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| Status |
Public on Feb 14, 2017 |
| Title |
CD103+CD49a-CD8 TRM, biological replicate 1 |
| Sample type |
SRA |
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| Source name |
CD103+CD49a- CD8 TRM
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| Organism |
Homo sapiens |
| Characteristics |
tissue origin: healthy skin
cell type: epidermal CD8+CD103+CD49a- tissue resident memory T cells
cell subset: CD49a-
donor: Subject 1
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| Treatment protocol |
Epidermis were separate from dermal tissue after dispase treatment overnight. The epidermal tissue were further digested by collagenase. The resulting cell suspension were stained and sorted by FACS based on surface markers.
Epidermal T cells were sorted from epidermal cell suspension according to their cellular markers (live CD45+CD3+CD4-CD103+ CD49+/-) by a MoFlo XDP sorter.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were sorted directly into Qiazol and stored at -80 degree before extraction using miRNeasy Mini Kit (Qiagen) according to manufacturer's protocol.
Library was constructed using SMART-Seq v4 Ultra Low Input RNA Kit (ClonTech) according to manufacturer's protocol.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
C0115EPI-CD8EpAp
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| Data processing |
Basecalling softwares: HCS1.5.15.1+ RTA1.13.48 +OLB 1.9.4; parameters are $OLB-1.9.4/bin/setupBclToQseq.py –b $BaseCalls -o $Bustard
Alignment: Bowtie alignment of gene reference, bowtie2-2.2.5, -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant -p 16 -k 200; BWA alignment of genome reference, bwa-0.7.10, -o 1 -e 63 -i 90 -L -k 2 -l 31 -t 4 -q 10
Filtering: Remove reads with adapters; Remove reads with unknown bases more than 10%; Remove low-quality reads (which are defined as reads having more than 50% bases with quality value <= 10).
Additional: TopHat alignment of genome reference (for AS, NovelTU, ExtendGene), TopHat v2.0.10, -p 16 --solexa1.3-quals --segment-length 30 --segment-mismatches 2 -r 20 --mate-std-dev 20 --library-type fr-unstranded
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Tab-delimited text files include expected.count values for each sample (*replicate#.txt) and all samples (all.gene.expected_count_ALL.txt). Gene ids in the processed data files (column 1) are the Gene IDs from the NCBI's Entrez Gene database (http://www.ncbi.nlm.nih.gov/gene/), and the "expected.count" values were obtained by the RSEM method.
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| Submission date |
Jun 22, 2016 |
| Last update date |
May 10, 2023 |
| Contact name |
Liv Eidsmo |
| E-mail(s) |
liv.eidsmo@ki.se
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| Phone |
0851772158
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| Organization name |
Karolinska Insitutet
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| Street address |
L8:02 Karolinska Univeristy Hospital
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| City |
Stockholm |
| ZIP/Postal code |
17177 |
| Country |
Sweden |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE83637 |
RNA-seq transcriptome analysis of epidermal CD8+CD103+CD49a+ and CD8+CD103+CD49- T cells from healthy human skin |
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| Relations |
| Reanalyzed by |
GSE232236 |
| BioSample |
SAMN05284378 |
| SRA |
SRX1871068 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2211621_CD103plusCD49aminusCD8_TRM_biological_replicate1.txt.gz |
91.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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