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TranscriptomicsNuclear SLIC-CAGE of human cortical neurons from Cornelia de Lange Syndrome patients and control individuals
We used SLIC-CAGE to map transcriptional start sites in cortical neurons from Cornelia de Lange Syndrome (CdLS) patients and control individuals. SLIC-CAGE was performed using nuclear RNA isolated from pre-frontal cortical grey matter. Usage of nuclear RNA allows enrichment of unstable RNAs, such as...
ORGANISM(S): Homo sapiens 
2021-02-27 | E-MTAB-9045 | biostudies-arrayexpress
TranscriptomicsRNA-seq of zebrafish embryos with mutations in a muscle-specific kinase and the giant titin protein
RNA-seq of zebrafish embryos with mutations in srpk3 (sa1890 allele) and/or ttn.1 (sa5562 allele). Each of the 24 samples (six samples for each of four genotypes) represents RNA from a pool of three 5 dpf zebrafish embryos.
ORGANISM(S): Danio rerio 
2024-02-09 | E-MTAB-12934 | biostudies-arrayexpress
TranscriptomicsRNA-seq of wild-type zebrafish embryos developmentally exposed to three addictive drugs
RNA-seq of wild-type Tüpfel long fin (TLF) zebrafish embryos developmentally exposed to three addictive drugs - 5 µM nicotine, 1.14 µM oxycodone and 5 µM amphetamine. Each of the 24 samples (6 samples per drug, plus 6 control samples) represents RNA from a pool of seven 5 dpf zebrafish embryos, expo...
ORGANISM(S): Danio rerio 
2022-01-24 | E-MTAB-11086 | biostudies-arrayexpress
TranscriptomicsWhole-genome bisulphite sequencing of met1-3/+
14 F1 individuals that resulted from crosses between a 420-CEN3 reporter line and met1-3/+ plants were subject to whole-genome bisulphite sequencing alongside Col wild-type and met1-3/+ controls
ORGANISM(S): Arabidopsis thaliana 
2015-10-10 | E-MTAB-3927 | biostudies-arrayexpress
TranscriptomicsCo-ordinate inhibiton of autism candidate genes by topoisomerase inhibitors [array]
Topoisomerases are necessary for the expression of neurodevelopmental genes, and are mutated in some patients with autism spectrum disorder (ASD). We have studied the effects of inhibitors of Topoisomerase 1 (Top1) and Topoisomerase 2 (Top2) enzymes on mouse cortical neurons. We find that topoisomer...
ORGANISM(S): Mus musculus 
2013-08-30 | E-GEOD-43899 | biostudies-arrayexpress
TranscriptomicsRNA-seq of Bur, Col and taf4b Arabidopsis thaliana meiocytes
Purified meiocytes from Col, Bur and taf4b Arabidopsis thaliana plants were extracted as previously described (Walker at al, 2018 Nat. Genet.), and cDNA used to produce libraries.
ORGANISM(S): Arabidopsis thaliana 
2019-12-31 | E-MTAB-7870 | biostudies-arrayexpress
TranscriptomicsATAC-seq analysis of the day-night rhythm in chromatin accessibility in PCM1+ left ventricular cardiomyocyte nuclei
This study investigated differential chromatin accessibility at zeitgeber time (ZT) 0 denoting the start of the light/inactive period in mice compared to ZT12 (the start of the dark/active) period to obtain insights into diurnal changes in transcription factor binding and gene regulatory pathways in...
ORGANISM(S): Mus musculus 
2024-02-29 | E-MTAB-13696 | biostudies-arrayexpress
GenomicsMouse ES cells expressing catalytically inactive Ring1B display impaired Ring1B and H3K27me3 deposition.
ChIP-seq for H3K27me3 and Ring1B was performed in WT mESCs and mESCs containing catalytically inactive Ring1B (I53A mutant). Cells expressing catalytically inactive Ring1B maintain the spatial distribution of Ring1B and H3K27me3 but at reduced levels. These findings support the notion that PRC2 recr...
ORGANISM(S): Mus musculus 
2015-09-20 | E-GEOD-69955 | biostudies-arrayexpress
GenomicsMapping meiotic crossovers in Arabidopsis using low-coverage whole-genome sequencing
Whole-genome DNA libraries were prepared from a population of just under 100 Col/Ler F1 backcrossed to Col. Low-coverage whole-genome sequencing was used to map meiotic crossovers in this population following the protocol described in Rowan et al., 2015, doi: 10.1534/g3.114.016501.
ORGANISM(S): Arabidopsis thaliana 
2015-10-15 | E-MTAB-3926 | biostudies-arrayexpress
TranscriptomicsHi-C and capture Hi-C for HPV16 infected human W12 cervical cell lines and normal cervical tissue
Two biological replicates Hi-C and HPV16-specific Region Capture Hi-C libraries were prepared for each of the W12 cell lines. Capture Hi-C was performed using HPV16-specific RNA baits. Hi-C libraries alone were prepared from normal cervix tissue (Ncx).
ORGANISM(S): Homo sapiens 
2021-06-18 | E-MTAB-10152 | biostudies-arrayexpress
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