. No normalization and background correction are performed first, then quantile normalization and background correction are done.

source_name: 4TO7 cells stably transduced with retrovirus vectors encoding TM4SF1 (pBabepuro-TM4SF1)

label_protocol: Biotinylated cRNA were prepared according to the standard Illumina protocol from total RNA.

treatment_protocol: The lentivirus pLKO vector expression TM4SF1 shRNAs (TRCN0000112785 and TRCN0000112787) was used to make stable cell line knocking down TM4SF1. The retrovirus pBabepuro vector expression TM4SF1 was used to make stable cell line expressing TM4SF1.

tag: cell line


title: 4T1 cells with shRNA #5 targeting TM4SF1, biological rep1 of 3

description: gene expression data from 4T1 cells stably transduced with lentiviral vectors encoding a shRNA targeting TM4SF1 (shTM4SF1-5)


title: mille-00271: 219C42_U133B

tag: diagnosis


title: 4TO7 cells with pBabepuro, biological rep1 of 3

description: gene expression data from 4TO7 cells stably transduced with retroviral vectors (pBabepuro)

source_name: 4TO7 cells stably transduced with retrovirus vectors (pBabepuro)


title: 4T1 cells with shRNA #1 targeting TM4SF1, biological rep3 of 3

description: gene expression data from 4T1 cells stably transduced with lentiviral vectors encoding a shRNA targeting TM4SF1 (shTM4SF1-1)


title: mille-00271: 66A84_U133A


title: 4TO7 cells with pBabepuro, biological rep2 of 3


title: 4T1 cells with scramble shRNA, biological rep1 of 3

description: gene expression data from 4T1 cells stably transduced with lentiviral vectors encoding a control shRNA (shscramble)


title: 4T1 cells with shRNA #1 targeting TM4SF1, biological rep1 of 3

source_name: 4T1 cells stably transduced with lentiviral vectors encoding a shRNA targeting TM4SF1 (shTM4SF1-1)


title: mille-00271: 265C40_U133A


title: 4T1 cells with shRNA #1 targeting TM4SF1, biological rep2 of 3


title: 4T1 cells with shRNA #5 targeting TM4SF1, biological rep2 of 3

source_name: 4T1 cells stably transduced with lentiviral vectors encoding a shRNA targeting TM4SF1 (shTM4SF1-5)


title: mille-00271: 236C55_U133B


title: mille-00271: 146B39_U133B


title: mille-00271: 308C93_U133B


title: mille-00271: 73A01_U133A


title: 4T1 cells with scramble shRNA, biological rep2 of 3

source_name: 4T1 cells stably transduced with lentiviral vectors encoding a control shRNA (shscramble)


title: 4T1 cells with scramble shRNA, biological rep3 of 3


title: mille-00271: 67A43_U133A


title: mille-00271: 212C21_U133B


title: mille-00271: 296C95_U133B


title: mille-00271: 67A43_U133B


title: 4T1 cells with shRNA #5 targeting TM4SF1, biological rep3 of 3


title: 4TO7 cells stably expressing TM4SF1, biological rep3 of 3


title: mille-00271: 267C04_U133A


title: mille-00271: 236C55_U133A


title: mille-00271: 254C80_U133A


title: mille-00271: 27C82_U133A


title: mille-00271: 176B74_U133B


title: mille-00271: 87A79_U133B


title: mille-00271: 303C36_U133B


title: mille-00271: 182B43_U133B


title: mille-00271: 274C81_U133A


title: 4TO7 cells stably expressing TM4SF1, biological rep2 of 3


title: mille-00271: 278C80_U133A


title: 4TO7 cells with pBabepuro, biological rep3 of 3


title: mille-00271: 237C56_U133B


title: mille-00271: 23C52_U133A


title: mille-00271: 143B81_U133B


title: mille-00271: 282C51_U133B


title: mille-00271: 142B05_U133A


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title: mille-00271: 297C26_U133B


title: mille-00271: 258C21_U133B


title: mille-00271: 209C10_U133B


title: meyer-00191: 382T3

source_name: Lung

value: lung cancer

tag: diseasestaging

value: female

tag: normalizedsmokinghistoryinpackyears

value: Lung

tag: histology

value: Lung Adenocarcinoma


title: meyer-00191: 266T1


title: meyer-00191: NL2378

value: Normal

value: Normal Cell


title: meyer-00191: 382T1


title: mille-00271: 136B04_U133A


title: meyer-00191: 341T1-2


title: mille-00271: 221C14_U133B


title: mille-00271: 270C93_U133A


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title: mille-00271: 40C57_U133B


title: mille-00271: 309C49_U133B


title: meyer-00191: 120T2


title: meyer-00191: COID9T1

value: Lung Carcinoid Tumor


title: mille-00271: 203B49_U133B


title: mille-00271: 174B41_U133B


title: mille-00271: 18C56_U133B


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title: mille-00271: 217C79_U133B


title: mille-00271: 49A07_U133B


title: meyer-00191: A3T1


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title: mille-00271: 140B91_U133B


title: meyer-00191: 172T4


title: meyer-00191: 366T1


title: mille-00271: 261C94_U133B


title: mille-00271: 246C75_U133B


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title: mille-00271: 62A02_U133B


title: mille-00271: 229C44_U133B


title: meyer-00191: A7T1


title: mille-00271: 160B16_U133B


title: mille-00271: 253C20_U133B


title: meyer-00191: COID4518


title: mille-00271: 100B08_U133B


title: meyer-00191: SQ3197

value: Squamous Cell Lung Carcinoma


title: mille-00271: 252C64_U133B

value: breast cancer


title: mille-00271: 44A53_U133B


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title: meyer-00191: 122T3


title: meyer-00191: SQ2557


title: mille-00271: 234C15_U133B


title: meyer-00191: SQ5T1


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title: mille-00271: 196B81_U133B


title: mille-00271: 238C87_U133B


title: mille-00271: 267C04_U133B


title: meyer-00191: SQ2921


title: meyer-00191: 304T1


title: meyer-00191: 179T2


title: meyer-00191: SQ3624


title: meyer-00191: 313T1


title: meyer-00191: SQ13T1


title: meyer-00191: 308T1


title: meyer-00191: 202T2


title: meyer-00191: 336T1


title: mille-00271: 184B38_U133B


title: meyer-00191: 212T1


title: mille-00271: 53A06_U133B


title: meyer-00191: 179T1


title: meyer-00191: SQ2572


title: mille-00271: 232C58_U133B


title: meyer-00191: A2T1


title: mille-00271: 104B91_U133B


title: meyer-00191: 353T1


title: meyer-00191: NL268n1


title: meyer-00191: NL1884


title: mille-00271: 233C91_U133B


title: mille-00271: 165B72_U133A


title: meyer-00191: 346T1-2


title: mille-00271: 245C22_U133B


title: meyer-00191: 346T1-1


title: mille-00271: 301C66_U133B


title: meyer-00191: 370T1


title: mille-00271: 105B13_U133B


title: mille-00271: 262C85_U133B


title: meyer-00191: COID2260


title: mille-00271: 83A37_U133B


title: mille-00271: 82A83_U133B


title: meyer-00191: 384T2


title: meyer-00191: 368T2


title: mille-00271: 10B88_U133B


title: mille-00271: 199B55_U133B


title: mille-00271: 227C50_U133B


title: meyer-00191: 236T1


title: meyer-00191: 158T1


title: meyer-00191: 221T1


title: mille-00271: 201B68_U133B


title: meyer-00191: 384T1


title: mille-00271: 250C78_U133B


title: mille-00271: 120B73_U133B


title: mille-00271: 290C91_U133B


title: mille-00271: 84A44_U133B


title: meyer-00191: 255T1-3


title: mille-00271: 164B81_U133B


title: meyer-00191: 255T1-1


title: meyer-00191: 255T1-2


title: mille-00271: 200B47_U133B


title: meyer-00191: SMCL5937

value: Small Cell Lung Carcinoma


title: meyer-00191: 258T1-3


title: mille-00271: 315C75_U133B


title: mille-00271: 222C26_U133B


title: meyer-00191: 258T1-1


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title: mille-00271: 76A44_U133B


