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Sample GSM7120260 Query DataSets for GSM7120260
Status Public on Sep 17, 2023
Title D330C101_ChIP_p50_D2-24h_Bmori-v4_H3K27me3_rep1_IP
Sample type SRA
 
Source name full embryo
Organism Bombyx mori
Characteristics tissue: full embryo
strain: p50
chip antibody: H3K27me3
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 IP
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 SAMN33955669
SRA SRX19799396

Supplementary file Size Download File type/resource
GSM7120260_log2_D330C101-D330C100_p50-D2-24h_H3K27me3_25bp.bigwig 92.3 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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