title: UUO 14 days, 010


title: Folic Acid 7 days, 006

status: Public on Oct 13 2018

type: RNA

city: Ann Arbor

first: Greg

last: Dressler

state: MI

address: 109 Zina Pitcher Drive

department: Pathology

country: USA

institute: University of Michigan

hyb_protocol: Following Labeling procedure, 3.75 ug of biotinylated cDNA were hybridized at 45C on Affymetrix Mouse HT MG-430 PM arrays, and were washed and stained using the Affymetrix Gene Atlas system (software version 1.0.4.267).

scan_protocol: Arrays were scanned using the Affymetrix Gene Atlas system (software version 1.0.4.267).

data_processing: Data was analyzed using the limma and affy Bioconductor packages implemented in the R-statistical environment version 3.3.0. RMA was used to fit log2 transformed expression values.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Kidney

label_protocol: cDNA were prepared according to the Nugen Ovation PicoSL WTA System V2 kit protocol from 20 ng total RNA (Ovation PicoSL WTA System V2 Manual, P/N M01226 v4). Subsequently, biotinylated cDNA were prepared according to the Nugen Encore Biotin Module from 3.75 ug of cDNA (Encore Biotin Module Manual, P/N M01111 v6).

extract_protocol: RNA was isolated from FACS sorted fibroblasts with Trizol according to the manufacturer's protocol.

treatment_protocol: Adult mice were subjected to Folic Acid induced Acute Kidney Injury and cells isolated at 3, 7, and 14 days post injury. Adults were subjected to unilateral ureteral obstruction (UUO) and cells isolated after 14 days.

tag: strain/background

tag: cell type

value: PDGFra-positive fibroblasts

tag: treatment

value: Folic acid-induced acute kidney injury

tag: time

value: 7 days


title: Folic Acid 3 days, 003

value: 3 days


title: Folic Acid 3 days, 002


title: Folic Acid 3 days, 001


title: UUO 14 days, 011

value: Unilateral ureteral obstruction (UUO)

value: 14 days


title: sexual_stage5 rep1_WT

status: Public on Aug 16 2018

type: SRA

city: East Lansing

first: Wonyong

last: Kim

state: Michigan

address: 612 Wilson Road, Room 166

department: Plant Biology

institute: Michigan State University

library_source: transcriptomic

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 High Output flow cell (v4) using Illumina HiSeq SBS reagents (v4) in a 1x50bp paired end format. Base calling was done by Illumina Real Time Analysis (RTA) v1.18.64 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v1.8.4.
Poor quality reads were trimmed and/or filtered out, and adapters and homopolymers were trimmed from raw reads, using the ngsShoRT program v2.2, with parameters -lqs 12 -tera_avg 20 -5a_mp 98 -rmHP_ml 10
Filtered reads were mapped to the repeat-masked genome (Ensembl version 32), using the HISAT2 program v2.0.4, with default parameters
De novo transcript assembly was performed using the StringTie program v1.3.0, with default parameters
Read counts for gene loci in the de novo annotations were calculated using the htseq-count program v0.6.1. Gene expression levels in counts-per-million (CPM) value were computed and normalized by effective library size estimated by trimmed mean of M values, using the edgeR R package v3.14.0.
Genome_build: Fusarium graminearum str. PH-1 Ensembl Genomes 32
Supplementary_files_format_and_content: tab-delimited text file include a matrix of log2-CPM values for all samples and the associated GTF file

organism: Fusarium graminearum

source_name: sexual_stage5 WT

extract_protocol:
Fungal hyphae were scraped out from carrot agar culture and frozen in liquid nitrogen, and total RNA was isolated using the standard Trizol extraction protocol with additional extraction steps.
The KAPA Stranded RNA-Seq Library Preparation Kit was used with 2 ug of total RNA for the construction of cDNA libraries.
Stranded RNA-seq with poly-A captured RNA samples

tag: strain

tag: tissue

value: ascospores

tag: genotype

value: wild-type


title: Folic Acid 14 days, 009


title: sexual_stage3 rep2_WT

source_name: sexual_stage3 WT

value: paraphyses


title: sexual_stage3 rep1_WT


title: sexual_stage1 rep3_WT

source_name: sexual_stage1 WT

value: ascogonia


title: sexual_stage2 rep1_WT

source_name: sexual_stage2 WT

value: perithecial wall


title: sexual_stage1 rep2_WT


title: sexual_stage2 rep3_WT


title: sexual_stage2 rep2_WT


title: day4_EB biol rep 2

status: Public on Aug 15 2018

city: Baltimore

first: Patrick

last: Cahan

state: MD

address: 733 North Broadway, MRB 653

department: ICE and Biomedical Engineering

institute: Johns Hopkins University School of Medicine

description:
BulkExpDat.csv
D4G45

data_processing:
Sequence data was processed according to Radley et al. 2017.
[citations] Radley, A.H., Schwab, R.M., Tan, Y., Kim, J., Lo, E.K.W., Cahan, P., 2017. Assessment of engineered cells using CellNet and RNA-seq. Nat. Protoc. 12, 1089–1102. https://doi.org/10.1038/nprot.2017.022
Genome_build: GRCm38.cdna release 80
Supplementary_files_format_and_content: csv file is an expression matrix with the rows as genes and the columns as samples. The expression was calculated by down-sampling  and normalizing the raw counts according to Radley et al. 2017.

molecule: polyA RNA

growth_protocol: Bry-GFP mESCs were maintained on mouse embryonic feeder (mEF) cells in Dulbecco’s Modified Eagles’ Medium (DMEM; Gibco) containing 15% FBS (Sigma-Aldrich), 1%PSG (Gibco), LIF (MTI Global Stem; 1,000 U/mL), and 2-mercaptoethanol (Sigma; 0.1 mM). mESCs were passaged every other day via trypsinization (TrypLE; Gibco) and complete dissociation of colonies by pipetting.

extract_protocol:
Embryoid bodies were dissociated by incubating them in TrypLE for 2 minutes at 37C and then vortexing them briefly. Total RNA was extracted from the counted cells using the Sigma GenElute Mammalian Total RNA kit.
Libraries were prepared according the TruSeq Stranded mRNA Sample Preparation Guide (Part # 15031047 Rev. E).
[citations] Craft, A.M., Ahmed, N., Rockel, J.S., Baht, G.S., Alman, B. a, Kandel, R. a, Grigoriadis, A.E., Keller, G.M., 2013. Specification of chondrocytes and cartilage tissues from embryonic stem cells. Development 140, 2597–610. https://doi.org/10.1242/dev.087890

treatment_protocol: To begin differentiation (day 0), cells were trypsinized, removed from feeder cells, and cultured in suspension in serum-free differentiation media (SFD; Craft et al. 2013) at a density of 75,000 cells/mL for 48 hours to form embryoid bodies (EBs). At this point (day 2), we induced primitive streak (PS) formation by culturing cells in SFD containing the following growth factors and inhibitors: Noggin (150ng/mL), Wnt3a (25ng/mL), and Activin A (9ng/mL). After, the 48-hour PS induction (day 4), cells were removed from primitive streak-inducing factors and cultured as cell aggregates in SFD containing bFGF (10ng/mL) for an additional 48 hours.

value: cells from ES-derived embryoid body

tag: biological replicate


title: sexual_stage0 rep1_WT

source_name: sexual_stage0 WT

value: vegetative hyphae


title: sexual_stage0 rep2_WT


title: day2_EB biol rep 2

description:
BulkExpDat.csv
D2G45


title: sexual_stage1 rep1_WT


title: day0_mESC biol rep 2

description:
BulkExpDat.csv
D0G45

source_name: mouse ESC

value: mouse embryonic stem cell


title: day4_EB biol rep 1

description:
BulkExpDat.csv
D4G44


title: day6_EB biol rep 1

description:
BulkExpDat.csv
D6G44


title: day0_mESC biol rep 1

description:
BulkExpDat.csv
D0G44


title: day2_EB biol rep 1

description:
BulkExpDat.csv
D2G44


title: sexual_stage0 rep3_WT


title: HM1_VEGF_3

status: Public on Jun 19 2018

city: Kyoto

first: Naoki

last: Horikawa

address: 54, Kawahara-cho, Shogoin, Sakyo-ku

department: Gynecology and Obstetrics

country: Japan

institute: Kyoto University

description:
VEGF-3
Gene expression data from HM-1 tumor treated with anti-VEGF antibody.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Mouse Transcriptome Assay 1.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed using Transcriptome Analysis Console with default analysis settings and global scaling as normalization method using RMA Express. These data were filtered and statistically analyzed using R software including genefilter package.

source_name: Subcutaneous tumor collected after treatment

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA.

growth_protocol: 1 million HM-1 cells were injected into right flank of B6C3F1 mice. Tumors were collected when long diameter of tumor reaches 1.5 cm.

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

treatment_protocol: 3 days after cell injection, anti-VEGF antibody or rat IgG isotype control were injected intraperitoneally into mice twice a week until sacrification.

tag: injected cells

value: HM-1 ovarian cancer cells

value: Subcutaneous tumor

value: Anti-VEGF antibody


title: HM1_control_4

description:
control-4
Gene expression data from HM-1 tumor treated with control.

value: Rat IgG control


title: HM1_VEGF_2

description:
VEGF-2
Gene expression data from HM-1 tumor treated with anti-VEGF antibody.


title: HM1_control_1

description:
control-1
Gene expression data from HM-1 tumor treated with control.


title: HM1_VEGF_4

description:
VEGF-4
Gene expression data from HM-1 tumor treated with anti-VEGF antibody.


title: HM1_control_2

description:
control-2
Gene expression data from HM-1 tumor treated with control.


title: HM1_VEGF_1

description:
VEGF-1
Gene expression data from HM-1 tumor treated with anti-VEGF antibody.


title: Experimental Group in vitro (EG in vitro)_male_BiolRep2-TechRep3_pool

status: Public on May 01 2018

city: Ankara

first: Bengi

last: CINAR KUL

address: İrfan Bastug Caddesi

department: Genetics

country: Turkey

institute: Ankara University

description:
DM-6
Experimental1_group_male_Biologic_Replica_2-Tech._Rep_3_pool
Replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with IlluminaGUI in R

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with PureLink RNA isolation kit (Ambion) in accordance with the prescribed protocol provided with the kit. Quality control was performed with MultiskanGo (Thermo) spectrophotometer.

