Digital gene and expression profiling of primary acute lymphoblastic leukemia (ALL) cells
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ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Jessica Nordlund
PROVIDER: E-GEOD-26878 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:We determined the genome-wide digital gene expression (DGE) profiles of primary acute lymphoblastic leukemia (ALL) cells from 28 patients and fractionated blood cells from healthy blood donors taking advantage of “second generation” sequencing technology. The patients included in the study represent distinct subtypes of B-cell precursor (BCP) ALL and T-cell lineage ALL (T-ALL) and the controls are fractionated CD19+ and CD3+ cells. Gene expression analysis of 28 ALL patient samples with different immunophenotypic backgrounds including T-ALL (n=4) and patients with BCP ALL with diverse cytogenetic backgrounds: High Hyperploidy (HeH) (n=10), t(9;22) BCR-ABL1 (n=3), t(12;21) ETV6-RUNX1 (n=4), dic(9;20) (n=3), t(1;19)TCF3-PBX1, MLL/11q23 (n=1) and undefined/non-recurrent aberrations (n=1). Fractionated b-cells (CD19+) and t-cells (CD3+) isolated from peripheral blood of healthy donors were used as controls. Sequencing libraries were prepared from 1 µg of total RNA using reagents from the NlaIII Digital Gene Expression Tag Profiling kit (Illumina Inc, San Diego, CA, USA). mRNA was captured on magnetic oligo(dT) beads and reverse transcribed into double-stranded cDNA. The cDNA was cleaved using the restriction enzyme NlaIII. An adapter sequence containing the recognition sequence for the restriction enzyme MmeI was ligated to the NlaIII cleavage sites. The adapter-ligated cDNA was digested with MmeI to release the cDNA from the magnetic bead, while leaving 17 base-pairs of sequence in the fragment. The fragments were dephosphorylated and purified by phenol-chloroform. A second adapter was ligated at the MmeI cleavage sites. The adapter-ligated cDNA fragments were amplified by PCR, and the PCR products were purified on a 6% polyacrylamide gel. The ~96 base pair PCR products were excised from the gel and eluted overnight, followed by ethanol precipitation and re-suspension. Purified libraries were quality controlled and quantified on a Bioanalyzer using DNA 1000 series or High Sensitivity chips. The DGE libraries were diluted to a 10 nM concentration and sequenced on one lane of an Illumina GAII or GAIIx for 18 cycles.
2011-12-20 | E-GEOD-26530 | biostudies-arrayexpress
Project description:We determined the genome-wide digital gene expression (DGE) profiles of primary acute lymphoblastic leukemia (ALL) cells from 28 patients and fractionated blood cells from healthy blood donors taking advantage of “second generation” sequencing technology. The patients included in the study represent distinct subtypes of B-cell precursor (BCP) ALL and T-cell lineage ALL (T-ALL) and the controls are fractionated CD19+ and CD3+ cells.
2011-12-20 | GSE26530 | GEO
Project description:Digital gene expression profiling of primary acute lymphoblastic leukemia cells
| PRJNA142169 | ENA
Project description:A drug sensitive stock of T.b.brucei (STIB247) was used to generate a drug resistant strain (247MelCyR), expressing 130-fold increase in resistance to the melaminophenyl arsenical Cymelarsan (MelCy) by subcurative treatment in mice. Expression of the Cymelarsan resistant phenotype was maintained in 247MelCyR following adaptation to procyclic form in vitro culture. Here we have compared the transcriptomes of the STIB247 and 247MelCyR strains from procyclic cell culture, using digital gene expression (DGE) analysis. Digital gene expression analysis was performed on RNA derived from 2 biological replicates each of Cymelarsan resistant (247MelCyR) and Cymelarsan sensitive (STIB 247), T.b.brucei procyclic cell culture.