title: meyer-00191: 158T2


title: meyer-00191: 258T2


title: meyer-00191: SMCL4T1


title: mille-00271: 235C20_U133B


title: meyer-00191: 260T1-2


title: meyer-00191: 259T1


title: mille-00271: 47A87_U133B


title: meyer-00191: 260T1-1


title: mille-00271: 254C80_U133B


title: mille-00271: 39C24_U133B


title: meyer-00191: 170T2


title: meyer-00191: 170T1


title: mille-00271: 142B05_U133B


title: mille-00271: 128B48_U133B


title: meyer-00191: 268T1


title: meyer-00191: 268T2-1


title: mille-00271: 216C61_U133B


title: meyer-00191: 268T2-2


title: meyer-00191: A31


title: mille-00271: 122B81_U133B


title: mille-00271: 313A87_U133B


title: meyer-00191: COID7T1


title: meyer-00191: 275T1


title: mille-00271: 147B19_U133B


title: meyer-00191: 258T1-2


title: meyer-00191: 130T1


title: mille-00271: 13B79_U133B


title: meyer-00191: NL1675


title: mille-00271: 7B96_U133B


title: meyer-00191: 320T1


title: mille-00271: 213C36_U133B


title: mille-00271: 170B15_U133B


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title: meyer-00191: 115T1


title: meyer-00191: 115T2


title: mille-00271: 275C70_U133B


title: meyer-00191: 334T1


title: meyer-00191: 334T2


title: meyer-00191: COID11T1


title: meyer-00191: COID13T1


title: mille-00271: 159B47_U133B


title: mille-00271: 223C51_U133B


title: mille-00271: 9B52_U133B


title: mille-00271: 99A50_U133B


title: mille-00271: 177B67_U133B


title: mille-00271: 145B10_U133B


title: meyer-00191: COID8T1


title: meyer-00191: 283T1


title: mille-00271: 70A79_U133B


title: mille-00271: 248C91_U133B


title: meyer-00191: NL3681


title: meyer-00191: 294T1


title: mille-00271: 189B83_U133B


title: mille-00271: 195B75_U133B


title: meyer-00191: 185T2


title: meyer-00191: 262T1-2


title: mille-00271: 208C06_U133B


title: mille-00271: 14B98_U133B


title: mille-00271: 79A35_U133B


title: meyer-00191: 232T1


title: meyer-00191: SQ20T1


title: mille-00271: 240C54_U133B


title: meyer-00191: 338T1-2


title: mille-00271: 42C57_U133B


title: mille-00271: 43C47_U133B


title: meyer-00191: 338T1-1


title: meyer-00191: 294T2


title: mille-00271: 150B81_U133B


title: meyer-00191: 163T3


title: meyer-00191: 114T1


title: meyer-00191: 163T1


title: mille-00271: 289C75_U133B


title: mille-00271: 94A16_U133B


title: meyer-00191: 114T2


title: meyer-00191: COID18T1


title: mille-00271: 75A01_U133B


title: mille-00271: 270C93_U133B


title: meyer-00191: 318T3


title: meyer-00191: 224T1


title: meyer-00191: 234T1


title: meyer-00191: 262T1-1


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title: mille-00271: 144B49_U133B


title: mille-00271: 48A46_U133B


title: meyer-00191: 169T2


title: mille-00271: 158B84_U133B


title: meyer-00191: 287T1


title: meyer-00191: 169T3


title: mille-00271: 288C57_U133B


title: mille-00271: 272C88_U133B


title: meyer-00191: 277T1


title: mille-00271: 316C65_U133B


title: mille-00271: 311A27_U133B


title: meyer-00191: COID10T1


title: meyer-00191: 335T2


title: meyer-00191: SQ14T1


title: mille-00271: 239C32_U133B


title: mille-00271: 173B43_U133B


title: meyer-00191: 327T3


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title: mille-00271: 50A91_U133B


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title: mille-00271: 37C06_U133B


title: meyer-00191: 374T1


title: meyer-00191: 340T1-2


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title: meyer-00191: 355T2


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title: meyer-00191: 131T1-2


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title: mille-00271: 27C82_U133B


