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| Status |
Public on Mar 17, 2020 |
| Title |
Caecum Control_replicate2 |
| Sample type |
SRA |
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| Source name |
Caecum sample at 9 day post infection from control group
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| Organism |
Capra hircus |
| Characteristics |
infection status: Control
tissue: caecum
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| Treatment protocol |
Two groups including one control and one virus infected of tissues including lung, spleen and caecum were used in the study. For the control group, healthy tissues of goats were collected and screened for the absence of PPRV antigen, and for the infected group tissues were isloated from goat infected with Izatnagar 94 PPRV at 9 day post infection. The tissues of both groups were collected in RNase free 1.5 ml centrifuge tube in RNA later.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from control and PPRV infected lung, spleen and caecum was isolated using the RNeasy Mini kit (Qiagen GmbH, Germany) according to the manufacturer’s protocol. The integrity and quantity of isolated RNA were assessed based on a Bioanalyzer (Agilent Technologies, Inc). The RNA integrity number (RIN) value of all the samples was found greater than 8, which is considered suitable for further processing.
Library was prepared using NEBNext Ultra RNA Library Prep Kit for Illumina (NewEngland Biolabs Inc.) following the manufacturer’s protocol. Approximately, 100ng of RNA from each sample was used for RNA library preparation. The quality of the libraries was assessed on Bioanalyzer and further quantified using a Qubit 2.0 Fluorometer (Life technologies) and by qPCR. Libraries were sequenced on Illumina – NextSeq500 following manufacturer’s protocol.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
lncRNAs and mRNAs expression in Caecum
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| Data processing |
Fastq files containing sequencing reads, each of control and infected samples were processed to remove adaptors and low-quality reads. Thereafter, filtered reads were mapped to goat genome(assembly ARS1) by Tophat software and transcripts were assembled by Cufflinks. Cuffmerge was further used to merge the replicate assemblies and to categorized the novel transcripts. Long non-coding RNAs were filtered according to transcript length (≥ 200 nt), classcode- “I’, “j”, “o”, “u” and “x”, ORF length ≤ 300 nt and protein domains. Long non-coding RNA transcripts were evaluated using coding potential calculator (CPC). At last, cuffdiff was used to carry out differential expression analysis of long non-coding transcripts and mRNA transcripts between the infected and control samples.
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| Submission date |
May 01, 2019 |
| Last update date |
Mar 18, 2020 |
| Contact name |
Ravi Kumar Gandham |
| E-mail(s) |
gandham71@gmail.com
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| Phone |
+919458687850
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| Organization name |
NIAB
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| Street address |
Gowlidoddy
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| City |
Hyderabad |
| State/province |
Telangana |
| ZIP/Postal code |
500032 |
| Country |
India |
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| Platform ID |
GPL21299 |
| Series (1) |
| GSE130552 |
Genome-wide identification and characterization of long non-coding RNAs and mRNAs in goat tissues infected with PPRV |
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| Relations |
| BioSample |
SAMN11547613 |
| SRA |
SRX5773279 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3742103_Caecum_Control_replicate2_gene.txt.gz |
1.0 Mb |
(ftp)(http) |
TXT |
| GSM3742103_Caecum_Control_replicate2_lnc.txt.gz |
358.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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