|
| Status |
Public on May 23, 2013 |
| Title |
dme_gd_pol_2to4h_1 |
| Sample type |
SRA |
| |
|
| Source name |
Pol II IP DNA from gd7 embryos expressing the transgene twiBAC-Yellow
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: whole gd7 embryos
tissue type: dorsal ectoderm
genotype: maternally gd7/gd7 mutants and zygotically expressing the transgene twiBAC-Yellow
chip antibody: Pol II (4H8, Millipore)
|
| Treatment protocol |
no treatment, only fixation of embryos in formaldehyde
|
| 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 |
| |
|
| Description |
Pol II IP DNA from gd7 embryos with one copy of a 25kb TwistBAC where the twi coding region has been replaced by the yellow sequence
|
| Data processing |
Reads were aligned to the UCSC dm3 genome with the addition of specific BAC sequences as pseudo-chromosomes with bowtie v0.12.7. Only uniquely aligning reads with up to two mismatches were retained. For paired-end samples, successfully aligned mate pairs were joined to a single fragment.
Genome Build:
gd_pol.bed: dm3
|
| |
|
| Submission date |
Mar 06, 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 (1) |
| GSE36310 |
Tissue specific Pol II Chip-Seq in the early fly embryo |
|
| Relations |
| SRA |
SRX127435 |
| BioSample |
SAMN00809025 |
