|
| Status |
Public on Nov 20, 2014 |
| Title |
cel_dcr1_2.5d |
| Sample type |
SRA |
| |
|
| Source name |
young adult nematodes
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
developmental stage: young adult
strain: fem-1
|
| Treatment protocol |
RNAi by feeding
|
| Growth protocol |
fem-1 strain, sterile control animals to compare to dcr-1 loss of function animals (induces sterility)
|
| 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 ce6 with TOPHAT2 2.06
quantification of wormbase transcript expression with cuffdiff 2.1.1 from CUFFLINKS suite
building coverage tracks with samtools and custom scripts
correction for different coverage along transcript length (see Suppl. methods) with custom script
Genome_build: ce6 (WS190)
Supplementary_files_format_and_content: wig files with coverage, text file (tab-separated), with FPKM expression values
cel.isoforms.fpkm_tracking cuffdiff output, tab-separated text
dcr1_2.5.fpkm.lfc tab-separated text: gene, mock FPKM (corrected), dcr-1 KD FPKM (corrected), Log2 fold-change
drosha_2.5.fpkm.lfc tab-separated text: gene, mock FPKM (corrected), drsh1 KD FPKM (corrected), Log2 fold-change
|
| |
|
| 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 |
GPL13657 |
| Series (2) |
| GSE55329 |
Transcriptome wide identification of Dicer binding in human and C. elegans reveals a variety of substrates (CEL RNA-Seq) |
| GSE55333 |
Transcriptome wide identification of Dicer binding in human and C. elegans reveals a variety of substrates |
|
| Relations |
| BioSample |
SAMN02664674 |
| SRA |
SRX475895 |
