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Sample GSM1412836

Query DataSets for GSM1412836

Status

Public on Apr 20, 2015

Title

Sample type

SRA

Source name

Mesendoderm

Organism

Mus musculus

Characteristics

cell type: ES-derived mesendoderm cells
treatment: none
strain: 129/Ola

Growth protocol

Mesendoderm cells were derived from T-GFP ES cells by LIF withdrawal (Fehling et al., 2003; Kubo et al., 2004). T-GFP cells were cultured in differentiation ES medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and without recombinant leukemia inhibitory factor (LIF, millipore) for six days. GFP positive cells were sorted out by fluorescent-activated cell sorting (FACS).

Extracted molecule

total RNA

Extraction protocol

RNA was extracted from FACS sorted ME cells. TRIzol reagent was added directly into the plate after cold 1 × PBS wash once. The total RNA was extracted according to manufacturer's instructions. mRNA was further isolated by Dynabeads mRNA purification kit (Life Technologies) according to manufacturer's instructions.
Library was prepared by illumina TruSeq Stranded mRNA LT Sample Prep Kit (RS-122-2101) according to the standard protocols of the manufacturer.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2000

Description

Sample 11
messenger RNA
processed data file: ESCs_RNA-Seq_profile.txt
Sample 11

Data processing

The sequencing company provided "clean reads" (i.e., low quality reads removed).
Basecalls performed using CASAVA version
ChIRP retrived DNA-Seq reads were aligned to the mm9 genome assembly using Bowtie version 1.0.0 with the default parameters
RNA-seq reads were aligned to the mm9 genome assembly using Tophat v2.0.11,allowing for uniquely mapped reads and mapping both spliced and unspliced reads.
FPKM was calculated by Cufflink 2.1.1
Peaks of each sample were called using MACS v. 1.4.2
Genome_build: mm9
Supplementary_files_format_and_content: RNA-seq: tab-delimited text files include FPKM values for wild-type or Haunt KO Samples; ChIRP-seq: bedgraph files were generated using MACS v. 1.4.2, including peaks called by default parameters.

Submission date

Jun 16, 2014

Last update date

May 15, 2019

Contact name

jinlong lu

E-mail(s)

bioyuyang@hotmail.com

Phone

5853098469

Organization name

University of Rochester