sense mrna seq library kit, by Lexogen - Product details

1

Bulk and Single-Cell RNA-Seq Protocols

Check if the same lab product or an alternative is used in the 5 most similar protocols

Whole RNA was isolated from cells using RNAeasy Mini Kit (Qiagen). For RNA isolation from bulk tumours, tumours were homogenized in Trizol and RNA was extracted using chloroform, followed by a clean-up step using the RNAeasy Mini Kit. For standard RNA-seq, libraries were generated using the Lexogen sense mRNA seq library kit using 500 ng – 1 μg of input RNA, for Quant-seq libraries were generated using the Lexogen Quant-seq 3’ mRNA seq kit using 500 ng input RNA, both according to manufacturer’s instructions. All libraries were quality controlled on a fragment analyser and quantified using the Qbit HS dsDNA kit (Thermo Scientific). Smart-seq analysis of 100 sorted DCs (DAPI^- CD45⁺ CD11c⁺ CD103⁺) or 100 sorted T cells (DAPI^- CD45⁺ CD3e⁺ CD8a⁺) was performed in-house using the Smart-seq2 protocol by Illumina^{59 (link)}. Library prep was performed according to manufacturer’s instruction using the Nextera kit after direct sorting into RNA lysis buffer. Sequencing was performed in-house on Illumina HiSeqV4 to obtain 50 bp single-end sequencing reads.

Haas L., Elewaut A., Gerard C.L., Umkehrer C., Leiendecker L., Pedersen M., Krecioch I., Hoffmann D., Novatchkova M., Kuttke M., Neumann T., de Silva I.P., Witthock H., Cuendet M.A., Carotta S., Harrington K.J., Zuber J., Scolyer R.A., Long G.V., Wilmott J.S., Michielin O., Vanharanta S., Wiesner T, & Obenauf A.C. (2021). Acquired resistance to anti-MAPK targeted therapy confers an immune-evasive tumour microenvironment and cross-resistance to immunotherapy in melanoma. Nature cancer, 2(7), 693-708.

+ Open protocol

+ Expand

2

Bulk and Single-Cell RNA-Seq Protocols

Check if the same lab product or an alternative is used in the 5 most similar protocols

Whole RNA was isolated from cells using RNAeasy Mini Kit (Qiagen). For RNA isolation from bulk tumours, tumours were homogenized in Trizol and RNA was extracted using chloroform, followed by a clean-up step using the RNAeasy Mini Kit. For standard RNA-seq, libraries were generated using the Lexogen sense mRNA seq library kit using 500 ng – 1 μg of input RNA, for Quant-seq libraries were generated using the Lexogen Quant-seq 3’ mRNA seq kit using 500 ng input RNA, both according to manufacturer’s instructions. All libraries were quality controlled on a fragment analyser and quantified using the Qbit HS dsDNA kit (Thermo Scientific). Smart-seq analysis of 100 sorted DCs (DAPI^- CD45⁺ CD11c⁺ CD103⁺) or 100 sorted T cells (DAPI^- CD45⁺ CD3e⁺ CD8a⁺) was performed in-house using the Smart-seq2 protocol by Illumina^{59 (link)}. Library prep was performed according to manufacturer’s instruction using the Nextera kit after direct sorting into RNA lysis buffer. Sequencing was performed in-house on Illumina HiSeqV4 to obtain 50 bp single-end sequencing reads.

Haas L., Elewaut A., Gerard C.L., Umkehrer C., Leiendecker L., Pedersen M., Krecioch I., Hoffmann D., Novatchkova M., Kuttke M., Neumann T., de Silva I.P., Witthock H., Cuendet M.A., Carotta S., Harrington K.J., Zuber J., Scolyer R.A., Long G.V., Wilmott J.S., Michielin O., Vanharanta S., Wiesner T, & Obenauf A.C. (2021). Acquired resistance to anti-MAPK targeted therapy confers an immune-evasive tumour microenvironment and cross-resistance to immunotherapy in melanoma. Nature cancer, 2(7), 693-708.

+ Open protocol

+ Expand

3

Chromatin and Transcriptome Profiling of ESCs

Check if the same lab product or an alternative is used in the 5 most similar protocols

ChIP for ChIP-seq assays was performed as described above except that we used 2.5 μg antibodies and 1.5 × 10⁷ ESCs for a transcription factor ChIP and 10 μg antibodies and 0.75 × 10⁷ ESCs for a histone ChIP. The ChIPed and input DNA libraries were generated and sequencing was performed on an Illumina GAIIx or Hi-seq genome analyzer according to the manufacturer’s protocols. FAIRE-seq assays were essentially performed as described previously (Simon et al. 2012 (link)) with 2 × 10⁶ ESCs per condition. Libraries for RNA-seq were generated with a SENSE mRNA-seq library kit (Lexogen) and sequencing was performed on an Illumina GAIIx genome analyzer according to the manufacturer’s protocols.

Yang S.H., Kalkan T., Morissroe C., Marks H., Stunnenberg H., Smith A, & Sharrocks A.D. (2014). Otx2 and Oct4 Drive Early Enhancer Activation during Embryonic Stem Cell Transition from Naive Pluripotency. Cell Reports, 7(6), 1968-1981.

+ Open protocol

+ Expand

Sense mrna seq library kit

Lab products found in correlation

3 protocols using sense mrna seq library kit

Bulk and Single-Cell RNA-Seq Protocols

Bulk and Single-Cell RNA-Seq Protocols

Chromatin and Transcriptome Profiling of ESCs

About PubCompare

Ready to get started?