|
| Status |
Public on May 05, 2015 |
| Title |
ESC_H33KO1_RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: 129xC57Bl/6 H3.3A/B-KO
cell type: Embryonic stem cells
cell line: H3.3 KO1
|
| Growth protocol |
ESCs (129xC57Bl/6J background) were cultured under standard conditions (KO-DMEM, 2 mM Glutamax, 15% ES grade fetal bovine serum, 0.1 mM 2-mercaptoethanol, and leukemia inhibitory factor (LIF)). For early passages, cells were maintained on an irradiated feeder layer. To remove feeders, cells were passaged at least two passages off of feeders onto gelatin-coated plates.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted from embryonic stem cells using the Qiagen Rneasy kit. 4 ug of RNA was used for library preparation.
Libraries were constructed according to the Illumina Tru-Seq protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
for gene expression analysis, reads were aligned to mm10 using TopHat v2.0.9 (-T -G --no-novel-juncs) and Bowtie v2.1.0 using 100bp segment length
differential gene expression analysis was performed using cufflinks/cuffdiff v2.2.0
for coverage file, reads were aligned to mm9 using bowtie 4.1.2 using –M 1 --best
wig file was created from bam file using igvtools
Genome_build: mm9
Supplementary_files_format_and_content: coverage file in wiggle format
|
| |
|
| Submission date |
Jul 06, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Laura Banaszynski |
| E-mail(s) |
Laura.banaszynski@utsouthwestern.edu
|
| Organization name |
UT Southwestern Medical Center
|
| Department |
Green Center for Reproductive Biology Sciences
|
| Street address |
5323 Harry Hines Blvd
|
| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75390-8511 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE59104 |
Histone H3.3 is required for endogenous retroviral element silencing and genome stability [RNA-Seq] |
| GSE59189 |
Histone H3.3 is required for endogenous retroviral element silencing and genome stability |
|
| Relations |
| BioSample |
SAMN02903883 |
| SRA |
SRX647221 |
| Named Annotation |
GSM1428580_ESC_H33KO1_RNA-seq.wig.gz |
