Expression profiles in Blast Bank samples with AML/RAEB
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE1427 | GEO | 2006/05/25
SECONDARY ACCESSION(S): PRJNA90077
REPOSITORIES: GEO
Similar Datasets
Project description:CD133-positive immature blasts were purified from bone marrow of the patients. Total RNA was extracted by RNeasy mini spin column (Qiagen, Inc). SUBMITTER_CITATION: Yamashita Y, Ohashi J, Hirai Y, Choi YL, Kaneda R, Fujiwara S-i, Arai Y, Akutsu M, Tsutsumi C, Miyazaki Y, Usuki K, Teramura M, Mitani K, Kano Y, O'Neill MC, Urabe A, Tomonaga M, Ozawa K & Mano H. Gene expression profiles of CD133-positive fractions predict the survival of individuals with acute myeloid leukemia 2006, Cancer Genomics & Proteomics, 3:169-182.
2008-06-12 | E-GEOD-1427 | biostudies-arrayexpress
Project description:Total RNA in mesenteric LNs from chow- or high fat diet-fed Ldlr–/– mice were isolated using an RNeasy mini kit (Qiagen) with on-column DNaseI digestion. The DNA array was conducted using a Mouse Oligo chip 24k (TORAY Industries Inc.) and a 3D-Gene® Scanner (TORAY Industries Inc.) by Kamakura Techno-Science, Inc. (TORAY Industries Inc.).
2021-02-21 | GSE167142 | GEO
Project description:Transcriptional changes were monitored in the wheat cultivar Renan 24 hours post i noculation with adapted and non-adapted Magnaporthe isolates using the Affymetrix wheat genome array GeneChip®. Wheat plants cv. Renan were grown in a peat and sand (1:1) mix at 23 C in a Sanyo Fitotron growth cabinet (Sanyo Gallenkamp PLC, Loughborough, U.K.) with a 16/8 h, light/dark cycle. Three Magnaporthe isolates were used in this expt, two wheat-adapted isolates (BR32, BR37) and one wheat non-adapted isolate (BR29). Magnaporthe isolates were grown for eleven days on Complete Media Agar at 25 C under a 16/8h, light/dark cycle. Conidia were harvested by flooding the plates with 5 mL of sterile inoculation solution [0.25% (w/v) gelatine and 0.01% (v/v) Tween 20] and scraping the conidia from the surface using a sterile glass rod. Conidia were filtered through sterile miracloth and the density adjusted to 1 x 10 5 conidia mL-1 with inoculation solution. Fourteen day old wheat seedlings mist inoculated with 4 mL of a Magnaporthe conidia suspension and plants were sealed in plastic propagators to maintain relative humidity c.100% and kept at 25 C in the dark for the first 24 hours post inoculation (hpi). Inoculation solution without Magnaporthe conidia was used as a mock-inoculation control. Leaf samples were collected 24 hpi for transcriptomics analysis from three independent biological experiments. Leaf tissue was ground under liquid nitrogen and total RNA extracted using a QIAquick RNeasy Plant Extraction Kit (Qiagen, Hilden, Germany), followed by TURBO DNaseTM (Ambion, Texas, U.S.A.) treatment. RNeasy Mini Spin column purification (Qiagen) was used to further purify RNA samples for array hybridisation. RNA quality checks, cRNA conversion and Affymetrix genome array hybridisation was carried out by the Nottingham Arabidopsis Stock Centre (NASC) array hybridisation service (http://affymetrix.arabidopsis.info/). ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Graham McGrann. The equivalent experiment is TA24 at PLEXdb.]
2011-08-31 | GSE31760 | GEO
Project description:affy_ath_2012_05 - affy_ath_2012_05 - The main objective is to determinate the influence of Ubiquitin-Like Proteases in plant transcriptional modulation. The experiment will also allow us to find what transcriptional cues are particularly affected in the mutants relatively to wild-type.-Seeds were stratified for 3 days at 4ºC in the dark. Afterwards, seeds were surface sterilized, sown onto MS media and grown at 23ºC, with 100 µE light condition, in long days (16h L/8h D). Each MS plate was dived in four, corresponding to a genotype (Col, AB, SIZ1 or SAB), and 10 seeds were sown per genotype. After 10 days, seedlings were collected and frozen in liquid nitrogen. Each replicate was made of ~40 seedlings coming from 4 different MS plates. Frozen plant material was grounded in an eppendorf tube using a mini pestle. RNA was extracted using RNeasy Plant Mini kit (QIAGEN cat.74904), following the manufacturer instructions (QIAGEN, Hilden, Germany). The RNA samples were DNase treated (Recombinant DNase I, Takara Biotechnology, Dalian, China) and subsequently cleaned by column using RNeasy Plant Mini kit (QIAGEN, Hilden, Germany).
