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Sample GSM4654018 Query DataSets for GSM4654018
Status Public on May 31, 2021
Title H3ChIP_AG_male_midgut
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 A747
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 SAMN15443095
SRA SRX8665083

Supplementary file Size Download File type/resource
GSM4654018_Agam_male_H3ChIPlog2FCInp_Rep1.bw 215.2 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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