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Sample GSM4139661 Query DataSets for GSM4139661
Status Public on Mar 18, 2021
Title iPS_BMP4_rep2
Sample type SRA
 
Source name cultured cells
Organism Mus musculus
Characteristics cell type: iPS
treatment: BMP4
Treatment protocol Single iPSCs (GFP+) and TSCCs(RFP+) were mixed adequately and then seeded into 5% Matrigel coated 12-well plate. The attached cells were cultured in ITSC medium to induce embryonic body(EB) formation. Two days later, cells were treated for another 24 hours in ITSC medium with or without BMP4. At day 3, single embryoid structure were confirmed carefully in fluorescence microscope. Proper single structure should be composed of two tightly attached colonies with green (iPSC-part) and red (TSC-part) fluorescent individually. Then picked and separated the structure into two individual parts with distinct fluorescent under stereomicroscope. Each part were transfer directly into 200uL RNase-free tube followed with smart-seq protocol. iPSCs or TSCCs only group were treated with the same protocol as described above.
Growth protocol mESC and iPSCs were grow in 5% matrigel coated 12-well culture plate with ITSC medium composed of 50% RPMI, 25% DMEM F-12, 25% Neurobasal A, 10% FBS, 0.5mM GlutaMAX, 0.1mM 2-mercaptoethanol, 0.5mM sodium pyruvate, 0.25x N2 supplement, 0.5x B27 supplement, plus 12.5 ng/ml FGF4 and 500ng/ml heparin.
Extracted molecule total RNA
Extraction protocol Pick single clone into 200uL Rnase-free tube with lysis buffer which prepared following the Smart-seq2 protocol (Picelli, 2014)
RNA-seq library was prepared following the Smart-seq2 protocol (Picelli, 2014)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Data processing Illumina Casava software was used for basecalling.
Sequenced reads were trimmed for adaptor sequences, and masked for low-complexity or low-quality sequences, then mapped to hg19 genome using Tophat2.
Fragments Per Kilobase per Million mapped reads (FPKM) of Refseq genes were caculated.
Table of gene names and FPKM values for each sample.
Genome_build: mm9
Supplementary_files_format_and_content: Table of gene names and FPKM values for each sample.
 
Submission date Oct 25, 2019
Last update date Mar 18, 2021
Contact name Jie Na
E-mail(s) jie.na@tsinghua.edu.cn
Phone +86-18618192150
Organization name Tsinghua University
Department Basic Medical Sciences, School of Medicine
Lab D115 School of Medicine
Street address Tsinghua University
City Beijing
State/province Beijing
ZIP/Postal code 100084
Country China
 
Platform ID GPL21273
Series (1)
GSE139379 Transcriptome analysis of assembled embryos using mouse induced pluripotent stem cells (iPSC) and trophectoderm stem cells (TSCC)
Relations
BioSample SAMN13112859
SRA SRX7055364

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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