Gene Expression Nebulas

PRJCA002326

BioProject PRJCA002326
Project Name Transcriptome of patients infected with SARS-CoV-2
Species Homo sapiens
Tissue Bronchoalveolar Lavage Fluid (BALF)
Disease Healthy Control,SARS-CoV-2 infection
Summary RNA-seq was employed to investigate host responses to SARS-CoV-2 infection in the bronchoalveolar lavage fluid (BALF) and peripheral blood mononuclear cells (PBMC) samples of COVID-19 patients.
Overall Design -
Protocol
  • Growth Protocol: -
  • Treatment Protocol: -; infected with SARS-CoV-2
  • Extract Protocol: -
  • Library Construction Protocol: One microgram of total RNAs extracted from PBMCs (Ficoll preparation) were used as input. Messenger RNAs were purified using oligo-dTs covalently coupled magnetic beads. Then, the RNAs were fragmented into small pieces by heating. First strand of cDNA was synthesized in the presence of specific chemicals to ensure that only RNAs were used as template. Double strand cDNAs were purified with Agencourt AMPure XP beads after the reaction. DNA library was constructed through end-repair, adaptor-ligation and PCR amplification. The intermediate products were size-selected after the adaptor-ligation using two rounds of Agencourt AMPure XP beads. Qualified double strand DNA library was transformed into single-stranded circular DNA library through DNA-denaturation and circularization. DNA nanoballs (DNBs) were generated from single-stranded circular DNA using rolling circle amplification (RCA). The DNBs were qualified using Qubit 2.0. Qualified DNBs were loaded on the flow cell and sequenced.; Total RNAs were extracted from BALF samples and quantified by Qubit RNA HS Assay Kit. The library preparation was performed with Trio RNA-Seq kit with AnyDeplete probe to remove human ribosomal RNAs. The resulting libraries were subject to 150 bp pair-end sequencing with an Illumina Miseq platform.
Sequencing
  • Molecule Type: polyA RNA; total RNA
  • Library Source:
  • Library Layout: PAIRED
  • Library Strand: Forward; -
  • Platform: ILLUMINA; BGISEQ
  • Instrument Model: Illumina NovaSeq 500; BGISEQ-500; Illumina MiSeq
  • Strand-Specific: Specific; Unspecific

GEN Sample

Display columns

Basic Information:
Sample Characteristic:
Biological Condition:
Experimental Variables:
Protocol:
Sequencing:
Assessing Quality:
Analysis:
Data Resource Project ID BioProject ID Sample ID Sample Name BioSample ID Sample Accession Experiment Accession Release Date Submission Date Update Date Species Race Ethnicity Age Age Unit Gender Source Name Tissue Cell Type Cell Subtype Cell Line Disease Disease State Development Stage Mutation Phenotype Case / Control Case Detail Control Detail Growth Protocol Treatment Protocol Extract Protocol Library Construction Protocol Molecule Type Library Layout Strand-Specific Library Strand Spike-In Strategy Platform Instrument Model Cell Number Reads Number Gbases AvgSpotLen1 AvgSpotLen2 Uniq Mapping Rate Multiple Mapping Rate Coverage Rate

Bulk Expression Profiles

Gene Name Gene Accession Condition BioProject ID Sample Biological Condition Raw Counts FPKM TPM Editing Box Plot
Cell Type Cell Line Tissue Disease Disease State Development Stage