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| Status |
Public on Sep 15, 2013 |
| Title |
3AB_input |
| Sample type |
SRA |
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| Source name |
S2 cells
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| Organism |
Drosophila melanogaster |
| Characteristics |
chip antibody: none
cell line: S2 DRSC: Schneider's line 2
treatment: 3AB treated
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| Treatment protocol |
10 million of S2 cells seeded in 4.5ml of media was incubated for 16 h after addition of 0.5 ml of water (Control) or 120mM of 3AB (3AB-12mM).
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| Growth protocol |
S2 cells were maintained in Schneider's medium + 10 % HI FBS
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were crosslinked with 1% formaldehyde for 10 min at room temperature. Crosslinking was quenched with glycine and nuclear lysates were sonicated to generate 200–1000 bp DNA fragments. Chromatin was pre-cleared overnight at 4oC with protein A sepharose beads and then incubated overnight with antibody at 4oC. Chromatin was then precipitated with Protein A Sepharose beads for 2 hours at 4oC. After washing and eluting from beads the crosslinking was reversed and DNA was isolated. To generate sequencing libraries, ChIP DNA was prepared for adaptor ligation by end repair (‘End-It DNA End Repair Kit’ - Epicentre Cat# ER0720) and addition of ‘A’ base to 3’ ends (Klenow 3’-5’ exo- NEB Cat# M0212S). Illumina adaptors (Illumina Cat# PE-102-1001) were titrated according to prepared DNA ChIP sample concentration, and ligated with T4 ligase (NEB Cat# M0202S). Ligated ChIP samples were PCR amplified using Illumina primers and Phusion DNA polymerase (NEB Cat# F-530L) and size selected for 200-300bp by gel extraction.
antibody reference: CP190, dCTCF and Su(Hw): Regulation of chromatin organization and inducible gene expression by a Drosophila insulator. Wood AM, Van Bortle K, Ramos E, Takenaka N, Rohrbaugh M, Jones BC, Jones KC, Corces VG. Mol Cell. 2011 Oct 7;44(1):29-38.
antibody reference: dCTCF, Su(Hw) and Mod(mdg4)2.2.: Drosophila CTCF tandemly aligns with other insulator proteins at the borders of H3K27me3 domains. Van Bortle K, Ramos E, Takenaka N, Yang J, Wahi JE, Corces VG. Genome Res. 2012 Sep 20.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Input in 3AB treated S2 cells
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| Data processing |
Alignment: Sequence reads were obtained and mapped to the D.melanogaster (DM3) genome using Bowtie 0.12.5 software using the default setting. Same number of reads from control and 3AB treated samples were used for peak calling by MACS .
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| Submission date |
Oct 04, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Chin-Tong Ong |
| E-mail(s) |
[email protected]
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| Organization name |
Temasek Life Sciences Lab
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| Department |
Developmental Biology
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| Lab |
Ong
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| Street address |
1 Research Link
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| City |
Singapore |
| ZIP/Postal code |
117604 |
| Country |
Singapore |
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| Platform ID |
GPL13304 |
| Series (2) |
| GSE41354 |
Distribution of insulator proteins CP190, dCTCF, Su(Hw) and Mod(mdg4)2.2 in Drosophila S2 cells in the presence or absence of dPARP inhibitor 3AB |
| GSE50769 |
Mapping the inter- and intra-chromosomal interactions of specific insulator binding sites with circular chromosome conformation capture (4C) assay (Gondor et al., 2008 Nature Protocol) |
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| Relations |
| SRA |
SRX191916 |
| BioSample |
SAMN01758668 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data not applicable for this record |
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