|
| Status |
Public on Dec 19, 2013 |
| Title |
alg-3/4 males 20°C mRNA |
| Sample type |
SRA |
| |
|
| Source name |
alg-3(tm1155); alg-4(ok1041); fog-2(q71) males 20°C
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
barcode: 5' barcode (C) GCTG
barcode: 3' barcode (1) CTGTAGGCACCATCAAT
genotype/variation: alg-3/4
culture conditions: 20°C
|
| Treatment protocol |
For mRNA sequencing, polyA RNA was purified from total RNA using the PolyATtract mRNA Isolation System (Promega); each sample was purified twice. The mRNA was fragmented by base hydrolysis at 95°C for 9.5 min in Sodium carbonate buffer, and 2’,3’-cyclic phosphates were resolved with T4 Polynucleotide Kinase (NEB). mRNA fragments with an average length of ~200 nt were purified from an 8% polyacrylamide/8M urea gel
|
| Growth protocol |
C. elegans worm grown at 20°C and 25°C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
3' ligation followed by circularization
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sample name: alg3420mseq
alg-3/4 males 20°C mRNA
mRNA profiling
|
| Data processing |
Remove 5' barcode and 3' barcode (or called linker)
Map the reads to WS215 genome and annotation
A custom PERL pipeline is used to summarize reads and generate histogram at single nt level.
Generic genome browse is used to visualize the data
Genome_build: WBcel215 (WormBase WS215)
Supplementary_files_format_and_content: txt format table for sequence and read number mapping the genome
|
| |
|
| Submission date |
Aug 08, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Craig Mello |
| Organization name |
University of Massachusetts Medical School
|
| Department |
Program in Molecular Medicine
|
| Lab |
Craig Mello
|
| Street address |
368 Plantatoin Street, Suite AS5-2047
|
| City |
Worcester |
| State/province |
MA |
| ZIP/Postal code |
01605 |
| Country |
USA |
| |
|
| Platform ID |
GPL13657 |
| Series (1) |
| GSE49672 |
Argonautes promote male fertility and provide a paternal memory of germline gene expression in C. elegans |
|
| Relations |
| BioSample |
SAMN02314098 |
| SRA |
SRX333010 |
