title: Testis_F2PW_ind783

description: testis

source_name: Testis, PWD/PhJ dam x WSB/EiJ sire F2, indiv 783


title: Testis_F2PW_ind442

status: Public on May 01 2014

type: RNA

city: Ploen

first: Leslie

middle: M

last: Turner

address: August-Thienemann Str 2

department: Evolutionary Genetics

country: Germany

institute: Max Planck Institute for Evolutionary Biology

description: testis

hyb_protocol: Hybridization was performed following the One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) Protocol from Agilent.

scan_protocol: Arrays were scanned using a High Resolution Microarray Scanner (Agilent) and raw images processed using Feature Extraction Software (Agilent). Raw images and the distribution of non-uniformity outliers were visually inspected for large spatial artifacts (e.g. caused by buffer leakage or dust particles). We used quality control metrics from Feature Extraction protocol GE1_QCMT_Dec08.

data_processing: We mapped the 41,174 non-control probe sequences from the Whole Mouse Genome Microarray to the mouse reference genome (NCBI37, downloaded March 2011) using BLAT (minScore = 55, default settings for all other options).  We excluded probes with multiple perfect matches, more than nine matches, matches to non-coding/intergenic regions only, and matches to more than one gene. A total of 36,323 probes (covering 19,742 Entrez Genes) were retained. Preprocessing of microarray data was performed using the BioConductor package Agi4x44PreProcess [91]. We used the “half” setting, which sets intensities below 0.5 to 0.5 following background subtraction, and an offset value of 50. The background signal was computed in Feature Extraction. During preprocessing, we filtered probes based on flags from Feature Extraction. Probes with signal above background in at least 10% of samples were retained (settings: wellaboveBG=TRUE, isfound=TRUE, wellaboveNEG=TRUE). We used default settings for quality-control flags. Following preprocessing, we removed probes for which the 98th percentile was <2-fold greater than background. The final data set includes 24,675 probes.

molecule: total RNA

organism: Mus musculus

source_name: Testis, PWD/PhJ dam x WSB/EiJ sire F2, indiv 442

label_protocol: We used single-color Quick-Amp Labeling Kits (Agilent) to amplify and label RNA. The yield (>2 μg) and specific activity (>9.0 pmol Cy3/μg cRNA) of labeling reactions was verified using a NanoDrop ND-1000 UV-VIS Spectrophotometer (NanoDrop, Wilmington, DE, USA).

growth_protocol: Pups were weaned into same-sex sibling groups at 21 days, and males were separated into individual cages at approx. 56 days. Males were killed for phenotyping at 70 (±5) days of age using carbon dioxide.

extract_protocol: We extracted RNA from testis using RNeasy kits (Qiagen, Hilden, Germany). RNA quality (RIN > 8) was verified using RNA 6000 Nano kits (Agilent) on a 2100 Bioanalyzer (Agilent).

treatment_protocol: The left testis was flash-frozen in liquid nitrogen upon dissection and stored at -80°. Frozen testis samples were transferred to RNAlater-ICE buffer (Invitrogen, Grand Island, NY, USA), shipped to the Max Planck Institute in Plön and stored at -80° until processing.

tag: strain

value: PWD/PhJ dam x WSB/EiJ sire F2

tag: tissue

value: testis


title: Tumor (H081081T)

city: Incheon

first: Farhan

last: Haq

address: 7-45, Songdo-dong, Yeonsu-gu

country: South Korea

institute: Gachon University

hyb_protocol: Samples passing these QC steps were next end-labeled with a biotinylated nucleoitde using Terminal Deoxynucleotidyl Transferase (TdT). The end-labeled products were added to a hybridization solution, denatured, and added to a CytoScan™ HD Array (one array per sample).

scan_protocol: After hybridization was complete, the DNA sample was removed from each microarray and replaced with Array Holding Buffer. Arrays were then washed on the Fluidics Station 450 using AGCC software (Affymetrix GeneChip® Command Console, Version 3.2.2) This protocol includes 6 cycles of 5 mixes/cycle with low stringency Wash Buffer A (6X SSPE, 0.01% Tween-20) at 25℃ followed by 24 cycles of 5 mixes/cycle with high stringency Wash Buffer B (0.6X SSPE, 0.01% Tween-20) at 45℃. Binding of the biotinylated targets was detected by incubating the array for 10 min in a Streptavidin–Phycoerythrin (SAPE) solution at 25℃ followed by a post stain wash comprised of 6 cycles of 5 mixes/cycle with Wash Buffer A at 25℃. A second round of staining was then completed using a 10 min incubation in Anti-Streptavidin Antibody Stain Solution at 25℃ followed by a third stain for 10 min in SAPE solution at 25℃ and a final wash consisting of 10 cycles of 6 mixes/cycle with Wash Buffer A at 30℃, filling of the array with Array Holding Buffer, and a hold at 25℃.

data_processing: CNV analysis was performed using the Affymetrix Cytoscan HD platform (CEL files). CNV data were analysed with the Nexus Copy Number software (BioDiscovery, CA, ver. 6.1).

label: biotin

organism: Homo sapiens

source_name: Liver

extract_protocol: Each DNA (250ng gDNA) aliquot was 96 well plate. Then, 24 of the samples on a plate were subjected to treatment with Nsp I restriction enzyme. After inactivation of the restriction enzyme, the sticky ends of the digested DNA were ligated to Nsp I adaptor/primers using T4 ligase. Aliquots from each ligated product were added to four separate plates for PCR amplification using a universal primer. The products of all four PCR reactions for each subject were combined and then purified with purification magnetic beads in 1.5ml microtube. The yield of each amplified DNA sample was assessed by UV spectrophotometry on a microplate reader. Any DNA showing lower than expected yield (≥ 3mg/ml) or an unusual size distribution was flagged and not processed further. Subsequently, each DNA was fragmented between 25 to 125 bp using partial DNase I digestion and the size distribution of the fragmented amplicons assessed by agarose gel electrophoresis (4% agarose in Tris-Acetate-EDTA buffer).

value: liver

tag: tumor size

tag: microvascular invasion

value: No

tag: early recurrence

tag: edmondson-steiner histological grade

tag: fibrosis stage

tag: alpha-fetoprotein levels


title: NC105.1-RFP vs. NC105.1-Cy5 at 4 h replicate 2

city: New York

first: Si

last: Li

state: New York

address: 12 Waverly Place

department: Biology

country: USA

institute: New York University

hyb_protocol: Equal amounts of sample and common biological reference cRNA were hybridized against the same microarray at 65°C for 17 hours and washed afterwards

scan_protocol: The slides were scanned using Agilent’s High-Resolution C Scanner and gene expression information was extracted from microarray scan data by Agilent Feature Extraction (FE) software

data_processing: Gene expression data was log2-transformed and normalized within array using a combined rank consistency filtering with LOWESS intensity normalization in FE. Between-array normalization was implemented using the Aquantile method in the Limma package in R (http://www.R-project.org/) to ensure the A-values (average intensities) have the same empirical distribution across arrays leaving the M-values (log2-ratios) unchanged

organism: Dictyostelium discoideum

source_name: Mechanically disaggregated D. discoideum cells

label_protocol: Samples were amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit together with positive control transcripts

growth_protocol: D. discoideum cells were grown on SM agar plates spread evenly with Klebsiella aerogenes (Ka). Approximately 1×105 spores were mixed with Ka and incubated at 22°C for approximately 44 hours

extract_protocol: Total RNA of NC105.1-RFP cell populations was extracted by QIAGEN RNeasy Micro Kit (Valencia, CA)

treatment_protocol: Equal amounts of RFP and non-RFP amoebae were mixed and spread evenly on two developing plates (1.5% KK2 agar) at a density of 1.6×106 cells/cm2 as biological replicates. Developing plates were incubated in a dark and humid environment at 22°C for 4 h, 8 h, 12 h, 16 h, and 20 h, respectively, before harvest. Samples collected at these different time points/developmental stages were mechanically disaggregated in disassociation buffer (KK2, 20mM EDTA) and subject to fluorescence-activated cell sorting (FACS) with a FACS Aria from BD Biosciences (San Jose, CA) immediately with a nozzle size of 70 μm

tag: time point

value: 4 h

source_name: Biological reference mixed from different time points

value: Mix of 0 h, 4 h, 8 h, 12 h, 16 h, and 20 h


title: NC105.1-RFP vs. NC105.1-Cy3 at 20 h replicate 2


title: Normal (H081081N)

label_protocol: The end-labeled products were added to a hybridization solution, denatured, and added to a CytoScan™ HD Array (one array per sample).


title: Testis_F2WP_ind1009

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1009

value: WSB/EiJ dam x PWD/PhJ sire F2


title: NC105.1-RFP vs. NC63.2-Cy3 at 20 h replicate 2


title: Liver_untreated_rep1

city: New Haven

first: Yasutaka

last: Okabe

state: CT

address: 300 Cedar Street

department: Immunobiology

institute: Yale University School of Medicine

description: SAMPLE 4

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

label: Biotin

source_name: Kupffer cells

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

growth_protocol: BMDMs were cultured in the presence of M-CSF for 7 days.

extract_protocol: RNA was extraceted by RNeasy micro with Dnase treatment

tag: gender

value: Male

tag: age

value: 8-10 week old

value: Liver

tag: cell type

value: macrophage


title: Lung_untreated_rep1

description: SAMPLE 3

source_name: Alveolar macrophages

value: Lung


title: Testis_F2PW_ind441

description: testis

source_name: Testis, PWD/PhJ dam x WSB/EiJ sire F2, indiv 441


title: Peritoneum_untreated_rep1

description: SAMPLE 1

source_name: Peritoneal macrophages

value: Peritoneal cavity


title: Nasopharyngeal carcinoma NPC15F

type: genomic

city: Singapore

first: Lizhen

last: Liu

address: 14 Medical Drive

country: Singapore

institute: Cancer Science Institute

description: Hybridized to 250K_Nsp

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The arrays were  washed using Affymetrix fluidics stations and scanned using the Gene Chip Scanner 3000.

data_processing: CEL files and CHP files (generated by Affymetrix GTYPE using the DM algorithm) were processed by CNAG/AsCNAR 3.0

molecule: genomic DNA

source_name: Nasopharyngeal carcinoma NPC15F

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from nasopharyngeal carcinoma biopsy tissues  at diagnosis using the Qiagen DNA Mini Kit. DNA quantity and quality was assessed using a Qubit® dsDNA HS Assay Kit as well as agarose gel electrophoresis.

tag: tumor type

value: nasopharyngeal carcinoma

tag: tissue type

value: biopsy tissues

value: male

tag: age (yr)

tag: smoking  history

value: NO

tag: primary tumor size (t)

tag: regional lymph node (n)

tag: metastasis (m)

tag: clinical stage

value: III


title: NC105.1-RFP vs. NC105.1-Cy3 at 20 h replicate 1

tag: strain


title: Tumor (H081077T)

tag: tissue

tag: tumor size

tag: microvascular invasion

tag: early recurrence

value: Yes


title: Tumor (H081048T)

value: liver

tag: edmondson-steiner histological grade

tag: fibrosis stage

tag: alpha-fetoprotein levels


title: NC105.1-RFP vs. NC63.2-Cy3 at 16 h replicate 2

tag: time point


title: Peritoneum_untreated_rep2

description: SAMPLE 2

tag: gender

tag: age

tag: cell type


title: Testis_F1WP_ind299

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F1, indiv 299

value: WSB/EiJ dam x PWD/PhJ sire F1

value: testis


title: Testis_F1WP_ind298

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F1, indiv 298


title: irs_ND_6731_MA2_25549_3rdreplicate_wildtype_8weeks

city: Houston

first: Chad

middle: A.

last: Shaw

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: BCM

description:
wildtype_8 weeks_3rd
BAC-Trap RNA

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix genechip scanner protocol

data_processing: data were analyzed in R using the GCRMA R package with defaults

source_name: BacTrap Purkinje Cells

label_protocol: Affymetrix IVT and labeling protocol was used with Enzo IVT labeling reagents followed by Affymetrix cleanup columns, according to manufacturer's protocols

growth_protocol: Four mice, two male and two female, for each replicated sample were euthanized with CO2 and their cerebella were dissected. Each genotype was assayed in triplicate.

extract_protocol: Qiagen RNeasy mini kit was used for RNA extraction and purification , according to manufacturer's protocols.

