|
| Status |
Public on Jan 23, 2020 |
| Title |
Hap1 CTRL + sterols |
| Sample type |
SRA |
| |
|
| Source name |
Hap1 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Hap1
dna content: Haploid
|
| Growth protocol |
Cells were plated and subsequently cultured in sterol-contaning or sterol-depletion medium for 24 hrs before extraction of RNA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with the Trizol protocol
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
3864_2_Ctrl_Hap1_sterol_depletion_ACAGTGA_S26
|
| Data processing |
Basecalling and demultiplexing was performed using the standard Illumina pipeline
The reads were mapped to the human reference genome (GRCh38) using TopHat (version 2.1.0).
TopHat was supplied with a known set of gene models based on Ensembl GTF version 77 and was guided to use the first-strand as the library-type. As additional parameters --prefilter-multihits and –no coverage were used.
Genecounts were generated using a custom script, based on HTSeq-count, that generates counts per gene.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-separated file with number of reads per gene/sample.
|
| |
|
| Submission date |
Jan 13, 2020 |
| Last update date |
Jan 23, 2020 |
| Contact name |
Noam Zelcer |
| Organization name |
AUMC
|
| Department |
Medical Biochemistry
|
| Street address |
Meibergdreef 9
|
| City |
Amsterdam |
| ZIP/Postal code |
1105AZ |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE143530 |
A suite of haploid genetic screens identifies SPRING as a novel determinant of SREBP signaling and cholesterol metabolism |
|
| Relations |
| BioSample |
SAMN13836409 |
| SRA |
SRX7546653 |