value: left lung lobe

tag: gender

value: male

value: C57BL/6 X BALBc

tag: developmental stage

value: day18 of gestation

tag: group

value: Experimental


title: Experimental Group in vitro (EG in vitro)_male_BiolRep3-TechRep1_pool

description:
DM-7
Experimental1_group_male_Biologic_Replica_3-Tech._Rep_1_pool
Replicate 1


title: Experimental Group in vitro (EG in vitro)_male_BiolRep3-TechRep2_pool

description:
DM-8
Experimental1_group_male_Biologic_Replica_3-Tech._Rep_2_pool
Replicate 2


title: Experimental Group in vitro (EG in vitro)_male_BiolRep1-TechRep3_pool

description:
DM-3
Experimental1_group_male_Biologic_Replica_1-Tech._Rep_3_pool
Replicate 3


title: Control_group_male_BiolRep3-TechRep3_pool

description:
K1M-9
Control_group_male_Biologic_Replica_3-Tech._Rep_3_pool
Replicate 3

value: Control


title: HM1_control_3

description:
control-3
Gene expression data from HM-1 tumor treated with control.


title: Experimental Group in vitro (EG in vitro)_male_BiolRep1-TechRep2_pool

description:
DM-2
Experimental1_group_male_Biologic_Replica_1-Tech._Rep_2_pool
Replicate 2


title: Experimental Group in vitro (EG in vitro)_male_BiolRep2-TechRep2_pool

description:
DM-5
Experimental1_group_male_Biologic_Replica_2-Tech._Rep_2_pool
Replicate 2


title: Control_group_male_BiolRep2-TechRep2_pool

description:
K1M-5
Control_group_male_Biologic_Replica_2-Tech._Rep_2_pool
Replicate 2


title: Control_group_male_BiolRep1-TechRep2_pool

description:
K1M-2
Control_group_male_Biologic_Replica_1-Tech._Rep_2_pool
Replicate 2


title: Control_group_male_BiolRep1-TechRep3_pool

description:
K1M-3
Control_group_male_Biologic_Replica_1-Tech._Rep_3_pool
Replicate 3


title: Control_group_male_BiolRep2-TechRep1_pool

description:
K1M-4
Control_group_male_Biologic_Replica_2-Tech._Rep_1_pool
Replicate 1


title: Experimental Group in vitro (EG in vitro)_male_BiolRep3-TechRep3_pool

description:
DM-9
Experimental1_group_male_Biologic_Replica_3-Tech._Rep_3_pool
Replicate 3


title: Control_group_male_BiolRep3-TechRep1_pool

description:
K1M-7
Control_group_male_Biologic_Replica_3-Tech._Rep_1_pool
Replicate 1


title: Experimental Group in vitro (EG in vitro)_male_BiolRep2-TechRep1_pool

description:
DM-4
Experimental1_group_male_Biologic_Replica_2-Tech._Rep_1_pool
Replicate 1


title: Control_group_male_BiolRep3-TechRep2_pool

description:
K1M-8
Control_group_male_Biologic_Replica_3-Tech._Rep_2_pool
Replicate 2


title: Control_group_male_BiolRep1-TechRep1_pool

description:
K1M-1
Control_group_male_Biologic_Replica_1-Tech._Rep_1_pool
Replicate 1


title: GF_10

status: Public on Apr 10 2018

city: Los Angeles

first: Calvin

last: Pan

address: 675 Charles Young Dr South

institute: UCLA

data_processing:
alignment with STAR 2.5.2b
feature quantification with STAR 2.5.2b
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text containing feature counts

source_name: gonadal fat

extract_protocol:
Upon sacrifice, tissues were instantly frozen in liquid nitrogen. Frozen tissues were homogenized in Qiazol, and following chloroform phase separation RNA was prepared from the pink phase using Qiagen miRNAeasy kits as per original protocol.  Total RNA quality was validated with BioANAlyzer (all samples had RIN>8)
RNA libraries were prepared by the sequencing facility at the UCLA Neurosciences Genomics Core using Illumina TruSeq Stranded kits v2

tag: Sex

value: M

tag: diet

value: high-fat/high-sucrose

value: sham surgery

tag: age

value: 16 weeks


title: GF_11


title: GF_3

value: gonadectomy


title: GF_9


title: GF_2


title: Lv_60

source_name: liver

value: F

value: chow


title: GF_1


title: Control_group_male_BiolRep2-TechRep3_pool

description:
K1M-6
Control_group_male_Biologic_Replica_2-Tech._Rep_3_pool
Replicate 3


title: placebo_e; 230FC

status: Public on Apr 25 2018

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Samples were hybridized to Affymetrix GeneChip Human Gene 1.1 ST array plates (Santa Clara, CA) according to manufacturer's instructions.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.36.1).

organism: Homo sapiens

source_name: Peripheral blood mononuclear cells, placebo treatment, after intervention, subject 230

label_protocol: One hundred nanogram of total RNA was used for whole transcript cDNA synthesis with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: Apparently healthy men and women aged 40–80 y were recruited from Wageningen and surroundings, in The Netherlands. Eligible for participation were nonsmoking men and women, with a BMI (in kg/m2) between 20 and 40 and systolic blood pressure (SBP) between 125 and 160 mm Hg on 2 separate occasions. Exclusion criteria included the presence of diabetes mellitus; cardiovascular, gastrointestinal, or liver disease; usage of antihypertensive or cholesterol-lowering medication or corticosteroids; adherence to a prescribed diet; unstable weight in the past 2 mo; ≥10 h/wk moderate to vigorous physical activity (≥3 metabolic equivalent tasks); and pregnancy or lactation. All subjects gave written informed consent for participation in this study, which was reviewed and approved by the local Medical Ethical Committee of Wageningen University. All procedures were executed according to the declaration of Helsinki. This study was registered at clinicaltrials.gov as NCT01691404.

extract_protocol: RNA was isolated (RNeasy Micro kit, Qiagen, Venlo, the Netherlands), quantified (Nanodrop ND 1000, Nanodrop technologies, Wilmington, Delaware USA) and integrity was checked by an Agilent 2100 Bioanalyser with RNA 6000 microchips (Agilent Technologies, South Queensferry, UK). Samples were included for microarray analysis if the RNA integrity number (RIN) was > 7.

treatment_protocol: The study was a randomized, double blind, placebo-controlled, cross-over trial in which subjects received two 4-week interventions; epicatechin (100mg/day) or placebo (microcrystalline cellulose). Details of the study have been previously described (Dower et al., 2015; PMID: 25934864). In brief, subjects received both interventions in random order with a wash-out period of 4-week between both interventions. Subjects consumed 2 capsules per day with a glass of water: one during breakfast and one during dinner. Subjects were asked to avoid consumption of epicatechin-rich foods throughout the study. Fasting peripheral blood mononuclear cells (PBMC) were collected before (T0) and after each intervention period (T4) using BD Vacutainer Cell Preparation Tubes. On the day prior to each study day, subjects received a standardized evening meal, refrained from alcohol consumption and strenuous exercise, and were not allowed to eat or drink anything except water after 10.00 pm.

value: placebo

tag: subjectid

tag: before/after supplementation

value: after


title: placebo_b; 230FC

source_name: Peripheral blood mononuclear cells, placebo treatment, before intervention, subject 230

value: before


title: placebo_e; 238GG

source_name: Peripheral blood mononuclear cells, placebo treatment, after intervention, subject 238


title: Experimental Group in vitro (EG in vitro) _male_BiolRep1-TechRep1_pool

description:
DM-1
Experimental1_group_male_Biologic_Replica_1-Tech._Rep_1_pool
Replicate 1


title: placebo_b; 238GG

source_name: Peripheral blood mononuclear cells, placebo treatment, before intervention, subject 238


title: Lv_58


title: Lv_59


title: Lv_57


title: GF_4


title: Lv_51


title: Lv_50


title: Lv_49


title: Lv_52


title: Lv_43


title: Lv_44


title: Lv_42


title: Lv_41


title: Lv_36


title: Lv_33


title: Lv_32


title: Lv_30


title: Lv_29


title: Lv_9


title: Lv_12


title: Lv_17


title: Lv_10


title: Lv_11


title: Lv_4


title: Lv_18


title: Lv_31


title: Lv_3


title: GF_60


title: GF_59


title: Lv_1


title: GF_52


title: GF_57


title: GF_58


title: GF_49


title: GF_50


title: GF_44


title: Lv_35


title: GF_43


title: Lv_34


title: GF_35


title: GF_41


title: Lv_19


title: Lv_20


title: GF_36


title: GF_34


title: GF_42


title: Lv_2


title: GF_32


title: GF_33


title: GF_30


title: GF_20


title: GF_29


title: GF_19


title: GF_17


title: GF_51


title: GF_12


title: GF_31


title: GF_18


title: R2-2_w/_rep1

status: Public on Mar 31 2018

city: Tsukuba

first: Kenji

last: Kubara

state: Ibaraki

address: Tokodai 5-1-3

department: Tsukuba Research Laboratories

institute: Eisai Co., Ltd.

description: Gene expression of KRAS mutant iPSCs cultured with bFGF for 5 days.

hyb_protocol: Six hundred nanograms of Cy3-RNAs were hybridized to a SurePrint G3 Human GE Microarray Kit 8x 60K ver. 1.0 (Agilent Technologies) for 17 h at 65°C and 10 rpm rotation by using a Gene Expression Hybridization Kit (Agilent Technologies). The microarrays were washed with a Gene Expression Wash Pack (Agilent Technologies).

scan_protocol: The microarrays were scanned with a G2505B Microarray Scanner (Agilent Technologies).

data_processing: Scanned images were quantified by using Feature Extraction software ver. 11 (Agilent Technologies). Raw data were normalized to the 75th percentile shift per array (chip) with GeneSpring GX ver.13.1 (Agilent Technologies).

source_name: R2-2_Mut, w/ bFGF, 5 days

label_protocol: The total RNA (200 ng) from each cell culture was converted to Cy3-labeled complementary RNAs (cRNAs) by using a One-Color Low Input Quick Amp Labeling Kit (Agilent Technologies) in accordance with the manufacturer’s protocol. Cy3-labeled cRNAs were purified with the RNeasy Mini Kit, and their purity and dye incorporation were assessed with the NanoDrop ND-1000 spectrophotometer and 2100 Bioanalyzer.

extract_protocol: Cells were treated with RLT lysis reagent. Total RNA was purified with the RNeasy Mini kit with DNase (Qiagen). The concentration of purified RNA was measured with a NanoDrop ND-1000 spectrophotometer (SCRUM Inc., Tokyo, Japan), and its quality was assessed with a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Cells were dissociated by TrypLE Select, and 100000 cells were seeded on vitronectin-coated 6-well plates in StemFit (Ajinomoto) containing Y-27632 (10 μM) with or without bFGF and cultured for 5 days. Medium was changed on day 1 to remove Y-27632 and on day 3.

