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| Status |
Public on Aug 31, 2017 |
| Title |
OSS_146_NUN_siPIWI_siPAF1 |
| Sample type |
SRA |
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| Source name |
OSS_NUN_siPIWI_siPAF1
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| Organism |
Drosophila melanogaster |
| Characteristics |
cell line: OSS
cell type: ovarian follicle cell culture
sirna knockdown of: both PAF1 and PIWI
rna extracted from: NUN pellets
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| Treatment protocol |
For each experiment, 500 pmoles siRNAs were electroporated into a 10cm plate of OSS cells using Amaxa kit V (program D013), and cells were cultured for 6 days before harvesting.
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| Growth protocol |
OSS cells were cultured in a customly assembled media comprised of fly extract, M13 media, FBS, insulin, and glutathione. See the full protocol from Lau et al, Genome Res, 2009.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from NUN pellets or cytoplasm lysates were extracted with the Tri-reagent protocol of Chomzcynski and and Sacchi, 1987.
New Englad Bioloabs, NEBNext Ultra Directional RNA Library Prep Kit for Illumina.
Eight libraries with different barcodes were multiplexed in each sequencing run. Separation of sequences by different barcodes was conducted during the on-instrument base-calling.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Illumina Nextseq 500 on instrument base calling
FastX initial quality score trimming and filtering of reads against structural RNAs, microRNAs, viral RNAs
Mapped to the Drosophila melanogaster reference genome, build Dm3 / Release 5, with Bowtie, allowing up to 2 mismatches
For just the 146_NUN set (siGFP, siPIWI, siPAF1 and siPIWI+siPAF1), a "jackpot" reads filter was applied to remove any sequences whose read count was greater than 50 reads.
SAM file of reads counted against RefSeq database of all Drosophila transcripts, counts per locus region and both strands measured
Genome_build: Drosophila melanogaster genome build Release 5.1, Dm3
Supplementary_files_format_and_content: text file tab-delimited tables of read counts mapped to refseq transcripts
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| Submission date |
Jul 25, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
NELSON LAU |
| E-mail(s) |
[email protected]
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| Organization name |
Boston University School of Medicine
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| Department |
Biochemistry
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| Street address |
72 E Concord St K219, Dept of Biochemistry
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| City |
BOSTON |
| State/province |
MA |
| ZIP/Postal code |
02118 |
| Country |
USA |
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| Platform ID |
GPL19132 |
| Series (1) |
| GSE84766 |
Paf1 modulates Piwi/piRNA silencing capacity in Drosophila |
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| Relations |
| Reanalyzed by |
GSM3281704 |
| BioSample |
SAMN05437376 |
| SRA |
SRX1973484 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2249873_processed_OSS_146_NUN_siPIWI_siPAF1.fastq-50-0.02.txt.gz |
1.3 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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