Ontology highlight
ABSTRACT:
PROVIDER: PRJNA600801 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10875200_1.fastq.gz | Fastqsanger.gz | |||
| SRR10875200_2.fastq.gz | Fastqsanger.gz | |||
| SRR10875201_1.fastq.gz | Fastqsanger.gz | |||
| SRR10875201_2.fastq.gz | Fastqsanger.gz | |||
| SRR10875202_1.fastq.gz | Fastqsanger.gz |
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Project description:We examine the use of high-throughput sequencing on binding sites recovered using a bacterial one-hybrid (B1H) system and find that improved models of transcription factor (TF) binding specificity can be obtained compared to standard methods of sequencing a small subset of the selected clones. We can obtain even more accurate binding models using a modified version of B1H selection method with constrained variation (CV-B1H). However, achieving these improved models using CV-B1H data required the development of a new method of analysis - GRaMS (Growth Rate Modeling of Specificity) - that estimates bacterial growth rates as a function of the quality of the recognition sequence. We benchmark these different methods of motif discovery using Zif268, a well characterized C2H2 zinc finger transcription factor on both a 28bp randomized library for the standard B1H method and on 6bp randomized library for the CV-B1H method for which forty-five different experimental conditions were tested: 5 time points and three different IPTG and 3-AT concentrations. We find that GRaMS analysis is robust to the different experimental parameters whereas other analysis methods give widely varying results depending on the conditions of the experiment. Finally, we demonstrate that the CV-B1H assay can be performed in liquid media, which produces recognition models that are similar in quality to sequences recovered from selection on solid media. All selections were performed using the bait transcription factor Zif268. 45 different B1H selections were performed on plates and the selected sites were multiplexed and sequenced in a single lane. A single selection was performed in liquid media and sequenced along with other multiplexed sets of sites in a separate lane. For the experiments performed on plates, the of the selections assays was varied (4, 8, 12, 18, 24 hours). The stringency of the selections was also varied by changing the concentration of IPTG (0, 10, 50 uM) and 3-AT (0.5, 1, 2 mM). The initial randomized library used for all selections was also sequenced in a single lane. The randomized portion of each transcription factor binding site is 6bp long and is immediately 5' of the constant sequence, GCGG, which is the consensus binding site for finger 1 of Zif268. Upstream of the randomized binding site is a 4bp randomized region referred to as the key region. The purpose of the key region is to detect possible PCR 'jackpotting.' The single liquid media experiment was run for 4 hours using 50uM IPTG and 5mM 3-AT. Four selections were performed using a prey library with a 28bp long randomized region and not fixed consensus site region. These selections were performed at either 36 or 48 hours using 10uM IPTG and 0, 2, or 5 mM 3-AT.
2011-04-28 | E-GEOD-26767 | biostudies-arrayexpress
Project description:High-througput Bacteria one hybrid (B1H) selections for all Drosophila homeodomain proteins
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Project description:By utilizing single-cell analysis at different stages of tumorigenesis, we demonstrated a developmental hierarchy of dynamic progenitor pools in murine sonic hedgehog-(SHH) MBs. We identified Olig2+ progenitors as transit-amplifying cells during initial tumorigenic phases. These cells are quiescent stem-like progenitors in full-blown tumors but enriched in therapy-resistant as well as recurrent medulloblastomas. Olig2 ablation or depletion of mitotic Olig2+ progenitors abrogated tumorigenesis. Transcriptome profiling and chromatin occupancy assays revealed that Olig2 activates oncogenic networks including HIPPO- Yap/Taz signaling and Aurora-A/MycN pathways. Co-targeting these oncogenic pathways induced sustained tumor growth arrest. Together, our single-cell analyses uncover unexpected glia-lineage-related Olig2+ progenitor pools critical for medulloblastoma initiation and suggest targeting Olig2-regulated oncogenic pathways as an avenue for therapy.
