|
| Status |
Public on Aug 10, 2021 |
| Title |
AL24 - Hmr_Flag_deltaC_induced |
| Sample type |
SRA |
| |
|
| Source name |
SL2 cells
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell line: SL2
ChIP: HMR
input id: AL20
construct: pMT HMR-dC-FLAG-HA
treatment: induced (CuSO4 250 uM)
|
| Growth protocol |
Drosophila SL2 cells stably transfected with FLAG-HA-HMR under a CuSO4 inducible promoter (pMT) were grown at 26˚C in Schneider Drosophila medium (Invitrogen) supplemented with 10% fetal calf serum and antibiotics (100 units/mL penicillin and 100 μg/mL streptomycin). Transfected cells were selected with 20 ug/mL Hygromycin B. Cells were grown to confluence in 550 mL flasks and induced for 20-24h with 250 uM CuSO4 before harvesting for chromatin immunoprecipitation.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin immunoprecipitation was essentially performed as in Gerland et al., PlosOne 2017. For each ChIP reaction, chromatin isolated from 1–2 x 10^6 cells was incubated either with 5 ug of mouse anti-FLAG (F1804, SIGMA-ALDRICH - RRID: AB262044) pre-coupled directly to Protein A/G Sepharose or with rat anti-HMR 2C10 (RRID: AB2569849) antibody pre-coupled to Protein A/G Sepharose through a rabbit IgG anti-rat.
Libraries for AL02-78 were prepared with Diagenode Microplex Library Prep Kit v2 (starting with 1ng of DNA), AL79-80 with "NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (starting with 2 ng of DNA)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Sequencing reads (50 bp, single end) were mapped to the Drosophila genome (version dm6) using bowtie2 (version 2.2.9) and filtered by mapping quality (-q 2) using samtools (version 1.3.1). Sequencing depth and input normalized coverages were generated by Homer (version 4.9). Enriched peaks were identified by Homer with the parameters -i input.dir -style factor -F 2 -size 200 for each replicate.
Genome_build: dm6
Supplementary_files_format_and_content: Peak list in bed format and input normalized tracks in bedgraph format
|
| |
|
| Submission date |
Dec 11, 2020 |
| Last update date |
Aug 10, 2021 |
| Contact name |
Tamas Schauer |
| E-mail(s) |
tamas.schauer@helmholtz-munich.de
|
| Organization name |
Helmholtz Zentrum München
|
| Department |
Institute of Epigenetics and Stem Cells
|
| Street address |
Feodor-Lynen-Straße 21
|
| City |
Munich |
| ZIP/Postal code |
81377 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13304 |
| Series (1) |
| GSE163058 |
Genome-wide ChIP-Seq profiling of a wild-type and a C-terminally truncated mutant of HMR |
|
| Relations |
| BioSample |
SAMN17059420 |
| SRA |
SRX9720892 |
