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Sample GSM1412837 Query DataSets for GSM1412837
Status Public on Apr 20, 2015
Title NPC
Sample type SRA
Source name Neural progenitor cells
Organism Mus musculus
Characteristics cell type: ES-derived neural progenitor cells
treatment: none
strain: 129/Ola
Growth protocol Neural progenitor cells were derived from 46C (Sox1-GFP knock-in). 46C cells were differentiated for 6 days in N2B27 medium as described before (Conti et al, 2005). GFP positive cells were sorted by fluorescent-activated cell sorting (FACS).
Extracted molecule total RNA
Extraction protocol RNA was extracted from FACS sorted NPC 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 12
messenger RNA
processed data file: ESCs_RNA-Seq_profile.txt
Sample 12
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 SAMN02863120
SRA SRX644380

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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