|
| Status |
Public on Apr 04, 2019 |
| Title |
RNA-seq in K562 cell line treated with JQ1 and Methotrexate for 1h, replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
K562 cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: K562
sample_type: cell line
treatment: JQMT
timepoint: 1h
|
| Growth protocol |
HAP1 cell lines were cultured in Iscove’s Modified Dulbecco’s Medium (IMDM, Gibco), supplemented with 10% Fetal Bovine Serum (FBS; Gibco) and incubated in 5% CO2 atmosphere at 37°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed with Qiagen RNeasy Mini Kit (Cat No. 74106) according to the manufacturer's instructions.
Total RNA was quantified using Qubit 2.0 Fluorometric Quantitation system (Life Technologies) and the RNA integrity number (RIN) was determined using Experion Automated Electrophoresis System (Bio-Rad). RNA-seq libraries were prepared with TruSeq Stranded mRNA LT sample preparation kit (Illumina) using Sciclone and Zephyr liquid handling robotics (PerkinElmer). Library amount was quantified using Qubit 2.0 Fluorometric Quantitation system (Life Technologies) and the size distribution was assessed using Experion Automated Electrophoresis System (Bio-Rad). For sequencing libraries were pooled, diluted and sequenced on Illumina HiSeq 3000 using 50 bp single-read chemistry.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
RNA-seq in K562 cell line treated with JQ1 and Methotrexate for 1h, replicate 2
|
| Data processing |
Base calls provided by the Illumina Realtime Analysis software were converted into BAM format using Illumina2bam and demultiplexed using BamIndexDecoder (https://github.com/wtsi-npg/illumina2bam)
Sequenced reads were trimmed for adaptor sequences
Reads were mapped to hg19 whole genome using bowtie2 v2.2.4 with the –very-sensitive parameter
Duplicate reads were marked and removed with picard tools version 1.118
Library quality was assessed with the phantomPeakQualtools scripts (Landt SG, Genome Research 2012).
Transcriptome analysis was performed using the Tuxedo suite. TopHat2 was supplied with reads passing vendor quality filtering (PF reads) and the Ensembl transcript set (Homo sapiens, e75, February 2014) as reference. TopHat2 analyses were run independently for each replicate.
Cufflinks (v2.2.1) was used to assemble transcripts from spliced read alignments, using the Ensembl e73 transcriptome as the reference as well as de novo assembly of transcript models.
Differential expression was assessed with Cuffdiff v2.2.1. Transcriptome sets of all replicates for each sample group were combined with Cuffmerge. Finally, cummeRbund and biomaRt were used to perform quality assessment and refine analysis results.
Genome_build: hg19
Supplementary_files_format_and_content: tsv file contains FPKM values for each sample at gene level
|
| |
|
| Submission date |
Dec 06, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Christoph Bock |
| E-mail(s) |
cbock@cemm.oeaw.ac.at
|
| Organization name |
CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences
|
| Street address |
Lazarettgasse 14
|
| City |
Vienna |
| ZIP/Postal code |
1090 |
| Country |
Austria |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE105786 |
MTHFD1 links folate metabolism to BRD4-mediated transcriptional regulation |
|
| Relations |
| BioSample |
SAMN08138715 |
| SRA |
SRX3450815 |
