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| Status |
Public on Nov 15, 2019 |
| Title |
N720_S510_6 scRNAseq |
| Sample type |
SRA |
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| Source name |
CP_LN
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Lymph node
passages: FACS purified cells
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| Extracted molecule |
total RNA |
| Extraction protocol |
Libraries were prepared by getting mRNA be reverse transcribed from an anchored oligo-dT primer that includes a universal priming site at the 5’ end. RT reactions also included a template-switch oligonucleotide to allow the incorporation of the universal priming site at cDNA 3’ ends. Whole transcriptome cDNA was then amplified by PCR for 22–24 cycles using universal priming sites primers and Kapa HiFi Hot Start ReadyMix. After post-PCR clean-up, amplified whole transcriptome cDNA was incorporated into barcoded Illumina Nextera libraries and sequenced to a depth of about 2 million 150bp paired-end reads/cell on a HiSeq 4000 (Illumina). and amplified for 14 PCR cycles. Libraries were pooled and paired-end sequenced (38bp+37bp).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
Normalized_LN_EC_CP.csv
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| Data processing |
Paired-end sequencing reads were then trimmed to remove adaptor sequences and low-quality basecalls using the utility Trimmomatic
Reads were subsequently aligned using Bowtie against a genomic repeat element database derived from RepeatMasker software to quantify and remove transcript reads considered to be irrelevant for the analysis in hand (rRNA, rRNA, LINEs, SINEs, etc
The remaining reads were aligned against the most recent human genome build, hg38, using the splice-site aware aligner, STAR
Transcripts were then quantified and normalized using the bioinformatics package, Cufflinks
Genome_build: hg38
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| Submission date |
Nov 14, 2019 |
| Last update date |
Nov 20, 2019 |
| Contact name |
Marcus Buggert |
| E-mail(s) |
marcus.buggert@ki.se
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| Organization name |
Karolinska Institutet
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| Department |
Microbiology
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| Street address |
C2:94; Karolinska Universitetssjukhuset Huddinge
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| City |
Stockholm |
| State/province |
PA |
| ZIP/Postal code |
141 86 |
| Country |
Sweden |
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| Platform ID |
GPL20301 |
| Series (1) |
| GSE110684 |
Identification and characterization of HIV-specific resident memory CD8+ T cells in human lymphoid tissue |
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| Relations |
| BioSample |
SAMN13286624 |
| SRA |
SRX7141644 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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