|
| Status |
Public on Jun 04, 2020 |
| Title |
DLD-1 cells transfected with NUP153-NeonGreen-AID and treated with Auxin for 2hr replicate1 |
| Sample type |
SRA |
| |
|
| Source name |
DLD-1 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: DLD-1
genotype: NUP153-NeonGreen-AID
agent: Auxin
time point: 2hr
|
| Treatment protocol |
All AID-tagged cell lines were treated with 1 mM auxin (I5148, Sigma Aldrich) for nucleoporins loss for 0hrs or 2/3hrs
|
| Growth protocol |
The human colorectal cancer cell line DLD-1 was cultured in DMEM supplemented with heat-inactivated 10% FBS, antibiotics, and 2 mM GlutaMAX in 5% CO2 atmosphere at 37°C. From 75 to 100K of AID-tagged cells were plated on each well of 6-well plate dishes for RNA isolation. Cells at 85% of confluency were washed with PBS and lysed with RLT buffer.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNAeasy Mini Kit (Qiagen). Extracted RNA was analyzed for 260/280 and RIN value on Bioanalyzer 2100 (Agilent).
TruSeq Standard Total RNA Library Prep Kit (Illumina, San Diego, CA) was used to generate RNA-Seq libraries for the Illumina-platforms. The libraries were prepared by the Molecular Genomics Core at the Eunice Kennedy Shriver National Institutes of Child Health and Human Development (Bethesda, MD) as per manufacture’s guideline using Ribo-Zero Gold.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Replicate 1
|
| Data processing |
We used CASAVA 1.8.2 for the base calling (Illumina, San Diego, CA).
We used STAR aligner version 2.6.1c (Dobin et al., 2013, PMID: 23104886) with the default parameters to map RNA-Seq reads to human reference genome (GRCh38, obtained from Ensembl.org).
We counted the short-reads at the gene level using featureCounts 1.5.2 (Liao et al., 2014, PMID: 24227677). We used "-O" (allowMultiOverlap) and "-p" (isPairedEnd) parameters.
Genome_build: Human reference genome GRCh38 (obtained from Ensembl.org, release 87).
Supplementary_files_format_and_content: Tab-limited text files have human gene IDs (Ensembl 87) as well as read counts from featureCounts.
|
| |
|
| Submission date |
Jun 07, 2019 |
| Last update date |
Jun 04, 2020 |
| Contact name |
Alexei Arnaoutov |
| E-mail(s) |
arnaouta@mail.nih.gov
|
| Organization name |
NICHD
|
| Department |
PCRM
|
| Street address |
49 Convent Dr, Bldg 49 Room 5A10
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE132363 |
Gene expression profiling of human DLD-1 cells after instant depletion of basket nucleoporins |
|
| Relations |
| BioSample |
SAMN11975419 |
| SRA |
SRX5985475 |
