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Sample GSM1846088 Query DataSets for GSM1846088
Status Public on Apr 26, 2016
Title R2
Sample type SRA
Source name RAday4 with mix3
Organism Mus musculus
Characteristics cell type: Embryonic Stem Cells
treatment: Day 4 - After the addition of retinoic acid
mix of spikes: mix3
ercc: mix1
Treatment protocol Four days old Ebs where treated for the next 4 days with 2uM RA (Retinoic Acid, Sigma R2625). Day of RA addition corresponds to the sample name RAday0. Four days RA tratment corresponds to the sample name RAday4.
Growth protocol Embryoid Bodies (Ebs) where generated by plating R1 mouse ES cells into 6cm low cell binding dishes as a single cell suspension (35000cells/ml) in 5ml of mES growth medium without Lif and incubating them for 4 days.
Extracted molecule total RNA
Extraction protocol RNA was prepared with RNeasy Mini kit (Qiagen)
Mouse IVT spike-in and ERCC mixes were added to the total RNA
1microgram of total RNA was processed using the Illumina TruSeq RNA Sample Preparation Kit v2 protocol and 700ng for the Illumina TruSeq Strand Specific total RNA with RiboZero Gold protocol (Illumina). Libraries were evaluated by Qubit and TapeStation. Sequencing libraries were constructed with barcodes to allow multiplexing of 9 samples on three lanes. Between 39-59 million paired-end 100-bp reads were sequenced per sample on Illumina HiSeq Rapid 2500 instrument using protocols RTA ( and HCS (
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Data processing Reads were demultiplexed the reads into the different samples
Reads were aligned to the mm10 genome built and the sequences of the External RNA Control Consortium (ERCC) using Tophat (v2.0.10)
RSEM (v1.2.18) was used to quantify transcripts by directly running bowtie (v2.1.0). The quantification was done on gene structures of RefSeq (mm10). Several transcripts used as spike-ins that were not present in the original gtf and were added.
For the RSEM run, the transcript library was prepared (rsem-prepare-reference) followed by rsem-calculate-expression (--bowtie2 --forward-prob 0 --paired-end).
Trinity’s script was used to merge the abundance estimation of the different samples and to obtain TMM normalized FPKM matrix
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file include TMM normalized FPKM values for each sample
Submission date Aug 06, 2015
Last update date May 15, 2019
Contact name Gilgi Friedlander
Organization name Weizmann Institute of Science
Street address Hertzel st
City Rehovot
ZIP/Postal code 76100
Country Israel
Platform ID GPL17021
Series (2)
GSE71802 RNA-Seq: assessment of transcript level analysis tools [seq]
GSE75139 RNA-Seq: assessment of transcript level analysis tools
SRA SRX1135684
BioSample SAMN03979450

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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