title: mille-00271: 162B98_U133B


title: meyer-00191: COID9794


title: mille-00271: 181B70_U133B


title: meyer-00191: 188T1


title: meyer-00191: 131T1-1


title: meyer-00191: 327T1


title: mille-00271: 220C70_U133B


title: meyer-00191: 269T1


title: meyer-00191: 218T1


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title: meyer-00191: 240T1


title: mille-00271: 226C06_U133B


title: mille-00271: 175B72_U133B


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title: meyer-00191: 183T1-2


title: meyer-00191: 375T2


title: meyer-00191: 340T1-1


title: mille-00271: 46A25_U133B


title: meyer-00191: 183T1-1


title: meyer-00191: 119T3


title: mille-00271: 180B38_U133B


title: mille-00271: 88A67_U133B


title: meyer-00191: 243T2


title: meyer-00191: 243T1


title: mille-00271: 33C30_U133B


title: meyer-00191: 301T1-2


title: mille-00271: 106B55_U133B


title: mille-00271: 73A01_U133B


title: meyer-00191: SMCL8T1


title: mille-00271: 152B99_U133B


title: mille-00271: 74A63_U133B


title: meyer-00191: 186T1


title: meyer-00191: 363T1


title: meyer-00191: 330T2


title: mille-00271: 257C87_U133B


title: mille-00271: 89A64_U133B


title: mille-00271: 179B28_U133B


title: meyer-00191: SQ6T1


title: mille-00271: 110B34_U133B


title: meyer-00191: NL2562


title: mille-00271: 15C94_U133B


title: meyer-00191: SMCL3T1


title: mille-00271: 22C62_U133B


title: mille-00271: 61A53_U133B


title: mille-00271: 244C89_U133B


title: meyer-00191: 187T1


title: meyer-00191: 351T1


title: meyer-00191: 285T2


title: mille-00271: 218C29_U133B


title: meyer-00191: COID5T1


title: mille-00271: 138B34_U133B


title: meyer-00191: 301T1-1


title: mille-00271: 72A92_U133B


title: mille-00271: 269C68_U133B


title: meyer-00191: 228T3


title: mille-00271: 191B79_U133B


title: mille-00271: 161B31_U133B


title: mille-00271: 64A59_U133B


title: meyer-00191: NL1179


title: mille-00271: 298C47_U133B


title: meyer-00191: 201T1


title: meyer-00191: 228T2


title: meyer-00191: 383T2


title: meyer-00191: 383T1


title: mille-00271: 131B79_U133B


title: meyer-00191: 187T2


title: mille-00271: 166B79_U133B


title: meyer-00191: SQ1670


title: meyer-00191: NL3104


title: mille-00271: 165B72_U133B


title: meyer-00191: 309T1


title: mille-00271: 294C04_U133B


title: mille-00271: 194B60_U133B


title: meyer-00191: 332T1


title: mille-00271: 260C91_U133B


title: meyer-00191: 247T1


title: meyer-00191: NL7530


title: mille-00271: 230C47_U133B


title: meyer-00191: COID4385


title: meyer-00191: SQ4T1


title: mille-00271: 283C22_U133B


title: meyer-00191: A4T1


title: mille-00271: 185B44_U133B


title: mille-00271: 225C52_U133B


title: meyer-00191: A19T1


title: mille-00271: 224C93_U133B


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title: meyer-00191: 317T1


title: mille-00271: 198B90_U133B


title: meyer-00191: 164T1a


title: mille-00271: 192B69_U133B


title: mille-00271: 210C72_U133B


title: meyer-00191: 178T3


title: mille-00271: 45A96_U133B


title: mille-00271: 274C81_U133B


title: mille-00271: 241C01_U133B


title: mille-00271: 279C61_U133B


title: meyer-00191: A10T1


title: meyer-00191: 352T1


title: mille-00271: 151B84_U133B


title: mille-00271: 277C64_U133B


title: meyer-00191: 261T1


title: meyer-00191: NL504


title: mille-00271: 171B77_U133B


title: meyer-00191: 302T3


title: mille-00271: 214C35_U133B


title: mille-00271: 6B85_U133B


title: meyer-00191: 249T1


title: meyer-00191: SMCL301


title: meyer-00191: 350T1-2


title: mille-00271: 169B79_U133B


title: mille-00271: 130B92_U133B


title: meyer-00191: 178T2


title: meyer-00191: 350T1-1


title: mille-00271: 71A50_U133B


title: mille-00271: 58A50_U133B


title: meyer-00191: 296T2


title: mille-00271: 188B13_U133B


title: meyer-00191: 302T4


title: meyer-00191: SQ4389


title: meyer-00191: 296T1


title: meyer-00191: SQ5897


title: mille-00271: 265C40_U133B


title: mille-00271: 206C05_U133B


title: mille-00271: 52A90_U133B


title: meyer-00191: 337T1


title: meyer-00191: COID3580


title: meyer-00191: 118T1


title: meyer-00191: 123T1


title: mille-00271: 251C14_U133B


title: meyer-00191: 123T2


title: mille-00271: 134B33_U133B


title: meyer-00191: 043T2


title: meyer-00191: 162T2


title: mille-00271: 205B99_U133B


title: meyer-00191: 136T2


title: meyer-00191: 210T1


title: meyer-00191: 177T1


title: mille-00271: 96A21_U133B


title: mille-00271: 187B36_U133B


title: meyer-00191: 250T1


title: mille-00271: 41C65_U133B


title: meyer-00191: 239T1


title: mille-00271: 247C76_U133B


title: mille-00271: 21C28_U133B


title: mille-00271: 102B06_U133B


title: mille-00271: 66A84_U133B


title: meyer-00191: SQ6147


title: meyer-00191: 111T2


title: mille-00271: 34C80_U133B


title: meyer-00191: NL6943


title: mille-00271: 135B40_U133B


title: mille-00271: 127B00_U133B


title: mille-00271: 291C17_U133B


title: mille-00271: 65A68_U133B


title: meyer-00191: 314T1


title: mille-00271: 69A93_U133B


title: meyer-00191: 356T1


title: mille-00271: 111B51_U133B


title: meyer-00191: COID6T1


title: mille-00271: 268C87_U133B


title: meyer-00191: COID3T1


title: meyer-00191: 213T1


title: meyer-00191: 331T1


title: mille-00271: 278C80_U133B


title: meyer-00191: SQ4172


title: mille-00271: 280C43_U133B


title: mille-00271: 242C21_U133B


title: meyer-00191: NL1698


title: meyer-00191: 379T2


title: mille-00271: 112B55_U133B


title: meyer-00191: 379T1


title: mille-00271: 231C80_U133B


title: mille-00271: 101B88_U133B


title: meyer-00191: 299T1


title: meyer-00191: 367T1


title: mille-00271: 51A98_U133B


title: meyer-00191: 299T2


title: mille-00271: 16C97_U133B


title: meyer-00191: 347T1-2


title: mille-00271: 207C08_U133B


title: meyer-00191: 347T1-1


title: mille-00271: 307C50_U133B


title: meyer-00191: 267T1


title: mille-00271: 113B11_U133B


title: mille-00271: 314B55_U133B


title: meyer-00191: 127T1


title: mille-00271: 85A03_U133B


title: meyer-00191: 207T1


title: meyer-00191: 311T2


title: meyer-00191: 311T1


title: meyer-00191: COID1429


title: mille-00271: 183B75_U133B


title: mille-00271: 155B52_U133B


title: meyer-00191: SQ10T1


title: mille-00271: 148B49_U133B


title: meyer-00191: NL6084


title: mille-00271: 125B43_U133B


title: mille-00271: 23C52_U133B


title: meyer-00191: 208T1

value: T1 v M1


title: meyer-00191: 360T1


title: mille-00271: 172B19_U133B


title: meyer-00191: 203T2


title: meyer-00191: 360T2


title: mille-00271: 202B44_U133B


title: mille-00271: 55A79_U133B


title: meyer-00191: 203T1


title: mille-00271: 197B95_U133B


title: mille-00271: 259C74_U133B


title: meyer-00191: 241T1

value: male


title: mille-00271: 136B04_U133B


title: meyer-00191: 253T1


title: mille-00271: 243C70_U133B


title: mille-00271: 5B97_U133B


title: meyer-00191: A1T1


title: meyer-00191: 315T1


title: meyer-00191: 226T2


title: meyer-00191: NL4353


title: meyer-00191: SQ7324


title: meyer-00191: 252T1


title: meyer-00191: NL6853


title: meyer-00191: COID4T1


title: meyer-00191: 362T1


title: meyer-00191: 305T1


title: meyer-00191: SQ8T1


title: mille-00271: 304C89_U133B


title: meyer-00191: A18T1


title: meyer-00191: SQ3529


title: meyer-00191: COID14T1


title: meyer-00191: 159T1


title: meyer-00191: A15T1


title: meyer-00191: 276T2


title: meyer-00191: 276T1


title: meyer-00191: COID12T1


title: Participant 12, Placebo

city: Calgary

first: Robert

last: Newton

state: Alberta

address: 3330 Hospital Dr NW

department: Snyder Institute for Chronic Diseases

country: Canada

institute: University of Calgary

hyb_protocol: standard Affymetrix procedures. GeneChip PrimeView Human Gene Expression Array were used.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G

data_processing: The data were processed (RMA normalization) using Affymetrix Expression Console.

source_name: Bronchial biopsy following placebo inhalation

label_protocol: standard Affymetrix procedures

growth_protocol: Endobronchial mucosal biopsies (3 – 5 from each subject) were taken from the segmental and subsegmental bifurcations of the right lung, starting distally and working proximally, as per our SOP. At the 2nd bronchoscopy,  endobronchial mucosal biopsies were taken from the left lung for consistency, using the same approaches. In each case, one or two biopsies were placed in Tissue Tek OCT for later fixing and histological examination. The remaining biopsies were snap frozen, prior to storage at -80 °C for later RNA extraction. All biopsy samples were inspected to confirm the presence of airway tissues.

extract_protocol: Biopsy samples stored at -80° C were subjected to homogenization using a TissueLyser (Qiagen) and then processed for RNA according to the RNeasy protocol (Qiagen).

treatment_protocol: Volunteers were randomized to receive inhaled budesonide (1600 µg) or placebo, both via Turbuhaler. Two to three weeks later, participants received either budesonide or placebo, as appropriate to complete both study arms. Six hours after placebo or a budesonide inhalation, bronchial biopsies were obtained via bronchoscopy.

tag: tissue

value: Bronchial biopsy

tag: treatment

value: Placebo


title: Participant 12, Budesonide

source_name: Bronchial biopsy following budesonide inhalation

value: Budesonide


title: meyer-00191: SMCL9T1


title: meyer-00191: COID16T1


title: Participant 11, Budesonide


title: Participant 10, Placebo


title: Participant 11, Placebo


title: meyer-00191: A5T1


title: meyer-00191: 167T2


title: meyer-00191: 167T1


title: Participant 10, Budesonide


title: meyer-00191: 157T1


title: meyer-00191: 157T2


title: meyer-00191: 238T2


title: Participant 8, Placebo


title: Participant 7, Placebo


title: meyer-00191: 230T1


title: Participant 6, Budesonide


title: WT and gprK Replicate 2

city: Daejeon

first: Kwang-Soo

last: Shin

department: Life Science

country: South Korea

institute: Daejeon University

description: Biological replicate 2 of WT and gprK mutant

hyb_protocol: After checking labeling efficiency, cyanine 3-labeled and cyanine 5-labeled cRNA target were combined and fragmented by adding 10X blocking agent and 25X fragmentation buffer and incubating at 60 oC for 30min. The fragmented cRNA was resuspended with 2X hybridization buffer and directly pipetted onto assembled Aspergillus fumigatus AF293_30K microarray (MYcroarray.com, USA). The arrays hybridized at 57oC for 17 h using Agilent Hybridization oven (Agilent Technology, USA).

scan_protocol: The hybridization images were visualized with Axon GenePix 4000B Scanner (Axon Instrument, CA)

data_processing: The average fluorescence intensity for each spot was calculated and local background was subtracted. All data normalization and selection of fold-changed genes were performed using GenoWiz 4.0 (Ocimumbiosolutions, India). Gene Pix Pro 6.0 (Axon Instruments, CA) was used for background subtraction and GenoWiz 4.0 (Ocimumbiosolutions, India) was used Loess normalization.

organism: Aspergillus fumigatus Af293

label_protocol: The synthesis of target cRNA probes and hybridization were performed using Agilent’s Low Input Quick Amp WT Labeling kit, two color (Agilent Technology, USA) according to the manufacturer’s instructions. Briefly, each 0.2 ug total RNA was mixed with WT primer mix and incubated at 65 oC for 10min. cDNA master mix (5X First strand buffer, 0.1M DTT, 10mM dNTP mix, RNase-Out, and MMLV-RT) was prepared and added to the reaction mixer. The samples were incubated at 40 oC for 2 hours and then the RT and dsDNA synthesis was terminated by incubating at 70 oC for 15min.   The transcription master mix was prepared as the manufacturer’s protocol (4X Transcription buffer, 0.1M DTT, NTP mix, 50% PEG, RNase-Out, Inorganic pyrophosphatase, T7-RNA polymerase, and Cyanine 3/5-CTP). Transcription of dsDNA was performed by adding the transcription master mix to the dsDNA reaction samples and incubating at 40 oC for 2 hours.

growth_protocol: About 106 conidia were inoculated in liquid MMY medium and cultured at 37℃ for 24h.

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

treatment_protocol: The prepared sample was homogenized using a Mini Bead beater in the presence of 1 ml of TRIzol® reagent (Invitrogen) and 0.3 ml of silica/zirconium beads (Biospec).

tag: strain

value: Wild type

value: gprK deletion strain


title: WT and double deletion Replicate 2

description: Biological replicate 2 of WT and double deletion mutant

source_name: ΔΔ2

value: gprK/rgsC deletion strain


title: meyer-00191: SQ1174

value: lung cancer

tag: age


title: Participant 8, Budesonide


title: Participant 5, Budesonide


title: Participant 3, Budesonide


title: Participant 3, Placebo


title: Participant 7, Budesonide


title: Participant 5, Placebo


title: Participant 4, Placebo


title: Participant 2, Budesonide


title: Participant 4, Budesonide


title: WT and double deletion Replicate 1

description: Biological replicate 1 of WT and double deletion mutant

source_name: ΔΔ1


title: Participant 6, Placebo


title: meyer-00191: 295T1

value: female

value: Lung


title: Participant 2, Placebo


title: WT and gprK Replicate 1

description: Biological replicate 1 of WT and gprK mutant


title: WT and rgsC Replicate 1

description: Biological replicate 1 of WT and rgsC mutant

value: rgsC deletion strain


title: Participant 1, Budesonide


title: MDM non treated at 24h donor #72

status: Public on Jun 10 2016

city: Paris

first: Santy

last: Marques-Ladeira

state: Ile de France

address: 12, rue Lhomond

country: France

institute: Institut Curie

hyb_protocol: not provided

scan_protocol: not provided

data_processing: Data was normalised by RMA and analysed with limma

label_protocol: not provided

growth_protocol: human PBMC were separated using Ficoll-Paque, monocytes were purified using CD14+ magnetic beads (Miltenyi), and MDM were differentiated for 7 days in RPMI with Glutamax (Gibco) supplemented with 10% FCS (Gibco) and pen/strep (Gibco) with 25ug/ml M-CSF (Miltenyi)

extract_protocol: cells were lysed in Qiazol, RNA extracted using NucleoSpin RNA (Machery Nagel)

treatment_protocol: VSVG-pseudotyped HIV-1 NL-AD8 was produced by PEI-transfection of HEK 293T and ultracentrifugation of supernatant on a sucrose cushion, and was used at 0,5 ug/ml p24 on macrophages. AZT was added at the time of infection at 25uM.

