|
| Status |
Public on Sep 18, 2017 |
| Title |
AML-2_repB |
| Sample type |
SRA |
| |
|
| Source name |
Transplated AML sorted from bone marrow
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
culture conditions: Before transplantation, MLL-AF9;NRASG12D AML cells were obtained from the Lowe laboratory and cultured in RPMI-1640 with GlutaMax (Gibco), supplemented with 10% heat-inactivated FBS (HyClone) and 1% Penicillin/Streptomycin (Gibco) under 7.5% CO2 culture conditions.
cell type: Sorted AML cell from bone marrow 14 days post transplantation
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were sorted following previously published gating strategies, shown in Figure S1 and RNA was extracted using NucleoSpin RNA XS (Machery Nagel), including DNase treatment.
Between 3000 and 10,000 cells were used as library input using Clontech’s SMARTer Ultra Low input RNA Sequencing Kit (Cat. No. 634823). cDNA was sheared to 300 bp on a Covaris LE220 and used as input for Clontech’s low input library preparation for Illumina Sequencing kit (Cat. no. 634947). Libraries were sequenced paired-end 100 bp on an Illumina HiSeq2500.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
all_hematopoiesis_catalog-vst.csv
|
| Data processing |
Map to mm10 using STAR aligner
Duplicate removal using PICARD
Calculate counts for coding genes or catalog using htseq-count. To calculate the number of fragments mapping to each catalog transcript in each library, overlapping catalog genes were merged together
DESeq2 was used to calculate variance stabalized transformed values
Genome_build: mm10
Supplementary_files_format_and_content: all_hematopoiesis_catalog-vsd.csv: relative abundance estimations,mjdelasv_GEO_lowinputlibraries-merged_lncRNAassembly.gtf:lncRNA catalog assembly
|
| |
|
| 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 |
GPL17021 |
| Series (2) |
| GSE90067 |
Comprenhensive lncRNA expression analysis through normal hematopoiesis and AML |
| GSE90072 |
lncRNA dependencies in acute myeloid leukemia |
|
| Relations |
| BioSample |
SAMN06041048 |
| SRA |
SRX2361769 |
