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Sample GSM2194988 Query DataSets for GSM2194988
Status Public on Dec 06, 2016
Title bulk RNA-seq M1283LRC
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: 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 M1283LRC
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 SAMN05220047
SRA SRX1835128

Supplementary file Size Download File type/resource
GSM2194988_M1283LRC.counts.txt.gz 196.1 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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