|
| Status |
Public on Jan 08, 2018 |
| Title |
shREN_RN2_repeat2 |
| Sample type |
SRA |
| |
|
| Source name |
murine MLL-AF9/NrasG12D AML cell line(RN2)
|
| Organism |
Mus musculus |
| Characteristics |
cell line: RN2
cell types: cells transduced with shRNA in LEP vector
mouse strain: C57/BL/6
treatment time: day 3 post-infection
|
| Treatment protocol |
For RNA-seq in cells transduced with dox-regulated shRNA, cells were treated with dox for 24 hrs prior to RNA extraction.
|
| Growth protocol |
RN2 cells derived from MLL-AF9/NrasG12D AML mouse model were cultured in RPMI with 10%FBS and P/S under 7.5% CO2. Bone marrow-derived myeloid progenitor cells were cultured in 10%FBS with 10 ng/ul SCF, 2 ng/ul IL-3, 2 ng/ul IL-6 and 50 uM beta-ME under 7.5% CO2. Human AML cell line was cultured in RPMI with 10%FBS and P/S under 7.5% CO2.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted using TRIzol following manufacture’s protocol. 2ug total RNA was used for constructing RNA-seq library
RNA-seq libraries were constructed using the Illumina TruSeq sample prep kit v2 following manufacture’s protocol. Briefly, RNA was polyA selected and enzymatically fragmented. cDNA was synthesized using Super Script II master mix, followed by end repair, A-tailing and PCR amplification.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
processed data file: shTAF12 VS shREN_RN2.txt
|
| Data processing |
Single-end 50bp sequencing reads were mapped into mm9 genome using TopHat with default settings
Structural RNAs were masked
Differentially expressed genes were identified using Cuffdiff, normalized to total mapped reads
Genome_build: mm9/hg19
Supplementary_files_format_and_content: txt files generated from Cuffdiff
|
| |
|
| Submission date |
Sep 27, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Yali XU |
| E-mail(s) |
yxu@cshl.edu
|
| Organization name |
Cold Spring Harbor Laboratory
|
| Street address |
1 Bungtown Road
|
| City |
Cold Spring Harbor |
| State/province |
NY |
| ZIP/Postal code |
11724 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE104308 |
A TFIID-SAGA perturbation that targets MYB and suppresses acute myeloid leukemia (RNA-seq) |
| GSE104309 |
A TFIID-SAGA perturbation that targets MYB and suppresses acute myeloid leukemia |
|
| Relations |
| BioSample |
SAMN07709328 |
| SRA |
SRX3219127 |