treatment_protocol: L7CGG90Fmr1:Pcp2 BAC (r(CGG)90 BAC) and wild-type:L7/Pcp2 BAC (WT BAC) transgenic mice used in this study have a 50% C57B6 and 50% FVB genetic background and were derived from the same parents by crossing L7CGG90Fmr1 heterozygote transgenics (100% C57B6 background) with L7/Pcp2eEGFPL10a BAC homozygous transgenics (100% FVB background). We removed cerebella and isolated translating mRNAs specifically from Purkinje neurons for microarray analysis via TRAP.

tag: genotype/variation

value: wildtype

tag: replicate

value: 8 weeks

value: cerebellum

value: Purkinje cells


title: Testis_F1WP_ind235

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F1, indiv 235


title: Testis_F2PW_ind440

description: testis

source_name: Testis, PWD/PhJ dam x WSB/EiJ sire F2, indiv 440

value: PWD/PhJ dam x WSB/EiJ sire F2


title: Normal (H081048N)


title: irs_ND_6731_MA2_25547_1streplicate_wildtype_8weeks

description:
wildtype_8 weeks_1st
BAC-Trap RNA

value: 50% C57B6 and 50% FVB genetic background


title: NC105.1-RFP vs. NC63.2-Cy3 at 16 h replicate 1

value: Mix of 0 h, 4 h, 8 h, 12 h, 16 h, and 20 h


title: irs_ND_6731_MA2_25548_2ndreplicate_wildtype_8weeks

description:
wildtype_8 weeks_2nd
BAC-Trap RNA


title: Normal (H081077N)


title: Normal (H090284N)


title: Tumor (H081003T)

value: No


title: irs_ND_6731_MA2_24811_3rdreplicate_CGG90Fmr1_8weeks

description:
L7CGG90Fmr1_8 weeks_3rd
BAC-Trap RNA

value: FMR1 mutant


title: Normal (H081003N)


title: NC105.1-RFP vs. NC105.1-Cy3 at 16 h replicate 2


title: NC105.1-RFP vs. NC63.2-Cy3 at 12 h replicate 2


title: Tumor (H080971T)


title: Testis_F1WP_ind234

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F1, indiv 234


title: irs_ND_6731_MA2_24810_2ndreplicate_CGG90Fmr1_8weeks

description:
L7CGG90Fmr1_8 weeks_2nd
BAC-Trap RNA


title: Tumor (H080939T)


title: irs_ND_6731_MA2_24809_1streplicate_CGG90Fmr1_8weeks

description:
L7CGG90Fmr1_8 weeks_1st
BAC-Trap RNA


title: Testis_F1PW_ind322

description: testis

source_name: Testis, PWD/PhJ dam x WSB/EiJ sire F1, indiv 322

value: PWD/PhJ dam x WSB/EiJ sire F1


title: Testis_F1PW_ind557

description: testis

source_name: Testis, PWD/PhJ dam x WSB/EiJ sire F1, indiv 557


title: NC105.1-RFP vs. NC105.1-Cy3 at 16 h replicate 1


title: irs_ND_6693_MA2_25554_2ndreplicate_wildtype_4weeks

description:
wildtype_4 weeks_2nd
BAC-Trap RNA

value: 4 weeks


title: NC105.1-RFP vs. NC105.1-Cy3 at 12 h replicate 2


title: irs_ND_6693_MA2_25555_3rdreplicate_wildtype_4weeks

description:
wildtype_4 weeks_3rd
BAC-Trap RNA


title: Normal (H080939N)

source_name: Liver


title: NC105.1-RFP vs. NC105.1-Cy3 at 12 h replicate 1

source_name: Mechanically disaggregated D. discoideum cells


title: Nasopharyngeal carcinoma NPC7D

description: Hybridized to 250K_Nsp

source_name: Nasopharyngeal carcinoma NPC7D

tag: tumor type

value: nasopharyngeal carcinoma

tag: tissue type

value: biopsy tissues

value: male

tag: age (yr)

tag: smoking  history

value: NO

tag: primary tumor size (t)

tag: regional lymph node (n)

value: IV


title: Normal (H080971N)

tag: tissue

value: liver


title: Tumor (H080931T)

tag: tumor size

tag: microvascular invasion

tag: early recurrence

value: Yes


title: NC105.1-RFP vs. NC63.2-Cy3 at 8 h replicate 1

source_name: Biological reference mixed from different time points

tag: strain

value: 8 h


title: Testis_F1PW_ind1207

description: testis

source_name: Testis, PWD/PhJ dam x WSB/EiJ sire F1, indiv 1207

value: testis


title: irs_ND_6693_MA2_25552_3rdreplicate_CGG90Fmr1_4weeks

description:
L7CGG90Fmr1_4 weeks_3rd
BAC-Trap RNA

value: cerebellum

value: Purkinje cells


title: irs_ND_6693_MA2_25553_1streplicate_wildtype_4weeks

description:
wildtype_4 weeks_1st
BAC-Trap RNA

value: 50% C57B6 and 50% FVB genetic background

value: wildtype


title: NC105.1-RFP vs. NC63.2-Cy3 at 8 h replicate 2

tag: time point

value: Mix of 0 h, 4 h, 8 h, 12 h, 16 h, and 20 h


title: Normal (H080931N)


title: Testis_F1PW_ind1204

description: testis

source_name: Testis, PWD/PhJ dam x WSB/EiJ sire F1, indiv 1204


title: Tumor (H080895T)

value: No

tag: edmondson-steiner histological grade

tag: fibrosis stage

tag: alpha-fetoprotein levels


title: Testis_F1PW_ind1206

description: testis

source_name: Testis, PWD/PhJ dam x WSB/EiJ sire F1, indiv 1206

value: PWD/PhJ dam x WSB/EiJ sire F1


title: irs_ND_6693_MA2_25551_2ndreplicate_CGG90Fmr1_4weeks

description:
L7CGG90Fmr1_4 weeks_2nd
BAC-Trap RNA

tag: genotype/variation

value: FMR1 mutant

tag: age

value: 4 weeks

tag: cell type


title: Normal (H080895N)


title: NC105.1-RFP vs. NC63.2-Cy3 at 4 h replicate 2

value: 4 h


title: NC105.1-RFP vs. NC105.1-Cy3 at 8 h replicate 2


title: Testis_F1PW_ind1205

description: testis

source_name: Testis, PWD/PhJ dam x WSB/EiJ sire F1, indiv 1205


title: NC105.1-RFP vs. NC105.1-Cy3 at 8 h replicate 1


title: C2C12 myoblast cell line - MYC transfected

city: Pieve Emanuele

first: Charlotte

middle: K Y

last: Ng

state: MI

address: Via Rita Montalcini 4

department: Biomedical Sciences

country: Italy

institute: Humanitas University

description: C2C12 myoblast cell line

hyb_protocol: According to manufacturer's instructions

data_processing: MAS5.0 method was used to process the data.

source_name: C2C12 myoblast cell line

growth_protocol: C2C12 cells were cultured in Dulbecco’s modified minimal essential medium (DMEM) supplemented with 10% fetal bovine serum (FBS) (Hyclone, Logan, UT, USA).

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

treatment_protocol: C2C12 mouse myoblast cells were introduced wild type MYOD1, MYOD1 L122R, MYC, and GFP by retroviral infection. For retrovirus production, the pcx4 and pBabe vectors system were used.  Retroviruses were obtained by using 293T cells as packaging cells, and were infected into C2C12 cell line and selected with 500 μg/ml Zeocin (Invitrogen, Carlsbad, CA, USA) for 1 week.

tag: cell line

tag: transfection

value: MYC transfected


title: irs_ND_6681_MA2_24808_3rdreplicate_CGG90Fmr1_12weeks

description:
L7CGG90Fmr1_12 weeks_3rd
BAC-Trap RNA

tag: replicate

value: 12 weeks


title: Tumor (H080854T)


title: NC105.1-RFP vs. NC63.2-Cy3 at 4 h replicate 1


title: NC105.1-RFP vs. NC63.2-Cy3 at 12 h replicate 1


title: Normal (H080854N)


title: irs_ND_6693_MA2_25550_1streplicate_CGG90Fmr1_4weeks

description:
L7CGG90Fmr1_4 weeks_1st
BAC-Trap RNA


title: C2C12 myoblast cell line - GFP transfected

description: C2C12 myoblast cell line

scan_protocol: According to manufacturer's instructions

value: GFP transfected


title: C2C12 myoblast cell line - MYOD1 L122R mutant transfected

description: C2C12 myoblast cell line

label_protocol: According to manufacturer's instructions

value: MYOD1 L122R mutant transfected


title: irs_ND_6681_MA2_24807_2ndreplicate_CGG90Fmr1_12weeks

description:
L7CGG90Fmr1_12 weeks_2nd
BAC-Trap RNA


title: irs_ND_6681_MA2_24806_1streplicate_CGG90Fmr1_12weeks

description:
L7CGG90Fmr1_12 weeks_1st
BAC-Trap RNA


title: irs_ND_6681_MA2_24446_3rdreplicate_wildtype_12weeks

description:
wildtype_12 weeks_3rd
BAC-Trap RNA


title: C2C12 myoblast cell line - wild-type MYOD1 transfected

description: C2C12 myoblast cell line

value: wild-type MYOD1 transfected


title: Tumor (H080775T)

value: liver


title: Normal (H080782N)


title: NC105.1-RFP vs. NC105.1-Cy3 at 4 h replicate 2


title: NC105.1-RFP vs. NC105.1-Cy3 at 4 h replicate 1


title: Normal (H080775N)


title: Tumor (H080774T)

value: Yes


title: NC105.1-RFP vs. NC63.2-Cy5 at 20 h replicate 2


title: C2C12 myoblast cell line - parental cells

description: C2C12 myoblast cell line

value: parental


title: irs_ND_6681_MA2_24445_2ndreplicate_wildtype_12weeks

description:
wildtype_12 weeks_2nd
BAC-Trap RNA

value: cerebellum

value: Purkinje cells


title: Tumor (H080782T)


title: Clinical Breast Cancer Specimen from disease free patient 207_disease.free

city: Milan

first: Maurizio

last: Callari

address: Via Amadeo, 42

institute: Fondazione IRCCS Istituto Nazionale dei Tumori

hyb_protocol: One μg of the biotinylated cRNA sample was mixed with the Hyb E1 hybridization buffer containing 37.5% (w/w) formamide and then hybridized at 58 °C overnight  to the HumanRef-6_v3 (Illumina, Inc, San Diego, CA)

scan_protocol: scanned with Illumina BeadArray Reader

data_processing: Microarray raw data where generated using the Illumina BeadStudio 3.8 software and processed using the lumi package of Bioconductor. After quality control, the Robust Spline Normalization was applied.

source_name: Clinical Breast Cancer Specimen

label_protocol: 800 ng of total RNA were reverse transcribed, labeled with biotin and amplified overnight using the Illumina RNA TotalPrep Amplification kit (Ambion, Austin, TX) according to manufacturer’s protocol

growth_protocol: Tissue samples collected at time of surgery were stored at -80°C until RNA extraction

extract_protocol: Tissue was pulverized using a Mikrodismembrator (Braun Biotech International , Germany). Total RNA was extracted with the Trizol reagent (Invitrogen, Carlsbad, CA) according to manufacture instructions and an additional DNase digestion was performed using the RNeasy kit (Qiagen, Valencia, CA).

