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SRP156330
Homo sapiens
9 Downloadable Samples
Illumina HiSeq 4000
Description
To investigate the differences of transcriptional activities between AUG-initiated c-Myc and CUG-initiated c-Myc , we performed a transcriptomic analysis using high throoughput RNA sequencing (RNA-seq). Overall design: Total RNA extracted from KMST6 fibroblast cells stably expressing AUG-initiated c-Myc, CUG-initiated c-Myc, and empty vector (negative control) was subjected to RNA-seq analysis. The sequencing libraries generated from the RNA were analyzed by Illumina Hiseq 4000. The sequencing reads were trimmed for adaptor sequence, and low-complexity or low-quality reads were removed. Subsequently, the sequencing reads were aligned to the human reference GRCh38 genome using Gencode v27 annotations by STAR. Read counts per gene were quantified using the HTSeq Python package.
Publication Title
Novel oncogene 5MP1 reprograms c-Myc translation initiation to drive malignant phenotypes in colorectal cancer.
Sample Metadata Fields
Subject
View Samples- Homo sapiens
- 2 Downloadable Samples
- Illumina HiSeq 4000
Description
To investigate the downstream targets of eIF5 mimic protein 1 (5MP1), also known as Basic Leucine Zipper and W2 domains 2 (BZW2; Ensembl:ENSG00000136261), we performed a transcriptomic analysis using high throoughput RNA sequencing (RNA-seq). Overall design: Total RNA extracted from HCT116 cells stably expressing 5MP1 and empty vector-transfected negative control HCT116 cells was subjected to RNA-seq analysis. The sequencing libraries generated from the RNA were analyzed by Illumina Hiseq 4000. The sequencing reads were trimmed for adaptor sequence, and low-complexity or low-quality reads were removed. Subsequently, the sequencing reads were aligned to the human reference GRCh38 genome using Gencode v27 annotations by STAR. Read counts per gene were quantified using the HTSeq Python package.
Publication Title
Novel oncogene 5MP1 reprograms c-Myc translation initiation to drive malignant phenotypes in colorectal cancer.
Sample Metadata Fields
Subject
View Samples- Homo sapiens
- 74 Downloadable Samples
- NextSeq 500
Description
In a cross-site study we evaluated the performance of ribosomal RNA removal kits from Illumina, Takara/Clontech, Kapa Biosystems, Lexogen, New England Biolabs and Qiagen on intact and degraded RNA samples. We found that all of the kits were capable of performing significant ribosomal depletion, though there were differences in their ease of use. All kits were able to remove ribosomal RNA to below 20% with intact RNA and identify ~14,000 protein coding genes from the Universal Human Reference RNA sample at >1FPKM. Analysis of differentially detected genes among kits suggested that transcript length may be a key factor in library production efficiency. These results provide a roadmap for labs on the strengths of each of these methods and how best to utilize them. Overall design: The Universal Human Reference RNA (Agilent) was diluted to 500 ng/ul in 200ul of RNase-free water and 3.94ul of the Spike-in RNA Variant Control E2 Mix (Lexogen) were added. The sample was split into two aliquots, one of which was then heated at 94° C for 1 hour and 27 minutes. 1ul of ERCC RNA Spike-In Mix 1 was added to both the intact and degraded samples. The final intact and degraded RNA samples were then diluted to 25 ng/uL and were distributed to each of the ten genomics core facilities (members of ABRF) for ribo-depletion and library preparation following vendor protocol. Each site prepared between one and four library types. Indices were assigned by the group to prevent overlapping among libraries. Libraries were pooled at an equimolar concentration from each kit using site-specific quantification and pooling SOPs and return each pool along with individual un-pooled libraries to the designated sequencing site. The sequencing site quantified each pool, multiplexed and sequenced over three high output paired-end 75bp runs on the Illumina NextSeq 500. contributor: The Association of Biomolecular Resource Facilities (ABRF) DNA Sequencing Research Group (DSRG) members
Publication Title
Cross-site comparison of ribosomal depletion kits for Illumina RNAseq library construction.
Sample Metadata Fields
Subject
View Samples- Saccharomyces cerevisiae
- 15 Downloadable Samples
- Illumina HiSeq 2000
Description
The nuclear exosome performs critical functions in non-coding RNA processing, and in diverse surveillance functions including the quality control of mRNP formation, and in the removal of pervasive transcripts. Most non-coding RNAs and pervasive nascent transcripts are targeted by the Nrd1p-Nab3p-Sen1p (NNS) complex to terminate Pol II transcription coupled to nuclear exosome degradation or 3´-end trimming. Prior to nuclear exosome activity, the Trf4p-Air2p-Mtr4p polyadenylation complex adds an oligo-A tail to exosome substrates. Inactivating exosome activity stabilizes and lengthens these A-tails. We utilized high-throughput 3´-end poly(A)+ sequencing to identify at nucleotide resolution the 3´ ends targeted by the nuclear exosome, and determine the sites of NNS-dependent termination genome-wide. Overall design: 3´-end mapping of wild-type and various nuclear exosome mutant strains, either using gene knockouts or the anchor away system to conditionally deplete FRB-tagged proteins from the nucleus
Publication Title
Common genomic elements promote transcriptional and DNA replication roadblocks.
