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Sample GSM280090 Query DataSets for GSM280090
Status Public on Apr 30, 2008
Title S2cell (AGO1IP), Flock house virus
Sample type SRA
 
Source name small RNA
Organisms Drosophila melanogaster; Flock House virus
Characteristics from transfected Schneider cells
Treatment protocol tissues and cells were harvested on ice
Growth protocol flies and Schneider cells were grown under standard conditions at 25 degrees.
Extracted molecule total RNA
Extraction protocol extraction of total RNA was with Trizol; extraction of small RNAs from immunoprecipitates was with Phenol/Chloroform; before adaptor ligation, small RNAs were PAGE isolated;
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina Genome Analyzer
 
Description small RNA from immunoprecipitate
Data processing the 5'end of the Solexa read corresponds to the small RNA's 5'end. The 3' linker was computationally removed at the end of all reads if possible; only sequences matching the Drosophila genome with 100% identity are reported with the exception of the AGO1 and AGO2 IP libraries from Schneider cells, where also seqeunces matching NCBI deposited seqeunces for the Flock House Virus with up to 3 mismatches are included.
 
Submission date Apr 07, 2008
Last update date Jun 11, 2013
Contact name Julius Brennecke
E-mail(s) brenneck@cshl.edu
Organization name Cold Spring Harbor Labs
Lab Greg Hannon
Street address 1 Bungtown Road
City Cold Spring Harbor
State/province NY
ZIP/Postal code 11724
Country USA
 
Platform ID GPL9402
Series (1)
GSE11086 Deep sequencing of Drosophila melanogaster small RNAs
Relations
BioSample SAMN02195357

Data table header descriptions
SEQUENCE
COUNT number of times sequenced

Data table
SEQUENCE COUNT
AAAAACACGTGAGAGAAAGCA 1
AAAACAATGACCCTAAAAGTT 1
AAAACAATGACCCTAAAAGTTT 1
AAAACCAACACTCGAAGAAC 0
AAAACCAACACTCGAAGAACG 0
AAAACCAACACTCGAAGAACGA 0
AAAACGAAGAACGCCTCCGA 0
AAAACGAAGAACGCCTCCGAA 0
AAAACGAAGAACGCCTCCGAAA 0
AAAACGCATCAATGTGGGAG 0
AAAACGCATCAATGTGGGAGA 0
AAAACGCCCAATGAGTGTC 0
AAAACGCCCAATGAGTGTCA 0
AAAACGCCCAATGAGTTTCT 1
AAAACGGCAACGATCCCATCG 0
AAAACGTACCACGTAATGGTA 0
AAAAGCTGAGCACTGTACAA 0
AAAAGGATGTCAGGAAAGCC 0
AAAAGGATGTCAGGAAAGCCG 0
AAAAGGTCGGTTATCACAAA 0

Total number of rows: 20338

Table truncated, full table size 474 Kbytes.




Supplementary file Size Download File type/resource
GSM280090_AGO1_IP_S2_raw_data.txt.gz 87.6 Mb (ftp)(http) TXT
Raw data provided as supplementary file
Processed data included within Sample table

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