|
| Status |
Public on Jul 25, 2013 |
| Title |
ChIP-seq TBP in pre-MBT embryos (replicate 1) |
| Sample type |
SRA |
| |
|
| Source name |
Staged embryos
|
| Organism |
Drosophila melanogaster |
| Characteristics |
Stage: pre-MBT 01to02h AEL
genotype: Oregon-R
ChIP: TBP
antibody vendor/catalog: rabbit poly-antibody against dTBP
|
| Growth protocol |
D. melanogaster embryos were collected and aged on yeasted apple juice plates at 25 °C and 60 % humidity.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Each ChIPs were performed as previously described (Zeitlinger 2007) using 200ul embryos for pre-MBT embryos and 50ul for older embryos. Libraries were prepared from the immunoprecipitated DNAs using the Paired-End DNA Sample Preparation Kit (Illumina: PE-102-1001) but with a modified protocol. To remove adapter dimers, biotin-labeled dATP (Invitrogen: 19524-016) was added in the A-tailing reaction after end-repair. After ligation to the PE adaptor, the samples were incubated with streptavidin beads (Invitrogen: 650-01) in 500ul binding buffer at room temperature for 15min. DNA bound to the beads was then washed twice with 800ul binding buffer with0.05% Tween 20, twice with NEB buffer 2 and resuspended in 31ul NEB buffer 2. The PCR reaction was then performed according to the Illumina protocol.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Base calls were performed using the default settings of CASAVA
Reads were aligned to the UCSC dm3 genome using Bowtie 0.12.8, allowing only unique alignments with up to 2 mismatches
Genome_build: UCSC dm3
Supplementary_files_format_and_content: BED file containing aligned reads after extending to estimated insert size of the library (fragment size of paired-end samples was determined by read pair alignments)
|
| |
|
| Submission date |
Oct 19, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Julia Zeitlinger |
| E-mail(s) |
jbz@stowers.org
|
| Organization name |
Stowers Institute for Medical Research
|
| Lab |
Zeitlinger Lab
|
| Street address |
1000 E 50th St
|
| City |
Kansas City |
| State/province |
MO |
| ZIP/Postal code |
64110 |
| Country |
USA |
| |
|
| Platform ID |
GPL11203 |
| Series (2) |
| GSE41700 |
A global change in RNA Polymerase II pausing during the Drosophila midblastula transition [ChIP-seq] |
| GSE41703 |
A global change in RNA Polymerase II pausing during the Drosophila midblastula transition |
|
| Relations |
| SRA |
SRX197583 |
| BioSample |
SAMN01773236 |
