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| Status |
Public on Aug 27, 2024 |
| Title |
12 weeks, Normal Weight, Rep 3 |
| Sample type |
SRA |
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| Source name |
Peripheral Blood Mononuclear Cells (PBMCs)
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| Organism |
Homo sapiens |
| Characteristics |
cell type: Peripheral Blood Mononuclear Cells (PBMCs)
visit time: 12 weeks
subject category: Normal Weight
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| Treatment protocol |
Blood samples from the pregnant women who were either normal weight or overweight at prepregnancy were collected at 12, 24, and 36 weeks of gestation for peripheral blood mononuclear cells isolation. PBMCs were isolated using FICO/Lite-LyphoH density gradient method.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Trizol/BCP and Rneasy mini kit (QIAgen) and quantified using Qubit Flurometer
messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand of cDNA was synthesized using random hexamer primers, followed by the second strand of cDNA synthesis. This was followed by end repair, A-tailing, adapter ligation, size selection, amplification and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
G38
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| Data processing |
Raw FASTQ files were trimmed of auto-detected adapter sequences and filtered for read quality using TrimGalore (0.6.5) in paired-end mode.
Reads were aligned against the GRCh38 reference genome using STAR (2.7.9a) in paired-end mode. Resultant BAM files were sorted by coordinate and gzip-compressed.
Aligned reads were counted using the FeatureCounts utlility from subread (2.0.1) in unstranded mode (s=0), using the same annotation GTF used to construct the STAR reference.
Assembly: GRCh38
Supplementary files format and content: EukmRNAseq_counts.csv: Comma-seperated Values (CSV) table, count matrix used for input into DESeq2. Genes are listed as rows, and columns represent unique samples. The last 5 columns are gene annotations extracted from the reference GTF using the ENSEMBL ids found in the row names.
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| Submission date |
Aug 01, 2024 |
| Last update date |
Aug 27, 2024 |
| Contact name |
Dhivyaa Rajasundaram |
| E-mail(s) |
dhr11@pitt.edu
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| Organization name |
University of Pittsburgh
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| Department |
Pediatrics
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| Street address |
4401 Penn Avenue
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| City |
Pittsburgh |
| State/province |
PA |
| ZIP/Postal code |
15224 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE273780 |
Maternal immune cell gene expression associates with maternal gut microbiome, milk composition and infant gut microbiome |
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| Relations |
| BioSample |
SAMN42995044 |
| SRA |
SRX25578175 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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