value: blood

tag: infection status

value: not infected

tag: infection duration

tag: cell type

value: Monocyte derived macrophage


title: MDM infected by HIV-1 + AZT at 24h donor #72

value: infected


title: MDM infected by HIV-1 + AZT at 24h donor #71


title: MDM non treated at 24h donor #71


title: MDM non treated at 8h donor #72

value: 8 h


title: MDM infected by HIV-1 at 24h donor #72


title: Participant 1, Placebo


title: cotyledon ethylene 25.5 h 3

city: Utrecht

first: Rashmi

last: Sasidharan

address: Hugo R. Kruytgebouw, Padualaan 8

department: Plant Ecophysiology

country: Netherlands

institute: Utrecht University

description: RMA expression value derived from Expression Console software; core-gene analysis

hyb_protocol: The samples were hybridized to the Affymetrix Gene 1.1 ST Arabidopsis Array Plate and washed on an Affymetrix GeneAtlas system followed by scanning of arrays at AROS Applied Biotechnology (http://arosab.com/services/microarrays/gene-expression/).

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

data_processing: Raw data (.CEL) were processed using Affymetrix Expression Console 1.4. RMA analysis was used to obtain .CHP files with Gene-level analysis. Indidvidual .CHP files were used in Affymetrix Transcriptome Analysis Console v3.0 for further comparisons between samples. For data analysis, R software environment and Bioconductor was also used.

label: Biotin

organism: Arabidopsis thaliana

source_name: cotyledon ethylene 25.5 h

label_protocol: Single-stranded cDNA was generated from the amplified cRNA, fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: After stratification at 4°C for 3 d in the dark, seeds were transferred for 2 h to control light conditions (see below) and then kept in dark (at 20°C) again for another 15 h. Subsequently seedlings were allowed a period of 24 h growth under control light conditions in Short-Day photoperiod conditions (15 h dark/9h light) before being transferred to 22.4 L glass desiccators with air-tight lids for specific treatments. Col-0 genotypes were grown at 21 ± 1 °C.

extract_protocol: Seedlings were dissected using BD PrecisionGlide Hypodermic 27 Gauge 1 1/4" Grey Needle with outer diameter = 0.41 mm (Becton Dickinson B.V., The Netherlands) to separately harvest the hypocotyl and cotyledon + shoot apical meristem (hereafter termed “cotyledon”). The roots were discarded. Samples were harvested at 1.5 h, 13.5 h and 25.5 h after the start of the treatments. For 13.5 h time point, which occurs during the dark period, dissection was carried out under low intensity green safelight (≈ 5 μmol m-2 s-1). For minimizing the effects of green light on gene expression, seedlings were kept in the dark until dissected and dissection was carried out in several rounds with each round involving maximum 2-3 seedlings. In total, 3 replicate experiments were carried out. In each replicate experiment, tissues were harvested from two independent technical replicates (each with 25 seedlings from the two technical replicate plates as mentioned in “Treatments” section above). Harvested material was immediately frozen in liquid nitrogen and stored at -80°C until further use. Frozen tissue was ground using tissue lyser and total RNA was isolated using RNeasy Mini Kit (QIAGEN, Germany). QIAGEN RNase-Free DNase set was used to eliminate Genomic DNA contamination by performing on-column DNase digestion. Extracted RNA was verified (for quality check) and quantified using NanoDropTM ND-1000 Spectrophotometer (Isogen Life Science, De Meern, The Netherlands). RNA samples were sent to AROS (AROS Applied Biotechnology A/S, Aarhus, Denmark). RNA was repurified on low-elution QIAGEN RNeasy columns, re-quantified with NanoDropTM 8000 UV-Vis Spectrophotometer and checked for quality with Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). RNA samples with RNA Integrity Number (RIN) value of > 7.5 were considered for further use. 50 ng RNA from each of the two independent technical replicates was mixed in the ratio 1:1 and the pooled sample was considered as one biological replicate for hybridization experiments. Thus, 3 biological replicates were obtained for the 3 replicate experiments. 100 ng of RNA sample was processed for cDNA synthesis, fragmentation and labelling was carried out for the RNA samples.

treatment_protocol: Control and ethylene desiccators were kept in control light conditions (Photosynthetically Active Radiation, PAR = 140 μmol m-2 s-1, blue light (400 nm-500 nm) = 29 μmol m-2 s-1 and R:FR = 2.1). Ethylene treatments were started by injecting ethylene into the desiccators (with 1 µl L-1 final concentration in the dessicator) and levels were verified with a Gas Chromatograph (GC955; Synspec, The Netherlands). Shade treatment was started by putting desiccators under a single layer of Lee Fern Green Filter (Lee Hampshire, UK) (PAR = 40 μmol m-2s-1, blue light (400 nm-500 nm) = 3 μmol m-2 s-1 and R:FR = 0.45).

value: ethylene

value: cotyledon

tag: time-point


title: MDM non treated at 8h donor #71


title: cotyledon shade 13.5 h 3

source_name: cotyledon shade 13.5 h

value: shade


title: MDM infected by HIV-1 at 8h donor #72


title: MDM infected by HIV-1 at 24h donor #69


title: cotyledon ethylene 1.5 h 3

source_name: cotyledon ethylene 1.5 h


title: MDM non treated at 8h donor #69


title: cotyledon shade 25.5 h 3

source_name: cotyledon shade 25.5 h


title: cotyledon shade 1.5 h 3

source_name: cotyledon shade 1.5 h


title: MDM infected by HIV-1 at 24h donor #71


title: MDM infected by HIV-1 + AZT at 24h donor #69


title: MDM infected by HIV-1 at 8h donor #69


title: cotyledon ethylene 13.5 h 3

source_name: cotyledon ethylene 13.5 h


title: cotyledon control 25.5 h 3

source_name: cotyledon control 25.5 h

value: control


title: cotyledon control 13.5 h 3

source_name: cotyledon control 13.5 h


title: MDM infected by HIV-1 at 8h donor #71


title: cotyledon control 1.5 h 3

source_name: cotyledon control 1.5 h


title: hypocotyl shade 25.5 h 3

source_name: hypocotyl shade 25.5 h

value: hypocotyl


title: MDM non treated at 24h donor #69


title: hypocotyl shade 1.5 h 3

source_name: hypocotyl shade 1.5 h


title: hypocotyl ethylene 25.5 h 3

source_name: hypocotyl ethylene 25.5 h


title: hypocotyl control 25.5 h 3

source_name: hypocotyl control 25.5 h


title: hypocotyl shade 13.5 h 3

source_name: hypocotyl shade 13.5 h


title: cotyledon shade 1.5 h 2


title: hypocotyl ethylene 1.5 h 3

source_name: hypocotyl ethylene 1.5 h


title: hypocotyl ethylene 13.5 h 3

source_name: hypocotyl ethylene 13.5 h


title: cotyledon shade 13.5 h 2


title: hypocotyl control 1.5 h 3

source_name: hypocotyl control 1.5 h


title: hypocotyl control 13.5 h 3

source_name: hypocotyl control 13.5 h


title: cotyledon shade 25.5 h 2


title: cotyledon control 1.5 h 2


title: cotyledon shade 13.5 h 1

source_name: cotyledon shade 13.5 h


title: cotyledon ethylene 25.5 h 2

source_name: cotyledon ethylene 25.5 h


title: cotyledon ethylene 25.5 h 1


title: cotyledon control 13.5 h 2


title: cotyledon shade 25.5 h 1

source_name: cotyledon shade 25.5 h


title: cotyledon ethylene 13.5 h 2


title: cotyledon shade 1.5 h 1

source_name: cotyledon shade 1.5 h


title: WT and rgsC Replicate 2

description: Biological replicate 2 of WT and rgsC mutant

value: Wild type


title: cotyledon ethylene 1.5 h 2

source_name: cotyledon ethylene 1.5 h


title: hypocotyl shade 25.5 h 2


title: cotyledon ethylene 1.5 h 1


title: cotyledon ethylene 13.5 h 1

source_name: cotyledon ethylene 13.5 h


title: hypocotyl ethylene 13.5 h 2


title: cotyledon control 13.5 h 1

source_name: cotyledon control 13.5 h


title: hypocotyl control 25.5 h 2


title: hypocotyl ethylene 1.5 h 2


title: cotyledon control 1.5 h 1

source_name: cotyledon control 1.5 h


title: cotyledon control 25.5 h 2

source_name: cotyledon control 25.5 h


title: hypocotyl shade 1.5 h 2

source_name: hypocotyl shade 1.5 h


title: hypocotyl shade 25.5 h 1

source_name: hypocotyl shade 25.5 h


title: cotyledon control 25.5 h 1


title: hypocotyl ethylene 25.5 h 2

source_name: hypocotyl ethylene 25.5 h


title: hypocotyl control 13.5 h 2


title: hypocotyl shade 1.5 h 1


title: hypocotyl ethylene 25.5 h 1


title: hypocotyl control 13.5 h 1


title: hypocotyl control 1.5 h 1


title: hypocotyl shade 13.5 h 2

source_name: hypocotyl shade 13.5 h


title: hypocotyl ethylene 1.5 h 1

source_name: hypocotyl ethylene 1.5 h


title: hypocotyl control 1.5 h 2


title: hypocotyl shade 13.5 h 1


title: hypocotyl ethylene 13.5 h 1

source_name: hypocotyl ethylene 13.5 h


title: hypocotyl control 25.5 h 1

source_name: hypocotyl control 25.5 h


title: normal FLSs 1

city: Nanjing

first: Yu

last: Zhang

state: Jiangsu

address: 305 East Zhongshan Road

department: Clinical Laboratory Science

country: China

institute: Jinling Hospital

description:
lncRNAs and mRNAs expression
normal 1

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × blocking agent and 1 μl of 25 × fragmentation buffer, heated to 60 °C for 30 min, and diluted with 25 μl 2 × GE hybridization buffer. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the Human LncRNA Array v3.0 slide (8 x 60K, Arraystar). The slides were incubated for 17 hours at 65°C in an Agilent hybridization oven then washed, fixed and scanned.

