|
| Status |
Public on Apr 20, 2015 |
| Title |
WTc-d0 |
| Sample type |
SRA |
| |
|
| Source name |
CJ7 mES cells
|
| Organism |
Mus musculus |
| Characteristics |
cell line: CJ7
cell type: embryonic stem cells
genotype/variation: WT
treatment: none
time: day0
strain: 129S1/SVImJ
|
| Treatment protocol |
Cells were washed once with cold PBS, and then add TRIzol for RNA total RNA extraction
|
| Growth protocol |
Wild-type ESCs or Haunt KO ESCs were maintained in strandard 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 supplied with 1000 U/ml recombinant leukemia inhibitory factor (LIF, millipore).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were harvested at 24 hours after plating. 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 1
messenger RNA
processed data file: ESCs_RNA-Seq_profile.txt
Sample 1
|
| 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 |
SAMN02863113 |
| SRA |
SRX644369 |
