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| Status |
Public on May 01, 2024 |
| Title |
Lx33-Sim1 |
| Sample type |
SRA |
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| Source name |
:Lung
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| Organism |
Homo sapiens |
| Characteristics |
tissue: :Lung
cell line: Lx33
cell type: SCLC
genotype: NA
treatment: Simurosertib
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| Extracted molecule |
total RNA |
| Extraction protocol |
Frozen tissues were weighed and homogenized in RLT and nucleic acids were extracted using the AllPrep DNA/RNA Mini Kit (QIAGEN, #80204) according to the manufacturer’s instructions. RNA was eluted in nuclease-free water.
Fresh cell pellet or frozen tumor samples were shipped to GENEWIZ for RNA isolation, library preparation, and RNA sequencing. Total RNA was extracted using the RNeasy Plus Universal mini kit following manufacturer’s instructions (Qiagen, Hilden, Germany). RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA). RNA samples and sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). Sequencing libraries were clustered on one flowcell lane and then loaded on the Illumina HiSeq instrument (4000 or equivalent) (RRID: SCR_020127) according to manufacturer’s instructions. Samples were sequenced using a 2x150bp paired end (PE) configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bclfiles) was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software (RRID: SCR_015058). One mismatch was allowed for index sequence identification.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
In-line UMI sequences were trimmed from the sequencing reads with Marianas (https://github.com/mskcc/Marianas) and aligned to human GRCh38 genome using STAR 2.7.0 (https://github.com/alexdobin/STAR) [25] with Ensembl v92 gene annotation.
Hybrid selection-specific metrics and alignment metrics were calculated for the BAM files using CalculateHsMetrics and CollectRnaSeqMetrics, respectively, from Picard Toolkit (https://github.com/broadinstitute/picard) to determine the quality of the capture.
We quantified RNA-seq reads with Kallisto v.0.45.053 to obtain transcript counts and abundances.
Transcript per million (TPM) normalization by size factors was done from Kallisto output files using Sleuth v0.30.0 run in gene mode.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file with TPM values over all genes for each sample.
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| Submission date |
Jan 04, 2024 |
| Last update date |
May 01, 2024 |
| Contact name |
Yingqian Ada Zhan |
| E-mail(s) |
[email protected]
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| Organization name |
MSKCC
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| Department |
EPIGENETICS RESEARCH CENTER
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| Street address |
430 East 67th Street
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| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10065 |
| Country |
USA |
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| Platform ID |
GPL20301 |
| Series (2) |
| GSE252568 |
CDC7 inhibition impairs neuroendocrine transformation in lung and prostate tumors through MYC degradation III |
| GSE252569 |
CDC7 inhibition impairs neuroendocrine transformation in lung and prostate tumors through MYC degradation |
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| Supplementary data files not provided |
| Raw data not provided for this record |
| Processed data are available on Series record |
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