tag: genotype/variation

value: KRAS G13C/WT

value: Male

value: induced pluripotent stem cells (iPSCs)

value: bFGF


title: AF22-sh411-CHIR-N2B27-2

status: Public on Mar 28 2018

city: Shinjuku-ku

first: Tsukasa

last: Sanosaka

state: Tokyo

address: 35 Shinanomachi

department: Department of Physiology

institute: Keio University School of Medicine

description:
replicate 2
SAMPLE 12

data_processing: The data were loaded into R for background correction, quantile normalization and log (base 2)   conversion with the limma package.

source_name: iPS derived Neural Stem Cells

label_protocol: Total RNA was reverse-transcribed, labeled with biotin using the Target Amp-Nano Labeling Kit for Illumina Expression BeadChip (Epicentre)

extract_protocol: RNA was extracted using QIAGEN RNeasy mini kit in accordance with the prescribed protocol. Quality control was performed with Agilent Bioanalyser.

tag: lentivirus

tag: condition


title: AF22-shCTRL-CHIR-N2-2

description:
replicate 2
SAMPLE 14

value: shCTRL


title: R2-1_w/_rep1

source_name: R2-1_Mut, w/ bFGF, 5 days

tag: cell type

tag: treatment


title: R2-1_w/o_rep1

description: Gene expression of KRAS mutant iPSCs cultured without bFGF for 5 days.

source_name: R2-1_Mut, w/o bFGF, 5 days


title: AF22-shCTRL-CHIR-N2-1

description:
replicate 1
SAMPLE 13


title: AF22-sh410-CHIR-N2B27-1

description:
replicate 1
SAMPLE 9


title: AF22-sh410-CHIR-N2-1

description:
replicate 1
SAMPLE 15


title: R2-2_w/o_rep1

source_name: R2-2_Mut, w/o bFGF, 5 days


title: OUH_miR_110

status: Public on Feb 16 2018

city: Odense

first: Ines

last: Block

address: J.B. Winsløws Vej 4

department: Department of Clinical Genetics

country: Denmark

institute: Odense University Hospital

description: Total RNA extracted from fresh frozen primary breast tumour of a female patient without relapse

hyb_protocol: Hybridization, washing, and scanning (Agilent G2565CA Microarray scanner) were performed according to the recommendations provided by Exiqon.

scan_protocol: Scanned images were imported into GenePixPro6.0 software (Molecular Devices) for quality control and raw data extraction.

data_processing: Signals from 3 spots were compiled, only human microRNAs were selected, the R-package limma was used for LOESS normalization and quantile normalization of raw signal intensities, and the ComBat function embedded in the sva R-package was used for adjustment of the normalized intensities and to eliminate potential batch effects

source_name: Primary breast tumour of patient without relapse

label_protocol: The miRCURY Power labeling kit (Exiqon), miRCURY LNA Array hybridization buffer (Exiqon) and miRCURY LNA Array Washing buffer kit (Exiqon) were used for sample labelling, hybridization and washing, respectively.

growth_protocol: not applicable

extract_protocol: Total RNA was isolated from tumor samples with Trizol (Invitrogen) and further purified with the RNeasy micro kit (Qiagen), including DNase treatment. NanoDrop Spectrophotometer (NanoDrop Technologies) was used for RNA quantification. The quality of extracted RNA was assessed with Bioanalyzer 2100 (Agilent Technologies) using the RNA 6000 Nano Kit (Agilent Technologies).

treatment_protocol: After surgical removal, tumor samples were snap-frozen and stored at -80°C.

tag: tissue

value: primary breast tumour

value: female

tag: pair no.

tag: metastasis (1= yes; 0=no)

tag: tumour type

value: ILC

tag: esr1 expression (1=yes; 0=no)

tag: lymph node status (1=positive; 0=negative)

tag: status at last follow up (1=dead, 0=alive)

source_name: common reference pool of all samples


title: OUH_miR_108

tag: gender

value: Papillary carcinoma


title: C2-2_w/_rep1

description: Gene expression of wild-type iPSCs cultured with bFGF for 5 days.

source_name: C2-2_WT, w/ bFGF, 5 days

value: KRAS WT/WT


title: AF22-sh411-CHIR-N2B27-1

description:
replicate 1
SAMPLE 11


title: AF22-sh410-1

description:
replicate 1
SAMPLE 3


title: C2-1_w/o_rep1

description: Gene expression of wild-type iPSCs cultured without bFGF for 5 days.

source_name: C2-1_WT, w/o bFGF, 5 days


title: AF22-sh410-2

description:
replicate 2
SAMPLE 4


title: C2-1_w/_rep1

source_name: C2-1_WT, w/ bFGF, 5 days


title: AF22-shCTRL-CHIR-N2B27-2

description:
replicate 2
SAMPLE 8


title: AF22-shCTRL-CHIR-N2B27-1

description:
replicate 1
SAMPLE 7


title: AF22-shCTRL-1

description:
replicate 1
SAMPLE 1


title: AF22-sh411-CHIR-N2-1

description:
replicate 1
SAMPLE 17


title: AF22-sh411-2

description:
replicate 2
SAMPLE 6


title: AF22-sh410-CHIR-N2B27-2

description:
replicate 2
SAMPLE 10


title: AF22-sh411-1

description:
replicate 1
SAMPLE 5


title: AF22-shCTRL-2

description:
replicate 2
SAMPLE 2


title: AF22-sh410-CHIR-N2-2

description:
replicate 2
SAMPLE 16


title: AF22-sh411-CHIR-N2-2

description:
replicate 2
SAMPLE 18


title: C2-2_w/o_rep1

source_name: C2-2_WT, w/o bFGF, 5 days


title: OUH_miR_107

description: Total RNA extracted from fresh frozen primary breast tumour of a female patient with relapse

source_name: Primary breast tumour of patient with relapse


title: OUH_miR_109


title: OUH_miR_106


title: OUH_miR_101

value: Carcinoma with metaplasia


title: OUH_miR_102


title: OUH_miR_105


title: OUH_miR_104


title: OUH_miR_100

value: IDC


title: OUH_miR_099


title: OUH_miR_098


title: OUH_miR_097


title: OUH_miR_096

value: Mucinous carcinoma


title: OUH_miR_093


title: OUH_miR_092


title: OUH_miR_090


title: OUH_miR_094


title: OUH_miR_091


title: OUH_miR_095


title: OUH_miR_089


title: OUH_miR_081


title: OUH_miR_084


title: OUH_miR_085


title: OUH_miR_086


title: OUH_miR_082


title: OUH_miR_088


title: OUH_miR_080


title: OUH_miR_079


title: OUH_miR_083


title: OUH_miR_077


title: OUH_miR_078


title: OUH_miR_103


title: OUH_miR_087


title: OUH_miR_076


title: OUH_miR_074


title: OUH_miR_073


title: OUH_miR_075


title: OUH_miR_070


title: OUH_miR_069


title: OUH_miR_068


title: OUH_miR_067


title: OUH_miR_056


title: OUH_miR_062


title: OUH_miR_061


title: OUH_miR_060


title: OUH_miR_058


title: OUH_miR_059


title: OUH_miR_065


title: OUH_miR_063


title: OUH_miR_072


title: OUH_miR_071


title: OUH_miR_052


title: OUH_miR_051


title: OUH_miR_054


title: OUH_miR_048


title: OUH_miR_050


title: OUH_miR_049


title: OUH_miR_053


title: OUH_miR_047


title: OUH_miR_066


title: OUH_miR_046


title: OUH_miR_055


title: OUH_miR_064


title: OUH_miR_057


title: OUH_miR_044


title: OUH_miR_041


title: OUH_miR_042


title: OUH_miR_043


title: OUH_miR_045


title: OUH_miR_039


title: OUH_miR_040


title: OUH_miR_025


title: OUH_miR_026


title: OUH_miR_024


title: OUH_miR_023


title: OUH_miR_031


title: OUH_miR_029


title: OUH_miR_027


title: OUH_miR_032


title: OUH_miR_030


title: OUH_miR_033


title: OUH_miR_022


title: OUH_miR_034


title: OUH_miR_036


title: OUH_miR_035


title: OUH_miR_037


title: OUH_miR_028


title: OUH_miR_021


title: OUH_miR_020


title: OUH_miR_019


title: OUH_miR_016


title: OUH_miR_017


title: OUH_miR_018


title: OUH_miR_038


title: OUH_miR_010


title: OUH_miR_011


title: OUH_miR_014


title: OUH_miR_015


title: OUH_miR_013


title: OUH_miR_009


title: OUH_miR_012


title: CONTR, HEMI, sample 2748 [reference set]

status: Public on Jan 14 2018

type: genomic

city: Heidelberg

first: Martin

last: Sill

address: Im Neuenheimer Feld 280

department: Division of Pediatric Neurooncology

country: Germany

institute: DKFZ

description: Methylation data from brain tumor sample.

hyb_protocol: Illumina protocol.

scan_protocol: Illumina iScan System according to the manufacturer's protocol

data_processing:
Bioconductor (Version 3.3) package minifi (Version 1.18) using function 'preprocessIllumina'
Average beta

label: biotin/DNP

molecule: genomic DNA

source_name: brain tumor

label_protocol: Illumina protocol.

extract_protocol: Illumina protocol.

treatment_protocol: Extraction of high molecular weight DNA from frozen tumor samples was carried out by use of a salting-out method or by ultracentrifugation over cesium chloride.

