Two mRNA expression profiles (GSE3960 and GSE54720) were obtained from NCBI-GEO (https://www.ncbi.nlm.nih.gov/geo/ ). The microarray data of GSE3960, which included 101 NB primary tumors and 1 fetal brain tissue was based on GPL8300 (Affymetrix Human Genome U95 Version 2 Array, Affymetrix Inc., Santa Clara, CA, USA); while microarray data of GSE54720 was based on the GPL13667 platform (Affymetrix Human Genome U219 Array, Affymetrix Inc., Santa Clara, CA, USA), and included 19 NB tumors and 4 non-pathological tissues. The combined cohort of TCGA, TARGET, and GTEx samples were obtained from UCSC Xena browser (TCGA TARGET GTEx cohort (https://xenabrowser.net/datapages/?cohort=TCGA%20TARGET%20GTEx&removeHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443 )), and there were 162 NB samples and 1280 normal tissues (128 normal adrenal gland and 1152 normal brain tissues).
Affymetrix human genome u219 array
Manufactured by Thermo Fisher Scientific
Sourced in United States
The Affymetrix Human Genome U219 Array is a microarray platform designed for transcriptome analysis. It provides comprehensive coverage of the human genome, with probes targeting over 500,000 transcript clusters. The array is a tool for researchers to study gene expression patterns and profiles.
Automatically generated - may contain errors
Lab products found in correlation
Affymetrix human genome u133 plus 2.0 array, by Thermo Fisher Scientific (5 mentions)
Ht human genome u133a array, by Thermo Fisher Scientific (2 mentions)
Affymetrix human genome u133a 2.0 array, by Thermo Fisher Scientific (2 mentions)
Affymetrix human genome u95 version 2 array, by Thermo Fisher Scientific (1 mentions)
Humanht 12 v4.0 expression beadchip, by Illumina (1 mentions)
Affymetrix human gene expression array, by Thermo Fisher Scientific (1 mentions)
Humanht 12 v3.0 expression beadchip, by Thermo Fisher Scientific (1 mentions)
Human genome u133 plus 2.0 array, by Thermo Fisher Scientific (1 mentions)
Paxgene blood rna kit, by Qiagen (1 mentions)
Paxgene blood rna tube, by Qiagen (1 mentions)
Human ht 12 v3 expression beadchips, by Illumina (1 mentions)
12 protocols using affymetrix human genome u219 array
1
Comparative Analysis of Neuroblastoma mRNA Profiles
2
Integrated Analysis of Dendritic Cell Maturation
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
The gene expression profiles of GSE52894, GSE72893, GSE75938 and GSE77969 were downloaded from GEO (https://www.ncbi.nlm.nih.gov/geo/geo2r/ ). The gene expression profiles GSE52894 were measured with GPL10558 platforms (Illumina HumanHT-12 v4.0 expression beadchip) and included sixteen samples from four monDCs types (immature, mature, tolerogenic and LPS-tolerogenic). The microarray data of GSE72893 was based on GPL10558 platforms (Illumina HumanHT-12 v4.0 expression beadchip) and consisted of four imDCs samples, four mature DCs samples and two Treg-conditioned DCs samples. GSE75938 was based on GPL15207 platforms (Affymetrix Human Gene Expression Array). The GSE75938 dataset contained 14 samples, including three sets of monocytes, derived imDCs and macrophage, mature DCs and macrophage. GSE77969 which was based on GPL13667 platforms (Affymetrix Human Genome U219 Array) consisted of three imDCs samples and three mature DCs samples. We chose imDCs and mature DCs samples from these 4 datasets for integrated analysis in the present study.
3
Sepsis Transcriptome Analysis Using Public Datasets
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Three public gene expression matrices (GSE54514, GSE65682, and GSE95233), comprising of gene expression data from sepsis patients (SP) and healthy controls (HC), were obtained from the Gene Expression Omnibus (GEO) databases. The GSE65682 dataset (GPL13667, [HG-U219] Affymetrix Human Genome U219 Array), consisting of 42 healthy samples and 760 sepsis samples, served as the training cohort, while the GSE54514 (GPL6947, Illumina HumanHT-12 V3.0 expression beadchip) and GSE95233 (GPL570, [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array) datasets, which included 58 healthy samples and 229 sepsis samples, were utilized as the test cohort. The R script “sva” was employed to normalize the data and eliminate any batch effects present in the three datasets (20 (link)). The definition of differentially expressed genes (DEGs) was established at |Fold change| ≥ 2, p (p. adjust) < 0.05. Mitochondria-related genes (MiRGs) were collected from the Mito-Carta, MitoMiner, IMPI 2, and UniProt databases.
4
Comprehensive PDA Gene Expression Analysis
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
PDA gene expression datasets (GSE62165 ,20 GSE125158 ,21 and GSE71989 22 ) were obtained from the NCBI Gene Expression Omnibus (GEO) database (http://www.ncbi.nlm.nih.gov/geo/ ), a public functional genomics data repository for storing high‐throughput gene expression datasets, sequence‐based data, and microarrays.23 GSE62165 (GPL13667 [HG‐U219] Affymetrix Human Genome U219 Array) is based on 118 PDA tissue samples and 13 noncancerous samples, GSE125158 (GPL6480, Agilent‐014850 Whole Human Genome Microarray 4x44K G4112F) is based on 17 PDA and 13 noncancerous samples, GSE71989 (GPL570 [HG‐U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array) is based on 13 PDA and nine noncancer samples.
