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Sample GSM4139667

Query DataSets for GSM4139667

Status

Public on Mar 18, 2021

Title

ITS_TSC_BMP4_rep2

Sample type

SRA

Source name

cultured cells

Organism

Mus musculus

Characteristics

cell type: ITS_TSC
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