|
| Status |
Public on Jun 01, 2017 |
| Title |
Brain-AD |
| Sample type |
SRA |
| |
|
| Source name |
human brain tissue from a patient with Alzheimer’s disease
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: brain from Alzheimer's disease patient
|
| Growth protocol |
For human embryonic stem cells (H1-hESC cell line; WiCell), cells were cultured in mTeSR1 (Stem Cell Technologies) on Matrigel matrix (BD) and were harvested between passages 50 and 55. For Brain-AD sample, total RNA materials (BioChain, Lot No. A703252) was provided by Elizabeth Tseng (PacBio Inc.) and Ting Hon (PacBio Inc.) as a gift.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted using RNeasy Plus Mini Kit (QIAGEN). Agilent RNA 6000 Pico Kit (Agilent) was used to assess the RNA quality, and Qubit RNA BR Assay Kit (ThermoFisher Scientific) was used to quantify the extracted RNA.
For Illumina sequencing, TruSeq Stranded mRNA Library Prep Kit was used to prepare library. For PacBio SMRT seqeuncing, library was prepared following Iso-Seq protocol (PacBio Inc.). For size selection of PacBio SMRT seqeuncing, the full-length cDNA was fractioned into four contiguous size ranges (0–1kb, 1–2kb, 2–3kb, >3kb) on a Sage ELF (Sage Science) before constructing SMRTbell templates.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Hisat2 (version 2.0.0-beta) was used to align Illumina short reads to reference genome with the parameters (“-k 1 - -rna-strandness RF - -no-mixed - -no-discordant”) for paired-end strand-specific data.
The SMRT Analysis software (version 2.3.0) was used to process PacBio long read data. In brief, Reads of Insert (ROI) were extracted from raw sequencing data requiring full passes ≥0 and predicted accuracy ≥70. Full-length non-chimera ROI and non-full-length non-chimera ROI were used for alignment. GMAP (version 2016-06-09) was used to align long reads to reference genome with the parameter “- -max-intronlength-middle 500000 - -max-intronlength-ends 500000 -z sense_force -n 0 -f samse - -split-output”.
IDP-APA (with PacBio long reads and Illumina short reads) was run using a reference isoform annotation library (GENCODE, version 25) to construct expressed isoforms and identify polyA sites.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files includ identified polyA sites for each expressed gene isoforms
|
| |
|
| Submission date |
Apr 12, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Kin Fai Au |
| E-mail(s) |
kinfai@med.umich.edu
|
| Phone |
734-615-5510
|
| Organization name |
University of Michigan
|
| Department |
Department of Computational Medicine and Bioinformatics
|
| Lab |
Room 2035, Palmer Commons
|
| Street address |
100 Washtenaw Avenue
|
| City |
Ann Arbor |
| State/province |
MI |
| ZIP/Postal code |
48109 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE97688 |
Alternative cleavage and polyadenylation analysis in an isoform-resolved way by Second- and Third-Generation Sequencing technologies |
|
| Relations |
| BioSample |
SAMN06711633 |
| SRA |
SRX2733980 |
