|
| Status |
Public on Jan 22, 2019 |
| Title |
HA_RnpS1_RNAseT1_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
ChIP Seq with RnpS1 HA tagged Cells, with Rnase T1
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell line: S2R+ Cells
cell type: Embryonic
chip antibody: anti-HA (F-7) (Santa Cruz, catalog# sc-7392, lot# I0916)
|
| Treatment protocol |
S2R+ cells were fixed with 1% formaldehyde for 3 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 µl of TE
After checking enrichment the recovered DNA was converted into libraries using NebNext Ultra DNA II library preperation kit, following manufacturer's protocol
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
ChIP Seq with RnpS1 HA tagged Cells, with Rnase T1 Rep1
cell culture
|
| Data processing |
The data was sequenced on a HiSeq2500 in a rapid run with a readlength of 68 bp single read (HiSeq Rapid SBS/Cluster Kit v2) . Demultiplexing and fastq file conversion was done using blc2fastq v. 1.8.4.
Mapping was performed using bowtie2 version 2.2.8 against ensemble release 84 of BDGP6. Parameters “-N 1 --phred 33 --fr --end-to-end --maxins 1000 --minins 0 --very-sensitive)
After mapping reads were filtered for uniquely mapping reads using the XS flag.
UCSC compatible library normalized bigwig tracks were produced using samtools version 1.2, ucsc tools (bedGraphToBigWig from 04-11-2012) and bedtools (v. 2.25.0) and custom scripts
Genome_build: BDGP6
Supplementary_files_format_and_content: UCSC compatible library size normalized bigwig tracks
|
| |
|
| Submission date |
Dec 14, 2016 |
| 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 |
GPL17275 |
| Series (2) |
| GSE92386 |
ChIP of RnpS1_HA [Promoter-proximal pausing mediated by the exon junction complex regulates splicing] |
| GSE92389 |
Promoter-proximal pausing mediated by the exon junction complex regulates splicing |
|
| Relations |
| BioSample |
SAMN06141544 |
| SRA |
SRX2422644 |
