|
| Status |
Public on Jul 19, 2022 |
| Title |
ChIP-seq CTCF-KO Su(Hw) replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
Cultured cells
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell line: CTCF 19.7-1c
mutation: CTCF[y+1]
antibody: anti-Su(Hw) from Schwartz et al. 2012
|
| Treatment protocol |
none
|
| Growth protocol |
Cells were grown to confluence in Schneider's medium (Lonza) supplemented with 10% FBS, 100U/ml of Penicillin G, 100ug/ml of Streptomycin sulfate
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Live cells were crosslinked with 1.8% formaldehyde for 10 min at 25C. Soluble chromatin was prepared and immunoprecipitation performed as described in Kahn et al. Nucleic Acids Res. 2016. 44:10132-10149
2ng of immunoprecipitated DNA were processed using NEBNext Ultra II DNA Library preparation Kit for Illumina (cat# E76455) and index oligonucleotides from NEBNext Multiplex Oligos for Illumina (cat# E7335).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Base calling and quality score assignment were done with HiSeq Control Software 2.2.58/RTA 1.18.64
Bcl to FastQ conversion was performed using None from the CASAVA software suite. The sequence read quality was reported in Sanger/phred33/Illumina 1.8+ scale.
Reads were aligned to the dm3 genome assembly using bowtie2 and the following parameters --phred33 -p 8.
Reads with MAPQ scores less than 30 were removed using samtools view -q 30
Genomic read count profiles were computed from the filtered bowtie2 alignments using pyicos convert software and the following parameters -f sam -F bed_wig -x 180 -O.
The resulted read count profiles were normalized to the number of corresponding MAPQ 30 filtered sequencing reads using custom R script
Assembly: dm3
Supplementary files format and content: Read count profiles in wig format
Supplementary files format and content: bed in dm6 transferred by UCSC liftover from above wig, example
|
| |
|
| Submission date |
Mar 16, 2022 |
| Last update date |
Jul 20, 2022 |
| Contact name |
Jia-Ming Chang |
| E-mail(s) |
chang.jiaming@gmail.com
|
| Organization name |
National Chengchi University
|
| Department |
Department of Computer Science
|
| Street address |
NO.64, Sec. 2, ZhiNan Rd., Wenshan District
|
| City |
Taipei |
| ZIP/Postal code |
11605 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL23702 |
| Series (2) |
| GSE198762 |
Topological screen identifies hundreds of Cp190 and CTCF dependent Drosophila chromatin insulator elements [ChIP-seq] |
| GSE198763 |
Topological screen identifies hundreds of Cp190 and CTCF dependent Drosophila chromatin insulator elements |
|
| Relations |
| BioSample |
SAMN26725056 |
| SRA |
SRX14474265 |
