|
| Status |
Public on Sep 16, 2016 |
| Title |
mRNA-seq_48hr_CX-5461 |
| Sample type |
SRA |
| |
|
| Source name |
H9 hESC treated with a 50 ng/mL final concentration of CX-5461 for 48 hours
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: H9
chip antibody: N/A
passage: 58-60
treatment: 50 ng/mL CX-5461 for 48 hours
|
| Growth protocol |
For CX-5461 treatment ,cells were grown to about 75 – 80% confluency. The cells were washed with PBS and 10 ml of RPMI 1640 (GE Healthcare # SH30027.01) was added with 1X B-27 supplement (life technologies # 17504-044) along with CX-5461 (selleckchem # 52684) to a final concentration of 50 ng/ml for 48 hours. Old media was removed and replaced with fresh media/CX-5461 at 24 hours.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA-seq: Trizol followed by 2 rounds of poly A selection.
Libraries were prepared by Illumina's Tru-seq Library Preparation Kit v2. Paired-end sequencing was carried out on Hi-Seq_v4 (PE50 runs).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
mRNA
hg19
|
| Data processing |
Illumina CASAVA version 1.8.2 software was used to create the fastq files from the bcl files for ChIP-seq. bcl2fastq version 1.8.4 was used for RNA-seq. ChIP fastq files were filtered using the fastx filter tool to have 80% of the reads with a Qual score of >= 20. The remaining reads were collapsed using the collapser tool to eliminate all PCR duplicates. The resulting FASTA file was aligned to a custom hg18 annotation that includes the rDNA consensus repeat as an added chromosome called 'chr24_rDNA' using Bowtie2 under default conditions. The aligned SAM files were converted to BAM using samtools then to BED format using BEDTools.
RNA-seq datsets were aligned to hg19 using Tophat2 using default conditions.
Differential gene expression for mRNA-seq datasets was determined by running DEseq2 in R Statistical Environment. Processed tag counts across genes tested are in processed data file 'mRNA-seq_GeneCounts_AllSamples.xlsx'.
Genome_build: mRNA-seq = hg19, ChIP-seq = hg18plusrDNA custom build
Supplementary_files_format_and_content: bed + counts
|
| |
|
| Submission date |
Jan 06, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Jessica L Woolnough |
| E-mail(s) |
jlmakofske@gmail.com
|
| Organization name |
Brigham and Women's Hospital
|
| Department |
Genetics
|
| Street address |
77 Avenue Louis Pasteur
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE76586 |
The control of rRNA synthesis during the directed differentiation of human embryonic stem cells precedes heterochromatin formation. |
|
| Relations |
| BioSample |
SAMN04386706 |
| SRA |
SRX1519712 |
