|
Status |
Public on Jul 22, 2014 |
Title |
Drosophila sechellia male body small RNA |
Sample type |
SRA |
|
|
Source name |
male bodies
|
Organism |
Drosophila sechellia |
Characteristics |
tissue: abdomen and thorax
|
Extracted molecule |
total RNA |
Extraction protocol |
Male bodies were isolated in bulk using sieves. Animals were flash frozen in liquid nitrogen followed by vortexing. This procedure severs heads from the thorax and abdomen allowing separation of these two body parts when sifted through chilled fine mesh sieves. Here we used a .600mm sieve to collect male bodies. Total RNA was then extracted from the bodies using TRIzol according to manufacturer protocol. For Illumina GAII Libraries: From total RNA, ~18-26 nt fraction was isolated using PAGE and cloned using ligation to adapters requiring 5' monophosphate and 3' OH. For Illumina HiSeq Library: Libraries were created with the Illumina truseq small RNA cloning kit using a modified protocol. Small RNAs in the 18-29nt size range were first isolated from total RNA by PAGE purification before cloning. PAGE purification was also performed after ligation of RNAs to 3’ and 5’ linkers before processing in subsequent steps. All enzymatic reactions and oligos were used as indicated by manufacturer.
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
size fractionation |
Instrument model |
Illumina Genome Analyzer II |
|
|
Data processing |
3' adapter sequences were trimmmed using the fastx_clipper utility reads < 15nt in size were filtered identical read sequences were collapsed using the fastq_collapser utility Supplementary_files_format_and_content: read count table files (columns are read read sequence and number of reads)
|
|
|
Submission date |
Mar 26, 2014 |
Last update date |
May 15, 2019 |
Contact name |
Jaaved Mohammed |
E-mail(s) |
jaavedm@stanford.edu
|
Organization name |
Stanford University
|
Department |
Chemical and Systems Biology
|
Lab |
Joanna Wysocka
|
Street address |
265 Campus Drive
|
City |
Stanford |
State/province |
CA |
ZIP/Postal code |
94305 |
Country |
USA |
|
|
Platform ID |
GPL10071 |
Series (1) |
GSE56244 |
Small RNAs from four Drosophila melanogaster-subgroup species |
|
Relations |
BioSample |
SAMN02708805 |
SRA |
SRX501656 |