tag: methylation class

value: CONTR, HEMI

tag: material

value: FFPE


title: OUH_miR_008


title: HGNET, MN1, sample 2779 [reference set]

value: HGNET, MN1


title: HGNET, MN1, sample 2777 [reference set]


title: HGNET, MN1, sample 2648 [reference set]


title: HGNET, MN1, sample 2681 [reference set]


title: HGNET, MN1, sample 2632 [reference set]


title: HGNET, MN1, sample 2778 [reference set]


title: OUH_miR_007


title: CONTR, REACT, sample 2656 [reference set]

value: CONTR, REACT


title: OUH_miR_005


title: OUH_miR_006


title: OUH_miR_004


title: PXA, sample 2629 [reference set]

value: PXA


title: PXA, sample 2630 [reference set]


title: HGNET, MN1, sample 2631 [reference set]


title: PXA, sample 2628 [reference set]


title: PXA, sample 2627 [reference set]


title: OUH_miR_003


title: OUH_miR_002


title: OUH_miR_001


title: PXA, sample 2626 [reference set]


title: PXA, sample 2625 [reference set]


title: PXA, sample 2624 [reference set]


title: CONTR, REACT, sample 2623 [reference set]


title: LGG, PA/GG ST, sample 2635 [reference set]

value: LGG, PA/GG ST


title: PXA, sample 2518 [reference set]


title: LGG, PA/GG ST, sample 2478 [reference set]


title: PXA, sample 2480 [reference set]


title: LGG, PA/GG ST, sample 2394 [reference set]


title: LGG, PA/GG ST, sample 2428 [reference set]


title: LGG, PA/GG ST, sample 2474 [reference set]


title: CONTR, REACT, sample 2433 [reference set]


title: CONTR, REACT, sample 2427 [reference set]


title: LGG, PA/GG ST, sample 2289 [reference set]


title: HGNET, MN1, sample 2265 [reference set]


title: CONTR, REACT, sample 2217 [reference set]


title: PXA, sample 2220 [reference set]


title: LGG, PA/GG ST, sample 1994 [reference set]


title: CONTR, REACT, sample 1956 [reference set]

value: Frozen


title: PXA, sample 2062 [reference set]


title: PXA, sample 2198 [reference set]


title: PXA, sample 2177 [reference set]


title: PXA, sample 2176 [reference set]


title: HGNET, MN1, sample 2042 [reference set]


title: PXA, sample 2481 [reference set]


title: HGNET, MN1, sample 1970 [reference set]


title: PXA, sample 1925 [reference set]


title: PXA, sample 1934 [reference set]


title: LGG, PA/GG ST, sample 1916 [reference set]


title: PXA, sample 1857 [reference set]


title: PXA, sample 1851 [reference set]


title: PXA, sample 1853 [reference set]


title: PXA, sample 1856 [reference set]


title: PXA, sample 1852 [reference set]


title: PXA, sample 2347 [reference set]


title: PXA, sample 2178 [reference set]


title: PXA, sample 1816 [reference set]


title: HGNET, MN1, sample 1774 [reference set]


title: LGG, PA/GG ST, sample 1730 [reference set]


title: PXA, sample 1710 [reference set]


title: PXA, sample 1683 [reference set]


title: HGNET, MN1, sample 1659 [reference set]


title: PXA, sample 1651 [reference set]


title: CONTR, REACT, sample 1632 [reference set]


title: LGG, PA/GG ST, sample 1918 [reference set]


title: PXA, sample 1639 [reference set]


title: PXA, sample 1645 [reference set]


title: LGG, PA/GG ST, sample 1623 [reference set]


title: HGNET, MN1, sample 1534 [reference set]


title: PXA, sample 1595 [reference set]


title: LGG, PA/GG ST, sample 1482 [reference set]


title: PXA, sample 1467 [reference set]


title: LGG, PA/GG ST, sample 1466 [reference set]


title: PXA, sample 1650 [reference set]


title: HGNET, MN1, sample 1167 [reference set]


title: CONTR, REACT, sample 1175 [reference set]


title: HGNET, MN1, sample 1171 [reference set]


title: PXA, sample 1115 [reference set]


title: CONTR, REACT, sample 1114 [reference set]


title: LGG, PA/GG ST, sample 1187 [reference set]


title: PXA, sample 1145 [reference set]


title: HGNET, MN1, sample 1737 [reference set]


title: LGG, PA/GG ST, sample 890 [reference set]


title: HGNET, MN1, sample 945 [reference set]


title: HGNET, MN1, sample 927 [reference set]


title: LGG, PA/GG ST, sample 856 [reference set]


title: LGG, PA/GG ST, sample 961 [reference set]


title: LGG, PA/GG ST, sample 855 [reference set]


title: CONTR, REACT, sample 864 [reference set]


title: HGNET, MN1, sample 841 [reference set]


title: LGG, PA/GG ST, sample 850 [reference set]


title: PXA, sample 802 [reference set]


title: PXA, sample 804 [reference set]


title: LGG, PA/GG ST, sample 805 [reference set]


title: PXA, sample 801 [reference set]


title: PXA, sample 1174 [reference set]


title: PXA, sample 799 [reference set]


title: CONTR, REACT, sample 761 [reference set]


title: LGG, PA/GG ST, sample 762 [reference set]


title: PXA, sample 2297 [reference set]


title: PXA, sample 798 [reference set]


title: CONTR, REACT, sample 760 [reference set]


title: LGG, PA/GG ST, sample 757 [reference set]


title: HGNET, MN1, sample 752 [reference set]


title: CONTR, HEMI, sample 681 [reference set]


title: CONTR, REACT, sample 759 [reference set]


title: CONTR, HEMI, sample 680 [reference set]


title: CONTR, HEMI, sample 679 [reference set]


title: CONTR, HEMI, sample 678 [reference set]


title: CONTR, REACT, sample 666 [reference set]


title: CONTR, HEMI, sample 677 [reference set]


title: CONTR, REACT, sample 659 [reference set]


title: CONTR, REACT, sample 660 [reference set]


title: PXA, sample 803 [reference set]


title: CONTR, REACT, sample 658 [reference set]


title: PXA, sample 800 [reference set]


title: LGG, PA/GG ST, sample 656 [reference set]


title: CONTR, REACT, sample 602 [reference set]


title: CONTR, HEMI, sample 384 [reference set]


title: CONTR, HEMI, sample 385 [reference set]


title: CONTR, HEMI, sample 382 [reference set]


title: CONTR, HEMI, sample 386 [reference set]


title: CONTR, HEMI, sample 387 [reference set]


title: CONTR, REACT, sample 370 [reference set]


title: CONTR, HEMI, sample 383 [reference set]


title: LGG, PA/GG ST, sample 69 [reference set]


title: CONTR, REACT, sample 33 [reference set]


title: CONTR, REACT, sample 113 [reference set]


title: CONTR, REACT, sample 75 [reference set]


title: CONTR, REACT, sample 661 [reference set]


title: HGNET, MN1, sample 470 [reference set]


title: CONTR, HEMI, sample 682 [reference set]


title: Non pregnant Fetal cotyledon_rep4

status: Public on Dec 30 2017

city: Karnal

first: Syed

middle: Azmal

last: Ali

state: Haryana

address: G.T. Road, ABTC, Proteomics and Cell Biology Lab

department: Animal Biotechnology

country: India

institute: National Dairy Research Institute

description: Gene expression before pregnancy rep4

hyb_protocol: 600ng of labeled cRNA sample were fragmented at 60ºC and hybridized on to Agilent's Bovine Gene Expression  8x15k Array (AMADID: 029411). Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours.

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

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

organism: Bos taurus

source_name: Fetal cotyledon tissue non pregnant rep4

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

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

treatment_protocol: The Gravid uteri tissue samples from pregnant buffalo were collected from local slaughter house. The samples were collected from the slaughtered animals and no animal was slaughtered purposely for tissue collection.

value: Fetal cotyledon

tag: Sex

tag: pregnant

value: no


title: Pregnant Fetal cotyledon_rep1

description: Gene expression after pregnancy rep1

source_name: Fetal cotyledon tissue pregnant rep1

value: yes


title: Non pregnant Fetal cotyledon_rep1

description: Gene expression before pregnancy rep1

source_name: Fetal cotyledon tissue non pregnant rep1

value: female


title: Pregnant Fetal cotyledon_rep2

description: Gene expression after pregnancy rep2

source_name: Fetal cotyledon tissue pregnant rep2


title: Untreated vempty vector, biological rep1

status: Public on Jul 07 2017

city: Montreal

first: Steven

last: Shao

state: Quebec

address: 2155 Guy Street, suite 500

country: Canada

institute: McGill University

description:
Gene expression from empty vector transduced human CD4+ T cells
EV-UT-1

hyb_protocol: 3.5µg DNA target was hybridized on GeneChip® Clariom S Human (Affymetrix) and incubated at 450C in the Genechip® Hybridization oven 640 (Affymetrix) for 17 hours at 60 rpm. GeneChips were then washed in a GeneChips® Fluidics Station 450 (Affymetrix) using Affymetrix Hybridization Wash and Stain kit according to the manufacturer’s instructions (Affymetrix).

scan_protocol: The microarrays were scanned on a GeneChip® scanner 3000 (Affymetrix).

data_processing: The data were analyzed using R with the pd.clariom.s.human, clariomshumantranscriptcluster.db, oligo, limma and gplots packages. RMA normalization and Log2 transformation were applied to the raw intensity values.

source_name: Untreated vempty vector

label_protocol: Sense-strand cDNA was synthesized from 100 ng of total RNA, and fragmentation and labeling were performed to produce ss DNA with the Affymetrix GeneChip® WT Terminal Labeling Kit according to manufacturer’s instructions (Affymetrix).

growth_protocol: Transduced T cells were expanded in exvivo-15 medium with 5% FBS.

extract_protocol: Total RNA was isolated using the Qiagen RNEasy Mini kit according to the manufacturer's suggested protocol. Total RNA was quantified using a NanoDrop Spectrophotometer ND-1000 (NanoDrop Technologies, Inc.) and its integrity was assessed using a 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Resting transduced T cells were activated with PHA with or without SGF.

