|
| Status |
Public on Dec 20, 2012 |
| Title |
Pol II ChIP-seq from Drosophila Toll10b mutant embryos, 8WG16 antibody, replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
Toll10b mutant
|
| Organism |
Drosophila melanogaster |
| Characteristics |
genetic background: embryos were collected from Toll10b/+ females obtained from a balanced stock (Toll10b/TM3, Sb, Ser and Toll10b/OR60)
time point: 02 to 04h AEL
chip antibody: Pol II (8WG16, Covance)
chip antibody manufacturer: Covance
chip antibody catalog #: 8WG16
|
| 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 |
ChIP-seq: DNA-protein-complexes were isolated with specific antibodies. Sequencing libraries were prepared following Illumina's instructions: DNA was end repaired using T4 DNA polymerase, DNA polymerase I large fragment (Klenow polymerase) and T4 polynucleotide kinase. A single 3'-A overhang was added to the blunted ends using Klenow 3'-5' exo- polymerase. Adapters with single 3'-T overhangs were ligated to the adenylated fragments, and after a size-selection step on a 2 % agarose gel (150-250 bp) the adapter modified DNA was PCR-amplified. Following cluster generation on the flowcell surface, the sequencing libraries were sequenced following Illumina's protocol.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
toll10b_pol_8wg16_1.bed; genome build: dm3
Reads were trimmed to 18bp and aligned to the UCSC dm3 genome with bowtie v0.12.7. Only uniquely aligning reads with up to two mismatches were retained. Aligned reads were then extended to the estimated average insert size of each library as measured by a Bioanalyzer.
|
| |
|
| Submission date |
Dec 09, 2011 |
| 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) |
| GSE34301 |
Poised RNA Polymerase II changes over developmental time and prepares genes for future expression (ChIP-seq data) |
| GSE34304 |
Poised RNA Polymerase II changes over developmental time and prepares genes for future expression |
|
| Relations |
| SRA |
SRX110772 |
| BioSample |
SAMN00764922 |
