Expression analysis of zebrafish TIF1g-deficient, cdc73 deficient and double-deficient embryos
Ontology highlight
ABSTRACT:
ORGANISM(S): Danio rerio
SUBMITTER: Xiaoying Bai
PROVIDER: E-GEOD-20432 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Publications
TIF1gamma controls erythroid cell fate by regulating transcription elongation.
Bai Xiaoying X Kim Jonghwan J Yang Zhongan Z Jurynec Michael J MJ Akie Thomas E TE Lee Joseph J LeBlanc Jocelyn J Sessa Anna A Jiang Hong H DiBiase Anthony A Zhou Yi Y Grunwald David J DJ Lin Shuo S Cantor Alan B AB Orkin Stuart H SH Zon Leonard I LI
Cell 20100701 1
Recent genome-wide studies have demonstrated that pausing of RNA polymerase II (Pol II) occurred on many vertebrate genes. By genetic studies in the zebrafish tif1gamma mutant moonshine we found that loss of function of Pol II-associated factors PAF or DSIF rescued erythroid gene transcription in tif1gamma-deficient animals. Biochemical analysis established physical interactions among TIF1gamma, the blood-specific SCL transcription complex, and the positive elongation factors p-TEFb and FACT. Ch ...[more]
Similar Datasets
Project description:Transcriptional profiling of the zebrafish embryonic host response to a systemic bacterial infection with Salmonella typhimurium (strain SL1027); comparison between traf6 knock-down and control morpholino treated embryos. All infection experiments were performed using mixed egg clutches of ABxTL strain zebrafish. Embryos injected with traf6 morpholino or a 5bp mismatch control morpholino were staged at 27 hours post fertilization (hpf) by morphological criteria and approximately 250 cfu of DsRed expressing Salmonella bacteria were injected into the caudal vein close to the urogenital opening. As a control an equal volume of PBS was likewise injected. Pools of 20-40 infected and control embryos were collected 8 hours post infection (hpi). The whole procedure was preformed in triplicate on separate days. Total RNA of the biological triplicates was pooled using equal amounts of RNA prior to RNAseq library preparation.
2010-08-01 | E-GEOD-21024 | biostudies-arrayexpress
Project description:Embryos were injected with antisense Morpholino Oligonucleotides (AMOs) targetting MyoD. The transcriptional profile of these knock down embryos was compared with embryos injected with control morpholino (CMO).
2011-06-22 | E-MEXP-3272 | biostudies-arrayexpress
Project description:Transcriptional profiling of embryonic zebrafish injected with a control morpholino or a morpholino that causes exclusion of TNNT2 exon 13. Zebrafish embryos were injected with a antisense morpholino oligo that induced missplicing of exon 13 of TNNT2 (TNNT2sp) or a control morpholino. At 96hpf these embryos were euthanized and RNA was collected.
2010-12-31 | E-GEOD-20179 | biostudies-arrayexpress
Project description:Transcriptional profiling of hdac1 morphant zebrafish embryos in comparison to standard control injected embryos. Embryos where injected at the one cell stage with either a translation blocking morpholino (Hdac1 ATG), splice blocking morpholino (Hdac1 Splice) or Hdac1 mismatch control morpholino (Hdac1 control). RNA was extracted and compared in a two-colour hybridisation to the comman reference Standard control morpholino injected embryos. Common reference experiment, hdac1 morphants vs. standard control morphants. Biological replicates: 2 (except Splice which was technical rather than biological)
2011-01-21 | E-GEOD-26708 | biostudies-arrayexpress
Project description:Transcriptional profiling of Xenopus laevis embryos and ectoderm (animal caps) comparing embryos injected with control morpholino with embryos injected with the morpholino mixture PVD2, which knocks down all three Xenopus PouV proteins. Whole embryos (WE) or animal caps (AC) were collected at late blastula (9) or early gastrula (10) stages from Control and PVD2 morphants. Two conditions: Control vs. PouV morpholino; Two tissues: whole embryos, animal caps .Two timepoints: stage 9 and 10. Biological replicates: 2 control replicates at stage 9 and 10 for whole embryos, 2 control replicates at stage 9 and 10 for animal caps, 2 PVD2 morpholino replicates at stage 9 and 10 for whole embryos, 2 control replicates at stage 9 and 10 for animal caps
2013-11-12 | E-GEOD-47578 | biostudies-arrayexpress
Project description:Transcriptional profiling of hdac1 morphant zebrafish embryos in comparison to standard control injected embryos. Embryos where injected at the one cell stage with either a translation blocking morpholino (Hdac1 ATG), splice blocking morpholino (Hdac1 Splice) or Hdac1 mismatch control morpholino (Hdac1 control). RNA was extracted and compared in a two-colour hybridisation to the comman reference Standard control morpholino injected embryos.
