 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Sep 29, 2023 |
| Title |
RV-Compen_8 |
| Sample type |
SRA |
| |
|
| Source name |
Right ventricle
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Right ventricle
Sex: F
primary disease_characterization: Compensated RV
secondary group_characterization: NA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Human RV tissues were manually dissected in cardiac biopsy or autopsy, according to the previously described protocol ( doi: 10.1161/CIRCULATIONAHA.120.047626 ), and Total RNA from each batch of RV samples were isolated separately using the RNeasy Mini Kit (Qiagen, Germantown, MA, USA) and snap-frozen. Purification of total RNA was performed as described in the RNeasy handbook, using DNase I digestion (RNase-Free DNase Set, Qiagen).
Following the RNA integrity measurement, approximately 10 ng of total RNA were used as starting material for library preparation using the SMARTer® Stranded Total RNA-seq Kit - Pico Input Mammalian, following manufacturers’ protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
processed-data-human.xlsx
count matrix column name: RV-Compen_8
|
| Data processing |
Raw fastqs were assessed for quality, adapter content, and duplication rates using FastQC. Trimmomatic version 0.39 was employed to trim reads following a quality drop (below a mean of Q15) in a window of five nucleotides
STAR mapping-b1: --outFilterMismatchNoverLmax 0.1 --outFilterScoreMinOverLread 0.9 --outFilterMatchNminOverLread 0.9 --outFilterMatchNmin 20 --alignIntronMax 200000 --alignMatesGapMax 2000 --alignEndsProtrude 10 ConcordantPair --outFilterMultimapNmax 1 --genomeDir GRCh38/indices/star_GRCh38_gencode.v27
STAR mapping-b2: mode: single-end, keep duplicates: no, keep multi-mapping: no, keep ribosomal: no, keep mitochondria: no --outFilterMismatchNoverLmax 0.1 --outFilterScoreMinOverLread 0.9 --outFilterMatchNminOverLread 0.9 --outFilterMatchNmin 20 --alignIntronMax 200000 --alignMatesGapMax 2000 --alignEndsProtrude 10 ConcordantPair --outMultimapperOrder Random --limitOutSAMoneReadBytes 10000000 --outFilterMultimapNmax 1 --genomeDir GRCh38/indices/star_GRCh38_gencode.v27
The number of reads that aligned to genes was counted using featureCounts version 1.6.5 from the Subread package. Only reads mapping at least partially inside exons were aggregated and counted per gene. Reads aligning to multiple regions or genes were excluded. -t exon -g gene_id -s 2; multi-mapping: no; duplicates: no
Raw count values for each organism were normalized separately using DESeq2 version 1.30.0, then transformed into regularized logarithm values for further analysis. Because we had two different batches of human samples, we performed a batch effect correction on this data using the sva package. The normalized and batch-corrected data were the basis of downstream analysis.
Assembly: hg38; (GRCh38.27)
Supplementary files format and content: excel file containing sheet 1: sample labels and mapping parameters
Supplementary files format and content: excel file containing sheet 2: matrix of raw read counts for genes*samples
|
| |
|
| Submission date |
Aug 15, 2023 |
| Last update date |
Sep 29, 2023 |
| Contact name |
Fatemeh Khassafi |
| E-mail(s) |
s.khassafi92@gmail.com
|
| Organization name |
Max Planck Institute
|
| Lab |
Soni Pullamsetti
|
| Street address |
Parkstrasse
|
| City |
Bad Nauheim |
| ZIP/Postal code |
61231 |
| Country |
Germany |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE240921 |
Transcriptional profiling of human adaptive and maladaptive right ventricular remodeling |
| GSE240941 |
Transcriptional profiling unveils molecular subgroups of adaptive and maladaptive right ventricular remodeling in pulmonary hypertension |
|
| Relations |
| BioSample |
SAMN36996261 |
| SRA |
SRX21375672 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
