|
| Status |
Public on Mar 01, 2019 |
| Title |
(HN)-SCC25_input |
| Sample type |
SRA |
| |
|
| Source name |
Head and neck squamous cell carcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: tongue
antibody: none
|
| Growth protocol |
Cells were grown DMEM-F12 media 10% FBS
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin was prepared from 2x10^7 SCC cells or 1x10^6 sorted cells using the ChIP-IT High Sensitivity kit (53040, Active Motif) according to manufacturers instructions.
Library prep was performed with ThruPLEX DNA-seq kit (Rubicon Genomics, R400427) using 200pg of ChIP DNA or KAPA Hyper Prep kit (KAPA, KK8505) using 1ng of ChIP DNA
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
epithelial
|
| Data processing |
Human assembly version hg19/NCBI GRCh37 build were used for sequence alignments with bowtie 45 version 2.1.0.
Sequences with MAPQ scores <30 were removed with samtools50 and duplicates were removed with picard-tools version 1.88
IGV viewer files were generated with igvtools count -z 5 -w 25 -e 250.
ChIP-seq peaks were called with MACS51 version 2.1.0 in comparison to input controls with the parameters -q 0.001 --nomodel --extsize 400.
Motif discovery was performed with MEME-ChIP52,53 using 200bp sequence surrounding peak summits.
Motif containing ChIP-seq peaks were analyzed with the GREAT: Genomic Regions Enrichment of Annotations Tool54, using default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: bed
|
| |
|
| Submission date |
Sep 22, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Markus Schober |
| E-mail(s) |
markus.schober@nyulangone.org
|
| Organization name |
New York University School of Medicine
|
| Department |
Dermatology
|
| Street address |
550 First Ave, Smilow 407
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10016 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE104137 |
Defining transcription factor networks that govers SCC growth [ChIP_seq_hg19] |
| GSE104145 |
Defining transcription factor networks that govers SCC growth |
|
| Relations |
| BioSample |
SAMN07687883 |
| SRA |
SRX3205371 |
