|
| Status |
Public on Sep 17, 2023 |
| Title |
D1221C18_ChIP_p50_D2-24h_Bmori-v4_H3K4me3_rep2_IP |
| Sample type |
SRA |
| |
|
| Source name |
full embryo
|
| Organism |
Bombyx mori |
| Characteristics |
tissue: full embryo
strain: p50
chip antibody: H3K4me3
|
| 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 |
SAMN33955674 |
| SRA |
SRX19799391 |
