|
Status |
Public on Jan 23, 2020 |
Title |
Hap1 SPRING KO clone 14/rescue - 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_5_Hap1_C12orf49_clone_14_rescue_IMDM_ACTTGAA_S29
|
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 |
SAMN13836406 |
SRA |
SRX7546656 |