tag: distant metastasis (0-none)

tag: dfs (months)

tag: age (y)

tag: histotype

value: CDI

tag: esr1 status (0-negative)

tag: erbb2 status (0-negative)

value: breast cancer specimen


title: Clinical Breast Cancer Specimen from patient developing distant metastasis 646_dev.meta

tag: tumor size

value: CLI

tag: tissue


title: NC105.1-RFP vs. NC63.2-Cy5 at 20 h replicate 1

tag: strain

tag: time point

value: Mix of 0 h, 4 h, 8 h, 12 h, 16 h, and 20 h


title: NC105.1-RFP vs. NC105.1-Cy5 at 20 h replicate 2


title: NC105.1-RFP vs. NC105.1-Cy5 at 20 h replicate 1


title: irs_ND_6681_MA2_24444_1streplicate_wildtype_12weeks

description:
wildtype_12 weeks_1st
BAC-Trap RNA

value: 50% C57B6 and 50% FVB genetic background

value: wildtype


title: Normal (H080774N)


title: Tumor (H080750T)

tag: microvascular invasion

value: No

tag: early recurrence

tag: edmondson-steiner histological grade

tag: fibrosis stage

tag: alpha-fetoprotein levels


title: Nasopharyngeal carcinoma NPC29F

description: Hybridized to 250K_Nsp

source_name: Nasopharyngeal carcinoma NPC29F

tag: tumor type

value: nasopharyngeal carcinoma

tag: tissue type

value: biopsy tissues

tag: gender

value: male

tag: age (yr)

tag: smoking  history

value: YES

tag: primary tumor size (t)

tag: regional lymph node (n)

tag: metastasis (m)

tag: clinical stage

value: IV


title: Clinical Breast Cancer Specimen from patient developing distant metastasis 690_dev.meta

tag: distant metastasis (0-none)

tag: dfs (months)

tag: age (y)

tag: tumor size

tag: histotype

tag: esr1 status (0-negative)

tag: erbb2 status (0-negative)

tag: tissue


title: Clinical Breast Cancer Specimen from patient developing distant metastasis 653_dev.meta


title: Clinical Breast Cancer Specimen from disease free patient 264_disease.free


title: NC105.1-RFP vs. NC63.2-Cy5 at 16 h replicate 2

tag: strain

tag: time point


title: 2BM_mock_CMP

city: Tokyo

first: Fumio

last: Nakahara

address: 4-6-1 Shirokanedai, Minato-ku

department: Division of Cellular Therapy, Advanced Clinical Research Center

country: Japan

institute: The Institute of Medical Science, The University of Tokyo

description: Gene expression data from mock transduced CMP

hyb_protocol: 10 micrograms of fragmented cRNA were hybridised (45degree CelsiusC, 16 hours). Hybridization was controled by use of the GeneChip Eukaryotic Hybridization Control Kit (Affymetrix). Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v4.

scan_protocol: Scanning was performed in an Affymetrix GeneChip scanner 3000 7G.

data_processing: Genechip analysis was performed using the Affymetrix GeneChip Operating Software v1.3. Signal value was calculated using MAS5 algorithm with target intensity=100.

source_name: mock transduced CMP

label_protocol: In vitro transcription was performed on 1 microgram of cDNA using the Enzo BioArray High Yield RNA transcript labelling kit (Enzo Diagnostics). The cRNA was cleaned using RNAeasy clean-up columns (Qiagen). The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.

growth_protocol: Iscove's modified Dulbecco's medium (IMDM) (Sigma-Aldrich) containing 20% FBS, 50 ng/mL mouse SCF, 20 ng/mL mouse TPO, and 20 ng/mL mouse IL-3, 20 ng/mL mouse IL-6 (all from R&D Systems) was used for culturing CMPs.

extract_protocol: Total RNA was extracted with RNeasy (QIAGEN) according to the manufacturers’ instructions. 3 micrograms of total RNA was reverse transcribed using the SuperScript III system for cDNA synthesis (Invitrogen) according to the protocol recommended by Affymetrix. The oligonucleotide used for priming was 5'-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3' (Invitrogen). Double-stranded cDNA was cleaned by phenol:chloroform extraction and the aqueous phase removed by centrifugation through Phase-lock Gel (Eppendorf).

treatment_protocol: Common myeloid progenitors (CMPs; Lineage negative, c-Kit positive, Sca-1 negative, Fc-gamma-receptor low, CD34 positive fraction) were sorted with a FACSAria cell sorter (Becton Dickinson). Retroviruses were generated by transfecting Plat-E packaging cells with retrovirus vector pMYs-Hes1-IRES-GFP or empty vector (pMYs-IRES-GFP) using FuGENE 6 (Roche Diagnostics). Infection of retrovirus harboring Hes1 (pMYs-Hes1-IRES-GFP) or empty vector (pMYs-IRES-GFP) into progenitors was performed using RetroNectin (Takara Bio).  One sample of Hes1-transfected CMPs and one sample of mock-transduced CMPs were analyzed with microarray. Hes1-transfected CMPs and Mock-transduced CMPs were isolated 36 hours after infection with a FACSAria cell sorter.

tag: cell type

value: common myeloid progenitor (CMP) from bone marrow

tag: transfection

value: empty vector (pMYs-IRES-GFP)


title: APL RATD subset, biological rep1

city: Shanghai

first: Jiang

last: Zhu

address: 197, rui-jin 2nd Road

country: China

institute: Shanghai institute of hematology

description: Gene expression data from ATRA-treated leukemia cells

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

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

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software (Agilent technologies, Santa Clara, CA, US).

source_name: Mouse APL bone marrow cells, treated with ATRA for 3-5 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: GFP positive APL cells were expanded in vivo through syngenic transplantation.

treatment_protocol: Once the repopulated GFP+ APL cells were detected in the peripheral blood of recipients, the bone marrow tissue was then treated with or without ATRA at the dose of 10mg/kg for 5 days before the bone marrow samples were collected.

value: ATRA treated bone marrow

tag: genotype

value: FVB N/J mice

tag: age

value: 8-10 weeks

value: APL RATD subset


title: 2BM_Hes1_CMP

description: Gene expression data from Hes1 transduced CMP

source_name: Hes1 transduced CMP

value: retrovirus vector pMYs-Hes1-IRES-GFP


title: NC105.1-RFP vs. NC105.1-Cy5 at 16 h replicate 2


title: Tumor (H080540T)

value: liver

tag: microvascular invasion

value: Yes

tag: early recurrence

tag: edmondson-steiner histological grade

tag: fibrosis stage

tag: alpha-fetoprotein levels


title: Clinical Breast Cancer Specimen from disease free patient 184_disease.free

tag: distant metastasis (0-none)

tag: dfs (months)

tag: age (y)

value: CDI

value: breast cancer specimen


title: APL RATD subset, biological rep2


title: Normal (H080540N)


title: Clinical Breast Cancer Specimen from patient developing distant metastasis 689_dev.meta

tag: tumor size

tag: histotype

tag: esr1 status (0-negative)


title: NC105.1-RFP vs. NC63.2-Cy5 at 16 h replicate 1

tag: strain

value: Mix of 0 h, 4 h, 8 h, 12 h, 16 h, and 20 h


title: APL TD subset, biological rep2

description: Gene expression data from spontaneously generated leukemia cells

source_name: Mouse APL bone marrow cells, untreated

tag: tissue

value: untreated bone marrow

value: APL TD subset


title: Clinical Breast Cancer Specimen from disease free patient 383_disease.free

tag: erbb2 status (0-negative)


title: Tumor (H080530T)

value: No


title: APL RAPD subset, biological rep2

tag: cell type

value: APL RAPD subset


title: Normal (H080530N)


title: NC105.1-RFP vs. NC63.2-Cy5 at 12 h replicate 1

tag: time point


title: NC105.1-RFP vs. NC105.1-Cy5 at 16 h replicate 1


title: NC105.1-RFP vs. NC63.2-Cy5 at 12 h replicate 2


title: Tumor (H080503T)


title: Clinical Breast Cancer Specimen from patient developing distant metastasis 676_dev.meta

value: CDI+CLI


title: Clinical Breast Cancer Specimen from disease free patient 215_disease.free


title: APL RAPD subset, biological rep1

tag: genotype

tag: age


title: Normal (H080503N)


title: APL PD subset, biological rep2

value: APL PD subset


title: NC105.1-RFP vs. NC105.1-Cy5 at 12 h replicate 2


title: Tumor (H080486T)

tag: microvascular invasion

tag: early recurrence


title: APL TD subset, biological rep1


title: NC105.1-RFP vs. NC105.1-Cy5 at 12 h replicate 1


title: Clinical Breast Cancer Specimen from disease free patient 147_disease.free


title: Normal (H080486N)


title: APL SC subset, biological rep2

value: APL SC subset


title: Clinical Breast Cancer Specimen from patient developing distant metastasis 693_dev.meta


title: NC105.1-RFP vs. NC63.2-Cy5 at 8 h replicate 2

value: 8 h


title: Tumor (H080411T)

tag: edmondson-steiner histological grade

tag: fibrosis stage


title: Clinical Breast Cancer Specimen from patient developing distant metastasis 630_dev.meta

tag: distant metastasis (0-none)


title: Clinical Breast Cancer Specimen from patient developing distant metastasis 650_dev.meta

tag: dfs (months)

value: CLI


title: APL PD subset, biological rep1

value: FVB N/J mice

value: 8-10 weeks


title: NC105.1-RFP vs. NC63.2-Cy5 at 8 h replicate 1


title: NC105.1-RFP vs. NC105.1-Cy5 at 8 h replicate 2


title: Normal (H080411N)


title: Clone C6_Dox replicate 3

city: Hannover

first: Adrian

last: Schwarzer

address: Carl-Neuberg-Str. 1

department: Experimental Hematology

institute: Hannover Medical School

description: Gene expression data from myeloid clone C6 under Doxycyclin

hyb_protocol: fragmented and biotin labeled cDNA was hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using an Affymetrix 3000 7G Scanner

data_processing: CEL files were background corrected, quantile normalized and summarized using the RMA package (Bioconductor). QC was performed with ArrayQualityMetrics (Bioconductor)

source_name: pRRL.TET.Evi1.IRES.EGFP myeloid clone C6 with Doxycyclin 1ug/ml

label_protocol: NuGen Encore Biotin labeling system (NuGEN Technologies)

growth_protocol: S3F11 medium:  murine stem cell factor (mSCF) 50 ng/ml, murine interleukin 3 (mIL-3) 20 ng/ml, human FMS like tyrosine kinase 3 ligand (hFlt-3) 50 ng/ml, and human interleukin 11 (hIL-11) 50 ng/ml

extract_protocol: Qiagen Rneasy Micro Kit followed by SPIA-cDNA amplification with Ovation Amplification System V2 (NuGEN Technologies, Bemmel, The Netherlands)

treatment_protocol: myeloid clone C6 cells cultured in S3F11 medium with or without Dox were pelleted and total RNA extracted with Qiagen Rneasy Micro Kit

tag: background strain

value: Rosa26rtTA C57BL/6J

value: hematopoietic progenitor clone C6


title: APL SC subset, biological rep1


title: NC105.1-RFP vs. NC105.1-Cy5 at 8 h replicate 1


title: Clinical Breast Cancer Specimen from disease free patient 352_disease.free

tag: age (y)

tag: tumor size


title: Clinical Breast Cancer Specimen from disease free patient 334_disease.free

tag: histotype

tag: esr1 status (0-negative)


title: Clinical Breast Cancer Specimen from patient developing distant metastasis 682_dev.meta

tag: tissue


title: Clone C6_Dox_Withdrawal replicate 3

description: Gene expression data from myeloid clone C6 48 hrs after Doxycyclin withdrawal

source_name: pRRL.TET.Evi1.IRES.EGFP myeloid clone C6 48hrs after Dox withdrawal


title: Clone C6_Dox replicate 1


title: Tumor (H080360T)

source_name: Liver

value: liver

value: Yes

tag: alpha-fetoprotein levels


title: Clone C6_Dox replicate 2

tag: cell type


title: NC105.1-RFP vs. NC63.2-Cy5 at 4 h replicate 2

source_name: Mechanically disaggregated D. discoideum cells

tag: strain

tag: time point

value: 4 h


title: NC105.1-RFP vs. NC63.2-Cy5 at 4 h replicate 1

value: Mix of 0 h, 4 h, 8 h, 12 h, 16 h, and 20 h


title: Normal (H080360N)


title: Tumor (H080357T)


title: Clinical Breast Cancer Specimen from patient developing distant metastasis 677_dev.meta

value: CDI

tag: erbb2 status (0-negative)

value: breast cancer specimen


title: Clinical Breast Cancer Specimen from patient developing distant metastasis 670_dev.meta


title: Tumor (H080217T)

tag: microvascular invasion


title: Normal (H080217N)


title: Clinical Breast Cancer Specimen from disease free patient 224_disease.free


title: Tumor (H080212T)

value: No

tag: early recurrence


title: NC105.1-RFP vs. NC28.1-Cy3 at 20 h replicate 1


title: Normal (H080357N)


title: NC105.1-RFP vs. NC105.1-Cy5 at 4 h replicate 1


title: MRC5 D30 HIF2a

city: Seattle

first: Hannele

last: Ruohola-Baker

state: Washington

address: 850 Republican

department: Biochemistry

institute: University of Washington

description: Reprogramming MRC5 cells infected with OSLN and HIF2α over-expression virus at day 30

hyb_protocol: 825 ng of both Cy3-labelled cRNA and Cy5-labelled cRNA (specific activity >8 pmol Cy3 or Cy5 per ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint Human GE 4x44K Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven using Agilent SureHyb-enabled hybridization chambers.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by compressed air.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using the Agilent-2Color scan setting for 4x44k arrays.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE2_107_Sep09 and Grid: 014850_D_F_20101031). Values in the HRB_Normalized_data.txt on the Series record are log2 transformed. We used normalize.qspline function in the affy Bioconductor package using R to process these data.

