|
| Status |
Public on Jul 24, 2020 |
| Title |
Anti-TAZ replicate2 |
| Sample type |
SRA |
| |
|
| Source name |
H1299 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: non-small cell lung cancer
cell line: H1299
antibodies: Anti-TAZ
|
| Treatment protocol |
H1299 cells were seeded on 150mm plates and serum starved for 18 hours.
|
| Growth protocol |
H1299 were cultured in RPMI-1640 (Gibco, USA) supplemented with 10% fetal bovine serum (Biological Industries, Israel) and 1% penicillin-streptomycin antibiotics solution. Cells were maintained at 37˚C with 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei. The chromatin solution was immunoprecipitated with either YAP antibody or TAZ antibody. The immunoprecipitations were performed using Pierce ChIP-grade Protein G magnetic beads (Thermo Fisher Scientific). Reverse cross-linking and DNA purification was performed by ChIP DNA Clean & Concentrator kit (Zymo Research, USA).
Libraries were prepared as described in Blecher-Gonen et al., Nat Protoc, 2013. 8(3): p. 539-54.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Raw fastq files were preprocessed with cutadapt to remove adapters and low-quality bases (parameters: --times 2 -q 20 -m 25). Reads were mapped to human genome (hg19) using bowtie2 (parameters: –local). Aligned duplicated reads were removed using samtools view (parameters: -h -F 4 for all reads and -f 0x2 for paired end reads). Remaining unique reads were indexed and sorted using samtools. Broad peaks were called using MACS2 against the input samples (parameters: --bw 300 -B -f --SPMR -keep-dup auto -q 0.01).
Genome_build: hg19
|
| |
|
| Submission date |
May 26, 2020 |
| Last update date |
Jul 25, 2020 |
| Contact name |
Moshe Oren |
| E-mail(s) |
moshe.oren@weizmann.ac.il
|
| Organization name |
Weizmann Institute of Science
|
| Street address |
234 Herzl
|
| City |
Rehovot |
| ZIP/Postal code |
7610001 |
| Country |
Israel |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE151199 |
Division of labor between YAP and TAZ in non-small cell lung cancer [ChIP] |
| GSE151201 |
Division of labor between YAP and TAZ in non-small cell lung cancer |
|
| Relations |
| BioSample |
SAMN15016528 |
| SRA |
SRX8400473 |
