|
| Status |
Public on Jul 26, 2016 |
| Title |
hg19_shMLL1_RNA_150410_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
HCT116
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Human colorectal tumor
passages: Low passages (6-10)
cell line: HCT116
chip antibody: N/A
|
| Treatment protocol |
Treatment with GSK126[5uM] or DMSO was administrated at 0- and 48-hour; harvesting cells at 96-hours.
|
| Growth protocol |
Cell medium was composed as follow: DMEM 1X (Thermo Fisher), 10% serum (Corning), 1X glutamine (Life Technologies), 1X penicillin/streptomycin (Life Technologies), cells were grown in a CO2 incubator (5% CO2) at 37˚C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using QIAGEN RNeasy kit.
Stranded Total RNA Preparation Kit with
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Cells lentiviral infected with MLL1 specific shRNA vector
|
| Data processing |
Basecalls were performed using Casava v1.8 and bcl2fastq v2.17 for Illumina HiSeq and NextSeq output,respectively.
Both ChIP-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
RNA-seq reads were aligned to UCSC hg19 and dm3 using Tophat version 2.0.9. Only uniquely mapping reads with at most two mismatches were retained.
To create RNA-seq coverage plots, the mapped RNA-seq reads were split according to strand, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
genome build: hg19
processed data files format and content: bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.
|
| |
|
| Submission date |
May 23, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Ali Shilatifard |
| E-mail(s) |
ash@northwestern.edu
|
| Organization name |
Northwestern University Feinberg School of Medicine
|
| Department |
Department of Biochemistry and Molecular Genetics
|
| Lab |
Shilatifard Lab
|
| Street address |
320 E Superior St
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60611 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE81795 |
An epigenetic mark of polycomb response elements implemented by Trx/MLL/COMPASS |
|
| Relations |
| BioSample |
SAMN05164212 |
| SRA |
SRX1794301 |
