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GenomicsNucleosome dynamics specifies genome-wide binding of the male germ cell gene regulator CTCFL and of CTCF [ChIP-Seq]
CTCF and CTCFL DNA binding profile in CTCFL induced and non-induced ES cells.CTCF is a highly conserved and essential zinc finger protein that in conjunction with cohesin organizes chromatin into loops, thereby regulating gene expression and epigenetic events. The function of CTCFL or BORIS, the tes...
ORGANISM(S): Mus musculus 
2012-07-25 | E-GEOD-34094 | biostudies-arrayexpress
TranscriptomicsNucleosome dynamics specifies genome-wide binding of the male germ cell gene regulator CTCFL and of CTCF [MoGene-1_0 Expression]
CTCFL binding to DNA and the effect of CTCFL expression in ES cells RNA extracted from CTCFL induced and non-induced ES cells was hybridized on Affymetrix Mouse Gene 1.0ST arrays
ORGANISM(S): Mus musculus 
2012-07-24 | E-GEOD-34092 | biostudies-arrayexpress
TranscriptomicsNucleosome dynamics specifies genome-wide binding of the male germ cell gene regulator CTCFL and of CTCF [Mouse430_2 Expression]
The effect of CTCFL mutation on the transcriptional program in testes Testis RNA extracted from CTCFL wildtype and mutant mice was hybridized on Affymetrix Mouse430_2 arrays
ORGANISM(S): Mus musculus 
2012-07-24 | E-GEOD-34091 | biostudies-arrayexpress
GenomicsNucleosome dynamics specifies genome-wide binding of the male germ cell gene regulator CTCFL and of CTCF
This SuperSeries is composed of the following subset Series: GSE34091: Nucleosome dynamics specifies genome-wide binding of the male germ cell gene regulator CTCFL and of CTCF [Mouse430_2 Expression] GSE34092: Nucleosome dynamics specifies genome-wide binding of the male germ cell gene regulator CTC...
ORGANISM(S): Mus musculus 
2012-07-24 | E-GEOD-34093 | biostudies-arrayexpress
TranscriptomicsSLIC-CAGE (Super-Low Input Carrier-CAGE) transcription start site mapping of mouse migratory and gonadal primordial germ cells, postnatal oocytes and early embryo
We used SLIC-CAGE to map transcription start sites (TSSs) of mouse primordial germ cells from embryonic days 9.5-16.5, postnatal oocytes (P6, P14 and MII), and early 2-cell and 4-cell mouse embryos. We use this TSS data to show that the mouse germline development starts with the somatic promoter co...
ORGANISM(S): Mus musculus 
2022-02-14 | E-MTAB-9757 | biostudies-arrayexpress
TranscriptomicsHigh-resolution genome-wide transcriptomics analysis of O. dioica during recovery from growth arrest
Polycistronic mRNAs transcribed from operons are resolved via the trans-splicing of a spliced leader (SL) RNA. The SL is also frequently trans-spliced to monocistronic transcripts. Using a modified cap analysis of gene expression (CAGE) protocol we mapped sites of SL trans-splicing genome-wide in th...
ORGANISM(S): Oikopleura dioica 
2015-01-26 | E-GEOD-50848 | biostudies-arrayexpress
TranscriptomicsGenome-wide map of spliced-leader-led trans-splice sites in Oikopleura dioica
Polycistronic mRNAs transcribed from operons are resolved via the trans-splicing of a spliced leader (SL) RNA. The SL is also frequently trans-spliced to monocistronic transcripts. Using a modified cap analysis of gene expression (CAGE) protocol we mapped sites of SL trans-splicing genome-wide in th...
ORGANISM(S): Oikopleura dioica 
2015-01-26 | E-GEOD-50849 | biostudies-arrayexpress
GenomicsIn vivo live imaging of RNA polymerase II transcription factories in primary cells
Transcription steps are marked by different modifications of the C-terminal domain of RNA polymerase II (RNAPII). Phosphorylation of Ser5 and Ser7 by cyclin-dependent kinase 7 (CDK7) as part of TFIIH marks initiation, whereas phosphorylation of Ser2 by CDK9 marks elongation. These processes are thou...
ORGANISM(S): Mus musculus 
2013-05-13 | E-GEOD-46849 | biostudies-arrayexpress
TranscriptomicsTranscription start site mapping of Saccharomyces cerevisiae grown in YPD media using the nAnTi-iCAGE protocol
We used nAnT-iCAGE – unbiased single-nucleotide resolution method for genome-wide transcription start site (TSS) capture, to produce libraries from Saccharomyces cerevisiae total RNA. Our goal was to investigate S. cerevisiae core-promoters and assess the rules of transcription initiation in BY4741 ...
ORGANISM(S): Saccharomyces cerevisiae S288c 
2022-02-01 | E-MTAB-7465 | biostudies-arrayexpress
TranscriptomicsCAGE-seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics (e.g. fast - green vs slow - red)
The core-promoter, a stretch of DNA surrounding the transcription-start-site (TSS), is a major integration-point for regulatory-signals controlling gene-transcription. Cellular-differentiation is marked by divergence in transcriptional-repertoire and cell- cycling behaviour between cells of differen...
ORGANISM(S): Danio rerio 
2020-06-19 | E-MTAB-8795 | biostudies-arrayexpress
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