 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Dec 01, 2013 |
| Title |
Lu019 |
| Sample type |
SRA |
| |
|
| Source name |
Tralpt_Ctrl
|
| Organism |
Drosophila melanogaster |
| Characteristics |
strain: Tralpt
tissue: ovary
rip antibody: none
|
| Growth protocol |
Oregon Red or transgenic newly-eclosed fruitflies were grown on corn syrup solids with yeast for 2~4 days before ovary dissection. HeLa cells are cultured in DMEM +10%FBS + penicilin/streptomycin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Lysates were clarified from dissected Drosophila ovaries or HeLa cells and RNA-Sm protein complexes were isolated with antibody. RNA was purified from the immunoprecipitate, reverse transcribed and made into doublestranded DNA. Libraries were prepared according to Illumina's instructions. Briefly, DNA was fragmented, ligated to adapters and PCR amplified with Illumina primers for 15 cycles. The resultant DNA was purified from an agarose gel and captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
RIP-seq
|
| Data processing |
A custom D. melanogaster expanded genome was made using the Drosophila genome (dm3, April 2006) and gene annotations. Filtered sequence reads (chastity >=0.6) were mapped to the expanded genome using Bowtie, allowing up to 2 mismatches and 10 mapped locations. Bowtie-mapped files were then analyzed using the ERANGE software to count the number of unique, spliced and multiple reads, and reads that mapped to putative new genes, measured as RPKM (reads per kb per million reads) values.
For HeLa RIP-seq, reads were processed using the Tophat/Cufflinks pipeline
To create the Drosophila wiggle files, sequence files were mapped to D. melanogaster expanded genome and output as sam files, and then converted to UCSC track files using samtools and BEDtools.
To create the human bedgraph files, sequence files were mapped to human genome and output as sam files, and then converted to UCSC track files using samtools and BEDtools.
Genome Build:
Lu019.final.rpkm: dm3
Lu019.newregions.txt: dm3
Lu019.wig: dm3
|
| |
|
| Submission date |
May 28, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Zhipeng Lu |
| E-mail(s) |
zhipengluchina@gmail.com
|
| Organization name |
Stanford University
|
| Department |
Department of Dermatology
|
| Lab |
Howard Chang
|
| Street address |
269 Campus Drive
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL9061 |
| Series (1) |
| GSE35842 |
RIP-seq analysis of eukaryotic Sm proteins identifies three major categories of Sm-containing ribonucleoproteins |
|
| Relations |
| Reanalyzed by |
GSM3283452 |
| SRA |
SRX287104 |
| BioSample |
SAMN02182766 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1149490_Lu019.final.rpkm.gz |
299.6 Kb |
(ftp)(http) |
RPKM |
| GSM1149490_Lu019.newregions.txt.gz |
4.3 Kb |
(ftp)(http) |
TXT |
| GSM1149490_Lu019.wig.gz |
31.9 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
|
|
|
|
 |
