|
| Status |
Public on Mar 26, 2024 |
| Title |
FT-SA11849 |
| Sample type |
SRA |
| |
|
| Source name |
RMG-II
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: RMG-II
cell type: Clear cell ovarian cancer
chip antibody: CTCF (Active Motif 61311)
|
| Growth protocol |
FT33, FT246 and FT282 lines were maintained in DMEM-F12 medium (Gibco, Invitrogen, Carlsbad) supplemented with 10% fetal bovine serum (Gibco). The HGSOC cell line UWB 1.289 was cultured in a mixture (1:1) of 50% RPMI and 50% MEGM medium with 3% FBS and Kuramochi was cultured in RPMI-1640 media supplemented with 10% FBS. The remaining cell lines were maintained according to the recommended conditions (ATCC). All cell lines were thawed and allowed to recover for 1 day before expansion. All cell lines were passaged and plated onto 150mm plates. Cells were harvested at 80% confluency to be fixed, pelleted and snap frozen.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Four 15-cm dishes of confluent cells were fixed in formaldehyde for 10 min, before quenching the fixation with glycine. Cells were collected, lysed in a sarkosyl-containing lysis buffer and sonicated to yield 100- to 300-bp genomic DNA fragments. Five micrograms of an antibody raised against H3K4me1 was incubated with blocked magnetic Dynabeads (Life Technologies) at 4 °C for 4 h. Antibody–bead conjugates were incubated with 100 μg of chromatin at 4 °C overnight, with constant agitation. Beads were washed extensively with RIPA buffer and then treated with RNase and proteinase K (both Qiagen). DNA was then eluted from the beads in TE buffer and cleaned up using the QIAquick PCR Purification kit (Qiagen).
Sequencing libraries were prepared using a ThruPlex DNA-seq kit (Rubicon R400407), pooled and sequenced on an Illumina HiSeq 5000 for 2 x 150 bp paired-end for an average of 40 million reads (Fulgent Genetics; Temple City, CA).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
HiSeq X Five |
| |
|
| Description |
ChIP-Seq for CTCF with Replicate 1 (R1) and Replicate 2 (R2) and Input available. Fastq provided for Replicate 1 (R1), Replicate 2 (R2) and Input.
RMGII_2D_CTCF_hg38.rep1-rep2.idr0.05.bfilt.regionPeak.narrowpeak.gz
|
| Data processing |
ChIP sequencing data was processed based on ENCODE phase 3 histone ChIP-Seq pipeline with modifications on the peak calling algorithm to retain peaks with p-value < 10e-9.
Reads were aligned to the reference human genome (hg38), filtered by read quality and duplicate reads removed. Peak calling was performed with MACS2 within the AQUOS pipeline, with pooled replicate peaks that overlap 50% or more of each individual replicate selected for the final peak set. When replicates were not available pseudo replicates were formed and pooled peaks selected in the same manner from these pseudo replicates. Narrowpeaks were retained for downstream analysis.
Assembly: hg38
Supplementary files format and content: narrowpeak
|
| |
|
| Submission date |
Mar 19, 2024 |
| Last update date |
Mar 26, 2024 |
| Contact name |
Michelle Renee Jones |
| E-mail(s) |
jonesmrx@cshs.org
|
| Organization name |
Cedars-Sinai Medical Center
|
| Department |
Biomedical Sciences
|
| Lab |
Center for Bioinformatics and Functional Genomics
|
| Street address |
8720 Alden Dv
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90048 |
| Country |
USA |
| |
|
| Platform ID |
GPL33758 |
| Series (1) |
| GSE261931 |
CTCF ChIP-Seq in a panel of 18 cell lines related to ovarian cancer |
|
| Relations |
| BioSample |
SAMN40546256 |
| SRA |
SRX23994309 |
