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Sample GSM4175069 Query DataSets for GSM4175069
Status Public on May 01, 2023
Title PTL sample50
Sample type SRA
 
Source name decidua
Organism Homo sapiens
Characteristics labortype: preterm spontaneous
deliverytype: vaginal vertex
gestationalage: 33
Extracted molecule total RNA
Extraction protocol Human placentae were obtained within one hour of delivery with signed informed consent under the protocols approved by the University of Iowa Institutional Review Board (201411731). Placenta decidual tissue samples were macroscopically isolated from the maternal-facing surface of the placenta. Samples were cut into small pieces and placed in RNAlater® solution (Applied Biosystems, Foster City, CA). Biopsies were obtained after written informed consent, according to the protocol approved by the University of Iowa and in accordance with the Department of Health and Human Services regulations at 45 CFR 46.
Total RNA was extracted from each tissue using the TRIzol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instruction and stored at -80˚C until used
RNA-seq libraries were prepared using TruSeq RNA Sample Prep Kit v2 (Illumina) and sequenced on an Illumina HiSeq 2000 to produce 27-49 million 2x100nt pair-end reads per sample.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing Raw RNA-seq reads were trimmed of adapter sequences and mapped against the Ensembl human genome (hg19; GRCh37.75) using the software STAR v2.4.1c with default parameters.
The percentage of mapped reads is 88.6%±2.9% (mean±s.d).
Abundance measurements were obtained using htseq-count v0.6.1 with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include raw read counts for each sample.
 
Submission date Nov 18, 2019
Last update date May 01, 2023
Contact name Amal Katrib
E-mail(s) akatrib@ucla.edu
Organization name University of California, Los Angeles
Street address 609 Charles E Young Dr E
City Los Angeles
State/province CA
ZIP/Postal code 90095
Country USA
 
Platform ID GPL11154
Series (1)
GSE140602 A Transcriptomic Snapshot of Labor Timing and Development in Human Decidua
Relations
BioSample SAMN13321569
SRA SRX7176357

Supplementary file Size Download File type/resource
GSM4175069_PTL_Lib50.txt.gz 194.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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