title: NC5-3

status: Public on Oct 23 2016

city: Beijing

first: Xiaoxia

last: Yang

address: 20 Dongda Street, Fengtai District

institute: Institute of Disease Control and Prevention, Academy of Military Medical Sciences

hyb_protocol: Cy3-labelled RNA was dried dried on the medium-high heat setting with a vacuum concentrator according to the manufacture's protocol. Then the dried reactions were hybridized with genechip overnight in Agilent hybridization oven. The chip slides were then washed using 2×aline sodium citrate (SSC) (containing 0.2% SDS) wash buffer at 42℃ for 5 min and 0.2×SSC for 5 min.

scan_protocol: The chips were then scanned on an Agilent Microarray Scanner (Model #G2565CA).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.The extracted data were then normalized with Agilent GeneSpring 12.0 by three main steps. First,a filtering step is done wherein both flag (gIsGeneDetected column) and error (gTotalProbeError column) is taken into account. Only those rows are used that have a flag value of 1. For each miRNA, if all flags are 0 then the signal value is taken as 0.1. Or GeneSpring uses only those rows for summarization which have value of 1. Then if the signal value passes the filter(greater than 3 times the error value), it is used and assigned with a value of 0 for error. Second,the multiple probes that map to a given systematic name are first summed up. The signal value is computed as the SUM of all values and not average. Summarization is based on the systematic name as explained above and is done before thresholding of signal values. Last,the data was then normalized to 90th percentile with Percentile Shift algorithms.

source_name: mice brain

label_protocol: 200ng of microRNA sample was dephosphorylated at the 5’ end using alkaline phosphatase (CIP) provided in the miRNA Complete Labeling and Hyb Kit (Agilent, USA) and 3’ end-linked with a Cyanine3-pCp using T4 RNA ligase.

extract_protocol: Whole mouse brain tissues were homogenized in in PBS using a high-throughput organization grinding machine (Scientz-48, Scientz, Ningbo, China). MicroRNA was extracted from homogenized brains using the miRNA Purification Kit (Kangwei, China) according to the manufacturer’s protocol. The concentration of RNA was determined by a Nanodrop ND-1000 Spectrophotometer (Thermo)

treatment_protocol: Specific pathogen-free 1-day suckling Kunming mice were intraperitoneal injected with 10*6 TCID50 (100ul) of Enterovirus 71. In comparison, a normal control group were set up and given DMEM medium.

value: Kunming

value: brain

tag: days post infection

tag: infection status

value: no

tag: pathological change


title: NC5-2

type: RNA

country: China

molecule: total RNA

organism: Mus musculus

tag: strain

tag: tissue


title: IF5-3

value: yes


title: NC5-1


title: IF3-3


title: IF5-1


title: IF5-2


title: IF3-2


title: NC3-1


title: Reoxygenation 24h rep2

city: Taipei

first: Liang-Chuan

last: Lai

state: Taiwan

address: 1 Jen-Ai Road, Sec 1

department: Physiology

country: Taiwan

institute: National Taiwan University

description: SAMPLE 11

scan_protocol: Standard NanoString scanning protocol.

data_processing: Geometric Mean normalization were carried out using commercial nSolverAnalysisSoftware.  nSolverAnalysisSoftware used for basecalling.

label: Color coded beads

organism: Homo sapiens

source_name: MCF-7_Reoxygenation 24h

label_protocol: The samples were prepared for nCounter miRNA expression profiling according to the manufacturer's recommendations (NanoString, Seattle, WA, USA).

growth_protocol: Culture withDMEM medium.

extract_protocol: Total RNA from the cells were isolated using TRIzol® reagent (Invitrogen, Calsbad, CA) and purified with RNeasy® mini kits (Qiagen).

treatment_protocol: 0.5% O2 hypoxia and reoxygenation.

tag: cell line

tag: cell type

value: Breast ductal carcinoma

tag: time point

value: 24 h upon reoxygenation


title: Reoxygenation 24h rep1

description: SAMPLE 10


title: Reoxygenation 24h rep3

description: SAMPLE 12


title: Reoxygenation 12h rep1

description: SAMPLE 7

source_name: MCF-7_Reoxygenation 12h

value: 12h upon reoxygenation


title: Reoxygenation 1h rep2

description: SAMPLE 5

source_name: MCF-7_Reoxygenation 1h

value: 1h upon reoxygenation


title: Reoxygenation 12h rep3

description: SAMPLE 9


title: Reoxygenation 12h rep2

description: SAMPLE 8


title: Reoxygenation 1h rep3

description: SAMPLE 6


title: Reoxygenation 1h rep1

description: SAMPLE 4


title: Reoxygenation 0h rep1

description: SAMPLE 1

source_name: MCF-7_Reoxygenation 0h

value: 0h (hypoxia control)


title: Control:biological rep2

status: Public on Oct 24 2016

city: Fujisawa

first: Tsukasa

last: Mori

state: Kanagawa

address: Kameino 1866

department: Bioresource Sciences

country: Japan

institute: Nihon University

description: Gene expression data from tail tissues of Rana pirica tadpoles without predators.

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

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000.  The data were analyzed with GeneChip Operating Software (GCOS) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

data_processing: The data were analyzed first with GCOS algorithm MAS 5 and then using GeneSpringGX11.5.1.

label: biotin

organism: Rana pirica

source_name: Tail tissues from tadpoles without predators for 8 days

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

growth_protocol: Tadpoles before growing hind limb.

extract_protocol: Total RNA was obtained using the Qiagen RNA medium preparation system.  RNA yield was measured by absorbance at 260 nm and the quality was assessed by confirming the integrity of the rRNA bands by electrophoresis.

treatment_protocol: Tail tissue was dissected from each tadpole, cut into small pieces, and collected together in a single tube containing RNAlaterTM (QIAGEN RNA stabilization reagent) for subsequent use in producing RNA probes for the functional microarray analysis. The tissues were stored at -80°C until RNA extraction.

value: tail

tag: stress


title: NC3-2


title: NC3-3


title: IF3-1


title: Salamander: biological rep1

description: Gene expression data from tail tissues of Rana pirica tadpoles with larval salamanders.

source_name: Tail tissues from tadpoles with Salamanders for 8 days

value: larval salamanders for 8 days


title: Reoxygenation 0h rep2

description: SAMPLE 2


title: Reoxygenation 0h rep3

description: SAMPLE 3


title: P1 VICs_calcified120211

city: AURORA

first: fei

last: li

state: CO

country: USA

institute: university of colorado

description: Gene expression data from VICs of calcified valves

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Canine 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were background corrected with the RMA algorithm using R and the Bioconductor's affy package.  All parameters were set at its default settings

source_name: VICs isolated from calcified human aortic valves

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: RNA was prepared using the RNEasy Mini Kit and QIAshredder columns (QIAGEN, Valencia, CA)

treatment_protocol: VICs were isolated from normal and calcified human aortic valves (n=5 each group). Then P0 VICs were sub-cultured to get P1 VICs. A fraction of P1 VICs subject to RNA extraction and microarray analysis.

value: Calcified aortic valve leaflets

value: valve interstitial cells (VICs)


title: P1 VICs_normal042506

description: Gene expression data from VICs of normal valves

source_name: VICs islolated from normal human aortic valves

value: normal aortic valve leaflets


title: P1 VICs_calcified101510


title: P1 VICs_calcified073009


title: P1 VICs_normal052507


title: P1 VICs_calcified080410


title: P1 VICs_nomal051310


title: CD8+Tcell_blood_resting_CD103+_rep3

city: Amsterdam

first: Perry

middle: D

last: Moerland

address: Meibergdreef 9

department: Epidemiology and Data Science

country: Netherlands

institute: Amsterdam UMC

description:
Sample name: 102201-41
CD8+CD16-CD56- T cells

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: The samples were scanned using the Illumina iScan array scanner

data_processing: Data were retrieved using Illumina's GenomeStudio v2011.1 software. Analyses were carried out with Bioconductor packages in the statistical software package R (version 3.0.0). Normexp-by-control background correction, quantile normalization, and log2 transformation (Shi et al, NAR, 2010) were performed on the Illumina sample and control probe profiles using the limma package (version 3.16.8), function neqc.

source_name: peripheral blood,CD8+ T cells,resting,CD103+

label_protocol: The Illumina TotalPrep-96 RNA Amplification Kit was used to generate biotin-labeled (biotin-16-UTP) amplified cRNA

growth_protocol: Heparinized peripheral blood samples were obtained prior to or during the surgical procedure. Peripheral blood mononuclear cells (PBMC) were isolated using standard density gradient techniques. Directly after lobectomy, a piece of peripheral lung tissue as far away from the tumor as possible was cut off by a pathologist. Lung mononuclear cells (LMC) were isolated from this tissue specimen as described(60). In brief, tissue specimens (1 x 1 cm) were sliced with a McIlwain tissue chopper into pieces of 1mm and incubated for 20 minutes in RPMI with 20mM Hepes, 15% fetal calf serum (FCS), 50 U/ml DNAse type I (Sigma-Aldrich) while shaking at 37˚C. Tissue pieces were carefully driyed with sterile gauzes and transferred to medium supplemented with collagenase type I 300 U/ml (Worthington). The material was incubated in this medium for 60 minutes while shaking at 37˚C. A cell suspension was obtained by grinding the tissue through a flow-through chamber. Mononuclear cells were isolated from the lung cell suspension by standard density gradient techniques. To exclude the possibility of contamination with peripheral blood, the erythrocyte counts were confirmed to be less than 5% of erythrocyte counts in the paired blood sample. Isolated cells were cryopreserved in liquid nitrogen for later analyzis. Due to the low frequency of CD103+ T-cells in peripheral blood this subset was obtained from non-related buffy coat donors. T-cell stimulation was performed by adding αCD3/28 Dynabeads (Lifetechnologies) in a 1:1 ratio (c:b) for a period of 16h.

extract_protocol: RNA was isolated from sorted cell samples with the Qiagen RNeasy Plus Micro kit according to manufacturer’s instructions.

treatment_protocol: PBMC or LMC were incubated with the following antibodies: αCD103 PE-Cy7 (eBioscience), αCD27 FITC (Sanquin), αCD45RA PerCP-Cy5 (eBioscience), αCD8 APC (BD). To prevent premature activation of T-cells following αCD3 staining this marker was left out of the phenotyping panel. Hence, NK cell contamination was prevented using CD16 PE (BD) and CD56 PE (BD) as negative selection criteria. Cells were labelled according to manufacturer’s instructions and washed and analyzed in PBS containing 0.5% (w/v) bovine serum albumin (BSA). Cells were analyzed or sorted with a purity >99% using a LSR Fortessa (BD Biosciences)  and ARIA III cell sorter (BD Biosciences) , respectively. analyzis was performed using FlowJo software (Tree Star Inc).

