|
Status |
Public on Nov 20, 2014 |
Title |
hek_drosha_siRNA1_18h |
Sample type |
SRA |
|
|
Source name |
cell culture
|
Organism |
Homo sapiens |
Characteristics |
cell line: HEK293 strain: HEK293 T-Rex FLAG:DICER1 FLP-IN transfection: DROSHA siRNA1, 18h
|
Treatment protocol |
RNAi by transfection
|
Extracted molecule |
polyA RNA |
Extraction protocol |
TRIZOL Default Illumina RNA-Seq for HiSeq2000 (TruSeq)
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
|
|
Data processing |
Illumina base calling, demultiplexing, and FASTQ conversion with CASAVA-1.8.2 alignment to hg19 with STAR quantification of GENCODE transcript expression with HT-seq normalized log2 fold-changes computed with edgeR Genome_build: hg19 Supplementary_files_format_and_content: text file (tab-separated), with read counts (HT-Seq) and normalized log2 fold-changes by edgeR Supplementary_files_format_and_content: tab-separated text: gene, log(CPM) [counts per million], normalized Log2 fold-change, P-value estimate (in absence of replicates this is unreliable and was not used).
|
|
|
Submission date |
Nov 19, 2014 |
Last update date |
May 15, 2019 |
Contact name |
Marvin Jens |
E-mail(s) |
marvin.jens@mdc-berlin.de
|
Phone |
+493094062989
|
Organization name |
Max Delbrueck Center for Molecular Medicine
|
Department |
Systems Biology of Gene Regulatory Elements
|
Lab |
Rajewsky lab
|
Street address |
Robert Rössle Str. 10 (H. 87)
|
City |
Berlin |
ZIP/Postal code |
13092 |
Country |
Germany |
|
|
Platform ID |
GPL11154 |
Series (2) |
GSE55333 |
Transcriptome wide identification of Dicer binding in human and C. elegans reveals a variety of substrates |
GSE63475 |
A variety of Dicer substrates in human and C. elegans (HEK RNA-seq) |
|
Relations |
BioSample |
SAMN03201485 |
SRA |
SRX763961 |