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Sample GSM7054545 Query DataSets for GSM7054545
Status Public on Apr 12, 2023
Title SEM::EGR3 biol rep 3
Sample type SRA
 
Source name proB cells
Organism Homo sapiens
Characteristics tissue: proB cells
cell line: SEM
cell type: B cell precursor leukemia
genotype: EGR3-overexpressing vector transfected
treatment: Induction of transgene expression through Doxycycline treatment 1 µg/mL 48 h prior to RNA prep
Treatment protocol Induction of transgene expression through Doxycycline treatment 1 µg/mL 48 h prior to RNA extraction
Growth protocol SEM cells were maintained in RPMI 1640 (RPMI-HA, Capricorn Scientific) supplemented with 10% FBS (FBS-11A, Capricorn Scientific), 2 mM L-glutamine (STA-B, Capricorn Scientific), 100 U/ml penicillin and 100 μg/ml streptomycin (PS-B, Capricorn Scientific). Cells were kept at 37°C in 5% CO2 and a relative humidity of 95%.
Extracted molecule polyA RNA
Extraction protocol RNA of 1x10^7 SEM cells was extracted using the RNeasy Mini Kit (Qiagen, Cat. No. / ID: 74104) according to the manufacturer's protocol
MACE-libraries were prepared at GenXPro GmbH using the Massive Analysis of cDNA Ends (MACE) Library Preparation Kit (v2.0) from GenXPro GmbH.
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina NextSeq 500
 
Data processing Illumina bcl2fastq software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence and bad quality as well as MACE specific polyA stretches; PCR artifacts were deduplicated based on Unique Molecular Identifier sequences
Cleaned reads were mapped onto GRCh38 genome using bowtie2 and raw counts were obtained using HTSeq
Assembly: GRCh38
Supplementary files format and content: Matrix table as tab-delimited text file with raw and normalized gene counts for every gene and every sample
Library strategy: MACE-seq
 
Submission date Feb 21, 2023
Last update date Apr 12, 2023
Contact name Marius Külp
E-mail(s) marius.kuelp@em.uni-frankfurt.de
Organization name Goethe University Hospital Frankfurt
Department Department of Medicine II, Hematology/Oncology
Lab Rieger lab
Street address Theodor-Stern-Kai 7
City Frankfurt am Main
ZIP/Postal code 60590
Country Germany
 
Platform ID GPL18573
Series (1)
GSE225710 Transcriptional effect of EGR3 overexpression in the cell line SEM
Relations
BioSample SAMN33401426
SRA SRX19463370

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

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