5
Transcriptome Analysis of Myelofibrosis
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Gene expression profiles of GSE26049, GSE53482, GSE61629 were downloaded from the GEO database (https://www.ncbi.nlm.nih.gov/geo/ ), which is a functional public genomics dataset including high throughput gene expression data, chips and microarray. Multiple sample sets were utilized in this study to avoid clinical bias and race among different studies. Totally 55 PMF samples and 73 normal samples were provided on platforms “GPL570, Affymetrix Human Genome U133 Plus 2.0 Array” (GSE26049, GSE61629) and “GPL13667, Affymetrix Human Genome U219 Array” (GSE53482). Of which, GSE26049 contained 9 PMF samples and 21 normal samples, GSE53482 included 42 PMF samples and 31 normal samples and GSE61629 provided 4 PMF samples and 21 control samples.
6
Whole Blood RNA Expression Profiling
7
Gene Expression Profiling of PMF Patients
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
The expression profile dataset of GSE53482 was downloaded from Gene Expression Omnibus (GEO; http://www.ncbi.nlm.nih.gov/geo/ ) (10 (link)). A total of 73 chips were available, including 42 peripheral blood (PB) cluster of differentiation (CD) 34+ cells from PMF patients (PB-PMF group), 16 peripheral blood CD34+ cells from healthy individuals (PB-control group), 15 bone marrow (BM) CD34+ cells of healthy individuals (BM-control group). In order to reduce the variables, only the expression microarray data from PB tissue were analyzed. Raw data from mRNA and miRNA profiles were collected using GPL13667 (HG-U219) Affymetrix Human Genome U219 Array and GPL14613 (miRNA-2_0) Affymetrix Multispecies miRNA-2_0 Array (Affymetrix Inc., Santa Clara, CA, USA), respectively.
8
Differential Gene Expression in Ovarian Cancer Spheroids
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Gene expression datasets were manually searched and gathered from the NCBI GEO database (www.ncbi.nlm.nih.gov/geo ), using “ovarian spheroids” as keywords and selected two datasets, i.e., GSE28799 and GSE80373. Dataset GSE28799 consists of the gene expression profile of six samples, expression (in triplicate) of ovarian carcinoma OVCAR-3 cell cultured in adherent culture medium (2D), and spheroid derived cells (3D) cultured in suspension culture. The platform for the experiments in dataset GSE28799 was GPL570 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array. Gene expression profile of eight samples was available in dataset GSE80373, which contains a quadruplicate of each HEY ovarian cancer 2D monolayer sample and 3D spheroid sample, where the experimental platform is used as GPL13667 ([HG-u219] Affymetrix Human Genome U219 Array).
9
Validation of Hub Genes in PMF
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
The identified hub genes were validated in third party GEO database: GSE53482 and GSE61629, which were set as testing sets. The gene expression profiles were downloaded from GEO database, and annotation file were provided by platforms “GPL570, Affymetrix Human Genome U133 Plus 2.0 Array” for GSE61629 and “GPL13667, Affymetrix Human Genome U219 Array” for GSE53482. The initial downloaded file was “.CEL” format, “RMA” algorithm by R (“rma” function) was conducted to perform background correction and data normalization to obtain standard gene expression profiles, followed by probe annotation. Based on manufacture-provided annotation files on platform, probe sets without corresponding genes were removed. The expression of hub genes in these GEO datasets were analyzed between normal group and PMF group to validate the significance of these genes.
10
HCC Genomic and Transcriptomic Analysis
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
The datasets GSE14520 and GSE63898 were downloaded from the expression database GEO (Gene Expression Omnibus, http://www.ncbi.nlm.nih.gov/geo/ ) (21 (link), 22 (link)). GSE14520 included a total of 488 samples, 241 samples were paired non-tumor samples, while the other 247 samples were HCC samples. Platform Information was [HG-U133A_2] Affymetrix Human Genome U133A 2.0 Array for 43 samples, and [HT_HG-U133A] Affymetrix HT Human Genome U133A Array for the other 445 samples. GSE63898 included 228 HCC and 168 cirrhotic samples, and the platform was [HG-U219] Affymetrix Human Genome U219 Array for all samples. The clinicopathological, mutation, deletion, amplification, copy number variation and/or survival data from HCC patients are available via the cBioportal (23 (link)), the TCGA data portal and/or reported in a previous publication (24 (link)). Of the 424 HCC patients in the TCGA cohort, matched mutation, deletion, amplification and copy number variation (CNV) data are available for 366 patients via cBioportal (23 (link)). We therefore included only these patients in our genetic alteration analyses. In addition, of the 424 HCC patients included in our gene expression analysis, corresponding complete clinical information are available for 236 patients from the TCGA cohort.
About PubCompare
Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.
We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.
However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.
Ready to get started?
Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required
Revolutionizing how scientists
search and build protocols!