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Status |
Public on Jun 04, 2020 |
Title |
DLD-1 cells transfected with AID-NeonGreen-TPR replicate1 |
Sample type |
SRA |
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Source name |
DLD-1 cells
|
Organism |
Homo sapiens |
Characteristics |
cell line: DLD-1 genotype: AID-NeonGreen-TPR agent: NA time point: NA
|
Treatment protocol |
All AID-tagged cell lines were treated with 1 mM auxin (I5148, Sigma Aldrich) for nucleoporins loss for 0hrs or 2/3hrs
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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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
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|
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.
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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 |
SAMN11975389 |
SRA |
SRX5985463 |