value: BC599 (buffy coat donor)

value: peripheral blood

value: CD8+CD16-CD56- T cells

tag: cd103 status

value: POS

tag: treatment status

value: resting

tag: slide

value: K


title: P1 VICs_normal042106


title: P1 VICs_calcified102710


title: P1 VICs_normal060607


title: CD8+Tcell_blood_resting_CD103-_rep4

description:
Sample name: 102201-35
CD8+CD16-CD56- T cells

source_name: peripheral blood,CD8+ T cells,resting,CD103-

tag: procedure

value: lung transplantation because of end-stage pulmonary disease (COPD)

value: NEG

value: E


title: CD8+Tcell_blood_resting_CD103+_rep1

description:
Sample name: 102201-37
CD8+CD16-CD56- T cells

value: BC002 (buffy coat donor)

value: G


title: CD8+Tcell_lung_stimulated_CD103+_rep4

description:
Sample name: 102201-32
CD8+CD16-CD56- T cells

source_name: lung,CD8+ T cells,stimulated,CD103+

value: lung

value: T-cell stimulation

value: B


title: CD8+Tcell_lung_resting_CD103-_rep5

description:
Sample name: 102201-33
CD8+CD16-CD56- T cells

source_name: lung,CD8+ T cells,resting,CD103-

value: C


title: CD8+Tcell_blood_resting_CD103+_rep2

description:
Sample name: 102201-38
CD8+CD16-CD56- T cells

value: BC146 (buffy coat donor)

value: H


title: CD8+Tcell_blood_stimulated_CD103-_rep4

description:
Sample name: 102201-36
CD8+CD16-CD56- T cells

source_name: peripheral blood,CD8+ T cells,stimulated,CD103-

value: F


title: CD8+Tcell_blood_stimulated_CD103-_rep3

description:
Sample name: 102201-30
CD8+CD16-CD56- T cells

value: peripheral blood

value: L


title: CD8+Tcell_lung_resting_CD103-_rep4

description:
Sample name: 102201-21
CD8+CD16-CD56- T cells

value: CD8+CD16-CD56- T cells


title: CD8+Tcell_blood_resting_CD103-_rep2

description:
Sample name: 102201-23
CD8+CD16-CD56- T cells

value: resting

value: I


title: CD8+Tcell_lung_stimulated_CD103+_rep3

description:
Sample name: 102201-20
CD8+CD16-CD56- T cells

value: lung transplantation because of end-stage pulmonary disease (COPD)

value: POS


title: CD8+Tcell_blood_stimulated_CD103-_rep2

description:
Sample name: 102201-24
CD8+CD16-CD56- T cells

value: NEG

value: J


title: CD8+Tcell_blood_resting_CD103-_rep3

description:
Sample name: 102201-29
CD8+CD16-CD56- T cells

value: K


title: CD8+Tcell_lung_stimulated_CD103-_rep3

description:
Sample name: 102201-16
CD8+CD16-CD56- T cells

source_name: lung,CD8+ T cells,stimulated,CD103-

value: lobectomy for a peripheral primary lung tumor

value: lung


title: CD8+Tcell_lung_resting_CD103+_rep4

description:
Sample name: 102201-31
CD8+CD16-CD56- T cells

source_name: lung,CD8+ T cells,resting,CD103+

value: A


title: CD8+Tcell_lung_resting_CD103-_rep3

description:
Sample name: 102201-15
CD8+CD16-CD56- T cells


title: CD8+Tcell_blood_resting_CD103-_rep1

description:
Sample name: 102201-17
CD8+CD16-CD56- T cells

value: C


title: CD8+Tcell_blood_stimulated_CD103-_rep1

description:
Sample name: 102201-18
CD8+CD16-CD56- T cells

value: T-cell stimulation

value: D


title: CD8+Tcell_lung_stimulated_CD103-_rep4

description:
Sample name: 102201-22
CD8+CD16-CD56- T cells

value: H


title: MELAS with m.A3243G mutation [array]

city: Jinan

first: Wei

last: Wang

state: Shandong

address: West Wenhua Road

department: Department of Neurology

institute: Qilu Hospital, Shandong University

description:
Muscle pool from 20 MELAS patients with m.A3243G mutation.
miRNA

hyb_protocol: Hybridization was performed overnight on a μParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies).

scan_protocol: Hybridization images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing:
Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (Locally-weighted Regression).
Averages are derived from LOWESS normalized data from all probes per miRNA.

source_name: Frozen muscle, MELAS

label_protocol: The assay started from 2 to 5 µg total RNA sample were 3'-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining.

extract_protocol: Total RNA was extracted using the Animal Tissue RNA Purification Kit (Norgen Biotek Corporation, Thorold, Canada), following the manufacturer's recommended protocol.

tag: disease status

value: Mitochondrial myopathy, Encephalopathy, Lactic Acidosis, and Stroke-like episodes (MELAS)

tag: genotype/variation

value: m.A3243G mutation

value: muscle


title: CD8+Tcell_lung_stimulated_CD103-_rep2

description:
Sample name: 102201-10
CD8+CD16-CD56- T cells

value: CD8+CD16-CD56- T cells


title: CD8+Tcell_lung_resting_CD103+_rep3

description:
Sample name: 102201-19
CD8+CD16-CD56- T cells

value: resting

value: E


title: Control without myopathy [array]

description:
Muscle pool from 20 healthy controls.
miRNA

source_name: Frozen muscle, healthy

value: healthy

value: control


title: CD8+Tcell_lung_stimulated_CD103-_rep1

description:
Sample name: 102201-04
CD8+CD16-CD56- T cells

value: NEG


title: muscle_control_rep4

status: Public on Oct 22 2016

city: Copenhagen N

first: Ole

middle: Hartvig

last: Mortensen

address: Panum 6.5.28, Blegdamsvej 3

department: Department of Biomedical Sciences

country: Denmark

institute: University of Copenhagen

description: Gene expression data from newborn hindleg skeletal muscle, maternal control diet offspring

hyb_protocol: 5.5 ug of fragmented cRNA wae hybridized for 16 hr at 45C on GeneChip Rat Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed with Bioconductor 3.1 and R 3.2.2 using built-in RMA with default settings

organism: Rattus norvegicus

source_name: Hindleg skeletal muscle, newborn, offspring of maternal control diet

label_protocol: Biotinylated cRNA was prepared from 100 ng RNA using the Ambion WT Expression Kit (Life Technologies) and the Affymetrix Whole Transcription (WT) Expression kit (Affymetrix) according to the manufacturer's instructions

extract_protocol: Total RNA was isolated by Qiazol (Qiagen) as described by the manufacturer and further purified using the RNeasy kit (Qiagen) as described by the manufacturer. Quality of RNA was assured using a Bioanalyzer (Agilent, Santa Clara, CA, USA) as described by the manufacturer

treatment_protocol: Pregnant Wistar rats were subjected to either a control, a low protein or a low protein + taurine supplementation diet from day 1 of gestation throughout gestation. Newborn hind leg skeletal muscle from three male offspring of each dam was excised and pooled, followed by RNA isolation

tag: gender

value: male

value: Wistar

value: Skeletal Muscle

tag: age

value: Newborn


title: muscle_lowprotein_rep2

description: Gene expression data from newborn hindleg skeletal muscle, maternal low protein diet offspring

source_name: Hindleg skeletal muscle, newborn, offspring of maternal low protein diet


title: muscle_control_rep1


title: CD8+Tcell_lung_stimulated_CD103+_rep2

description:
Sample name: 102201-08
CD8+CD16-CD56- T cells

value: lobectomy for a peripheral primary lung tumor

value: lung

value: POS


title: CD8+Tcell_lung_resting_CD103+_rep2

description:
Sample name: 102201-07
CD8+CD16-CD56- T cells

value: G


title: CD8+Tcell_lung_resting_CD103-_rep1

description:
Sample name: 102201-03
CD8+CD16-CD56- T cells

value: C


title: muscle_lowprotein_rep3


title: muscle_lowprotein_rep4


title: CD8+Tcell_lung_resting_CD103+_rep1

description:
Sample name: 102201-01
CD8+CD16-CD56- T cells

value: A


title: CD8+Tcell_lung_stimulated_CD103+_rep1

description:
Sample name: 102201-02
CD8+CD16-CD56- T cells

value: T-cell stimulation

value: B


title: muscle_lowprotein_rep1


title: CD8+Tcell_lung_resting_CD103-_rep2

description:
Sample name: 102201-09
CD8+CD16-CD56- T cells

value: CD8+CD16-CD56- T cells

value: resting

value: I


title: muscle_lowprotein_taurine_rep3

description: Gene expression data from newborn hindleg skeletal muscle, maternal low protein diet + taurine supplementation offspring

source_name: Hindleg skeletal muscle, newborn, offspring of maternal low protein diet + taurine supplementation


title: muscle_lowprotein_taurine_rep1


title: muscle_control_rep2


title: Adipocyte treated with LCM, biological rep3

city: Los Angeles

first: Steve

last: Mittelman

state: CA

address: 4546 W Sunset Blvd

department: Endocrinology

institute: Children's Hospital Los Angeles

description:
Gene expression data from 3T3-L1 adipocytes treated with LCM for 24 hours
AL-3

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse MoEx-1_0-st GeneChips.  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 corrected for background and normalized, using Oligo Package in R

source_name: Murine 3T3-L1 adipocyte treated with LCM

growth_protocol: 3T3-L1 pre-adipocytes were differentiated into adipocytes with an adipogenic cocktail for 7 days. Adipocytes were maintained in RPMI 1640 media supplemented with 10% FBS.

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

treatment_protocol: 3T3-L1 adipocytes were treated with LCM (leukemia cell conditioned media made by 8093 murine acute lymphoblastic leukemia cells growing in RPMI1640 supplemented with 10% FBS, IL-3 and BME for 48 hours) for 24 hours.

value: 3T3-L1 Adipocyte cell line

tag: cell line source

value: obtained from ATCC

value: under 6 passages

tag: treatment

value: LCM


title: Adipocyte treated with LCM, biological rep1

description:
Gene expression data from 3T3-L1 adipocytes treated with LCM for 24 hours
AL-1


title: Adipocyte control, biological rep3

description:
Gene expression data from 3T3-L1 adipocytes
AO-3

source_name: Murine 3T3-L1 adipocyte

value: control


title: 121002-non-cancerous lung tissue

city: Kunming

first: Yanliang

last: Zhang

state: Yunnan province

address: No. 295, Xichang Road

department: Department of Clinical Laboratory

institute: First Affiliated Hospital of Kunming Medical University

description: Gene expression of 121002-non-cancerous lung tissue.

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized in an Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2x SSC at 42℃ for 5 min, and 0.2x SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and GeneSpring software was used to analyze the raw data, which are normalized by percentile normalization.

source_name: non-cancerous lung tissue from 121002

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine's linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer.

value: lung cancer

value: non-cancerous lung tissue

value: female

tag: geographic location

value: Xuanwei County, China

tag: patient id


title: Adipocyte treated with LCM, biological rep2

description:
Gene expression data from 3T3-L1 adipocytes treated with LCM for 24 hours
AL-2


title: HCC827-BR2

city: Miaoli County

first: Shih Sheng

last: Jiang

address: No. 35 Keyan Road, Zhunan County

department: National Institute of Cancer Research

institute: National Health Research Institutes

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Quantile normalization.

source_name: BIBW2992-resistant clone 2 derived from HCC827 cells

label_protocol: Biotinylated cRNA were prepared with the TargetAmp Nano-G Bioti- aRNA Labeling kit (Epicentre) for Illumina arrays.

extract_protocol: Total RNA was extracted with QIAGEN RNeasy mini kit according to  protocol provided in the kit by the  manufacturer. Quality control was performed with Agilent Bioanalyser.

tag: phenotype


title: 120901-non-cancerous lung tissue

description: Gene expression of 120901-non-cancerous lung tissue.

source_name: non-cancerous lung tissue from 120901

tag: tissue


title: 121203-non-cancerous lung tissue

description: Gene expression of 121203-non-cancerous lung tissue.

source_name: non-cancerous lung tissue from 121203

value: male


title: 120502_non-cancerous lung tissue

description: Gene expression of 120502_non-cancerous lung tissue.

source_name: non-cancerous lung tissue from 120502


title: Adipocyte control, biological rep1

description:
Gene expression data from 3T3-L1 adipocytes
AO-1

tag: cell line


title: Adipocyte control, biological rep2

description:
Gene expression data from 3T3-L1 adipocytes
AO-2


title: CD38+ mature luminal cells from patient 4

first: Andrew

middle: Scott

last: Goldstein

address: 610 Charles E Young Dr East

department: Urology

institute: University of California, Los Angeles

description:
BE ML 4
Gene expression data from CD38+ luminal cells isolated from benign human prostate

hyb_protocol: Biotinylated cDNA was hybridized to the Affymetrix Human Genome U133 Plus 2.0 Chip

scan_protocol: Chips were scanned using an Affymetrix GeneChip Scanner 7G

data_processing:
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
affymetrix-algorithm-name = ExpressionStat
affymetrix-algorithm-version = 5.0
program-name = Expression Console
program-id = 1.2.0.20

label: Biotin

source_name: Benign human prostate patient 4

label_protocol: Biotinylated cDNA were prepared from total RNA using the standard Affymetrix protocol.

growth_protocol: Tissue was collected from UCLA's Translational Pathology Core Laboratories within 24 hours of patients undergoing radical prostatectomy at UCLA

extract_protocol: RNA was isolated from sorted cells using the RNeasy Micro kit (QIAGEN) and amplified with the NuGEN Pico kit according to standard manufacturer protocols.

treatment_protocol: Tissues were dissociated to single cells using standard protocols described in Goldstein et al, Nature Protocols, 2011

tag: subject id

value: patient 4

value: Benign human prostate

tag: cell subpopulation

value: CD38+ mature luminal cells


title: 121202-non-cancerous lung tissue

description: Gene expression of 121202-non-cancerous lung tissue.

