|
| Status |
Public on Jan 31, 2024 |
| Title |
PL_M_72408 |
| Sample type |
SRA |
| |
|
| Source name |
Placenta: fetal surface at delivery
|
| Organism |
Homo sapiens |
| Characteristics |
subject id: 72408
tissue: Placenta: fetal surface at delivery
sample collection_method: Biopsy after delivery
sample trimester: Third trimester
sample gestational_age_in_days: 254
fetal sex: Male
fetal race: Caucasian
fetal ethnicity: NonHispanic
mode of_conception: Spontaneous/unassisted
rna integrity_number: 9.4
sequencing plate_name: Plate5-Pisarska2019
matched sample: _both_trimesters_available: FALSE
|
| Treatment protocol |
Fresh placenta tissue collected after chorionic villus sampling or delivery, submerged in RNAlater RNA stabilizing reagent (QIAGEN), and stored at -80C to preserve RNA quality until further processing.
|
| Growth protocol |
Singleton human pregnancies conceived without fertility treatment ("spontaneous" or "unassisted" pregnancy). Chorionic villus sampling confirmed normal karyotype for all subjects, including those without tissue collected at first trimester. All pregnancies resulted in live births, including those without tissue collected at delivery.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Placenta tissue was submerged in RNAlater RNA stabilization reagent (QIAGEN) and stored at -80C until further processing. Tissue was thawed on ice and homogenized using sonication and/or by passing tissue through needles, then total RNA was isolated using the AllPrep DNA/RNA/miRNA Universal kit (QIAGEN). Polyadenylated RNA was selected during the library preparation process.
For library preparation, 1 ug of the total RNA elution was used with the Illumina TruSeq Stranded mRNA library preparation kit (Illumina), with polyA mRNA selection then cDNA synthesis using SuperScript II reverse transcriptase (Invitrogen) and random primers. The cDNA was converted into double stranded DNA and PCR-amplified, then purified with Agencourt AMPure XP beads (Beckman Coulter). Sample libraries were multiplexed and sequenced on a NovaSeq 6000 platform (Illumina) using 75bp single-end mRNA-sequencing, with average 30 million reads per sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
RawCounts_124CVS-43Placenta.csv.gz
TPM_124CVS-43Placenta.csv.gz
FPKM_124CVS-43Placenta.csv.gz
DESeq2_First-versus-Third-Trimester_sexAdjusted_124CVS-43PL.csv.gz
|
| Data processing |
Raw sequencing data was demultiplexed and converted to fastq format by using bcl2fastq v2.20 (Illumina, San Diego, California).
Sequencing reads were aligned to the human genome using STAR v2.6.1 and RSEM v1.2.28 with default parameters, using a custom human GRCh38 transcriptome reference downloaded from GENCODEgenes.org which contained all protein coding and long non-coding RNA genes based on human GENCODE version 23 annotation.
Each gene was fitted into a negative binomial generalized linear model to compare first versus third trimester (adjusted for fetal sex). The Wald test was applied to get pvalues and the Benjamini-Hochberg false discovery rate procedure was applied to get adjusted pvalues (padj) or FDR values. Differential expression analysis was performed for the full cohort (124 first trimeter samples and 43 third trimester samples) as well as a sub-cohort of 23 subjects (46 samples) with matched data. Fetal sex differences were also analyzed at each trimester.
Assembly: GENCODE release 23
Supplementary files format and content: "RawCounts_124CVS-43Placenta.csv.gz" is a matrix of GENCODE/Ensembl Gene IDs with gene symbols (rows) and sample titles (columns). Values are raw sequencing counts which were used as input for DESeq2 differential expression analysis. Gene ID information is from the GENCODE human genome annotations.
Supplementary files format and content: "TPM_124CVS-43Placenta.csv.gz" is a matrix of GENCODE/Ensembl Gene IDs with gene symbols (rows) and sample names (columns). Values are transcripts per million which are useful to rank gene expression.
Supplementary files format and content: "FPKM_124CVS-43Placenta.csv.gz" is a matrix of GENCODE/Ensembl Gene IDs with gene symbols (rows) and sample names (columns). Values are fragments per million (FPKMs) which are useful to rank gene expression.
Supplementary files format and content: "DESeq2_First-versus-Third-Trimester_sexAdjusted_124CVS-43PL.csv.gz" is the differential expression analysis results spreadsheet comparing human placenta at first versus third trimester, adjusted for fetal sex. Individual sample columns at the end of the file are counts normalized by sequencing depth but not by gene length, which DESeq2 refers to as "baseMeans" or "normalized counts". Column descriptions are above the header row, describing the data source ("biomaRt" refers to Ensembl.org's BioMart server accessed through bioconductor package biomaRt, "DESeq2" means it is output from the DESeq2 analysis, etc).
|
| |
|
| Submission date |
Nov 09, 2023 |
| Last update date |
Jan 31, 2024 |
| Contact name |
Margareta D Pisarska |
| Organization name |
Cedars-Sinai Medical Center
|
| Department |
Obstetrics and Gynecology
|
| Lab |
Pisarska Lab
|
| Street address |
8635 West Third Street Suite 160
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90048 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE247382 |
High-throughput mRNA-seq atlas of human placenta at first and third trimester, all live births |
|
| Relations |
| BioSample |
SAMN38183713 |
| SRA |
SRX22465956 |
