|
| Status |
Public on Dec 22, 2011 |
| Title |
ELL-309 ChIP-Seq |
| Sample type |
SRA |
| |
|
| Source name |
Schneider's Drosophila Line 2
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell type: S2; Schneider's Drosophila Line 2; Marco Blanchette's Lab
cell line: S2
antibody: in house Rabbit anti-ELL-fl (aa 1-1079)
|
| Treatment protocol |
Cells were fixed for 10 minutes in 1% formaldehyde, quenched with the addition of 1/10 volume of 2.5 M Glycine in PBS for 10 minutes, cells were washed twice in PBS, resuspended in hypotonic buffer and nutated for 10 minutes.3x10e7 cells were pelleted and resuspended in 1.3 ml RIPA buffer with 0.5% Sarkosyl.Cells were sonicated in polyethylene 15 ml tubes for 15 minutes, high output, in a Bioruptor Diagenode) at 4 degrees. Debris was pelleted 10 minutes at 20,000 x g 4° C. ChIP was performed with 200 µl of chromatin and 5 µg of antibodies, and scaled up 10 fold for ChIP-seq.
|
| Growth protocol |
Drosophila chromatin immunoprecipitation was performed with S2 cells grown in Schneider's media with 10% FBS at room temperature.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP libraries were prepared with the Illumina DNA Sample Kit (Part# 0801-0303) according to Illumina's instructions and sequenced on the Genome Analyzer IIx following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
Chromatin IP against ELL-FL
|
| Data processing |
Sequencing reads were acquired through the primary Solexa image analysis pipeline, where bases were called and reads were filtered for quality, according to default Solexa standards. Filtered reads were then aligned to the fly genome (UCSC dm3) using the Bowtie (10) alignment tool, version 0.12.7. Only those sequences that matched uniquely to the genome with up to two mismatches were retained for subsequent analysis.Enriched regions of ChIP-seq signal were determined by the âMACSâ (11) peak-finding program, version 1.4.0rc2. Sequence reads for each ChIP-seq dataset and their associated whole-cell extract controls were used for the input and control file, respectively. The effective genome size was configured appropriately for the fly datasets, and the p-value cutoff was set to 1.00e-05 and a fold-change greater than five, or FDR < 1%. All other MACS parameters were left default.
|
| |
|
| Submission date |
Sep 14, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Alexander (Garrett) Garruss |
| E-mail(s) |
asg@stowers.org
|
| Organization name |
Stowers Institute for Medical Research
|
| Lab |
Shilatifard
|
| Street address |
1000 East 50th Street
|
| City |
Kansas CIty |
| State/province |
Missouri |
| ZIP/Postal code |
64110 |
| Country |
USA |
| |
|
| Platform ID |
GPL11203 |
| Series (1) |
| GSE32120 |
The little elongation complex (LEC) regulates small nuclear RNA transcription |
|
| Relations |
| SRA |
SRX097620 |
| BioSample |
SAMN00718945 |
