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Status |
Public on Jan 24, 2021 |
Title |
Pol II ChIP in 2-4hrs OregonR embryos Rep1 |
Sample type |
SRA |
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Source name |
2-4hrs OregonR embryo
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Organism |
Drosophila melanogaster |
Characteristics |
tissue: embryos chip antibody: anti-RPB3 rabbit polyclonal, custom (GenScript) developmental stage: 2-4h
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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 |
SAMN10087044 |
SRA |
SRX4712934 |
Supplementary file |
Size |
Download |
File type/resource |
GSM3394955_Dme_emb_Rpb3_2-4h_1.bw |
72.3 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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