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Sample GSM3324234 Query DataSets for GSM3324234
Status Public on Aug 09, 2018
Title Human placenta 1 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 SAMN09783547
SRA SRX4520642

Supplementary file Size Download File type/resource
GSM3324234_Hu_placenta_1_THE1B_capture-seq_Tophat2.bigwig 10.1 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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