scan_protocol: The slides were scanned using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: The scanned were images were analysed using the Agilent Feature Extraction software version 11.0.1.1. Data normalization was carried out using Agilent GeneSpring GX. After quantile normalization of the raw data, LncRNAs and mRNAs that at least 1 out of 6 samples have flags in Present or Marginal were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs between two groups were identified through Volcano Plot filtering.

source_name: fibroblast-like synoviocytes from trauma patient

label_protocol: Each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method. The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000

growth_protocol: Tissue specimens were minced into small pieces and digested for 2 hours with 2 mg/ml of type II collagenase (Invitrogen, Carlsbad, CA, USA) in high-glucose Dulbecco’s modified Eagle’s medium (DMEM) at 37°C. After centrifugation at 210 × g for 5 minutes, the precipitate was resuspended with 1 ml of high-glucose DMEM containing 10% fetal bovine serum (FBS), 100 units/ml penicillin, and 100 units/ml streptomycin, and then cultured in 25-cm2 cell culture flasks (Corning) in a humidified 5% CO2 incubator. After 10 hours, 4 ml of high-glucose DMEM containing 10% FBS was added to the cell culture flask. All experiments were conducted using cells at passage 3.

extract_protocol: Total RNA was isolated from fibroblast-like synoviocytes using Agient total RNA isolation Mini kit (Agilent Technologies, Santa Clara, CA, USA) following the manufacture's recommended protocol. The quality and the concentration of the RNA samples were monitored at absorbance ratios of A260/A280 and A260/A230 using a NanoDrop 8000 spectrophotometer.

tag: subject status

value: trauma patient

tag: Sex

value: male

value: 61 years

value: fibroblast-like synoviocytes


title: normal FLSs 2

description:
lncRNAs and mRNAs expression
normal 2

value: female

value: 47 years


title: RA FLSs 3

description:
lncRNAs and mRNAs expression
RA 3

source_name: fibroblast-like synoviocytes from rheumatoid arthritis patient

value: rheumatoid arthritis patient

value: 49 years


title: normal FLSs 3

description:
lncRNAs and mRNAs expression
normal 3

value: 45 years


title: RA FLSs 2

description:
lncRNAs and mRNAs expression
RA 2

value: 48 years


title: RA FLSs 1

description:
lncRNAs and mRNAs expression
RA 1

value: 63 years


title: patient 3

city: Turku

first: Gun

last: West

address: Tykistökatu 6B6

department: Pathology

country: Finland

institute: Turku University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: quantile normalization

source_name: fibroblasts

label_protocol: Standard Illumina label protocol

extract_protocol: Total RNA was extracted with QIAGEN RNeasy kit followed by convertion into cDNA using Tetro cDNA Synthesis kit

value: fibroblasts

tag: disease state

value: normal


title: patient 7

value: severe dilated cardiomyopathy with conduction defect, cardiac transplantation


title: 24h H2O - mock (Rep 3)

city: Gent

first: Patrick

last: Willems

address: Technologiepark 927

department: PSB

country: Belgium

institute: Ghent University

description: At day 7 hydrogen peroxide (H2O2) was added to a final concentration of 10mM. Control plants were treated with the same volume of H2O. Seedlings were grown for 24h under the same controlled conditions.

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C and at 60 rounds/min. The GeneChips were washed and stained in the Affymetrix Fluidics Station 400 and 450.

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

data_processing: Normalized using GCRMA using an updated probe annotation (TAIRGv18.0.0)

source_name: 24h H2O - mock, seedling

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5 microg total RNA.

growth_protocol: We used wild-type Arabidopsis thaliana Columbia-0 plants. Seeds were surface-sterilized by fumigation overnight and cold treated at 4ºC for 3-4 days before germination. Seeds were distributed in 96-well plates (5 seeds/well) containing half-strength liquid Murashige and Skoog (MS) medium supplemented with 1% sucrose (0.2 ml/well). Plants were grown under controlled environmental conditions (16h/8h light/dark, 100 μmol m−2 s−1 light intensity, 21ºC, 70% relative humidity).

extract_protocol: For each replicate plant leaf material was pooled from 4-5 individual plants and total RNA was isolated using Trizol Reagent (Life Technologies, Gaithersburg, USA).

tag: accession

value: 7 days

tag: developmental stage

value: seedling

tag: stress

value: control

value: leaf


title: control 4


title: 24h 10mM H2O2 (Rep 2)

source_name: 24h 10mM H2O2, seedling

treatment_protocol: At day 7 hydrogen peroxide (H2O2) was added to a final concentration of 10mM. Control plants were treated with the same volume of H2O. Seedlings were grown for 24h under the same controlled conditions.


title: control 3


title: control 1


title: patient 6

value: dilated cardiomyopathy with conduction defect


title: 24h H2O - mock (Rep 2)


title: patient 4


title: ambient CO2 (rep 1)

description: After 6 weeks plants were transferred to low CO2 conditions (100 ppm) during 24 h or kept at 400 ppm CO2 (control condition).

data_processing: Normalised using GCRMA using an updated probe annotation (TAIRGv18.0.0)

source_name: Leaves

growth_protocol: Plants were grown in soil under normal (400 ppm) CO2 conditions under a short day light regime.

value: ambient CO2

value: 6 weeks


title: patient 1

value: mild dilated cardiomyopathy


title: low CO2 (rep 2)

treatment_protocol: After 6 weeks plants were transferred to low CO2 conditions (100 ppm) during 24 h or kept at 400 ppm CO2 (control condition).

value: low CO2


title: low CO2 (rep 3)


title: 24h H2O - mock (Rep 1)


title: patient 2

value: mild conduction defect


title: ambient CO2 (rep 3)


title: control 2


title: 24h 10mM H2O2 (Rep 1)


title: patient 5


title: 24h 10mM H2O2 (Rep 3)


title: low CO2 (rep 1)


title: ambient CO2 (rep 2)


title: CANE [28922]

type: genomic

city: Bethesda

first: Dayna

last: Dreger

address: 50 South Drive

department: NHGRI

institute: National Institutes of Health

hyb_protocol: Resuspended DNA was loaded onto BeadChips arrays and hybridized overnight at at 48oC.  Single-base extension and allele-specific staining was performed by hand.

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Image data was analyzed using GenomeStudio with GT module (Illumina).

molecule: genomic DNA

organism: Canis lupus familiaris

source_name: whole blood

label_protocol: 200ng of genomic DNA was amplified in an overnight reaction at 37oC. The amplified DNA was enzymatically fragmented, precipitated with isopropanol, and resuspended in hybridization buffer.

extract_protocol: Genomic DNA was extracted from whole blood using Proteinase K and phenol/chloroform with standard protocols.

tag: breed

value: Cane Corso


title: PTWD_9118

value: Portuguese Water dog


title: CANE [27352]


title: PTWD_5874


title: PTWD_6247


title: CANE [28921]


title: CANE [27048]


title: PTWD_6621


title: PTWD_5838


title: PTWD_6145


title: ITGY_28387

value: Italian Greyhound


title: ITGY_28393


title: PTWD_5827


title: ITGY_28390


title: PTWD_5862


title: SSNZ_11494

value: Standard Schnauzer


title: ITGY_26972


title: SSNZ_11497


title: ITGY_28389


title: SSNZ_11495


title: ITGY_8506


title: SSNZ_11493


title: SSNZ_11496


title: ITGY_8502


title: SSNZ_3180


title: PTWD_5676


title: ITGY_27353


title: SSNZ_7420


title: SSNZ_11491


title: SALU_28384

value: Saluki


title: SSNZ_3181


title: IBIZ_1228

value: Ibizan Hound


title: ITGY_15288


title: GPYR_27750

value: Great Pyrenees


title: IBIZ_1316


title: ITGY_6386


title: IBIZ_1088


title: ANAT_7334

value: Anatolian Shepherd


title: GPYR_8830


title: IBIZ_1230


title: GPYR_12349


title: GPYR_27751


title: GPYR_8836


title: ANAT_7584


title: IBIZ_1128


title: IBIZ_1146


title: IBIZ_1281


title: IBIZ_1084


title: NEAP_23564

value: Neapolitan Mastiff


title: ANAT_7063


title: SALU_28391


title: IBIZ_1086


title: ANAT_7680


title: IBIZ_1148


title: NEAP_23554


title: ANAT_7066


title: ANAT_7069


title: GPYR_4168


title: NEAP_23555


title: GPYR_4971


title: STBD_12750

value: Saint Bernard


title: STBD_12747


title: STBD_6463


title: NEAP_23550


title: SALU_27915


title: STBD_27082


title: GPYR_6369


title: STBD_12748


title: GPYR_8839


title: NEAP_23567


title: SALU_27301


title: 10.WT p(+) Isotype

city: Kumamoto

first: Hiroyuki

last: Oshiumi

address: 1-1-1 Honjo Chuo-ku

institute: Kumamoto University

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

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

data_processing:
Data analysis was performed with AffymetrixTM microarray suite software version 5 (MAS 5.0 Affymetrix) and GeneSpringTM software version 6.1 (Silicon Genetics, San Carlos, CA)
The default settings of MAS 5.0 were used to calculate scaled gene expression values for each sample.

