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Sample GSM4521386

Query DataSets for GSM4521386

Status

Public on Dec 14, 2020

Title

T86_P003

Sample type

SRA

Source name

T86

Organism

Homo sapiens

Characteristics

cell_number: 72
tissue: TONSIL
Sex: F

Extracted molecule

total RNA

Extraction protocol

Sorted cells were processed using the Smart-seq2 protocol with minor changes (Picelli et al., 2013). Sequencing was done to the average depth of 0.7 million reads per cell with 43bp reads (single end) after demultiplexing. Blood samples were additionally sequenced for V(D)J analysis to and average depth of 0.84 million reads per cell with 150 bp reads (paired end) after demultiplexing.
Smart-Seq2

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2000

Data processing

The reads were aligned to the human genome (hg19 –GRCh38) and spike-in sequences (from the External RNA Controls Consortium) using STAR v2.5.3a (Dobin et al., 2013), and filtered for uniquely mapping reads. Counts per gene were calculated for each transcript in Ensembl release 92 using rpkmforgenes (Ramsköld et al., 2009). The following rpkmforgenes options were used: -readcount -fulltranscript -mRNAnorm -rmnameoverlap -bothendsceil
Genome_build: hg19 –GRCh38
Supplementary_files_format_and_content: Tab delimited files include metadata, barcodes and features of each plate. We also included a matrix containing estimated counts.

Submission date

May 07, 2020

Last update date

Dec 15, 2020

Contact name

Luca Mazzurana

E-mail(s)

luca.mazzurana@ki.se

Organization name

Karolinska Institutet

Street address

Alfred Nobels Aleè 8

City

Huddinge

ZIP/Postal code

14152

Country

Sweden

Platform ID

GPL11154

Series (1)

GSE150050

Tissue-specific transcriptional imprinting and heterogeneity in human innate lymphoid cells revealed by full-length single-cell RNA-sequencing

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BioSample

Supplementary file	Size	Download	File type/resource
GSM4521386_T86_P003.tar.gz	2.3 Mb	(ftp)(http)	TAR
Processed data provided as supplementary file
Processed data are available on Series record
Raw data not provided for this record