|
| Status |
Public on Sep 25, 2019 |
| Title |
051917CD2+GFPred |
| Sample type |
SRA |
| |
|
| Source name |
low-GFP mesodermal cells
|
| Organism |
Drosophila melanogaster |
| Characteristics |
strain: reporter insertion pool crossed to twi:CD2
cell population: CD2+GFPred
|
| Treatment protocol |
Single-cell suspensions were prepared from dechorionated embryos and stained with Alexa647-anti-rat CD2 (Biorad MCA154A647), then CD2-positive and -negative populations were sorted as controls before low-GFP CD2+ populations were sorted to provide informative pools of silencers.
|
| Growth protocol |
Transformant male flies containing random picks from a pool of silencer reporter constructs were crossed to twi:CD2 virgin females in population cages. Embryos were collected for 2.25 hours from pre-layed cages and aged 11 hours at 18°.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total genomic DNA from sorted cells was used as template for nested PCR recovery of barcoded library inserts with common vector primers.
Size-selected amplicons were sheared by sonication, end-repaired, and A-tailed before ligation of Illumina PE adaptors and PCR enrichment.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Reads were filtered for the presence of common primer sequences, indicating that they originated from a barcoded end of a library element, and barcode sequences were extracted. Barcode lookup produced a table of insert read counts per library element per sample. These steps used a custom Perl program, available upon request.
Within each experiment, triplicate low-GFP mesodermal cell readcounts were compared to readcounts from input cell populations (not sorted for GFP status) with the original DESeq package and commands estimateSizeFactors, estimateVarianceFunctions, and nbinomTest.
Genome_build: n/a
Supplementary_files_format_and_content: count tables (reads per library insert barcode in each sorted cell sample)
Supplementary_files_format_and_content: DESeq results from nbinomTest give average corrected abundance is experimental and control conditions, fold change, and raw and adjusted p-values for each library element.
|
| |
|
| Submission date |
Sep 24, 2019 |
| Last update date |
Sep 26, 2019 |
| Contact name |
Stephen Gisselbrecht |
| E-mail(s) |
steveg@alum.mit.edu
|
| Phone |
857-540-2853
|
| Organization name |
Brigham and Women's Hospital
|
| Department |
Division of Genetics, Department of Medicine
|
| Lab |
Martha L. Bulyk
|
| Street address |
77 Avenue Louis Pasteur, Rm 468
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL17275 |
| Series (2) |
| GSE137949 |
Transcriptional silencers in Drosophila serve a dual role as transcriptional enhancers in alternate cellular contexts [HiChIP] |
| GSE137958 |
Transcriptional silencers in Drosophila serve a dual role as transcriptional enhancers in alternate cellular contexts |
|
| Relations |
| BioSample |
SAMN12832951 |
| SRA |
SRX6902236 |
