 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Sep 01, 2014 |
| Title |
strain9_x_strain160-Input-Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Strain9_x_Strain160
|
| Organism |
Drosophila virilis |
| Characteristics |
strain: Strain9 x Strain160
chip-antibody: none, sonicated input
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Flies were put on yeast for 2-3 days and 100 ovaries per IP condition were dissected. Ovaries were fixed for 10 min at RT using 1% paraformaldehyde (PFA) followed by 5 min quenching at RT by directly adding glycine (final concentration 25mM) and 3 washes in PBS. Ovaries were slightly dounced in Farnham Buffer (5mM HEPES pH8.0; 85mM KCl; 0.5% NP-40/Igepal; NaCl Protease Inhibitor Cocktail; NaF 10mM; Na3VO4 0.2mM), palleted, followed by strong douncing in RIPA Buffer (20mM Tris pH7.4; 150mM; 1% NP-40/Igepal; 0.5% Sodium Deoxycholate; 0.1% SDS; Protease Inhibitor Cocktail; NaF 10mM; Na3VO4 0.2mM) prior to sonication using a Bioruptor from Diagenode on medium power for 20 cycles (30sec ON, 30sec OFF). Samples were then centrifuged, supernatant collected and pre-cleared for 2h at 4ºC using Dynabeads Protein G (Invitrogen). Antibodies were conjugated to Dynabeads Protein G for 2h at 4ºC. A sample of 5% of the pre-cleared supernatant was saved as input control fraction and the rest was incubated with the antibody-conjugated beads for 2h at 4ºC. The beads were washed 5 times at 4ºC using LiCl IP Buffer (10mM Tris ph7.5; 500mM LiCL; 1% NP-40/Igepal; 1% Sodium Deoxycholate), once with TE. Samples were digested in Proteinase K Buffer (200mM Tris ph7.4; 25mM EDTA; 300mM NaCL; 2% SDS) with 100µg of proteinase K. Samples for 3h at 55ºC and revers-crosslinked overnight at 65ºC. DNA was extracted following standard phenol-chloroform extraction and concentration was measured by Qubit.
Libraries were generated following Illumina's DNA Sample Prep Kit protocol
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
strain9_x_strain160-Input-Rep2
|
| Data processing |
base calling: Casava1.8
read alignment, RNA-seq data: TopHat 2.0.8
read alignment, ChIP-seq data: Bowtie 0.12.7
bedgraph track generation: custom-written python script
Genome_build: droVir2
Supplementary_files_format_and_content: bedgraph of read coverage, normalized to RPM (Read Per Million)
|
| |
|
| Submission date |
Jul 31, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Georgi Kolev Marinov |
| Organization name |
STANFORD UNIVERSITY
|
| Department |
Genetics
|
| Street address |
279 Campus Drive West, Beckman Center, B-257A/259
|
| City |
Stanford |
| State/province |
California |
| ZIP/Postal code |
94305-5101 |
| Country |
USA |
| |
|
| Platform ID |
GPL13313 |
| Series (1) |
| GSE59965 |
A trans-generational epigenetic process defines piRNA biogenesis in Drosophila virilis |
|
| Relations |
| BioSample |
SAMN02948123 |
| SRA |
SRX667341 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1462853_strain9_x_strain160-Input-Rep2.bedGraph.gz |
62.6 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
