 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jun 18, 2014 |
| Title |
SRA ChIRP-seq |
| Sample type |
SRA |
| |
|
| Source name |
NTERA2
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: NTERA2 pluripotent stem cell line
chirp oligonucletide: Customed oligo probes targeting lncRNA SRA
|
| Growth protocol |
DMEM with 10% FBS
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Sheared chromatin was pulled down by SRA probes or p68 antibody.
Library was prepared using MicroPlex Library Preparation kit (Diagenode, C05010010).
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Sample 1
|
| Data processing |
library strategy: ChIRP-Seq
Basecalls performed using RTA v1.17.21.3
Demultiplexing and alignment using CASAVA package v1.8.2, which uses the aligner ELANDv2
Peak calling performed using MACS1.4, which generated bed files
Genome_build: hg19
Supplementary_files_format_and_content: bed files report MACS peaks
|
| |
|
| Submission date |
Jun 18, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Gary Felsenfeld |
| E-mail(s) |
garyf@intra.niddk.nih.gov
|
| Organization name |
NIDDK, NIH
|
| Lab |
LMB
|
| Street address |
9000 Rockville Pike
|
| City |
BETHESDA |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE58641 |
Genome-wide map of long non-coding RNA steroid receptor RNA activator (SRA) and its associated RNA heliase p68 in human pluripotent stem cells NTERA2 |
|
| Relations |
| BioSample |
SAMN02866397 |
| SRA |
SRX610812 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1415922_NTERA2_SRA.bed.gz |
68.5 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
