|
| Status |
Public on Feb 01, 2018 |
| Title |
D17-105042_CZ_d_S3 |
| Sample type |
SRA |
| |
|
| Source name |
Universal Human Reference RNA_CZ_d_S3
|
| Organism |
Homo sapiens |
| Characteristics |
kit: SMARTer Pico (CZ)
state: heat degraded
site: S3
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Reads were aligned against hg19 / ENSEMBL 75 using STAR v. 2.5.1b with the following flags -runThreadN 8 --runMode alignReads with default ENCODE options except --alignIntronMin 10
Gene expression was quantitated using RSEM v. 1.2.30 with the following flags for all libraries: rsem-calculate-expression --paired-end --calc-pme --alignments -p 8 --forward-prob 0 against an annotation matching the STAR SA reference, with the exception of the positively-stranded CZ libraries, for which --forward-prob was set to 1. Posterior mean estimates (pme) of counts were retrieved, ribosomal RNA counts removed and expression in reads per kilobase of modeled exon per million mapped reads (RPKM) or transcripts per million (TPM) were computed on the remaining count matrices. Similar scripts and pipelines were used for ERCC and SIRV mapping and quantitation.
Genome_build: hg19 / ENSEMBL 75
|
| |
|
| Submission date |
Jun 16, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jyothi Thimmapuram |
| E-mail(s) |
jthimmap@purdue.edu
|
| Phone |
765-496-6252
|
| Organization name |
Purdue University
|
| Department |
Bioinformatics Core
|
| Street address |
YONG 1022, 155 S. Grant Street
|
| City |
West Lafayette |
| State/province |
IN |
| ZIP/Postal code |
47907 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE100127 |
Cross-Site Comparison of Ribosomal Depletion Kits for Illumina RNAseq Library Construction |
|
| Relations |
| BioSample |
SAMN07249803 |
| SRA |
SRX2925726 |
