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  2. RNA-seq + siRNA knockdown followed by RNA-seq + shRNA knockdown followed by RNA-seq + CRISPR genome editing followed by RNA-seq + CRISPRi followed by RNA-seq + PAS-seq

RNA-seq of long RNAs (paired-end, stranded)

Alternate accession: ENCPL086BPC

Status
released
Title
RNA-seq of long RNAs (paired-end, stranded)
Assays
RNA-seq, siRNA knockdown followed by RNA-seq, shRNA knockdown followed by RNA-seq, CRISPR genome editing followed by RNA-seq, CRISPRi followed by RNA-seq, PAS-seq
Description
ENCODE pipeline for paired-ended and stranded bulk RNA-seq data. RNA libraries generated from mRNAs (poly-A(+)), rRNA-depleted total RNA, or poly-A(-) populations that are size-selected to be longer than approximately 200 bp may be run through this pipeline. More information regarding references used for this pipeline and exogenous RNA spike-in controls are described in the pipelines overview document.
Lab
ENCODE Processing Pipeline
Award PI
J. Michael Cherry, Stanford
Pipeline standards
Bulk RNA-seq Data Standards

Pipeline schematic

Documents

pipeline protocol
Description excerpt: Bulk RNA-seq pipeline: Includes overview, references, and spike-ins…
Attachment PDF Icon
Bulk RNA-seq pipeline overview.pdf
Description
Bulk RNA-seq pipeline: Includes overview, references, and spike-ins information about the pipeline
Submitted by
Kathrina Onate
Lab
J. Michael Cherry, Stanford