NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1149493 Query DataSets for GSM1149493
Status Public on Dec 01, 2013
Title Lu028
Sample type SRA
 
Source name VFP-LSm11_IP
Organism Drosophila melanogaster
Characteristics strain: nosGal4 VFP-LSm11
tissue: ovary
rip antibody: GFP
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:
Lu028.final.rpkm: dm3
Lu028.newregions.txt: dm3
Lu028.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 GSM3283455
SRA SRX287107
BioSample SAMN02182769

Supplementary file Size Download File type/resource
GSM1149493_Lu028.final.rpkm.gz 296.7 Kb (ftp)(http) RPKM
GSM1149493_Lu028.newregions.txt.gz 2.3 Kb (ftp)(http) TXT
GSM1149493_Lu028.wig.gz 24.7 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap