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Sample GSM652442 Query DataSets for GSM652442
Status Public on Nov 03, 2011
Title mouse_TG_RNA-seq
Sample type SRA
 
Source name pool of thyroid gland tissues, IFN-alpha transgenic
Organism Mus musculus
Characteristics strain: mixed (~75% C57BL/6, ~25% CBA/J)
genotype: transgenic mice overexpressing IFN-alpha under control of bovine thyroglobulin promoter
age: ~6 months
tissue: thyroid
Treatment protocol Confluent human primary thyroid cultures were exposed to human IFNα (5,000 U/ml) for 0, 12 or 24 hours, followed by RNA isolation.
Growth protocol Human thyroid primary cells were prepared from fresh, non-cancerous thyroid tissue adjacent to thyroid tumors that were removed at surgery. Tissue was minced and incubated in 200 U/ml of collagenase solution for 1 hour at 37°C. Cells were harvested and cultured in DMEM supplemented with 10% FBS, penicillin (100 U/ml), and streptomycin (100 µg/ml) (P0). Cells were passaged at 1:2 dilution and cultured until confluent.
Extracted molecule total RNA
Extraction protocol According to the Illumina mRNA Sequencing Sample Preparation Guide. Briefly, 2ug total RNA was hybridized to poly-dT magnetic beads to capture polyA mRNA molecules. Chemical fragmentation, first-strand synthesis with RTase, randomers second-strand synthesis. Then, end repair, 3' A overhang, multiplex adapter ligation (from Illumina indexing kit), size selection by electrophoresis and cut at 200bp. 18 cycles of PCR with a primer bearing an indexing barcode.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer IIx
 
Description RNA-seq of thyroid tissue of IFN-alpha tansgenic mice.
Data processing Single reads split by barcode into individual files using PERL script. The reads with good quality were aligned to reference sequence (RefSeq) databases of human (UCSC hg18) or mouse (UCSC mm9) genomes, RefSeq exons, splicing junctions and contamination databases including ribosome and mitochondria sequences using the BWA alignment algorithm, and the alignment files in SAM format were generated. After filtering reads mapped to contamination databases, the reads that have one or no mismatch and are uniquely aligned to each exon and splicing-junction sites were extracted and then counted. The read count for each RefSeq transcript was calculated by combining the counts for exons and splicing junctions of the corresponding transcript. The read count at exon, splice-junction, transcript and gene levels were summarized and normalized to relative abundance in Fragments Per Kilobase of exon model per Million (FPKM) in order to compare transcription level among samples.
 
Submission date Jan 10, 2011
Last update date May 15, 2019
Contact name Weijia Zhang
E-mail(s) weijia.zhang@mssm.edu
Phone 212-241-2883
Organization name Mount Sinai School of Medicine
Department Department of Medicine
Lab Bioinformatics Lab
Street address 1425 Madison Avenue
City New York
State/province NY
ZIP/Postal code 10029
Country USA
 
Platform ID GPL11002
Series (1)
GSE25115 Interferon-alpha mediates the development of autoimmunity by direct tissue toxicity and through immune-cell recruitment mechanisms
Relations
SRA SRX038876
BioSample SAMN00191577

Data table header descriptions
SEQUENCE Unique sequence read
COUNT Count

Data table
SEQUENCE COUNT
GGATACCCATGGCAACAAAAAAAATCTCTCCCACTGGAAACCAAGAAGCA 1
TTCATGCCCTTTGTCAAGCGCCTCAACTACGTAAGCCTGGTGAAGCCCAG 1
GACTGGCTGCCCCAGCCCACCCCCCCCGGCAGCCTCGTCTCCTTGCCCTT 1
GGAGGCAGCGAAAGTCCGAGCTTCCCCCCGTATGCGGCCCGGCCATCCAG 1
TGGAATCAGAAGGAGCTGCAGCTTATAGCCTCTCCGCAACAACGTAATAT 1
CCCAGCTACTCAGCTGATTACGTCAATAGTAATTTTTCAACATTTAAGAA 1
CTAAAATGTGACAGCGAGTCTCCTTGACTAAGCCTTGCTCTTCCATCCTT 1
ATTTTATGCATATGACCGTTTGCCTGCACCGGAACCATATGCACGCGAGA 1
GTTTTGTAAAGGACACACTAAGGAACAGCAGAGCGCTCGCAACTTGCCGG 2
CGGGGGGTGACCGGCAGATGAAATTCTAGAGCCCGCAGAATGGCGTCCTG 1
GGGGAATAGGTACCCGGGGCCCCCACTGGCCAGCTGACCCCCTCCCCGAC 1
CAAACTTGAAGCTTTATGAGGAAAGACCCACGGTCGAAGTTGCATCCCTA 1
CAGGGCATGCCGGACCGACGAGTAGAACCAGCAGAGGAACCCGAAGAAAC 1
CTTGCCTGTCTGTCCCTTCCGATTGTGCCTAGCGATTACCACCCAGCAGA 1
GTTGCTTTGGGGGGAACACCCCCTCAGCGCCTGTGAGGGAGGTTGTTACT 1
TGGAGGGCGAGGATGACCCTGACCGCCACATGAAGCACTCCTTCCGGACC 1
CTTGAAATCCTCATTAAAGATACACTGGGTCTCCCAGTCGCTGGGCAAAC 1
CGAAGACGAAGAAGCCGGAGACCTTGAAGCCCGGGCGAGCAGCGTTGGTG 1
GTTGGGTGCCAACAATGTCCGGCAGGGCAGTGCCACTCAATGGTGTGTGC 2
CCGCAAAGCAGTGCTCCCAAGCAGGGTCCACTGCATCCCTGGATGACGCT 1

Total number of rows: 5077268

Table truncated, full table size 262822 Kbytes.




Supplementary file Size Download File type/resource
GSM652442_mouse_TG_mm9.BED.gz 35.0 Mb (ftp)(http) BED
GSM652442_mouse_TG_mm9_refseq.txt.gz 213.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data included within Sample table
Processed data provided as supplementary file

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