source_name: Wild-type_CD8α+ DCs after PolyIC stimulation with isotype control IgG

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: CD8alpha positive dendritic cells were isolated from mouse spleen

extract_protocol: Total RNA was extracted with Rneasy Kit (Qiagen).

treatment_protocol: Cells were mock or polyIC stimulated for 8 hr with isotype control IgG or anti-IFNAR antibody

tag: strain background

tag: genotype/variation

value: Wild-type

value: spleen

value: CD8alpha positive dendritic cells

tag: treatment group


title: 8.IPS1KO p(+) IFNAR1

source_name: IPS-1 KO_CD8α+ DCs after PolyIC stimulation with anti-IFNAR antibody

value: IPS-1 KO

tag: tissue


title: STBD_1075


title: GPYR_8840


title: 9.WT p(-) Isotype

source_name: Wild-type_CD8α+ DCs after Mock stimulation with isotype control IgG


title: STBD_12749


title: STBD_6460


title: SALU_27308


title: SALU_27932


title: 7.IPS1KO p(-) IFNAR1

source_name: IPS-1 KO_CD8α+ DCs after Mock stimulation with anti-IFNAR antibody


title: 11.WT p(-) IFNAR1

source_name: Wild-type_CD8α+ DCs after Mock stimulation with anti-IFNAR antibody


title: 5.IPS1KO p(-) Isotype

source_name: IPS-1 KO_CD8α+ DCs after Mock stimulation with isotype control IgG


title: 6.IPS1KO p(+) Isotype

source_name: IPS-1 KO_CD8α+ DCs after PolyIC stimulation with isotype control IgG


title: 12.WT p(+) IFNAR1

source_name: Wild-type_CD8α+ DCs after PolyIC stimulation with anti-IFNAR antibody


title: 3.TICAM1KO p(-) IFNAR1

source_name: TICAM-1 KO_CD8α+ DCs after Mock stimulation with anti-IFNAR antibody

value: TICAM-1 KO


title: 4.TICAM1KO p(+) IFNAR1

source_name: TICAM-1 KO_CD8α+ DCs after PolyIC stimulation with anti-IFNAR antibody


title: 2.TICAM1KO p(+) Isotype

source_name: TICAM-1 KO_CD8α+ DCs after PolyIC stimulation with isotype control IgG


title: 1.TICAM1KO p(-) Isotype

source_name: TICAM-1 KO_CD8α+ DCs after Mock stimulation with isotype control IgG


title: SSNZ_27424


title: STBD_27063


title: SALU_27302


title: FONN DNA [29862]

value: Fonni's Dog


title: FONN DNA [29861]


title: STBD_27062


title: NEAP_23551


title: SALU_27314


title: SALU_27317


title: CIRN DNA [26441]

value: Cirneco dell'Etna


title: FONN DNA [29860]


title: FONN DNA [29859]


title: FONN DNA [29858]


title: Zbtb32-/- 6 [BMPC]

city: Tucson

first: Deepta

last: Bhattacharya

state: Arizona

address: 1656 E. Mabel Street, MRB 217

department: Department of Immunobiology

institute: University of Arizona

hyb_protocol: Following fragmentation with NuGen Encore Biotin Module,2.5 ug of cDNA were hybridized into the GeneChip Hybridization Oven 640 for 18 hr at 45C on Gene 1.0 ST Array. GeneChip were washed and stained in the Affymetrix Fluidics Station 450

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

data_processing:
The data was analyzed with the Affymetrix GeneChip Command Console. Microarray expression data was processed using Command Console (Affymetrix, Inc) and the raw (.CEL) files generated were analyzed using Expression Console software with Affymetrix default RMA Gene analysis settings.(Affymetrix, Inc).  Probe summarization (Robust Multichip Analysis, RMA), quality control analysis, and probe annotation were performed according to recommended guidelines (Expression Console Software, Affymetrix, Inc.).
CEL files were imported into ArrayStar (DNASTAR) for analysis. Data were normalized with the RMA algorithm, and values represent log2 intensities.

source_name: bone marrow plasma cells

label_protocol: Affymetrix GeneChip WT Pico kit and Encore Biotin module kit was used to generate, label, and fragment cRNA.

growth_protocol: CD45.2 wild type and Zbtb32-/- splenocytes from NP-CGG-immune donors were transferred into CD45.1 recipients and challenged with NP-CGG. B220- CD138+ Ly6g- CD11b- CD45.1- CD45.2+ NP+ plasma cells were isolated from the bone marrow 7 days later by fluorescence activated cell sorting.

extract_protocol: Macherey-Nagel Nucleospin RNA XS kit

value: bone marrow

tag: markers

tag: genotype


title: FONN DNA [29857]


title: CIRN DNA [26635]


title: SALU_27311


title: PTWD_27192

value: Portuguese Water dog


title: Zbtb32-/- 5 [BMPC]


title: TIMB DNA [25314]

value: Tibetan Mastiff


title: Zbtb32-/- 4 [BMPC]


title: CIRN DNA [26277]


title: CIRN DNA [26437]


title: TIMB DNA [25313]


title: MAAB DNA [24539]

value: Mastino Abruzzese


title: CIRN DNA [26438]


title: Unknown Dog DNA [24534]

value: Unknown


title: TIMB DNA [25310]


title: VPIN DNA [24547]

value: Volpino Italiano


title: TIMB DNA [25311]


title: Zbtb32-/- 3 [BMPC]


title: LVMD DNA [24544]

value: Levriero Meridionale


title: MAAB DNA [24546]


title: Wild Type 5 [BMPC]


title: CANE DNA [24548]

value: Cane Corso


title: Zbtb32-/- 2 [BMPC]


title: Wild Type 4 [BMPC]


title: CANE DNA [24520]


title: CPAT DNA [24532]

value: Cane Paratore


title: LVMD DNA [24542]


title: VPIN DNA [24536]


title: Wild Type 2 [BMPC]


title: TIMB DNA [25312]


title: Wild Type 1 [BMPC]


title: Wild Type 3 [BMPC]


title: VPIN DNA [24529]


title: Zbtb32-/- 4 [resting MBC]

source_name: memory B cells

label_protocol: Nugen Ovation Pico kit and Encore Biotin module kit was used to generate, label, and fragment cRNA.

growth_protocol: Splenocytes from unimmunized wild type or Zbtb32-/- mice were isolated, stained with fluorescently conjugated antibodies, and CD19+ CD80+ CCR6+ IgD- IgM- were purified by fluorescence activated cell sorting.

extract_protocol: Qiagen RNeasy micro kit

value: CD19+ CD80+ CCR6+ IgD- IgM-


title: Zbtb32-/- 5 [resting MBC]


title: CPAT DNA [24540]


title: Wild Type 6 [BMPC]


title: VPIN DNA [24518]


title: CANE DNA [24509]


title: SLOU DNA [24407]

value: Sloughi


title: Zbtb32-/- 3 [resting MBC]

value: spleen


title: CANE DNA [24515]


title: SLOU DNA [24408]


title: Wild Type 2 [resting MBC]


title: Zbtb32-/- 1 [BMPC]


title: Wild Type 4 [resting MBC]


title: Zbtb32-/- 2 [resting MBC]


title: Wild Type 3 [resting MBC]


title: Wild Type 1 [resting MBC]


title: CANE DNA [24519]


title: SALU DNA [24402]

value: Saluki


title: SLOU DNA [24409]


title: SALU DNA [24403]


title: Zbtb32-/- 1 [resting MBC]


title: Zbtb32-/- 5 [MBC]

growth_protocol: CD45.2 wild type and Zbtb32-/- splenocytes from NP-CGG-immune donors were transferred into CD45.1 recipients and challenged with NP-CGG. CD19+ CD80+ CCR6+ IgD- IgM- NP+ CD45.1- CD45.2+ CD11b- Ly6g- CD117- CD11b memory B cells were isolated from the spleen 7 days later by fluorescence activated cell sorting.


