|
| Status |
Public on Feb 15, 2022 |
| Title |
Clone EM2 replicate 1 (RNA-seq) |
| Sample type |
SRA |
| |
|
| Source name |
Clone EM2
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: ER-/PR- IBC
cell line: SUM149PT_EM2
cell line origin: SUM149PT
|
| Treatment protocol |
No treatment
|
| Growth protocol |
Grown according to ATCC recommendations
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA extraction performed by Rneasy Plus kit acording to directions
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
FASTQ files were generated using bcl2fastq v2.20.0.422 from Illumina Inc.
Raw reads were trimmed with Cutadapt (v2.4) and aligned to hg38 using STAR (2.7.2b) with parameters “--outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 10 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 –alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1”
Gene-level abundance estimates were generated using RSEM (v1.3.2) using the rsem-calculate-expression command with the parameters “--strandedness reverse --fragment-length-mean 313 --fragment-length-sd 91”.
Genome_build: hg38
Supplementary_files_format_and_content: txt files, RSEM output for each sample. Gene Identifers are from ENSEMBL v97
|
| |
|
| Submission date |
Apr 21, 2021 |
| Last update date |
Feb 15, 2022 |
| Contact name |
Diwakar Pattabiraman Pattabiraman |
| E-mail(s) |
Diwakar.R.Pattabiraman@Dartmouth.edu
|
| Organization name |
Geisel School of Medicine at Dartmouth
|
| Department |
Molecular and Systems Biology
|
| Lab |
Pattabiraman lab
|
| Street address |
1 Medical Center Drive
|
| City |
LEBANON |
| State/province |
NH |
| ZIP/Postal code |
03765 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE172609 |
Phenotypic heterogeneity driven by plasticity of the intermediate EMT state governs disease progression and metastasis in breast cancer [RNA-seq] |
| GSE172613 |
Phenotypic heterogeneity driven by plasticity of the intermediate EMT state governs disease progression and metastasis in breast cancer |
|
| Relations |
| BioSample |
SAMN18823900 |
| SRA |
SRX10654395 |
