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Sample GSM959258

Query DataSets for GSM959258

Status

Public on Jul 15, 2013

Title

CLAMP ChIP Kc cells control RNAi replicate 2

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)

[email protected]

Organization name

Brown University

Street address

185 Meeting St.