|
| Status |
Public on May 14, 2022 |
| Title |
ATAC_231_GATA3_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
MDA-MB-231
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-MB-231
genotype: MDA-MB-231_GATA3
passages: <20
|
| Treatment protocol |
Increasing number of NMuMG cells were used to optimize the ATAC seq protocol. Cells are cultured using DMEM+10% FBS medium. To collect the cell pellet, cells were washed with 1X PBS, and trypsinize with 0.25% Trypsin-EDTA (1X). Cells are counted by the Countess cell counter (Invitrogen)
|
| Growth protocol |
DMEM (with L-Glutamine, and 15 mM HEPES) + 10% FBS was used for NMuMG cells. DMEM + 10%FBS was used for MDA-MB-231 cells.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
MinElute (before PCR, Qiagen) and AMPure XP (after PCR, Beckman Coulter) were used for DNA purification.
Cells were lysed with CSK buffer (10 mM PIPES pH 6.8, 100 mM NaCl, 300 mM sucrose, 3 mM MgCl2, 0.1% Triton X-100). Nuclei were treated with Tn5 Transposase (Illumina). The total of 8 PCR cycles were performed to recover and amplify the DNA fragments at open chromatin.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Reads were filtered based on a mean base quality score >20.
Adapter sequences were removed with the Cutadapt function.
Reads were mapped to the mm10 or hg19 genome using Bowtie 0.12.8 with parameters '-I 0 -X 2000 -m 1'.
The offset parameters suggested by Buenrostro et al (Nat. Methods, 2013) were applied to each mapped read.
Alignments to chrM were filtered out with samtools.
Duplicate reads were removed using MarkDuplicates.jar from picard-tools-1.107 package.
Signal tracks were generated from either the full ATAC-seq fragment or only the 9bp footprint at 5' ends of reads, via conversion to bedGraph via Bedtools v2.17.0 genomeCoverageBed followed by conversion to bigWig format by UCSC utility bedGraphToBigWig.
Peak calls were made by PeaKDEck with parameters '-sig 0.0001 -bin 300 -back 3000 -npBack 2500000'.
Assembly: mm10, hg19
Supplementary files format and content: coverage tracks in bigWig format
Supplementary files format and content: peak calls in BED format
|
| |
|
| Submission date |
May 11, 2022 |
| Last update date |
May 17, 2022 |
| Contact name |
Archana Dhasarathy |
| E-mail(s) |
archana.dhasarathy@und.edu
|
| Phone |
7017774285
|
| Organization name |
UNIVERSITY OF NORTH DAKOTA
|
| Department |
Biomedical Sciences
|
| Lab |
Dhasarathy Lab
|
| Street address |
501 N. Columbia Road, STOP 9061, STOP 9061
|
| City |
Grand Forks |
| State/province |
ND |
| ZIP/Postal code |
58202-9061 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE202791 |
ATAC-seq Optimization for Cancer Cells |
|
| Relations |
| BioSample |
SAMN28194814 |
| SRA |
SRX15237449 |
