|
| Status |
Public on Jul 17, 2016 |
| Title |
Female Miranda CLAMP input Replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
Female Miranda CLAMP input
|
| Organism |
Drosophila miranda |
| Characteristics |
genotype: wild type
chip antibody: none
developmental stage: 3rd instar larvae
|
| Growth protocol |
Melanogaster flies were maintained at 21 degree Celcius, and Miranda flies at 18 degree Celcius
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Standard ChIP seq protocol - larvae were homogenized in liquid nitrogen followed by lysis and sonication, chromatin was immunoprecipitated with CLAMP antibody.
ChIP-seq libraries were prepared with the illumina TruSeq DNA Prep kit
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
ChIP-seq reads were aligned to the D. melanogaster (dm3) and D. miranda (reference 15, please see the paper) genome assembly using Bowtie with with parameters “-m 1 -I 50 -X 500 --solexa-quals –best”
The positions with anomalously high read counts are potential amplification artifacts and were removed from consideration
Peaks in the ChIP-Seq fragments distribution were identified using the SPP software package with default parameters
Overlapping peaks of two replicates were used in the analysis.
Genome_build: dm3 for D. melanogaster, DroMir_2.2 for D. miranda [PMID 25688566]
Supplementary_files_format_and_content: peak files were generated using spp; scores show the enrichment
|
| |
|
| Submission date |
Jun 16, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Michael Tolstorukov |
| E-mail(s) |
tolstorukov@molbio.mgh.harvard.edu
|
| Organization name |
Massachusetts General Hospital
|
| Department |
Molecular Biology
|
| Street address |
185 Cambridge Street
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02114 |
| Country |
USA |
| |
|
| Platform ID |
GPL22022 |
| Series (2) |
| GSE83435 |
Expansion of GA dinucleotide repeats increases the density of CLAMP binding sites on the X-chromosome to promote Drosophila dosage compensation [ChIP-Seq] |
| GSE83444 |
Expansion of GA dinucleotide repeats increases the density of CLAMP binding sites on the X-chromosome to promote Drosophila dosage compensation |
|
| Relations |
| BioSample |
SAMN05255822 |
| SRA |
SRX1850486 |
