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| Status |
Public on Dec 21, 2012 |
| Title |
chicken_c_kidney |
| Sample type |
SRA |
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| Source name |
chicken_kidney
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| Organism |
Gallus gallus |
| Characteristics |
tissue: kidney
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| Treatment protocol |
RNALater
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| Growth protocol |
standard lab/farm conditions
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| Extracted molecule |
total RNA |
| Extraction protocol |
Animals were sacrificed with no input from the authors (i.e. each group/facility utilized their standard method). Tissues samples were isolated from each organ, placed into an appropriate volume of RNALater, and incubated at 4C overnight. Each sample was then homogenized in a bead-mill in a phenol/chlorofom solution and RNA was isolated by and treated with DNAse on a Qiagen miRNEasy column.
Strand-specific libraries were generated using the standard RNA-Seq protocol / dUTP method, with the “second-day” done on the Beckman-Coulter SPRIworks machine. Briefly, before second-strand synthesis, samples are precipitated first and the second strand is made using a dNTP solution that replaces dTTP with dUTP. Before the final PCR step, libraries are treated with an enzyme that removes dUTP from dsDNA.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Sample 130
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| Data processing |
Base-calling: Illumina Real Time Analysis, scoring metric v1.5
Long-read (76-108bp libraries) were mapped with TopHat v1.1.4 with the following additional parameters: --no-novel-indels, -r [inner length], --segment-length 20, --solexa-1.3-quals, --coverage-search -g [species.gtf]
junctions from all long read (76-108bp libraries) were combined and all libraries were mapped by TopHat v1.1.4 with the following parameters: --no-novel-indels, -r [inner length], --segment-length 20, --solexa-1.3-quals, --coverage-search, -j [species_junction_file.bed] -g [species.gtf]
Cufflinks v1.0.2 was run on the long read libraries with the following parameters: --min-isoform-fraction 0.00, --pre-mrna-fraction 0.00, -g [species.gtf], --max-intron-length 100000, -u, -b [genome.fa], --library-type ff-firststrand
Transcripts from libraries within a species were combined with CuffCompare v1.0.2 with the following parameters: -r [species.gtf]
Cufflinks v1.0.2 was run on all libraries with the following parameters: --min-isoform-fraction 0.05, --pre-mrna-fraction 0.10, -G [combined_species.gtf from above], --max-intron-length 100000, -u, -b [genome.fa], --library-type ff-firststrand
Transcripts from libraries from each individual were combined with CuffCompare v1.0.2 with the following parameters: -r [combined_species.gtf]
Genome_build: mouse: mm9, rat: rn4, cow: bt4, chicken: gg3, rhesus: rhemac2, human: hg19
Supplementary_files_format_and_content: mapped reads
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| Submission date |
Oct 17, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Jason Merkin |
| E-mail(s) |
jmerkin@mit.edu, jjmerkin@gmail.com
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| Organization name |
MIT
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| Department |
Biology
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| Lab |
Burge
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| Street address |
31 Ames St
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
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| Platform ID |
GPL16133 |
| Series (1) |
| GSE41637 |
Evolutionary dynamics of gene and isoform regulation in mammalian tissues |
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| Relations |
| SRA |
SRX196392 |
| BioSample |
SAMN01766942 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1020768_chicken_c_kidney.transcripts.gtf.gz |
33.0 Mb |
(ftp)(http) |
GTF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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