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| Status |
Public on Nov 04, 2019 |
| Title |
E55-2 |
| Sample type |
SRA |
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| Source name |
E55, embryonic skin sample
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| Organism |
Capra hircus |
| Characteristics |
tissue: skin
developmental stage: embryo
age: E55
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| Extracted molecule |
total RNA |
| Extraction protocol |
For RNA-seq, total RNA was extracted from each embryo, 10 mg of total RNA was used for RNA sequencing (RNA-seq) library preparation. Polyadenylated mRNAs were purified and concentrated with Magnetic Beads Oligo (dT) (Invitrogen, Carlsbad, CA, USA) before used for directional RNA-seq library preparation. Purified mRNAs were iron fragmented at 95oC followed by end repair and 5' adaptor ligation. Then, reverse transcription was performed with RT primer harboring 3' adaptor sequence and randomized hexamer. The cDNAs were purified and amplified and PCR products corresponding to 200-500 bps were purified, quantified and applied to Illumine NextSeq 500 system 151 nt pair-end sequencing by ABlife, Inc. (Wuhan, China).
Total RNA was extracted by using TRIzol® reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions, and RQ1 DNase (Promega, Madison, WI, USA) was used to remove contaminating genomic DNA. The quality and quantity of the purified RNA was monitored at the ratios of A260/A280 and A260/230 on SmartSpec Plus Spectrophotometer (BioRad, Philadelphia, PA, USA). RNA integrity was further verified by 1.5% agarose gel electrophoresis.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
The cashmere goat, which produces cashmere wool, is a breed of Capra hircus.
expressed_gene_RPKM.txt
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| Data processing |
Illumina Casava1.9 software used for basecalling.
3' adapter (GATCGGAAGAGC) trimmed with fastx_clipper
mapped using tophat2 --microexon-search --no-coverage-search --b2-N 1
detecting different expression gene using edgeR
Genome_build: Capra hircus CHIR_1.0
Supplementary_files_format_and_content: tab-delimited text file includes gene RPKM values for each Sample. FASTA file (cds.fa) compatible with RPKM table.
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| Submission date |
Jan 05, 2016 |
| Last update date |
Nov 04, 2019 |
| Contact name |
Dong Chen |
| Organization name |
ABLife, Inc.
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| Department |
Center for Genome Analysis
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| Street address |
388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone
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| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430075 |
| Country |
China |
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| Platform ID |
GPL21299 |
| Series (1) |
| GSE76538 |
Transcriptome profiling reveals transcriptional and alternative splicing regulation in the early embryonic development of hair follicles in the cashmere goat |
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| Relations |
| BioSample |
SAMN04384520 |
| SRA |
SRX1517372 |
| 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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