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Evaluation of protocols for rRNA depletion-based RNA sequencing of nanogram inputs of mammalian total RNA

Next generation RNA-Sequencing (RNA-seq) is a flexible approach that can be applied to e.g. global quantification of transcript expression, the characterization of RNA structure such as splicing patterns and profiling of expressed mutations. Many RNA-seq protocols require up to microgram levels of total RNA input amounts to generate high quality data, and thus remain impractical for the limited starting material amounts typically obtained from rare cell populations, such as those from early developmental stages or from laser micro-dissected clinical samples. Here, we present an assessment of the contemporary ribosomal RNA depletion-based protocols, and identify those that are suitable for inputs as low as 1-10 ng of intact total RNA and 100-500 ng of partially degraded RNA from formalin-fixed paraffin-embedded tissues.

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Studies are experimental investigations of a particular phenomenon, e.g., case-control studies on a particular trait or cancer research projects reporting matching cancer normal genomes from patients.

Study ID Study Title Study Type
EGAS00001003849 Transcriptome Analysis

This table displays only public information pertaining to the files in the dataset. If you wish to access this dataset, please submit a request. If you already have access to these data files, please consult the download documentation.

ID File Type Size Located in
EGAF00002637464 fastq.gz 7.9 GB
EGAF00002637465 fastq.gz 8.3 GB
EGAF00002637466 fastq.gz 63.8 MB
EGAF00002637467 fastq.gz 69.0 MB
EGAF00002637468 fastq.gz 76.4 MB
EGAF00002637469 fastq.gz 82.2 MB
EGAF00002637470 fastq.gz 8.5 GB
EGAF00002637471 fastq.gz 9.0 GB
EGAF00002637472 fastq.gz 84.9 MB
EGAF00002637473 fastq.gz 90.3 MB
EGAF00002637474 fastq.gz 145.2 MB
EGAF00002637475 fastq.gz 155.7 MB
EGAF00002637476 fastq.gz 607.3 MB
EGAF00002637477 fastq.gz 604.1 MB
EGAF00002637478 fastq.gz 78.8 MB
EGAF00002637479 fastq.gz 84.0 MB
EGAF00002637480 fastq.gz 494.7 MB
EGAF00002637481 fastq.gz 511.1 MB
EGAF00002637482 fastq.gz 60.8 MB
EGAF00002637483 fastq.gz 64.5 MB
EGAF00002637484 fastq.gz 69.2 MB
EGAF00002637485 fastq.gz 73.0 MB
EGAF00002637486 fastq.gz 695.1 MB
EGAF00002637487 fastq.gz 697.6 MB
EGAF00002637488 fastq.gz 78.9 MB
EGAF00002637489 fastq.gz 83.2 MB
EGAF00002637490 fastq.gz 94.1 MB
EGAF00002637491 fastq.gz 99.5 MB
EGAF00002637492 fastq.gz 146.0 MB
EGAF00002637493 fastq.gz 156.5 MB
EGAF00002637494 fastq.gz 683.1 MB
EGAF00002637495 fastq.gz 688.3 MB
EGAF00002637496 fastq.gz 459.7 MB
EGAF00002637497 fastq.gz 471.6 MB
EGAF00002637498 fastq.gz 85.2 MB
EGAF00002637499 fastq.gz 90.1 MB
EGAF00002637500 fastq.gz 713.5 MB
EGAF00002637501 fastq.gz 721.0 MB
EGAF00002637502 fastq.gz 156.8 MB
EGAF00002637503 fastq.gz 172.0 MB
EGAF00002637504 fastq.gz 101.4 MB
EGAF00002637505 fastq.gz 107.1 MB
EGAF00002637506 fastq.gz 99.2 MB
EGAF00002637507 fastq.gz 105.0 MB
EGAF00002637508 fastq.gz 482.6 MB
EGAF00002637509 fastq.gz 488.9 MB
EGAF00002637510 fastq.gz 77.6 MB
EGAF00002637511 fastq.gz 83.7 MB
EGAF00002637512 fastq.gz 537.9 MB
EGAF00002637513 fastq.gz 548.7 MB
EGAF00002637514 fastq.gz 93.7 MB
EGAF00002637515 fastq.gz 100.0 MB
EGAF00002637534 fastq.gz 763.2 MB
EGAF00002637535 fastq.gz 792.4 MB
EGAF00002637536 fastq.gz 670.8 MB
EGAF00002637537 fastq.gz 704.0 MB
EGAF00002637538 fastq.gz 990.9 MB
EGAF00002637539 fastq.gz 1.0 GB
EGAF00002637540 fastq.gz 589.5 MB
EGAF00002637541 fastq.gz 615.7 MB
EGAF00002637542 fastq.gz 1.2 GB
EGAF00002637543 fastq.gz 1.2 GB
EGAF00002637544 fastq.gz 699.8 MB
EGAF00002637545 fastq.gz 729.5 MB
64 Files (56.1 GB)