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Status
Public on Jun 05, 2009
Title
Piwi IP from Armi Mutant
Sample type
SRA
Source name
ovaries
Organism
Drosophila melanogaster Characteristics
tissue: ovaries
Treatment protocol
Trizol/Phenol Cholorofom extractions
Growth protocol
24 degrees C
Extracted molecule
total RNA
Extraction protocol
Trizol
Library strategy
RNA-Seq
Library source
transcriptomic
Library selection
size fractionation
Instrument model
Illumina Genome Analyzer II
Description
small RNA sequencing
Data processing
The 36nt long Illumina reads were stripped of the 3’ linker and the resulting small RNA sequences were mapped to the Release 5 genome excluding the Uextra portion. Only reads matching the fly genome 100% were used for further analysis. For annotation, we used Flybase for protein coding genes, UCSC for non-coding RNAs and transposons/repeats (repeat masker tracks) and the most recent miRNA catalog. To control for sequencing depth, small RNA counts were normalized to the same total number after subtracting those matching abundant cellular RNAs such as rRNAs and tRNAs. For the piRNA analysis, we selected small RNAs, which exceeded 22 nt in length and were not annotated as miRNA, tRNA, rRNA, snoRNA, snRNA or smRNA.
Submission date
Jun 04, 2009
Last update date
Jun 11, 2013
Contact name
Colin Dean Malone
E-mail(s)
colin.malone@med.nyu.edu Phone
708-602-2170
Organization name
NYU Medical Center
Department
Skirball Institute - Developmental Genetics
Lab
Lehmann Lab
Street address
NYUMC, Skirball Institute, 540 1st Ave, 4-10
City
New York
State/province
NY
ZIP/Postal code
10016
Country
USA
Platform ID
GPL9061 Series (1)
GSE15186 Specialized piRNA pathways act in germline and somatic tissues of the Drosophila ovary
Relations BioSample
SAMN02198702
Data table header descriptions SEQUENCE seqlen the small RNA sequence length, in nucleotides
mapnum the number of times the small RNA matches the respective genome sequence
COUNT number of times sequenced
Data table SEQUENCE seqlen mapnum COUNT AAAAAAAAAGCGTCGTGTTTGAAGGT
26
1
1
AAAAAAAAGAGAGAAGGCCGAGACCT
26
3
1
AAAAAAAATAAAAGAATTAGTAATAAA
27
1
1
AAAAAAACGGAGCTCAGCGCGCACAC
26
1
1
AAAAAAACGTGGATTAAATGATGAGT
26
1
1
AAAAAAACTCAAGAGGCTGTACATA
25
1
1
AAAAAAAGAAATCGCGCAAGAAACATT
27
1
1
AAAAAAAGGAAAAAAAATAAGATATTC
27
4
1
AAAAAAATATCAGAGGACAATTATC
25
1
2
AAAAAACATGAGCTTGGCGAG
21
1
1
AAAAAACCCGTCAGTTGTACACGTG
25
1
1
AAAAAAGAGAGAAGGCCGAGACCTT
25
3
1
AAAAAAGCCGCTGGGGCCGAACAA
24
1
1
AAAAAAGTAGCAGTGGAAGATTGAATG
27
1
1
AAAAAAGTAGTCACGAAGGACCTGTT
26
6
1
AAAAAATATGAGAAAACTCGCAGTT
25
1
1
AAAAAATGGAAACAGAAAATGCTGTC
26
1
1
AAAAAATGGATATGGTAATTGAGCCAAT
28
1
1
AAAAAATTGAGGGCGTCAGAATCACTT
27
7
1
AAAAACAAAAAGATGGGAAAG
21
1
1
99119 3253 Kbytes .Supplementary file Size Download File type/resource GSM412772_Armi_Mutant_Piwi_IP_NonMappers.csv.gz
588.2 Kb
(ftp) (http) CSV
Processed data included within Sample table