title: Zbtb32-/- 4 [MBC]


title: Zbtb32-/- 3 [MBC]


title: Zbtb32-/- 2 [MBC]


title: SALU DNA [24265]


title: Wild Type 6 [MBC]


title: Wild Type 5 [resting MBC]


title: Zbtb32-/- 1 [MBC]


title: Wild Type 3 [MBC]


title: Wild Type 4 [MBC]


title: AZWK DNA [23342]

value: Azawahk


title: Wild Type 2 [MBC]


title: Wild Type 5 [MBC]


title: Mtb infected-CC11050 treated 2

city: Newark

first: Selvakumar

last: Subbian

state: NJ

address: 225 Warren St, Rm# W250.Q

department: New Jersey Medical School,

institute: Rutgers Biomedical and Health Sciences, Rutgers The State University of NJ

hyb_protocol: standard protocol used can be found at <http://www.cag.icph.org> from the center for advanced genomics of the Public Health Research Institute was used for all the experiments

data_processing: Data from the scanned images were extracted using the software from Affymetrix and processed using PARTEK Genomics Suite

source_name: Mtb infected-CC11050 treated_lung

label_protocol: Total RNA samples were reverse transcribed and labled with biotin as suggested by the array manufacturer (affymetrix)

growth_protocol: B6D2F1 mice were infected with Mtb CDC1551 at ~2log10 (on day 0). At14 days post infection, one group of infected mice were treated with CC11050 at 50mg/kg.  Uninfected mice were included as control. Lung tissue was isolated  from all mice at 28 days post infection and used for total RNA isolation.

extract_protocol: Total RNA from the mouse lungs were isolated using TRIzol reagent (Invitrogen, CA, USA) and purified using RNA mini prep columns (Qiagen, CA, USA) according to the instructions of the manufacturers

treatment_protocol: The compound was used at 50mg/kg body weight, dissolved in distilled water and administered through gavage five days a week.

tag: strain

tag: infected with

value: Mtb CDC1551 at ~2log10

tag: treated with

value: CC11050 at 50mg/kg

tag: timepoint

value: At 28 days post-infection

value: lung


title: Wild Type 1 [MBC]


title: Mtb infected-CC11050 treated 4

scan_protocol: standard protocol used can be found at <http://www.cag.icph.org> from the center for advanced genomics of the Public Health Research Institute  was used for all the experiments


title: Mtb infected-CC11050 treated 1


title: AZWK DNA [23341]


title: Mtb infected-no treatment 3

source_name: Mtb infected-no treatment_lung

value: none (untreated control)


title: Mtb infected-no treatment 2


title: AZWK DNA [23339]

source_name: whole blood


title: Mtb infected-no treatment 1


title: Mtb infected-CC11050 treated 3


title: No infection control 4

source_name: No infection control_lung

value: none (uninfected control)


title: Mtb infected-no treatment 4


title: AZWK DNA [23340]


title: SALU DNA [23362]


title: No infection control 2


title: SALU DNA [24003]


title: SLOU DNA [24401]


title: SALU DNA [13122]


title: SALU DNA [22847]


title: AZWK DNA [15369]


title: SALU DNA [22848]


title: SALU DNA [23361]


title: liver-m-VPS33B-ko-3

city: London

first: Paul

last: Gissen

state: London

address: Gower Street

department: LMCB

country: United Kingdom

institute: UCL

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on Affymetrix Mogene 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: RMA processing using 'oligo' Bioconductor package in R

source_name: mouse liver, male, Vps33b liver-sepcific ko

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

growth_protocol: 10 week old mice were fed 0.5% cholic acid supplemented chow (TestDiet® Europe, London, UK) for 2 weeks and sacrificed immediately after

extract_protocol: Extraction of total RNA was performed using the RNAeasy Microkit (Qiagen, UK)

value: liver

value: Vps33b liver-sepcific ko

value: male


title: liver-m-VPS33B-ko-1


title: liver-f-VPS33B-ko-4

source_name: mouse liver, female, Vps33b liver-sepcific ko

value: female


title: liver-m-control-1

source_name: mouse liver, male, control

value: wild type


title: SLOU DNA [23547]


title: liver-m-VPS33B-ko-2


title: liver-m-control-2


title: Memory CD8+  (5452241003_D)

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

data_processing: The data was log2-transformed and quantile normalized using Partek® Genomics Suite® (PGS) software v6.6©

source_name: spleen

label_protocol: Biotinylated cRNA were prepared with the TargetAmp Nano-g Biotin-aRNA Labeling Kit

growth_protocol: Cells were isolated from spleens

extract_protocol: Total RNA from all cell samples was isolated using TRIzol Reagent (Invitrogen).

tag: cell type

value: CD8+ T cells

tag: sub population

value: Memory CD8+


title: in vitro LSEC-primed CD8+ (5452647001_D)

value: in vitro LSEC-primed CD8+


title: liver-f-control-3

source_name: mouse liver, female, control

tag: Sex


title: Naive CD8+ (5452647001_B)

value: Naive CD8+


title: in vivo LSEC-primed CD8+ (5541244065_E)

value: in vivo LSEC-primed CD8+


title: in vitro DC-primed CD8+ (5452241003_B)

value: in vitro DC-primed CD8+


title: in vivo LSEC-primed CD8+ (5541244065_C)


title: liver-f-control-4


title: Naive CD8+ (5452647001_A)


title: in vitro LSEC-primed CD8+ (5452647001_C)


title: in vivo LSEC-primed CD8+ (5541244065_D)


title: No infection control 1


title: in vivo LSEC-primed CD8+ (5541244065_F)


title: Naive CD8+ (5452241003_F)


title: in vitro DC-primed CD8+ (5452647001_F)


title: in vivo LSEC-primed CD8+ (5541244065_A)


title: in vivo LSEC-primed CD8+ (5541244065_B)


title: in vitro DC-primed CD8+ (5452241003_E)


title: in vitro DC-primed CD8+ (5452647001_E)


title: in vitro LSEC-primed CD8+ (5452241001_D)


title: Memory CD8+ (5452241001_E)


title: Memory CD8+ (5452241001_C)


title: Naive CD8+ (5452241001_A)


title: in vitro LSEC-primed CD8+ (5452241003_A)


title: liver-f-VPS33B-ko-6


title: Naive CD8+ (5452241001_B)


title: ARB_9

city: Bronx

first: Pilib

last: Ó Broin

address: 1301 Morris Park Ave

institute: Albert Einstein College of Medicine

description:
313V0
Gene expression data from ACEI/ARB group

hyb_protocol: Total RNA samples hybridized to the Affymetrix Hugene 1.0 st chip according to the protocols provided by the manufacturer.

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip 3000 7G scanner, software AGCC v2.0

data_processing: Probe intensities were extracted from Affymetrix CEL files, normalized and summarized at the transcript cluster level using the Robust Multiarray Average method from the R/Bioconductor (http://bioconductor.org) oligo package. Array quality control was performed to remove arrays that significantly differed in initial overall probe intensity. Expression values were analyzed on the log base 2 scale. Significance testing was performed by fitting gene-wise linear models using the limma Bioconductor package, and genes were ranked for differential expression using Benjamini & Hochberg adjusted p-values and log-posterior odds of differential expression. Gene set analysis was performed using the limma romer method. Gene set used were taken from the Molecular Signatures Database (MSigDB) Pathogenesis Based Transcripts (PBT; http://transplants.med.ualberta.ca/Nephlab/data/gene_lists.html) gene sets from the University of Alberta, Edmonton. Analysis for changes in gene expression of Gene Ontology (GO) categories was performed using the GOstats Bioconductor package to calculate Hypergeomtric p-values for over or under-representation of each GO term.

source_name: Biopsy from ACEI/ARB group patient

label_protocol: Labelled as per manufacturer's instruction in Ambion Whole Transcript Expression Kit (Catalog Number 4425209, Ambion, Austin, TX) and Affymetix Genechip Whole Transcript Terminal Labeling Kit (Catalog Number 900671, Affymetrix, Santa Clara, CA)

extract_protocol: One biopsy core was collected into a vial containing 1ml of RNALater® (Ambion, Catalog Number AM7023), stored at -20°C for 24 hours and then transferred to -70°C until RNA isolation. Renal tissue and glomerular content in all cores was verified by Pathology department technical personnel using a dissecting microscope and any non-renal tissue was removed.

tag: treatment

value: ARB

value: kidney biopsy


title: ACEI_2

description:
210V0
Gene expression data from ACEI/ARB group

value: ACEI


title: ARB_5

description:
252V0
Gene expression data from ACEI/ARB group


title: ARB_7

description:
311V0
Gene expression data from ACEI/ARB group


title: ACEI_3

description:
254Vex
Gene expression data from ACEI/ARB group


title: ARB_2

description:
163V0
Gene expression data from ACEI/ARB group


title: ARB_3

description:
206V0
Gene expression data from ACEI/ARB group


title: ARB_8

description:
312V0
Gene expression data from ACEI/ARB group


title: ARB_4

description:
246V0
Gene expression data from ACEI/ARB group


title: Control_13

description:
307V0
Gene expression data from control group

source_name: Biopsy from control group patient

value: control


title: Control_16

description:
330V0
Gene expression data from control group


title: Control_14

description:
309V0
Gene expression data from control group


title: ARB_1

description:
156V0
Gene expression data from ACEI/ARB group


title: Control_15

description:
322V0
Gene expression data from control group


title: ARB_6

description:
293V0
Gene expression data from ACEI/ARB group


title: Control_12

description:
286V0
Gene expression data from control group


title: ACEI_1

description:
125V0
Gene expression data from ACEI/ARB group


title: ACEI_4

description:
324V0
Gene expression data from ACEI/ARB group


title: back fetus at 14.5 dpc, biological rep4

city: Mexico

first: Sara

last: Frias

state: Distrito Federal

address: Insurgentes Sur 3700-C 6o piso

department: Investigación en Genetica Humana/Medicina, Genómica y Toxicología Ambiental

country: Mexico

institute: Instituto Nacional de Pediatría/Instituto de Investigaciones Biomedicas, UNAM

description:
miRNA expression data from skin from the back at 14.5 dpc
total RNA including short RNAs (<200nt)

hyb_protocol: Denaturalized samples were placed to a GeneChip miRNA Array 3.0 and hybridized at 48°C and 60 rpm for 17 hours in an Affymetrix Hybridization Oven 645; stained and washed in the Affymetrix GeneChip Fluidic Station 450.

