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.
2020-01-17 | GSE138445 | GEO
Project description:Raw fastq files from paired-end, Illumina-based sequencing on NovaSeq6000
2021-11-01 | GSE160615 | GEO
Project description:Raw fastq files from paired-end, Illumina-based sequencing on NovaSeq6000
2021-11-01 | GSE160791 | GEO
Project description:HPV positive head and neck cancer (HNC) are thought to have different etiology from HPV-unrelated HNC. There are indications that HPV positive HNC have better survival and that treatment options could be optimized in this set of tumours. In this study, we sought to evaluate miRNA profiles in the different groups of HNC based on cancer subsite (oral or oropharyngeal) and HPV presence (positive/negative; based on both viral DNA and RNA presence) all in comparison with normal tonsillar tissue from approximately aged subjects. From 61 enrolled patients, 22 were selected for NGS small RNA sequencing using Illumina small RNA library preparation kits and sequencing reagents on Nextseq 500 machine. Only samples with RIN >= 7 were included. manufacturers protocol was followed for library preparation. Indexing was done with indexes 1-22, and final libraries were normalizes to same amount after QBit measurement. Sequencing was done on Nextseq 500 machine and subsequent analyisis in Basespace (illumina). Raw fastq files were subsequently additionally trimmed of adapter sequences using FastQc Basespace app and differential expression evaluated with SmallRNA app. Customized plots were obtained after importing SmallRNA app calculated counts to DeSeq2 package in R and reanalysis therein.
2019-02-20 | E-MTAB-7030 | biostudies-arrayexpress