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| Status |
Public on Aug 24, 2020 |
| Title |
Brain_M2 Sample 39 |
| Sample type |
SRA |
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| Source name |
Hatchling Brain cells
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| Organism |
Crocodylus porosus |
| Characteristics |
age: Runts hatchlings 359 days, Normal hatchlings 373 days
size: Runt hatchlings were 386.2 ± SD 23.6 mm and normal hatchlings were 740.2 ± 73.5 mm
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| Treatment protocol |
no treatment protocols were imposed. Runt crocodiles developed under the same growth conditions as the normal crocodiles and it was the purpose of this work to understand any underlying transcriptional reasons for these differences.
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| Growth protocol |
as all growth protocols for the crocodiles were described in a previously published manuscript, can we add something like “Animal housing was previously described in Finger, J.W. Jr., Thomson, P.C., Adams, A.L., Benedict, S. Moran, C., Isberg, S.R. (2015) Reference levels for corticosterone and immune function in farmed saltwater crocodiles (Crocodylus porosus) hatchlings using current Code of Practice guidelines. General and Comparative Endocrinology 212:63-72.”
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| Extracted molecule |
total RNA |
| Extraction protocol |
Tissue types were flash frozen in liquid nitrogen. Tissue types were stored in RNAlater. Total RNA was isolated using Trizol, RNeasy Mini Kit (Qiagen) and the Directt-Zol RNA Miniprep Kit (Zymo Research Inc.).
All libraries were constructed using NEBNext Small RNA Library Prep for Illumina (NEB Inc.)
Small RNA sequencing (Deep sequencing)
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| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
Brain_M2
small RNA
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| Data processing |
Demultiplexing and BaseCalling performed with bcl2fastq (v2)
FastxToolkit (v. 0.0.14) used to filter and quality check of the raw seqeuncing reads. Nucleotide distribution plots, Quality boxplots were generated from these QC reads.
Bowtie (v 1.2.0) used to index the genome
miRDeep2 (v 2.0.0.8) was first trained with avian miRNA from miRBase v.21 (Chicken and Zebrafinch). Then miRDeep2 was used to predict all known and novel miRNAs in C. porosus. miRDeep2 was used to calculate expression of all predicted miRNAs as well.
miRanda (v. 3.3a) and RNAhybrid (v. 2.1.2) ) were used to identify putative targets of the miRNAs. Targets identified by miRanda were finally retiend due to their overall robustness.
To identify relationship of miRNAs and Transposable elemnets (TEs), RepeatMasker (v. 4.0.6) was used to identify all TEs. RepBase version 20150807 was utilised. Bedtools (v.2.26.0) was used to understand overlapping of miRNAs and TEs.
MapMI (version 1.5.9-b31) was used to determine phylogenetic distributions of the orthologous C porosus miRNAs relative to other vertebrates.
Genome_build: MDVP00000000
Supplementary_files_format_and_content: Microsoft excel file containing library size normalized expression values for predicted miRNAs in the study
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| Submission date |
May 13, 2020 |
| Last update date |
Aug 24, 2020 |
| Contact name |
ARNAB GHOSH |
| Organization name |
Texas Tech University
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| Department |
Biology
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| Street address |
2500 Broadway
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| City |
Lubbock |
| State/province |
Texas |
| ZIP/Postal code |
79409 |
| Country |
USA |
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| Platform ID |
GPL28534 |
| Series (1) |
| GSE150461 |
Identification and characterization of microRNAs (miRNAs) and their transposable element origins in the saltwater crocodile, Crocodylus porosus |
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| Relations |
| BioSample |
SAMN14910654 |
| SRA |
SRX8335617 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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