|
| Status |
Public on Jan 22, 2019 |
| Title |
Control KD_K4Me3_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
ChIP Seq of K4Me3 in Ctrl KD
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell line: S2R+
cell type: Embryonic
chip antibody: Ab8580 (anti H3K4Me3)
|
| Treatment protocol |
S2R+ cells were fixed with 1% formaldehyde for 10 min at room temperature, and harvested in SDS buffer resuspended in RIPA buffer (140 mM NaCl, 10 mM Tris-HCl [pH 8.0], 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% DOC), and lysed by sonication. The lysate was cleared by centrifugation, and incubated with respective antibodies overnight at 4¡C. Antibody complexes bound to protein G beads, were washed once with 140mM RIPA, four times with 500mM RIPA, one with LiCl buffer and twice with T.E buffer for 10 minutes each at 4¡C.
|
| Growth protocol |
Drosophila S2R+ cells were cultured in Schneider Cell’s Medium (GIBCO, Cat No-21720) supplemented with 10% FBS and 2% Penicillin/Streptomycin
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was recovered after reverse crosslinking and phenol chloroform extraction. After precipitating and pelleting, DNA was dissolved in 30 _l of TE
After checking enrichment the recovered DNA was converted into libraries using NebNext Ultra DNA library preperation kit, following manufacturer's protocol
NebNext UltraII
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Samples were sequencing on an Illumian NextSeq500 and demultiplexed using bcl2fastq v2.19
Mapping was done using bowtie2 (v. 2.2.8) against BDGP6 fo the Drosophila genome
Bigwig tracks were produced using bedTools (v.2.25) and bedGraphToBigwig
Genome_build: BDGP6
Supplementary_files_format_and_content: sequencing depth normalised bigwig tracks
|
| |
|
| Submission date |
Nov 15, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jean-Yves Roignant |
| Organization name |
Institute of molecular Biology
|
| Lab |
Roignant
|
| Street address |
Ackermannweg 4
|
| City |
Mainz |
| ZIP/Postal code |
55128 |
| Country |
Germany |
| |
|
| Platform ID |
GPL19132 |
| Series (2) |
| GSE92389 |
Promoter-proximal pausing mediated by the exon junction complex regulates splicing |
| GSE106904 |
ChIP of K4Me3 in Ctr condition and Mago knockdown [Promoter-proximal pausing mediated by the exon junction complex regulates splicing] |
|
| Relations |
| BioSample |
SAMN08027410 |
| SRA |
SRX3393634 |
