|
| Status |
Public on Aug 09, 2018 |
| Title |
Human placenta 2 Capture-seq |
| Sample type |
SRA |
| |
|
| Source name |
villous placenta >39 weeks gestational age
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: placenta
|
| Treatment protocol |
Two human placentas were collected by cesarean section at 39 weeks 1 day and 39 weeks 2 days gestational age (IRB protocol: CCHMC IRB 2013-2243).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was purified from term placentas using a combination of TRIzol and Qiagen columns.
RNA-seq libraries were prepared using the SureSelect Strand-Specific RNA Library Prep for Illumina Multiplexed Sequencing kit (Agilent). For capture-sequencing, pre-amplified RNA-seq libraries were enriched for THE1B containing transcripts using a custom panel of 120 nt THE1B RNA oligos and the SureSelectXT RNA Target Enrichment kit (Agilent). Libraries were sequenced as 75 bp paired-end reads on an Illumina HiSeq machine.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
Capture-seq
|
| Data processing |
Reads were aligned to the human genome (hg19) using Tophat2 ( -I 100000 --max-segment-intron 100000 -r 300)
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files generated from bam files using Deeptools
|
| |
|
| Submission date |
Aug 08, 2018 |
| Last update date |
Aug 09, 2018 |
| Contact name |
Caitlin E Dunn |
| E-mail(s) |
caitlin.dunn@cchmc.org
|
| Organization name |
Cincinnati Children's Hospital Medical Center
|
| Department |
Division of Human Genetics
|
| Lab |
Muglia Lab
|
| Street address |
3333 Burnet Avenue
|
| City |
Cincinnati |
| State/province |
Ohio |
| ZIP/Postal code |
45229 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (2) |
| GSE118285 |
Long terminal repeat THE1B is a candidate enhancer for placenta-specific gene regulation [RNA-Seq] |
| GSE118289 |
Long terminal repeat THE1B is a candidate enhancer for placenta-specific gene regulation |
|
| Relations |
| BioSample |
SAMN09783559 |
| SRA |
SRX4520643 |