tag: cell

value: CD4+ T cell

tag: lentivirally transduced with

value: Empty Vector

tag: activated with

value: 0.5 μg/ml of phytohemagglutinin (PHA) in the absence of SGF003


title: SGF treated wild-type, biological rep1

description:
Gene expression from wild-type FOXP3 transduced human CD4+ T cells treated with SGF
WT-SGF-1

source_name: SGF treated wild-type

value: Wild-type FOXP3

value: 0.5 μg/ml of phytohemagglutinin (PHA) in the presence of SGF003 (8 μg/mL)


title: Non pregnant Fetal cotyledon_rep3

description: Gene expression before pregnancy rep3

source_name: Fetal cotyledon tissue non pregnant rep3


title: Non pregnant Fetal cotyledon_rep2

description: Gene expression before pregnancy rep2

source_name: Fetal cotyledon tissue non pregnant rep2


title: Untreated A384T, biological rep1

description:
Gene expression from A384T FOXP3 transduced human CD4+ T cells
AT-UT-1

source_name: Untreated A384T

value: A384T FOXP3


title: Untreated R397W, biological rep1

description:
Gene expression from R397W FOXP3 transduced human CD4+ T cells
RW-UT-1

source_name: Untreated R397W

value: R397W FOXP3


title: SGF treated wild-type, biological rep2

description:
Gene expression from wild-type FOXP3 transduced human CD4+ T cells treated with SGF
WT-SGF-2


title: SGF treated A384T, biological rep1

description:
Gene expression from A384T FOXP3 transduced human CD4+ T cells treated with SGF
AT-SGF-1

source_name: SGF treated A384T


title: Untreated wild-type, biological rep2

description:
Gene expression from wild-type FOXP3 transduced human CD4+ T cells
WT-UT-2

source_name: Untreated wild-type


title: Untreated wild-type, biological rep1

description:
Gene expression from wild-type FOXP3 transduced human CD4+ T cells
WT-UT-1


title: MB_SubtypeStudy_55761

status: Public on Jun 13 2017

city: Toronto

first: Florence

middle: M G

last: Cavalli

state: Ontario

address: PGCRL, 686 Bay Street

department: Developmental and Stem Cell

institute: The Hospital for Sick Children

hyb_protocol: As directed by affimetrix

scan_protocol: As directed by affimetrix

data_processing:
Expression data were analyzed in the R environment (v3.1.1). We used the affy package (v1.44.0) and the custom chip definition file (CDF) hugene11sthsensgcdf (v19.0.0) (from http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/19.0.0/ensg.asp) to load and summarize the expression of 21,641 Ensembl (ENSG) genes and process the data. Samples flagged by the arrayQualityMetrics Bioconductor package (v3.22.0) were removed due to low quality.  Expression data were normalized using the rma method.
The expression table (available on the series record) contains the normalized log2 gene expression values. The first 5 columns contain annotations; the Probe.Set.Name and description given by the Brainarray CDF package used (v19) and the corresponding Ensembl gene ID, HGNC symbol and ID retrieved from ensembl v77 (Otober 2014). This version of Ensembl has been used since the Brain array CDF package used (v19) has been released in November 2014.

source_name: Fresh frozen

label_protocol: As directed by affimetrix

extract_protocol: Snap frozen tissue was homogenized using the Precellys 24 tissue homogenizer in Trizol Reagent. RNA was extracted from the homogenized tissue according to the manufacturer's instructions for Trizol Reagent. RNA was measured with nanoDrop and Agilent Bioanalyzer for quantity and quality.

value: medulloblastoma

tag: subgroup

tag: subtype


title: SGF treated empty vector, biological rep1

description:
Gene expression from empty vector transduced human CD4+ T cells treated with SGF
EV-SGF-1

source_name: SGF treated empty vector


title: SGF treated empty vector, biological rep2

description:
Gene expression from empty vector transduced human CD4+ T cells treated with SGF
EV-SGF-2


title: Pregnant Fetal cotyledon_rep4

description: Gene expression after pregnancy rep4

source_name: Fetal cotyledon tissue pregnant rep4

tag: tissue


title: Untreated R397W, biological rep2

description:
Gene expression from R397W FOXP3 transduced human CD4+ T cells
RW-UT-2


title: Untreated vempty vector, biological rep2

description:
Gene expression from empty vector transduced human CD4+ T cells
EV-UT-2


title: SGF treated R397W, biological rep1

description:
Gene expression from R397W FOXP3 transduced human CD4+ T cells treated with SGF
RW-SGF-1

source_name: SGF treated R397W


title: Pregnant Fetal cotyledon_rep3

description: Gene expression after pregnancy rep3

source_name: Fetal cotyledon tissue pregnant rep3


title: SGF treated R397W, biological rep2

description:
Gene expression from R397W FOXP3 transduced human CD4+ T cells treated with SGF
RW-SGF-2


title: MB_SubtypeStudy_55762


title: Untreated A384T, biological rep2

description:
Gene expression from A384T FOXP3 transduced human CD4+ T cells
AT-UT-2


title: MB_SubtypeStudy_55763


title: SGF treated A384T, biological rep2

description:
Gene expression from A384T FOXP3 transduced human CD4+ T cells treated with SGF
AT-SGF-2


title: MB_SubtypeStudy_55759

value: SHH


title: MB_SubtypeStudy_55755


title: MB_SubtypeStudy_55757


title: MB_SubtypeStudy_55760


title: MB_SubtypeStudy_55758


title: MB_SubtypeStudy_55752


title: MB_SubtypeStudy_55753


title: MB_SubtypeStudy_55749


title: MB_SubtypeStudy_55756


title: MB_SubtypeStudy_55754

value: WNT


title: MB_SubtypeStudy_55750


title: MB_SubtypeStudy_55740


title: MB_SubtypeStudy_55748


title: MB_SubtypeStudy_55751


title: MB_SubtypeStudy_55744


title: MB_SubtypeStudy_55733


title: MB_SubtypeStudy_55742


title: MB_SubtypeStudy_55743


title: MB_SubtypeStudy_55735


title: MB_SubtypeStudy_55746


title: MB_SubtypeStudy_55741


title: MB_SubtypeStudy_55747


title: MB_SubtypeStudy_55736


title: MB_SubtypeStudy_55738


title: MB_SubtypeStudy_55745


title: MB_SubtypeStudy_55734


title: MB_SubtypeStudy_55739


title: MB_SubtypeStudy_55731


title: MB_SubtypeStudy_55737


title: MB_SubtypeStudy_55732


title: MB_SubtypeStudy_55730


title: MB_SubtypeStudy_55728


title: MB_SubtypeStudy_55726


title: MB_SubtypeStudy_55717


title: MB_SubtypeStudy_55727


title: MB_SubtypeStudy_55722


title: MB_SubtypeStudy_55721


title: MB_SubtypeStudy_55715


title: MB_SubtypeStudy_55729


title: MB_SubtypeStudy_55723


title: MB_SubtypeStudy_55719


title: MB_SubtypeStudy_55725


title: MB_SubtypeStudy_55711


title: MB_SubtypeStudy_55713


title: MB_SubtypeStudy_55724


title: MB_SubtypeStudy_55704


title: MB_SubtypeStudy_55712


title: MB_SubtypeStudy_55714


title: MB_SubtypeStudy_55706


title: MB_SubtypeStudy_55705


title: MB_SubtypeStudy_55709


title: MB_SubtypeStudy_55708


title: MB_SubtypeStudy_55720


title: MB_SubtypeStudy_55710


title: MB_SubtypeStudy_55718


title: MB_SubtypeStudy_55707


title: MB_SubtypeStudy_55698


title: MB_SubtypeStudy_55699


title: MB_SubtypeStudy_55700


title: MB_SubtypeStudy_55701


title: MB_SubtypeStudy_55695


title: MB_SubtypeStudy_55696


title: MB_SubtypeStudy_55692


title: MB_SubtypeStudy_55691


title: MB_SubtypeStudy_55697


title: MB_SubtypeStudy_55689


title: MB_SubtypeStudy_55688


title: MB_SubtypeStudy_55693


title: MB_SubtypeStudy_55694


title: MB_SubtypeStudy_55702


title: MB_SubtypeStudy_55686


title: MB_SubtypeStudy_55687


title: MB_SubtypeStudy_55679


title: MB_SubtypeStudy_55683


title: MB_SubtypeStudy_55716


title: MB_SubtypeStudy_55685


title: MB_SubtypeStudy_55678


title: MB_SubtypeStudy_55681


title: MB_SubtypeStudy_55677


title: MB_SubtypeStudy_55682


title: MB_SubtypeStudy_55680


title: MB_SubtypeStudy_55676


title: MB_SubtypeStudy_55684


title: MB_SubtypeStudy_55690


title: MB_SubtypeStudy_55674


title: MB_SubtypeStudy_55672


title: MB_SubtypeStudy_55675


title: MB_SubtypeStudy_55673


title: MB_SubtypeStudy_55671


title: MB_SubtypeStudy_55666


title: MB_SubtypeStudy_55668


title: MB_SubtypeStudy_55670


title: MB_SubtypeStudy_55659


title: MB_SubtypeStudy_55703


title: MB_SubtypeStudy_55669


title: MB_SubtypeStudy_55662


title: MB_SubtypeStudy_55661


title: MB_SubtypeStudy_55655


title: MB_SubtypeStudy_55657


title: MB_SubtypeStudy_55656


title: MB_SubtypeStudy_55658


title: MB_SubtypeStudy_55664


title: MB_SubtypeStudy_55667


title: MB_SubtypeStudy_55653


title: MB_SubtypeStudy_55649


title: MB_SubtypeStudy_55654


title: MB_SubtypeStudy_55663


title: MB_SubtypeStudy_55660


title: MB_SubtypeStudy_55650


title: MB_SubtypeStudy_55665


title: MB_SubtypeStudy_55648


title: MB_SubtypeStudy_55646


title: MB_SubtypeStudy_55644


title: MB_SubtypeStudy_55647


title: MB_SubtypeStudy_55645


title: MB_SubtypeStudy_55641


title: MB_SubtypeStudy_55642


title: MB_SubtypeStudy_55632


title: MB_SubtypeStudy_55633


title: MB_SubtypeStudy_55652


title: MB_SubtypeStudy_55630


title: MB_SubtypeStudy_55637


title: MB_SubtypeStudy_55643


title: MB_SubtypeStudy_55640


title: MB_SubtypeStudy_55636


title: MB_SubtypeStudy_55628


title: MB_SubtypeStudy_55639


title: MB_SubtypeStudy_55638


title: MB_SubtypeStudy_55629


title: MB_SubtypeStudy_55635


title: MB_SubtypeStudy_55634


title: MB_SubtypeStudy_55631


title: MB_SubtypeStudy_55620


title: MB_SubtypeStudy_55627


title: MB_SubtypeStudy_55624


title: MB_SubtypeStudy_55626


title: MB_SubtypeStudy_55618


title: MB_SubtypeStudy_55625


title: MB_SubtypeStudy_55623


title: MB_SubtypeStudy_55617


title: MB_SubtypeStudy_55619


title: MB_SubtypeStudy_55621


title: MB_SubtypeStudy_55613


title: MB_SubtypeStudy_55604


title: MB_SubtypeStudy_55605


title: MB_SubtypeStudy_55614


title: MB_SubtypeStudy_55622


title: MB_SubtypeStudy_55609


title: MB_SubtypeStudy_55615


title: MB_SubtypeStudy_55616


title: MB_SubtypeStudy_55606


title: MB_SubtypeStudy_55601


title: MB_SubtypeStudy_55610


title: MB_SubtypeStudy_55607


title: MB_SubtypeStudy_55602


title: MB_SubtypeStudy_55611


title: MB_SubtypeStudy_55612


title: MB_SubtypeStudy_55600


title: MB_SubtypeStudy_55603


title: MB_SubtypeStudy_55608


title: MB_SubtypeStudy_55594


title: MB_SubtypeStudy_55599


title: MB_SubtypeStudy_55598


title: MB_SubtypeStudy_55593


title: MB_SubtypeStudy_55597


title: MB_SubtypeStudy_55592


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title: MB_SubtypeStudy_55574


