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Status |
Public on Nov 26, 2016 |
Title |
34_ICAR_SCNT_61 |
Sample type |
SRA |
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Source name |
Endometrium_Inter-caruncle_SCNT_34d
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Organism |
Bos taurus |
Characteristics |
tissue source: Endometrium tissue: Inter-caruncle gestation day: 34 group: somatic cell nuclear transfer (SCNT)
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Extracted molecule |
polyA RNA |
Extraction protocol |
Total RNA was extracted from snap frozen tissues using the guanidinium thiocyanate-phenol-chloroform method (Chomczynski and Sacchi, 2006) (TRIzol® Reagent, Invitrogen, Carlsbad, CA) following the manufacturer’s instructions with slight modifications. A purification with acid phenol:chloroform (pH 4.5, Ambion) was added prior to RNA precipitation with isopropanol. RNA samples were purified with the RNeasy® Mini Kit (Qiagen, Boston, MA), quantified, and assayed for purity on a 2100 Bioanalyzer (Agilent, Santa Clara, CA). Three µg of total RNA was used for the polyA+ library construction using a TruSeq SBS Sequencing Kit Version 3
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
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Data processing |
Base-calling was performed by Casava v1.8.2 Sequences were aligned to the cattle (Bos taurus) genome (Btau4) using the TopHat software, allowing for 2 mismatches for each block of 25 nucleotides. The unaligned sequences were trimmed at the 3’ end to 75 nt and realigned; the process was then repeated once more, with unaligned reads trimmed to 50 nt in length. The three files with aligned sequences were merged, and the sequences were filtered to retain those matched to a unique position in the reference genome, with mapping quality greater than 30 and containing up to 3 mismatches. Duplicate reads were removed by Picard tools Sequence reads were counted according to overlaps on exon models obtained from the ensGene database from the UCSC genome browser. The database was downloaded in January 2011 using R software and processed using the Bioconductor packages rtracklayer, Rsamtools, GenomicRanges and GenomicFeatures. A set of genes that was not annotated in the Ensembl database but that was annotated in the refGene database from the UCSC genome browser was analyzed in conjunction with the Ensembl annotation. The reads that overlapped to an exon model were used for downstream analyses. Genome_build: btau4 Supplementary_files_format_and_content: unfiltered_reads_count_EET.txt: reads count for extra-embryonic tissues and exon length unfiltered_reads_count_END.txt: reads count for endometrial tissues and exon length
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Submission date |
Oct 19, 2015 |
Last update date |
May 15, 2019 |
Contact name |
Fernando H Biase |
E-mail(s) |
fbiase@vt.edu
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Phone |
540-231-9520
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Organization name |
Virginia Tech
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Department |
School of Animal Sciences
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Lab |
Biase lab
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Street address |
175 West Campus Drive
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City |
Blacksburg |
State/province |
VA |
ZIP/Postal code |
24061 |
Country |
USA |
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Platform ID |
GPL15749 |
Series (1) |
GSE74152 |
Massive dysregulation of genes involved in cell signaling and placental development in cloned cattle conceptus and maternal endometrium |
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Relations |
BioSample |
SAMN04194387 |
SRA |
SRX1354447 |
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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