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Sample GSM3878577 Query DataSets for GSM3878577
Status Public on Jun 04, 2020
Title gelatin_std_2
Sample type SRA
Source name C57BL6/J WT mESC
Organism Mus musculus
Characteristics strain background: C57BL6/J
cell type: Embryonic stem cell
culture condition: gelatin coated dish under Std medium
Growth protocol WT mESCs derived from inbred mouse (Bruce 4 C57BL/6J, male, EMD Millipore, Billerica, MA) were cultured on either LN511 or gelatin coated dish under either Std or 2i medium.
Extracted molecule total RNA
Extraction protocol C57BL/6J WT mESCs were conditioned on either gelatin or LN511 coated dish in either Std or 2i medium for 2 weeks.
Then, RNA was recovered from 1x106 cells using the NucleoSpin RNA kit (Macherey-Nagel, Düren, Germany).
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Description gelatin_std_2_GGCTAC_L001
Data processing All reads are mapped to mm10 using TopHat (version 2.1.1)
FPKM are quantified using Cufflinks (version 2.1.1)
Genome_build: mm10
Supplementary_files_format_and_content: genes.fpkm.csv and isoforms.fpkm.csv files include RPKM values at gene- and transcript-level, respectively
Submission date Jun 12, 2019
Last update date Jun 04, 2020
Contact name Itoshi NIKAIDO
Organization name RIKEN
Department Center for Biosystems Dynamics Research
Lab Laboratory for Bioinformatics Research
Street address 2-1 Hirosawa
City Wako
State/province Saitama
ZIP/Postal code 351-0198
Country Japan
Platform ID GPL17021
Series (2)
GSE132591 RNA-seq analysis of mESCs cultured on either Laminin-511 or gelatin coated dishes in either Std or 2i medium
GSE132593 Genome-wide kinetic properties of transcriptional bursting in mouse embryonic stem cells
BioSample SAMN12037552
SRA SRX6047931

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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