|
| Status |
Public on Aug 31, 2016 |
| Title |
villous_S3 |
| Sample type |
SRA |
| |
|
| Source name |
placental villous tissue
|
| Organism |
Homo sapiens |
| Characteristics |
ercc spike-in pool: Mix_1
fetal sex: Male
gestational age (weeks): 39.29
tissue: placental villous tissue
|
| Treatment protocol |
Placenta samples were collected and dissected post-delivery and incubated in RNAlater solution at 4 degrees celcius for 24 hours before being stored at -80 degrees celcius.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from 16 placental samples using TRIzol following the manufacturer’s protocol. All samples were spiked with mix 1 or mix 2 of the 96 External RNA Controls Consortium (ERCC) ExFold RNA transcripts.
Ribosomal RNAs were depleted from samples using Ribo-Zero Gold. and sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA Sample Preparation kits. Sequencing was performed on the Illumina Hi-Seq 2500 using a 100bp paired-end protocol at the Australian Cancer Genomics Facility in Adelaide.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Libraries were sequenced on the Illumina Hi-Seq 2500. Basecalls were performed with CASAVA version 1.8.
Sequence adapters were trimmed using AdapterRemoval with options --trimns, --minlength 20. Trimmed RNA-Seq reads were aligned to known UCSC hg19 genes and the hg19 genome using Bowtie 2 v2.1.0 and TopHat v2.0.9 with options --library-type=fr-firststrand --mate-inner-dist -20 --mate-std-dev 180. UCSC hg19 reference genome and transcriptome was obtained through Illumina iGenomes (https://support.illumina.com/sequencing/sequencing_software/igenome.html).
Aligned RNA-Seq reads were summarised using the summarizeOverlaps algorithm with the UCSC known genes hg19 GTF file using the the options overlapMode=``Union'', ignoreStrand=FALSE, singleEnd=FALSE, fragments=TRUE to generate a table of unique read counts per gene for each sample.
Genome_build: hg19
Supplementary_files_format_and_content: A count table of uniquely mapped read pairs overlapping genes.
|
| |
|
| Submission date |
Jan 21, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Sam Buckberry |
| E-mail(s) |
sam.buckberry@uwa.edu.au
|
| Organization name |
The University of Western Australia
|
| Street address |
35 Stirling Highway, Crawley
|
| City |
Perth |
| State/province |
WA |
| ZIP/Postal code |
6009 |
| Country |
Australia |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE77085 |
Deep RNA sequencing of the human placental transcriptome |
|
| Relations |
| BioSample |
SAMN04432819 |
| SRA |
SRX1539762 |
