|
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 |
E-mail(s) |
bioyuyang@hotmail.com
|
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 |
|
Relations |
BioSample |
SAMN02863120 |
SRA |
SRX644380 |