source_name: non-cancerous lung tissue from 121202


title: 110902_non-cancerous lung tissue

description: Gene expression of 110902_non-cancerous lung tissue.

source_name: non-cancerous lung tissue from 110902


title: 120401_non-cancerous lung tissue

description: Gene expression of 120401_non-cancerous lung tissue.

source_name: non-cancerous lung tissue from 120401


title: CD38+ mature luminal cells from patient 3

description:
BE ML 3
Gene expression data from CD38+ luminal cells isolated from benign human prostate

source_name: Benign human prostate patient 3

value: patient 3


title: HCC827-BR1

source_name: BIBW2992-resistant clone 1 derived from HCC827 cells


title: BNL CL.2 cells with RAW 264.7 cells, rep3

city: Barcelona

first: Marco

last: Constante

address: C/ Dr. Aiguader, 88

country: Spain

institute: CRG

description: BNL CL.2 cells cultured for 24h with RAW 264.7 cells

hyb_protocol: Done following Expression Wash, Stain and Scan User Manual (P/N 702731 Rev. 3)

data_processing: The raw data was read and preprocessed using the affy package developed within the Bioconductor project in the R statistical programming environment (Gentleman et al, 2004). Data were preprocessed using the rma (robust multi-array average) expression measure.

source_name: BNL CL.2 cells with RAW 264.7 cells

growth_protocol: Cells were grown in DMEM with 10% FBS 1% PS

extract_protocol: Extraction of total RNA was performed with Qiagen Rneasy mini kit according to the manufacturers instructions

treatment_protocol: BNL CL.2 Cells were trypsinized and incubated with more BNL CL.2 cells in an insert or with RAW 264.7 cells in the insert with or without iron, where appropriate

value: BNL CL.2

tag: tissue origin

value: liver


title: BNL CL.2 cells with RAW 264.7 cells, rep2

scan_protocol: Done following Expression Wash, Stain and Scan User Manual (P/N 702731 Rev. 3)


title: CD38+ mature luminal cells from patient 1

description:
BE ML 1
Gene expression data from CD38+ luminal cells isolated from benign human prostate

source_name: Benign human prostate patient 1

value: patient 1


title: CD38-lo luminal progenitor-enriched cells from patient 4

description:
BE LP 4
Gene expression data from CD38-lo luminal cells isolated from benign human prostate


title: HCC827

source_name: Human non-small cell carcinoma cell line HCC827

value: BIBW2992 sensitive


title: BNL CL.2 cells alone, rep2

description: BNL CL.2 cells cultured for 24h alone

source_name: BNL CL.2 cells alone

label_protocol: Done following Expression Wash, Stain and Scan User Manual (P/N 702731 Rev. 3)


title: BNL CL.2 cells with RAW 264.7 cells, rep1


title: BNL CL.2 cells alone, rep3

description: BNL CL.2 cells cultured for 24h alone


title: 110901_non-cancerous lung tissue

description: Gene expression of 110901_non-cancerous lung tissue.

source_name: non-cancerous lung tissue from 110901


title: 121203_lung carcinoma tissue and paired non_cancerous lung tissue

type: mixed

description:
Sample name: 121203
529552A02_A.pair: raw data file for lung carcinoma sample.
529552A02_P.pair: raw data file for non-cancerous lung sample.

hyb_protocol: The labeled DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-20h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html).

scan_protocol: Arrays were scanned on a NimbleGen MS 200 Microarray Scanner per manufacturer's protocol.

data_processing: Arrays were processed using NimbleGen's standard protocol with NimbleScan 2.6 extraction.

molecule: genomic DNA

source_name: lung carcinoma tissue from 121203

label_protocol: 0.5 µg genomic DNA was directly labeled by Klenow random priming with Cy3 nonamers and Cy5 Nonamers, per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

extract_protocol: Genomic DNA was prepared using the Qiagen Mini kit following the manufacturer's recommendations. DNA was quantified using a NanoDrop-1000 spectrophotometer.

value: lung carcinoma tissue


title: CD38+ mature luminal cells from patient 2

description:
BE ML 2
Gene expression data from CD38+ luminal cells isolated from benign human prostate

source_name: Benign human prostate patient 2

value: patient 2


title: 121202_lung carcinoma tissue and paired non_cancerous lung tissue

description:
Sample name: 121202
529550A03_A.pair: raw data file for lung carcinoma sample.
529550A03_P.pair: raw data file for non-cancerous lung sample.

source_name: lung carcinoma tissue from 121202


title: 120901_lung carcinoma tissue and paired non_cancerous lung tissue

description:
Sample name: 120901
529609A02_A.pair: raw data file for lung carcinoma sample.
529609A02_P.pair: raw data file for non-cancerous lung sample.

source_name: lung carcinoma tissue from 120901

source_name: non-cancerous lung tissue from 120901


title: 121002_lung carcinoma tissue and paired non_cancerous lung tissue

description:
Sample name: 121002
529609A03_A.pair: raw data file for lung carcinoma sample.
529609A03_P.pair: raw data file for non-cancerous lung sample.

source_name: lung carcinoma tissue from 121002

source_name: non-cancerous lung tissue from 121002


title: 110902_lung carcinoma tissue and paired non-cancerous lung tissue

description:
Sample name: 110902
529564A03_A.pair: raw data file for lung carcinoma sample.
529564A03_P.pair: raw data file for non-cancerous lung sample.

source_name: lung carcinoma tissue from 110902


title: 120502_lung carcinoma tissue and paired non-cancerous lung tissue

description:
Sample name: 120502
529550A02_A.pair: raw data file for lung carcinoma sample.
529550A02_P.pair: raw data file for non-cancerous lung sample.

source_name: lung carcinoma tissue from 120502

source_name: non-cancerous lung tissue from 120502


title: 120401_lung carcinoma tissue and paired non-cancerous lung tissue

description:
Sample name: 120401
529550A01_A.pair: raw data file for lung carcinoma sample.
529550A01_P.pair: raw data file for non-cancerous lung sample.

source_name: lung carcinoma tissue from 120401

source_name: non-cancerous lung tissue from 120401


title: muscle_control_rep3

description: Gene expression data from newborn hindleg skeletal muscle, maternal control diet offspring

source_name: Hindleg skeletal muscle, newborn, offspring of maternal control diet

tag: strain

value: Wistar

value: Skeletal Muscle

value: Newborn


title: BNL CL.2 cells with RAW 264.7 cells and FAC, rep2

description: BNL CL.2 cells cultured for 24h with RAW 264.7 cells and 100 micromolar FAC


title: Benign basal cells from patient 3

description:
BE BAS 3
Gene expression data from basal cells isolated from benign human prostate

source_name: Benign human prostate patient 3

value: Benign basal cells


title: Benign basal cells from patient 4

description:
BE BAS 4
Gene expression data from basal cells isolated from benign human prostate

source_name: Benign human prostate patient 4


title: BNL CL.2 cells alone, rep1

description: BNL CL.2 cells cultured for 24h alone

source_name: BNL CL.2 cells alone


title: Benign basal cells from patient 2

description:
BE BAS 2
Gene expression data from basal cells isolated from benign human prostate


title: CD38-lo luminal progenitor-enriched cells from patient 1

description:
BE LP 1
Gene expression data from CD38-lo luminal cells isolated from benign human prostate

source_name: Benign human prostate patient 1


title: muscle_lowprotein_taurine_rep4

description: Gene expression data from newborn hindleg skeletal muscle, maternal low protein diet + taurine supplementation offspring

source_name: Hindleg skeletal muscle, newborn, offspring of maternal low protein diet + taurine supplementation


title: CD38-lo luminal progenitor-enriched cells from patient 3

description:
BE LP 3
Gene expression data from CD38-lo luminal cells isolated from benign human prostate


title: CD38-lo luminal progenitor-enriched cells from patient 2

description:
BE LP 2
Gene expression data from CD38-lo luminal cells isolated from benign human prostate

source_name: Benign human prostate patient 2


title: BNL CL.2 cells with FAC, rep2

description: BNL CL.2 cells cultured for 24h with 100 micromolar FAC

source_name: BNL CL.2 cells with FAC


title: Benign basal cells from patient 1

description:
BE BAS 1
Gene expression data from basal cells isolated from benign human prostate


title: BNL CL.2 cells with FAC, rep3


title: BNL CL.2 cells with FAC, rep1


title: BNL CL.2 cells with RAW 264.7 cells and FAC, rep1


title: 110901_lung carcinoma tissue and paired non-cancerous lung tissue

description:
Sample name: 110901
529564A02_A.pair: raw data file for lung carcinoma sample.
529564A02_P.pair: raw data file for non-cancerous lung sample.

source_name: lung carcinoma tissue from 110901

value: lung cancer

value: female

source_name: non-cancerous lung tissue from 110901

value: non-cancerous lung tissue


title: Mouse colon stromal cells, Vehicle 1

status: Public on Oct 21 2016

city: Stanford

first: Philip

last: Beachy

address: 265 Campus Drive

institute: Stanford University

hyb_protocol: Microarray hybridization was performed by the Stanford Protein and Nucleic Facility using Mouse Genome 430 2.0 Affymetrix arrays

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

data_processing: Microarray data was analyzed using R and Bioconductor

source_name: colons

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

growth_protocol: Gli1+ positive cells were marked in all mice by giving tamoxifen to Gli1 CreER; R26 mTmG mice daily (40 mg/ml) on days 1-3

extract_protocol: colons were dissected from ice, flushed with PBS and then homogenized in Trizol (Invitrogen) and purified with the PureLink Mini Kit (Invitrogen)

treatment_protocol: Treatment mice were given SAG21k at a dose of 0.5 mg/kg ip twice daily from day +7 to day +10, Vehicle treated mice were given PBS by ip injection on days +7 to +10

value: male

value: Gli1 expressing stromal cells

value: vehicle


title: Mouse colon, SAG21k 3

source_name: colon

treatment_protocol: Treatment mice were given SAG21k at a dose of 0.5 mg/kg ip twice daily from day -5 to day +10, Vehicle treated mice were given PBS by ip injection on days -5 to +10

value: colon


title: Mouse colon stromal cells, SAG21k 2


title: Mouse colon, SAG21k 1


title: Mouse colon stromal cells, Vehicle 3


title: Mouse colon stromal cells, Vehicle 2


title: Mouse colon stromal cells, SAG21k 3


title: Mouse colon, Vehicle 2


title: Mouse colon, SAG21k 2


title: Mouse colon, Vehicle 3


title: Mouse colon stromal cells, SAG21k 1


title: Mouse colon, Vehicle 1


title: FIB 3

city: Salamanca

first: Beatriz

middle: Roson

last: Burgo

address: Campus Miguel de Unamuno

department: Cancer Research Centre

institute: Consejo Superior de Investigaciones Científicas & Universidad de Salamanca

hyb_protocol: Affymetrix manufacture's protocol for Human Exon Array 1.0 ST

data_processing:
Data was processed within R/Bioconductor, using affy package tools. RMA normalization function was applied. Probeset sumarization into ENSEMBL genes (v57) was performed with the CDF genemapperhumanexon1.0cdf_3.0 from GATExplorer (http://bioinfow.dep.usal.es/xgate/mapping/mapping.php?content=rprogram)
probes2genes-Human_Exon_1.0.txt (tab-delimited-file). CDF R-package: genemapperhumanexon1.0cdf_3.0. Both available at: 'http://bioinfow.dep.usal.es/xgate/' These files contain the probe sequences and array coordinates that unambiguously map probes to gene loci.
HumanGeneAnnotation_Ensembl57.txt (tab-delimited-file) The genome build used to annotate the genes and map the probes.

source_name: Dermal Fibroblasts

growth_protocol: MSCs were isolated from mononuclear cell fraction by Ficoll-Paque, plated and expanded in DMEM (10%FCS, 1%Penicillin/Streptomycin) until passage 3 (incubated at 37ºC and 5% CO2)

extract_protocol: Total RNA from cultured populations was extracted using TRIzol reagent according to the manufactures’s instructions (Invitrogen).

