|
| Status |
Public on Aug 13, 2013 |
| Title |
M1BP sequencing reads |
| Sample type |
SRA |
| |
|
| Source name |
S2R+ cells
|
| Organism |
Drosophila melanogaster |
| Characteristics |
antibody: M1BP antisera generated in a rabbit using recombinant M1BP isolated from E. coli.
cell line: S2R+
|
| Treatment protocol |
Crosslinked chromatin was prepared from cells as described by Petesch, S.J. and J.T. Lis (2008) Cell 134, p 74-84
|
| Growth protocol |
Cells were grown in Schneider's media with 10% FBS at 24 degrees C
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Crosslinked chromatin from 20 million cells was immunoprecipitated by either M1BP antisera or preimmune sera. DNA precipitated from two biologically independent experiments was combined and subjected to library preparation for SOLiD sequencing
DNA libraries were prepared as described by Motallebipour et al. (2009) Genome Biology 10, R129
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
AB SOLiD System 2.0 |
| |
|
| Description |
sequencing reads for DNA crosslinked to M1BP
|
| Data processing |
Sequence reads were obtained and mapped to the Drosophila melanogaster dm3 (April, 2006) genome using Bowtie 1.1.2 with a seed length of 28 nucleotides.
All unique reads mapping with two or fewer mismatches were retained.
The reads on both strands were shifted 50 base pairs towards the center of the ChIP'ed DNA fragments and binned into 25 nucleotide widows to make bedgraph files for both M1BP ChIP-seq and Pre-immune ChIP-seq results.
Genome_build: dm3 (April, 2006)
|
| |
|
| Submission date |
Aug 13, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
David Scott Gilmour |
| E-mail(s) |
[email protected]
|
| Phone |
814-863-8905
|
| Organization name |
Penn State University
|
| Department |
Biochemistry and Molecular Biology
|
| Lab |
Gilmour
|
| Street address |
465 North Frear
|
| City |
University Park |
| State/province |
Pennsylvania |
| ZIP/Postal code |
16802 |
| Country |
USA |
| |
|
| Platform ID |
GPL9521 |
| Series (2) |
| GSE46630 |
The newly identified transcription factor M1BP ad GAGA factor orchestrate distinct mechanisms of transcriptional regulation on paused genes |
| GSE49842 |
ChIP-seq analysis of M1BP in Drosophila S2R+ cells |
|
| Relations |
| BioSample |
SAMN02316508 |
| SRA |
SRX334936 |