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title: MB_SubtypeStudy_55570


title: MB_SubtypeStudy_55565


title: MB_SubtypeStudy_55562


title: MB_SubtypeStudy_55567


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title: input-of-Sall4-ChIP-in-TT2-shTet2

status: Public on Oct 07 2016

city: Beijing

first: Zhuqiang

last: Zhang

address: 15 Datun Road, Chaoyang District.

country: China

institute: Institute of Biophysics, CAS

description: input of SALL4A ChIP in TT2 cells transfected with shTet2#3

library_source: genomic

data_processing:
Basecalls performed by BGI, Shenzhen
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie version 0.12.7 with only unique mapped reads were kept
Data were filtered using samtools to remove potential PCR duplicates
peaks were called using MACS (v1.4.2)
RNA-Seq data were mapped by TopHat and quantitified by Crosslinks.
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using IGV tools with fragment extension 300 bp

source_name: TT2 mES cells treated with shRNA of Tet2 (shTet2#3).

growth_protocol: TT2 mouse ESCs were cultured on dishes coated with 0.1% gelatin (Millipore) without feeder cells. The medium contained Dulbecco’s Modified Eagle’s Medium (DMEM, Sigma, D9443), 10% Knockout Serum Replacement (KSR, Life Technologies), 1% dialyzed fetal bovine serum (FBS, Life Technologies), 3.5 mg/ml D-glucose (Amresco), 1× non-essential amino acids (Millipore), 1× β-mercaptoethanol (Millipore), 1,000 U/ml leukaemia inhibitory factor (LIF, Millipore), 105 μg/ml L-leucine (Sigma, L8912), 89 μg/ml L-arginine:HCl (for heavy medium, R10, Cambridge Isotope Laboratories, CNLM-539-0.5; for light medium, R0, Sigma, A8094) and 91 μg/ml L-lysine:HCl (for heavy medium, K8, Cambridge Isotope Laboratories, CNLM-291-0.5; for light medium, K0, Sigma, L8662).

extract_protocol:
Cells for ChIP assays were crosslinked in 1% formaldehyde for 8-10 min at room temperature. The reaction was terminated by adding 2 M glycine to a final concentration of 125 mM. After being washed with PBS, the cells were resuspended in lysis buffer 1 (50 mM HEPES, pH 7.9, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% IGEPAL CA-630 and 0.25% Triton X-100) and incubated for 10 min on ice. After centrifugation, the cells were resuspended in lysis buffer 2 (10 mM Tris-HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA and 0.5 mM EGTA) and incubated for 10 min at room temperature. The chromatin fraction was resuspended in lysis buffer 3 (10 mM Tris-HCl, pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxycholate and 0.5% sodium N-lauroyl sarcosine) and sonicated into 200-400 base-pair (bp) fragments (Bioruptor, Diagenode). Chromatin fragments were immunoprecipitated overnight with antibodies against SALL1, SALL4A and TET1. The protein-antibody complexes were incubated with pre-washed Dynabeads Protein A or G (Life Technologies) for 1 hr. The beads were sequentially washed with the following buffers: once with FA-lysis buffer (150 mM NaCl, 1% Triton X-100, 50 mM HEPES, pH 7.9, 2 mM EDTA and 0.5% sodium deoxycholate), twice with FA high salt buffer (500 mM NaCl, 1% Triton X-100, 50 mM HEPES, pH 7.9, 2 mM EDTA and 0.5% sodium deoxycholate), once with LiCl buffer (250 mM LiCl, 0.5% IGEPAL CA-630, 0.5% sodium deoxycholate, 1 mM EDTA and 10 mM Tris-HCl, pH 8.0) and twice with TE buffer (10 mM Tris-HCl, pH 8.0 and 1 mM EDTA). Protein complexes were eluted by incubation with 250 μl of freshly prepared elution buffer (1% SDS and 100 mM sodium bicarbonate) for 15 min at room temperature. The elution step was repeated once, and the eluted fractions were combined.  For ChIP of bio-SALL4A, chromatin fragments were incubated with Dynabeads M-280 Streptavidin (Life Technologies) equilibrated with PBS + 1% BSA. Triton X-100 was added to a final concentration of 1%. Protein-bound beads were washed sequentially with following buffers: 2% SDS twice, FA high salt buffer twice, LiCl buffer (250 mM LiCl, 1% IGEPAL CA-630, 0.5% sodium deoxycholate, 1 mM EDTA and 10 mM Tris-HCl, pH 8.0) once and TE buffer twice. Protein complexes were eluted by incubating the beads in 300 μl of elution buffer at 65℃ with agitation at 800 rpm overnight.  After crosslinking reversal and RNase A and proteinase K treatment, DNA was extracted with phenol-chloroform and precipitated with ethanol.  For DNA immunoprecipitation assays, genomic DNA was isolated by conventional phenol extraction and proteinase K treatment. The purified genomic DNA was sonicated into 200-400 bp fragments. Adapter-ligated DNA libraries were constructed. DNA fragments were denatured in 0.4 M NaOH by incubation at 95℃ for 10 min and then placed on ice immediately and neutralised by adding an equal volume of 2 M ammonium acetate. Samples (3 μg) of the adapter-ligated DNA libraries were immunoprecipitated with 5 μg of mC or hmC antibodies, and 5 μg of DNA with 0.2 μl of caC anti-serum.  For mRNA deep sequencing analysis, total RNA was isolated by TRIzol Reagent (Life Technologies), and mRNA with a poly (A) tail was purified and subjected to sequencing library construction.
The ChIP-seq libraries were constructed using NEBNext DNA Sample Prep Master Mix (NEB).DNA libraries were subjected to size-selection using AMPure XP beads (Beckman Coulter) and PCR amplification (18-20 cycles for ChIP-seq DNA libraries and 12-16 cycles for DIP-seq libraries).

tag: strain background

value: (C57BL/6NCrlj x CBA/JNCrlj)F1

tag: cell line

tag: cell type

value: embryonic stem cells

tag: genotype/variation

value: Tet2 shRNA transgene

tag: chip antibody


title: input-of-Sall4-ChIP-in-TT2-shScr-2nd

description: input of SALL4A ChIP in TT2 cells transfected with scrambled shRNA (2nd)

source_name: TT2 mES cells treated with scrambled shRNA (shScr-2nd)

value: scrabled shRNA transgene


title: Sall4-ChIP-in-TT2-shTet2

description: SALL4A ChIP in TT2 cells transfected with shTet2#3

value: Monoclonal antibody against SALL4A was generated with the immunogenic peptide TSGPNSRDLM in mice at Abmart.


title: Sall4-ChIP-in-TT2-shScr-2nd

description: SALL4A ChIP in TT2 cells transfected with scrambled shRNA (2nd)


title: MB_SubtypeStudy_55008


title: MB_SubtypeStudy_55006


title: MB_SubtypeStudy_55007


title: MB_SubtypeStudy_55011


title: MB_SubtypeStudy_55002


title: MB_SubtypeStudy_55001


title: MB_SubtypeStudy_55010


title: MB_SubtypeStudy_55003


title: MB_SubtypeStudy_55004


title: CD8-Tcells_in vitro_48h_20mM_R-2-HG, 3

status: Public on Jul 27 2016

first: Lukas

last: Bunse

description:
SAMPLE6
3999521008_F

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Gene expression microarrays were scanned using the Illumina iScan-Scanner according to "Standard Illumina Scanning Protocol" Part # 11322355.

data_processing: Intensity values were normexp background corrected and quantile-normalized using control probes according to Shi et al. 2010.

source_name: CD8 T cells + R-2-HG

label_protocol: Standard Illumina labeling protocol.

growth_protocol: T-cells were isolated using biotinylated anti-CD3 (clone 145-2C11) and anti-biotin beads (1:10, Miltenyi Biotec) using magnetic-activated cell sorting (MACS) technology. CD4+ and CD8+ T-cells were separated with the CD4 T-cell isolation kit, human (order no. 130-096-533) or by CD4 MicroBeads, human (order no. 130-045-101) on isolated T-cells using MACS according to manufacturer's instructions (Miltenyi Biotec). CD4+ and CD8+ T-cells were kept in RPMI-1640 with 10 % FBS, 100 U/ml penicillin, 100 μg/ml streptomycin, 0.1 mM non-essential amino acids solution, and 5e−5 M 2-mercaptoethanol.

extract_protocol: Total T-cells mRNA were extracted using RNeasy RNA isolation kit (Qiagen) including DNase digestion according to manufacturer’s instructions.

treatment_protocol: T-cells were treated with R-2-HG for 48 h before overnight stimulation with PMA (20 ng/ml) and ionomycin (1 μg/ml).

tag: disease status

value: healthy

value: CD8+ T cells

tag: treatment

value: R-2-hydroxyglutarate (R-2-HG)

tag: treatment duration

tag: sample type

value: treated

tag: donor id


title: CD8-Tcells_in vitro_48h_vehicle, 4

description:
SAMPLE7
3999521008_G

source_name: CD8 T cells + vehicle

value: vehicle

value: control


title: CD8-Tcells_in vitro_48h_vehicle, 3

description:
SAMPLE5
3999521008_E


title: CD4-Tcells_in vitro_48h_vehicle, 5

description:
SAMPLE11
3999521008_K

source_name: CD4 T cells + vehicle

value: CD4+ T cells


title: CD4-Tcells_in vitro_48h_20mM_R-2-HG, 5

description:
SAMPLE12
3999521008_L

source_name: CD4 T cells + R-2-HG


title: CD8-Tcells_in vitro_48h_vehicle, 5

description:
SAMPLE9
3999521008_I


title: CD8-Tcells_in vitro_48h_vehicle, 1

description:
SAMPLE1
3999521008_A


title: CD8-Tcells_in vitro_48h_20mM_R-2-HG, 5

description:
SAMPLE10
3999521008_J


title: CD8-Tcells_in vitro_48h_vehicle, 2

description:
SAMPLE3
3999521008_C


title: CD8-Tcells_in vitro_48h_20mM_R-2-HG, 2

description:
SAMPLE4
3999521008_D


title: CD8-Tcells_in vitro_48h_20mM_R-2-HG, 1

description:
SAMPLE2
3999521008_B


title: CD8-Tcells_in vitro_48h_20mM_R-2-HG, 4

description:
SAMPLE8
3999521008_H


title: dkfz_MB_15-0001

status: Public on Feb 25 2016

first: Marcel

last: Kool

department: Pediatric Neurooncology

institute: German Cancer Research Center DKFZ

description: Gene expression data from a brain tumor sample

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 = 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).