source_name: Fibroblasts MRC5

label_protocol: Cyanine-3 (Cy3) and cyanine-5 (Cy5) labeled cRNA was prepared from 200 ng total RNA using Agilent’s Low Input Quick Amp Two-Color Labeling Kit according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Reprogramming cells were cultured using the following condition: Dulbecco's modified Eagle's medium/Ham's F-12 medium (DMEM/F12) containing glutamax with 20% knockout serum replacer (SR), 1 mM sodium pyruvate, 0.1 mM nonessential amino acids, 50 U/mL penicillin, 50 μg/mL streptomycin (all from Invitrogen, Carlsbad, CA), 0.1 mM β-mercaptoethanol (Sigma- Aldrich, St. Louis, MO), and 4 ng/mL basic fibroblast growth factor (FGF; Peprotech, Rocky Hill, NJ). Cells were passaged using 1.2 U/mL dispase dissolved in phosphate- buffered saline (PBS) containing 20% knockout SR (all from Invitrogen)

extract_protocol: RNA was extracted from cells adherent on plates using Trizol reagent (Invitrogen)

treatment_protocol: On the day before the infection, MRC5 and IMR90 (ATCC) at passage 30-35 were seeded onto 0.1% Gelatin coated 35mm plate in DMEM media with 10% FBS (Invitrogen) and 1% Penicillin-Streptomycin (Invitrogen). On day 0, cells were infected with equal amount of Oct4, Sox2, Lin28 and Nanog lentivirus (OSLN, generated from Addgene constructs #21162 and 21163, Yu et al 2009) for 4-12 hours with 4ng/ml hexadimethrine bromide (Polybrene, Invitrogen). Alternatively (fig.1I), spin infection was performed at 3500rpm during 1h30 at 30oC and media was changed 12h later. On day 2, cells were transferred into 10cm plate for further expansion, and on day 6 cells were trypsinized and counted using nucleocounter (Chemometec). 4x104 cells were seeded on 35mm matrigel (BD Biosciences)-coated plate, or alternatively, 1.5x105 cells on 10cm matrigel-coated plate. hESC media was changed every other day from day 7 to the end of the reprogramming process. Empty vector or HIF2α over-expressing retroviruses were infected into fibroblasts using the same titer in the presence of Polybrene at 4 ng/ml (Invitrogen) together with OSLN on day 0. Medium was changed after 4-12 hours of infection. Other procedure after day 0 follow the same condition done in iPSC reprogramming process.

tag: cell line

tag: infection

value: OSLN and HIF2α over-expression

tag: day


title: Clone C6_Dox_Withdrawal replicate 1


title: Clinical Breast Cancer Specimen from disease free patient 400_disease.free

tag: distant metastasis (0-none)

tag: dfs (months)

value: other


title: Clinical Breast Cancer Specimen from disease free patient 141_disease.free

tag: age (y)


title: Clone C6_Dox_Withdrawal replicate 2

tag: background strain


title: NC105.1-RFP vs. NC28.1-Cy3 at 20 h replicate 2

source_name: Biological reference mixed from different time points


title: NC105.1-RFP vs. NC105.1-Cy3 at 20 h replicate 2


title: Clinical Breast Cancer Specimen from disease free patient 198_disease.free

tag: tumor size

tag: histotype

value: CDI+CLI


title: MRC5 D30 EV

description: Reprogramming MRC5 cells infected with OSLN and empty vector at day 30

value: OSLN and Empty Vector


title: IMR90 D30 HIF2a

description: Reprogramming IMR90 cells infected with OSLN and HIF2α over-expression virus at day 30

source_name: Fibroblasts IMR90


title: NC105.1-RFP vs. NC105.1-Cy3 at 20 h replicate 1


title: NC105.1-RFP vs. NC105.1-Cy5 at 4 h replicate 2


title: Normal (H080212N)

tag: tissue


title: Clinical Breast Cancer Specimen from disease free patient 398_disease.free

tag: esr1 status (0-negative)


title: IMR90 D12 HIF2a

description: Reprogramming IMR90 cells infected with OSLN and HIF2α over-expression virus at day 12


title: NC105.1-RFP vs. NC28.1-Cy3 at 16 h replicate 2


title: IMR90 D30 EV

description: Reprogramming IMR90 cells infected with OSLN and empty vector at day 30


title: IMR90 D12 EV

description: Reprogramming IMR90 cells infected with OSLN and empty vector at day 13


title: Tumor (H080204T)

tag: edmondson-steiner histological grade

tag: fibrosis stage

tag: alpha-fetoprotein levels


title: MRC5 D12 HIF2a

description: Reprogramming MRC5 cells infected with OSLN and HIF2α over-expression virus at day 12


title: Clinical Breast Cancer Specimen from disease free patient 303_disease.free

tag: erbb2 status (0-negative)


title: Normal (H080204N)


title: Clinical Breast Cancer Specimen from disease free patient 418_disease.free


title: Tumor (H080196T)

tag: microvascular invasion


title: NC105.1-RFP vs. NC28.1-Cy3 at 16 h replicate 1

tag: strain

tag: time point


title: NC105.1-RFP vs. NC105.1-Cy3 at 16 h replicate 2


title: Normal (H080174N)


title: Clinical Breast Cancer Specimen from disease free patient 415_disease.free


title: Normal (H080196N)


title: NC105.1-RFP vs. NC28.1-Cy3 at 12 h replicate 2


title: Normal (H080750N)


title: Tumor (H080174T)

tag: early recurrence


title: Clinical Breast Cancer Specimen from disease free patient 225_disease.free


title: Molt4 farnesol treated replicate 3

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression in Molt4 cells after treatment with farnesol.

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNA was fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data was obtained using the Agilent Feature Extraction software (v9.5), using the 1-color defaults for all parameters.

source_name: Molt4 cells treated with farnesol

label_protocol: Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

growth_protocol: Human T lymphoblastic leukemia Molt4-hyg  were provided by Dr. Y.A. Hannun (Department of Medicine, Duke University Medical Center, Durham, NC) and  cultured in RPMI-1640 medium supplemented with 10% heat-inactivated fetal bovine serum, 2 mM L-glutamine, penicillin, and streptomycin.

extract_protocol: RNA was isolated using Qiagen Rneasy midi or mini prep kits. RNA quality will be analyzed by agarose gel electrophoresis and by the Bioanalyzer.

treatment_protocol: Molt4 cells were treated with 75 uM farnesol (in DMSO) or vehicle for 4 hrs before RNA was isolated.

tag: cell line

tag: treatment

value: 75 uM farnesol


title: Molt4 farnesol treated replicate 2


title: NC105.1-RFP vs. NC28.1-Cy3 at 12 h replicate 1


title: Clinical Breast Cancer Specimen from disease free patient 340_disease.free

tag: distant metastasis (0-none)

tag: dfs (months)


title: NC105.1-RFP vs. NC105.1-Cy3 at 12 h replicate 2


title: Tumor (H080074T)


title: Clinical Breast Cancer Specimen from patient developing distant metastasis 692_dev.meta

tag: age (y)


title: Molt4 vehicle treated replicate 2

description: Gene expression in Molt4 cells after treatment with vehicles.

source_name: Molt4 cells treated with vehicle

value: vehicle


title: Molt4 vehicle treated replicate 3


title: Molt4 farnesol treated replicate 1


title: NC105.1-RFP vs. NC105.1-Cy3 at 12 h replicate 1


title: Normal (H080074N)


title: Clinical Breast Cancer Specimen from patient developing distant metastasis 610_dev.meta

tag: tumor size


title: MRC5 D12 EV

description: Reprogramming MRC5 cells infected with OSLN and empty vector at day 12

tag: infection

tag: day


title: Tumor (H080061T)

tag: tissue


title: Clinical Breast Cancer Specimen from patient developing distant metastasis 620_dev.meta

tag: histotype

value: CLI

tag: esr1 status (0-negative)


title: Normal (H080061N)


title: Clinical Breast Cancer Specimen from disease free patient 148_disease.free


title: Tumor (H080037T)

tag: edmondson-steiner histological grade

tag: fibrosis stage

tag: alpha-fetoprotein levels


title: Molt4 vehicle treated replicate 1


title: NC105.1-RFP vs. NC28.1-Cy3 at 8 h replicate 2

tag: strain

value: 8 h


title: E16 embryo_rep3

city: Paris

first: Matthias

last: Groszer

address: 17, rue du Fer à Moulin

department: Developmental Neuroscience

country: France

institute: INSERM U839

description:
miRNA expression in BPs at E16
E16_16_WT

hyb_protocol: After labeling samples were purified using MicroBioSin 6 column (Bio-Rad) according to manufacturer's protocol, then samples were completely dried using a vacuum concentrator at 45 to 55°C as per Agilent hybridization protocol, samples were then resuspended in 17 ul nuclease-free water; Agilent's miRNA Hyb Kit was used for hybridization sample preparation and manufacturer's protocol followed.  Agilent microRNA spike controls were also prepared using Spike-In kit (Agilent) and 1ul Hyb Spike-In solution (3rd Dilution) was added to each sample.  Samples were hybridized to Agilent mouse miRNA microarrays (V2) (G4472B) at 55°C for 20 hours in a rotating (20 rpm) Agilent Hybridization oven.  After hybridization, microarrays were washed 5 min. at room temperature with GE Wash Buffer 1 (Agilent) and 5 min. with 37°C GE Wash buffer 2 (Agilent). After wasing slides were scanned immediately.

scan_protocol: Immediately after washing slides were scanned on Agilent Microarray Scanner (G2505C) and the TIFF images extracted using the Agilent Feature Extraction software (version 10.7.3.1).

data_processing: The scanned images were analyzed by using Agilent Feature Extraction software (version 10.7.3.1) to obtain raw signal intensities.  After removing control probes, background substracted signal intensity (gBGSubSignal) for the detected probes (gIsWellAboveBG=1) were used for analysis.  Probes detected in one array and not in others were not considered during analysis; Further outlier probes were removed and data were quantile normalized (Bolstad BM et al., 2003).

source_name: Mouse embryonic cortex_E16 stage_replicate3

label_protocol: Cyanine-3 labeling was performed in 100ng of total RNA sample using Agilent's miRNA labeling kit following manufacturer's protocol.

