|
Status |
Public on Mar 23, 2011 |
Title |
0-24h Embryo PolII ChIP-Seq extraction4_seq1 aliquote 1 |
Sample type |
SRA |
|
|
Source name |
0-24h Embryo PolII ChIP-Seq extraction4_seq1 channel_1
|
Organism |
Drosophila melanogaster |
Characteristics |
developmental stage: Mixed Embryos 0-24h
|
Growth protocol |
Embryo collection protocol
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Cross linking and chromatin extraction protocol for Drosophila ChIP experiments. Chromatin IP of a chromatin extract with an antibody. Generation of a genomic library suitable for Illumina sequencing, using the standard Illumina protocol. This includes a 150-200bp size selection step. Load sample onto flow cell at a (usually 2-8 pM, variable) concentration and run on an Illumina Genome Analyzer II for single-end sequencing for 36 or 76 nt. Image data is then deconvoluted using the most current versions of Firecrest, Bustard, and Gerald (or equivalents).
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina Genome Analyzer |
|
|
Description |
channel ch1 is input DNA;
|
Data processing |
Illumina_seq_maq_processing:DM:1 protocol. Using the MAQ command-line tool v.0.7.1, reads are converted from Illumina FASTQ to Sanger FASTQ to Binary FASTQ. The Drosophila genome v.5.1 is then converted into binary fasta format. Then the reads are mapped back to the Drosophila genome using maq 0.7.1 with a maximum of 3 mismatches per read and a mapview file is created which is then read into a local relational database. Processed data are obtained using following parameters: genome version is 5.1 ChIPseq_analysis:DM:1 protocol. * WIG Track Generation: o Tracks are read into SPP and informative tags are selected using SPP's select.informative.tags function. o Local sequencing anomalies are removed with SPP's remove.local.tag.anomalies function. o Input subtracted ChIP density wiggle track is output with a step size of 100 and a bandwidth of 100 using SPP's get.smoothed.tag.density function. The tags are shifted 1/2 of the optimal shift size discovered with get.binding.characteristics. o To combine replicates, all the reads were pooled together and the tag shift was estimated as the mean tag shift between the replicates. * GFF3 Peak Call Generation: o MAQ files were converted to ELAND using an in-house script. o The PeakSeq preprocessing scripts were run by an in-house pipeline automation script. o The PeakSeq v.1.01 C++ code was run with the default parameters and a maximum q-val of .05. o To combine replicates, overlapping windows of enrichment between the two sets were combined, and the rest were discarded.
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Submission date |
Mar 21, 2011 |
Last update date |
May 15, 2019 |
Contact name |
DCC modENCODE |
E-mail(s) |
help@modencode.org
|
Phone |
416-673-8579
|
Organization name |
Ontario Institute for Cancer Research
|
Lab |
modENCODE DCC
|
Street address |
MaRS Centre, South Tower, 101 College Street, Suite 800
|
City |
Toronto |
State/province |
Ontario |
ZIP/Postal code |
M5G 0A3 |
Country |
Canada |
|
|
Platform ID |
GPL9058 |
Series (1) |
GSE28068 |
24 Hour RNA PolII ChIP-Seq experiment |
|
Relations |
SRA |
SRX050605 |
BioSample |
SAMN00253861 |