|
Status |
Public on Nov 20, 2014 |
Title |
hek_mock_2.5d |
Sample type |
SRA |
|
|
Source name |
cell culture
|
Organism |
Homo sapiens |
Characteristics |
strain: HEK293 T-Rex FLAG:DICER1 FLP-IN cell line: HEK293
|
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 TOPHAT2 2.06 quantification of GENCODE17 transcript expression with cuffdiff 2.1.1 from CUFFLINKS suite building coverage tracks with samtools and custom scripts Genome_build: hg19 Supplementary_files_format_and_content: wig files with coverage, text file (tab-separated), with FPKM expression values hek.isoforms.fpkm_tracking cuffdiff output, tab-separated text hek.polya.lfc tab-separated text: gene, mock FPKM, DICER1 KD FPKM, DROSHA KD FPKM, Log2 fold-change (DICER1/MOCK), Log2 fold-change (DROSHA/MOCK)
|
|
|
Submission date |
Feb 25, 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) |
GSE55326 |
Transcriptome wide identification of Dicer binding in human and C. elegans reveals a variety of substrates (HEK RNA-Seq) |
GSE55333 |
Transcriptome wide identification of Dicer binding in human and C. elegans reveals a variety of substrates |
|
Relations |
BioSample |
SAMN02664662 |
SRA |
SRX475877 |