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| Status |
Public on Apr 19, 2012 |
| Title |
veg09_04 |
| Sample type |
SRA |
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| Source name |
vegetative strain ALXC9
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| Organism |
Oxytricha trifallax |
| Characteristics |
strain: ALXC2
Stage: vegetative
rna subset: small RNA
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was purified using the mirVana miRNA Isolation kit using the total RNA purification protocol. 1µg of total RNA was used to prepare smallRNA libraries using the TruSeq small RNA Sample Prep Kit (Illumina) following standard protocol.
small RNA sequencing runs were size selected for inserts of 15-45 bases in length prior to the run. Reads were set to 100 base paired-end reads and ended up with complete overlap of the sequence in both directions. For the processed data, we only chose to look at the 77% of raw reads that were identical in both directions.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Illumina smallRNA TruSeq
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| Data processing |
100base paired-end reads obtained.All 11 libraries in a single lane of a Illumina HiSeq2000
Indexing and trimming of linker sequences
Reads of at least 16nt that are 100% identical in both directions were further processed (77% of total)
Bowtie was used to align libraries to non-coding RNAs from Oxytricha trifallax as a filter
Bowtie was used to align reads that survive the filter to the Oxytricha macronuclear genome partial assembly WGS2.1.1.
Genome_build: Oxytricha trifallax macronuclear genome WGS2.1.1 partial assembly
Supplementary_files_format_and_content: Tab-delimited files. For all 7 libraries from mating cells, the txt files list all distinct 26-28nt long RNAs from the library that survived the non-coding RNA filter. Table shows #_of_occurrences, sequence, sequence_length
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| Submission date |
Apr 18, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Alan M Zahler |
| E-mail(s) |
[email protected]
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| Phone |
8314595131
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| Organization name |
UC Santa Cruz
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| Department |
MCD Biology
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| Lab |
Zahler Lab
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| Street address |
Sinsheimer Labs
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| City |
Santa Cruz |
| State/province |
CA |
| ZIP/Postal code |
95064 |
| Country |
USA |
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| Platform ID |
GPL15459 |
| Series (1) |
| GSE37390 |
Mating of the stichotrichous ciliate Oxytricha trifallax induces production of a class of 27nt small RNAs derived from the parental macronucleus |
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| Relations |
| SRA |
SRX143239 |
| BioSample |
SAMN00858096 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data not provided for this record |
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