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Sample GSM1673357 Query DataSets for GSM1673357
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
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
BioSample SAMN03579579
SRA SRX1015887

Supplementary file Size Download File type/resource
GSM1673357_DM_CTTGT_L001_R1_001_tails.txt.gz 6.8 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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