2011-01-21 | GSE26708 | GEO
Project description:Transcriptional profiling of hdac1 ATG morphant zebrafish embryos in comparison to standard control injected embryos. Embryos where injected at the one cell stage with either a translation blocking morpholino (Hdac1 ATG) or Standard control morpholino (StCo). RNA was extracted at 12, 18 and 27hpf from both sets of embryos and compared with a two-colour hybridisation. Timecourse experiment, hdac1 ATG morphants vs. standard control morphants. Biological replicates: 3
2011-01-21 | E-GEOD-26709 | biostudies-arrayexpress
Project description:Transcriptional profiling of the zebrafish embryonic host response to a systemic bacterial infection with Salmonella typhimurium (strain SL1027); comparison between traf6 knock-down and control morpholino treated embryos. Two-way factorial dual colour design with factor 1 'infection with Salmonella enterica serovar Typhimurium (S. typhimurium)' and factor 2 'morpholino knock-down of traf6' using a common reference made from the sample pool. All infection experiments were performed using mixed egg clutches of ABxTL strain zebrafish. Embryos injected with traf6 morpholino or a 5bp mismatch control morpholino were staged at 27 hours post fertilization (hpf) by morphological criteria and approximately 250 cfu of DsRed expressing Salmonella bacteria were injected into the caudal vein close to the urogenital opening. As a control an equal volume of PBS was likewise injected. Pools of 20-40 infected and control embryos were collected 8 hours post infection (hpi). For the microarray analysis, the whole procedure was preformed in triplicate on separate days. The triplicates are marked 1,2 and 3.
2010-08-01 | E-GEOD-20310 | biostudies-arrayexpress
Project description:Transcription factors play diverse roles during embryonic development, combinatorially controlling multiple cellular states in a spatially and temporally defined manner. Resolving the dynamic transcriptional profiles that underlie these patterning processes is essential for understanding embryogenesis at the molecular level. Here we show how temporal, tissue-specific changes in embryonic transcription factor function can be discerned by integrating caged morpholinos (cMOs) with photoactivatable fluorophores, fluorescence-activated cell sorting (FACS), and microarray technologies. As a proof of principle, we have dynamically profiled No tail-a (Ntla)-dependent genes at different stages of axial mesoderm development in zebrafish, discovering and characterizing discrete sets of transcripts that are coincident with either notochord cell fate commitment or differentiation. Our studies demonstrate how optically controlled chemical tools can be use to probe developmental processes with spatiotemporal precision and reveal the sequential activation of distinct transcriptomes within a cell lineage by a single transcriptional factor. Zebrafish zygotes were injected with a mixture of ntla caged morpholino (cMO) and caged fluorescein dextran (cFD), and a 100 µm-diameter region of the shield was UV-irradiated at 6 hours post fertilization (hpf). The UV irradiation generated an active morpholino targeting the ntla 5'UTR and simultaneously labeled the cells with green fluorescence. By 36 hpf, the irradiated, green-fluorescent cells contributed to the medial floor plate rather than the notochord, consistent with earlier proposals that Ntla acts as a transcriptional switch between these two cell fates. Combining these caged reagents with microarray analysis identified transcriptional changes coincident with loss of ntla at 9 hpf and subsequent notochord fate respecification. Zebrafish zygotes were injected with a mixture of ntla cMO/cFD, and a 100 µm-diameter region of the shield was UV-irradiated at 6 hpf. Control embryos were injected with cFD and similarly irradiated at 6 hpf. Experimental and control sets of embryos were enzymatically dissociated at 9 hpf, green-fluorescent cells were isolated by FACS, and collected in trizol. Thirty embryos were used for each experiment or controls, each yielding approximately 8,000 green fluorescent cells. Five biological replicates were performed along with five paired controls. Total RNA was isolated from each sample, reverse transcribed, and amplified using WTA2 TransPlex Complete Whole Transcriptome Amplification kit (Sigma) using a miniaturized procedure and manufacturer-recommended incubation steps. The synthesized cDNA was sent to Nimblegen for dye labeling and hybridization. Samples were hybridized to the Nimblegen 2007 (Zv 7) Danio rerio Gene Expression Array chip using one dye per chip. Raw probe data (.pair file) was subjected to RMA, normalization, background correction, and generation of gene expression summary (.calls file) by Nimblegen. Processed data was analyzed in ArrayStar software (DNAStar). Significantly affected genes (fold change > 2 and p-value < 0.10) were identified using a moderated t-test.