extract_protocol: Total RNA was extracted from FACS isolated BPs by using mirVanaTM kit (Ambion) following manufacturer's protocol

tag: developmental stage

value: Brain cortex

tag: cell type

value: Basal progenitors


title: NC105.1-RFP vs. NC28.1-Cy3 at 8 h replicate 1

tag: time point


title: Normal (H080037N)

value: liver


title: E16 embryo_rep1

description:
miRNA expression in BPs at E16
E16_8_WT

source_name: Mouse embryonic cortex_E16 stage_replicate1


title: Clinical Breast Cancer Specimen from disease free patient 425_disease.free

source_name: Clinical Breast Cancer Specimen

tag: erbb2 status (0-negative)


title: Clinical Breast Cancer Specimen from patient developing distant metastasis 681_dev.meta

tag: distant metastasis (0-none)


title: NC105.1-RFP vs. NC105.1-Cy3 at 8 h replicate 1


title: Clinical Breast Cancer Specimen from disease free patient 205_disease.free

tag: dfs (months)


title: Tumor (H080025T)

tag: microvascular invasion

tag: early recurrence


title: E16 embryo_rep2

description:
miRNA expression in BPs at E16
E16_14_WT

source_name: Mouse embryonic cortex_E16 stage_replicate2


title: E16 embryo_rep4

description:
miRNA expression in BPs at E16
E16_94_WT

source_name: Mouse embryonic cortex_E16 stage_replicate4


title: E13 embryo_rep4

description:
miRNA expression in BPs at E13
E13_67_WT

source_name: Mouse embryonic cortex_E13 stage_replicate4


title: NC105.1-RFP vs. NC28.1-Cy3 at 4 h replicate 2


title: NC105.1-RFP vs. NC105.1-Cy3 at 16 h replicate 1


title: Normal (H080025N)


title: E13 embryo_rep3

description:
miRNA expression in BPs at E13
E13_66_WT

source_name: Mouse embryonic cortex_E13 stage_replicate3


title: NC105.1-RFP vs. NC105.1-Cy3 at 8 h replicate 2


title: Normal (H080015N)


title: Tumor (H072999T)

tag: tumor size


title: E13 embryo_rep2

description:
miRNA expression in BPs at E13
E13_62_WT

source_name: Mouse embryonic cortex_E13 stage_replicate2


title: NC105.1-RFP vs. NC28.1-Cy3 at 4 h replicate 1


title: Clinical Breast Cancer Specimen from patient developing distant metastasis 687_dev.meta

tag: age (y)


title: Clinical Breast Cancer Specimen from patient developing distant metastasis 649_dev.meta

tag: tissue


title: Clinical Breast Cancer Specimen from patient developing distant metastasis 662_dev.meta

tag: histotype


title: Normal (H072999N)


title: NC105.1-RFP vs. NC105.1-Cy3 at 4 h replicate 1


title: Clinical Breast Cancer Specimen from disease free patient 254_disease.free

tag: esr1 status (0-negative)


title: Tumor (H080015T)

value: Yes

tag: edmondson-steiner histological grade


title: Tumor (H072992T)

tag: fibrosis stage


title: Clinical Breast Cancer Specimen from disease free patient 260_disease.free


title: Normal (H072992N)


title: E13 embryo_rep1

description:
miRNA expression in BPs at E13
E13_55_WT

source_name: Mouse embryonic cortex_E13 stage_replicate1


title: Clinical Breast Cancer Specimen from disease free patient 463_disease.free


title: Clinical Breast Cancer Specimen from disease free patient 227_disease.free


title: NC105.1-RFP vs. NC28.1-Cy5 at 20 h replicate 2


title: NC105.1-RFP vs. NC105.1-Cy5 at 20 h replicate 2


title: Clinical Breast Cancer Specimen from disease free patient 330_disease.free


title: NC105.1-RFP vs. NC28.1-Cy5 at 16 h replicate 2


title: Tumor (H072969T)

tag: alpha-fetoprotein levels


title: NC105.1-RFP vs. NC28.1-Cy5 at 20 h replicate 1

tag: strain


title: Clinical Breast Cancer Specimen from patient developing distant metastasis 611_dev.meta


title: Normal (H072969N)


title: Tumor (H072961T)


title: NC105.1-RFP vs. NC28.1-Cy5 at 16 h replicate 1


title: NC105.1-RFP vs. NC105.1-Cy5 at 20 h replicate 1


title: Tumor (H072932T)


title: Normal (H072961N)


title: Normal (H072932N)


title: Tumor (H072926T)


title: NC105.1-RFP vs. NC105.1-Cy5 at 16 h replicate 1


title: NC105.1-RFP vs. NC105.1-Cy5 at 16 h replicate 2


title: Clinical Breast Cancer Specimen from patient developing distant metastasis 685_dev.meta


title: Clinical Breast Cancer Specimen from patient developing distant metastasis 674_dev.meta


title: NC105.1-RFP vs. NC105.1-Cy5 at 12 h replicate 2


title: Normal (H072926N)


title: NC105.1-RFP vs. NC105.1-Cy5 at 12 h replicate 1


title: NC105.1-RFP vs. NC28.1-Cy5 at 12 h replicate 1


title: NC105.1-RFP vs. NC28.1-Cy5 at 12 h replicate 2


title: Clinical Breast Cancer Specimen from disease free patient 312_disease.free


title: Clinical Breast Cancer Specimen from disease free patient 471_disease.free


title: NC105.1-RFP vs. NC28.1-Cy5 at 8 h replicate 2


title: Tumor (H072896T)


title: NC105.1-RFP vs. NC105.1-Cy3 at 4 h replicate 2

value: 4 h


title: Clinical Breast Cancer Specimen from disease free patient 344_disease.free


title: Clinical Breast Cancer Specimen from patient developing distant metastasis 688_dev.meta


title: Clinical Breast Cancer Specimen from disease free patient 408_disease.free


title: WT primary OBLs, biological rep 2

city: Rehovot

first: Omri

last: Bauer

address: Herzl

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

description: SAMPLE 4

hyb_protocol: 2ug ss cDNA in 80 ul total volume were hybridized to a Mouse Gene 1.0 ST array using Affymetrix hybridization kit materials and hybridized for 17 hours at 45° at 60rpm. Post-hyb washes were done with Affymetrix wash solutions on the FS450 station using FS450_0007 protocol.

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

data_processing: Data analysis was done using the Partek Genome Suite software (Partek Inc., St. Louis, Missouri 63141, http://www.partek.com), using RMA.

source_name: WT primary OBLs

label_protocol: 200ng TotalRNA were used for labeling. cDNA samples were generated and labeled using Affymetrix WT-cDNA synthesis and labeling kit

growth_protocol: OBL progenitor cells were isolated from neonatal mouse calvaria bone, according to standard protocol. Cells were then allowed to differentiate to OBLs in an osteogenic medium (containing ascorbate and glycerol phosphate) for 21 days (at 37°C/5% CO2). Medium was refreshed 3 times/week.

extract_protocol: Total RNA was isolated by PerfectPure RNA tissue kit (# 2302410, 5 PRIME, Germany) according to the manufacturer's instructions.

treatment_protocol: Comparison of OBLs extracted from Runx3fl/fl/Col1a1-cre and WT

tag: genotype/variation

value: wild type

tag: tissue origin

value: neonatal mouse calvaria bone

value: Myoblast

value: primary osteoblasts (OBLs)


title: NC105.1-RFP vs. NC28.1-Cy5 at 8 h replicate 1

tag: time point

value: Mix of 0 h, 4 h, 8 h, 12 h, 16 h, and 20 h


title: Runx3f/f/Col1a1-cre primary OBLs, biological rep 2

description: SAMPLE 3

source_name: Runx3f/f/Col1a1-cre primary OBLs

tag: cell type


title: WT primary OBLs, biological rep 1

description: SAMPLE 2


title: Normal (H072896N)

source_name: Liver


title: Clinical Breast Cancer Specimen from disease free patient 203_disease.free

tag: distant metastasis (0-none)

value: CDI

tag: erbb2 status (0-negative)

value: breast cancer specimen


title: Clinical Breast Cancer Specimen from patient developing distant metastasis 644_dev.meta

tag: dfs (months)


title: NC105.1-RFP vs. NC105.1-Cy5 at 8 h replicate 2

source_name: Mechanically disaggregated D. discoideum cells


title: IL-10-deficient liver DSS colitis 7 days rep 4

city: Charlestown

first: Bobby

last: Cherayil

state: Massachusetts

address: Building 114, 16th Street

department: Pediatrics

institute: Massachusetts General Hospital

description: IL10 KO DSS d

hyb_protocol: Following fragmentation, 5.5 micrograms of cDNA were hybridized for 16 hours at 45 degrees C on GeneChip Mouse 2.0 ST Array in an Affymetrix GeneChip hybridization oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G running Affymetrix Gene Command Console ver 3.2.

data_processing: The data was normalized by robust multichip analysis (RMA) using the Bioconductor package (v.2.12) in R (v.3.0.1).

label_protocol: Biotinylated cDNA was prepared according to the standard Affymetrix protocol from 0.1 micrograms of total RNA using amplification kit (Ambion WT Expression Kit, Lot #1210014), followed by labeling 5.5 micrograms of cDNA using Affymetrix WT Terminal Labelin Kit (Lot #4182035).

growth_protocol: Mice were maintained under specific pathogen-free conditions.

extract_protocol: Mice were euthanized on completion of 7 days of DSS treatment. At necropsy, segments of liver were excised and homogenized in Trizol reagent. Total RNA was prepared according to the manufacturer's guidelines.

treatment_protocol: The mice were given 3% DSS in their drinking water for 7 days to induce colitis.

tag: strain background

tag: gender

value: female

tag: age

value: 6 weeks

value: IL-10 knockout

tag: treated with

value: 3% dextran sulfate sodium (DSS) in the drinking water for 7 days


title: Normal (H072849N)

tag: tissue


title: NC105.1-RFP vs. NC105.1-Cy5 at 8 h replicate 1

value: 8 h

source_name: Biological reference mixed from different time points


title: Tumor (H072820T)

tag: tumor size

tag: microvascular invasion

value: No

tag: early recurrence


title: Clinical Breast Cancer Specimen from patient developing distant metastasis 661_dev.meta

tag: age (y)

tag: histotype

tag: esr1 status (0-negative)


title: Clinical Breast Cancer Specimen from patient developing distant metastasis 622_dev.meta


title: NC105.1-RFP vs. NC28.1-Cy5 at 4 h replicate 2

tag: strain


title: Tumor (H072849T)

tag: edmondson-steiner histological grade

tag: fibrosis stage

tag: alpha-fetoprotein levels


title: Runx3f/f/Col1a1-cre primary OBLs, biological rep 1

description: SAMPLE 1

tag: genotype/variation

tag: tissue origin

tag: cell type


title: Clinical Breast Cancer Specimen from disease free patient 144_disease.free

tag: distant metastasis (0-none)

tag: dfs (months)

tag: erbb2 status (0-negative)


title: Normal (H072820N)

tag: tissue


title: Tumor (H072813T)

tag: tumor size


title: IL-10-deficient liver DSS colitis 7 days rep 2

description: IL10 KO DSS b

tag: strain background

tag: gender

tag: age

tag: treated with


title: AML-54

city: Columbus

first: Ramiro

last: Garzon

address: 460 12th street

institute: Ohio State University

hyb_protocol: Labeled targets from 5 μg of total RNA was used for hybridization on each OSU-CCC  miRNA microarray custom version 3. All the probes on these microarrays are 40-mer oligonucleotides spotted by contacting technologies and covalently attached to a polymeric matrix. The microarrays were hybridized in 6× SSPE (0.9 M sodium chloride/60 mM sodium phosphate/8 mM EDTA, pH 7.4)/30% formamide at 25°C for 18 h, washed in 0.75× TNT (Tris·HCl/sodium chloride/Tween 20) at 37°C for 40 min, and processed by using direct detection of the biotin-containing transcripts by Streptavidin-Alexa647 conjugate

scan_protocol: Processed slides were scanned by using a PerkinElmer ScanArray XL5K Scanner with the laser set to 635 nm, at power 80 and PMT 70 settings, and a scan resolution of 10 μm.

data_processing: miRNA microarray images were analyzed using GENEPIX PRO. Average values of the replicate spots of each miRNA were background subtracted; log2-transformed and normalized using quantiles.

source_name: Bone marrow mononuclear cells

label_protocol: Five micrograms of total RNA were separately added to reaction mix in a final volume of 12 μl, containing 1 μg of [3′-(N)8-(A)12-biotin-(A)12-biotin-5′] oligonucleotide primer. The mixture was incubated for 10 min at 70°C and chilled on ice. With the mixture remaining on ice, 4 μl of 5× first-strand buffer, 2 μl of 0.1 M DTT, 1 μl of 10 mM dNTP mix, and 1 μl of SuperScript II RNaseH- reverse transcriptase (200 units/μl) was added to a final volume of 20 μl, and the mixture was incubated for 90 min in a 37°C water bath. After incubation for first-strand cDNA synthesis, 3.5 μl of 0.5 M NaOH/50 mM EDTA was added into 20 μl of first-strand reaction mix and incubated at 65°C for 15 min to denature the RNA/DNA hybrids and degrade RNA templates. Then, 5 μl of 1 M Tris·HCI (pH 7.6, Sigma) was added to neutralize the reaction mix, and labeled targets were stored in 28.5 μl at -80°C until chip hybridization.     Five micrograms of total RNA were separately added to reaction mix in a final volume of 12 μl, containing 1 μg of [3′-(N)8-(A)12-biotin-(A)12-biotin-5′] oligonucleotide primer. The mixture was incubated for 10 min at 70°C and chilled on ice. With the mixture remaining on ice, 4 μl of 5× first-strand buffer, 2 μl of 0.1 M DTT, 1 μl of 10 mM dNTP mix, and 1 μl of SuperScript II RNaseH- reverse transcriptase (200 units/μl) was added to a final volume of 20 μl, and the mixture was incubated for 90 min in a 37°C water bath. After incubation for first-strand cDNA synthesis, 3.5 μl of 0.5 M NaOH/50 mM EDTA was added into 20 μl of first-strand reaction mix and incubated at 65°C for 15 min to denature the RNA/DNA hybrids and degrade RNA templates. Then, 5 μl of 1 M Tris·HCI (pH 7.6, Sigma) was added to neutralize the reaction mix, and labeled targets were stored in 28.5 μl at -80°C until chip hybridization.

