|
| Status |
Public on Jun 30, 2023 |
| Title |
AB12_Subject 12 adenomyosis baseline [RNA_seq] |
| Sample type |
SRA |
| |
|
| Source name |
Endometrial Biopsy
|
| Organism |
Homo sapiens |
| Characteristics |
subject id: Subject 12
subject status: diagnosed with diffuse adenomyosis
treatment/time point: adenomyosis baseline
tissue: Endometrial Biopsy
|
| Treatment protocol |
Twelve women diagnosed with diffuse adenomyosis were administered for six months with a daily dose of 5mg vaginal bromocriptine. Endometrial biopsies were collected at baseline and at the end of treatment.
|
| Growth protocol |
Not applicable
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from tissue stored in RNA later using RNeasy total RNA Kit (Qiagen, Hilden, Germany) as per the manufacturer protocol.
cDNA library was constructed using well established Smart-seq2 protocol (Picelli et al. 2013, Picelli et al. 2014), tagmentation step was accomplished using Nextera XT kit (Illumina) , miRNA sequencing was performed as per the Hagemann et al 2018 protocol and sequencing was done in Illumina NextSeq 550® at the bioinformatics expression analysis facility at Karolinska University hospital, Sweden.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Bioinformatic analyses were performed using Partek Flow Genomic Analysis Software (Partek, St. Louis, Missouri, USA).
Sequenced raw FASTQ files were trimmed for adapters and contaminants such as ribosomal DNA, mitochondrial DNA respectively.
Trimmed reads were mapped to the reference genome hg38 using STAR aligner.
Mapped reads were further filtered and quantified to transcripts and genes using hg38 assembly and Ensemble transcripts release 99 for mRNA nad miRbase v22 for miRNA.
Genome_build: hg38
Supplementary_files_format_and_content: Filtered Gene Counts in a txt format
|
| |
|
| Submission date |
Apr 07, 2021 |
| Last update date |
Jun 30, 2023 |
| Contact name |
Nageswara Rao Boggavarapu |
| E-mail(s) |
nagsdsh@gmail.com
|
| Organization name |
Karolinska Institutet
|
| Department |
Women and Children health
|
| Lab |
Bioclinicum J9:30
|
| Street address |
Visionsgatan 4
|
| City |
Solna |
| State/province |
stockholm |
| ZIP/Postal code |
17164 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL21697 |
| Series (1) |
| GSE171653 |
Bromocriptine reduces endometrial cell growth in women with adenomyosis by targeting glucose metabolism |
|
| Relations |
| BioSample |
SAMN18649383 |
| SRA |
SRX10534979 |
