|
| Status |
Public on Oct 18, 2011 |
| Title |
SuUR_3SG_orc2_ChIP |
| Sample type |
SRA |
| |
|
| Source name |
third instar salivary gland from SuUR
|
| Organism |
Drosophila melanogaster |
| Characteristics |
genotype: SuUR
antibody: orc2 (steve bell lab, MIT)
tissue: third instar salivary gland
|
| Treatment protocol |
Salivary glands were hand dissected from committed wandering third instar larvae directly into EBR medium and frozen within less than 30 min in liquid nitrogen. When enough were collected, ChIP was performed with anti-orc2 from Steve Bell lab (MIT)
|
| Growth protocol |
Drosophila were grown on standard cornmeal, molasses agar media.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was prepared using Illumina ChIP sample prep kit according to instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Data processing |
Alignment: Images acquired were processed by the bundled Illumina image extraction pipeline v1.6 and mRNA-Seq reads were aligned to BDGP Release 5/DM3 using ELAND, using the first 25 bases of a read as a seed. Each matched seed was then extended up to 36 bases and scored to break any ties between multi-matches. For mRNA expression counts, unique reads in the genome that landed within any known exons were counted. The counts were normalized by the mRNA length to get the final RPKM values (reads per KB per million reads).
Peaks: The ChIPâseq reads were mapped back to the Drosophila melanogaster genome (Flybase v.5.2) using MAQ (v.0.7.1) with a maximum of three mismatches per read. For the SG cells, we then used the SPP package to remove anomalous reads and detect peaks using the WTD method. We used maximum estimated enrichment cutoffs of 2.105 and 2.092 in the OrR and SuUR mutant samples respectively as determined by the SPP packagesâs MSER function.
|
| |
|
| Submission date |
Sep 06, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Terry L. Orr-Weaver |
| E-mail(s) |
weaver@wi.mit.edu
|
| Phone |
617-258-5251
|
| Organization name |
Whitehead Institute for Biomedical Research
|
| Lab |
Orr-Weaver
|
| Street address |
9 Cambridge Center
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL9061 |
| Series (2) |
| GSE31899 |
ChIP-Seq of ORC2 bound to third instar salivary gland DNA in WT and mutant Drosophila, analyzed by Illumina sequencing |
| GSE31900 |
Developmental Control of Gene Copy Number by Repression of Replication Initiation and Fork Progression |
|
| Relations |
| SRA |
SRX097296 |
| BioSample |
SAMN00718794 |
