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Sample GSM1412830 Query DataSets for GSM1412830
Status Public on Apr 20, 2015
Title WTc-d2
Sample type SRA
Source name CJ7 mES cells (-LIF, day2)
Organism Mus musculus
Characteristics cell line: CJ7
cell type: embryonic stem cells
genotype/variation: WT
treatment: LIF withdrawal
time: day2
strain: 129S1/SVImJ
Growth protocol ESCs were cultured in ESC differentiation 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 two days.
Extracted molecule total RNA
Extraction protocol Differentiated ES cells were harvested at day 2 of LIF withdrawal. 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 5
messenger RNA
processed data file: ESCs_RNA-Seq_profile.txt
Sample 5
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
Phone 5853098469
Organization name University of Rochester
Lab Gorbunova & Seluanov Labs
Street address 213 Hutchinson Hall
City Rochester
State/province NY
ZIP/Postal code 14627
Country USA
Platform ID GPL13112
Series (1)
GSE58514 Opposing roles for the lncRNA Haunt and its genomic locus in regulating HOXA gene activation during embryonic stem cell differentiation
BioSample SAMN02863116
SRA SRX644373

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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