extract_protocol: Total RNA was extracted with Trizol  (Invitrogen) according to the manufacturer’s protocol.

tag: disease state

value: AML

tag: response

value: CR

tag: npm1 mutation

value: Positive

value: Bone marrow mononuclear cells


title: Clinical Breast Cancer Specimen from disease free patient 271_disease.free

tag: age (y)

tag: histotype

tag: esr1 status (0-negative)


title: NC105.1-RFP vs. NC28.1-Cy5 at 4 h replicate 1

tag: strain

tag: time point

value: 4 h


title: Normal (H072813N)

value: liver


title: AML-53

value: No CR

value: Negative

tag: cell type


title: IL-10-deficient liver DSS colitis 7 days rep 3

description: IL10 KO DSS c

tag: genotype/variation


title: Wild-type liver DSS colitis 7 days rep 4

description: WT DSS d

source_name: Wild-type liver DSS colitis 7 days

value: wild-type


title: AML-52


title: Clinical Breast Cancer Specimen from patient developing distant metastasis 694_dev.meta

tag: distant metastasis (0-none)

tag: dfs (months)

value: CDI

tag: erbb2 status (0-negative)


title: Tumor (H072777T)

tag: tissue

tag: tumor size

tag: microvascular invasion

tag: early recurrence

tag: edmondson-steiner histological grade

tag: fibrosis stage

tag: alpha-fetoprotein levels


title: NC105.1-RFP vs. NC105.1-Cy5 at 4 h replicate 2

value: Mix of 0 h, 4 h, 8 h, 12 h, 16 h, and 20 h


title: IL-10-deficient liver DSS colitis 7 days rep 1

description: IL10 KO DSS a

tag: strain background

tag: gender

value: female

tag: age

tag: treated with


title: Normal (H072777N)


title: Wild-type liver DSS colitis 7 days rep 3

description: WT DSS c

value: 6 weeks


title: Tumor (H072749T)

value: Yes


title: AML-51

tag: disease state

tag: response

tag: npm1 mutation


title: Clinical Breast Cancer Specimen from disease free patient 250_disease.free

tag: distant metastasis (0-none)

tag: age (y)

tag: histotype

value: CDI+CLI

tag: esr1 status (0-negative)

value: breast cancer specimen


title: Clinical Breast Cancer Specimen from patient developing distant metastasis 660_dev.meta

tag: dfs (months)

tag: tumor size

tag: erbb2 status (0-negative)

tag: tissue


title: AML-49

tag: cell type


title: AML-50


title: Normal (H072749N)


title: AML-48


title: Tumor (H072658T)

tag: microvascular invasion

value: No

tag: early recurrence

tag: edmondson-steiner histological grade

tag: fibrosis stage

tag: alpha-fetoprotein levels


title: NC105.1-RFP vs. NC105.1-Cy5 at 4 h replicate 1

tag: strain

tag: time point


title: Wild-type liver DSS colitis 7 days rep 2

description: WT DSS b

tag: strain background

tag: gender

tag: age

tag: genotype/variation

tag: treated with

value: 3% dextran sulfate sodium (DSS) in the drinking water for 7 days


title: Normal (H072658N)


title: Normal (H072623N)


title: Tumor (H072623T)


title: Wild-type liver DSS colitis 7 days rep 1

description: WT DSS a


title: Tumor (H072601T)


title: Clinical Breast Cancer Specimen from patient developing distant metastasis 672_dev.meta

tag: distant metastasis (0-none)

tag: dfs (months)

tag: age (y)

tag: histotype

tag: esr1 status (0-negative)


title: Clinical Breast Cancer Specimen from disease free patient 276_disease.free

tag: tumor size

tag: erbb2 status (0-negative)

tag: tissue


title: AML-43

tag: disease state

value: AML

tag: response

tag: npm1 mutation

tag: cell type


title: AML-44


title: AML-46

value: CR


title: AML-45

value: Bone marrow mononuclear cells


title: AML-47

value: Positive


title: Clinical Breast Cancer Specimen from disease free patient 152_disease.free


title: Clinical Breast Cancer Specimen from disease free patient 191_disease.free


title: Normal (H072601N)

value: liver


title: Tumor (H072543T)

tag: microvascular invasion

tag: early recurrence

tag: edmondson-steiner histological grade

tag: fibrosis stage

tag: alpha-fetoprotein levels


title: Clinical Breast Cancer Specimen from disease free patient 295_disease.free

tag: distant metastasis (0-none)

value: CLI


title: Clinical Breast Cancer Specimen from patient developing distant metastasis 671_dev.meta

tag: dfs (months)


title: AML-42


title: AML-41


title: Tumor (H072525T)


title: Normal (H072543N)


title: AML-40

value: Negative


title: Normal (H072525N)


title: AML-39

value: No CR


title: Clinical Breast Cancer Specimen from disease free patient 193_disease.free

tag: age (y)

value: CDI


title: Tumor (H072511T)


title: Clinical Breast Cancer Specimen from disease free patient 445_disease.free

tag: histotype


title: AML-38


title: Clinical Breast Cancer Specimen from patient developing distant metastasis 673_dev.meta

tag: esr1 status (0-negative)


title: Normal (H072511N)


title: AML-37


title: AML-36


title: Clinical Breast Cancer Specimen from patient developing distant metastasis 614_dev.meta

tag: tumor size


title: AML-35


title: Clinical Breast Cancer Specimen from patient developing distant metastasis 638_dev.meta

tag: erbb2 status (0-negative)


title: Clinical Breast Cancer Specimen from disease free patient 387_disease.free

tag: tissue


title: Clinical Breast Cancer Specimen from patient developing distant metastasis 686_dev.meta


title: Normal (H072447N)


title: AML-34

tag: disease state


title: Clinical Breast Cancer Specimen from disease free patient 128_disease.free


title: Tumor (H072441T)


title: Normal (H072441N)


title: AML-33

tag: response


title: Clinical Breast Cancer Specimen from patient developing distant metastasis 639_dev.meta


title: Clinical Breast Cancer Specimen from patient developing distant metastasis 640_dev.meta


title: Tumor (H072447T)


title: AML-32

tag: npm1 mutation


title: Tumor (H072059T)


title: Tumor (H072103T)


title: AML-31

tag: cell type


title: AML-30


title: AML-28


title: AML-29


title: Clinical Breast Cancer Specimen from disease free patient 310_disease.free


title: Tumor (H072056T)

tag: microvascular invasion


title: Clinical Breast Cancer Specimen from patient developing distant metastasis 618_dev.meta


title: Clinical Breast Cancer Specimen from patient developing distant metastasis 680_dev.meta


title: Normal (H072059N)


title: Clinical Breast Cancer Specimen from disease free patient 346_disease.free


title: Normal (H072056N)


title: AML-27


title: Tumor (H072032T)

tag: early recurrence


title: Normal (H072103N)


title: Clinical Breast Cancer Specimen from disease free patient 430_disease.free


title: AML-25


title: Clinical Breast Cancer Specimen from patient developing distant metastasis 612_dev.meta


title: AML-24


title: AML-26


title: Tumor (H072012T)

tag: edmondson-steiner histological grade


title: Normal (H072032N)


title: AML-23


title: Clinical Breast Cancer Specimen from patient developing distant metastasis 667_dev.meta


title: Clinical Breast Cancer Specimen from disease free patient 419_disease.free


title: Clinical Breast Cancer Specimen from patient developing distant metastasis 659_dev.meta


title: Clinical Breast Cancer Specimen from patient developing distant metastasis 647_dev.meta


title: Tumor (H071941T)

tag: fibrosis stage


title: Clinical Breast Cancer Specimen from patient developing distant metastasis 663_dev.meta


title: Normal (H071941N)


title: Tumor (H071904T)

tag: alpha-fetoprotein levels


title: AML-22


title: Clinical Breast Cancer Specimen from disease free patient 318_disease.free

tag: distant metastasis (0-none)


title: AML-21


title: AML-19


title: AML-20


title: Clinical Breast Cancer Specimen from patient developing distant metastasis 668_dev.meta

tag: dfs (months)


title: Tumor (H071899T)


title: Normal (H071904N)


title: Normal (H072012N)


title: Clinical Breast Cancer Specimen from disease free patient 98_disease.free

tag: age (y)

value: other


title: AML-18


title: Normal (H071899N)


title: AML-17


title: AML-15


title: AML-16


title: Normal (H071859N)


title: Tumor (H071859T)


title: Clinical Breast Cancer Specimen from disease free patient 232_disease.free

tag: histotype


title: Tumor (H071591T)


title: Clinical Breast Cancer Specimen from disease free patient 237_disease.free

tag: esr1 status (0-negative)


title: Clinical Breast Cancer Specimen from disease free patient 214_disease.free

tag: tumor size


title: AML-13


title: AML-14


title: Clinical Breast Cancer Specimen from patient developing distant metastasis 691_dev.meta

tag: erbb2 status (0-negative)


title: Tumor (H071380T)

tag: tissue


title: AML-12

tag: disease state


title: Clinical Breast Cancer Specimen from patient developing distant metastasis 656_dev.meta


title: Clinical Breast Cancer Specimen from patient developing distant metastasis 652_dev.meta


title: Normal (H071380N)


title: Tumor (H070599T)


title: AML-11

tag: response


title: AML-10

tag: npm1 mutation


title: Normal (H070599N)


title: AML-9

tag: cell type


title: Clinical Breast Cancer Specimen from patient developing distant metastasis 648_dev.meta


title: Tumor (H070487T)

tag: microvascular invasion


title: Clinical Breast Cancer Specimen from disease free patient 416_disease.free


title: Normal (H071591N)


title: Normal (H070487N)


title: Clinical Breast Cancer Specimen from disease free patient 158_disease.free


title: Clinical Breast Cancer Specimen from patient developing distant metastasis 617_dev.meta


title: Tumor (H062262T)

tag: early recurrence


title: Clinical Breast Cancer Specimen from patient developing distant metastasis 624_dev.meta


title: AML-7


title: AML-6


title: AML-8


title: Normal (H062262N)


title: Clinical Breast Cancer Specimen from patient developing distant metastasis 678_dev.meta


title: Normal (H062024N)


title: Clinical Breast Cancer Specimen from disease free patient 350_disease.free


title: Clinical Breast Cancer Specimen from patient developing distant metastasis 654_dev.meta


title: Clinical Breast Cancer Specimen from disease free patient 450_disease.free


title: Clinical Breast Cancer Specimen from disease free patient 361_disease.free


title: Tumor (H061840T)

tag: edmondson-steiner histological grade


title: Tumor (H062024T)

tag: fibrosis stage


title: AML-5


title: AML-4


title: AML-3


title: Normal (H061840N)


title: AML-2


title: Clinical Breast Cancer Specimen from patient developing distant metastasis 655_dev.meta


title: Tumor (H061464T)

tag: alpha-fetoprotein levels


title: Clinical Breast Cancer Specimen from disease free patient 137_disease.free

tag: distant metastasis (0-none)


title: Clinical Breast Cancer Specimen from disease free patient 455_disease.free

tag: dfs (months)


title: Normal (H061464N)


title: Tumor (H061394T)


title: Normal (H061394N)


title: Treatment 4th group Replicate 3

first: Changquan

last: Ling

state: Shanghai

address: No. 800,Xiangyin Road

department: Department of Traditional Chinese Medicine

institute: Second Military Medical University

description: Biological replicate 3 of 3. HepG2 cells, treated with 200 nM triptolide for 24 h, harvested after several passages.

hyb_protocol: After stopping the labeling procedure, the Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.16.0) (Exiqon) according to array manual. The total 25 μL mixture from Hy3TM-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min and then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA), which provides an active mixing action and constant incubation temperature to improve hybridization uniformity and enhance signal. Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon), and finally dried by centrifugation for 5 min at 400 rpm. Then the slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>50 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, differentially expressed miRNAs were identified through Fold Change filtering. Hierarchical clustering was performed using MEV software (v4.6, TIGR).

source_name: HepG2  human hepatocellular carcinoma cells

label_protocol: One microgram of each sample was 3'-end-labeled with Hy3TM fluorescent label, using T4 RNA ligase by the following procedure: RNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C, and was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture. The labeling reaction was incubated for 1 h at 16°C, and terminated by incubation for 15 min at 65°C.

growth_protocol: The cells were grown in Dulbecco’s Modified Eagle Medium (Gibco BRL) with 10% fetal bovine serum (Gibco BRL) and were maintained in an atmosphere of 5% CO2 in a humidified 37 °C incubator.

