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| Status |
Public on Oct 02, 2024 |
| Title |
BmGATA_Mock |
| Sample type |
SRA |
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| Source name |
BmN cells
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| Organism |
Bombyx mori |
| Characteristics |
cell line: BmN cells
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were collected and cross-linked with 1% formaldehyde for 10 min at 25˚C. The reaction was then quenched by addition of glycine to a final concentration of 125 mM. Afterwards, cells were lysed and chromatin was obtained on ice. Chromatin was sheared to a mean fragment size of 200-500 base pairs. The samples were immunoprecipitated by anti-HA antibody (Abcam, 9110).
Sequencing libraries were generated using VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme, ND607) following the instructions.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Raw data was cleaned by Trim Galore (Version 0.6.6) with the parameters "-q 25 --phred33 --length 36 -e 0.1 --stringency 5" and maped to silkworm genome using Bowtie 2 (Version 2.4.4). Afterwards, the resulted SAM files were converted into BAM format using SAMtools (Version 1.12), and MACS2 (Version 2.2.7.1) was adopted for peaks calling with the parameters "-p 0.1 -f BAMPE -g 4.6e8".
Assembly: SilkBase November 2016
Supplementary files format and content: bigWig files indicating binding density for each ChIP-seq sample
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| Submission date |
Sep 27, 2024 |
| Last update date |
Oct 02, 2024 |
| Contact name |
Shudi Zhao |
| E-mail(s) |
shudi.zhao@zju.edu.cn
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| Organization name |
Zhejiang University
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| Street address |
Yuhangtang Road No.866
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| City |
Hangzhou |
| ZIP/Postal code |
310058 |
| Country |
China |
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| Platform ID |
GPL29210 |
| Series (1) |
| GSE278205 |
Binding density of BmGATA on silkworm genome |
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| Relations |
| BioSample |
SAMN43826135 |
| SRA |
SRX26124742 |
| SRA |
SRX26124741 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8541808_ChIP_BmGATA_Mock.bw |
61.8 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
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