NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM3044963 Query DataSets for GSM3044963
Status Public on Feb 06, 2019
Title RNASeq_RMCO2
Sample type SRA
 
Source name Cord blood CD34 cells
Organism Homo sapiens
Characteristics mutation status: RUNX1mut transduced
harvest time: NA
cell type: Cord blood CD34 cells
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from 1x10e6 iPSC control and RUNX1mut cells using the RNeasy mini kit (Qiagen) and performing on-column DNaseI treatment. Ribosomal RNA was depleted by using the ribo-zero rRNA removal kit (Illumina). RNA was fragmented in 300 bp fragments by incubation for 7.5 minutes in fragmentation buffer (200 mM Tris-acetate, 500 mM Potassium Acetate, 150 mM Magnesium Acetate (pH 8.2)). First strand cDNA synthesis was performed using superscript III (Life Technologies), followed by synthesis of the second cDNA strand. Libraries were generated using the Kapa hyper prep kit (KAPA Biosystems).
Libraries were generated using the Kapa hyper prep kit. End repair and A-tailing was performed on the double strand DNA using end repair and A-tailing buffer. Subsequently, the adapters were ligated and a post-ligation cleanup was performed using Agencourt AMPure XP reagent. The libraries were amplified by PCR using the Kapa Hifi hotstart readymix and primer mix, 10 cycles. Samples were purified using the Qiaquick MinElute PCR purification kit and 300 bp fragments were selected from E-gel and the size was checked on the agilent bioanalyzer. Samples were sequenced on the Illumina NextSeq 500.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing For expression analyses, the hg19 reference genome index was first generated using STAR aligner with UCSC gene annotation. Paired-end reads were mapped to the indexed genome in two-pass mode with default parameters, to increase alignment accuracy and sensitivity. Stranded gene-level read counts were enumerated at the same time. Expression quantification for each RefSeq gene was performed by Cuffnorm function in Cufflinks, to estimate Fragments Per Kilobase per Million aligned reads value (FPKM). All alignment files were scaled to RPKM-normalized read coverage files using deepTools for visualization.
Genome_build: hg19
Supplementary_files_format_and_content: Gene-level read counts were enumerated by STAR tool. bigWig files were generated using deepTools by scaling read depth to RPKM-normalized coverage
 
Submission date Mar 15, 2018
Last update date Nov 11, 2021
Contact name Joost Martens
E-mail(s) joost.martens@ru.nl
Phone 0243780645
Organization name Radboud University
Department RIMLS
Lab Molecular Biology
Street address Geert Grooteplein 28
City Nijmegen
State/province Nederland
ZIP/Postal code 6525GA
Country Netherlands
 
Platform ID GPL18573
Series (2)
GSE111918 RUNX1 mutations lead to a myeloid differentiation block by altering the RUNX1 transcriptional program (RNA-Seq)
GSE111919 RUNX1 mutations lead to a myeloid differentiation block by altering the RUNX1 transcriptional program
Relations
BioSample SAMN08720335
SRA SRX3800488

Supplementary file Size Download File type/resource
GSM3044963_RMCO2_Mylene_CB.bw 45.8 Mb (ftp)(http) BW
GSM3044963_RMCO2_Mylene_CB_ReadsPerGene.out.tab.gz 146.7 Kb (ftp)(http) TAB
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap