|
| Status |
Public on Nov 20, 2014 |
| Title |
hek_drosha_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 |
SAMN02664661 |
| SRA |
SRX475879 |
