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Arabidopsis thaliana
94 Downloadable Samples
Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis.
Sample Metadata Fields
Age, Specimen part, Treatment
View Samples- Arabidopsis thaliana
- 75 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Plant organs are comprised of distinct cell types with unique assemblages of mRNAs. This is a collection of CEL files of mRNA profiles of the total steady-state mRNAs and polysomal mRNAs of distinct cell types of the whole root and shoot of 7-d-old Arabidopsis thaliana seedlings. The cell type specific mRNA populations are those present in ribosome-mRNA complexes. This sub-population of mRNAs was obtained by first establishing a collection of Arabidopsis lines that express a FLAG-epitope tagged ribosomal protein L18 (RPL18) directed by promoters expressed in specific cell types and regions. Thirteen different promoter:FLAG-RPL18 lines were used. The targeted cell types and promoters included root atrichoblast (non-hair) epidermal cells (pGL2), root endodermis (pSCR), root stelar xylem and pericycle (pWOL, pSHR), root phloem companion cells (phloem CC) (pSUC2, pSultr2;2), root proliferating cells (pRPL11C), root cortex meristematic cells (pCO2), root cortex elongation/maturation cells (pPEP), shoot mesophyll (pRBCS), shoot epidermis (pCER5), shoot guard cells (pKAT1), shoot bundle sheath (pSultr2;2), shoot phloem CC (pSUC2) and shoot trichomes (pGL2). A CaMV 35S promoter:FLAG-RPL18 line was used to obtain the polysomal mRNA of multiple cell types. The immunopurification of ribosome-mRNA complexes of specific cell types/regions was accomplished by the method described in Zanetti et al. (Plant Physiology, 138, 624-635; 2005). Hybridization of the immunopurified mRNAs to the Affymetrix ATH1 DNA microarray platform and subsequent data analysis permitted the identification of transcripts that are enriched or depleted in specific cell types/regions of roots and shoots. The dataset includes samples from cell types/regions from seedlings grown under control conditions and cell types/regions of seedlings exposed to low oxygen stress (hypoxia) for 2 h.
Publication Title
Profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis.
Sample Metadata Fields
Age, Specimen part, Treatment
View Samples- Arabidopsis thaliana
- 19 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Plant organs are comprised of distinct cell types with unique assemblages of mRNAs. This is a collection of CEL files of mRNA profiles of the total steady-state mRNAs and polysomal mRNAs of distinct cell types of the root tip of 7-d-old Arabidopsis thaliana seedlings. The cell type specific mRNA populations are those present in ribosome-mRNA complexes. This sub-population of mRNAs was obtained by first establishing a collection of Arabidopsis lines that express a FLAG-epitope tagged ribosomal protein L18 (RPL18) directed by promoters expressed in specific cell types and regions. Four different promoter:FLAG-RPL18 lines were used. The targeted cell types and promoters included root endodermis (pSCR) and root stelar xylem and pericycle (pWOL, pSHR). A CaMV 35S promoter:FLAG-RPL18 line was used to obtain the polysomal mRNA of multiple cell types. The immunopurification of ribosome-mRNA complexes of specific cell types was accomplished by the method described in Zanetti et al. (Plant Physiology, 138, 624-635; 2005). Hybridization of the immunopurified mRNAs to the Affymetrix ATH1 DNA microarray platform and subsequent data analysis permitted the identification of transcripts that are enriched or depleted in specific cell types of root tips. The dataset includes samples from cell types from seedlings grown under control conditions and cell types of seedlings exposed to low oxygen stress (hypoxia) for 2 h.
Publication Title
Profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis.
