|
| Status |
Public on Jan 13, 2017 |
| Title |
DON2531A845 |
| Sample type |
SRA |
| |
|
| Source name |
HUES2 Embryonic stem cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HUES2
cell type: embryonic stem cell derived macrophage
macrophage batch: WTA
macrophage samhd1: wildtype
macrophage culture time in hours: 1
macrophage culture media: conditioned media with LPS
|
| Growth protocol |
Macrophages grown on fibronectin coated polaris chip in XVIVO 15 + MCSF + FCS + PS
LPS 100ng/ml in either XVIVO 15 + FCS + MCSF or from previously cultured Macrophages exposed to same batch of LPS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
FluidigmC1 RNAseq protocol: cDNA was generated using SMARTer Ultra Low RNA Kit (Clontech)
Nextera XT DNA Library Preparation Kit (Illumina); Illumina RNAseq HiSeq4000 75bp PE
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Adapter trimming: RNA-seq reads were trimmed for Nextera and Illumina adapter sequences using skewer-v0.1.125
Alignment: Reads in gzipped fastq format were aligned using Hisat2 version-2.0.0-beta with default parameters to a modified reference genome comprising the human genome, Homo sapiens GRCh37 - human_g1k_v37, and fasta sequences for ERCC spike-ins
Mark Duplicates: Duplicate reads were marked using MarkDuplicates.jar implemented in Picard tools v1.92
Read counts: Reads mapping uniquely to genes annotated in ENSEMBL release 75 were counted using featureCounts implemented in subread-v1.5.0
Genome_build: GRCh37
Supplementary_files_format_and_content: Count_table.txt: raw read counts for all 63677 ENSEMBL annotated genes
Supplementary_files_format_and_content: additional_file_2.xlsx: Contains multiple excel sheets with Sheet1= tpm table (subset for 13873 expressed genes);
Supplementary_files_format_and_content: additional_file_2.xlsx: Sheet2= cell metadata with information regarding chip, sequencing batch, imaging, and QC metrics;
Supplementary_files_format_and_content: additional_file_2.xlsx: Sheet3= wildtype differential expression;
Supplementary_files_format_and_content: additional_file_2.xlsx: Sheet4= knockout differential expression
|
| |
|
| Submission date |
Oct 17, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Eshita Sharma |
| Organization name |
Wellcome Trust Centre for Human Genetics
|
| Department |
Bioinformatics
|
| Street address |
Roosevelt Drive, Headington
|
| City |
Oxford |
| State/province |
Oxfordshire |
| ZIP/Postal code |
OX3 7BN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE87849 |
The Nature and Nurture of Cell Heterogeneity: Accounting for Macrophage Gene-environment Interactions with Single-cell RNA-Seq |
|
| Relations |
| BioSample |
SAMN05913930 |
| SRA |
SRX2250198 |