treatment_protocol: No drug treatment applied

tag: isolation protocol

value: Primary culture

tag: cell type

value: Dermal Fibroblasts


title: FIB 2

scan_protocol: Affymetrix manufacture's protocol for Human Exon Array 1.0 ST


title: BNL CL.2 cells with RAW 264.7 cells and FAC, rep3

value: BNL CL.2

value: liver


title: ADMSC 3

source_name: Mesenchymal Stem/Stromal Cells from Adipose tissue

label_protocol: Affymetrix manufacture's protocol for Human Exon Array 1.0 ST

value: Primary culture - 3th passage


title: PLMSC 2

source_name: Mesenchymal Stem/Stromal Cells from Placenta (Chorionic tissue)


title: HSPC 1

source_name: Hematopoietic CD34+ cells

value: Immunomagnetic selection

value: Hematopoietic CD34+ cells


title: FIB 1


title: HSPC 3


title: ADMSC 2

value: Mesenchymal Stem/Stromal Cells from Adipose tissue


title: BMMSC 1

source_name: Mesenchymal Stem/Stromal Cells from Bone Marrow


title: BMMSC 3

value: Mesenchymal Stem/Stromal Cells from Bone Marrow


title: HSPC 2


title: ADMSC 1


title: PLMSC 3

value: Mesenchymal Stem/Stromal Cells from Placenta (Chorionic tissue)


title: muscle_lowprotein_taurine_rep2

value: Wistar

value: Skeletal Muscle

value: Newborn


title: Para-carcinoma_patient 4

city: Chongqing

first: Zhenyu

last: Zhong

address: No. 1 Yixueyuan Road

institute: Chongqing Medical University

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Scanned images were imported into Agilent Feature Extraction software for raw data extraction. Quantile normalization of raw data and subsequent data processing were performed using the R software package.

source_name: Adjacent normal tissue

label_protocol: RNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNA was isolated from frozen tissues stored in liquid nitrogen using TRIzol (Invitrogen) according to manufacturer’s recommendations. RNA quantity and quality were determined by OD260 using a NanoDrop ND-1000 spectrophotometer and RNA integrity was assessed by electrophoresis on a denaturing agarose gel.

value: patient 4

tag: patient diagnosis

value: bladder cancer

value: Adjacent normal

value: male


title: PLMSC 1


title: Fibroblasts, 24 h, 200 J/m2, repeated UVB, rep1

city: Yokohama

first: Kazuyuki

last: Yo

address: 560 Kashio-cho, Totsuka-ku

department: Skin Research Department

institute: POLA Chemical Industries, Inc.

description: Gene expression in fibroblasts 24 hours after three daily irradiations with 200 J/m2 UVB

hyb_protocol: 1 μg of each labeled cRNA (pmol Cy3/μg cRNA) was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed and fixed.

scan_protocol: The hybridized array was scanned with using the Agilent DNA Microarray Scanner G2505C using one color scan setting for 8*60K array slides.

data_processing:
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze the scanned images.
Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent). LncRNAs were further analyzed when their expression was detectable in at least 6 out of 18 samples/ in at least one third of the samples.

source_name: Primary neonatal skin fibroblasts, 24hr, 200 J/m2 repeated UVB, replicate 1

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 using Arraystar Flash RNA Labeling Kit (Arraystar, Rockville, MD).

growth_protocol: Primary human fibroblasts were established from neonatal foreskin, and were incubated in Dulbecco's Modified Eagle's Medium supplemented with 10% heat-inactivated fetal bovine serum and 1% penicillin/streptomycin at 37℃ with 5% CO2.

extract_protocol: Total RNA was isolated using RNeasy Mini Kit (Qiagen, Hilden, Germany) following manufacture's protocol. RNA was quantified using a NanoDrop-1000 spectrophotometer and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: Fibroblasts were washed twice by PBS, then irradiated through a thin cover of PBS with UVA or UVB.

value: Primary neonatal skin fibroblasts


title: Bladder carcinoma tissue_patient 3

source_name: Bladder carcinoma tissue

value: patient 3

value: Bladder carcinoma


title: Para-carcinoma_patient 1

value: patient 1


title: Bladder carcinoma tissue_patient 2

value: patient 2


title: Para-carcinoma_patient 3


title: Bladder carcinoma tissue_patient 1


title: Bladder carcinoma tissue_patient 4


title: Fibroblasts, sham, parallel to repeated UVR, rep3

description: Gene expression in fibroblasts harvested parallel to samples with  three daily UV irradiations

source_name: Primary neonatal skin fibroblasts, sham with repeated UVR, replicate 3


title: BMMSC 2

value: Primary culture - 3th passage


title: Fibroblasts, 24 h, 100 kJ/m2, repeated UVA, rep2

description: Gene expression in fibroblasts 24 hours after three daily irradiations with 100 kJ/m2 UVA

source_name: Primary neonatal skin fibroblasts, 24hr, 100 kJ/m2 repeated UVA, replicate 2


title: Fibroblasts, 24 h, 500 J/m2, single UVB, rep1

description: Gene expression in fibroblasts 24 hours after single irradiation with 500 J/m2 UVB

source_name: Primary neonatal skin fibroblasts, 24hr, 500 J/m2 single UVB, replicate 1


title: CLL_Tumor_SS216_Tumor

type: genomic

city: Boston

first: Sunita

middle: R

last: Setlur

address: 221 Longwood Avenue

institute: Brigham and Women's Hospital

description: processed data file: SS216Final.txt

hyb_protocol: Standard protocols detailed by the manufacturer (Affymetrix Inc.) was used for array hybridization. The arrays were hybridized using the Hybridization Oven 645.

scan_protocol: The arrays were scanned according to the standard protocol using the Gene Chip Scanner 3000 (Affymetrix Inc)

data_processing:
Raw data was processed using the Affymetrix Chromosome Analysis Suite [version -2.0.1.2 (r5919)], genome build hg19. Reference model file used was "CytoScanHD_Array.na32.3.v1.REF_MODEL" and the annotation file used was "CytoScanHD_Arra_na32.3.annot.db".
A cutoff of 25 probes and 200kb (50 kb on gene overlapping regions) for deletion CNAs or 400kb (50 kb on gene overlapping regions) for gain CNAs was used.  A size cut off of 10 MB genome-wide and 3 MB within genic regions was used to detect LOH events. All CNAs and LOHs were manually reviewed. The TXT format file of the final data can be found in a tar archive on the series record.

source_name: Blood CLL_Tumor_SS216_Tumor

label_protocol: Samples for Affymetrix CytoScan HD arrays were labelled following fragmentation according to the manufacturer’s protocol.

extract_protocol: Tumor and saliva DNA were extracted using QIAamp Blood DNA (Qiagen Inc, Valencia, CA) and Oragene DNA (Oragene, Ontario, Canada) kits respectively, according to the manufacturer’s directions.

treatment_protocol: B cell enrichment was performed using Easy Sep Human B cell Enrichment Kit (StemCell Technologies Inc, Vancouver, Canada) for samples with WBC count lower than 25K or absolute lymphocyte count <20K. For samples with lymphocyte count >25K, peripheral blood mononuclear cells (PBMC) were separated using conventional Ficoll-Hypaque separation according to manufacturer’s instructions (StemCell Techonologies Inc, Vancouver, Canada).

value: blood

tag: tissue source

value: CLL -Tumor

tag: 17p status

value: Copy Neutral LOH


title: CLL_Tumor_SS208_Tumor

description: processed data file: SS208Final.txt

source_name: Blood CLL_Tumor_SS208_Tumor

value: Deleted


title: CLL_Tumor_SS206_Tumor

description: processed data file: SS206Final.txt

source_name: Blood CLL_Tumor_SS206_Tumor


title: Fibroblasts, sham, parallel to repeated UVR, rep2

source_name: Primary neonatal skin fibroblasts, sham with repeated UVR, replicate 2

tag: gender


title: CLL_Tumor_SS207_Tumor

description: processed data file: SS207Final.txt

source_name: Blood CLL_Tumor_SS207_Tumor


title: Para-carcinoma_patient 2

tag: age


title: CLL_Tumor_SS204_Tumor

description: processed data file: SS204Final.txt

source_name: Blood CLL_Tumor_SS204_Tumor


title: Fibroblasts, 24 h, 100 kJ/m2, repeated UVA, rep1

source_name: Primary neonatal skin fibroblasts, 24hr, 100 kJ/m2 repeated UVA, replicate 1


title: Fibroblasts, 24 h, 500 J/m2, single UVB, rep2

source_name: Primary neonatal skin fibroblasts, 24hr, 500 J/m2 single UVB, replicate 2


title: Fibroblasts, 24 h, 200 kJ/m2, single UVA, rep1

description: Gene expression in fibroblasts 24 hours after single irradiation with 200 kJ/m2 UVA

source_name: Primary neonatal skin fibroblasts, 24hr, 200 kJ/m2 single UVA, replicate 1


title: CLL_Tumor_SS203_Tumor

description: processed data file: SS203Final.txt

source_name: Blood CLL_Tumor_SS203_Tumor


title: Fibroblasts, 6 h, 500 J/m2, single UVB, rep2

description: Gene expression in fibroblasts 6 hours after single irradiation with 500 J/m2 UVB

source_name: Primary neonatal skin fibroblasts, 6hr, 500 J/m2 single UVB, replicate 2


title: Fibroblasts, sham, parallel to single UVR, rep3

description: Gene expression in fibroblasts harvested parallel to samples with single UV irradiation

source_name: Primary neonatal skin fibroblasts, sham with single UVR, replicate 3


title: Fibroblasts, sham, parallel to single UVR, rep2

source_name: Primary neonatal skin fibroblasts, sham with single UVR, replicate 2


title: CLL_Tumor_SS202_Tumor

description: processed data file: SS202Final.txt

source_name: Blood CLL_Tumor_SS202_Tumor


title: CLL_Tumor_SS200_Tumor

description: processed data file: SS200FinalV2.txt

source_name: Blood CLL_Tumor_SS200_Tumor


title: Fibroblasts, 6 h, 200 kJ/m2, single UVA, rep1

description: Gene expression in fibroblasts 6 hours after single irradiation with 200 kJ/m2 UVA

source_name: Primary neonatal skin fibroblasts, 6hr, 200 kJ/m2 single UVA, replicate 1


title: Fibroblasts, 24 h, 200 kJ/m2, single UVA, rep2

source_name: Primary neonatal skin fibroblasts, 24hr, 200 kJ/m2 single UVA, replicate 2


title: CLL_Tumor_SS199B_Tumor

description: processed data file: SS199Final.txt

source_name: Blood CLL_Tumor_SS199B_Tumor


title: Fibroblasts, 6 h, 500 J/m2, single UVB, rep1

source_name: Primary neonatal skin fibroblasts, 6hr, 500 J/m2 single UVB, replicate 1


title: CLL_Tumor_SS199A_Tumor

description: processed data file: SS199Final.txt

source_name: Blood CLL_Tumor_SS199A_Tumor


title: CLL_Tumor_SS198_Tumor

description: processed data file: SS198Final.txt

source_name: Blood CLL_Tumor_SS198_Tumor


title: CLL_Tumor_SS197_Tumor

description: processed data file: SS197Final.txt

source_name: Blood CLL_Tumor_SS197_Tumor


title: Fibroblasts, sham, parallel to repeated UVR, rep1

source_name: Primary neonatal skin fibroblasts, sham with repeated UVR, replicate 1


title: CLL_Tumor_SS194_Tumor

description: processed data file: SS194Final.txt

source_name: Blood CLL_Tumor_SS194_Tumor


title: Fibroblasts, sham, parallel to single UVR, rep1

source_name: Primary neonatal skin fibroblasts, sham with single UVR, replicate 1


title: CLL_Tumor_SS193_Tumor

description: processed data file: SS193Final.txt

source_name: Blood CLL_Tumor_SS193_Tumor


title: CLL_Tumor_SS190_Tumor

description: processed data file: SS190Final.txt

source_name: Blood CLL_Tumor_SS190_Tumor


title: CLL_Tumor_SS189B_Tumor

description: processed data file: SS189Final.txt

source_name: Blood CLL_Tumor_SS189B_Tumor


title: CLL_Tumor_SS189A_Tumor

description: processed data file: SS189Final.txt

source_name: Blood CLL_Tumor_SS189A_Tumor


title: CLL_Tumor_SS188_Tumor

description: processed data file: SS188Final.txt

source_name: Blood CLL_Tumor_SS188_Tumor


title: CLL_Tumor_SS192_Tumor

description: processed data file: SS192FinalV2.txt

source_name: Blood CLL_Tumor_SS192_Tumor


title: Fibroblasts, 24 h, 200 J/m2, repeated UVB, rep2

source_name: Primary neonatal skin fibroblasts, 24hr, 200 J/m2 repeated UVB, replicate 2


title: CLL_Tumor_SS186_Tumor

description: processed data file: SS186FinalV2.txt

source_name: Blood CLL_Tumor_SS186_Tumor


title: CLL_Tumor_SS185_Tumor

description: processed data file: SS185Final.txt

source_name: Blood CLL_Tumor_SS185_Tumor


title: CLL_Tumor_SS184_Tumor

description: processed data file: SS184Final.txt

source_name: Blood CLL_Tumor_SS184_Tumor


title: CLL_Tumor_SS191_Tumor

description: processed data file: SS191Final.txt

source_name: Blood CLL_Tumor_SS191_Tumor


title: CLL_Tumor_SS183_Tumor

description:
processed data file: SS183(Only Tumor Sample)FinalV2.txt
There is no matched normal sample for the SS183 tumor sample due to poor data quality.

