|
| Status |
Public on Jan 31, 2013 |
| Title |
3_ACAGTGA |
| Sample type |
SRA |
| |
|
| Source name |
m6ATracer-GFP+/DamLaminB1+
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HT1080
clone: m6A-Tracer
treatment protocol: Doxycycline -/ Shield +
|
| Treatment protocol |
The samples 1/4/7/10 were grown for 4 days in the presence of 50ng/ml Doxycycline. The samples 2/5/8/11 were grown for 3 days in the presence of Doxycycline, and 24hr prior to the RNA isolation, without doxycycline to induce the expression of the m6A-Tracer or m6A-Tracer-VP16. The samples 3/6/9/12 were grown for 3 days in the presence of Doxycycline, and 24hr prior to the RNA isolation, without doxycycline and in the presence of 500nM Shield1 to induce Dam-LMNB1.
|
| Growth protocol |
The cell lines were cultured in DMEM 1X (Gibco) supplemented with 10% Fetal Bovine Serum (Thermo Scientific HyClone) and 1% Pen 1% Strep.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol. Sequencing libraries were constructed using Illumina TruSeq RNA PART# 15008136 REVISION A.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sample 3
|
| Data processing |
Basecalling and filtering were performed using standard software of the Illumina HiSeq 2000.
Reads were aligned to the human genome, GRCh37, using TopHat (version 1.4.0) and Bowtie (version 0.12.7), using default settings and a model annotation file (GTF version 66).
Supplementary_files_format_and_content: absolute_genecounts.txt: readcounts per gene, generated by htseq-count
|
| |
|
| Submission date |
Aug 14, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Bas van Steensel |
| E-mail(s) |
b.v.steensel@nki.nl
|
| Phone |
+ 31 20 512 2040
|
| Fax |
+31 20 669 1383
|
| URL |
http://www.nki.nl/nkidep/vansteensel
|
| Organization name |
Netherlands Cancer Institute
|
| Department |
division of Molecular Biology
|
| Lab |
van Steensel group
|
| Street address |
Plesmanlaan 121
|
| City |
Amsterdam |
| ZIP/Postal code |
1066 CX |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE40111 |
Stochastic genome - nuclear lamina contacts are linked to histone H3K9 dimethylation (RNA-seq data) |
| GSE40112 |
Stochastic genome - nuclear lamina contacts are linked to histone H3K9 dimethylation |
|
| Relations |
| SRA |
SRX176602 |
| BioSample |
SAMN01113233 |
