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Sample GSM959255 Query DataSets for GSM959255
Status Public on Jul 15, 2013
Title CLAMP ChIP Kc cells control RNAi replicate 1 Input
Sample type SRA
 
Source name CLAMP ChIP Kc cells control RNAi
Organism Drosophila melanogaster
Characteristics cell line: Kc
Treatment protocol RNAi treatment for 6 days at 25 C
Extracted molecule genomic DNA
Extraction protocol Standard Illumina ChIP-seq (Tru-seq) protocol
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
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.
 
Submission date Jul 11, 2012
Last update date May 15, 2019
Contact name Erica Larschan
E-mail(s) Erica_Larschan@brown.edu
Organization name Brown University
Street address 185 Meeting St.
City Providence
ZIP/Postal code 02912
Country USA
 
Platform ID GPL13304
Series (1)
GSE39271 Synergistic interactions between CLAMP and MSL complex facilitate Drosophila dosage compensation
Relations
SRA SRX159163
BioSample SAMN01087358

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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