source_name: Blood CLL_Tumor_SS183_Tumor


title: CLL_Tumor_SS182_Tumor

description: processed data file: SS182Final.txt

source_name: Blood CLL_Tumor_SS182_Tumor


title: CLL_Tumor_SS181A_Tumor

description: processed data file: SS181FinalV2.txt

source_name: Blood CLL_Tumor_SS181A_Tumor


title: CLL_Tumor_SS180_Tumor

description: processed data file: SS180Final.txt

source_name: Blood CLL_Tumor_SS180_Tumor


title: CLL_Tumor_SS177_Tumor

description: processed data file: SS177FinalV2.txt

source_name: Blood CLL_Tumor_SS177_Tumor


title: CLL_Tumor_SS179_Tumor

description: processed data file: SS179Final.txt

source_name: Blood CLL_Tumor_SS179_Tumor


title: CLL_Tumor_SS178_Tumor

description: processed data file: SS178FinalV2.txt

source_name: Blood CLL_Tumor_SS178_Tumor


title: CLL_Tumor_SS181B_Tumor

description: processed data file: SS181FinalV2.txt

source_name: Blood CLL_Tumor_SS181B_Tumor


title: CLL_Tumor_SS175C_Tumor

description: processed data file: SS175FinalV2.txt

source_name: Blood CLL_Tumor_SS175C_Tumor


title: CLL_Tumor_SS176_Tumor

description: processed data file: SS176Final.txt

source_name: Blood CLL_Tumor_SS176_Tumor


title: CLL_Tumor_SS175B_Tumor

description: processed data file: SS175FinalV2.txt

source_name: Blood CLL_Tumor_SS175B_Tumor


title: Fibroblasts, 6 h, 200 kJ/m2, single UVA, rep2

source_name: Primary neonatal skin fibroblasts, 6hr, 200 kJ/m2 single UVA, replicate 2


title: CLL_Tumor_SS173_Tumor

description: processed data file: SS173Final.txt

source_name: Blood CLL_Tumor_SS173_Tumor


title: CLL_Tumor_SS175A_Tumor

description: processed data file: SS175FinalV2.txt

source_name: Blood CLL_Tumor_SS175A_Tumor


title: CLL_Tumor_SS172_Tumor

description: processed data file: SS172Final.txt

source_name: Blood CLL_Tumor_SS172_Tumor


title: CLL_Tumor_SS171_Tumor

description: processed data file: SS171Final.txt

source_name: Blood CLL_Tumor_SS171_Tumor


title: PM_testes_adult_3

city: Lexington

first: Mark

last: Evers

state: Kentucky

address: 800 Rose Street

department: College of Medicine

institute: University of Kentucky

data_processing: RNA was processed on the Nanostring nCounter platform to assay gene expression. Background subtraction was performed to account for background signal and counts were normalized to the mean of two housekeeping genes, EF1A_A and EF1A_B

organism: Petromyzon marinus

source_name: Adult Testes

growth_protocol: Fertilized embryos were incubated in 10% Holfretter's solution at 18° C throughout development.

extract_protocol: Embryos were frozen in liquid nitrogen and extracted using the Direct-zol RNA mini-prep (Zymo Research)

tag: developmental stage

value: Adult

value: testes


title: CLL_Tumor_SS170_Tumor

description: processed data file: SS170FinalV2.txt

source_name: Blood CLL_Tumor_SS170_Tumor


title: CLL_Tumor_SS187_Tumor

description: processed data file: SS187Final.txt

source_name: Blood CLL_Tumor_SS187_Tumor


title: CLL_Tumor_SS168_Tumor

description: processed data file: SS168FinalV2.txt

source_name: Blood CLL_Tumor_SS168_Tumor


title: PM_testes_adult_2


title: PM_testes_adult_1


title: CLL_Tumor_SS167_Tumor

description: processed data file: SS167FinalV2.txt

source_name: Blood CLL_Tumor_SS167_Tumor


title: CLL_Tumor_SS169_Tumor

description: processed data file: SS169FinalV2.txt

source_name: Blood CLL_Tumor_SS169_Tumor


title: PM_embryo_D5_3

source_name: Whole Embryos

value: D5 embryos

value: whole embryo


title: PM_embryo_D5_2


title: CLL_Normal_SS216_Normal

description: processed data file: SS216Final.txt

source_name: Saliva CLL_Normal_SS216_Normal

value: saliva

value: CLL -Matched Normal


title: PM_embryo_D5_1


title: CLL_Normal_SS207_Normal

description: processed data file: SS207Final.txt

source_name: Saliva CLL_Normal_SS207_Normal


title: CLL_Normal_SS208_Normal

description: processed data file: SS208Final.txt

source_name: Saliva CLL_Normal_SS208_Normal


title: CLL_Normal_SS206_Normal

description: processed data file: SS206Final.txt

source_name: Saliva CLL_Normal_SS206_Normal


title: PM_embryo_D4_3

value: D4 embryos


title: CLL_Normal_SS203_Normal

description: processed data file: SS203Final.txt

source_name: Saliva CLL_Normal_SS203_Normal


title: CLL_Tumor_SS174_Tumor

description: processed data file: SS174Final.txt

source_name: Blood CLL_Tumor_SS174_Tumor


title: CLL_Normal_SS202_Normal

description: processed data file: SS202Final.txt

source_name: Saliva CLL_Normal_SS202_Normal


title: PM_embryo_D4_2


title: CLL_Normal_SS200_Normal

description: processed data file: SS200FinalV2.txt

source_name: Saliva CLL_Normal_SS200_Normal


title: CLL_Normal_SS198_Normal

description: processed data file: SS198Final.txt

source_name: Saliva CLL_Normal_SS198_Normal


title: PM_embryo_D4_1


title: CLL_Normal_SS199_Normal

description: processed data file: SS199Final.txt

source_name: Saliva CLL_Normal_SS199_Normal


title: CLL_Normal_SS197_Normal

description: processed data file: SS197Final.txt

source_name: Saliva CLL_Normal_SS197_Normal


title: CLL_Normal_SS194_Normal

description: processed data file: SS194Final.txt

source_name: Saliva CLL_Normal_SS194_Normal


title: CLL_Normal_SS193_Normal

description: processed data file: SS193Final.txt

source_name: Saliva CLL_Normal_SS193_Normal


title: PM_embryo_D3_2

value: D3 embryos


title: CLL_Tumor_SS166_Tumor

description: processed data file: SS166Final.txt

source_name: Blood CLL_Tumor_SS166_Tumor


title: PM_embryo_D3_1


title: CLL_Tumor_SS165_Tumor

description: processed data file: SS165FinalV2.txt

source_name: Blood CLL_Tumor_SS165_Tumor


title: PM_embryo_D2.5_3

value: D2.5 embryos


title: CLL_Normal_SS190_Normal

description: processed data file: SS190Final.txt

source_name: Saliva CLL_Normal_SS190_Normal


title: CLL_Normal_SS189_Normal

description: processed data file: SS189Final.txt

source_name: Saliva CLL_Normal_SS189_Normal


title: CLL_Normal_SS192_Normal

description: processed data file: SS192FinalV2.txt

source_name: Saliva CLL_Normal_SS192_Normal


title: CLL_Normal_SS188_Normal

description: processed data file: SS188Final.txt

source_name: Saliva CLL_Normal_SS188_Normal


title: CLL_Normal_SS191_Normal

description: processed data file: SS191Final.txt

source_name: Saliva CLL_Normal_SS191_Normal


title: PM_embryo_D2.5_1

source_name: Whole Embryos


title: CLL_Normal_SS204_Normal

description: processed data file: SS204Final.txt

source_name: Saliva CLL_Normal_SS204_Normal


title: CLL_Normal_SS186_Normal

description: processed data file: SS186FinalV2.txt

source_name: Saliva CLL_Normal_SS186_Normal


title: PM_embryo_D2.5_2


title: CLL_Normal_SS187_Normal

description: processed data file: SS187Final.txt

source_name: Saliva CLL_Normal_SS187_Normal


title: CLL_Normal_SS185_Normal

description: processed data file: SS185Final.txt

source_name: Saliva CLL_Normal_SS185_Normal


title: CLL_Normal_SS182_Normal

description: processed data file: SS182Final.txt

source_name: Saliva CLL_Normal_SS182_Normal


title: PM_embryo_D3_3


title: PM_embryo_D2_3

value: D2 embryos


title: PM_embryo_D2_2


title: CLL_Normal_SS180_Normal

description: processed data file: SS180Final.txt

source_name: Saliva CLL_Normal_SS180_Normal


title: CLL_Normal_SS181_Normal

description: processed data file: SS181FinalV2.txt

source_name: Saliva CLL_Normal_SS181_Normal


title: CLL_Normal_SS179_Normal

description: processed data file: SS179Final.txt

source_name: Saliva CLL_Normal_SS179_Normal


title: CLL_Normal_SS178_Normal

description: processed data file: SS178FinalV2.txt

source_name: Saliva CLL_Normal_SS178_Normal


title: PM_embryo_D2_1


title: CLL_Normal_SS176_Normal

description: processed data file: SS176Final.txt

source_name: Saliva CLL_Normal_SS176_Normal


title: CLL_Normal_SS177_Normal

description: processed data file: SS177FinalV2.txt

source_name: Saliva CLL_Normal_SS177_Normal


title: CLL_Normal_SS175_Normal

description: processed data file: SS175FinalV2.txt

source_name: Saliva CLL_Normal_SS175_Normal


title: PM_embryo_D1_3

value: D1 embryos


title: PM_embryo_D1_2


title: CLL_Normal_SS174_Normal

description: processed data file: SS174Final.txt

source_name: Saliva CLL_Normal_SS174_Normal


title: PM_embryo_D1_1


title: CLL_Normal_SS172_Normal

description: processed data file: SS172Final.txt

source_name: Saliva CLL_Normal_SS172_Normal


title: CLL_Normal_SS170_Normal

description: processed data file: SS170FinalV2.txt

source_name: Saliva CLL_Normal_SS170_Normal


title: CLL_Normal_SS184_Normal

description: processed data file: SS184Final.txt

source_name: Saliva CLL_Normal_SS184_Normal


title: CLL_Normal_SS168_Normal

description: processed data file: SS168FinalV2.txt

source_name: Saliva CLL_Normal_SS168_Normal


title: CLL_Normal_SS167_Normal

description: processed data file: SS167FinalV2.txt

source_name: Saliva CLL_Normal_SS167_Normal


title: CLL_Normal_SS166_Normal

description: processed data file: SS166Final.txt

source_name: Saliva CLL_Normal_SS166_Normal


title: CLL_Normal_SS165_Normal

description: processed data file: SS165FinalV2.txt

source_name: Saliva CLL_Normal_SS165_Normal


title: CLL_Normal_SS173_Normal

description: processed data file: SS173Final.txt

source_name: Saliva CLL_Normal_SS173_Normal


title: g2 3

city: Frankfurt

first: Darja

last: Karpova

address: Sandhofstrasse 1

department: Cell Therapeutics

country: Germany

institute: German Red Cross Blood Donor Service

hyb_protocol: The balanced aRNAs were suspended in Agilent 2X Gene Expression buffer (55ul), Agilent 10X Blocking agent (11ul), and Kreablock (6ul).  The hybridization solutions were applied to Agilent Mouse v2 8x60K microarrays (G4852B-074809).  Hybridization was carried out at 65C for 20 hours.  Washing procedures were carried out according to Agilent gene expression protocols.

scan_protocol: Slides were scanned on an Agilent C-class Microarray scanner to detect Cy5 fluorescence, according to manufacturer's specifications.

data_processing: Gridding and analysis of images was performed using Feature Extraction (v11.5.1.1, Agilent Technologies).

