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| Status |
Public on Jan 05, 2018 |
| Title |
toll10b 2-4h dl ChIP-Seq rep 1 |
| Sample type |
SRA |
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| Source name |
2-4h toll10b embryo
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| Organism |
Drosophila melanogaster |
| Characteristics |
genotype/variation: toll10b
tissue: embryo
chip antibody: anti-dl rabbit polyclonal, custom (GenScript)
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| Treatment protocol |
Embryos were dechorionated in 100% bleach for ~1 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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| Growth protocol |
Fly stocks Toll10b (Meso) and gd7 (Ecto) were kind gifts from Mike Levine (UC Berkeley). gd7/gd7 females were crossed to gd7/+ males, and Toll10b, e /TM3, Sb, Ser, e females were crossed to Toll10b, e/TM3, Sb, Ser, e males. Offspring of these crosses were used for embryo collections. Embryos were collected on apple juice plates for 2 h and then matured at 25C for another 2 h (2-4h after egg deposition (AED)).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-seq libraries were constructed following He et al. (2011)
ChIP-seq and ChIP-nexus 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
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
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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, normalized to reads per million and saved in BigWig format
For ChIP-nexus samples, custom barcode sequences were removed from the first 9bp of each read and sequencing adapters were trimmed from the 3' end using cutadapt v1.3. Remaining reads with length >= 22bp 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 separated by strand and reduced to a single base at the 5' end. Genome-wide coverage counts were calculated for each strand separately and normalized to reads per million
Genome_build: UCSC dm6
Supplementary_files_format_and_content: BigWig files contain pileup counts for each base
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| Submission date |
Oct 11, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Julia Zeitlinger |
| E-mail(s) |
[email protected]
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| Organization name |
Stowers Institute for Medical Research
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| Lab |
Zeitlinger lab
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| Street address |
1000 E 50th Street
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| City |
Kansas City |
| State/province |
MO |
| ZIP/Postal code |
64110 |
| Country |
USA |
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| Platform ID |
GPL11203 |
| Series (1) |
| GSE104839 |
Capicua controls Toll/IL-1 signaling targets independently of RTK regulation |
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| Relations |
| BioSample |
SAMN07775288 |
| SRA |
SRX3270979 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2808636_toll10b_dl_chipseq_1_normalized.bw |
36.3 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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