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| Status |
Public on Feb 25, 2022 |
| Title |
Input_rep2 |
| Sample type |
SRA |
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| Source name |
S2
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| Organism |
Drosophila melanogaster |
| Characteristics |
cell type: Drosophila S2 cells
treatment: None
antibody: None
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| Treatment protocol |
None
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| Growth protocol |
Drosophila S2 cells were maintained in Schneider’s medium (Gibco) supplemented with 10% FBS (Sigma) and 1% penicillin–streptomycin (Sigma).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin samples were incubated with specific antibodies in the ChIP Lysis buffer (20 mM Tris-HCl pH8.1, 150 mM NaCl, 2 mM EDTA, 1% TritonX-100 and 0.05% SDS) overnight at 4℃. The protein-DNA complexes were immobilized on pre-washed protein A/G beads (20μl per reaction). The bound fractions were washed 3 times with the Lysis buffer, and twice with the Low Salt Wash buffer (10 mM Tris-HCl, 250 mM LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% Na-deoxylcholate), and once with 10 mM Tris-HCl pH8.0. Elution and reverse crosslinking were carried out in the Elution buffer (50 mM Tris-HCl pH8.0, and 1% SDS) at 65℃ for 5 hours. After 1 hour of RNase A (1unit/μl) at 37℃ and Proteinase K (1unit/μl) digestion at 55℃, DNA samples were then purified using PCR extraction kit (QIAGEN #28006).
The precipitated DNA samples were prepared for DNA deep sequencing according to manufacturer’s guidelines (SWIFT, #21096).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
HiSeq X Ten |
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| Data processing |
Raw reads were first trimmed to filter adapters and low-quality reads using trim_galore (0.6.4_dev) and aligned to the mm10 genome using Bowtie2 (v 2.2.5).
PCR duplicates were removed using samtools (v1.7) rmdup.
Genome coverage bigwig files were generated by deeptools (v 3.0.2) bamCoverage.
Genome_build: dm3
Supplementary_files_format_and_content: Genome coverage bigwig files
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| Submission date |
Oct 29, 2021 |
| Last update date |
Feb 26, 2022 |
| Contact name |
Yang Shi |
| E-mail(s) |
yshi@hms.harvard.edu
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| Organization name |
Fudan university
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| Street address |
NO. 138, Yi-Xue-Yuan Road
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| City |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
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| Platform ID |
GPL23702 |
| Series (2) |
| GSE144404 |
Dynamic Control of Chromatin-associated m6A Methylation Regulates Nascent RNAs Stability |
| GSE186853 |
Dynamic Control of Chromatin-associated m6A Methylation Regulates Nascent RNAs Stability [ChIP-seq Dm] |
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| Relations |
| BioSample |
SAMN22786689 |
| SRA |
SRX12839276 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5662352_S2_Input_Rep2_bs5_noNorm.bw |
20.6 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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