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Sample GSM2231219 Query DataSets for GSM2231219
Status Public on Jun 12, 2017
Title Prepub_3
Sample type SRA
Source name Hypothalamus
Organism Capra hircus
Characteristics strain: Anhuai goats
tissue: Hypothalamus
development stage: Prepuberty
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, 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
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
BioSample SAMN05381031
SRA SRX1936146

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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