|
| Status |
Public on Mar 01, 2022 |
| Title |
4681-M |
| Sample type |
SRA |
| |
|
| Source name |
Whole blood
|
| Organism |
Homo sapiens |
| Characteristics |
case_control_status: Control
participant_type: Mother
family: 4681
study_phase: Discovery
age_years: _
Sex: F
self_declared_ancestry: White
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Blood samples (EDTA tubes) were collected from all research subjects by venipuncture. DNA and RNA were extracted simultaneously from 1ml fresh whole blood, using the AllPrep DNA/RNA Mini kit (Qiagen).
Globin mRNAs were depleted from RNA samples using the GLOBINclear kit (Invitrogen). Stranded library preparation and eukaryotic transcriptome resequencing were performed using the BGISeq-500 next generation sequencing platform with paired end 100bp reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Description |
Whole blood of healthy control subject (Mother of 4681-P)
|
| Data processing |
Trim-Galore! was used to perform adaptor trimming and filtering of raw reads.
Kallisto was used to align reads to the GENCODE 32 human transcriptome (Genome build hg38).
Transcript-level counts were summarized to gene level counts using tximport.
Genome_build: RNA-Seq reads aigned to GENCODE 32 human transcriptome (Genome build hg38)
Supplementary_files_format_and_content: Raw counts. Rownames represent genes (ENTREZ gene IDs), column names represent samples
|
| |
|
| Submission date |
Dec 20, 2021 |
| Last update date |
Jun 28, 2022 |
| Contact name |
Caroline Dive |
| E-mail(s) |
[email protected]
|
| Organization name |
Cancer Research UK Manchester Institute
|
| Street address |
Cancer Research UK Manchester Institute, The University of Manchester, Wilmslow Road
|
| City |
Manchester |
| ZIP/Postal code |
M20 4BX |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL23227 |
| Series (2) |
| GSE191274 |
Whole blood RNA-Seq of individuals with Sotos syndrome and healthy control subjects |
| GSE191277 |
Sotos syndrome and healthy control subjects |
|
| Relations |
| BioSample |
SAMN24247289 |
| SRA |
SRX13456319 |
