|
| Status |
Public on Sep 01, 2012 |
| Title |
sRNAs from Contig 22226.0 IES1+ strain backcrossed to wild-type strain at 19 hr |
| Sample type |
SRA |
| |
|
| Source name |
Oxytricha mating cells
|
| Organism |
Oxytricha trifallax |
| Characteristics |
genotype: Contig22226.0 IES1+ strain backcrossed to wild-type parental strain at 19 hr
time: 19h
|
| Treatment protocol |
Contig22226.0 IES1+ strain was obtained by injection of Contig22226.0 IES1-containing piRNA in the mating pairs of wild-type strains JRB310 and JRB510. The clonal line of Contig22226.0 IES1+ was mated with wild-type JRB510, and total RNA was extracted at ~19 hr post mixing.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA at ~19 hr was directly used for library construction following ng Illumina® TruSeq™ Small RNA Sample Preparation protocol with two different barcodes, and these two libraries were sequenced together as a partial control lane on Illumina HiSeq 2000.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
CTGATC; AAGCTA
|
| Data processing |
The raw sequencing data from a control Illumina lane were first filtered by requiring the presence of sequences "TCACGATCAGATCTC" or "TCACTAGCTTATCTC" (15bp sequences with barcodes inside) in the read. This filtered fastq file is provided here as the raw file. Then 3’ adapter is trimmed by requiring a perfect 15bp match to “TGGAATTCTCGGGTG” (the 5'-end of the 3' adapter). Reads that contain “N” or shorter than 18bp were discarded. The remaining reads were collapsed using FASTX Tool kit Collapser (http://hannonlab.cshl.edu/fastx_toolkit/index.html), and those that contain telomeric sequences “CCCCAAAACCCC” or “GGGGTTTTGGGG” were removed. The non-redundant, telomere-reads removed dataset was provided here as the processed fasta file. The SHiMP output of the reads mapping against Contig22226.0 MAC and MIC contigs are provided as processed datafiles, after removing those mappings with more than two mismatches.
Genome_build: not applicable
Supplementary_files_format_and_content: not applicable
|
| |
|
| Submission date |
Aug 13, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Wenwen Fang |
| E-mail(s) |
[email protected]
|
| Phone |
6092581933
|
| Organization name |
Princeton University
|
| Department |
EEB
|
| Lab |
Landweber
|
| Street address |
323 Guyot Hall, Washington Rd
|
| City |
Princeton |
| State/province |
NJ |
| ZIP/Postal code |
08544 |
| Country |
USA |
| |
|
| Platform ID |
GPL15459 |
| Series (1) |
| GSE40081 |
sRNA profiling during Oxytricha conjugation |
|
| Relations |
| SRA |
SRX176183 |
| BioSample |
SAMN01112994 |
