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| Status |
Public on May 01, 2023 |
| Title |
NSVD sample72 |
| Sample type |
SRA |
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| Source name |
decidua
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| Organism |
Homo sapiens |
| Characteristics |
labortype: term spontaneous
deliverytype: vaginal vertex
gestationalage: 39
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| 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.
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| Submission date |
Nov 18, 2019 |
| Last update date |
May 01, 2023 |
| Contact name |
Amal Katrib |
| E-mail(s) |
akatrib@ucla.edu
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| Organization name |
University of California, Los Angeles
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| Street address |
609 Charles E Young Dr E
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| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE140602 |
A Transcriptomic Snapshot of Labor Timing and Development in Human Decidua |
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| Relations |
| BioSample |
SAMN13321577 |
| SRA |
SRX7176349 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4175061_NSVD_Lib72.txt.gz |
192.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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