2013-09-01 | GSE43883 | GEO
Project description:The parasite Plasmodium falciparum is responsible for severe malaria, which remains a major cause of death, particularly in sub-Saharan Africa. The reference strain NF54 (or its subclone 3D7) is commonly used for controlled human malaria infection (CHMI), but recently strains with a different geographic and genomic background have become available for CHMI, including 7G8, which was subcloned from the Brazilian isolate IMTM22 in 1984 (Burkot TR et al. 1984. Infectivity to mosquitoes of Plasmodium falciparum clones grown in vitro from the same isolate. Trans R Soc Trop Med Hyg 78 (3):339-41. doi: 10.1016/0035-9203(84)90114-7). To provide the first RNA-seq reference dataset for 7G8 ring stage parasites and validate our qPCR primer set targeting all var gene variants above 6 kb encoded in the 7G8 genome according to current guidelines and best practices, we thawed an aliquot from the Sanaria 7G8 parasite working cell bank (Lot: SAN03-021214 dated 20. February 2014) thawed and cultured for 13 parasite generations at a hematocrit of 5% in human O+ erythrocytes. Parasites were kept synchronous by regular sorbitol treatment. Ring-stage infected erythrocytes were lysed with Trizol, and total RNA was purified using column-based purification (Qiagen RNeasy Mini Mit), including DNase treatment on the column and control for absence of genomic DNA contamination by qPCR. Total RNA samples were cleared of human globin mRNA using magnetic bead isolation technology (GLOBINclear kit). After quality control of RNA samples and optimized preparation of cDNA libraries for AT-rich genomes for Illumina sequencing, RNA-seq was performed at BGI Genomics (Shenzhen, China) on the HiSeq 4000 to generate 100 bp paired-end sequencing reads.
2022-09-22 | E-MTAB-12157 | biostudies-arrayexpress
Project description:RNA from A673 cells with shRNA-mediated knockdown of GFP (4 libraries), EWS-FLI1 (4 libraries), or lnc277 (7 libraries) was isolated with TRIzol (Invitrogen). Each sample was DNase treated and further purified on an RNeasy Mini column (Qiagen) before quality analysis on an Agilent 2100 Bioanalyzer. For each sample, 100-150ng of RNA was synthesized into cDNA, sheared on a Covaris ultrasonicator, and amplified using the NuGen Encore Complete kit (NuGen) to produce strand-specific and rRNA-depleted libraries. Samples were multiplexed (4/lane) for 2x100bp paired-end sequencing on an Illumina HiSeq 2000
2014-11-01 | GSE60949 | GEO
Project description:Different Th cells were generated in vitro, and then the total RNA was extracted with Rneasy Mini Kit (qiagen).
2018-12-12 | GSE123624 | GEO
Project description:In this experiment the transcriptome reprogramming in wheat during host and nonhost interaction with Magnaporthe sp. was analyzed in a time-series approach. Seven days old wheat plants of cv. Renan were mock-inoculated or inoculated with adapted Magnaporthe isolate Br116.5 from wheat or non-adapted isolate CD180 from Pennisetum. After 6, 12, 24 and 48 hours the abaxial epidermis was sampled. Total RNA was extracted using the RNeasy Plant Mini Kit with on-column DNase digestion (Qiagen, Hilden, Germany), and hybridized to Agilent 44k oligonucleotide arrays.
2017-12-02 | E-MTAB-5635 | biostudies-arrayexpress
Project description:In this experiment the transcriptome reprogramming in barley during host and nonhost interaction with Magnaporthe sp. was analyzed in a time-series approach. Seven days old barley plants of cv. Vada were mock-inoculated or inoculated with adapted Magnaporthe isolate TH6772 from rice or non-adapted isolate CD180 from Pennisetum. After 6, 12, 24 and 48 hours the abaxial epidermis was sampled. Total RNA was extracted using the RNeasy Plant Mini Kit with on-column DNase digestion (Qiagen, Hilden, Germany), and hybridized to Agilent 44k oligonucleotide arrays.
2017-12-02 | E-MTAB-5634 | biostudies-arrayexpress
Project description:Monocytes were isolated from 30 ml of whole blood from each of 19 women, 10 with high BMD and 9 with low BMD, using monocyte negative isolation kit from Dynal Biotech Inc. Total RNA was extracted from monocytes using Qiagen RNeasy Mini Kit. Targets were produced for each subject using standard Affymetrix procedures from about 4ug of total RNA. Hybridization was made for each subject. Comparison was performed between 10 high BMD and 9 low BMD subjects. Keywords = microarray Keywords = monocyte Keywords = osteoporosis Keywords = HDC Keywords = CCR3 Keywords = GCR Keywords: other
2005-07-01 | GSE2208 | GEO