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| Status |
Public on Apr 16, 2010 |
| Title |
bam H3K4me3 ChIP-seq |
| Sample type |
SRA |
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| Source name |
bam testis
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| Organism |
Drosophila melanogaster |
| Characteristics |
cell type: bam testis
antibody: H3K4me3
antibody manufacturer: Abcam
antibody catalog number: ab8580
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| Growth protocol |
Flies were raised using standard medium at 25oC unless stated otherwise. The bam1/TM3 and bam114-97 /TM6B stocks were obtained from Bloomington Drosophila Stock Centers.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
For each modified histone and Pol II ChIP experiment, we dissected 200 pairs of bam testes in cold PBS and grouped them in 200ml PBS which contained protease inhibitor (Roche complete mini, # 11836153001) and 0.5mM PMSF (MP Biomedicals, #195381). We then added 5.5ml 37% fresh formaldehyde (Supelco, # 47083-U) and incubated at 37oC for 15 mins. The testes were washed twice with 450ml cold 1x PBS (with inhibitors and PMSF). Then 200ml lysis buffer (50mM Tris-HCl, pH7.6, 1mM CaCl2, 0.2% Triton X-100, 5mM butyrate, 1x proteinase inhibitor cocktail, and 0.5mM fresh PMSF) was added and the tissues were homogenized thoroughly followed by incubation at room temperature (RT) for 10 mins. Chromatin was sheared into approximately 200 bp fragments by sonication using Microtip (Misonix, Inc, Microson XL-2000). Chromatin was prepared and ChIP-seq experiments were performed similarly as described previously ( Barski A, et al. Cell 2007) with the following antibodies: Pol II (Abcam ab5408), H3K4me3 (Abcam ab8580), H3K27me3 (Millipore/Upstate 07-449), H3K36me3 (Abcam ab9050).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
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| Description |
Chromatin IP against H3K4me3
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| Data processing |
The 25-bp sequencing reads were obtained from the Illumina Genome Analyzer (GA) Pipeline. All reads were aligned to the Drosophila genome (dm3) using the ELAND (Efficient Local Alignment of Nucleotide Data) software, allowing up to two mismatches with the reference sequence. Only uniquely mapped reads were retained. For multiple identical reads, at most three copies were retained to reduce the possibility of biases from PCR amplification. The output of the GA Pipeline was converted to browser extensible data (BED) files. The bedgraph files used for visualization on the UCSC browser were generated from the uniquely mapped reads using a 4-bp window as previously described ( Barski A, et al. Cell 2007).
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| Submission date |
Dec 07, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
Dustin E Schones |
| E-mail(s) |
[email protected]
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| Organization name |
City of Hope
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| Street address |
1500 E Duarte Rd.
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| City |
Duarte |
| State/province |
CA |
| ZIP/Postal code |
91010 |
| Country |
USA |
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| Platform ID |
GPL9061 |
| Series (1) |
| GSE19325 |
Monovalent and unpoised status of most genes in undifferentiated cell-enriched Drosophila testis |
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| Relations |
| SRA |
SRX017854 |
| BioSample |
SAMN00010229 |
| Named Annotation |
GSM480446_dm3-bam-H3K4me3.bed.gz |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM480446_dm3-bam-H3K4me3.bed.gz |
11.6 Mb |
(ftp)(http) |
BED |
| GSM480446_dm3-bam-H3K4me3.bedgraph.gz |
6.6 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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