|
| Status |
Public on Dec 02, 2020 |
| Title |
DLD1 BRCA2-/- sgALC1_5uM Ola_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Horizon Discovery
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: DLD1
cell-type: epithelial-like
genotype: This is a pseudodiploid human cell line with the modal chromosome number of 46, occurring in 86% of cells. The rate of polyploidy was high at 17.1%. The karyotype of the line was 46,XY,-2,+dir dup(2)(p13-p23). The Y chromosome was slightly longer than N22 and had a large segment of heterochromatic, fluorescent distal q arms.
transduction: sgALC1
treatment: Ola
|
| Treatment protocol |
Cell were transduced with lentivirus vector either expressing Negative sgRNA or sgRNA for ALC1.DLD1 cells were either treated with DMSO or 1uM olaparib for 4 hours.UWB1.289 cells were either treated with DMSO or 1uM talizoparib for 4 hours.
|
| Growth protocol |
DLD1 BRCA2-/- were cultured in RPMI 1640 with GlutaMAX media and supplemented with 10% FBS and 1x penicillin-streptomycin (P/S). DLD1 BRCA2-/- cells were maintained at 3% oxygen. UWB1.289 cells were cultured in 1:1 (MEGM:RPMI) media supplemented with 10% FBS and 1xP/S. UWB1.289 were cultured at atmospheric oxygen.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
50K cells were pelleted at 800 x g and washed with 50mL of ice cold 1 x PBS followed by 2min treatment with 50 uL lysis buffer. After pelleting nuclei, nuclei were re-suspended in 50uL of transposition buffer (25uL of 2x TD buffer, 22.5ul of molecular biology grade water and 2.5uL Tn5 transposase (Illumina, cat# FC-121-1030) to tag the accessible chromatin for 45min at 37C. Tagmented DNA was purified with MinElute Reaction Cleanup kit and amplified with 5 cycles. Additional number of PCR cycles was determined from the side re-action and ranged from 10-12 total cycles of PCR. Two to three replicates were performed for each condition. Libraries were purified using QiaQuick PCR purification kit and eluted in 20uL EB buffer.
Indexed libraries were assessed for nucleosome patterning on the Agilent TapeStation 2200 and paired-end sequenced (38bp+38bp) on Illumina NextSeq 550.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Reads from ATAC-seq experiments were trimmed with Trim Galore
Reads were aligned to the primary assembly including all the chromosomes and contigs using BWA
Reads mapped to contigs, ENCODE blacklist and marked as duplicates were discarded
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files for genome browser viewing
|
| |
|
| Submission date |
May 20, 2020 |
| Last update date |
Dec 02, 2020 |
| Contact name |
Robert Babak Faryabi |
| E-mail(s) |
faryabi@pennmedicine.upenn.edu
|
| Phone |
215-573-8220
|
| Organization name |
University of Pennsylvania
|
| Department |
Pathology
|
| Lab |
Faryabi Lab
|
| Street address |
Room 553 BRB II/III, 421 Curie Boulevard
|
| City |
Philadelphia |
| State/province |
Pennsylvania |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL21697 |
| Series (1) |
| GSE150955 |
ALC1 and PARP activities coordinate chromatin accessibility and viability in homologous recombination deficient cells (ATAC-seq) |
|
| Relations |
| BioSample |
SAMN14984968 |
| SRA |
SRX8371228 |