source_name: BM LSK SLAM, G-CSF, 2 days (4 doses) mouse 3

label_protocol: cDNAs were chemically labeled with Kreatech ULS RNA labeling kit (Kreatech Diagnostics).  Per reaction, 3ug of each RNA (+water=16ul) was mixed with Kreatech 10x labeling buffer (2ul) and Kreatech cy5/DY-ULS (2ul).  The reactions were incubated at 85C for 15 minutes in the dark and placed on ice for 3 minutes.  Labeled cDNA was purified with Qiagen PCR purification columns according to manufacturer’s protocol.  cDNAs were quantitated on a Nanodrop spectrophotometer. Detailed protocol can be found at http://www.kreatech.com/fileadmin/user_upload/Documenten/PDF/12_man_EA-021-022-023__D0.6.pdf

growth_protocol: HSCs harvested directly from mouse by flow cytometry

extract_protocol: RNA was prepared using the NucleoSpin® RNA XS Isolation kit (Macherey-Nagel, Bethlehem, PA, USA) following the manufacturer's recommendations.  The protocol includes an on-column DNase digestion. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: HSCs from control mice or after 2 or 5 days of G-CSF treatment or 14 days after POL5551 infusion start

value: bone marrow

value: male

tag: treatment

value: G-CSF (100 ug/kg/injection, q12h, 2 days


title: g5 1

source_name: BM LSK SLAM, G-CSF, 5 days (9 doses) mouse 1

value: G-CSF (100 ug/kg/injection, q12h, 5 days


title: g5 3

source_name: BM LSK SLAM, G-CSF, 5 days (9 doses) mouse 3


title: g5 2

source_name: BM LSK SLAM, G-CSF, 5 days (9 doses) mouse 2


title: CLL_Normal_SS171_Normal

description: processed data file: SS171Final.txt

source_name: Saliva CLL_Normal_SS171_Normal


title: CLL_Normal_SS169_Normal

description: processed data file: SS169FinalV2.txt

source_name: Saliva CLL_Normal_SS169_Normal


title: pol 2

source_name: BM LSK SLAM, POL5551 infusion mouse 2

value: POL5551 treated (continuos infusion, 2 wks, 100 mg/kg/day)


title: g2 1

source_name: BM LSK SLAM, G-CSF, 2 days (4 doses) mouse 1


title: Ccl2-/- monocyte, biological replicate 2

first: Barrett

middle: J

last: Rollins

state: MA

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

description: Monocytes pooled from peripheral blood of 5 mice of the same genotype

hyb_protocol: Samples were hybridized with GeneChip Mouse Gene 1.0 ST Arrays (Affymetrix) and scanned at the Dana-Farber Cancer Institute Microarray Core Facility.

data_processing: Scanned fluorescent images were analyzed using the dChip software. Comparison among samples was conducted using the parameters E/B or B/E >1.2 AND E-B or B-E >100.

source_name: Ccl2-/- monocyte

growth_protocol: Adult mouse monocytes isolated from peripheral blood

extract_protocol: Purified monocytes were centrifuged, and total RNA was isolated using RNeasy (QIAGEN, Valencia, CA). RNA quality was assessed using a Nanodrop spectrophotometer and Bioanalyzer.

treatment_protocol: not applicable

value: Balb/c

tag: genotype


title: Ccr2-/- monocyte, biological replicate 1

source_name: Ccr2-/- monocyte


title: Wild type monocyte, biological replicate 2

source_name: Wild type monocyte

value: wild-type


title: pol 1

source_name: BM LSK SLAM, POL5551 infusion mouse 1


title: Ccr2-/- monocyte, biological replicate 2


title: Ccr2-/- monocyte, biological replicate 3


title: pol 3

source_name: BM LSK SLAM, POL5551 infusion mouse 3


title: Ccl2-/- monocyte, biological replicate 3


title: ctr 1

source_name: BM LSK SLAM, sham-op, mouse 1

value: sham-op


title: Wild type monocyte, biological replicate 1


title: Ccl2-/- monocyte, biological replicate 1


title: ctr 2

source_name: BM LSK SLAM, sham-op, mouse 2


title: Wild type monocyte, biological replicate 3


title: ctr 3

source_name: BM LSK SLAM, sham-op, mouse 3


title: g2 2

source_name: BM LSK SLAM, G-CSF, 2 days (4 doses) mouse 2


title: SM/J mouse liver, treated animal 1

city: Chapel Hill

first: Merrie

last: Mosedale

state: North Carolina

address: 301 Pharmacy Lane, Kerr Hall CB#7569

department: Division of Pharmacotherapy and Experimental Therapeutics

institute: UNC Eshelman School of Pharmacy

hyb_protocol: Samples were hybridized to the Affymetrix GeneChip Mouse Genome 430 2.0 Array using the Hybridization, Wash and Stain kit (Affymetrix). The hybridization cocktail was applied to arrays and incubated at 45°C for 16 hours. Following hybridization, arrays were washed and stained using standard Affymetrix procedures.

scan_protocol: GeneChip were scanned with an Affymetrix Gene Chip Scanner.

data_processing: Data were processed using the Affymetrix Power Tools program apt-probeset-summarize. Probes overlapping SNPs in MDP strains were removed and intensity data were RMA (Robust Multi-array Analysis) transformed.

source_name: SM/J liver, PF-04287881 treated

label_protocol: RNA samples were converted into labeled target antisense RNA (cRNA) using the Single-Round RNA Amplification and Biotin Labeling System (Enzo). Purified cRNA was fragmented using a 5X fragmentation buffer.

growth_protocol: Eight female mice in each of four strains (MA/MyJ, NZW/LacJ, SM/J, WSB/EiJ) were 8-10 weeks old at the start of the study.

extract_protocol: Twenty-four (24) hours after the final dose, mice were sacrificed, livers were excised, and left liver lobe tissue was flash frozen in liquid nitrogen. Total liver RNA was isolated with the RNeasy total RNA isolation kit (Qiagen) according to manufacturer’s instructions.

treatment_protocol: Four mice per strain were dosed with vehicle (sterile water) and four with PF-04287881 (600 mg/kg) once daily by oral gavage for seven days.

value: left liver lobe

value: SM/J

tag: kupffer cell vacuolation

value: No

tag: single cell necrosis


title: SM/J mouse liver, treated animal 4

tag: tissue


title: SM/J mouse liver, treated animal 2


title: NZW/LacJ mouse liver, treated animal 3

source_name: NZW/LacJ, PF-04287881 treated

value: NZW/LacJ

value: Yes


title: SM/J mouse liver, treated animal 3


title: NZW/LacJ mouse liver, control animal 4

source_name: NZW/LacJ liver, vehicle treated

value: vehicle


title: SM/J mouse liver, control animal 3

source_name: SM/J liver, vehicle treated


title: NZW/LacJ mouse liver, treated animal 1


title: SM/J mouse liver, control animal 1


title: SM/J mouse liver, control animal 2


title: SM/J mouse liver, control animal 4


title: NZW/LacJ mouse liver, control animal 2


title: NZW/LacJ mouse liver, control animal 3


title: NZW/LacJ mouse liver, treated animal 4


title: WSB/EiJ mouse liver, treated animal 3

source_name: WSB/EiJ, PF-04287881 treated

value: WSB/EiJ


title: NZW/LacJ mouse liver, control animal 1


title: WSB/EiJ mouse liver, treated animal 2


title: WSB/EiJ mouse liver, control animal 3

source_name: WSB/EiJ liver, vehicle treated


title: NZW/LacJ mouse liver, treated animal 2


title: WSB/EiJ mouse liver, control animal 2


title: MA/MyJ mouse liver, treated animal 4

source_name: MA/MyJ liver, PF-04287881 treated

value: MA/MyJ


title: WSB/EiJ mouse liver, control animal 4


title: WSB/EiJ mouse liver, control animal 1


title: WSB/EiJ mouse liver, treated animal 1


title: MA/MyJ mouse liver, treated animal 2


title: MA/MyJ mouse liver, treated animal 1


title: MA/MyJ mouse liver, treated animal 3


title: MA/MyJ mouse liver, control animal 2

source_name: MA/MyJ liver, vehicle treated


title: MA/MyJ mouse liver, control animal 4


title: MA/MyJ mouse liver, control animal 3


title: MA/MyJ mouse liver, control animal 1


title: HE1-dox_rep1

city: Freiburg

first: Pierre

middle: Daniel

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

institute: University Medical Center Freiburg

hyb_protocol: Hybridisation samples were prepared for a 8-pack microarray using 600 ng cRNA each according to the hybridisation protocol from Agilent: One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling), loaded onto the 8-pack array slide and hybridized at 65 °C overnight

scan_protocol: After washing the microarray was scanned on an Agilent C Scanner using the Profile AgilentG3_GX_1Color for 8x60K microarrays (Dye channel: Green; Scan region: Scan Area (61 x 21.6 mm); Scan resolution (μm): 3; Tiff: 20 bit)

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) (protocol GE1_107_Sep09, Grid: 028005_D_GeneList_20131202 and platform Agilent SurePrint G3 Mouse GE 8x60K). The raw data output by Feature Extraction Software was analyzed using the LIMMA R package with quantile normalisation and background subtraction.

label_protocol: 25 ng RNA was labelled with Cyanine 3-CTP according to the sample preparation protocol from Agilent: One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling). Amplified labelled RNA samples were purified by using Qiagen's RNeasy mini spin columns and cRNA quantified by using a Nanodrop

growth_protocol:
A Flag-tagged dominant negative FOS (dnFOS) construct was PCR-amplified from CMV plasmid (CMV500-8584hep-fosLZ(MO), A-FOS, kindly provided by Charles Vinson (Olive et al, 1997)) and HindIII as well as Not1 sites were introduced. The GFP of the p2lox plasmid (kindly provided by Michael Kyba (Kyba et al, 2002)) was exchanged for Flag-tagged dnFOS. A2lox ESCs (a gift from Michael Kyba (Kyba et al, 2002)) or Bry-GFP ESCs were cultured as described before (Gilmour et al, 2014; Regha et al, 2015). Briefly, cells were grown on mitomycin C-inactivated mouse embryonic feeder cells (MEFs) in DMEM medium supplemented with 15% FCS (Stem Cell Technologies), 1mM sodium pyruvate, 1mM glutamine, 100 units per ml penicillin and 100g/ml streptomycin, 25mM HEPES buffer, 1 × non-essential amino acids, 0.15mM MTG and 103 units per ml LIF (ESGRO mLIF, Millipore ESG1107). Medium was changed every day and cells were passaged every 2nd day using TrypLE Express (Thermo Fisher). For transfection with p2lox-dnFOS plasmid, 2.5x106 A2lox ESCs were resuspended in 100 µl PBS (Sigma D8537), 20 µg of each p2lox-dnFOS plasmid and Cre-expressing plasmid were added and cells were electroporated at 240V, 7ms settings on a EPI 2500 electroporator (Fischer). Cells were plated quickly on NEO-resistant feeder cells in ESC medium and 1 day later selection was started by adding 300µg/ml G418. Clones were picked after 6 days of selection, assessed for their differentiation ability and transgene expression upon doxycycline addition.
ESCs were cultured for one day on gelatinized plates in DMEM ESC medium and for another day on gelatinized plates in IMDM ESC medium in the presence of LIF. Subsequently, cells were differentiated as embryoid bodies (EBs) in 15cm bacterial-grade dishes at 1.25x106 cells per 50 ml for 3.75 days in IMDM differentiation medium without LIF. EBs were then dispersed to single cells by TrypLE Express treatment and Flk1pos cells were purified using MACS technology. Purified Flk1pos cells were cultured in gelatinized T150 tissue culture-grade flask at 1.2x106 cells per flask in blast culture medium (IMDM supplemented with 10% FCS, 100 units per ml penicillin and 100ug/ml streptomycin, 1 mM glutamine, 0.45 mM MTG, 0.18 mg ml−1 Human transferrin (Roche 10652202001) 25 μg ml−1 ascorbic acid, 20% D4T conditioned media, 5 μg l−1 recombinant mouse Vascular Endothelial Growth Factor (Peprotech: 450-32), 10 μg l−1 mIL-6 (Peprotech: 216–16)).

extract_protocol: RNA was extracted from cells using TRIzol® (Invitrogen) according to manufacturers instruction. First strand cDNA synthesis was carried out using M-MLV reverse transcriptase (Invitrogen) according to manufacturers instructions using 1-2 μg of RNA.

treatment_protocol: cells were treated with 1µg/ml doxycycline for the duration indicated in each experiment.

value: hemogenic endothelium 1 IVD cells

tag: dox treatment

tag: ap-1 status

value: without AP-1


title: SM-dox_rep1

source_name: SM-dox

value: smooth muscle IVD cells


title: Prog-dox_rep1

source_name: Prog-dox

value: hematopoietic progenitor IVD cells


title: HE2_rep1

value: hemogenic endothelium 2 IVD cells

value: with AP-1


title: HE2-dox_rep1


title: Prog_rep1

source_name: Prog


title: FLK24dox_rep1

value: d1 blast culture Flk1+ IVD cells


title: FLk_rep1

source_name: FLk

value: hemangioblast Flk1+ IVD cells


title: FLK24h_rep1


title: HE1_rep2


title: Pro-dox_rep2

source_name: Pro-dox


title: HE2_rep2


title: SM_rep2

source_name: SM


title: SM_rep1


title: Prog_rep2


title: SM_rep3


title: FLK5hdox_rep1

value: 5h blast culture Flk1+ IVD cells


title: HE1-dox_rep2


title: HE2-dox_rep2


title: FLK5h_rep1


title: HE1_rep1


title: FLK5hdox_rep2


title: PiNN 49

city: Dummerstorf

first: Siriluck

last: Ponsuksili

address: Wilhelm-stahl-allee 2

institute: FBN

description:
Musculus longissimus dorsi tissue from adult pig taken 24h before slaughter
miRNA expression data from skeletal muscle of adult pig breed (PiNN).

