|
| Status |
Public on Sep 04, 2012 |
| Title |
ser5p_r2 |
| Sample type |
SRA |
| |
|
| Source name |
wing imaginal discs
|
| Organism |
Drosophila melanogaster |
| Characteristics |
genotype/variation: LID RNAi mutant
developmental stage: third instar larvae
tissue: wing imaginal discs
chip antibody: POLIISER5 [anti-PolIIS5P]
antibody vendor: Abcam
antibody catalog number: ab5131
|
| Treatment protocol |
LID RNAi strain was obtained from NIG-FLY and it was combined with lidk06801. For every sample, around 800 wing imaginal discs were dissected in PBS
|
| Growth protocol |
CantonS or lidk06801;act5Cgal4>lid RNAi larvae were grown at 25ºC until they became wall-climbing third instar larvae.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Discs were crosslinked in 1.8% formaldehyde solution and sonicated. DNA-protein complexes were immunoprecipitated with anti-PolIIS5P (ab5131) or anti-PolIIS2P (ab5095) antibodies. Libraries were prepared according to Illumina's instructions accompanying the ChIP-Seq DNA Sample Prep Kit (Part# IP-102-1001). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 16 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced for 40 (H3K4me3) and 36 (LID) nucleotides on the Genome Analyzer II following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Data processing |
Reads were aligned to the dm3 genome with Bowtie 0.12.5, setting the parameters -n 2 -m 1
Peaks were called with Bioconductor htSeqTools package, using functions enrichedRegions and enrichedPeaks succesively
Genome_build: dm3
Supplementary_files_format_and_content: bed files with "aligned" in the file name contain aligned reads as returned by Bowtie.
Supplementary_files_format_and_content: Peaks were called with Bioconductor.
|
| |
|
| Submission date |
Sep 04, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
David Rossell |
| E-mail(s) |
[email protected]
|
| Organization name |
IRB Barcelona
|
| Street address |
Baldiri Reixac 10
|
| City |
Barcelona |
| ZIP/Postal code |
08028 |
| Country |
Spain |
| |
|
| Platform ID |
GPL9061 |
| Series (2) |
| GSE27081 |
Drosophila dKDM5/LID regulates H3K4me3 dynamics at the transcription start site of actively transcribed developmental genes |
| GSE40599 |
POLIISER5 and POLIISER2 ChIP-Seq in mutant RNAi LID Drosophila Melanogaster |
|
| Relations |
| SRA |
SRX182775 |
| BioSample |
SAMN01161952 |
