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Sample GSM3120485 Query DataSets for GSM3120485
Status Public on Jun 14, 2018
Title S377_rabbit_WT4_CD4_p1_SC
Sample type SRA
 
Source name Tumor B16F10 melanoma
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: Tumor
genotype/variation: wild type
Treatment protocol Tumor infiltrating CD8+ T cells were isolated from WT and IL27ra KO B16F10 melanoma bearing mice.
Extracted molecule total RNA
Extraction protocol 5 µl lysis buffer comprised of Buffer TCL (Qiagen) plus 1% 2-mercaptoethanol.
Plates were then spun down for one minute at 3000rpm and immediately frozen at -80°C. Cells were thawed and RNA was isolated with 2.2x RNAClean SPRI beads (Beckman Coulter Genomics) without final elution. The beads were then air-dried and processed immediately for cDNA synthesis. Samples were then processed using the Smart-seq2 protocol. This was followed by making a 25µl reaction mix for each PCR and performing 21 cycles for cDNA amplification. Then 0.25 ng cDNA from each cell and ¼ of the standard Illumina NexteraXT reaction volume were used in both the tagmentation and final PCR amplification steps
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description Single cell RNAseq
R5_rsem.genes.counts.matrix.TMM_normalized.FPKM
Data processing paired reads were mapped to mouse annotation mm10 using Bowtie (allowing a maximum of one mismatch in seed alignment, and suppressing reads that had more than 10 valid alignments).
TPMs were computed using RSEM, and log2(TPM+1) values were used for subsequent analyses.
filtered out low quality cells and cell doublets, maintaining for subsequent analysis the cells that had (1) 1,000-4,000 detected genes (defined by at least one mapped read), (2) at least 200,000 reads mapped to the transcriptome, and (3) at least 50% of the reads mapped to the transcriptome, ending with a total of 707 CD4+ and 825 CD8+ WT TILs and 376 CD4+ and 394 CD8+ IL27ra KO TILs.
Genome_build: mm10
 
Submission date Apr 27, 2018
Last update date Jun 14, 2018
Contact name Asaf Madi
E-mail(s) [email protected]
Organization name BWH
Department Neurology
Lab Ana Carrizosa Anderson
Street address 60 Fenwood Road, BTM 10016F
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platform ID GPL17021
Series (2)
GSE113811 Single cell RNAseq of Wild Type and IL27ra KO Tumor infiltrating lymphocytes isolated from B16F10 melanoma batch 5
GSE113968 The induction and transcriptional regulation of the co-inhibitory gene module in T cells by IL-27
Relations
BioSample SAMN08996661
SRA SRX4005420

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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