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GSE108868
Homo sapiens
2 Downloadable Samples
Affymetrix Human Gene 2.0 ST Array (hugene20st)
Description
MS-275 and hydroxyurea treatment influences whole gene expression including DNA damage response and cell cycle checkpoint signaling.
Publication Title
HDAC1 and HDAC2 integrate checkpoint kinase phosphorylation and cell fate through the phosphatase-2A subunit PR130.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Drosophila melanogaster
- 20 Downloadable Samples
Illumina HiSeq 1500
Description
The goal of this study was to identify genes that are differentially expressed in animals that lack the histone methyltransferase Ash1 that generates H3K36 di-methylation Overall design: Comparison of the transcriptome in 3rd leg and haltere imaginal discs (T3 discs) and in wing imaginal discs (T2 discs) between wild-type animals and in animals that were homozgyous for the ash1[22] null mutation
Publication Title
Regulation and function of H3K36 di-methylation by the trithorax-group protein complex AMC.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 8 Downloadable Samples
- Illumina HiSeq 1500
Description
Inhibition of ZNF768 function was achieved by conditional over expression expression of the C-terminal zinc finger of ZNF768 for 12h. For preparation of total RNA cells were resuspended in TRIzol reagent (Life Technologies) at 0.9Mio/ml and snap-frozen. After thawing RNA was extracted from 0.4ml of TriZol lysate using the direct-zol RNA Miniprep (Zymo Research, Irvine CA, USA) as described in the manufacturer's protocol. RNA was assessed for purity by UV-vis spectrometry (Nanodrop) and for integrity by Bioanalyzer (Agilent Bioanalyzer 2100, Agilent, Santa Clara USA)). RNA was of high purity (abs. 260/280 >1.9, abs 269/239>2.1) and integrity (Bioanalyzer RIN>9 ) and thus used for further processing. For production of RNA-seq libraries total RNA was DNAse treated (dsDNAse, Fermentas) and 100 ng of this RNA was processed with a strand-specific protocol (RNA-seq complete kit, NuGEN, San Carlos, USA). In brief the RNA was reverse transcribed to cDNA with a reduced set of hexamer primers, avoiding excessive representation of rRNA in the cDNA. Second strand cDNA synthesis was done in presence of dUTP. After ultrasonic fragmentation of the cDNA and end repair, Illumina-compatible adapter were ligated. Adapters contained uracil in one strand, allowing complete digestion of the second-strand derived DNA. After strand selection the libraries were amplified, assessed for correct insert size on the Agilent Bioanalyser and diluted to 10nM. Barcoded libraries were mixed in equimolar amounts and sequenced on an Illumina HiSeq1500 in single-read mode with a read length of 100 b. Overall design: ZNF768-deltaN
Publication Title
MIR sequences recruit zinc finger protein ZNF768 to expressed genes.
Sample Metadata Fields
Treatment, Subject
View Samples- Drosophila melanogaster
- 20 Downloadable Samples
- Illumina HiSeq 1500
Description
We report here mRNA-seq data of adult male Drosophila head tissues. We compare two different ages: young and midlife as well as chm/chameau (CG5229) heterozygous mutants. Overall design: Comparison of ageing effect (young vs. midlife) in wild-type and mutant.
Publication Title
Life span extension by targeting a link between metabolism and histone acetylation in Drosophila.
Sample Metadata Fields
Sex, Subject
View Samples- Homo sapiens
- 12 Downloadable Samples
- Illumina HiSeq 2000
Description
The aim of the RNA-seq was to identify the KMT9 transcriptome in PC-3M cells. The MCF10A breast epithelial cells that do not express KMT9a were used to show that the siRNA against KMT9 show no off-target effects. Overall design: 12 samples correponding to 4 times 3 replicates were used for the study
Publication Title
KMT9 monomethylates histone H4 lysine 12 and controls proliferation of prostate cancer cells.
Sample Metadata Fields
Specimen part, Cell line, Treatment, Subject
View Samples- Homo sapiens
- 6 Downloadable Samples
- IlluminaHiSeq2000
Description
The aim of the study is to identify AR target gens in LNCaP cells Overall design: 6 samples correponding to 2 times 3 replicates were used for the study
Publication Title
Assembly of methylated KDM1A and CHD1 drives androgen receptor-dependent transcription and translocation.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 3 Downloadable Samples
- Illumina HiSeq 2000
Description
In this study, we investigate the anti-aging response induced by dietary restriction (DR) on gene expression level. For this, we carried out Ribosomal RNA depleted Total RNA sequencing in 16 weeks old Ercc1?/- ad libidum (AL), DR and wt mice. Overall design: Total RNA was extracted from fresh liver samples from 16 weeks old Ercc1?/- AL, DR and wt mice. Ribosomal RNA was depleted from the extracts by using RiboMinus kit (Ambion) then sequenced according to the Illumina TruSeq v3 protocol on HiSeq2000 platform.
Publication Title
Restricted diet delays accelerated ageing and genomic stress in DNA-repair-deficient mice.
Sample Metadata Fields
Age, Specimen part, Subject
View Samples