|
| Status |
Public on Oct 02, 2020 |
| Title |
BmN4_crosslinked_H3K4me3_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
ovary-derived cells
|
| Organism |
Bombyx mori |
| Characteristics |
cell type: ovary-derived cells
|
| Treatment protocol |
For 20E-related eperiments, BmN4 cells were treated with 20E for 48 hours (for treated samples), or DMSO for 48 hours (for control samples). For 20-washout experiment, BmN4 cells were treated with 20E for 48 hours and then grown in conditioned medium without 20E for an additional 5 days (for mRNAseq) or an additional 10 days (for CENP-T ChIP-seq).
|
| Growth protocol |
Cultured silkworm ovary-derived BmN4 and T. ni Hi5 cell lines were maintained in Sf-900 II SFM medium supplemented with (BmN4,) or without (Hi5) 10% fetal bovine serum , antibiotic-antimycotic and 2mM L-glutamine at 27°C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-seq: DNA-protein complexes (either cross-linked with formaldehyde or not) were isolated with specific antibody after chromatin solubilization using MNase and sonication. isolated DNA was purified using phenol/chloroform/isoamyl alcohol extraction method.
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
mRNA-seq: Total RNA was extracted from cells using Trizol reagent.
All steps of Illumina library preparation and sequencing were carried out at the Curie Institute’s sequencing platform using TruSeq ChIPseq protocol or TruSeq Stranded mRNA protocol.
ChIP-seq or mRNA-seq
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
BmN4_H3K4me3_native_rep2
|
| Data processing |
Adapter-trimmed chIP-seq reads were aligned to the B. mori genome assembly or T. ni genome assembly using Bowtie2- 2.2.9 Alignment files (sam) were converted to bam, sorted, indexed. Duplicates were removed using Picard Tools (v 2.6.0). ChIp-seq scores were visualized in IGV as bigwig files representing average log2 ratio of (IP/Input) in genome-wide 1 kb windows generated using Deeptools bamCompare function.
Adapter trimmed mRNA-seq reads were aligned to the B. mori genome assembly or T. ni genome assembly using STAR-2.7.0a. Alignment files (sam) were converted to bam, sorted, indexed and used to generate 1 kb resolution BPM-normalized bigwig tracks using Deeptools bamCoverage function. Unique, multimapping and duplicate reads were included.
Genome_build: Bombyx mori: genome assembly downloaded from Silkbase: http://silkbase.ab.a.u-tokyo.ac.jp
Genome_build: Trichoplusia ni: GenBank Assembly Accession: GCA_003590095.1
Supplementary_files_format_and_content: ChIP-seq: bigwig files generated using RPKM-normalized Bam files for IP and Input using Deeptools bamCompare function. Each bigwig fille represents average log2 ratio of IP/Input in genome-wide 1kb windows.
Supplementary_files_format_and_content: mRNA-seq: bigwig files genrated using Deeptools bamCoverage function. Each bigwig file represents bins per million mapped reads (BPM) in genome-wide 1 kb windows.
|
| |
|
| Submission date |
Oct 01, 2020 |
| Last update date |
Oct 06, 2020 |
| Contact name |
Ines Anna Drinnenberg |
| Organization name |
Institut Curie
|
| Street address |
26 Rue d'Ulm
|
| City |
Paris |
| ZIP/Postal code |
75005 |
| Country |
France |
| |
|
| Platform ID |
GPL16216 |
| Series (1) |
| GSE158902 |
Formation of the CenH3-deficient holocentromere in Lepidoptera avoids actie chromatin |
|
| Relations |
| BioSample |
SAMN16337396 |
| SRA |
SRX9233131 |
