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| Status |
Public on Jan 24, 2021 |
| Title |
Pol II ChIP in 14-17hrs OregonR embryos Rep1 |
| Sample type |
SRA |
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| Source name |
14-17hrs OregonR embryo
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| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: embryos
chip antibody: anti-RPB3 rabbit polyclonal, custom (GenScript)
developmental stage: 14-17h
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| Treatment protocol |
Embryos were dechorionated in 5% bleach for ~2-3 min, washed with water, fixed for 15 min shaking on a vortexer, speed 7 with 1.8% formaldehyde in heptane, washed with PBT-glycine and PBT, and frozen in liquid nitrogen until used.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-seq was performed according to He et al. (2011) and He et al. (2015) with whole cell extract (WCE) derived from 100 mg embryos per ChIP
ChIP-seq libraries were constructed following He et al. (2011)
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
base calling, read filtering and demultiplexing were performed by Illumina CASAVA 1.8.2 with default settings.
For ChIP-seq samples, reads were aligned to the reference genome using bowtie v1.0.0, retaining only uniquely aligning reads with a maximum of 2 mismatches. Aligned reads were extended to each library's estimated insert size. Genome-wide coverage counts were calculated, and saved in BigWig format
Genome_build: dm6
Supplementary_files_format_and_content: BigWig files contain pileup counts for each base
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| Submission date |
Sep 18, 2018 |
| Last update date |
Jan 26, 2021 |
| Contact name |
Julia Zeitlinger |
| E-mail(s) |
jbz@stowers.org
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| Organization name |
Stowers Institute
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| Street address |
1000 E 50th St
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| City |
Kansas City |
| ZIP/Postal code |
64110 |
| Country |
USA |
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| Platform ID |
GPL13304 |
| Series (2) |
| GSE120152 |
Two promoter types induce tissue-specific effector genes in the late Drosophila embryo [ChIP-Seq] |
| GSE120157 |
Two promoter types induce tissue-specific effector genes in the late Drosophila embryo |
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| Relations |
| BioSample |
SAMN10087037 |
| SRA |
SRX4712932 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3394953_Dme_emb_Rpb3_14-17h_1.bw |
136.5 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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