|
| Status |
Public on Jan 22, 2019 |
| Title |
B_tot-PolII_controlKD_Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
ChIP Seq of Pol II in Ctrl KD
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell line: S2R+
cell type: Embryonic
pulldown: RBP1 (Diagenode Cat No-15200004)
|
| 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 |
| |
|
| Description |
imb_roignant_2017_18_JA_ChIP_Ctrl_PolII_2
|
| Data processing |
Samples were sequencing on an Illumian NextSeq500 and demultiplexed using bcl2fastq v2.19. The libraries contain a Yeast spike in.
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 |
| GSE106908 |
ChIP of PolII from cells with Mago knockdown, control knockdown, and RnpS1 knockdwon [Promoter-proximal pausing mediated by the exon junction complex regulates splicing] |
|
| Relations |
| BioSample |
SAMN08027430 |
| SRA |
SRX3393676 |