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

tag: cell line

tag: cell passage

value: human hepatocellular carcinoma cells

tag: treatment

value: Triptolide 200 nM 24 h


title: Clinical Breast Cancer Specimen from disease free patient 327_disease.free

tag: age (y)

tag: tumor size

tag: histotype

tag: esr1 status (0-negative)


title: Treatment 4th group Replicate 2

description: Biological replicate 2 of 3. HepG2 cells, treated with 200 nM triptolide for 24 h, harvested after several passages.

scan_protocol: Then the slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).


title: AML-1

tag: disease state

tag: response


title: Tumor (H061350T)

first: Farhan

last: Haq

address: 7-45, Songdo-dong, Yeonsu-gu

institute: Gachon University

hyb_protocol: Samples passing these QC steps were next end-labeled with a biotinylated nucleoitde using Terminal Deoxynucleotidyl Transferase (TdT). The end-labeled products were added to a hybridization solution, denatured, and added to a CytoScan™ HD Array (one array per sample).

scan_protocol: After hybridization was complete, the DNA sample was removed from each microarray and replaced with Array Holding Buffer. Arrays were then washed on the Fluidics Station 450 using AGCC software (Affymetrix GeneChip® Command Console, Version 3.2.2) This protocol includes 6 cycles of 5 mixes/cycle with low stringency Wash Buffer A (6X SSPE, 0.01% Tween-20) at 25℃ followed by 24 cycles of 5 mixes/cycle with high stringency Wash Buffer B (0.6X SSPE, 0.01% Tween-20) at 45℃. Binding of the biotinylated targets was detected by incubating the array for 10 min in a Streptavidin–Phycoerythrin (SAPE) solution at 25℃ followed by a post stain wash comprised of 6 cycles of 5 mixes/cycle with Wash Buffer A at 25℃. A second round of staining was then completed using a 10 min incubation in Anti-Streptavidin Antibody Stain Solution at 25℃ followed by a third stain for 10 min in SAPE solution at 25℃ and a final wash consisting of 10 cycles of 6 mixes/cycle with Wash Buffer A at 30℃, filling of the array with Array Holding Buffer, and a hold at 25℃.

data_processing: CNV analysis was performed using the Affymetrix Cytoscan HD platform (CEL files). CNV data were analysed with the Nexus Copy Number software (BioDiscovery, CA, ver. 6.1).

tag: tissue


title: Clinical Breast Cancer Specimen from patient developing distant metastasis 629_dev.meta

tag: erbb2 status (0-negative)


title: Normal (H061350N)


title: Treatment 3rd group Replicate 3

description: Biological replicate 3 of 3. HepG2 cells, treated with 200 nM triptolide for 12 h, harvested after several passages.

tag: cell type

value: Triptolide 100 nM 24 h


title: Treatment 3rd group Replicate 2

description: Biological replicate 2 of 3. HepG2 cells, treated with 200 nM triptolide for 12 h, harvested after several passages.


title: Treatment 4th group Replicate 1

description: Biological replicate 1 of 3. HepG2 cells, treated with 200 nM triptolide for 24 h, harvested after several passages.


title: Treatment 2nd group Replicate 3

description: Biological replicate 3 of 3. HepG2 cells, treated with 100 nM triptolide for 24 h, harvested after several passages.

value: Triptolide 200 nM 12 h


title: Clinical Breast Cancer Specimen from patient developing distant metastasis 675_dev.meta

value: breast cancer specimen


title: Clinical Breast Cancer Specimen from patient developing distant metastasis 651_dev.meta


title: Clinical Breast Cancer Specimen from disease free patient 230_disease.free


title: Clinical Breast Cancer Specimen from disease free patient 268_disease.free


title: Tumor (H061195T)

tag: microvascular invasion

value: No

tag: early recurrence

tag: edmondson-steiner histological grade


title: Tumor (H061142T)

tag: fibrosis stage

tag: alpha-fetoprotein levels


title: Normal (H061195N)


title: Normal (H061142N)


title: Tumor (H061095T)

value: Yes


title: Normal (H061095N)


title: Clinical Breast Cancer Specimen from patient developing distant metastasis 637_dev.meta

tag: distant metastasis (0-none)

tag: dfs (months)


title: Treatment 1st group Replicate 2

description: Biological replicate 2 of 3. HepG2 cells, treated with 100 nM triptolide for 12 h, harvested after several passages.

tag: cell line

tag: cell passage

tag: treatment

value: Triptolide 100 nM 12 h


title: Treatment 1st group Replicate 1

description: Biological replicate 1 of 3. HepG2 cells, treated with 100 nM triptolide for 12 h, harvested after several passages.


title: Treatment 2nd group Replicate 2

description: Biological replicate 2 of 3. HepG2 cells, treated with 100 nM triptolide for 24 h, harvested after several passages.


title: Clinical Breast Cancer Specimen from patient developing distant metastasis 635_dev.meta

tag: age (y)

tag: tumor size

tag: histotype


title: Clinical Breast Cancer Specimen from disease free patient 477_disease.free

tag: esr1 status (0-negative)


title: Control group Replicate 3

description: Biological replicate 3 of 3. Control HepG2 cells, untreated, harvested after several passages.


title: Clinical Breast Cancer Specimen from disease free patient 223_disease.free

tag: tissue


title: Clinical Breast Cancer Specimen from patient developing distant metastasis 684_dev.meta

tag: erbb2 status (0-negative)


title: Tumor (H061039T)


title: Clinical Breast Cancer Specimen from patient developing distant metastasis 645_dev.meta


title: Control group Replicate 1

description: Biological replicate 1 of 3. Control HepG2 cells, untreated, harvested after several passages.

tag: cell type


title: Treatment 1st group Replicate 3

description: Biological replicate 3 of 3. HepG2 cells, treated with 100 nM triptolide for 12 h, harvested after several passages.


title: Normal (H060877N)


title: Control group Replicate 2

description: Biological replicate 2 of 3. Control HepG2 cells, untreated, harvested after several passages.


title: Normal (H061039N)


title: Tumor (H060877T)

tag: microvascular invasion


title: Tumor (H060891T)

tag: early recurrence


title: Tumor (H060859T)

tag: edmondson-steiner histological grade


title: Tumor (H060795T)

tag: fibrosis stage


title: Normal (H060859N)


title: Normal (H060795N)


title: Normal (H060891N)


title: T_cells_rep2

city: Jouy en Josas

first: pierre

last: Sibille

address: domaine de Vilvert, bât 440

department: Virologie et Immunologie Moléculaires

institute: INRA

hyb_protocol: Complementary RNA (cRNA) samples were linearly amplified and labeled with cyanine 3 starting from 12 to 50 ng of total RNA. Following fragmentation, labeled cRNA were hybridized on Agilent “SurePrint G3 Chicken Custom Gene Expression 8x60K Microarray” (Design ID 038072), for 17 hrs, at 65°C under 10 rpm.

scan_protocol: slides were scanned using an Agilent G2565CA microarray Scanner System, at a 3 µm resolution in a 20-bit scan mode, according to the “AgilentG3_GX_1Color” protocol

data_processing: Raw gene expression data were background corrected using the normexp method and quantile normalized with the limma package through Bioconductor in the R statistical environment (version 2.15.0). Independent biological triplicates (B cells) and quadruplicates (cDC, MP and T cells) were performed by using cells isolated from 4 different animals. Quality control of the expression data was assessed by boxplots of raw expression data, density plots of normalized data, scatter plots and calculation of the Pearson's correlation coefficients between arrays, using the Ringo package.

organism: Gallus gallus

label_protocol: RNA labeling was performed using the one-color Low Input Quick Amp Labeling kit (Agilent Technologies) following the manufacturer’s recommendations. Each RNA sample (50 ng) was amplified and cyanin 3 (Cy3) -labelled, and subsequently the complementary RNA (cRNA) was checked for quality on Nanodrop and Agilent 2100 Bioanalyzer.

extract_protocol: When insufficient total RNA amounts for hydridization was obtained (< 50 ng), the RNA from the sorted subsets of distinct spleen pools were mixed

treatment_protocol: Spleen from 4 different exsanguinated chicken were used for cell isolation. Spleens were crushed on stainless steel mesh, and cell suspension was digested with DNAse / Collagenase D before 1.077 histopaque gradient centrifugation. Four populations were separated according to cell surface staining : B and T cells were respectively labeled with 2 µg/ml phycoerythrin (PE)-conjugated anti Bu-1 AV20 monoclonal antibody (mAb) and PE-conjugated anti chicken CD3 CT-3 mAb respectively; macrophage population (MP) was sorted after labelling with 2 µg/ml PE-conjugated KUL01 mAb ; for cDC candidate cell sorting, splenocytes were first stained with the 8F2 hybridoma cell supernatant directed to the putative chicken CD11c, followed by 50 µg/ml Alexa647-conjugated goat anti-mouse Fab (Jackson Immuno Research), and subsequently reacted with a cocktail of FITC -conjugated mAb anti chicken MHC-II, PE -conjugated KUL01, anti Bu-1, and anti CD3 mAbs. Putative cDCs were sorted as 8F2+, MHC-II+, KUL01-, BU-1-, CD3- cells. Hybridizations were performed at the Platform Biopuces et Séquençage (IGBMC, 67400 Illkirch, France, http://www.igbmc.fr/grandesstructures/cbi/).

tag: gender

value: female

value: spleen

value: spleen mononuclear cells

tag: cell subtype

value: T cells

tag: fluorescence sorted cell population


title: T_cells_rep4


title: T_cells_rep3


title: Tumor (H060776T)

city: Incheon

label_protocol: The end-labeled products were added to a hybridization solution, denatured, and added to a CytoScan™ HD Array (one array per sample).

extract_protocol: Each DNA (250ng gDNA) aliquot was 96 well plate. Then, 24 of the samples on a plate were subjected to treatment with Nsp I restriction enzyme. After inactivation of the restriction enzyme, the sticky ends of the digested DNA were ligated to Nsp I adaptor/primers using T4 ligase. Aliquots from each ligated product were added to four separate plates for PCR amplification using a universal primer. The products of all four PCR reactions for each subject were combined and then purified with purification magnetic beads in 1.5ml microtube. The yield of each amplified DNA sample was assessed by UV spectrophotometry on a microplate reader. Any DNA showing lower than expected yield (≥ 3mg/ml) or an unusual size distribution was flagged and not processed further. Subsequently, each DNA was fragmented between 25 to 125 bp using partial DNase I digestion and the size distribution of the fragmented amplicons assessed by agarose gel electrophoresis (4% agarose in Tris-Acetate-EDTA buffer).

value: liver

tag: alpha-fetoprotein levels


title: Clinical Breast Cancer Specimen from disease free patient 213_disease.free

tag: distant metastasis (0-none)

tag: dfs (months)


title: Dendritic-cells_rep1

source_name: Dendritic-cells

value: putative conventional Dendritic cells

value: CD3- Bu-1-, KUL01-, MHCII+, 8F2+(putative CD11c)


title: macrophages_rep4

source_name: macrophages

value: macrophage spleen population


title: Normal (H060776N)


title: macrophages_rep1


title: macrophages_rep2


title: T_cells_rep1


title: Tumor (H060690T)


title: B_cells_rep2

value: control B cells


title: B_cells_rep4


title: Dendritic-cells_rep3


title: B_cells_rep1


title: Tumor (H060674T)


title: macrophages_rep3


title: Normal (H060674N)


title: Dendritic-cells_rep2


title: Tumor (H060670T)


title: Normal (H060690N)


title: Tumor (H060664T)


title: Normal (H060664N)


title: Tumor (H060638T)


title: Normal (H060638N)


title: Normal (H060617N)


title: Normal (H060670N)


title: 48h_P_X1(2)

city: Evanston

first: Christian

middle: Paul

last: Petersen

state: IL

address: 2205 Tech Drive, Hogan 2-100

department: Molecular Biosciences

institute: Northwestern University

description: Gene expression in neoblasts after 48h tail regeneration

hyb_protocol: Hybridizations were performed according to manufacturerer's protocol

scan_protocol: Scan was performed according to manufacturer's protocol

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Schmidtea mediterranea

source_name: X1 neoblasts, posterior-facing wounds, 48h regeneration, replicate 2

label_protocol: WTA2 whole genome amplification (Sigma) followed by Kreatech labeling with Cy5

growth_protocol: Asexual planarians, strain CIW4 Schmidtea mediterranea, were cultured at 19 degrees in 1x planarian water after amputation of heads and tails.

