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Sample GSM3173587 Query DataSets for GSM3173587
Status Public on Feb 16, 2020
Title ML-2-ctrl
Sample type SRA
Source name Acute myeloid leukemia cells
Organism Homo sapiens
Characteristics treatment: GFP overexpression
Extracted molecule total RNA
Extraction protocol Total RNA from different samples were extracted (Rnaeasy mini kit, Qiagen), and used for construction of sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
Data processing The raw sequencing reads were filtered for adapter and low quality sequences using cutadapt (Martin, 2011) and custom scripts. Low quality reads were defined as sequencing reads with more than 5% unknown bases (ā€˜Nā€™) and reads with more than 50% of the bases.
Alignment, expression estimation and tests for differential expression were processed by RSEM 1.2.31 (Li and Dewey, 2011) and EBSeq Version 1.10.0 (Leng et al, 2013). Resulting values were indicated by Transcript Per Million (TPM).
Genome_build: Human genome (GRCh38)
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample.
Submission date Jun 04, 2018
Last update date Feb 18, 2020
Contact name Chi Ho Lin
Phone +852 2831 5511
Organization name The University of Hong Kong
Department Centre for PanorOmic Sciences
Street address 6th Floor, The Hong Kong Jockey Club Building for Interdisciplinary Research, 5 Sassoon Road, Pokfulam
City Hong Kong
ZIP/Postal code Hong Kong
Country Hong Kong
Platform ID GPL18460
Series (1)
GSE115284 RNA-seq of ML-2 acute myeloid leukemia cells overexpressed with GFP, FST317 and FST344
BioSample SAMN09317870
SRA SRX4159102

Supplementary file Size Download File type/resource
GSM3173587_ML-2-ctrl.txt.gz 971.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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