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Sample GSM2306952

Query DataSets for GSM2306952

Status

Public on Dec 08, 2016

Title

04-A10.CC019

Sample type

SRA

Source name

lung

Organism

Homo sapiens

Characteristics

diagnosis: Control
patientid: CC019

Extracted molecule

total RNA

Extraction protocol

Cells were isolated from two normal controls and six IPF tissue samples prepared as described for FACS except that cells were sorted initially with CD326 prior to single cell isolation. For single cell analysis cell capture, lysis, reverse transcription and cDNA amplification were performed on the C1 IFC for mRNA-seq on Fluidigm C1 Single-Cell Auto Prep System following the manufacturer’s protocol.
Medium sized C1 mRNA-Seq chips were used to capture each cell-cycle fraction. The C1 Auto-prep system captures the dissociated single cells across 96 wells and performs cell lysis, cDNA synthesis with reverse transcription and PCR reaction using the SMARTer Ultra Low Input RNA Kit v3 (ClonTech, Mountain View, CA). Cells captured across the 96 wells are manually inspected as a quality control measure to remove empty well, doublets or debris containing wells. cDNA from several representative cells are checked by High Sensitivity DNA chips using Fragment Analyzer (Advanced Analytical) and all cDNA libraries are quantitated via Qubit (Thermo Fisher Scientific, Carlsbad, CA). Libraries for each of the 96 captured cells are prepared using the Illumina Nextera XT DNA sample preparation kit with 96 dual barcoded indices

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NextSeq 500

Data processing

Briefly, the analytic pipeline consisted of four components that included: gene pre-filtering and normalization, reiterative cell type mapping (hierarchical clustering followed by PCA), cell specific signature genes identification, and driving forces prediction for each cell type. Detailed methods and code for this analytic pipeline are found in “SINCERA: A pipeline for single-cell RNA-Seq profiling analysis.” (3) and are available on line at https://research.cchmc.org/pbge/sincera.html as an open access program.
Genome_build: gencode 23
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

Submission date

Sep 09, 2016

Last update date

May 15, 2019

Contact name

Jie Tang

E-mail(s)

jie.tang@cshs.org

Organization name

Cedars Sinai Medical Center

Street address

8700 Beverly Blvd