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Status
Public on Apr 30, 2009
Title
Vasa 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
Mar 11, 2009
Last update date
May 15, 2019
Contact name
Colin Dean Malone
E-mail(s)
[email protected] 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 SRA
SRX005005 BioSample
SAMN02197894
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 AAAAAAAAACGAAAAGCACAGTATG
25
1
1
AAAAAAAAACGGAAAAATG
19
2
1
AAAAAAAAAGAACAGCATGA
20
1
1
AAAAAAAAAGCGAAGGGAAAT
21
1
1
AAAAAAAAAGGGCAATCA
18
31
14
AAAAAAAAAGGGCAATCAATGC
22
31
2
AAAAAAAACAGTAATTGGTTTTAGTC
26
1
1
AAAAAAAACCTAACTTACAATGTGT
25
7
1
AAAAAAAACTCTTGGTCTGAG
21
1
1
AAAAAAAAGAGCAAAAGGAAAC
22
1
1
AAAAAAAAGAGGATGGAAAAT
21
14
1
AAAAAAAAGGAGGAGGAGC
19
1
1
AAAAAAAAGGGAGAGAAAA
19
1
1
AAAAAAAAGGGCAATCA
17
31
5
AAAAAAAAGGGCAATCAATG
20
31
7
AAAAAAAAGGGCAATCAATGC
21
31
6
AAAAAAAAGGGCAATCAATGCC
22
31
3
AAAAAAAAGTTGGCATCTAGGTCAGAG
27
1
1
AAAAAAAATAACCGTCACTA
20
1
1
AAAAAAAATCGTTGCACCGTT
21
2
1
382600 11951 Kbytes .Supplementary file Size Download File type/resource GSM379064_Vasa_Mutant_NonMappers.csv.gz
8.3 Mb
(ftp) (http) CSV
SRA Run Selector Processed data included within Sample table Raw data are available in SRA
