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| Status |
Public on Aug 20, 2009 |
| Title |
input |
| Sample type |
SRA |
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| Source name |
larvae
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| Organism |
Drosophila melanogaster |
| Characteristics |
antibody: input
developmental stage: larvae
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| Growth protocol |
Flies were kept on standard cornmeal-molasses medium at 25 °C. Two yellow+-marked attP landing sites were used, attP18 and attP3, inserted at positions 6648525 bp and 20201600 bp of the X chromosome, respectively (R5.18) (Markstein et al. 2008). Briefly, TrojanHorse/TrojanHorseD/TrojanElephant DNA was injected into y1 w67c23 P{y+ attP=CaryP}; M{Avic\RFPE.3xP3, vas-int.B}ZH-102D embryos. The integrase source was a kind gift of Johannes Bischoff and Konrad Basler. Flies with colored eyes were selected in G1 progeny from a cross with the y w stock and bred to homozygosity. Accuracy and integrity of insertions was verified by PCR. P{mini-white+ MSL3-TAP-pCaSpeR3-1}; msl31 background (Alekseyenko et al. 2006) was introduced by standard genetic crosses. When needed for ChIP purposes, male larvae were obtained by crossing the TrojanHorse (or TrojanElephant); MSL3-TAP; msl31 females with FM7c, P{GAL4-Kr.C}DC1, P{UAS-GFP.S65T}DC5, sn+/Y; MSL3-TAP; msl31 males, and sexed based on their non-GFP phenotype. For embryo sorting, Sxl/PE-GFP transgene integrations on the X (G5B) or the third chromosome (G78A), expressing GFP under the early Sxl promoter specifically in female embryos were recombined into TrojanHorse and TrojanHorseD stocks.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Preparation of chromatin and libraries from sexed larvae for ChIP-seq was performed as described in Alekseyenko et al., Cell 134(4): 599-609.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
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| Description |
chromatin input of TrojantElephant mutant larvae
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| Data processing |
Alignment: reads were aligned against D.melanogaster dm3 assembly using bowtie (using -m 1 option)
Processed data: ChIP and input ratios were calculated using sliding 7Kbp window. The 99% confidence interval (CI) was determined at each window position based based on the counts using Poisson model. The conservative enrichment profile reports lower CI bound if it is above 0 (on log2 scale), and upper CI bound if it is below 0. Positions at which CI included 0 were reported with the enrichment value of 0.
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| Submission date |
Aug 19, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
Peter Kharchenko |
| Organization name |
Harvard Medical School
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| Department |
DBMI
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| Lab |
Kharchenko
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| Street address |
10 Shattuck St.
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platform ID |
GPL9058 |
| Series (1) |
| GSE17729 |
Long range spreading of dosage compensation in Drosophila captures transcribed autosomal genes inserted on X |
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| Relations |
| SRA |
SRX011652 |
| BioSample |
SAMN00003956 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data not provided for this record |
| Raw data are available in SRA |
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