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Sample GSM3004628 Query DataSets for GSM3004628
Status Public on Sep 11, 2018
Title TALL_JS_18 (total RNA)
Sample type SRA
Source name bone marrow
Organism Homo sapiens
Characteristics subgroup: IMM
Extracted molecule total RNA
Extraction protocol RNA was extracted using the miRNAeasy mini kit (Qiagen). TruSeq Stranded Total RNA (w/RiboZero Gold) sample prep kit (Illumina) was used for the preparation of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Data processing fastq files were aligned to GRCh38 primary annotation with STARv2.4.2a using a 2-pass strategy. In the first pass gencode.v25 was used as guide, in the second pass all sjdb files from the first pass were used as guide
Genes were quantified by STARv2.4.2a on Gencode.v25
Genome_build: GRCh38
Supplementary_files_format_and_content: reads per gene as generated by STAR2.4.2a
Submission date Feb 14, 2018
Last update date Sep 11, 2018
Contact name Karen Verboom
Organization name Ghent University
Department Pediatrics and Genetics
Lab Center for Medical Genetics Ghent
Street address De Pintelaan 185
City Ghent
ZIP/Postal code 9000
Country Belgium
Platform ID GPL18573
Series (2)
GSE110636 Total RNA-seq in a primary T-ALL patient cohort
GSE110637 T-ALL
BioSample SAMN08537236
SRA SRX3700744

Supplementary file Size Download File type/resource 390.4 Kb (ftp)(http) TAB
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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