|
| Status |
Public on Jan 31, 2024 |
| Title |
310_Control |
| Sample type |
SRA |
| |
|
| Source name |
Control
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: endometrium
disease state: Control
age: 36
mesntrual cycle phase: SE
history of endometriosis: no
hypermenorrhea: yes
dysmenorrhea: no
fertility: yes
polyps: no
myomas: no
laparoscopy: no
hormones: no
smoker: yes
|
| Treatment protocol |
Samples were fixed with paraformaldehyd 4% ON and embedded in paraffin
|
| Growth protocol |
endometrial biopsies were obtained by a Cornier Pipelle
|
| Extracted molecule |
total RNA |
| Extraction protocol |
High Pure FFPET-RNA Isolation Kit (Roche) following manufacturer’s instructions.
Library preparation was obtained using TruSeq_Stranded Total_RNA_LT, w/ Ribo-Zero Gold, Set_A kit. According to standard protocols, purified amplicons were pooled in equimolar amounts and paired-end sequenced via flow cell at 2x50nt on an Illumina Hi-Seq-2000 platform
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sample ID:
310
|
| Data processing |
Quality of reads was checked with FastQC software23. Preprocessing of reads was performed with fastx-toolkit24 and specific aScidea perl scripts property of aScidea S.L. (Ascidea Computational Biology Solutions, S.L., Sant Cugat, Spain) to filter regions of low quality. Raw reads with good quality were mapped using Tophat_2.1.125 and Bowtie2_2.2.826.
The Homo sapiens genome version GRCh38 was used as reference. Genomic annotations were obtained from Illumina iGenomes27.
The transcript isoform level and gene level counts were calculated and fragments per kilobase per million reads mapped (FPKM) were normalized using Cufflinks_2.2.1 software28.
Resulting p-values were adjusted using Benjamini and Hochberg method29 to obtain false discovery rate (FDR). Lists of differentially expressed genes (DEGs) were filtered by ln(fold change)(FC) > 1 and q-value < 0.05. Main statistical analyses were performed using the Bioconductor Project30.
Different comparisons were done using CLC_Genomics Workbench 8.0.2 software31. The comparisons made were as follows: DIE (n = 4) versus control (n = 19); OE (n = 8) versus control (n = 19); Adeno (n = 6) versus control (n = 19); DOA (DIE + OE + Adeno; n = 18) versus control (n = 19).
Genome_build: GRCh38
Supplementary_files_format_and_content: txt files containing the read distribution in each sample and the bamstats per sample
Supplementary_files_format_and_content: xlsx. File contains the fragments per kilobase million (fpkm) per sample and per each transcript
|
| |
|
| Submission date |
Jan 18, 2022 |
| Last update date |
Jan 31, 2024 |
| Contact name |
Xavier Santamaria |
| E-mail(s) |
juls.vallve@gmail.com, xsantamaria@bioliquid.es
|
| Phone |
935950444
|
| Organization name |
Bioliquid Inovative Genetics SLU
|
| Street address |
Av. Diagonal 463 Bis Pl. 4
|
| City |
Barcelona |
| State/province |
Barcelona |
| ZIP/Postal code |
08036 |
| Country |
Spain |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE193928 |
Discovery study in endometrial samples using RNA-HighSeq to build classifiers to differentiate between control patients and adenomyosis, ovarian endometriosis and deep infiltrating endometriosis |
|
| Relations |
| BioSample |
SAMN25076093 |
| SRA |
SRX13824334 |