2012-03-01 | E-GEOD-31880 | biostudies-arrayexpress
Project description:Transcription factors play diverse roles during embryonic development, combinatorially controlling multiple cellular states in a spatially and temporally defined manner. Resolving the dynamic transcriptional profiles that underlie these patterning processes is essential for understanding embryogenesis at the molecular level. Here we show how temporal, tissue-specific changes in embryonic transcription factor function can be discerned by integrating caged morpholinos (cMOs) with photoactivatable fluorophores, fluorescence-activated cell sorting (FACS), and microarray technologies. As a proof of principle, we have dynamically profiled No tail-a (Ntla)-dependent genes at different stages of axial mesoderm development in zebrafish, discovering and characterizing discrete sets of transcripts that are coincident with either notochord cell fate commitment or differentiation. Our studies demonstrate how optically controlled chemical tools can be use to probe developmental processes with spatiotemporal precision and reveal the sequential activation of distinct transcriptomes within a cell lineage by a single transcriptional factor. Zebrafish zygotes were injected with a mixture of ntla caged morpholino (cMO) and caged fluorescein dextran (cFD), and a 100 µm-diameter region of the posterior chordamesoderm 125 μm anterior to the center of Kupffer’s vesicle was UV-irradiated at 12 hours post fertilization (hpf). The UV irradiation generated an active morpholino targeting the ntla 5'UTR and simultaneously labeled the cells with green fluorescence. By 36 hpf, the irradiated, green-fluorescent cells contributed to both notochord and floor plate, but the notochord cells were partially vacuolated and disorganized. Combining these caged reagents with microarray analysis identified transcriptional changes coincident with loss of ntla at 16 hpf and subsequent notochord differentiation. Zebrafish zygotes were injected with a mixture of ntla cMO/cFD, and a 100 µm-diameter region of the posterior chordamesoderm 125 μm anterior to the center of Kupffer’s vesicle was UV-irradiated at 12 hpf. Control embryos were injected with cFD and similarly irradiated at 12 hpf. Experimental and control sets of embryos were enzymatically dissociated at 16 hpf, green-fluorescent cells were isolated by FACS, and collected in trizol. Thirty embryos were used for each experiment or controls, each yielding approximately 8,000 green fluorescent cells. Five biological replicates were performed along with five paired controls. Total RNA was isolated from each sample, reverse transcribed, and amplified using WTA2 TransPlex Complete Whole Transcriptome Amplification kit (Sigma) using a miniaturized procedure and manufacturer-recommended incubation steps. The synthesized cDNA was sent to Nimblegen for dye labeling and hybridization. Samples were hybridized to the Nimblegen 2007 (Zv 7) Danio rerio Gene Expression Array chip using one dye per chip. Raw probe data (.pair file) was subjected to RMA, normalization, background correction, and generation of gene expression summary (.calls file) by Nimblegen. Processed data was analyzed in ArrayStar software (DNAStar). Significantly affected genes (fold change > 2 and p-value < 0.10) were identified using a moderated t-test.
2012-03-01 | E-GEOD-31881 | biostudies-arrayexpress