|
| Status |
Public on May 01, 2015 |
| Title |
PolyA+_TF screening_C/EBPb |
| Sample type |
SRA |
| |
|
| Source name |
MLL-AF9/NrasG12D murine cell line
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: Acute myeloid leukemia
genotype: MLL-AF9/NrasG12D
shRNA: shC/EBPb.1459 (C/EBPb_1), shC/EBPb.1460 (C/EBPb_2)
treatment: none
|
| Treatment protocol |
To profile the basal transcription level, we performed PolyA+ (illumina TruSeq) in a murine AML RN2 cell lines. To define the genes affected by target TF knockdown, RN2 cells which express dox-inducible shRNAs were cultured with Doxycyclin for 48 hour before harvest. To define the rapid downregulated genes in response to JQ1 and C646 in RN2 cell, we performed RNA-seq in RN2 exposing to each 500nM JQ1 or 10uM C646 for 6 hour. Especially, 10uM of C646 was replenished every 2 hour with unstable nature of C646 in this culture.
|
| Growth protocol |
Cultures were maintained in RPMI medium 1640 supplemented with 10% FBS, 1% Pen/Strep.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted using Trizol reagent.
These libraries were made following the instructions of illumina Truseq RNA sample prep kit v2.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
RNA-Seq
|
| Data processing |
Sequenced reads were trimmed for adaptor sequence to map with mouse genome (mm9) using Tophat with default parameters.
Cufflinks software was used to compare gene expression profiles by calculting Reads Per Kilobase of exon per Megabase of library size (RPKM) for each sample.
For biological replicates of experiments, two individual shRNAs (for HAT and TF knockdown RNA-Seq) or two independent drug treated cells (for JQ1 and C646 RNA-Seq) were used to prepare total RNA.
To define the expressed genes in further analysis of PolyA+ RNA-Seq, only the genes over RPKM=1 and status=OK from Cuffdiff analysis were considered.
Processed data files contain a list of filtered genes with averaged RPKM from two biological replicates.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample.
|
| |
|
| Submission date |
Feb 18, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Jae Seok Roe |
| E-mail(s) |
jroe@yonsei.ac.kr
|
| Organization name |
Yonsei University
|
| Street address |
Yonsei-ro, 50
|
| City |
Seoul |
| ZIP/Postal code |
03722 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE66068 |
BET Bromodomain Inhibition Suppresses the Function of Hematopoietic Transcription Factors in Acute Myeloid Leukemia [RNA-Seq] |
| GSE66123 |
BET Bromodomain Inhibition Suppresses the Function of Hematopoietic Transcription Factors in Acute Myeloid Leukemia |
|
| Relations |
| BioSample |
SAMN03354697 |
| SRA |
SRX884103 |
