|
| Status |
Public on Feb 19, 2018 |
| Title |
LOUCY_Untreated_Exp2_Rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Leukemia cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LOUCY
treatment: Untreated
experiment number: 2
|
| Growth protocol |
Cells were grown in RPMI-1640 (Gibco) supplemented with 10% FCS (HyClone) and 1% penicillin/streptomycin (PAA Laboratories)
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted using the RNeasy Mini Kit (Qiagen).
Libraries were constructed using the Smart-seq2 method (Picelli et al., Full-length RNA-seq from single cells using Smart-seq2. Nat Protocols 2014). cDNA was generated using SuperScript II (Invitrogen) and oligo-dT30VN primers (Biomers.net), pre-amplified using KAPA HiFi HotStart ReadyMix (KAPA Biosystems) and purified using Agencourt AMPure XP (Beckman Coulter). Tagmentation and library preparation was performed using the Nextera XT DNA Library Preparation Kit (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
FASTQ files were aligned to the human genome (hg38) using STAR version 2.5.1b.
Reads mapping to gene exons were counted using the Subread (version 1.4.5-p1) featureCounts tool and the hg38 annotation.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using edgeR (version 3.10.5). Only genes detected at greater than 1 count per million (cpm) in at least 4 samples were included for analysis.
Genome_build: hg38
Supplementary_files_format_and_content: Table of RPKM values for all samples for all genes expressed at greater than 1 cpm in at least 4 samples
|
| |
|
| Submission date |
Jun 30, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Christopher Booth |
| Organization name |
University of Oxford
|
| Department |
Weatherall Institute of Molecular Medicine
|
| Street address |
John Radcliffe Hospital
|
| City |
Oxford |
| State/province |
Oxfordshire |
| ZIP/Postal code |
OX3 9DS |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE100694 |
Ezh2 and Runx1 Mutations Collaborate to Initiate Lympho-Myeloid Leukemia in Early Thymic Progenitors [Human cell line RNA-seq] |
| GSE100695 |
Ezh2 and Runx1 Mutations Collaborate to Initiate Lympho-Myeloid Leukemia in Early Thymic Progenitors |
|
| Relations |
| BioSample |
SAMN07304682 |
| SRA |
SRX2975044 |
