title: IsoSeq analysis and functional annotation of the infratentorial ependymoma tumor tissue on PacBio RSII platform.
abstract: Here, we sequenced and functionally annotated the long reads (1-2 kb) cDNAs library of an infratentorial ependymoma tumor tissue on PacBio RSII by Iso-Seq protocol using SMRT technology. 577 MB, data was generated from the brain tissues of ependymoma tumor patient, producing 1,19,313 high-quality reads assembled into 19,878 contigs using Celera assembler followed by Quiver pipelines, which produced 2952 unique protein accessions in the nr protein database and 307 KEGG pathways. Additionally, when we compared GO terms of second and third level with alternative splicing data obtained through HTA Array2.0. We identified four and twelve transcript cluster IDs in Level-2 and Level-3 scores respectively with alternative splicing index predicting mainly the major pathways of hallmarks of cancer. Out of these transcript cluster IDs only transcript cluster IDs of gene PNMT, SNN and LAMB1 showed Reads Per Kilobase of exon model per Million mapped reads (RPKM) values at gene-level expression (GE) and transcript-level (TE) track. Most importantly, brain-specific genes--PNMT, SNN and LAMB1 show their involvement in Ependymoma.
authors: Advanced Molecular Science Research Centre (Centre for Advanced Research), King George's Medical University, Lucknow 226003, India.
authors: Neetu
authors: N
authors: Singh
authors: Imperial Life Sciences, 463 Phase City 2nd, Sector 37, Gurgaon, Haryana 122001, India.
authors: Dinesh Kumar
authors: DK
authors: Sahu
authors: Department of Periodontics, King George's Medical University, Lucknow 226003, India.
authors: Rebecca
authors: R
authors: Chowdhry
authors: Department of Biochemistry, King George's Medical University, Lucknow 226003, India.
authors: Archana
authors: A
authors: Mishra
authors: Department of Pathology, King George's Medical University, Lucknow 226003, India.
authors: Madhu Mati
authors: MM
authors: Goel
authors: Department of Neuro Surgery, King George's Medical University, Lucknow, Uttar Pradesh 226003, India.
authors: Mohd
authors: M
authors: Faheem
authors: Department of Neuro Surgery, King George's Medical University, Lucknow, Uttar Pradesh 226003, India.
authors: Chhitij
authors: C
authors: Srivastava
authors: Department of Neuro Surgery, King George's Medical University, Lucknow, Uttar Pradesh 226003, India.
authors: Bal Krishna
authors: BK
authors: Ojha
authors: Department of Pediatric Surgery, All India Institute of Medical Sciences, New Delhi 110029, India.
authors: Devendra Kumar
authors: DK
authors: Gupta
authors: Department of Surgical Oncology, King George's Medical University, Lucknow, Uttar Pradesh 226003, India.
authors: Ravi
authors: R
authors: Kant
keywords: Annotation; Ependymoma; Isoseq; PacBio