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| Status |
Public on Jul 15, 2013 |
| Title |
mRNA-seq CLAMP RNAi SL2 |
| Sample type |
SRA |
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| Source name |
mRNA-seq CLAMP RNAi SL2
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| Organism |
Drosophila melanogaster |
| Characteristics |
cell line: SL2
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| Treatment protocol |
RNAi treatment for 6 days at 25 C
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| Extracted molecule |
total RNA |
| Extraction protocol |
Standard Illumina mRNA-seq (Tru-seq) protocol
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Alignment to Drosophila Melanogaster genome, dm3 assembly, with bowtie software, allowing at most 1 mismatch and discarding reads that do not align uniquely (parameters: -v 1 -m 1 )
Aligned reads from sample replicates were pooled
To produce wig files read counts from both input and ChIP samples were calculated within 20bp bins across the genome. A pseudocount of one was added to both input and ChIP counts to prevent undefined ratios. Counts were further normalized by the total number of reads in the sample. Enrichment within each bin was then calculated as the log(2) ratio of sample-size normalized ChIP read counts to sample-size normalized input read counts.
Genome_build: dm3
Supplementary_files_format_and_content: Scores in wig files represent input-normalized CLAMP enrichment, calculated from pooled replicates in control S2 cells, control KC cells, and S2 cells treated with MSL2 RNAi.
Supplementary_files_format_and_content: RPKM values were calculated from each RNA-Seq sample by first computing the total number reads that overlap the coding sequence of each gene. These counts were then normalized to RPKM by normalizing to coding sequence length and by total sample reads.
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| Submission date |
Jul 11, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Erica Larschan |
| E-mail(s) |
[email protected]
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| Organization name |
Brown University
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| Street address |
185 Meeting St.
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| City |
Providence |
| ZIP/Postal code |
02912 |
| Country |
USA |
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| Platform ID |
GPL13304 |
| Series (1) |
| GSE39271 |
Synergistic interactions between CLAMP and MSL complex facilitate Drosophila dosage compensation |
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| Relations |
| Reanalyzed by |
GSM3278693 |
| SRA |
SRX159175 |
| BioSample |
SAMN01087370 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM959267_rnaseq_s2cells_clamp_rnai_paired_rep1.rpkm.gz |
350.1 Kb |
(ftp)(http) |
RPKM |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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