source_name: brain tumor

label_protocol: Standard Affymetrix protocol

extract_protocol: Total RNA from biopsy samples was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using the TRIzol reagent (Invitrogen, Carlsbad, USA), and subsequently passed over a RNeasy Mini Spin Column (Qiagen, Hilden, Germany) for the removal of small fragments. Integrity control and sample quantitation of total extracted RNA was performed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).

tag: affymetrix id

tag: institutional tumor diagnosis

value: MB

tag: molecular subgroup

tag: gender

value: M

tag: age (years)

tag: tumor location

value: cerebellar


title: dkfz_MB_15-0022


title: dkfz_MB_15-0003


title: dkfz_MB_15-0046

value: F


title: dkfz_MB_15-0017


title: dkfz_MB_15-0007


title: dkfz_MB_15-0042


title: dkfz_MB_15-0016


title: dkfz_MB_15-0036


title: dkfz_MB_15-0018


title: dkfz_MB_15-0014


title: dkfz_MB_15-0045


title: dkfz_MB_15-0032


title: dkfz_MB_15-0005


title: dkfz_MB_15-0044


title: dkfz_MB_15-0035


title: dkfz_MB_15-0039


title: dkfz_MB_15-0028


title: dkfz_MB_15-0019


title: dkfz_MB_15-0020


title: dkfz_MB_15-0010


title: dkfz_MB_15-0024


title: dkfz_MB_15-0029


title: dkfz_MB_15-0030


title: dkfz_MB_15-0021


title: dkfz_MB_15-0009


title: MB_SubtypeStudy_55012

tag: tissue

value: medulloblastoma

tag: subgroup

value: SHH

tag: subtype


title: dkfz_MB_15-0037


title: dkfz_MB_15-0031


title: dkfz_MB_15-0008


title: dkfz_MB_15-0038


title: dkfz_MB_15-0027


title: dkfz_MB_15-0023


title: dkfz_MB_15-0033


title: dkfz_MB_15-0034


title: dkfz_MB_15-0025


title: dkfz_MB_15-0002


title: dkfz_MB_15-0004


title: dkfz_MB_15-0015


title: dkfz_MB_15-0006


title: dkfz_MB_15-0013


title: dkfz_MB_15-0041


title: dkfz_MB_15-0040


title: dkfz_MB_15-0026


title: dkfz_MB_15-0011


title: dkfz_MB_15-0043


title: MB_SubtypeStudy_55009


title: MB_SubtypeStudy_55005


title: dkfz_MB_15-0012


title: Multi-region sample MB8-4

status: Public on Dec 31 2015

first: Marc

last: Remke

address: 555 University Ave. Rm 1504

department: Laboratory Medicine and Pathobiology

hyb_protocol: As directed by Affymetrix.

scan_protocol: As directed by Affymetrix.

data_processing: Cel files were imported to Partek Genomics Suite. Robust Multi-array average (RMA) was used as normalization method.

source_name: Primary human brain tumor sample

label_protocol: As directed by Affymetrix.

extract_protocol: Total RNA was extracted from frozen medulloblastoma tissue using the Trizol method (Invitrogen) as directed by the manufacturer.  RNA integrity was assessed using the Agilent 2100 Bioanalyzer prior to processing for the Gene Array.  Samples with RIN values equal to / greater 7 were included in the study.

tag: patientid

tag: age

value: Male


title: Multi-region sample MB9-4


title: Multi-region sample MB8-3


title: Multi-region sample MB8-5


title: Multi-region sample MB9-3


title: Multi-region sample MB9-1


title: Multi-region sample MB7-1


title: Multi-region sample MB8-1


title: Multi-region sample MB9-5


title: Multi-region sample MB9-2


title: Multi-region sample MB6-6

value: Female


title: Multi-region sample MB7-5


title: Multi-region sample MB6-5


title: Multi-region sample MB5-9


title: Multi-region sample MB5-8


title: Multi-region sample MB6-1


title: Multi-region sample MB7-3


title: Multi-region sample MB7-2


title: Multi-region sample MB7-6


title: Multi-region sample MB9-6


title: Multi-region sample MB8-2


title: Multi-region sample MB5-3


title: Multi-region sample MB5-4


title: Multi-region sample MB6-3


title: Multi-region sample MB6-2


title: Multi-region sample MB7-4


title: Multi-region sample MB5-6


title: Multi-region sample MB6-4


title: Multi-region sample MB5-5


title: Multi-region sample MB5-2


title: Multi-region sample MB5-1


title: Multi-region sample MB4-9


title: Multi-region sample MB4-4


title: Multi-region sample MB2-7


title: Multi-region sample MB4-1


title: Multi-region sample MB4-6


title: Multi-region sample MB4-7


title: Multi-region sample MB4-5


title: Multi-region sample MB4-8


title: Multi-region sample MB4-3


title: Multi-region sample MB2-8


title: Multi-region sample MB2-4


title: Multi-region sample MB4-2


title: Multi-region sample MB1-3


title: Multi-region sample MB2-1


title: Multi-region sample MB1-4


title: Multi-region sample MB2-3


title: Primary medulloblastoma sample_MB-1210

data_processing: CHP files were generated by Expression Console using Affymetrix default analysis settings and Robust Multi-array average (RMA) as normalization method.

tag: histology

value: LCA

tag: follow-up

tag: death


title: Primary medulloblastoma sample_MB-1204


title: Multi-region sample MB2-5


title: Multi-region sample MB1-5


title: Primary medulloblastoma sample_MB-131


title: Primary medulloblastoma sample_MB-729

value: Classic


title: Primary medulloblastoma sample_MB-2168

value: Desmoplastic


title: Primary medulloblastoma sample_MB-610


title: Primary medulloblastoma sample_MB-1072

value: Medulloblastoma


title: Multi-region sample MB2-6


title: Primary medulloblastoma sample_MB-518


title: Primary medulloblastoma sample_MB-1348


title: Primary medulloblastoma sample_MB-508


title: Multi-region sample MB2-2


title: Primary medulloblastoma sample_MB-124


title: Primary medulloblastoma sample_MB-338


title: Multi-region sample MB1-2


title: medulloblastoma M13

status: Public on Oct 21 2015

city: Utrecht

first: Judith

middle: M.

last: Boer

address: Heidelberglaan 25

institute: Prinses Maxima Centrum

description: Gene expression data from pediatric medulloblastoma

hyb_protocol: Affymetrix hybridization kit was used including fragmentation according to Affymetrix's protocol. Hybridization was done on Affymetrix U133 Plus 2.0 arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 400

scan_protocol: The arrays were scanned using the Affymetrix Genechip scanner

data_processing: Data were summarized using MAS5 in R using the Affy package, followed by variance stabilization normalization using the vsn package

source_name: pediatric brain tumor

label_protocol: 8ul 125ng/ul was used as input for the Affymetrix in vitro one cycle kit, followed by IVT labelling (Affymetrix)

growth_protocol: Fresh-frozen tumor samples collected at Erasmus MC Sophia Children's Hospital, Rotterdam, The Netherlands between 1990 and 2004. Before RNA extraction, 4-um cryosections were prepared from the same tissue blocks and stained with hematoxylin and eosin to confirm tumor histology.

extract_protocol: RNA was isolated by homogenizing tissue samples in Trizol reagent using a tissue homogenizer. Total RNA was isolated according to the manufacturer's instructions.

tag: type

value: without radiological visible leptomeningeal metastases

value: primary


title: medulloblastoma M8


title: cerebellum S132

description: Gene expression data from adult cerebellum

source_name: adult brain control

value: cerebellum


title: medulloblastoma M118

value: with radiological visible leptomeningeal metastases


title: medulloblastoma M112


title: medulloblastoma M19


title: medulloblastoma M116


title: cerebellum S1

value: control


title: medulloblastoma M5


title: medulloblastoma M12


title: medulloblastoma M6


title: medulloblastoma M4


title: medulloblastoma M119


title: medulloblastoma M111


title: cerebellum S176


title: cerebellum S57


title: medulloblastoma M7


title: medulloblastoma M114


title: medulloblastoma M110


title: medulloblastoma M107


title: medulloblastoma M115


title: medulloblastoma M120


title: medulloblastoma M109


title: cerebellum S135


title: medulloblastoma M17


title: medulloblastoma M106


title: medulloblastoma M108


title: medulloblastoma M102


title: MB_patient_21

status: Public on Apr 15 2015

city: Taipei

first: Tsung-Han

last: Hsieh

address: No.250, Wusing St., Xinyi Dist., Taipei City 112, Taiwan (R.O.C.)

department: Institute of Microbiology and Immunology

country: Taiwan

institute: Taipei Medical University

description:
Gene expression data from pediatic CNS MB patient
SAMPLE 21

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

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

data_processing: RMA through R based affymetrix module

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 15 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)

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

tag: subject status

value: medulloblastoma patient

value: male

tag: tissue type

value: pediatric brain tumor

tag: histopathological diagnosis

value: MB, with myogenic and melanotic differentiations

tag: tumor site

value: cerebellar vermis


title: MB_patient_8

description:
Gene expression data from pediatic CNS MB patient
SAMPLE 8

value: MB, classic


title: MB_patient_19

description:
Gene expression data from pediatic CNS MB patient
SAMPLE 19


title: medulloblastoma M10

value: medulloblastoma


title: MB_patient_12

description:
Gene expression data from pediatic CNS MB patient
SAMPLE 12

value: MB, demoplastic


title: MB_patient_7

description:
Gene expression data from pediatic CNS MB patient
SAMPLE 7


title: MB_patient_22

description:
Gene expression data from pediatic CNS MB patient
SAMPLE 22

value: female


title: MB_patient_14

description:
Gene expression data from pediatic CNS MB patient
SAMPLE 14

value: MB, anaplastic


title: MB_patient_4

description:
Gene expression data from pediatic CNS MB patient
SAMPLE 4


title: MB_patient_20

description:
Gene expression data from pediatic CNS MB patient
SAMPLE 20


title: MB_patient_5

description:
Gene expression data from pediatic CNS MB patient
SAMPLE 5


title: EPNPFB_0943_1

status: Public on Feb 27 2015

city: Aurora

first: Andrew

middle: M

last: Donson

state: CO

department: Pediatrics

institute: CU Anschutz Medical Campus

description: reanalysis of GSM1217918

hyb_protocol: Following fragmentation, 11.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

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

data_processing: Microarray .CEL file data was background corrected and normalized using the gcRMA algorithm, resulting in log 2 expression values. The Affymetrix HG-U133 plus 2 microarray contains 54,675 probe sets including multiple probe sets for the same gene. In order to reduce error associated with multiple testing we used only a single probe set for each gene that possessed the highest gcRMA expression level across all our samples. This filtered list of the best expressed probe sets contained 21,050 genes. This list was further filtered to remove probe sets that were expressed below a threshold level that denoted absence of expression in any sample.

