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Sample GSM3770577 Query DataSets for GSM3770577
Status Public on Apr 21, 2023
Title A375_CMVCDK13_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: overexpress CDK13 R860Q
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 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.
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.
 
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 SAMN11659484
SRA SRX5846397

Supplementary file Size Download File type/resource
GSM3770577_A375_CMVCDK13_SE_input_comb.bw 129.4 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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