|
| Status |
Public on Dec 18, 2022 |
| Title |
PolII_Input_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
MRC-5 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MRC-5 cells
chip antibody: input
|
| Growth protocol |
MRC5 cells were cultured in DMEM medium (Gibco) supplemented with 10% fetal bovine serum (Corning), 1,000 Units/ml Penicillin-Streptomycin (Gibco) at 37°C in a humidified incubator at 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
After fixation, cells were lysed and sonication with a Bioruptor Plus sonication device (Diagenode). Sonication was conducted for 25 cycles, with 30 sec on/off at high intensity. ChIP was performed by incubating the sonicated sample with either Rpb1 NTD (D8L4Y) Rabbit mAb #14958 or Acetyl-Histone H3 (Lys27) (D5E4) XP Rabbit mAb #8173 (Cell Signaling Technologies) and the protein A/G agarose beads. Beads were washed and eluted in 200μl of elution buffer (50 mM Tris-HCl at pH 8.0, 10 mM EDTA, 1.0% SDS). The eluates were de-cross-linked and the DNA purified using the Qiagen PCR purification kit.
Libraries were prepared with the Illumina Chip-SEQ Kit multiplexed with IDT unique dual index barcodes. Library quality control was assessed using Bioanalyzer High Sensitivity DNA Analysis kit (Agilent) and sequenced on an Illumina NovaSEQ6000 (100bp paired-end reads).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned to the reference genome using Bowtie2 version 2.2.6
bigWig files were created using deepTools
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files
|
| |
|
| Submission date |
Apr 05, 2021 |
| Last update date |
Dec 18, 2022 |
| Contact name |
Mary Hummel |
| E-mail(s) |
m-hummel@northwestern.edu
|
| Phone |
847-322-6438
|
| Organization name |
Northwestern University
|
| Street address |
303 E. Chicago Ave
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60611 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE171509 |
Pol II and H3K27Ac occupancy of the human genome in MRC5 cells |
| GSE171522 |
HCMV epigenome and transcriptome during early lytic infection |
|
| Relations |
| BioSample |
SAMN18620490 |
| SRA |
SRX10515082 |