extract_protocol: RNA was extracted in trizol followed by purification of the aqueous phase using RNAeasy kits. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer

treatment_protocol: Tissues ~200 microns from amputation sites were diced and mascerated in 1xCMF (calcium-magnesium free media) with collagenase, labeled with Hoechst dye and propidium iodide, and FACS sorted as the population of G2/S/M cells of high DNA content

tag: strain

value: neoblasts

tag: regeneration type

value: tail


title: 24h_P_X1(3)

description: Gene expression in neoblasts after 24h tail regeneration

source_name: X1 neoblasts, posterior-facing wounds, 24h regeneration, replicate 3


title: 48h_P_X1(1)

source_name: X1 neoblasts, posterior-facing wounds, 48h regeneration, replicate 1


title: BXPC3_DDR1shRNA_rep3

city: Santa Monica

first: Mike

last: Mattie

state: CA

address: 1800 Stewart Street

department: Applied Molecular Biology

institute: Agensys Inc

description: Gene expression

hyb_protocol: 1650 ng of labeled cRNA was fragmented by incubation with 10 µl of 10X Blocking Reagent and 25X Fragmentation Buffer in a 50 µl reaction volume for 30 minutes at 65 °C. 50 µl of 2X GE Hybridization Buffer HI-RPM was added to fragmented cRNA and hybridization mixes then placed onto Agilent Human GE 4X44K v2 microarrays. Hybridization was done for 17 hours at 65 °C by rotating at 10 rpm. Microarray slides were washed in GE Wash Buffer 1 for 2 minutes and pre-warmed GE Wash Buffer 2 for 2 minutes at room temperature.

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

data_processing: The scanned images were analyzed with Feature Extraction Software 10 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: BXPC3 DDR1 shRNA, replicate 3

label_protocol: Cyanine 3-CTP labeled cRNA target was prepared using One-Color Low Input Quick Amp kit and One Color Spike-In kit (Agilent Technologies) using 200 ng input RNA (RIN>8.0) according to manufacturer protocols.  Labeled cRNA was purified using RNeasy Mini kit (QIAGEN) according to manufacturer recommendation.  Labeled cRNA was quantified on a NanoDrop ND-1000 UV Spectrophotometer using Microarray/RNA-40 measurement.  Specific activity of Cyanine 3 was calculated in pmol /µg with a minimum threshold of 15 pmol/µg.

growth_protocol: BXPC3 cell lines were plated at 2 million cells/10 cm dish in triplicate and grown RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum.   The cultures were incubated for 72 hours at 37 ºC in a humidified incubator with 5% CO2 prior to harvest for RNA isolation.

extract_protocol: Total RNA was isolated from cells with TRIzol Reagent (Life Technologies, Carlsbad, USA) according to manufacturer protocol.  RNA was digested with DNase I-Amp Grade (Life Technologies) on-column and purified using an RNeasy Mini kit (QIAGEN, Valencia, USA) according to manufacturer protocols.  RNA quality and quantification were performed by analyzing RNA in RNA Nano 6000 chips in a Bioanalyzer2100 following manufacturer protocol (Agilent Technologies, Santa Clara, USA).

value: Pancreatic cancer cell line


title: BXPC3_DDR1shRNA_rep1

description: Gene expression

source_name: BXPC3 DDR1 shRNA, replicate 1


title: BXPC3_NTshRNA_rep2

description: Gene expression

source_name: BXPC3 NT shRNA, replicate 2


title: 72h_P_X1(2)

description: Gene expression in neoblasts after 72h tail regeneration

source_name: X1 neoblasts, posterior-facing wounds, 72h regeneration, replicate 2


title: 0h_P_X1(3)

description: Gene expression in neoblasts after 0h tail regeneration

source_name: X1 neoblasts, posterior-facing wounds, 0h regeneration, replicate 3


title: 72h_P_X1(1)

source_name: X1 neoblasts, posterior-facing wounds, 72h regeneration, replicate 1


title: BXPC3_DDR1shRNA_rep2

description: Gene expression

source_name: BXPC3 DDR1 shRNA, replicate 2


title: BXPC3_NTshRNA_rep1

description: Gene expression

source_name: BXPC3 NT shRNA, replicate 1


title: BXPC3_Parental_rep3

description: Gene expression

source_name: BXPC3 parental, replicate 3


title: 24h_P_X1(1)

source_name: X1 neoblasts, posterior-facing wounds, 24h regeneration, replicate 1


title: 0h_P_X1(2)

source_name: X1 neoblasts, posterior-facing wounds, 0h regeneration, replicate 2


title: 72h_P_X1(3)

source_name: X1 neoblasts, posterior-facing wounds, 72h regeneration, replicate 3


title: BXPC3_NTshRNA_rep3

description: Gene expression

source_name: BXPC3 NT shRNA, replicate 3


title: Tumor (H060616T)

source_name: Liver

tag: tumor size


title: 24h_P_X1(2)

source_name: X1 neoblasts, posterior-facing wounds, 24h regeneration, replicate 2


title: 0h_P_X1(1)

source_name: X1 neoblasts, posterior-facing wounds, 0h regeneration, replicate 1


title: Normal (H060616N)


title: 72h_A_72(3)

description: Gene expression in neoblasts after 72h head regeneration

source_name: X1 neoblasts, anterior-facing wounds, 72h regeneration, replicate 3

value: head


title: Tumor (H060607T)


title: 48h_P_X1(3)

source_name: X1 neoblasts, posterior-facing wounds, 48h regeneration, replicate 3


title: 72h_A_X1(2)

source_name: X1 neoblasts, anterior-facing wounds, 72h regeneration, replicate 2


title: Normal (H060607N)


title: Tumor (H060566T)


title: Normal (H060566N)


title: Tumor (H060555T)


title: Treatment 3rd group Replicate 1

description: Biological replicate 1 of 3. HepG2 cells, treated with 200 nM triptolide for 12 h, harvested after several passages.

source_name: HepG2  human hepatocellular carcinoma cells

tag: cell line

tag: cell passage

value: human hepatocellular carcinoma cells

tag: treatment

value: Triptolide 100 nM 24 h


title: Tumor (H060515T)

tag: tissue

value: No


title: Normal (H060515N)


title: Treatment 2nd group Replicate 1

description: Biological replicate 1 of 3. HepG2 cells, treated with 100 nM triptolide for 24 h, harvested after several passages.

tag: cell type

value: Triptolide 200 nM 12 h


title: Tumor (H060509T)

tag: microvascular invasion

tag: early recurrence

value: Yes


title: 72h_A_X1(1)

source_name: X1 neoblasts, anterior-facing wounds, 72h regeneration, replicate 1


title: 48h_A_X1(3)

description: Gene expression in neoblasts after 48h head regeneration

source_name: X1 neoblasts, anterior-facing wounds, 48h regeneration, replicate 3


title: Weaned piglets' jejunum Replicate 3

first: Lihui

address: 800 Dongchuang Road

department: School of Agriculture and Biology

institute: Shanghai Jiaotong University

description:
Gene expression in 25d old weaned piglet's jejunum
Weaned-rep3

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions

scan_protocol: Slides were scanned by Agilent Microarray Scanner (G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

organism: Sus scrofa

source_name: Weaned piglets' jejunum

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit (Agilent technologies), following the manufacturer’s instructions. Cy3 was used to label the samples from the control sucking individuals and the weaned animals.

growth_protocol: A total of fourty 21-d old pigs (Duroc × Landrace) from 4 litters (10 piglets per litter) were assigned randomly to control (suckling) and weaning groups on the basis of their litter origins (n = 20/ group). Piglets in control group continued to be nursed by sows, whereas piglets in weaning group were weaned and moved from the farrowing pens to nursery pens without mixing any litters (5 piglets per pen), and had ad libitum access to the basal diet and water with 14.48 MJ/kg DE and 20.50% CP (N × 6.25).

extract_protocol: Total RNA of jejunum tissues was extracted following the Trizol Reagent instructions (Invitrogen), and checked for a RNA integrity number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies).Qualified total RNA was further purified by RNeasy mini kit (Qiagen) and RNase-Free DNase Set (Qiagen). Only those samples that had an OD260/OD280 ratio of approximately 2.0 and showed no degradation (RNA integrity number ≥ 7.0) were used to generate labeled targets.

treatment_protocol: At 25 d of age, 1 piglet closed to the average weight was randomly chosen from each litter, resulting in 4 piglets per treatment. Animals were then anesthetized by intramuscular injection of sodium pentobarbital (50 mg/kg BW) and then euthanized. Jejunal samples, approximately 2 cm in length, were resected from the middle portion of the jejunum, washed in PBS, and frozen in liquid N2 and stored at - 80°C before used for the isolation of total RNA.

value: jejunum

tag: age

value: day 25

tag: protocol

value: weaned


title: Control suckling piglets' jejunum Replicate 4

description:
Gene expression in 25d old suckling piglet's jejunum
Control-rep4

source_name: Control suckling piglets' jejunum

value: control


title: Normal (H060509N)

value: liver


title: Normal (H060555N)


title: 48h_A_X1(2)

source_name: X1 neoblasts, anterior-facing wounds, 48h regeneration, replicate 2


title: Weaned piglets' jejunum Replicate 4

description:
Gene expression in 25d old weaned piglet's jejunum
Weaned-rep4


title: 24h_A_X1(2)

description: Gene expression in neoblasts after 24h head regeneration

source_name: X1 neoblasts, anterior-facing wounds, 24h regeneration, replicate 2


title: Control suckling piglets' jejunum Replicate 3

description:
Gene expression in 25d old suckling piglet's jejunum
Control-rep3


title: 24h_A_X1(1)

source_name: X1 neoblasts, anterior-facing wounds, 24h regeneration, replicate 1


title: Tumor (H060417T)

tag: edmondson-steiner histological grade

tag: fibrosis stage


title: 24h_A_X1(3)

source_name: X1 neoblasts, anterior-facing wounds, 24h regeneration, replicate 3


title: BXPC3_Parental_rep2

description: Gene expression

source_name: BXPC3 parental, replicate 2


title: Weaned piglets' jejunum Replicate 1

description:
Gene expression in 25d old weaned piglet's jejunum
Weaned-rep1


title: Control suckling piglets' jejunum Replicate 1

description:
Gene expression in 25d old suckling piglet's jejunum
Control-rep1


title: BXPC3_Parental_rep1

description: Gene expression

source_name: BXPC3 parental, replicate 1


title: Control suckling piglets' jejunum Replicate 2

description:
Gene expression in 25d old suckling piglet's jejunum
Control-rep2


title: HeLa cells 6

first: Suk Min

last: JANG

address: 25 rue du Dr-Roux

department: Biologie Development

institute: Institut Pasteur

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) and scanned.

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

data_processing:
Data were processed using EASANA from GenoSplice technology. GC background correction were applied to probe intensities (core), gene and exon level expression were summarized from the corrected intensities and then quantile normalized.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: HeLa_DYRK1A depletion

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: HeLa cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Gibco) with 100 U/ml penicillin-streptomycin and incubated at 37°C with 7% CO2.

extract_protocol: RNA was extracted using the High Pure RNA Isolation Kit (Roche REF 11 828 665 001).

treatment_protocol: siRNA were transfected into HeLa cells at a final concentration of 50 nM using DharmaFECT1 (T-2001). Cells were harvested three days after transfection.

value: HeLa

value: Cervical cancer cells

tag: transfected with

value: siRNA against DYRK1A

tag: genotype/variation

value: depletion of DYRK1A


title: 0h_A_X1(3)

description: Gene expression in neoblasts after 0h head regeneration

source_name: X1 neoblasts, anterior-facing wounds, 0h regeneration, replicate 3

value: neoblasts


title: 0h_A_X1(2)

source_name: X1 neoblasts, anterior-facing wounds, 0h regeneration, replicate 2