Ontology highlight
ABSTRACT:
PROVIDER: PRJNA683929 | ENA |
REPOSITORIES: ENA
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Project description:The mammary glands of adult female mice were divided into ductal tissue and terminal end buds (TEBs). Basal and luminal epithelial cells were FACS sorted and nuclei extracted for 75bp paired-end ATAC-seq profiling using an Illumina NextSeq 500 sequencer.
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Project description:The mammary glands of adult female mice were divided into ductal tissue and terminal end buds (TEBs). Basal and luminal epithelial cells were FACS sorted and RNA extracted for 75bp paired-end RNA-seq profiling using an Illumina NextSeq 500 sequencer.
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Project description:Total RNA was extracted using RNAble (Eurobio), then cleaned-up with RNeasy columns (Qiagen), then sequenced. The libraries were prepared following the TruSeq Stranded mRNA protocol (Illumina), starting from 1 μg of high quality total RNA. Paired end (2 × 75 bp) sequencing was performed on an Illumina Nextseq 500 platform(Illumina).
2020-01-13 | E-MTAB-7768 | biostudies-arrayexpress
Project description:Undamaged utricular sensory epithelia from P2, P4, and P6 mice were isolated using FACS and underwent Smartseq-2 protocol for single cell RNA seq. Data was generated using Illumina NextSeq 500, paired end, 75-150bp reads with median depth of ~0.5 million reads per cell.
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Project description:Determining the role of DDX17 in the formation of DNA:RNA-hybrids around active DNA double-strand breaks (DSBs) using DRIP-seq in the damaged induced via AsiSI (DIvA) cell system that induced DSBs at known genomic loci in response to hydroxytamoxifen (OHT) treatment via and AsiSI enzyme fused to an oestrogen receptor. Sequencing was done using either control or DDX17 siRNA, and mock or 4 hours 300nM OHT treatment. Paired-end 150 cycles was completed on an Illumina NextSeq 500 and library prep was completed using the NEB NEBNext Ultra II library prep kit.
2022-11-08 | E-MTAB-10814 | biostudies-arrayexpress
Project description:Double-strand DNA breaks (DSBs) continuously arise and are a source of mutations and chromosomal rearrangements. Here, we present DSBCapture, a sequencing-based method that captures DSBs in situ and directly maps these at single nucleotide resolution enabling the study of DSB origin. DSBCapture shows substantially increased sensitivity and data yield compared to other methods. Employing DSBCapture, we uncovered a striking relationship between DSBs and elevated transcription within nucleosome-depleted chromatin. 6 library samples, 75 base pairs (50 bp for the EcoRV library) custom protocol (DSBCapture or BLESS) sequenced as paired-end reads on Illumina NextSeq 500 (MiSeq for EcoRV library): 1 replicate for the EcoRV library, 1 replicate for the library coming from the U2OS AID-DlvA cell line with AsiSI restriction enzyme, 2 replicates for the BREAk-seq NHEK libraries and 2 replicates for the BLESS NHEK libraries. 4 RNA-Seq library samples from HEK Gibco cells, single-end sequencing on the Illumina NextSeq 500, 75 base pairs.
2016-07-18 | E-GEOD-78172 | biostudies-arrayexpress
Project description:RNA-seq experiment to study the role of Pat1b in HEK293T cells. HEK293T cells were treated twice with siRNA with Lipofectamine 2000 then harvested after 48hours. Total RNA was extracted with TriReagent. Ribo-Zero TruSeq stranded mRNA libraries were prepared for each sample and sequenced on Illumina NextSeq 500 Sequencing System providing around 100 million reads per sample (around 75 bp paired-end reads).
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Project description:Purpose: Determine if alveolar macrophage express different transcriptional programs when CD44 expression is lost. Methods: Alveolar macrophages were isolated from the bronchoalveolar lavage of 6-10 week old CD44+/+ and CD44-/- female mice. RNA was isolated an sequenced using Illumina NextSeq 500. RNA was sequenced by the UBC Biomedical Research Center. RNA quality, 18S and 28S ribosomal RNA with RIN = 9.6, was determined by Agilent 2100 Bioanalyzer following standard protocol for NEBnext Ultra ii Stranded mRNA (New England Biolabs). Sequencing was performed on the Illumina NextSeq 500 with paired end 42bp 42bp reads. De-multiplexed read sequences were then aligned to the Mus musculus (mm10) reference sequence using Spliced Transcripts Alignment to a Reference, STAR (https://www.ncbi.nlm.nih.gov/pubmed/23104886), aligners. Results and conclusion: Multiple pathways were abnormal in CD44-/- alveolar macrophages, in particular those involved in lipid metabolism and immune signaling.
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2017-11-20 | GSE95445 | GEO
Project description:1.Comparison of chromatin occupancy of H2BUb and RNA Polymerase II in SHP-1 WT and KO MCF7 cells. Paired end sequencing (2X100 bp) was performed on the Illumina HiSeq X ten. 2.Identification of the SHP-1 binding site in MCF7 cells using ChIP Seq. Paired end sequencing (2X100 bp) was performed on the Illumina Nextseq 2000 platform.
2022-06-01 | E-MTAB-10295 | biostudies-arrayexpress