Sample Metadata Fields
Age, Specimen part, Treatment
View Samples- Homo sapiens
- 4 Downloadable Samples
Illumina HiSeq 2500
Description
To determine the impact of ?Np63a knockdown on steady-state mRNA levels, we performed poly(A)-enriched RNA-seq analysis of lung squamous cell carcinoma line H226 (inducible shControl and shp63) in the presence of 1µg/mL doxycycline to induce shRNA expression. Overall design: Poly(A)+ RNA for two independent biological replicates was purified from H226 cells (inducible shControl and shp63) incubated treated for six days with 1 µg/mL doxycycline. a TruSeq Stranded mRNA Library Prep Kit (Illumina). Libraries were sequenced on an Illumina HiSeq 2000 system at the University of Colorado Cancer Center Genomics and Microarray Core facility. Reads were aligned (TopHat2) to the Human reference genome (GRCh37/hg19) and gene-level counts (HTseq-count) were used for differential expression analysis (DESeq2).
Publication Title
ΔNp63α Suppresses TGFB2 Expression and RHOA Activity to Drive Cell Proliferation in Squamous Cell Carcinomas.
Sample Metadata Fields
Specimen part, Cell line, Treatment, Subject
View Samples- Homo sapiens
- 12 Downloadable Samples
- Ion Torrent Proton
Description
To determine effects of p53 activation on levels of RNA associated with polysomes, we performed RNA-seq analysis of colorectal carcinoma cell line HCT116, breast carcinoma line MCF7, and osteosarcoma line SJSA treated with MDM2 inhibitor Nutlin. Overall design: Polysomal RNA was extracted from HCT116, MCF7 and SJSA cells treated with Nutlin, polyA enriched and subjected to RNA-seq protocol.
Publication Title
Identification of a core TP53 transcriptional program with highly distributed tumor suppressive activity.
Sample Metadata Fields
Cell line, Treatment, Subject
View Samples- Homo sapiens
- 35 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
To define the contribution of CDK8 versus CDK19 to gene expression control, we performed a series of microarray assays for cells where each kinase was stably knocked down.
Publication Title
HIF1A employs CDK8-mediator to stimulate RNAPII elongation in response to hypoxia.
Sample Metadata Fields
Cell line, Treatment
View Samples- Homo sapiens
- 16 Downloadable Samples
- IonTorrentProton
Description
To determine the effects of depleting TIP60, CDK8, or HIF1A on the transcriptional response to hypoxia, we performed RNAseq analysis of four HCT116 colorectal carcinoma cell lines (shNT, HIF1A-/-, shTIP60 and shCDK8) in normoxic and hypoxic (24hrs, 1% O2) conditions. Overall design: PolyA RNA for two independent biological replicates was purified from HCT116 cells stably expressing an shRNA against a non-targeting control (shNT), TIP60 (shTIP60) or CDK8 (shCDK8), or genetically deleted HIF1A (HIF1A-/-) subjected to 24hrs 1% O2 (hypoxia) or maintained under ambient oxygen (21%; normoxia) was sequenced on the Ion Torrent platform. Reads were aligned to the human genome and gene-level counts were used for differential expression analysis.
Publication Title
The TIP60 Complex Is a Conserved Coactivator of HIF1A.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 34 Downloadable Samples
- Illumina HiSeq 2500
Description
RNA was sequenced from individuals Disomic and Trisomic for chromosome 21 to identify consistent changes in gene expression across individuals Overall design: Cells were cultured at subconfluency and RNA harvested for sequencing
Publication Title
Trisomy 21 consistently activates the interferon response.
Sample Metadata Fields
Sex, Age, Subject
View Samples
SRP078911- Mus musculus
- 12 Downloadable Samples
- Illumina HiSeq 2500
Description
RNA was sequenced from Normal and DP 16 mice to identify consistent changes in gene expression across cohorts Overall design: Cells were cultured at subconfluency and RNA harvested for sequencing
Publication Title
Trisomy 21 consistently activates the interferon response.
Sample Metadata Fields
Subject
View Samples- Homo sapiens
- 6 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Global analysis of p53-regulated transcription identifies its direct targets and unexpected regulatory mechanisms.
Sample Metadata Fields
Cell line, Treatment
View Samples