|
| Status |
Public on Jun 16, 2021 |
| Title |
HEK293_RNA_Seq |
| Sample type |
SRA |
| |
|
| Source name |
HEK293
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293
|
| Treatment protocol |
-
|
| Growth protocol |
Cells were cultured in complete DMEM medium (Sigma), 10% fetal bovine serum (Sigma), 2 mg/ml L-alanyl-Lglutamine (Biological Industries Israel), 100 U/ml penicillin, 0.1 mg/ml streptomycin (Biological Industries Israel) at 37 °C in a humidified atmosphere with 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Trizol reagent (Sigma).
Deep sequencing libraries were prepared using TruSeq Stranded mRNA library preparation kits as per the manufacturer’s instructions. Sequencing of 125-bp paired-end reads was performed using an Illumina HiSeq 2000.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
paired reads were trimmed to keep only the first 100 bps
Raw reads were aligned to human genome assembly hg19 using tophat2 (Kim et al. 2013) with default parameters
Only uniquely mapped reads were kept and PCR duplicated were removed
Fragments Per Kilobase Million (FPKM) normalized reads were calculated using Cufflinks (Trapnell et al. 2010)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample
|
| |
|
| Submission date |
Feb 06, 2020 |
| Last update date |
Jun 16, 2021 |
| Contact name |
Matan Sorek |
| E-mail(s) |
matan.sorek@mail.huji.ac.il
|
| Phone |
972-2-6585144
|
| Organization name |
The Hebrew University of Jerusalem
|
| Department |
Genetics
|
| Lab |
Prof. Eran Meshorer
|
| Street address |
Edmond J. Safra Campus
|
| City |
Jerusalem |
| ZIP/Postal code |
91904 |
| Country |
Israel |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE144906 |
Intron looping is mediated during transcription by U1 snRNP and RNA polymerase II [RNA-Seq] |
| GSE145092 |
Intron looping is mediated by U1 snRNP and RNA polymerase II co-transcriptionally |
|
| Relations |
| BioSample |
SAMN14052700 |
| SRA |
SRX7692089 |
