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| Status |
Public on Dec 18, 2018 |
| Title |
ce_krit1_rep1 |
| Sample type |
SRA |
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| Source name |
entire organism
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| Organism |
Caenorhabditis elegans |
| Characteristics |
genotype: Kri-1 null (ccm1/kri-1(ok1251) knock out)
age: 24 hours past the L4 state
cell type: entire organism
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| Extracted molecule |
total RNA |
| Extraction protocol |
For human samples, RNAs was extracted using an RNA isolation kit (RNeasy® Micro Kit, Qiagen, Hilden, Germany). For mouse and C. elegans samples, RNA was extracted using the TRIzol protocol (ThermoFisher, Waltman, MA).
RNA libraries were prepared for sequencing using commercially low-input strand specific RNA-Seq kits (Clontech, California, USA) for human specimens and TruSeq Stranded mRNA Sample Prep Kit (Illumina, San Diego, CA) for mouse and C. elegans samples
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Raw sequencing QC assessement: FastQC v0.115
Alignment: STAR v2.5.3a
Post alignement QC assessment: RSeQC and Picard tools v2.9.0
Gene transcripts assembly: featureCounts
Differentially expressed genes analysis: DESeq2
Genome_build: UCSC human genome model: hg19; GENCODE mouse genome model: GRCm38 V13 (release_M13); ENSEMBLE worm genome model: c. elegans WBcel235 V87 (release-87)
Supplementary_files_format_and_content: tab-delimited text files include gene features raw counts values summarized by featureCouts for each Sample.
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| Submission date |
Dec 17, 2018 |
| Last update date |
Dec 18, 2018 |
| Contact name |
Yan Li |
| E-mail(s) |
yli22@bsd.uchicago.edu
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| Phone |
7738344316
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| Organization name |
The University of Chicago
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| Department |
Center for Research Informatics
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| Street address |
900 East 57th St.
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| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
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| Platform ID |
GPL22765 |
| Series (1) |
| GSE123968 |
Comprehensive Transcriptome Analysis of Cerebral Cavernous Malformation Across Multiple Species and Genotypes |
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| Relations |
| BioSample |
SAMN10603551 |
| SRA |
SRX5141971 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3517844_ce_krit1_rep1_IA82-merged.cordSorted.bam.feature.count.txt.gz |
178.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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