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| Status |
Public on Apr 20, 2021 |
| Title |
HESN_21 |
| Sample type |
SRA |
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| Source name |
Ectocervix
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| Organism |
Homo sapiens |
| Characteristics |
group: HESN
subjectid: P034
Sex: female
tissue: Ectocervix
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
The ectocervical biopsies that were stored in RNA-later were thawed and RNA was isolated and purified using AllPrep DNA/RNA Mini Kit (QIAGEN, Hilden, Germany) and the QIAcube Connect (QIAGEN). Poly-A containing mRNA transcripts were purified, fragmented and converted to cDNA. The cDNA fragments were amplified, barcoded and sequenced using NextSeq 550 (Illumina, San Diego, CA, USA). All ectocervical biopsies displayed good quality of isolated RNA and generated >10 million reads each.
We used the low sample (LS) library prep workflow from the TruSeq Stranded mRNA Reference Guide (1000000040498 v00). The samples were split into six seperate runs and sequenced with single end 75 bp reads
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
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| Data processing |
Base calling and demultiplexing of the Bcl2 files was performed using the bcl2fastq program.
Indexing of the human reference genome (hg38/GRCh38) was done using STAR (Spliced Transcripts Alignment to a Reference).
The resulting fastq files were aligned and uniquely mapped reads were counted and mapped to annotated exons using data from UCSC (University of Santa Cruz) genome browser (http://genome.ucsc.edu/) as reference.
Read counts were normalized to counts per million (CPM) and log2 scale with the edgeR package in Bioconductor.
Genome_build: hg38/GRCh38
Supplementary_files_format_and_content: Comma seperated files with raw gene counts and TMM-CPM-log2 normalized values respectively for each gene in each sample
Supplementary_files_format_and_content: Comma seperated file with metadata,
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| Submission date |
Jan 19, 2021 |
| Last update date |
Apr 20, 2021 |
| Contact name |
Kristina Broliden |
| E-mail(s) |
[email protected]
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| Organization name |
Karolinska Institutet
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| Department |
Dept. of Medicine Solna
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| Lab |
Kristina Broliden
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| Street address |
Visionsgatan 4, J7:20
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| City |
Stockholm |
| State/province |
Solna |
| ZIP/Postal code |
171 64 |
| Country |
Sweden |
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| Platform ID |
GPL21697 |
| Series (1) |
| GSE165132 |
HIV-exposed seronegative sex workers express high levels of regulatory T cells, low levels of T cell activation and an intact ectocervical tissue microenvironment |
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| Relations |
| BioSample |
SAMN17384926 |
| Supplementary data files not provided |
| Raw data not provided for this record |
| Processed data are available on Series record |
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