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| Status |
Public on Oct 23, 2024 |
| Title |
LCS9483_pPTC |
| Sample type |
SRA |
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| Source name |
Placenta
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Placenta
cell line: Cytotrophoblast
cell type: Cytotrophoblast
genotype: SV40-T immortalized
treatment: None
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol reagent (hermofisher, 15596018) following the manufacturer's procedure.
The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) with RIN number > 7.0. Approximately 5ug of total RNA was used to deplete ribosomal RNA according to the manuscript of the Ribo-Zero Gold rRNA Removal Kit (Illumina, cat.MRZG12324, San Diego, USA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Placental trophoblast, no treatment
No treatment
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| Data processing |
A cDNA library constructed by the pooled RNA was sequenced run with Illumina NovaseqTM 6000 sequence platform.Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads.To get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
we aligned reads of all samples to the homo sapiens reference genome(ftp://ftp.ensembl.org/pub/release-101/fasta/gallus_gallus/dna/) using HISAT2(https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package
The mapped reads of each sample were assembled using StringTie(http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8).
After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
RNAs differential expression analysis was performed by Deseq2 software between two different group and two different samples. The genes/transcripts with the parameter of pvalue < 0.05 and fold change > 2 or fold change <0.5.
Assembly: hg38
Supplementary files format and content: gene expression text files include raw counts and FPKM values for each Sample
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| Submission date |
Dec 19, 2023 |
| Last update date |
Oct 23, 2024 |
| Contact name |
Manuel Jr Sabalo Vidal |
| E-mail(s) |
[email protected]
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| Phone |
+639771270097
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| Organization name |
UTMB
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| Department |
Department of Obstetrics and Gynecology
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| Lab |
Menon Laboratory
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| Street address |
301 University Drive
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| City |
Galveston |
| State/province |
Texas |
| ZIP/Postal code |
77555 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE250585 |
Establishment and comparison of human term placenta-derived trophoblast cells |
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| Relations |
| BioSample |
SAMN38932161 |
| SRA |
SRX22970034 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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