Journal: Nucleic Acids Research

Article Title: Grouped-seq for integrated phenotypic and transcriptomic screening of patient-derived tumor organoids

doi: 10.1093/nar/gkab1201

Figure Lengend Snippet: Performance characterization of the Grouped-seq platform. ( A ) Mapped read and gene numbers across 192 microwells of the SMARchip. ( B ) Heatmap of correlation coefficients between any two of microwells. ( C ) Top 15 genes with the highest expression levels in all the microwells. ( D ) Quantitative capability of the Grouped-seq evaluated by ERCC sample. ( E ) Mixed-species experiment with human (A549) and mouse (3T3) cells performed on a single SMARchip. ( F ) High correlation between the Grouped-seq and the off-chip TruSeq. ( G ) Read and gene numbers of 192 microwells obtained at different sequencing depth from 0.025, 0.05, 0.1, 0.5, to 1 M reads per microwell. ( H ) UMI correction rates at different sequencing depth. UMI correction rate is defined as the ratio of read number to UMI number. ( I ) Limit of detection (LOD) of the gene expression level that can be detected at the different sequencing depths. The counts per million (CPMs) of the genes obtained at the 1-M sequencing depth are used as the standards and the LOD of a sequencing depth is defined as the upper limit of the CPMs (obtained at 1-M sequencing depth) of the genes that can be detected at least once with this sequencing depth.

Article Snippet: Meantime, 10 5 of A549 cells from the same batch were collected to extract total RNA using a RNeasy column (Qiagen) and a sequencing library was prepared from the total RNA using the Illumina TruSeq poly(A) + RNA-Seq library construction according to the manufacturer's instruction.

Techniques: Expressing, Sequencing

Journal: BMC Genomics

Article Title: Influence of RNA extraction methods and library selection schemes on RNA-seq data

doi: 10.1186/1471-2164-15-675

Figure Lengend Snippet: Experimental workflow. HEK 293 T cells were used to assess the influence of RNA extraction protocols in the RNA-seq data after sequencing with poly(A)+ or RiboZero procedure. The HEK293 nuclear and cytoplasmic RNA fractions provided a benchmark for the Ribozero sequencing.

Article Snippet: The fraction of junction reads were the highest, for Qiagen RNA/poly(A)+ RNA-seq and cytoplasmic RNA/RiboZero RNA-seq representing ~10,5%, of the mapped reads, (Additional file : Table S4).

Techniques: RNA Extraction, RNA Sequencing Assay, Sequencing

Journal: BMC Genomics

Article Title: Influence of RNA extraction methods and library selection schemes on RNA-seq data

doi: 10.1186/1471-2164-15-675

Figure Lengend Snippet: BRAF gene coverage. Snap shot (UCSC browser) representing the normalized read coverage for each method and the protocol dependence of the intronic reads. From top to bottom the experimental groups are the following: Poly (A) Qiagen total RNA, Poly (A) TRIzol total RNA, RiboZero Qiagen total RNA, RiboZero TRIzol total RNA, RiboZero cytoplasmic RNA, RiboZero nuclear RNA.

Article Snippet: The fraction of junction reads were the highest, for Qiagen RNA/poly(A)+ RNA-seq and cytoplasmic RNA/RiboZero RNA-seq representing ~10,5%, of the mapped reads, (Additional file : Table S4).

Techniques:

Journal: Wellcome Open Research

Article Title: The genome sequence of the sallow kitten, Furcula furcula (Clerck, 1759)

doi: 10.12688/wellcomeopenres.18112.1

Figure Lengend Snippet: Genome data for Furcula furcula , ilFurFurc1.1.

Article Snippet: PolyA RNA-Seq Illumina , ERR9434990.

Techniques:

Journal: Wellcome Open Research

Article Title: The genome sequence of common ivy, Hedera helix L., 1753

doi: 10.12688/wellcomeopenres.19662.1

Figure Lengend Snippet: Genome data for Hedera helix , drHedHeli1.2.

Article Snippet: PolyA RNA-Seq Illumina , ERR9435019 , .

Techniques: DNA Sequencing

Journal: NPJ Breast Cancer

Article Title: Effect of cross-platform gene-expression, computational methods on breast cancer subtyping in PALOMA-2 and PALLET studies

doi: 10.1038/s41523-024-00658-y

Figure Lengend Snippet: Intrinsic breast cancer molecular-subtyping methods in PALLET

Article Snippet: Strand-specific, poly-A+ RNAseq libraries for sequencing on the Illumina platform were prepared as previously described .

Techniques:

Journal: NPJ Breast Cancer

Article Title: Effect of cross-platform gene-expression, computational methods on breast cancer subtyping in PALOMA-2 and PALLET studies

doi: 10.1038/s41523-024-00658-y

Figure Lengend Snippet: a Pie chart of subtype distributions by the RNAseq-AIMS and RNAseq-PAM50.sgMd.TC subtyping methods for PALLET samples. b Odds ratios and 95% CIs for non-CCCA by breast cancer RNAseq-AIMS and RNAseq-PAM50.sgMd.TC subtype in PALLET. LET letrozole, n number of patients in the subtype treatment group, PAL palbociclib.

Article Snippet: Strand-specific, poly-A+ RNAseq libraries for sequencing on the Illumina platform were prepared as previously described .

Techniques: