|
| Status |
Public on Jun 01, 2015 |
| Title |
DM_CTTGT_L001_R1_001 |
| Sample type |
SRA |
| |
|
| Source name |
Fly Ovary
|
| Organism |
Drosophila melanogaster |
| Characteristics |
3' linker: NEB+Ext
tissue: ovary
|
| Treatment protocol |
Cells were treated with hydroxyurea at 5 mM for 15 min[C].
|
| Growth protocol |
HeLa cells were plated at 2X10^5 cells per 10 cm dish and synchronized by double thymidine block. Cells were treated with HU for 15 minutes 3 hrs after release into S-phase and RNA prepared.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with Trizol.
Libraries were prepared with Illumina sequences using two limited rounds of PCR after ligation of a custom linker to the 3' end of the RNA; cDNA was synthesized either with a primer to the custom linker (Sample2), or the same primer with 3 A's added to the 3' end (Sample1). Sample3 was prepared using only the H2A primer; Samples 4 and 5 were prepared using primers for H2A, H2B, H3, and H4.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
Fly Ovary
|
| Data processing |
Basecalls performed using CASAVA v. 1.8.2
Reads were aligned to hg19 or dm3 (including custom chromosome containing histone genes) using Bowtie2
The AppEnD algorithm was used to identify 3' tails
Genome_build: hg19, dm3
Supplementary_files_format_and_content: tab-delimited text files containing 3' tails generated using AppEnD
|
| |
|
| Submission date |
May 01, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
William F Marzluff |
| E-mail(s) |
marzluff@med.unc.edu
|
| Organization name |
The University of North Carolina at Chapel Hill
|
| Street address |
207 Fordham Hall
|
| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599 |
| Country |
USA |
| |
|
| Platform ID |
GPL16479 |
| Series (1) |
| GSE68471 |
EnD-Seq and AppEnD: Sequencing 3' ends to identify non-templated tails and degradation intermediates |
|
| Relations |
| BioSample |
SAMN03579579 |
| SRA |
SRX1015887 |