2011-07-28 | E-GEOD-23288 | biostudies-arrayexpress
Project description:TRI6 is a positive regulator of the trichothecene gene cluster and the production of trichothecene mycotoxins (deoxynivalenol [DON] and acetylated forms such as 15-ADON) in the cereal pathogen F. graminearum. As a global transcriptional regulator, TRI6 expression is modulated by nitrogen-limiting conditions, sources of nitrogen and carbon, pH, and light. However, the mechanism by which these diverse environmental factors affect TRI6 expression remains under-explored. In our effort to understand how nutrients affect TRI6 regulation, comparative digital expression profiling was performed with a wildtype F. graminearum and a Δtri6 mutant strain, grown in nutrient-rich conditions. Analysis showed that TRI6 negatively regulates genes of the branched-chain amino acid (BCAA) metabolic pathway. Feeding studies with deletion mutants of MCC, encoding methylcrotonyl-CoA-carboxylase, one of the key enzymes of leucine metabolism, showed that addition of leucine specifically down regulated TRI6 expression and reduced 15-ADON accumulation. Constitutive expression of TRI6 in the Δmcc mutant strain restored 15-ADON production. A combination of cellophane breach assays and pathogenicity experiments on wheat demonstrated that disrupting the leucine metabolic pathway significantly reduced disease. These findings suggest a complex interaction between one of the primary metabolic pathways with a global regulator of mycotoxin biosynthesis and virulence in F. graminearum. Triplicate samples of digital gene expression profiling data for the Tri6 mutant and wildtype strains were compared. **Please note that the raw data files for the current study are no longer available, and therefore are not included in the submission.
2015-08-01 | E-GEOD-71604 | biostudies-arrayexpress
Project description:This experiment contains Phytophthora sojae samples and RNA-seq data from experiment E-GEOD-29561 (https://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29651/) to understand gene expression during the P. sojae life cycle. The transcriptome of the oomycete plant pathogen Phytophthora sojae was profiled at 5 different developmental stages: mycelia (MY), zoosporangia (SP), zoospores (ZO), cysts (CY) and germinating cysts (GC); based on a 3'-tag digital gene expression (DGE) protocol. More than 90 million clean sequence tags were generated and compared to the P. sojae genome and its 19,027 predicted genes. A total of 14,969 genes were detected, of which 10,044 were deemed reliable because they mapped to unambiguous tags. A web-based server named the Phytophthora Transcriptional Database (PTD) has been established.
2011-09-01 | E-MTAB-4039 | biostudies-arrayexpress
Project description:Using global gene expression profiling in T-cells from untreated Mcs5a resistant and susceptible congenic rats, we asked if signatures of potential risk-decreasing mechanisms could be identified. On two independent sample sets, we applied microarray (MA) or digital gene expression (DGE) analysis comparing T-cells from Mcs5a resistant and susceptible congenic rats. This file contains the DGE data. T-cell RNA sample pools were compared between the susceptible (susc.; n=3 pools) and the resistant (Mcs5a; n=3 pools) congenic lines
2011-11-29 | E-GEOD-33975 | biostudies-arrayexpress
Project description:This series of single cell RNA sequencing data aims to investigate the heterogeneity of cellular hieararchies among pediatric acute myeloid leukemia and acute lymphoblastic leukemia with NUP98-rearrangement.
2025-07-24 | GSE287716 | GEO
Project description:The transcriptome of the oomycete plant pathogen Phytophthora sojae was profiled at 10 different developmental and infection stages based on a 3'-tag digital gene expression (DGE) protocol. More than 90 million clean sequence tags were generated and compared to the P. sojae genome and its 19,027 predicted genes. A total of 14,969 genes were detected, of which 10,044 were deemed reliable because they mapped to unambiguous tags. A comparison of the whole-library genes expression patterns suggested four groups: 1) mycelia and zoosporangia (MY and SP); 2) zoospores and cysts (ZO and CY); 3) germinating cysts (GC); 4) five infection site libraries (IF1.5 to IF24h). The libraries from the different groups showed major transitional shifts in gene expression. From the ten libraries, 722 gene expression pattern clusters were obtained and the top 16 ones, containing more than half of the genes, comprised enriched genes with different functions including protein localization, triphosphate metabolism, signaling process, and non-coding RNA metabolism. An evaluation of the average expression level of 30 pathogenesis related gene families revealed that most were infection induced, but with diverse expression patterns and levels. A web-based server named the Phytophthora Transcriptional Database (PTD) has been established. The five axenically grown stages were mycelia (MY), zoosporangia (SP), zoospores (ZO), cysts (CY), and germinating cysts (GC). The five infection stages, 1.5, 3, 6, 12 and 24 h after inoculation onto susceptible soybean leaf tissues (IF1.5h to IF24h).
2011-09-01 | E-GEOD-29651 | biostudies-arrayexpress