|
| Status |
Public on Feb 08, 2019 |
| Title |
input_DNA_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
inpu_DNA_ovaries
|
| Organism |
Drosophila melanogaster |
| Characteristics |
genotype: w1118
tissue: ovary
chip antibody: input
|
| Growth protocol |
Approximately 1000 ovary pairs were used in each ChIP-Seq experiment from young w1118 females raised at 25°C, 70% humidity on standard Drosophila medium
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Dissected ovaries were fixed in 1% formaldehyde, lysed and sonicated. Part of the lysate was kept for the input DNA, the rest was incubated with pre-immune serum or with the anti-dLsd1 antibody. Antibody complexes were recovered with a mixture of protein A- and G-Sepharose. The DNA was recovered by phenol-chloroform extraction and ethanol precipitation.
For the library preparation, ChIP DNA (10 ng) was blunt-ended and phosphorylated, and a single 'A' nucleotide was added to the 3' ends of the fragments in preparation for ligation to an adapter that has a single-base 'T' overhang. The ligation products was purified and size-selected by agencourt AMPure XP beads. Purified DNA was PCR-amplified to enrich for fragments that have adapters on both ends.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Reads in fastq files were pre processed with fastx toolkit version 0.0.13.2: fastq_masker fastq_masker -Q33 -q 20 -r N -v -I (mimimum quality threshold : 20, with low quality nucleotides replaced by 'N'
Reads were aligned to the reference Drosophila genome (BDGP6 build based on the Flybase release 6.13, dm6) using bwa software (version 0.6.2-r126) with standard parameters.
Multimapping reds were removed using samtools version 0.1.18
ChIP-seq narrow peaks were called against the input and pre-immune using MACS2 software with the options --nomodel -p 0.001
Genome_build: dm6
|
| |
|
| Submission date |
Feb 08, 2018 |
| Last update date |
Feb 08, 2019 |
| Contact name |
Luisa Di Stefano |
| E-mail(s) |
[email protected]
|
| Phone |
(33) 5 61 55 85 99
|
| Organization name |
Université Paul Sabatier - Toulouse III
|
| Lab |
Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération
|
| Street address |
LBCMCP - CNRS UMR5088 - IFR 109 Bât 4R3-B1 118 route de Narbonne
|
| City |
Toulouse Cedex 9 |
| State/province |
France |
| ZIP/Postal code |
31062 |
| Country |
France |
| |
|
| Platform ID |
GPL13304 |
| Series (1) |
| GSE110331 |
Genome-wide study of the role of the histone demethylase dLsd1 in oogenesis |
|
| Relations |
| BioSample |
SAMN08498343 |
| SRA |
SRX3663168 |
