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| Status |
Public on Dec 21, 2022 |
| Title |
Blood_Cd1c_BK114 |
| Sample type |
SRA |
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| Source name |
Blood
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Blood
cell type: Dendritic Cells Cd1c+
diagnosis: Control
library type: Low Input
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using RNeasy Micro Kit (Qiagen) and was quantified and purity checked using a NanoDrop ND-1000 (Thermo Scientific, Waltham, MA, USA). RNA integrity was verified using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Stranded library: 200 ng of total RNA were used with NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs) to construct index-tagged cDNA libraries. Libraries were quantified using a Qubit™ dsDNA HS assay with the Qubit fluorometer (Life Technologies, Carlsbad, California). Average library size and the size distribution were determined using a DNA 1000 assay in an Agilent 2100 Bioanalyzer. Libraries were normalized to 10nM using Tris-Cl 10mM, pH8.5 with 0.1% Tween 20.
Low Input library: Low Input RNAs were used to amplify the cDNA using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech-Takara). 1 ng of amplified cDNA was used to generate barcoded libraries using the Nextera XT DNA library preparation kit (Illumina). Libraries were quantified using a Qubit™ dsDNA HS assay with the Qubit fluorometer (Life Technologies, Carlsbad, California). Average library size and the size distribution were determined using a DNA 1000 assay in an Agilent 2100 Bioanalyzer. Libraries were normalized to 10nM using Tris-Cl 10mM, pH8.5 with 0.1% Tween 20.
Libraries were applied to an Illumina flow cell for cluster generation (SR Cluster Kit cBot) and sequence-by-synthesis single reads of 60 base length using the SBS Kit (Illumina) were generated on the HiSeq 2500 or the HiSeq 4000 following the standard sequencing protocol. Reads were further processed using the bcl2fastq package (Illumina) to split reads according to adapter indexes and produce fastq files. RNA-Seq was performed at the Genomics Unit of the Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Illumina Casava software used for basecalling and bcl2fastq for demultiplexing.
Sequenced reads quality was evaluated from FastQC.
Reads were trimmed for Illumina adaptors with cutadapt.
Reference Genome was indexed from RSem (Li B et al. 2011) and sequence reads were aligned using RSem.
RNA-Seq data were normalized using Transcripts Per Million (TPM) Trimmed Mean of M values (Robinson MD and A Oshlack 2010).
Genome_build: Human sequenced genome GRCh38 v91
Supplementary_files_format_and_content: *.rsem.genes.results.txt: Tab-delimited text files include raw, TPM and RPKM (Reads Per Kilobase Million) values for each sample.
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| Submission date |
Aug 28, 2020 |
| Last update date |
Dec 21, 2022 |
| Contact name |
Enrique Vazquez de Luis |
| E-mail(s) |
quiquevzquez@gmail.com
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| Organization name |
CNIC
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| Lab |
Genomics Unit
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| Street address |
Melchor Fernandez Almagro, 3
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| City |
Madrid |
| State/province |
Madrid |
| ZIP/Postal code |
28029 |
| Country |
Spain |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE157047 |
Interplay of NLRC4/NLRP3 inflammasomes and Fc-ˠ-Receptors on CD1c+ DC Associates with Pathogenic IFNˠ+IL17+ T cells and RA Severity |
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| Relations |
| BioSample |
SAMN15931210 |
| SRA |
SRX9029418 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4751517_BK114_CD1c.GRCh38v91.rsem.genes.results.txt.gz |
1.2 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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