|
| Status |
Public on Feb 05, 2022 |
| Title |
Monocytes_Control_F1 |
| Sample type |
SRA |
| |
|
| Source name |
Monocytes
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Monocytes
treatment: Vehicle
strain: C57BL/6
|
| Treatment protocol |
Monocytes were either treated with LPS or LPS plus 9CisRA
|
| Growth protocol |
Cultured bone marrow derived monocytes were purified using a purification kit
|
| Extracted molecule |
total RNA |
| Extraction protocol |
cell pellets were resuspended in lysis buffer, pelleted, and tagmented using the enzyme and buffer provided in the Nextera Library Prep Kit (Illumina). Tagmented DNA was then purified using the MinElute PCR purification kit (Qiagen), amplified with 10 cycles of PCR, and purified using Agencourt AMPure SPRI beads (Beckman Coulter). Resulting material was quantified using the KAPA Library Quantification Kit for Illumina platforms (KAPA Biosystems), and sequenced with PE42 sequencing on the NextSeq 500 sequencer (Illumina).
Resulting material was quantified using the KAPA Library Quantification Kit for Illumina platforms (KAPA Biosystems), and sequenced with PE42 sequencing on the NextSeq 500 sequencer (Illumina).
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
bcl2fastq2 (v2.20) (processing of Illumina base-call data and demultiplexing)
Samtools (v0.1.19) (processing of BAM files)
BEDtools (v2.25.0) (processing of BED files)
wigToBigWig (v4) (generation of bigWIG files)
Subread (v1.5.2) (counting of reads in BAM files for DESeq2)
|
| |
|
| Submission date |
Feb 02, 2022 |
| Last update date |
Feb 06, 2022 |
| Contact name |
JEHAN ALAM |
| E-mail(s) |
[email protected]
|
| Phone |
(402) 686-7021
|
| Organization name |
Baylor College of Medicine
|
| Street address |
Baylor One Plaza
|
| City |
Houston |
| State/province |
TEXAS |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE195961 |
Reduced RXRa signaling increases dry eye disease inducing gdT17 cells in the conjunctiva [Sequencing] |
| GSE195962 |
Reduced RXRa signaling increases dry eye disease inducing gdT17 cells in the conjunctiva |
|
| Relations |
| BioSample |
SAMN25597894 |
| SRA |
SRX14020135 |
