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| Status |
Public on Oct 01, 2024 |
| Title |
mRNA_BmGATA_Mock_rep3 |
| Sample type |
SRA |
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| Source name |
BmN cells
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| Organism |
Bombyx mori |
| Characteristics |
cell line: BmN cells
treatment: Mock
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| Extracted molecule |
total RNA |
| Extraction protocol |
For RNA-seq, BmN cells (1e6) with indicated treatments were harvested and total RNA of the cells was extracted using Trizol. For ChIP-seq, 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).
For RNA-seq, a total amount of 1.5 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB) following the instructions. For ChIP-seq, 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 |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| 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". For RNA-seq, cleaned data was maped to silkworm genome using HISAT2 (Version 2.2.1). The resulted SAM file was transformed to BAM file and sorted by SAMtools (Version 1.12). Mapped reads at the exons of each gene were counted via featureCounts, which is a part of the Subread (Version 2.0.1). For ChIP-seq, cleaned data was maped 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: tab-delimited narrowPeak files includes narrow peaks for each ChIP-seq sample
Supplementary files format and content: tab-delimited text files includes raw counts for each RNA-seq sample
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| Submission date |
Sep 26, 2024 |
| Last update date |
Oct 01, 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) |
| GSE278146 |
Transcriptional regulatory role of BmGATA |
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| Relations |
| BioSample |
SAMN43826140 |
| SRA |
SRX26124747 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8540784_mRNA_BmGATA_Mock_rep3.txt.gz |
941.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
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