|
| Status |
Public on Dec 06, 2016 |
| Title |
bulk RNA-seq M1283nonLRC |
| Sample type |
SRA |
| |
|
| Source name |
PDX Sample ALL-199
|
| Organism |
Homo sapiens |
| Characteristics |
patient: BCP-ALL pediatric
mouse id: NOD scid gamma
cell type: PDX cell
cell status: non-LRC
|
| Growth protocol |
human patient cells are grown as patient-derived xenograft cells in immunodeficient NOD scid gamma mice and re-isolated from bone marrow
|
| Extracted molecule |
total RNA |
| Extraction protocol |
cDNA synthesis protocol: Cells were sorted into lysis buffer composed of 0.2 % Triton X-100 (Sigma) and 2 U/μl of RNAse Inhibitor (Life Technologies). ERCC spike-in controls (Life Technologies) were added to the cell lysis mix at 1:5,000 dilution. RNA was cleaned-up from the crude lysate with Agencourt RNAclean XP SPRI beads (Beckman-Coulter). cDNA was synthesized and pre-amplified from 5 μl of lysate according to the Smart-seq2 protocol (Picelli et al., 2013)
0.2-1 ng of pre-amplified cDNA was used as input for tagmentation by the Nextera XT Sample Preparation Kit (Illumina), where amplification was performed for 12-14 PCR cycles.
Cells were isolated from the murine bone marrow, enriched by a MACS step and sorted for the population of interest. All steps were performed at 4°C.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
M1283non
|
| Data processing |
Sequencing reads were demultiplexed from the Nextera (i5 and i7) indices using deML (Renaud 2014, Bioinformatics)
Demultiplexed reads were aligned to the human genome (hg19) and ERCC reference using NextGenMap (Sedlazeck et al., 2013)
Count data was generated from mapped reads using featureCounts (Liao et al., 2014) on ENSEMBL gene models (GRCh38.74)
Genome_build: hg19
Supplementary_files_format_and_content: [.txt] processed data files are text files with count data, where columns equal to samples and rows equal to genes
|
| |
|
| Submission date |
Jun 09, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Christoph Ziegenhain |
| E-mail(s) |
ziegenhain@bio.lmu.de
|
| Organization name |
Ludwig-Maximilians University Munich
|
| Department |
Department Biology II
|
| Lab |
Anthropology & Human genomics
|
| Street address |
Großhaderner Str. 2
|
| City |
Martinsried |
| State/province |
Bavaria |
| ZIP/Postal code |
82152 |
| Country |
Germany |
| |
|
| Platform ID |
GPL18460 |
| Series (1) |
| GSE83142 |
Identification of rare, dormant and therapy resistant stem cells in acute lymphoblastic leukemia |
|
| Relations |
| BioSample |
SAMN05220048 |
| SRA |
SRX1835129 |
