|
| Status |
Public on Sep 05, 2020 |
| Title |
CNTT1 |
| Sample type |
SRA |
| |
|
| Source name |
peritoneal macrophages_CNT-T- treated rat
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Wistar
age: 8 weeks old
injected particles: MWCNT-CNT-T (tangled)
time point: 15 days after injection
cell type: Peritoneal macrophages
|
| Treatment protocol |
Peritoneal macrophages from CNT-7 or CNT-T-treated rats sacrificed after 15 days, were separated and isolated using flow cytometry cell sorting (FACSAria III, BD Biosciences).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using RNeasy mini kit (Cat. # 74104) from Qiagen. RNA quantity was measured with Qubit™ RNA HS Assay Kit (Thermofisher); the RNA integrity and quality were assessed using an Agilent Bioanalyzer using the Agilent RNA 6000 Nano kit. All RNA used had an RNA Integrity Number between 9 and 10.
Libraries were prepared starting from 100 ng of total RNA using the Illumina® TruSeq® Stranded mRNA Sample Preparation Kits following the standard protocol.
Libraries were sequenced using an Illumina HiSeq1500 platform. Approximately 50 million paired-end reads (2x125bp) per sample were obtained.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
CNTT1
|
| Data processing |
All sequencing data were analyzed using the Automated Reproducible MOdular workflow for preprocessing and differential analysis of RNA-seq data (ARMOR) pipeline
Reads were mapped using Salmon to the transcriptome index which was built using all Ensembl cDNA sequences obtained in the Rattus_norvegicus.Rnor_6.0.cdna.all.fa file
Estimated transcript abundances from Salmon were imported into R using the tximeta package and analyzed for differential gene expression with edgeR
Genome_build: Rattus_norvegicus.Rnor_6.0.cdna.all.fa
Supplementary_files_format_and_content: RNA.seq.counts.csv include the counts as estimated by Salmon
|
| |
|
| Submission date |
Sep 04, 2020 |
| Last update date |
Sep 05, 2020 |
| Contact name |
Jérôme Ambroise |
| E-mail(s) |
jambroise83@gmail.com
|
| Organization name |
Université catholique de Louvain
|
| Department |
Institut de Recherche Expérimentale et Clinique
|
| Street address |
Avenue Hippocrate 54
|
| City |
Woluwé |
| ZIP/Postal code |
1200 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL18404 |
| Series (1) |
| GSE157487 |
Monocytic ontogeny of regenerated macrophages characterizes the mesotheliomagenic responses to carbon nanotubes |
|
| Relations |
| BioSample |
SAMN16058335 |
| SRA |
SRX9075346 |