Sample Metadata Fields
Subject
View Samples- Homo sapiens
- 12 Downloadable Samples
Illumina HumanHT-12 V4.0 expression beadchip
Description
Compares shFOXO4 vs. Control in LNCaP grown in culture, or in nude mice as primary orthotopic tumors or lymph node metastases
Publication Title
A genome-wide RNAi screen identifies FOXO4 as a metastasis-suppressor through counteracting PI3K/AKT signal pathway in prostate cancer.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 6 Downloadable Samples
- IlluminaGenomeAnalyzerIIx
Description
We report the effects of Rapamycin treatment on the transcriptome of normal human dermal fibroblasts isolated from foreskin (designated 2DD). We sequenced mRNA from 2 replicates of proliferative (PRO) quiescent (QUI, serum starved) or treated with 500nM Rapamycin for 5 days (RAP). Comparative analyses with PRO transcripts a baseline indicate that genes that changed expression from Rapamycin treated fibroblasts are significantly different from those of quiescence cells. Rapamycin treated cells showed a significant enrichment for cytokines from the Il-6 cascade. Overall design: Examination of mRNAs from proliferative, quiescent (serum starvation) and Rapamycin (5oonM, 5days) treated 2DD normal human dermal/foreskin fibroblasts.
Publication Title
Concordance between RNA-sequencing data and DNA microarray data in transcriptome analysis of proliferative and quiescent fibroblasts.
Sample Metadata Fields
No sample metadata fields
View Samples- Gallus gallus
- 8 Downloadable Samples
- Affymetrix Chicken Genome Array (chicken)
Description
Inner ear auditory and vestibular tissues differ in their responses to mechanical stimuli.
Publication Title
Distinct energy metabolism of auditory and vestibular sensory epithelia revealed by quantitative mass spectrometry using MS2 intensity.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 30 Downloadable Samples
- NextSeq 500
Description
Development requires the cooperation of tissue-specific and ubiquitously expressed transcription factors, such as Sp-family members. However, the molecular details of how ubiquitous factors participate in developmental processes are still unclear. We previously showed that during the differentiation of embryonic stem cells lacking Sp1 DNA binding activity (Sp1deltaDBD/deltaDBD cells), early blood progenitors are formed. However, gene expression during differentiation becomes progressively deregulated and terminal differentiation is severely compromised. Here we studied the cooperation of Sp1 and its closest paralogue Sp3 in hematopoietic development and demonstrate that Sp1 and Sp3 binding sites largely overlap. Sp3 cooperates with Sp1deltaDBD/deltaDBD but is unable to support hematopoiesis in the complete absence of Sp1. Using single cell gene expression analysis, we show that the lack of Sp1 DNA binding leads to a distortion of cell fate decision timing, indicating that stable chromatin bi nding of Sp1 is required to maintain robust differentiation trajectories. Overall design: RNA-Seq in ESC, Flk, HE1, HE2 and progenitor cells with WT, Sp1deltaDBD or Sp3KO
Publication Title
Robust hematopoietic specification requires the ubiquitous Sp1 and Sp3 transcription factors.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Hordeum vulgare
- 15 Downloadable Samples
- Affymetrix Barley Genome Array (barley1)
Description
FN044, FN211, FN242 and FN303 are the fast neutron generated mutants in cv. Steptoe background. These 4 mutants have lesion mimic phenotype and increase disease resistance to stem rust. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, ling zhang. The equivalent experiment is BB54 at PLEXdb.]
Publication Title
A cation/proton-exchanging protein is a candidate for the barley NecS1 gene controlling necrosis and enhanced defense response to stem rust.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 2 Downloadable Samples
- NextSeq 500
Description
Development requires the cooperation of tissue-specifically and ubiquitously expressed transcription factors, such as Sp-family members. However, the molecular details of how ubiquitous factors participate in developmental processes are still unclear. We previously showed that during the differentiation of embryonic stem cells lacking Sp1 DNA binding activity (Sp1DDBD/DDBD cells), early blood progenitors are formed. However, gene expression during differentiation becomes progressively deregulated and terminal differentiation is blocked. Here we studied the cooperation of Sp1 and its homologue Sp3 in hematopoietic development and demonstrate that Sp1 and Sp3 binding sites largely overlap. Sp3 cooperates with Sp1DDBD/DDBD cells but is unable to support hematopoiesis in the complete absence of Sp1. Using single cell gene expression analysis, we show that the lack of Sp1 DNA binding leads to a distortion of cell fate decision timing, indicating that stable chromatin binding of Sp1 is required to maintain robust differentiation trajectories. Overall design: Chromium 10X - Single-cell RNA-seq of Sp1 wild-type and Sp1 DNA binding domain mutant cells
Publication Title
Robust hematopoietic specification requires the ubiquitous Sp1 and Sp3 transcription factors.
Sample Metadata Fields
Specimen part, Subject
View Samples