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 42C on Affymetrix GeneChip miRNA arrays. GeneChips were washed and processed to detect biotin-containing transcripts by Streptavidin-PE (Phycoerythrin) conjugate.

scan_protocol: Scanning using the GeneChip scanner 3000 were performed according to Affymetrix protocols

data_processing: Data were analysed with Expression Console and quantify by med polish

organism: Sus scrofa

source_name: skeletal muscle

label_protocol: Biotinylated cRNA were prepared from miRNA according to FlashTag Biotin RNA Labeling Kit for Affymetrix GeneChip miRNA arrays (Genisphere, Hatfield, PA, USA) according to the manufacturer’s recommendations Affymetrix GeneChip miRNA Array protocols (Affymetrix, Santa Clara, CA, USA)

extract_protocol: Total RNA was isolated using Qiagen miReasy Mini kit TRI Reagent (Qiagen, Hilden, Germany) according to the manufacturer’s protocol for small-RNA. Then small RNA was cleaned up using the Rneasy MinElute Clean up kit  (Qiagen, Hilden, Germany).

tag: breed

value: Pietrain

value: adult


title: PiNN 62


title: PiNN 35


title: PiNN 41


title: PiNN 21


title: SM-dox_rep2


title: PiNN 36


title: PiNN 47


title: PiNN 19


title: FLK_rep2

source_name: FLK


title: PiNN 22


title: PiNN 20


title: FLK24dox_rep2


title: Duroc 46

description:
Musculus longissimus dorsi tissue from adult pig taken 24h before slaughter
miRNA expression data from skeletal muscle of adult pig breed (Duroc).

value: Duroc


title: Early-lactation vs. Dry-lactation

city: Xi'an

first: Zhi

last: Chen

state: Select a State or Province

address: 22 Xinong Road, Yangling

department: Shaanxi Key Laboratory of Molecular Biology for Agriculture

institute: College of Animal Science and Technology, Northwest A&F University,  China

data_processing:
Screening for miRNAs involved in the early-lactation and dry-lactation. In the first round of screening, all the miRNAs with four-fold change and p-value smaller than 0.05 were chose as candidates (S1-first screening). Then we took a second round of screening to confirm the expression of the candidates above, and some miRNAs were excluded with the same criterion (S2-second screening).
S1_raw.xlsx: Raw data from first screening. Capra hircus primary miRNAs, Bos taurus primary miRNAs from miRBase and overlapping data. The samples were a balanced mixture of three goats (at the same period) in early-lactation and dry-lactation, respectively. The expression of 18s rRNA was used as a normalization control.
S2_raw.xlsx: Raw data from second screening. Samples of goat in different periods were tested separately, and the averages for each period were calculated. The expression of 18s rRNA was used as a normalization control.
146_miRNAs_differentially_expressed.xlsx: 146 miRNAs whose expression changed between early-lactation and dry-lactation.

label: FAM

organism: Capra hircus

source_name: Mammary epithelial cells, early-lactation

label_protocol: S-Poly(T) miRNA assay.

growth_protocol: Dairy goats used in the study were taken from the elite herd of Xinong Sasnen Dairy Goats in the experimental farm of Northwest A&F University of China. Three healthy goats were selected at the age of three-year-old with similar body weight in early-lactation (15 days after parturition) and peak-lactation (60 days after parturition). All goats gave birth to kids in the second lactation. We deal with those goats with euthanasia via bloodletting.

extract_protocol: Mammary gland tissues were surgically collected from goats at the same breeding environment in the two lactations. Three samples were pooled and snap-frozen immediately in liquid nitrogen. Total RNA was extracted using Trizol reagent (Invitrogen, USA) according to the manufacturer's instructions. The quantity and quality of RNA were determined using a NanoDrop ND-1000 spectrophotometer (NanoDrop, USA), and the RNA were stored at -80C before use.

value: Xinong Saanen dairy goat

value: mammary gland

tag: lactation stage

value: early

source_name: Mammary epithelial cells, dry-lactation

value: dry


title: Duroc 43


title: Duroc 42


title: Hypoxia-6day

status: Public on Oct 20 2016

city: HOUSTON

first: anil

middle: k

last: sood

state: TEXAS

address: 7777 knight road, unit 173

department: Gyn Oncology and Rep Medicine

institute: UT MD Anderson Cancer Center

description:
Gene expression after 6day in hypoxia condition
A2780_6d
total miRNA

hyb_protocol: miRNA Microarray System with miRNA Complete Labeling and Hyb kit. Agilent G4170-90011 V2.2

scan_protocol: Agilent Scanner G2505B at 5 um in green

data_processing: Agilent FE v 9.5.3.1

source_name: A2780 Cells, 6day, Hypoxia-1% O2

growth_protocol: Cells were maintained in 5% CO2 at 37°C in RPMI 1640 supplemented with 10-15% fetal bovine serum (FBS) and 0.1% gentamicin sulfate. For Hypoxia treatments, cells were incubated in an oxygen-controlled hypoxia chamber at 1% O2 for respective treatment intervals.

extract_protocol: RNA was isolated using miRVANA RNA isolation kit (Lifetechnologies). RNA qulaity was meassured using Agilent Bioanalsyer, with atleast RIN<8.

treatment_protocol: Hypoxia - 1% O2 for 6hr, 48hr, 6day. Normoxia - 21% O2 was used as control for all comparisons.

tag: cell line

value: epithelial ovarian cancer cell line A2780

value: Female

tag: stress

value: Hypoxia

tag: time


title: Hypoxia-6hr

description:
Gene expression after 6hr in hypoxia condition
A2780_6h
total miRNA

source_name: A2780 Cells, 6hr, Hypoxia-1% O2

label_protocol: miRNA Microarray System with miRNA Complete Labeling and Hyb kit. Agilent G4170-90011 V2.2


title: Hypoxia-48hr

description:
Gene expression after 48hr in hypoxia condition
A2780_48h
total miRNA

source_name: A2780 Cells, 48hr, Hypoxia-1% O2


title: Duroc 32


title: Duroc 59


title: Duroc 28


title: Duroc 24


title: Normoxia control

description:
Gene expression after 0hr in hypoxia condition
A2780_0h
total miRNA

source_name: A2780 Cells, Cultured in 21% O2

value: control


title: FLK5h_rep2

tag: cell type


title: Duroc 38


title: FLK24h_rep2


title: Duroc 31


title: Hippocampus_6752351035_Control_4

city: Woolloongabba

first: Suyinn

last: Chong

state: QLD

address: 37 Kent St

country: Australia

institute: Mater Research Institute - The University of Queensland

description: SAMPLE 10

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data was processed using GenomeStudio (1.9.0) following the manufacturer's protocol

source_name: Hippocampus, Control

label_protocol: Standard Illumina Labelling protocol

extract_protocol: Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen) kit, following the manufacturer's protocol.

treatment_protocol: Voluntary maternal consumption of 10% (v/v) ethanol from 0.5 to 8.5 days post-coitum

tag: strain

value: 3 weeks

value: Male

value: Hippocampus

value: Control


title: Hippocampus_6752351023_Control_2

description: SAMPLE 8

tag: gender


title: Hippocampus_6285422061_Control_6

description: SAMPLE 12

tag: age

value: 12 weeks


title: Hippocampus_6285422061_Control_4

description: SAMPLE 10


title: Hippocampus_6752351035_EtOH_4

description: SAMPLE 4

source_name: Hippocampus, EtOH

value: prenatal alcohol exposure


title: Hippocampus_6752351023_EtOH_3

description: SAMPLE 3


title: Hippocampus_6285422061_Control_5

description: SAMPLE 11


title: Hippocampus_6752351035_EtOH_5

description: SAMPLE 5


title: Hippocampus_6752351023_Control_1

description: SAMPLE 7


title: Hippocampus_6752351035_EtOH_6

description: SAMPLE 6


title: Hippocampus_6285422061_Control_3

description: SAMPLE 9


title: Hippocampus_6285422061_EtOH_5

description: SAMPLE 5


title: Hippocampus_6285422052_EtOH_2

description: SAMPLE 2


title: Caudate putamen_6285449051_Control_5

description: SAMPLE 11

source_name: Caudate putamen, Control

value: Caudate putamen


title: Hippocampus_6285422052_EtOH_3

description: SAMPLE 3


title: Hippocampus_6285422052_EtOH_1

description: SAMPLE 1


title: Hippocampus_6752351035_Control_5

description: SAMPLE 11


title: Hippocampus_6752351023_EtOH_1

description: SAMPLE 1


title: Hippocampus_6285422052_Control_2

description: SAMPLE 8


title: Caudate putamen_6285449051_Control_4

description: SAMPLE 10


title: Hippocampus_6285422061_EtOH_6

description: SAMPLE 6


title: Hippocampus_6285422052_EtOH_4

description: SAMPLE 4


title: Hippocampus_6752351023_Control_3

description: SAMPLE 9


title: Hippocampus_6285422052_Control_1

description: SAMPLE 7


title: Hippocampus_6752351023_EtOH_2

description: SAMPLE 2


title: Caudate putamen_6285449051_Control_6

description: SAMPLE 12


title: Caudate putamen_6285449042_Control_2

description: SAMPLE 8


title: Caudate putamen_6285449042_Control_3

description: SAMPLE 9


title: strain Newman, anaerobic growth, '882 treated, rep 2

city: Rochester

first: Paul

last: Dunman

state: NY

address: 601 Elmwood Avenue

department: Microbiology and Immunology

institute: University of Rochester

description: Gene expression data from '882 treated anaerobically grown S. aureus strain Newman biological replicate 2

hyb_protocol: 1.5 ug of RNA were hybrized for 16 hr at 45C on an S. aureus Affymetrix GeneChip.  GeneChips were washed and stained in an Affymetrix Fluidics Station using ProKaryotic GE-wash2 protocol.

scan_protocol: GeneChips were scanned in an Affymetrix 7G GeneArray Scanner

data_processing: The data were analyzed with Microarray Suite version 5.0 using Affymetrix default analysis settings (Algorithm: ExpressionStat 5.0).

organism: Staphylococcus aureus

label_protocol: 10 micrograms of each sample was labeled per Affymetrix (Santa Clara, CA) instructions for prokaryotic arrays (reverse transcribed, DNase I fragmentation and 3' biotinylated).

growth_protocol: S. aureus strain Newman or isogenic ΔsaeRS mutant cells were grown to mid-exponential phase (Optical Density 600nm of 0.5) in trypic soy broth at 37C with no aeration.  Cells were then treated with 25 µM '882 or equal volume of vehicle (DMSO) for 10 min.

extract_protocol: Culture samples were mechanically disrupted in a Bullet Blender (Next Advance; Averill Park, NY) using 0.5 mm RNase-free zirconium oxide beads.  Following disruption, total bacterial RNA was precipitated using isopropyl alcohol precipitation, washed with 70% ethanol and resuspended in deionized water.

