|
| Status |
Public on Dec 01, 2017 |
| Title |
CD24Neg_45-U-Neg_4 |
| Sample type |
SRA |
| |
|
| Source name |
Small intestine epithelium
|
| Organism |
Mus musculus |
| Characteristics |
cell type: CD24Neg
antibodies: Anti-CD24 (Biolegend), anti-CD45 D Pharmingen Cat. No. 553080, Ulex europaeus agglutinin I (UEA)(custom conjugation)
|
| Treatment protocol |
not applicable
|
| Growth protocol |
not applicable
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA (miRNeasy kit, Qiagen) from the flow sorted cells was used to prepare libraries using the TruSeq RNA sample preparation kit (Illumina).
as per instructions from the TruSeq RNA sample preparation kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
100BP reads were trimmed to 50BP and aligned to the NCBIM37.67 transcriptome using Bowtie version 0.12.8 using parameters as recommended by MMSeq guidelines
Gene expression estimates were calculated using the MMSeq workflow
Genome_build: NCBIM37.67 (transcriptome)
Supplementary_files_format_and_content: MMSeq gene expression estimates (FPKM)
|
| |
|
| Submission date |
Dec 10, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Chandra Chilamakuri |
| E-mail(s) |
datasubmissions@cruk.cam.ac.uk
|
| Organization name |
Cancer Research UK Cambridge Institute
|
| Street address |
Robinson Way
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 0RE |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE53190 |
Hydroxymethylcytosine in mouse intestinal differentiation [RNA-Seq] |
|
| Relations |
| BioSample |
SAMN02440001 |
| SRA |
SRX389708 |
