|
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 |