treatment_protocol: An equal volume of ice cold acetone:ethanol (1:1) was added to inactivate bacterial ribonucleases

tag: strain background

value: Newman

tag: genotype/variation

value: Wild type

tag: growth condition

value: Anaerobic growth

tag: sample

value: Whole cell

tag: treated with

value: 882 for 10min


title: strain Newman, anaerobic growth, '882 treated, rep 1

description: Gene expression data from '882 treated anaerobically grown S. aureus strain Newman biological replicate 1


title: strain saeRS, anaerobic growth, '882 treated, rep 1

description: Gene expression data from '882 treated anaerobically grown S. aureus strain ΔsaeRS biological replicate 1

source_name: Newman with ΔsaeRS_'882

value: saeRS


title: Caudate putamen_6285449051_EtOH_4

description: SAMPLE 4

source_name: Caudate putamen, EtOH

tag: tissue

tag: treatment


title: Caudate putamen_6285449042_Control_1

description: SAMPLE 7


title: strain Newman, anaerobic growth, DMSO treated, rep 2

description: Gene expression data from DMSO treated anaerobically grown S. aureus strain Newman biological replicate 2

value: DMSO for 10min


title: strain saeRS, anaerobic growth, DMSO treated, rep 1

description: Gene expression data from DMSO treated anaerobically grown S. aureus strain ΔsaeRS biological replicate 1

source_name: Newman with ΔsaeRS_DMSO


title: strain saeRS, anaerobic growth, DMSO treated, rep 2

description: Gene expression data from DMSO treated anaerobically grown S. aureus strain ΔsaeRS biological replicate 2


title: Caudate putamen_6285449051_EtOH_5

description: SAMPLE 5


title: Caudate putamen_6285449042_EtOH_3

description: SAMPLE 3


title: Caudate putamen_6285449042_EtOH_2

description: SAMPLE 2


title: strain Newman, anaerobic growth, DMSO treated, rep 1

description: Gene expression data from DMSO treated anaerobically grown S. aureus strain Newman biological replicate 1


title: case-SNX 49L

city: Erlangen

first: Steffen

last: Uebe

address: Kussmaulallee 4

department: Humangenetisches Institut

institute: Uniklinikum Erlangen

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneScan 3000 7G.

data_processing: Data were normalized using the Robust Multi-array Average (GC-RMA) algorithm, and analyzed with the Partek Genomics Suite

source_name: musculus soleus of the ischemic left hindlimb

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Extraction of total RNA was performed using the Qiagen RNA isolation kit according to the manufacturer's instructions.

value: musculus soleus

tag: operation

value: 5/6 nephrectomy


title: Caudate putamen_6285449051_EtOH_6

description: SAMPLE 6


title: case-SNX 20L


title: ctrl-sham 17L

source_name: musculus soleus of the nonischemic left hindlimb

value: sham


title: strain saeRS, anaerobic growth, '882 treated, rep 2

description: Gene expression data from '882 treated anaerobically grown S. aureus strain ΔsaeRS biological replicate 2


title: case-SNX 20R

source_name: musculus soleus of the ischemic right hindlimb


title: ctrl-sham 15R

source_name: musculus soleus of the nonischemic right hindlimb


title: case-SNX 18R


title: ctrl-sham 17R


title: case-SNX 37L


title: case-SNX 49R


title: ctrl-sham 15L


title: case-SNX 37R


title: ctrl-sham 13R


title: case-SNX 18L


title: Caudate putamen_6285449042_EtOH_1

description: SAMPLE 1


title: case-SNX 12L


title: ctrl-sham 11L


title: ctrl-sham 11R


title: Saliva Sample from control individual #1

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

hyb_protocol: The labeled RNA samples were heat denatured and hybridized to microarray slide and incubated at 55°C for 20 hours.

scan_protocol: After hybridization, microarray slides were washed and scanned in Agilent Microarray Scanner with Surescan High Resolution Technology (Agilent Technologies, Santa Clara, CA).

data_processing: Feature Extraction v10.7.3.1 (Agilent Technologies, CA) software was utilized to extract all features of the scanned image. Raw data were normalized by quantile normalization using Bioconductor software with R version 2.15.

source_name: Saliva Sample from control individual

label_protocol: 100 ng of total RNA from each sample were labeled with Cy3 using “Agilent miRNA Labeling and Hyb Kit” according to the manufacturer’s protocol.

extract_protocol: MiRNA profiling of seven saliva samples (three from patients with TSCC, four from healthy control individuals) were performed using Agilent 8X60K Human V19 miRNA microarray comprised of 2006 probes including control probes from Sanger miRBase (Release 19). All related reagents were purchased from Agilent Inc.

tag: disease state

value: control

tag: individual

value: individual 1

tag: biomaterial

value: saliva


title: Saliva Sample from control individual #2

value: individual 2


title: case-SNX 12R


title: Duroc 58

source_name: skeletal muscle

tag: breed

value: Duroc

value: adult


title: Saliva Sample from control individual #4

value: individual 4


title: Saliva Sample from (Tongue Cancer) TCa patient #1

value: TSCC

value: patient 1


title: Saliva Sample from (Tongue Cancer) TCa patient #2

value: patient 2


title: Saliva Sample from (Tongue Cancer) TCa patient #3

value: patient 3


title: ctrl-sham 13L


title: Saliva Sample from control individual #3

value: individual 3


title: Hippocampus_6752351035_Control_6

description: SAMPLE 12

value: 3 weeks

value: Male

value: Hippocampus

value: Control


title: 15477.Yeo.42_HTA-2_0

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

hyb_protocol: Hybridization cocktails containing ~5.5 ug of fragmented and labeled DNA target were prepared and applied to GeneChip Human Splice Junction arrays. Hybridization was performed for 16 hours using the Fluidics 450 station.

scan_protocol: Arrays were scanned using the Affymetrix 3000 7G scanner and GeneChip Operating Software version 1.4 to produce .CEL intensity files.

data_processing:
Data processed using Affymetrix package (Affy Power Tools) apt-probeset-summarize. Iter-plier algorithm used to quantify probesets.
HTA-2_0.r3.pgf

source_name: iPSC-MNs

label_protocol: WT Terminal Labeling Kit, Affymetrix

growth_protocol: iPSC-MNs were differentiated from MSP and control individuals

extract_protocol: RNA was extracted by standard Trizol extraction.

treatment_protocol: iPSC-MNs were treated with puromycin or saline for 24 hours

tag: genotype

value: VCP R155H

value: saline

tag: disease

value: MSP

tag: tissue type

value: iPSC-MN


title: 15457.Yeo.22_HTA-2_0

value: hnRNP A2/B1 D290V


title: 15476.Yeo.41_HTA-2_0


title: 15471.Yeo.36_HTA-2_0


title: 15464.Yeo.29_HTA-2_0

value: WT


title: 15474.Yeo.39_HTA-2_0

value: puromycin


title: 15451.Yeo.16_HTA-2_0


title: 15472.Yeo.37_HTA-2_0


title: 15475.Yeo.40_HTA-2_0


title: 15465.Yeo.30_HTA-2_0


title: 15460.Yeo.25_HTA-2_0


title: 15468.Yeo.33_HTA-2_0


title: 15463.Yeo.28_HTA-2_0


title: 15473.Yeo.38_HTA-2_0


title: 15461.Yeo.26_HTA-2_0


title: 15469.Yeo.34_HTA-2_0


title: 15449.Yeo.14_HTA-2_0


title: 15456.Yeo.21_HTA-2_0


title: 15466.Yeo.31_HTA-2_0


title: 15452.Yeo.17_HTA-2_0


title: 15454.Yeo.19_HTA-2_0


title: 15453.Yeo.18_HTA-2_0


title: 15467.Yeo.32_HTA-2_0


title: 15458.Yeo.23_HTA-2_0


title: 15455.Yeo.20_HTA-2_0


title: 15450.Yeo.15_HTA-2_0


title: 15470.Yeo.35_HTA-2_0


title: 15448.Yeo.13_HTA-2_0


title: 15459.Yeo.24_HTA-2_0


title: 15462.Yeo.27_HTA-2_0


title: 15447.Yeo.12_HTA-2_0


title: 15437.Yeo.2_HTA-2_0


title: 15440.Yeo.5_HTA-2_0


title: 15441.Yeo.6_HTA-2_0


title: 15442.Yeo.7_HTA-2_0


title: 15436.Yeo.1_HTA-2_0


title: 15445.Yeo.10_HTA-2_0


title: 15443.Yeo.8_HTA-2_0


title: 15444.Yeo.9_HTA-2_0


title: 15446.Yeo.11_HTA-2_0


title: primaryAstro_IFNg_12hr_rep2

city: Philadelphia

first: daniel

last: beiting

state: PA

address: 380 S. University Ave

department: Pathobiology

institute: University of Pennsylvania

description: replicate 2

data_processing: The data were quantile normalized without background subtraction using Illumina GenomeStudio V1.8

source_name: primary mouse astrocytes, IFNg stimulated for 12 hrs

label_protocol: Biotin labeled complementary RNA (cRNA) was made using the Illumina TotalPrep RNA Amplification Kit

growth_protocol: Astrocytes were isolated from mixed glial cultures derived from the cerebral cortex of 1-3 day old neonatal mice, as previously described (Wilson E.H., et al., 2010, Journal of Clinical Investigation 120: 1368-1379). After 12 days of cultures, astrocytes (>90% GFAP+) were plated at a density of 1x10^5 cells/cm^2 in 12-well plates.

extract_protocol: Total RNA was isolated using the Qiagen Rneasy Plus Kit

treatment_protocol: Cells were left untreated, or were treated with either 10ng/ml of recombinant IFN-γ (Peprotech) or Universal Type I Interferon (PBL Assay Science) for 12 hrs

value: IFNg stimulated for 12 hrs

tag: strain

tag: cell type

value: Astrocytes derived from mixed glial cultures from the cerebral cortex of 1-3 day old neonatal mice


title: primaryAstro_IFNa_12hr_rep1

description: replicate 1

source_name: primary mouse astrocytes, IFNa stimulated for 12 hrs

value: IFNa stimulated for 12 hrs


title: primaryAstro_IFNg_12hr_rep1

description: replicate 1


title: primaryAstro_unstimulated_rep2

description: replicate 2

source_name: primary mouse astrocytes, untreated

value: untreated


title: 14284.Yeo.21.sh_(HTA-2_0)

data_processing:
Cel files were analyzed using Expression Console (build 1.4.1.46, Affymetrix), with RMA normalization and DABG probe-level detection. Only probesets with detection p-value ≤ 0.05 in more than half of the microarray samples were considered for downstream analysis. All probes corresponding to cassette exons profiled on the microarray (comprising exclusion junction, upstream and downstream inclusion junction, and inclusion exonic probes) were identified and normalized against the average signal on a per-gene basis to remove gene expression changes. Student’s t-test was performed on residuals for inclusion probes and exclusion probes separately to identify robust splicing changes, which were quantified by SepScore ( defined as the normalized change in exclusion minus the normalized change in inclusion).
HTA-2_0.r1.pgf
HTA-2_0.r1.Psrs.mps

treatment_protocol: iPSC-MNs were treated with ASO against hnRNP A2/B1 or nontarget ASO for 28 days

value: hnRNP A2/B1 ASO 2


title: 15438.Yeo.3_HTA-2_0


title: primaryAstro_IFNa_12hr_rep2

description: replicate 2


title: primaryAstro_unstimulated_rep1

description: replicate 1


title: 14274.Yeo.11.sh_(HTA-2_0)


title: 14280.Yeo.17.sh_(HTA-2_0)

value: hnRNP A2/B1 ASO 1


title: 14285.Yeo.22.sh_(HTA-2_0)


title: 14276.Yeo.13.sh_(HTA-2_0)

value: nontarget ASO


title: 14278.Yeo.15.sh_(HTA-2_0)


title: 14269.Yeo.6.sh_(HTA-2_0)


title: 14271.Yeo.8.sh_(HTA-2_0)


title: 14283.Yeo.20.sh_(HTA-2_0)


title: 14281.Yeo.18.sh_(HTA-2_0)


title: 14282.Yeo.19.sh_(HTA-2_0)


title: 15439.Yeo.4_HTA-2_0


title: 14270.Yeo.7.sh_(HTA-2_0)


title: 14273.Yeo.10.sh_(HTA-2_0)