scan_protocol: GeneChip miRNA Array 3.0 were scanned using the Affymetrix GeneChip Scanner 3000 HR

data_processing: The array data were normalized by global normalization using the miRNA QC Tool of the Expression Console software (Affymetrix). Transcriptome Analysis Console software (Affymetrix) was used to identify differentially expressed miRNAs at each stage and for the  hierarchical clustering analysis.

source_name: One litter of Mus musculus fetus (14.5 dpc)

label_protocol: Total RNA including short RNAs was labeled with the kit FlashTag ® Biotin HSR (Genisphere/Affymetrix, Santa Clara, CA, USA) according  to manufacturer's instrucions; ) the labeling efficiency was tested with the Enzyme Linked Oligosorbent Assay (ELOSA) QC Assay.

growth_protocol: Scheduled mattings were carried out in order to obtain fetus at specific developmental stages, gestational age of the fetus was determined by the day of appearance of the vaginal plug (0.5 dpc) and confirmed by morphological criteria.

extract_protocol: Total RNA extraction including short RNAs (<200nt) was performed with RNA Mini elute kit (Qiagen) according to manufacturer's protocol.

treatment_protocol: Pregnant females were sacrificed at 13.5 dpc or 14.5 dpc, the fetus were dissected, external ear –pinna- and skin from the back tissues were dissected in iced cooled PBS nuclease free under stereomicroscope and kept in RNAlater (Ambion) at -80°C until their processing.

tag: age

value: Skin from the back


title: Control_11

description:
267V0
Gene expression data from control group


title: No infection control 3

value: none (uninfected control)

value: At 28 days post-infection

value: lung


title: liver-f-VPS33B-ko-5

value: liver

value: Vps33b liver-sepcific ko


title: ear fetus at 14.5 dpc, biological rep4

description:
miRNA expression data from external ear (pinnae) at 14.5 dpc
total RNA including short RNAs (<200nt)

value: External ear (pinna)


title: CXCR4 p.Ser344fs baseline replicate 3

city: Boston

first: Zachary

middle: Richard

last: Hunter

address: 450 Brookline Ave, Mayer 544

institute: Dana-Farber Cancer Institute

description: Gene expression data from CXCR4 c.1030_1041delinsGT  transduced BCWM.1 cell lines at baseline

hyb_protocol: Hybridization was preformed following manufactures instructions

scan_protocol: GeneChip Scanner 3000 7G

data_processing: CEL files were loaded into bioconductor and normalized using rma() from the oligo package. Data was then analyzed using limma.

source_name: CXCR4 p.Thr311fs expressing BCWM.1

label_protocol: Labeling was preformed following manufactures instructions

growth_protocol: Five days after transduction, GFP positive cells were sorted and used for functional studies. Cells were cultured in 10% FBS

extract_protocol: RNA was extracted using the AllPrep mini kit (Qiagen, Valencia, CA) as per manufactures protocol.

treatment_protocol: Cells were harvested at baseline and post 2 hour stimulation with 50nM CXCL12

value: Baseline

tag: cxcr4 mutation

tag: batch


title: Control_9

description:
141V0
Gene expression data from control group


title: in vitro DC-primed CD8+ (5452241001_F)

value: CD8+ T cells


title: CXCR4 p.Ser344fs CXCL12 stimulated replicate 3

description: Gene expression data from CXCR4 c.1030_1041delinsGT transduced BCWM.1 cell lines following two hour CXCL12 stimulation

value: Stimulated


title: CXCR4 p.Ser344fs CXCL12 stimulated replicate 1


title: CXCR4 p.Ser344fs CXCL12 stimulated replicate 2


title: Control_7

description:
104V0
Gene expression data from control group


title: CXCR4 p.Ser344fs baseline replicate 2


title: Control_6

description:
97V0
Gene expression data from control group


title: CXCR4 p.Ser344fs baseline replicate 1


title: Control_5

description:
96V0
Gene expression data from control group


title: CXCR4 p.Thr311fs baseline replicate 3

description: Gene expression data from CXCR4 c.932_933insT transduced BCWM.1 cell lines at baseline

source_name: CXCR4p.Thr311fs expressing BCWM.1


title: CXCR4 p.Thr311fs CXCL12 stimulated replicate 2

description: Gene expression data from CXCR4 c.932_933insT transduced BCWM.1 cell lines following two hour CXCL12 stimulation


title: CXCR4 p.Ser338* CXCL12 stimulated replicate 2

description: Gene expression data from CXCR4 c.1013C>G transduced BCWM.1 cell lines following two hour CXCL12 stimulation

source_name: CXCR4 p.Ser338* expressing BCWM.1


title: Control_3

description:
43V0
Gene expression data from control group


title: Control_2

description:
11V0
Gene expression data from control group


title: cat2-2 atrbohF rep1

description: After 3 weeks of growth under mild photorespiratory-promoting conditions, leaf tissue from the three different genotypes (cat2, cat2 rbohD and cat2 rbohF) was harvested in triplicate.

data_processing: Normalised using GCRMA

source_name: Leaves

growth_protocol: Plants were grown in air from seeds under a 16 h/8 h day/night regime, relative humidity was 65%, and an irradiance of 200 μmol·m-2·s-1 was used to drive oxidative stress in the cat2 background plants. Arabidopsis Col-0, cat2, cat2 rbohD and cat2 rbohF were 3 week old before sampling.

extract_protocol: Three biological replicates were generated each consisting of a pool of leaves from at least 8 plants. Total RNA was isolated using Trizol Reagent (Life Technologies, Gaithersburg, USA).

treatment_protocol: After 3 weeks of growth in mild photorespiratory-promoting conditions, leaf tissue from the three different genotypes was harvested in triplicate. Design: 3 replicates x 3 genotypes (cat2, cat2 rbohD and cat2 rbohF)

value: 3 weeks

tag: ecotype

value: cat2 rbohF


title: CXCR4 p.Thr311fs CXCL12 stimulated replicate 3


title: CXCR4 p.Thr311fs baseline replicate 2


title: cat2-2 atrbohD rep1

tag: genotype/variation

value: cat2 rbohD


title: CXCR4 p.Ser338* baseline replicate 3

description: Gene expression data from CXCR4 c.1013C>G transduced BCWM.1 cell lines at baseline


title: cat2-2 atrbohF rep3


title: CXCR4 p.Ser338* CXCL12 stimulated replicate 3


title: cat2-2 atrbohF rep2


title: cat2-2 atrbohD rep2


title: CXCR4 wild-type CXCL12 stimulated replicate 3

description: Gene expression data from CXCR4 WT transduced BCWM.1 cell lines following two hour CXCL12 stimulation

source_name: CXCR4 WT expressing BCWM.1

value: wild-type


title: Control_10

description:
235V0
Gene expression data from control group

value: kidney biopsy


title: CXCR4 p.Thr311fs baseline replicate 1


title: Control_8

description:
132V0
Gene expression data from control group


title: cat2-2 rep 2


title: Control_1

description:
3V0
Gene expression data from control group


title: CXCR4 p.Ser338* CXCL12 stimulated replicate 1


title: CXCR4 p.Thr311fs CXCL12 stimulated replicate 1


title: CXCR4 p.Ser338* baseline replicate 1


title: cat2-2 rep 3


title: Control_4

description:
80V0
Gene expression data from control group


title: CXCR4 p.Ser338* baseline replicate 2


title: meyer-00180: FEAST_p_TCGA_B20_21_Expression_HT_HG-U133A_96-HTA_D11_516298

status: Public on Jun 09 2016

city: Rockville

first: Mervi

last: Heiskanen

address: 9609 Medical Center Drive, 1W378

department: CBIIT

institute: NCI

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

source_name: brain

tag: diseasestate

value: Glioblastoma Multiforme

tag: organismpart

value: Brain

tag: clinicaldiagnosis

value: Untreated primary (De Nova) GBM

value: Male

tag: cancersite

tag: clinical diagnosis

tag: individual

tag: sample

tag: tissue anatomic site

tag: pathologic status

tag: histologic diagnosis


title: meyer-00180: TARRE_p_MultiPlate_TCGA_SS_MA_Ref_HT_HG-U133A_96-HTA_D05_586190

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

tag: Sex


title: meyer-00180: 5500024032848101507002_Collaborator082307.H09

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

value: GLIOBLASTOMA MULTIFORME

value: GBM

value: OVERLAPPING LESION OF BRAIN

value: MALIGNANT