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Sample GSM2786536 Query DataSets for GSM2786536
Status Public on Jan 01, 2018
Title DOHH2
Sample type SRA
 
Source name DOHH2 cell line
Organism Homo sapiens
Characteristics cell line: DOHH2
Extracted molecule total RNA
Extraction protocol Samples were centrifuged for 5 minutes at 1000 RPM, and supernatant was removed without disturbing the cell pellet. Cells were resuspended using 1000 uL of HGT Lysis buffer to maintain original concentration of 4 millions cells per 1000 uL. The lysis buffer cell suspension was placed in 95 degrees Celsius for fifteen (15) minutes. After allowing to cool at room temperature for ten (10) minutes, Proteinase K was added at 1/20 Lysis Buffer volume and samples were incubated at 50 for 180 minutes. Samples were run as singletons. Samples were plated initially at a concentration of 10000 cells per well (10000 cells/35 uL).
Samples submitted were individually barcoded and purified using AMPure XP beads and quantitated using KAPA Library Quantification kit. The library was sequenced at 4pM on an Illumina NextSeq using High Output, 75 cycle, v2 kit with two index reads.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description Sample 2
Targeted RNA-Seq
Processed data file: Raw_counts.txt
Processed data file: Normalized_counts.txt
Data processing Illumina Casava1.7 software used for basecalling. Four fastq files per sample.
The HTG EdgeSeq Parser was used to align reads to the probe list to collate the data. Data are provided as raw counts data and median normalized.
Genome_build: hg38
Supplementary_files_format_and_content: Raw_counts.txt: Tab-delimited text file includes raw counts values.
Supplementary_files_format_and_content: Normalized_counts.txt: Tab-delimited text file includes median normalized values.
 
Submission date Sep 17, 2017
Last update date May 15, 2019
Contact name Francesco Bertoni
E-mail(s) francesco.bertoni@ior.iosi.ch
Phone +41 91 820 0367
Organization name IOR
Department Lymphoma & Genomics Research Program
Street address Via V. Vela 6
City Bellinzona
State/province Ticino
ZIP/Postal code 6500
Country Switzerland
 
Platform ID GPL18573
Series (1)
GSE103934 Targeted RNA-Seq of Human Lymphoma Cell Line
Relations
BioSample SAMN07661061
SRA SRX3194393

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data is available on Series record

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