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Project description:RNA-binding proteins govern neural progenitor hierarchy during development and tumorigenesis
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Project description:Effect of the low phytic acid mutation on gene expression of developing seeds of M955, a low phytic acid barley genotype with >90% reduction in phytic acid in mature seeds. Expression analysis using the Barley1 GeneChip was performed on total RNA from developing seeds (7DAA) of M955 lpa and wt sib-selections. Sib-selections were from BC2 populations of M955 with Harrington as the recurrent parent. Material was grown in field trials in two years 2003 and 2004. In 2003 expression analysis was done from 2 lpa and 3 wt sib-selections, and in 2004 analysis was done from 2 lpa and 2 wt sib-selections. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, David Bowen. The equivalent experiment is BB22 at PLEXdb.] genotype: M955 LPA sib-selection - year: 2003(2-replications); genotype: M955 LPA sib-selection - year: 2004(2-replications); genotype: M955 WT sib-selection - year: 2003(3-replications); genotype: M955 WT sib-selection - year: 2004(2-replications)
2011-11-22 | E-GEOD-33395 | biostudies-arrayexpress
Project description:By utilizing single-cell analysis at different stages of tumorigenesis, we demonstrated a developmental hierarchy of dynamic progenitor pools in murine sonic hedgehog-(SHH) MBs. We identified Olig2+ progenitors as transit-amplifying cells during initial tumorigenic phases. These cells are quiescent stem-like progenitors in full-blown tumors but enriched in therapy-resistant as well as recurrent medulloblastomas. Olig2 ablation or depletion of mitotic Olig2+ progenitors abrogated tumorigenesis. Transcriptome profiling and chromatin occupancy assays revealed that Olig2 activates oncogenic networks including HIPPO- Yap/Taz signaling and Aurora-A/MycN pathways. Co-targeting these oncogenic pathways induced sustained tumor growth arrest. Together, our single-cell analyses uncover unexpected glia-lineage-related Olig2+ progenitor pools critical for medulloblastoma initiation and suggest targeting Olig2-regulated oncogenic pathways as an avenue for therapy.
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Project description:By utilizing single-cell analysis at different stages of tumorigenesis, we demonstrated a developmental hierarchy of dynamic progenitor pools in murine sonic hedgehog-(SHH) MBs. We identified Olig2+ progenitors as transit-amplifying cells during initial tumorigenic phases. These cells are quiescent stem-like progenitors in full-blown tumors but enriched in therapy-resistant as well as recurrent medulloblastomas. Olig2 ablation or depletion of mitotic Olig2+ progenitors abrogated tumorigenesis. Transcriptome profiling and chromatin occupancy assays revealed that Olig2 activates oncogenic networks including HIPPO- Yap/Taz signaling and Aurora-A/MycN pathways. Co-targeting these oncogenic pathways induced sustained tumor growth arrest. Together, our single-cell analyses uncover unexpected glia-lineage-related Olig2+ progenitor pools critical for medulloblastoma initiation and suggest targeting Olig2-regulated oncogenic pathways as an avenue for therapy.
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Project description:By utilizing single-cell analysis at different stages of tumorigenesis, we demonstrated a developmental hierarchy of dynamic progenitor pools in murine sonic hedgehog-(SHH) MBs. We identified Olig2+ progenitors as transit-amplifying cells during initial tumorigenic phases. These cells are quiescent stem-like progenitors in full-blown tumors but enriched in therapy-resistant as well as recurrent medulloblastomas. Olig2 ablation or depletion of mitotic Olig2+ progenitors abrogated tumorigenesis. Transcriptome profiling and chromatin occupancy assays revealed that Olig2 activates oncogenic networks including HIPPO- Yap/Taz signaling and Aurora-A/MycN pathways. Co-targeting these oncogenic pathways induced sustained tumor growth arrest. Together, our single-cell analyses uncover unexpected glia-lineage-related Olig2+ progenitor pools critical for medulloblastoma initiation and suggest targeting Olig2-regulated oncogenic pathways as an avenue for therapy.
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