|
| Status |
Public on May 31, 2021 |
| Title |
H3ChIP_AG_male_midgut_Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Dissected midgut
|
| Organism |
Anopheles gambiae |
| Characteristics |
genotype/variation: wild-type
gender: male
tissue: Dissected midgut
chip antibody: Histone H3 antibody (mAb), MABI 0301 (39763 Active Motif)
|
| Treatment protocol |
Male and female Anopheles were collected and anesthetized with CO2. Midguts were dissected.
|
| Growth protocol |
A. gambiae mosquitoes were maintained in standard insectary conditions (28°, 75–80% humidity, 12-hr/12-hr light/dark cycle).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Anopheles gambiae midguts were dissected and fixed in PBS containing 0.2% Formaldehyde (15 min at RT). Chromatin was extracted using a sucrose cushion followed by Micrococcal Nuclease treatment and 10 cycles of sonication in a Bioruptor Pico. The lysate was clarified by centrifugation before immunoprecipitation, washes, elution by reverse crosslinking at 65deg for 14h. After RNaseA and ProteinaseK treatment, the DNA from Input and Immunoprecipitation was purified using Phenol-Chloroform Extraction and Ethanol precipitation.
NEB Next Ultra II.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
Parkour-ID A887
|
| Data processing |
Paired-end reads were mapped to AgamP4_ensembl with bowtie2 (Galaxy version v2.2.6.2) using default parameters. To generate readCount normalized coverage bigwig files, we calculated the log2 ratio versus the Input using a binsize of 5 bp with deepTools bamCompare v2.4.2. Duplicate reads and reads with a mapping quality <10 were removed, the X chromosome was ignored for scaling.
Genome_build: AgamP4_ensembl
Supplementary_files_format_and_content: bigWig files of uniquely mapped reads.
|
| |
|
| Submission date |
Jul 03, 2020 |
| Last update date |
May 31, 2021 |
| Contact name |
Asifa Akhtar |
| E-mail(s) |
akhtarlab_data@ie-freiburg.mpg.de
|
| Organization name |
Max Planck Institute of Immunobiology and Epigenetics
|
| Department |
Chromatin Regulation
|
| Lab |
Akhtar Lab
|
| Street address |
Stuebeweg 51
|
| City |
Freiburg |
| ZIP/Postal code |
79108 |
| Country |
Germany |
| |
|
| Platform ID |
GPL25232 |
| Series (2) |
| GSE153778 |
Two distinct mechanisms for X chromosome dosage compensation in Anopheles and Drosophila [ChIP-seq] |
| GSE153780 |
Two distinct mechanisms for X chromosome dosage compensation in Anopheles and Drosophila |
|
| Relations |
| BioSample |
SAMN15443094 |
| SRA |
SRX8665084 |