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

extract_protocol:
[collection protocol] Tumor samples were snap frozen in liquid nitrogen or transferred to RNAlater immediately after surgical removal as part of patient care. All samples were collected with appropriate IRB approval (COM-IRB#95-500 and 09-0906 )
RNeasy (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.

tag: disease state

value: brain tumor

value: posterior fossa group B ependymoma


title: EPNPFB_0965_1

description: analysis of ependymoma surgical specimen


title: MB_patient_2

description:
Gene expression data from pediatic CNS MB patient
SAMPLE 2

tag: gender


title: EPNPFB_0930_2

description: reanalysis of GSM1217917


title: MB_patient_16

description:
Gene expression data from pediatic CNS MB patient
SAMPLE 16


title: MB_patient_18

description:
Gene expression data from pediatic CNS MB patient
SAMPLE 18

value: cerebellum, left


title: MB_patient_15

description:
Gene expression data from pediatic CNS MB patient
SAMPLE 15


title: MB_patient_10

description:
Gene expression data from pediatic CNS MB patient
SAMPLE 10


title: MB_patient_13

description:
Gene expression data from pediatic CNS MB patient
SAMPLE 13

value: cerebellum, right


title: MB_patient_11

description:
Gene expression data from pediatic CNS MB patient
SAMPLE 11

value: cerebellum


title: EPNPFB_0987_1


title: EPNPFB_1067_1


title: MB_patient_9

description:
Gene expression data from pediatic CNS MB patient
SAMPLE 9


title: MB_patient_17

description:
Gene expression data from pediatic CNS MB patient
SAMPLE 17


title: MB_patient_3

description:
Gene expression data from pediatic CNS MB patient
SAMPLE 3


title: MB_patient_1

description:
Gene expression data from pediatic CNS MB patient
SAMPLE 1


title: MB_patient_6

description:
Gene expression data from pediatic CNS MB patient
SAMPLE 6


title: EPNPFB_0930_1

description: reanalysis of GSM1217916


title: EPNPFB_0816_1

description: reanalysis of GSM1217907


title: EPNPFB_0897_1


title: EPNPFB_0911_1


title: EPNPFA_1010_1

value: posterior fossa group A ependymoma


title: EPNPFB_0816_2

description: reanalysis of GSM1217908


title: EPNPFB_0770_1

description: reanalysis of GSM1217901


title: EPNPFB_0483_2

description: reanalysis of GSM1217888


title: EPNPFA_0459_1

description: reanalysis of GSM1217885


title: EPNPFA_0321_1

description: reanalysis of GSM1217874


title: EPNPFA_0821_1

description: reanalysis of GSM1217909


title: EPNPFA_0319_1

description: reanalysis of GSM1217872


title: EPNPFA_0459_2

description: reanalysis of GSM1217886


title: EPNPFB_0727_1

description: reanalysis of GSM1217899


title: EPNPFB_0811_2

description: reanalysis of GSM1217905


title: EPNPFB_0781_1

description: reanalysis of GSM1217902


title: EPNPFA_0928_1


title: EPNPFA_1048_1


title: EPNPFB_0246_2

description: reanalysis of GSM1217868


title: EPNPFA_0839_1


title: EPNPFA_0321_2

description: reanalysis of GSM1217875


title: EPNPFB_0364_2

description: reanalysis of GSM1217878


title: EPNPFA_0871_1

description: reanalysis of GSM1217914


title: EPNPFA_0758_1

description: reanalysis of GSM1217900


title: EPNPFA_0691_2

description: reanalysis of GSM1217895


title: EPNPFA_0848_1

description: reanalysis of GSM1217911


title: EPNPFA_0507_2

description: reanalysis of GSM1217891


title: EPNPFA_0319_2

description: reanalysis of GSM1217873


title: EPNPFA_0318_1

description: reanalysis of GSM1217871


title: EPNPFA_0195_2

description: reanalysis of GSM1217863


title: medulloblastoma M9

description: Gene expression data from pediatric medulloblastoma

value: without radiological visible leptomeningeal metastases

value: primary


title: 036/08_cerebellar cortex

status: Public on Aug 29 2014

city: London

first: Mina

last: Ryten

address: Queen Square

department: Department of Molecular Neuroscience

country: United Kingdom

institute: UCL Institute of Neurology

description: This entry supercedes previous accession: GSM1135238

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 95° for 5 minutes, then 45° for 5 minutes. • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001.

scan_protocol: Affymetrix GeneChip Scanner 3000 7G.

data_processing:
Data were processed using Affymetrix Power Tools 1.14.3. Arrays were pre-processed using RMA quantile normalization with background correction. Gene level summary signals were generated by calculating the Winsorized mean (10% and 90%) of all probe sets annotated to a transcript.
Probe group file: HuEx-1_0-st-v2.r2.pgf
Meta-probeset file: Core_adapted_from_netaffyx31
Transcript assignments are based on genome build hg19
Core exons only are included in this analysis

source_name: post-mortem brain tissue, individual ID 036/08, cerebellar cortex

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal labelling kit (Affymetrix).

growth_protocol: Not applicable.

extract_protocol: Total RNA was extracted using the miRNeasy kit (Qiagen, UK). cDNA synthesis and amplification were performed using the Ambion┬«WT Expression Kit (Ambion, UK).

treatment_protocol: Not applicable.

tag: individual id

tag: brain region

value: cerebellar cortex

tag: disease status

value: neurologically and neuropathologically normal

tag: brain bank

value: MRC Sudden Death Brain & Tissue Bank in Edinburgh

tag: Cause of death

value: Suspension by ligature

tag: Sex

value: Female

tag: age at death (in years)

tag: post-mortem interval (in hours)

tag: ancestry

value: European

tag: brain ph

tag: rin


title: 07_37_cerebellar cortex

source_name: post-mortem brain tissue, individual ID 07_37, cerebellar cortex

value: Sun Health Research Institute

value: Respiratory failure

value: Male


title: 001/06_cerebellar cortex

description: This entry supercedes previous accession: GSM1135219

source_name: post-mortem brain tissue, individual ID 001/06, cerebellar cortex


title: 023/08_cerebellar cortex

description: This entry supercedes previous accession: GSM1135242

source_name: post-mortem brain tissue, individual ID 023/08, cerebellar cortex


title: 025/05_cerebellar cortex

description: This entry supercedes previous accession: GSM1135226

source_name: post-mortem brain tissue, individual ID 025/05, cerebellar cortex


title: 06_02_cerebellar cortex

source_name: post-mortem brain tissue, individual ID 06_02, cerebellar cortex

value: renal failure


title: 035/09_cerebellar cortex

description: This entry supercedes previous accession: GSM1135252

source_name: post-mortem brain tissue, individual ID 035/09, cerebellar cortex


title: 028/08_cerebellar cortex

description: This entry supercedes previous accession: GSM1135266

source_name: post-mortem brain tissue, individual ID 028/08, cerebellar cortex

value: Ruptured aortic aneurysm


title: 021/08_cerebellar cortex

description: This entry supercedes previous accession: GSM1135209

source_name: post-mortem brain tissue, individual ID 021/08, cerebellar cortex


title: 00_38_cerebellar cortex

source_name: post-mortem brain tissue, individual ID 00_38, cerebellar cortex


title: 007/09_cerebellar cortex

description: This entry supercedes previous accession: GSM1135228

source_name: post-mortem brain tissue, individual ID 007/09, cerebellar cortex

value: Road traffic accident


title: 032/08_cerebellar cortex

description: This entry supercedes previous accession: GSM1135240

source_name: post-mortem brain tissue, individual ID 032/08, cerebellar cortex


title: 07_73_cerebellar cortex

source_name: post-mortem brain tissue, individual ID 07_73, cerebellar cortex


title: 08_55_cerebellar cortex

source_name: post-mortem brain tissue, individual ID 08_55, cerebellar cortex


title: 005/09_cerebellar cortex

description: This entry supercedes previous accession: GSM1135237

source_name: post-mortem brain tissue, individual ID 005/09, cerebellar cortex


title: 014/08_cerebellar cortex

description: This entry supercedes previous accession: GSM1135200

source_name: post-mortem brain tissue, individual ID 014/08, cerebellar cortex


title: 022/08_cerebellar cortex

description: This entry supercedes previous accession: GSM1135257

source_name: post-mortem brain tissue, individual ID 022/08, cerebellar cortex

value: pulmonary embolism


title: 018/09_cerebellar cortex

description: This entry supercedes previous accession: GSM1135235

source_name: post-mortem brain tissue, individual ID 018/09, cerebellar cortex


title: 024/10_cerebellar cortex

description: This entry supercedes previous accession: GSM1135202

source_name: post-mortem brain tissue, individual ID 024/10, cerebellar cortex


title: 01_37_cerebellar cortex

source_name: post-mortem brain tissue, individual ID 01_37, cerebellar cortex


title: 018/06_cerebellar cortex

description: This entry supercedes previous accession: GSM1135189

source_name: post-mortem brain tissue, individual ID 018/06, cerebellar cortex


title: 012/10_cerebellar cortex

description: This entry supercedes previous accession: GSM1135281

source_name: post-mortem brain tissue, individual ID 012/10, cerebellar cortex


title: 029/09_cerebellar cortex

description: This entry supercedes previous accession: GSM1135255

source_name: post-mortem brain tissue, individual ID 029/09, cerebellar cortex


title: 012/09_cerebellar cortex

description: This entry supercedes previous accession: GSM1135193

source_name: post-mortem brain tissue, individual ID 012/09, cerebellar cortex


title: 034/08_cerebellar cortex

description: This entry supercedes previous accession: GSM1135254

source_name: post-mortem brain tissue, individual ID 034/08, cerebellar cortex


title: 033/08_cerebellar cortex

description: This entry supercedes previous accession: GSM1135243

source_name: post-mortem brain tissue, individual ID 033/08, cerebellar cortex