|
| Status |
Public on Dec 29, 2012 |
| Title |
small_RNA-seq_plusRA |
| Sample type |
SRA |
| |
|
| Source name |
NTera2/D1 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: NTera2/D1
treatment: RA
|
| Treatment protocol |
For induction, the cells were treated with 1 μM atRA (retinoic acid) for 2 days.
|
| Growth protocol |
Ntera2/D1 cells (American Type Culture Collection) were kept in minimum essential medium α (Invitrogen) plus 10% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
10 µg total RNAs were first added the SRA 3' and 5' adaptors by T4 RNA Ligase 2, truncated and T4 RNA ligase, respectively. The ligated product was then reverse-transcribed with the provided RT primers (Illumina) by using the SuperScript III kit (Invitrogen). The RT product was then subjected to PCR amplification with the provided PCR primers (Illumina). The separation of the PCR products was done in the 6% TBE gel. The gel slice corresponding to 100 -150 bp was cut out and passed through punched eppendorf tubes by centrifugation. The PCR products were eluted out of the gel with the SRA NaCl solution overnight. After EtOH precipitation, the library was ready for use.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Data processing |
The image analysis and base calling were performed by using Illumina's Genome Analysis pipeline.
The 3′ adaptor sequence was removed using FASTX .
The clipped reads were aligned to a custom DR2-Alu sequence database by using Novoalign.
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited text file that lists small RNA-seq reads that align to a custom database of DR2-Alu sequences
|
| |
|
| Submission date |
Nov 27, 2012 |
| Last update date |
Jun 11, 2013 |
| Contact name |
MICHAEL G ROSENFELD |
| E-mail(s) |
mrosenfeld@ucsd.edu
|
| Organization name |
HHMI/UCSD
|
| Street address |
9500 Gilman Drive
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL9115 |
| Series (2) |
| GSE42563 |
DICER- and AGO3-dependent generation of retinoic acid-induced DR2 Alu RNAs regulates human stem cell proliferation (RNA-seq) |
| GSE42602 |
DICER- and AGO3-dependent generation of retinoic acid-induced DR2 Alu RNAs regulates human stem cell proliferation |
|
| Relations |
| BioSample |
SAMN02197190 |
