GSM1853289: cy84_Primary_CD45_pos_C01_S409_comb; Homo sapiens; RNA-Seq - SRA

SRX1148856: GSM1853289: cy84_Primary_CD45_pos_C01_S409_comb; Homo sapiens; RNA-Seq
1 ILLUMINA (NextSeq 500) run: 597,761 spots, 38.3M bases, 20.1Mb downloads

Submitted by: Gene Expression Omnibus (GEO)

Study: Single cell RNA-seq analysis of melanoma

PRJNA292832 • SRP062392 • All experiments • All runs

show Abstracthide Abstract

To understand the diversity of expression states within melanoma tumors, we obtained freshly resected samples, dissagregated the samples, sorted into single cells and profiled them by single-cell RNA-seq. Overall design: Tumors were disaggregated, sorted into single cells, and profiled by Smart-seq2. *Raw data files absent for samples GSM1851356 and GSM1851494.* **Submitter declares reads will be made available through dbGaP.** Please note that the processed data file (melanoma_single_cell_revised_v2.txt) contains two additional sample characteristis ("classification (based on inferred cnvs)" and "cell types for non-malignant cells").

Sample: cy84_Primary_CD45_pos_C01_S409_comb

SAMN03991953 • SRS1032908 • All experiments • All runs

Organism: Homo sapiens

Library:

Instrument: NextSeq 500

Strategy: RNA-Seq

Source: TRANSCRIPTOMIC

Selection: cDNA

Layout: PAIRED

Construction protocol: RNA and DNA were isolated using the Qiagen minikit following the manufacturers recommendations. Whole Transcriptome amplification (WTA) was performed with a modified SMART-Seq2 protocol, with Maxima Reverse Transcriptase (Life Technologies) used in place of superscript II. WTA products were cleaned with Agencourt XP DNA beads and 70% ethanol (Beckman Coulter) and Illumina sequencing libraries were prepared using Nextera XT (Illumina), as previously described (15). The 96 samples of a multiwall plate were pooled together, and cleaned with two 0.8x DNA SPRIs (Beckman Coulter). Library quality was assessed with a high sensitivity DNA chip (Agilent) and quantified with a high sensitivity dsDNA Quant Kit (Life Technologies). Samples were sequenced on an Illumina NextSeq 500 instrument using 30bp paired-end reads.

Experiment attributes:

GEO Accession: GSM1853289

Links:

NCBI link: NCBI Entrez (gds)

The SRA run(s) below contain human sequence (more...)(less...)

These data are available through the dbGaP authorized access system. Request access to:

Study: Single cell RNA-seq analysis of melanoma

Runs: 1 run, 597,761 spots, 38.3M bases, 20.1Mb

Run	# of Spots	# of Bases	Size	Published
SRR2162259	597,761	38.3M	20.1Mb	2020-03-16

ID:: 1671968

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