|
| Status |
Public on Jun 12, 2017 |
| Title |
Pub_2 |
| Sample type |
SRA |
| |
|
| Source name |
Hypothalamus
|
| Organism |
Capra hircus |
| Characteristics |
strain: Anhuai goats
tissue: Hypothalamus
development stage: Puberty
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Hypothalamic tissues were surgically removed immediately frozen, and. RNA derived from goat hypothalamus was obtained using TRIzol Reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Total RNA was used as input material for the RNA sample preparations. Ribosomal RNA was removed by Epicentre Ribo-zero™ rRNA Removal Kit (Epicentre, USA). Sequencing libraries were generated using the rRNA-depleted RNA by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). Products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the libraries were sequenced on an Illumina Hiseq 4000 platform and 150 bp paired-end reads were generated.
Inorder to identify the lncRNAs,the preliminary scanning was conducted by Scripture (beta2) and Cufflinks (v2.1.1) in a reference-based approach, follwed by coding poteintial analysis using CNCI (v2), CPC (0.9-r2) and Pfam Scan (v1.3).
Cuffdiff (v2.1.1) was used to calculate FPKMs of both lncRNAs and coding genes in each sample (Trapnell,C.et al.2010).
Genome_build: CHIR_1.0
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample. The file lncRNA_sequence.txt contains the sequences for the lncRNA IDs contained in "lncRNA_FPKM.txt".
|
| |
|
| Submission date |
Jul 12, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Fugui Fang |
| E-mail(s) |
[email protected]
|
| Phone |
+8655165786357
|
| Organization name |
Anhui Agricultural University
|
| Department |
College of Animal Sciences and Technology
|
| Street address |
No. 130 of Changjiang West Road
|
| City |
Hefei |
| State/province |
Anhui |
| ZIP/Postal code |
230036 |
| Country |
China |
| |
|
| Platform ID |
GPL22146 |
| Series (1) |
| GSE84301 |
Transcriptome analysis of hypothalamuses from pubertal and prepubertal goats |
|
| Relations |
| BioSample |
SAMN05381027 |
| SRA |
SRX1936142 |
