|
| Status |
Public on Apr 21, 2023 |
| Title |
A375_CMV_SE_input |
| Sample type |
SRA |
| |
|
| Source name |
A375 melanoma cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: A375
tissue: melanoma cell line
chip antibody: none
antibody manu.: n/a
antibody catalog: n/a
antibody lot: n/a
cdk13 status: control (overexpress CLOVER)
|
| Growth protocol |
For ChIP-seq from human melanoma cells, one replicate (line 1) of A375 human melanoma cells expressing pLENTI-CMV CLOVER or pLENTI-CMV CDK13 R860Q as derived above in “Stable Human Cell Lines” from methods were used. Cells were grown in DMEM with 10% FBS with glutamine/penicillin/streptomycin. Equal cell number (approximately 40x106) were fixed and used for each IP.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclear cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 200-400 bp were immunoprecipitated using different antibodies.
Libraries were performed using the NEBNextMultiplex Oligos for Illumina kit (NEB) according to instructions. Samples were sequenced with 100bp reads, either single or paired end depending on the experiment.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Raw reads were aligned twice: first to the dm6 revision of the D. melanogaster genome to remove exogenous spike-in reads using bowtie version 1.2.2 with parameters -k 1 -m 1; unmapped reads were then aligned to the hg19 revision of the human genome.
hg19
Supplementary_files_format_and_content: bigWig files were created from the alignment bam file using the R with the GenomicAlignments package and with gr.cov and export.bw from rtracklayer
|
| |
|
| Submission date |
May 16, 2019 |
| Last update date |
Apr 21, 2023 |
| Contact name |
Richard A Young |
| E-mail(s) |
young_computation@wi.mit.edu
|
| Phone |
617-258-5219
|
| Organization name |
Whitehead Institute for Biomedical Research
|
| Lab |
Young Lab
|
| Street address |
9 Cambridge Center
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE131330 |
Oncogenic CDK13 Mutations Impede Nuclear RNA Surveillance (humanChIPseq) |
| GSE131334 |
Oncogenic CDK13 Mutations Impede Nuclear RNA Surveillance |
|
| Relations |
| BioSample |
SAMN11659443 |
| SRA |
SRX5846392 |
