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| Status |
Public on Feb 06, 2014 |
| Title |
Input DNA, rep1 |
| Sample type |
SRA |
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| Source name |
Input DNA
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| Organism |
Drosophila melanogaster |
| Characteristics |
strain: Oregon R (wild type)
tissue: whole-embryo
time point: 2-4hr after egg laying (AEL)
chip antibody: Anti Twist
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| Growth protocol |
D. melanogaster embryos were collected and aged on yeasted apple juice plates at 25 °C and 60 % humidity.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA-protein-complexes were isolated with specific antibodies. During Illumina library preparation, the samples are run on a 2% gel at 90V for ~2 hr, and fragments corresponding to ~50 bp, ~75, and ~100 bp inserts are cut out of the gel (slices are ~25bp thick). The final libraries are run a BioAnalyzer to measure the actual average insert size.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Description |
wce_ext107_1
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| Data processing |
Reads were aligned uniquely to the UCSC dm3 genome, using bowtie and allowing for up to 3 mismatches.
Peakzilla, SISSRs (Jothi et al., 2008) version 1.4, Spp (Kharchenko et al., 2008) version 1.8 and GPS (Guo et al., 2010) version 0.10.1 were run with default parameters.
MACS (Zhang et al., 2008) version 1.4.1 was run with an mfold parameter 3,30 and the gsize parameter approproiate for dm3
QuEST (Valouev et al., 2008) version 2.4 was run with FDR analysis (if possible), for transcription factor binding sites, recommended (or relaxed) peak calling parameters. cisGenome (Ji et al., 2008) version 2.0 was run with default parameters and required aln files.
PeakRanger read extension length parameter was run using peakzilla’s estimated fragment length.
Genome_build: UCSC dm3
Supplementary_files_format_and_content: BED formated annotations to UCSC dm3 genome
wce_ext107_1.bed: dm3
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| Submission date |
Sep 06, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Samuel Richard Meier |
| E-mail(s) |
srm@stowers.org
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| Phone |
816-926-4455
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| Organization name |
Stowers Institute for Medical Research
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| Lab |
Computational Biology
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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) |
| GSE40664 |
Identification of transcription factor binding sites from ChIP-seq data at high-resolution |
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| Relations |
| SRA |
SRX183886 |
| BioSample |
SAMN01162395 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM998953_wce_ext107_1.bed.gz |
85.3 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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