Ontology highlight
ABSTRACT:
PROVIDER: PRJEB81277 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Transcriptomic profile of human adipose tissue progenitor cells was performed as follows. For AmpliSeq transcriptome sequencing library construction, AmpliSeq™ Library PLUS, AmpliSeq Transcriptome Human Gene Expression Panel and AmpliSeq CD indexes SetA kits were purchased from Illumina and sequencing libraries were constructed as described in AmpliSeq for Illumina Transcriptome Human Gene Expression Panel reference guide (Illumina). Equimolar concentrations of libraries were pooled at 4 nM and denatured and diluted as described in Denature and Dilute Libraries Guide (Illumina) and adjusted to final concentration of 1.4 pM. Resulting library was sequenced on NextSeq 500 using NextSeq 500/550 High Output v2 kit with 2 X 151 bp cycle. Generated raw files were converted to FASTQ files and used for data analysis. AmpliSeq transcriptome FASTQ files were analyzed on Array studio V10.0 (Omicsoft, Qiagen). Following raw read QC, first and last 10 bases were trimmed and mapped to reference genome Human.B38. The read count data was generated using GeneModel RefGene20170606. Resulting data was normalized by DESeq package, transformed to log2 value and used for ANOVA analyses.
2023-01-12 | GSE222749 | GEO
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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Project description:Small RNA sequencing (tRF-seq) was performed on A375 human melanoma cells with CRISPR/Cas9-mediated knockout of DUS1L and wild-type control cells, with three biological replicates per group. Small RNA libraries were prepared using the NEBNext Small RNA Library Prep Set for Illumina and sequenced on an Illumina NextSeq 500 platform to generate single-end FASTQ files. Sequencing quality was assessed using FastQC, and 3' adaptor sequences were trimmed with cutadapt. Clean reads were aligned to the human tRNA genome using MINTmap to obtain read count-based expression profiles of tRNA-derived fragments (tRFs).
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