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Sample GSM7120266 Query DataSets for GSM7120266
Status Public on Sep 17, 2023
Title D577C39_ChIP_p50_D2-24h_Bmori-v4_H3K9me3_rep2_Input
Sample type SRA
 
Source name full embryo
Organism Bombyx mori
Characteristics tissue: full embryo
strain: p50
chip antibody: none (input)
Growth protocol ~200 p50 diapaused eggs harvest after release 24h at 25°C
Extracted molecule genomic DNA
Extraction protocol Eggs were placed in 1% formaldehyde before chorions were broken with a piston pellet to allow embryos fixation for 10 min. After quenching and cell lysis, embyo tissus were ruptured and chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the KAPA HyperPrep Library Preparation Kit complemented with Illumina TruSeq DNA UD Indexes. Libraries were amplified using 8-14 cycles on the thermocycler. Post amplification libraries were size selected at 250-600bp in length using SPRIselect beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity screenTapes.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NovaSeq 6000
 
Description ChIP Input
Data processing Library were sequenced on Novaseq.
Adapter sequences were trimmedfrom reads using trimgalore.
ChIP-seq reads were aligned to our custom Bmori_v4 genome assembly using Bowtie2 v2.3.5.1. Only uniquely mapping reads with a mapping quality higher than 10 were retained.
To create ChIP-seq coverage plots, log2 IP/Input ratio files have been generated at 25pb resolution using bamCompare from deepTools and reformatted in the bigWig file format.
Assembly: Bmori_v4
Supplementary files format and content: bigWig
 
Submission date Mar 28, 2023
Last update date Sep 17, 2023
Contact name Héloïse Muller
E-mail(s) heloise.muller@curie.fr
Organization name Institut Curie
Lab UMR3664
Street address 26 rue d'Ulm
City Paris
ZIP/Postal code 75005
Country France
 
Platform ID GPL29210
Series (2)
GSE228397 Unique territorial and sub-chromosomal organization revealed in the holocentric moth Bombyx mori [ChIP-seq]
GSE228401 Unique territorial and sub-chromosomal organization revealed in the holocentric moth Bombyx mori
Relations
BioSample SAMN33955663
SRA SRX19799402

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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