|
| Status |
Public on Jun 12, 2019 |
| Title |
IMR-90 PDL52 2 |
| Sample type |
SRA |
| |
|
| Source name |
Lung
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: IMR-90
cell type: Human Diploid Lung Fibroblast
tissue: Lung
treatment: Replicative exhaustion
passages: PDL52
|
| Growth protocol |
Cultured in DMEM supplemented with 10% FBS (Gibco), 1% antibiotics, 1% antimycotics, and 1% NEAA (Invitrogen).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Standard paired-end illumina preparation: Illumina Hiseq 2x150bp configuration single index per lane, RNA library preparation with rRNA depletion
Total RNA was extracted using TriPure (Roche)
RiboRNA depletion was done using RiboRNA depletion nano kit (Qiagen), cDNA synthesis was made with Ovation RNA-seq System V2 (NuGEN), Library prep was made with TruSeq ChIP Sample Preparation Kit (Illumina), Hiseq PE Cluster Kit (Illumina) and Hiseq SBS Kit (Illumina) was used for clustering and sequencing
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
IMR-90 replicative senescence
|
| Data processing |
BCL files were de-multiplexed and converted to standard FASTQ files using bcl2fastq program.
The reads were cleaned usning cutadapt program
The reads were aligned using STAR aligner (v2.4) using hg19 Ensembl v82 annotation database
Read counts were generated using featureCounts software
Genome_build: hg19
Supplementary_files_format_and_content: txt
|
| |
|
| Submission date |
May 05, 2019 |
| Last update date |
Jun 12, 2019 |
| Contact name |
Supriyo De |
| Organization name |
NIA-IRP, NIH
|
| Department |
Laboratory of Genetics and Genomics
|
| Lab |
Computational Biology & Genomics Core
|
| Street address |
251 Bayview Blvd
|
| City |
Baltimore |
| State/province |
Maryland |
| ZIP/Postal code |
21224 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE130727 |
Transcriptome Signature of Cellular Senescence |
|
| Relations |
| BioSample |
SAMN11578994 |
| SRA |
SRX5794340 |
