|
| Status |
Public on Sep 18, 2017 |
| Title |
9665_1_B |
| Sample type |
SRA |
| |
|
| Source name |
RN2 cells (MLL-AF9/NRASG12D)
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL6
knockdown: lncRNA_124982
shRNA: hp1
clonal cell line: B
|
| Treatment protocol |
Cells were transduced with a retroviral vector expressing an inducible shRNA. Infection percentage was kept to less than 30%. Single cell derived clonal cell lines were tested for homogeneous expression of the reported genes. Two cell lines per knockdown were used for further studies.
|
| Growth protocol |
MLL-AF9;NRASG12D AML cells were cultured in RPMI-1640 with GlutaMaxTM (Gibco), supplemented with 10% heat-inactivated FBS (HyClone) and 1% Penicillin/Streptomycin (Gibco) under 7.5% CO2 culture conditions.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA extraction using TriZol
TruSeq Stranded Total RNA Library Prep Kit (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
9665_vst.txt
|
| Data processing |
Reads were mapped to the mm10 genome assembly yielding at least 106 aligned reads per sample
HTSeq-count was used to calculate gene counts and subsequently input them into DESeq2 for quality control analysis, size normalization and variance dispersion corrections.
Genome_build: mm10
Supplementary_files_format_and_content: variance estabilized transformation calculated using DESeq2 for all replicated of both hairpins tagetting a given lncRNA, and Renilla controls
|
| |
|
| Submission date |
Nov 18, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
M Joaquina Delas |
| E-mail(s) |
joaquina.delas@crick.ac.uk, j.delas@ucl.ac.uk
|
| Organization name |
The Francis Crick Institute
|
| Department |
Briscoe Lab
|
| Street address |
1 Midland Road
|
| City |
London |
| ZIP/Postal code |
NW1 1AT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE90059 |
RNAseq analysis of AML cells upon lncRNA knockdown |
| GSE90072 |
lncRNA dependencies in acute myeloid leukemia |
|
| Relations |
| BioSample |
SAMN06040812 |
| SRA |
SRX2360544 |
